Chemistry Books

Book SynopsisSupramolecular chemistry deals with the organisation of molecules into defined assemblies using non-covalent interactions, including weaker and reversible interactions such as hydrogen bonds, and metal-ligand interactions. The aspect of stereochemistry within such chemical architectures, and in particular chirality, is of special interest as it impacts on considerations of molecular recognition, the development of functional materials, the vexed question of homochirality, nanoscale effects of interactions at interfaces, biocatalysis and enzymatic catalysis, and applications in organic synthesis. Chirality in Supramolecular Assemblies addresses many of these aspects, presenting a broad overview of this important and rapidly developing interdisciplinary field. Topics covered include: Origins of molecular and topological chirality Homochirogenesis Chirality in crystallinity Host-guest behavior Chiral influences in functionaTable of ContentsList of Contributors xi Preface xiii 1 Principles of Molecular Chirality 1Jean]Claude Chambron and F. Richard Keene 1.1 General Introduction 1 1.2 Geometrical Chirality 2 1.3 Topological Chirality 25 1.4 Conclusion 39 References 39 2 Homochirogenesis and the Emergence of Lifelike Structures 44Pedro Cintas 2.1 Introduction and Scope 44 2.2 The Racemic State: Mirror Symmetry Breaking 45 2.3 Asymmetric Oligomerization 49 2.4 Biochirality in Active Sites 58 2.5 Conclusions 61 Acknowledgements 61 References 61 3 Aspects of Crystallization and Chirality 65Roger Bishop 3.1 Introduction 65 3.2 Crystal Space Groups 65 3.3 Fundamentals of Crystallization for a Racemic Mixture 69 3.4 More Complex Crystallization Behavior 71 3.5 Multiple Crystal Forms 74 3.6 Conglomerates Revisited 85 References 90 4 Complexity of Supramolecular Assemblies 94Jonathan A. Kitchen and Philip A. Gale 4.1 Introduction 94 4.2 Generating Supramolecular Chirality through Assembly of Achiral Components 96 4.3 Enantioselective Supramolecular Assemblies 121 4.4 Conclusions and Future Outlook 134 References 134 5 Chirality in the Host]Guest Behaviour of Supramolecular Systems 142Nicholas H. Evans and Paul D. Beer 5.1 An Introduction to Chiral Recognition and its Importance 142 5.2 Chiral Hosts for Chiral Guests 143 5.3 Conclusions: Summary and Future Directions 155 References 156 6 Chiral Influences in Functional Molecular Materials 159David B. Amabilino 6.1 Introduction 159 6.2 Functional Molecular Materials in Different States 161 6.3 Switching 168 6.4 Conducting Materials 171 6.5 Magnetic Materials 173 6.6 Sensors 177 6.7 Conclusions and Outlook 180 Acknowledgements 181 References 181 7 Chirality in Network Solids 190David R. Turner 7.1 Introduction 190 7.2 Chirality in Inorganic Network Solids 191 7.3 Synthesis of Chiral Coordination Polymers 192 7.4 Applications of Chiral Coordination Polymers 207 7.5 Summary and Outlook 209 References 210 8 Chiral Metallosupramolecular Polyhedra 218Jack K. Clegg and John C. McMurtrie 8.1 Introduction 218 8.2 Basic Design Principles 219 8.3 Chiral Polyhedra from Achiral Components 221 8.4 Stereochemical Communication 231 8.5 Resolution of Racemic Metallo]Supramolecular Polyhedra 236 8.6 Chiral Polyhedra from Chiral Molecular Components 239 8.7 Conclusions and Outlook 250 References 251 9 Chirality at the Solution/Solid]State Interface 257Iris Destoop and Steven De Feyter 9.1 Self]Assembly at the Solution / Solid]State Interface 257 9.2 Chirality Expression at the Solution / Solid]State Interface 258 9.3 Chiral Induction / Amplification at the Solution / Solid]State Interface 266 9.4 Towards Applications 278 9.5 Conclusions 282 References 282 10 Nanoscale Aspects of Chiral Nucleation and Propagation 285Edward G. Latter and Rasmita Raval 10.1 Introduction 285 10.2 Systems of Discussion 288 10.3 Conclusions 303 References 304 11 Chirality in Organic Hosts 307Daniel Fankhauser and Christopher J. Easton 11.1 Introduction 307 11.2 Chiral Hosts in Analytical Applications 307 11.3 Chiral Hosts in Asymmetric Reactions 313 11.4 Conclusion 337 Acknowledgements 338 References 338 12 Chirality Related to Biocatalysis and Enzymes in Organic Synthesis 343Declan P. Gavin and Anita R. Maguire 12.1 Introduction 343 12.2 Biocatalysis 344 12.3 Biocatalytic Methodologies: Kinetic/Dynamic Kinetic Resolution and Asymmetric Transformations/Chemoselective Desymmetrizations 348 12.4 Optimization of Biocatalyst Performance 351 12.5 Protein Engineering 352 12.6 Hydrolysis/Reverse Hydrolysis 356 12.7 Redox Reactions 366 12.8 C]C and Other C]X Bond Formation 380 12.9 Future and Outlook 385 References 385 Index 407

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Book SynopsisThis series provides inorganic chemists and materials scientists with a forum for critical, authoritative evaluations of advances in every area of the discipline. Volume 59 continues to report recent advances with a significant, up-to-date selection of contributions by internationally-recognized researchers. The chapters of this volume are devoted to the following topics: Iron Catalysis in Synthetic Chemistry A New Paradigm for Photodynamic Therapy Drug Design: Multifunctional, Supramolecular DNA Photomodification Agents Featuring Ru(II)/Os(II) Light Absorbers Coupled to Pt(II) or Rh(III) Bioactive Sites Selective Binding of Zn2+ Complexes to Non-Canonical Thymine or Uracil in DNA or RNA. Progress Toward the Electrocatalytic Production of Liquid Fuels from Carbon Dioxide Monomeric Dinitrosyl Iron Complexes: Synthesis and Reactivity Interactions of Nitrosoalkanes/arenes, Nitrosamines, Nitrosothiols, and Alkyl Nitrites with Metals AminoTable of ContentsChapter 1 Iron Catalysis in Synthetic Chemistry 1 SUJOY RANA, ATANU MODAK, SOHAM MAITY, TUHIN PATRA, AND DEBABRATA MAITI Chapter 2 A New Paradigm for Photodynamic Therapy Drug Design: Multifunctional, Supramolecular DNA Photomodification Agents Featuring Ru(II)/Os(II) Light Absorbers Coupled to Pt(II) or Rh(III) Bioactive Sites 189 JESSICA D. KNOLL AND KAREN J. BREWER Chapter 3 Selective Binding of Zn2‡ Complexes to Non-Canonical Thymine or Uracil in DNA or RNA 245 KEVIN E. SITERS, STEPHANIE A. SANDER, AND JANET R. MORROW Chapter 4 Progress Toward the Electrocatalytic Production of Liquid Fuels from Carbon Dioxide 299 JOEL ROSENTHAL Chapter 5 Monomeric Dinitrosyl Iron Complexes: Synthesis and Reactivity 339 CAMLY T. TRAN, KELSEY M. SKODJE, AND EUNSUK KIM Chapter 6 Interactions of Nitrosoalkanes/arenes, Nitrosamines, Nitrosothiols, and Alkyl Nitrites with Metals 381 NAN XU AND GEORGE B. RICHTER-ADDO Chapter 7 Aminopyridine Iron and Manganese Complexes as Molecular Catalysts for Challenging Oxidative Transformations 447 ZOEL CODOLA, JULIO LLORET-FILLOL, AND MIQUEL COSTAS Subject Index 533 Cumulative Index 561

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Book SynopsisThis book describes techniques of synthesis and self-assembly of macromolecules for developing new materials and improving functionality of existing ones. Because self-assembly emulates how nature creates complex systems, they likely have the best chance at succeeding in real-world biomedical applications. Employs synthetic chemistry, physical chemistry, and materials science principles and techniques Emphasizes self-assembly in solutions (particularly, aqueous solutions) and at solid-liquid interfaces Describes polymer assembly driven by multitude interactions, including solvophobic, electrostatic, and obligatory co-assembly Illustrates assembly of bio-hybrid macromolecules and applications in biomedical engineeringTable of ContentsList of Contributors ix Preface xiii 1 A Supramolecular Approach to Macromolecular Self-Assembly: Cyclodextrin Host/Guest Complexes 1Bernhard V. K. J. Schmidt and Christopher Barner-Kowollik 1.1 Introduction, 1 1.2 Synthetic Approaches to Host/Guest Functionalized Building Blocks, 3 1.2.1 CD Functionalization, 3 1.2.2 Suitable Guest Groups, 5 1.3 Supramolecular CD Self-Assemblies, 7 1.3.1 Linear Polymers, 7 1.3.2 Branched Polymers, 12 1.3.3 Cyclic Polymer Architectures, 17 1.4 Higher Order Assemblies of CD-Based Polymer Architectures Toward Nanostructures, 17 1.4.1 Micelles/Core-Shell Particles, 17 1.4.2 Vesicles, 19 1.4.3 Nanotubes and Fibers, 20 1.4.4 Nanoparticles and Hybrid Materials, 21 1.4.5 Planar Surface Modification, 22 1.5 Applications, 23 1.6 Conclusion and Outlook, 26 References, 26 2 Polymerization-Induced Self-Assembly: The Contribution of Controlled Radical Polymerization to The Formation of Self-Stabilized Polymer Particles of Various Morphologies 33Muriel Lansalot, Jutta Rieger, and Franck D’Agosto 2.1 Introduction, 33 2.2 Preliminary Comments Underlying Controlled Radical Polymerization, 36 2.2.1 Introduction, 36 2.2.2 Major Methods Based on a Reversible Termination Mechanism, 37 2.2.3 Major Methods Based on a Reversible Transfer Mechanism, 39 2.3 Pisa Via CRP Based on Reversible Termination, 40 2.3.1 PISA Using NMP, 40 2.3.2 Using ATRP, 46 2.4 Pisa Via CRP Based on Reversible Transfer, 48 2.4.1 Using RAFT in Emulsion Polymerization, 48 2.4.2 Using RAFT in Dispersion Polymerization, 61 2.4.3 Using TERP, 70 2.5 Concluding Remarks, 71 Acknowledgments, 73 Abbreviations, 73 References, 75 3 Amphiphilic Gradient Copolymers: Synthesis and Self-Assembly in Aqueous Solution 83Elise Deniau-Lejeune, Olga Borisova, Petr Št¡epánek, Laurent Billon, and Oleg Borisov 3.1 Introduction, 83 3.2 Synthetic Strategies for The Preparation of Gradient Copolymers, 86 3.2.1 Preparation of Gradient Copolymers by Controlled Radical Copolymerization, 87 3.2.2 Preparation of Block-Gradient Copolymers Using Controlled Radical Polymerization, 106 3.3 Self-Assembly, 110 3.3.1 Gradient Copolymers, 110 3.3.2 Diblock-Gradient Copolymers, 111 3.3.3 Triblock-Gradient Copolymers, 113 3.4 Conclusion and Outlook, 114 Abbreviations, 115 References, 117 4 Electrostatically Assembled Complex Macromolecular Architectures Based on Star-Like Polyionic Species 125Dmitry V. Pergushov and Felix A. Plamper 4.1 Introduction, 125 4.2 Core-Corona Co-Assemblies of Homopolyelectrolyte Stars Complexed with Linear Polyions, 127 4.3 Core-Shell-Corona Co-Assemblies of Star-Like Micelles of Ionic Amphiphilic Diblock Copolymers Complexed with Linear Polyions, 130 4.4 Vesicular Co-Assemblies of Bis-Hydrophilic Miktoarm Stars Complexed with Linear Polyions, 133 4.5 Conclusions, 137 Acknowledgment, 137 References, 137 5 Solution Properties of Associating Polymers 141Olga Philippova 5.1 Introduction, 141 5.2 Structures of Associating Polyelectrolytes, 142 5.3 Associating Polyelectrolytes in Dilute Solutions, 142 5.3.1 Intramolecular Association, 145 5.3.2 Intermolecular Association, 147 5.4 Associating Polyelectrolytes in Semidilute Solutions, 151 5.5 Conclusions, 155 References, 155 6 Macromolecular Decoration of Nanoparticles for Guiding Self-Assembly in 2D and 3D 159Christian Kuttner, Munish Chanana, Matthias Karg, and Andreas Fery 6.1 Introduction, 159 6.2 Guiding Assembly by Decoration with Artificial Macromolecules, 160 6.2.1 Decoration of Nanoparticles, 161 6.2.2 Distance Control in 2D and 3D, 166 6.2.3 Breaking the Symmetry, 171 6.3 Guiding Assembly by Decoration with Biomacromolecules, 173 6.3.1 DNA-Assisted Assembly, 173 6.3.2 Protein-Assisted Assembly, 177 6.4 Application of Assemblies, 181 6.5 Conclusions and Outlook, 183 References, 184 7 Self-Assembly of Biohybrid Polymers 193Dawid Kedracki, Jancy Nixon Abraham, Enora Prado, and Corinne Nardin 7.1 Introduction, 193 7.1.1 Amphiphiles, 194 7.1.2 Packing Parameter and Interfacial Tension, 195 7.1.3 Interaction Forces in Self-Assembly, 196 7.2 Self-Assembly of Biohybrid Polymers, 198 7.2.1 Polymer-DNA Hybrids, 198 7.2.2 Polypeptide Block Copolymers, 204 7.2.3 Block Copolypeptides, 205 7.3 Self-Assembly Driven Nucleation Polymerization, 207 7.3.1 Polymer-DNA Hybrids, 209 7.3.2 Polymer-Peptide Hybrids, 209 7.3.3 DNA-Peptide Hybrids, 212 7.4 Self-Assembly Driven by Electrostatic Interactions, 213 7.4.1 DNA/Polymer Bio-IPECs, 216 7.4.2 DNA/Copolymer Bio-IPECs, 216 7.5 Conclusion, 218 References, 219 8 Biomedical Application of Block Copolymers 231Martin Hrubý, Sergey K. Filippov, and Petr Št¡epánek 8.1 Introduction, 231 8.2 Diblock and Triblock Copolymers, 234 8.3 Graft and Statistical Copolymers, 240 8.4 Concluding Remarks, 245 Acknowledgment, 245 References, 245 Index 251

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Book SynopsisThis book is based on a graduate course and suitable as a primer for any newcomer to the field, this book is a detailed introduction to the experimental and computational methods that are used to study how solid surfaces act as catalysts.Table of ContentsPreface viii 1 Heterogeneous Catalysis and a Sustainable Future 1 2 The Potential Energy Diagram 6 2.1 Adsorption, 7 2.2 Surface Reactions, 11 2.3 Diffusion, 13 2.4 Adsorbate–Adsorbate Interactions, 15 2.5 Structure Dependence, 17 2.6 Quantum and Thermal Corrections to the Ground-State Potential Energy, 20 3 Surface Equilibria 26 3.1 Chemical Equilibria in Gases, Solids, and Solutions, 26 3.2 The Adsorption Entropy, 31 3.3 Adsorption Equilibria: Adsorption Isotherms, 34 3.4 Free Energy Diagrams for Surface Chemical Reactions, 40 Appendix 3.1 The Law of Mass Action and the Equilibrium Constant, 42 Appendix 3.2 Counting the Number of Adsorbate Configurations, 44 Appendix 3.3 Configurational Entropy of Adsorbates, 44 4 Rate Constants 47 4.1 The Timescale Problem in Simulating Rare Events, 48 4.2 Transition State Theory, 49 4.3 Recrossings and Variational Transition State Theory, 59 4.4 Harmonic Transition State Theory, 61 5 Kinetics 68 5.1 Microkinetic Modeling, 68 5.2 Microkinetics of Elementary Surface Processes, 69 5.3 The Microkinetics of Several Coupled Elementary Surface Processes, 74 5.4 Ammonia Synthesis, 79 6 Energy Trends in Catalysis 85 6.1 Energy Correlations for Physisorbed Systems, 85 6.2 Chemisorption Energy Scaling Relations, 87 6.3 Transition State Energy Scaling Relations in Heterogeneous Catalysis, 90 6.4 Universality of Transition State Scaling Relations, 93 7 Activity and Selectivity Maps 97 7.1 Dissociation Rate-Determined Model, 97 7.2 Variations in the Activity Maximum with Reaction Conditions, 101 7.3 Sabatier Analysis, 103 7.4 Examples of Activity Maps for Important Catalytic Reactions, 105 7.4.1 Ammonia Synthesis, 105 7.4.2 The Methanation Reaction, 107 7.5 Selectivity Maps, 112 8 The Electronic Factor in Heterogeneous Catalysis 114 8.1 The d-Band Model of Chemical Bonding at Transition Metal Surfaces, 114 8.2 Changing the d-Band Center: Ligand Effects, 125 8.3 Ensemble Effects in Adsorption, 130 8.4 Trends in Activation Energies, 131 8.5 Ligand Effects for Transition Metal Oxides, 134 9 Catalyst Structure: Nature of the Active Site 138 9.1 Structure of Real Catalysts, 138 9.2 Intrinsic Structure Dependence, 139 9.3 The Active Site in High Surface Area Catalysts, 143 9.4 Support and Structural Promoter Effects, 146 10 Poisoning and Promotion of Catalysts 150 11 Surface Electrocatalysis 155 11.1 The Electrified Solid–Electrolyte Interface, 156 11.2 Electron Transfer Processes at Surfaces, 158 11.3 The Hydrogen Electrode, 161 11.4 Adsorption Equilibria at the Electrified Surface–Electrolyte Interface, 161 11.5 Activation Energies in Surface Electron Transfer Reactions, 162 11.6 The Potential Dependence of the Rate, 164 11.7 The Overpotential in Electrocatalytic Processes, 167 11.8 Trends in Electrocatalytic Activity: The Limiting Potential Map, 169 12 Relation of Activity to Surface Electronic Structure 175 12.1 Electronic Structure of Solids, 175 12.2 The Band Structure of Solids, 179 12.3 The Newns–Anderson Model, 184 12.4 Bond-Energy Trends, 186 12.5 Binding Energies Using the Newns–Anderson Model, 193 Index 195

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Book SynopsisThe book starts with an exposition of the relevant properties of ions and continues with a description of their solvation in the gas phase. The book contains a large amount of factual information in the form of extensive tables of critically examined data and illustrations of the points made throughout.Table of ContentsPreface ix 1 Introduction 1 1.1 The Significance and Phenomenology of Ions in Solution 1 1.2 List of Symbols and Abbreviations 5 2 Ions and Their Properties 10 2.1 Ions as Isolated Particles 10 2.1.1 Bare Ions 11 2.1.2 Ions in Clusters 26 2.2 Sizes of Ions 30 2.3 Ions in Solution 35 2.3.1 Thermodynamics of Ions in Aqueous Solutions 38 2.3.1.1 Heat Capacities of Aqueous Ions 38 2.3.1.2 Entropies of Aqueous Ions 39 2.3.1.3 Enthalpies of Formation of Aqueous Ions 43 2.3.1.4 Gibbs Energies of Formation of Aqueous Ions 44 2.3.1.5 Ionic Molar Volumes in Aqueous Solutions 44 2.3.2 Other Properties of Aqueous Ions 49 2.3.2.1 Ionic Conductivities in Aqueous Solutions 49 2.3.2.2 Ionic Self]Diffusion in Aqueous Solutions 50 2.3.2.3 Ionic Effects on the Viscosity 51 2.3.2.4 Ionic Effects on the Relaxation of NMR Signals 55 2.3.2.5 Ionic Dielectric Decrements 55 2.3.2.6 Ionic Effects on the Surface Tension 56 References 58 3 Solvents for Ions 63 3.1 Solvent Properties that Suit Ion Dissolution 63 3.2 Physical Properties of Solvents 64 3.2.1 Volumetric Properties 64 3.2.2 Thermodynamic Properties 69 3.2.3 Electrical, Optical, and Magnetic Properties 70 3.2.4 Transport Properties 75 3.3 Chemical Properties of Solvents 77 3.3.1 Structuredness 77 3.3.2 Solvent Properties Related to their Ion Solvating Ability 80 3.3.2.1 Polarity 81 3.3.2.2 Electron Pair Donicity and Ability to Accept a Hydrogen Bond 83 3.3.2.3 Hydrogen Bond Donicity and Electron Pair Acceptance 84 3.3.2.4 Softness 85 3.3.3 Solvents as Acids and Bases 86 3.3.4 Miscibility with and Solubility in Water 88 3.3.5 Spectroscopic and Electrochemical Windows 90 3.4 Properties of Binary Aqueous Cosolvent Mixtures 90 3.4.1 Physical Properties of Binary Aqueous Mixtures with Cosolvents 90 3.4.1.1 Thermodynamic Properties of the Mixtures 92 3.4.1.2 Some Electrical, Optical, and Transport Properties of the Mixtures 98 3.4.2 Chemical Properties of Binary Aqueous Mixtures with Cosolvents 98 3.4.2.1 Structuredness 98 3.4.2.2 Properties Related to the Ion Solvating Ability 101 References 104 4 Ion Solvation in Neat Solvents 107 4.1 The Solvation Process 107 4.2 Thermodynamics of Ion Hydration 109 4.2.1 Gibbs Energies of Ion Hydration 109 4.2.1.1 Accommodation of the Ion in a Cavity 110 4.2.1.2 Electrostatic Interactions 110 4.2.2 Entropies of Ion Hydration 116 4.2.3 Enthalpies of Ion Hydration 116 4.3 Transfer Thermodynamics into Nonaqueous Solvents 117 4.3.1 Selection of an Extra]Thermodynamic Assumption 117 4.3.2 Thermodynamics of Transfer of Ions into Nonaqueous Solvents 118 4.3.2.1 Gibbs Energies of Transfer 118 4.3.2.2 Enthalpies of Transfer 126 4.3.2.3 Entropies of Transfer 130 4.3.2.4 Ionic Heat Capacities in Nonaqueous Solvents 130 4.3.2.5 Ionic Volumes in Nonaqueous Solvents 133 4.4 The Structure of Solvated Ions 135 4.4.1 Hydration Numbers from Diffraction Studies 138 4.4.2 Hydration Numbers from Computer Simulations 139 4.4.3 Hydration Numbers from Bulk Properties 141 4.4.4 Solvation Numbers in Nonaqueous Solvents 147 4.5 The Dynamics of Solvated Ions 147 4.5.1 The Mobility of Ions in Solution 147 4.5.2 Rate of Solvent Exchange Near Ions 150 4.6 Acid/Base Properties of Ions in Solution 151 References 153 5 Mutual Effects of Ions and Solvents 156 5.1 Ion Effects on the Structure of Solvents 156 5.1.1 Experimental Studies of Ion Effects on the Structure of Solvents 156 5.1.1.1 Self]diffusion of Water Molecules 156 5.1.1.2 Viscosity B]Coefficients 157 5.1.1.3 NMR Signal Relaxation 159 5.1.1.4 Dielectric Relaxation 159 5.1.1.5 Vibrational Spectroscopy 160 5.1.1.6 X]Ray Absorption and Scattering 162 5.1.1.7 Structural Entropy 163 5.1.1.8 Transfer from Light to Heavy Water 165 5.1.1.9 Internal Pressure 168 5.1.1.10 Some Other Experimental Results 170 5.1.2 Computer Simulations of Ion Effects on the Structure of Solvents 170 5.2 Ion Effects on the Dynamics of the Solvent 171 5.2.1 Mean Residence Times of Solvent Molecules Near Ions 171 5.2.2 Experimental Studies of Ion Effects on the Solvent Orientation Dynamics 174 5.2.2.1 Ultrafast Infrared Spectroscopy 174 5.2.2.2 High]frequency Dielectric Relaxation Spectroscopy 176 5.2.2.3 NMR Relaxation Times 178 5.2.3 Computer Simulations of Reorientation Times 180 5.3 Solvent Effects on the Properties of Ions in Solution 180 5.3.1 Bulk Properties 180 5.3.2 Molecular Properties 186 References 187 6 Ions in Mixed Solvents 193 6.1 Ion Transfer into Solvent Mixtures 194 6.2 Properties of Ions in Solvent Mixtures 199 6.2.1 Thermodynamic Properties of Ions in Mixed Solvents 199 6.2.2 Transport Properties of Ions in Mixed Solvents 203 6.3 Preferential Solvation of Ions 205 6.3.1 Spectroscopic Studies 207 6.3.2 Results from Thermodynamic Data 210 6.3.2.1 The QLQC Method 211 6.3.2.2 The IKBI Method 213 6.3.2.3 Treatments Based on Stepwise Solvent Replacements 215 References 216 7 Interactions of Ions with Other Solutes 219 7.1 Ion–Ion Interactions 219 7.1.1 Activity Coefficients of Electrolyte Solutions 220 7.1.2 Ion Hydration Related to Ion–Ion Interactions 223 7.2 Ion Association 227 7.2.1 Electrostatic Theory of Ion Association 230 7.2.1.1 Activity Coefficients of Neutral Ion Pairs 231 7.2.2 Methods for Studying Ion Association 232 7.2.3 Thermodynamic Quantities Pertaining to Ion Association 234 7.2.4 Aggregation of Ions in Solutions 237 7.3 Salting]in and Salting]out 239 7.3.1 Empirical Setschenow Constant Data 240 7.3.2 Interpretation of Salting Phenomena 240 References 244 8 Applications of Solutions of Ions 247 8.1 Applications in Electrochemistry 248 8.1.1 Batteries and Supercapacitors 248 8.1.2 Solvent]Independent pH and Electrode Potential Scales 251 8.2 Applications in Hydrometallurgy 257 8.3 Applications in Separation Chemistry 259 8.3.1 Solvent Extraction of Alkali Metal Cations 259 8.3.2 Solvation of Ionizable Drug Molecules 262 8.4 Applications to Chemical Reaction Rates 264 8.5 Solvated Ions in Biophysical Chemistry 269 8.5.1 The Hofmeister Series 270 8.5.1.1 The Anion Hofmeister Series 270 8.5.1.2 The Cation Hofmeister Series 271 8.5.1.3 Interpretation of the Hofmeister series 272 8.5.2 Water Structure Effects of Ions 275 8.5.3 Some Aspects of Protein Hydration 277 References 279 Author Index 000 Subject Index 000

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Book SynopsisCovers the area of lipidomics from fundamentals and theory to applications Presents a balanced discussion of the fundamentals, theory, experimental methods and applications of lipidomics Covers different characterizations of lipids including Glycerophospholipids; Sphingolipids; Glycerolipids and Glycolipids; and Fatty Acids and Modified Fatty Acids Includes a section on quantification of Lipids in Lipidomics such as sample preparation; factors affecting accurate quantification; and data processing and interpretation Details applications of Lipidomics Tools including for Health and Disease; Plant Lipidomics; and Lipidomics on Cellular Membranes Table of ContentsForeword xix Preface xxi Abbreviations xxv Part I Introduction 1 1 Lipids and Lipidomics 3 1.1 Lipids, 3 1.1.1 Definition, 3€ 1.1.2 Classification, 4 1.1.2.1 Lipid MAPS Approach, 7 1.1.2.2 Building Block Approach, 10 1.2 Lipidomics, 13 1.2.1 Definition, 13 1.2.2 History of Lipidomics, 14 References, 16 2 Mass Spectrometry for Lipidomics 21 2.1 Ionization Techniques, 21 2.1.1 Electrospray Ionization, 22 2.1.1.1 Principle of Electrospray Ionization, 22 2.1.1.2 Features of Electrospray Ionization for Lipid Analysis, 28 2.1.1.3 Advent of ESI for Lipid Analysis: Nano-ESI and Off-Axis Ion Inlets, 30 2.1.2 Matrix-Assisted Laser Desorption/Ionization, 30 2.2 Mass Analyzers, 32 2.2.1 Quadrupole, 32 2.2.2 Time of Flight, 33 2.2.3 Ion Trap, 35 2.3 Detector, 36 2.4 Tandem Mass Spectrometry Techniques, 37 2.4.1 Product-Ion Analysis, 37 2.4.2 Neutral-Loss Scan, 39 2.4.3 Precursor-Ion Scan, 39 2.4.4 Selected Reaction Monitoring, 39 2.4.5 Interweaving Tandem Mass Spectrometry Techniques, 40 2.5 Other Recent Advances in Mass Spectrometry for Lipid Analysis, 42 2.5.1 Ion-Mobility Mass Spectrometry, 43 2.5.2 Desorption Electrospray Ionization, 43 References, 45 3 Mass Spectrometry-Based Lipidomics Approaches 53 3.1 Introduction, 53 3.2 Shotgun Lipidomics: Direct Infusion-Based Approaches, 54 3.2.1 Devices for Direct Infusion, 54 3.2.2 Features of Shotgun Lipidomics, 55 3.2.3 Shotgun Lipidomics Approaches, 56 3.2.3.1 Tandem Mass Spectrometry-Based Shotgun Lipidomics, 56 3.2.3.2 High Mass Accuracy-Based Shotgun Lipidomics, 56 3.2.3.3 Multidimensional MS-Based Shotgun Lipidomics, 57 3.2.4 Advantages and Drawbacks, 63 3.2.4.1 Tandem Mass Spectrometry-Based Shotgun Lipidomics, 63 3.2.4.2 High Mass Accuracy-Based Shotgun Lipidomics, 63 3.2.4.3 Multidimensional Mass Spectrometry-Based Shotgun Lipidomics, 64 3.3 LC-MS-Based Approaches, 65 3.3.1 General, 65 3.3.1.1 Selected Ion Monitoring for LC-MS, 66 3.3.1.2 Selected/Multiple Reaction Monitoring for LC-MS, 67 3.3.1.3 Data-Dependent Analysis after LC-MS, 67 3.3.2 LC-MS-Based Approaches for Lipidomics, 68 3.3.2.1 Normal-Phase LC-MS-Based Approaches, 68 3.3.2.2 Reversed-Phase LC-MS-Based Approaches, 69 3.3.2.3 Hydrophilic Interaction LC-MS-Based Approaches, 71 3.3.2.4 Other LC-MS-Based Approaches, 72 3.3.3 Advantages and Drawbacks, 72 3.3.4 Identification of Lipid Species after LC-MS, 73 3.4 MALDI-MS for Lipidomics, 74 3.4.1 General, 74 3.4.2 Analysis of Lipid Extracts, 74 3.4.3 Advantages and Drawbacks, 75 3.4.4 Recent Advances in MALDI-MS for Lipidomics, 76 3.4.4.1 Utilization of Novel Matrices, 76 3.4.4.2 (HP)TLC-MALDI-MS, 78 3.4.4.3 Matrix-Free Laser Desorption/Ionization Approaches, 78 References, 79 4 Variables in Mass Spectrometry for Lipidomics 89 4.1 Introduction, 89 4.2 Variables in Lipid Extraction (i.e., Multiplex Extraction Conditions), 89 4.2.1 The pH Conditions of Lipid Extraction, 89 4.2.2 Solvent Polarity of Lipid Extraction, 90 4.2.3 Intrinsic Chemical Properties of Lipids, 90 4.3 Variables in the Infusion Solution, 91 4.3.1 Polarity, Composition, Ion Pairing, and Other Variations in the Infusion Solution, 91 4.3.2 Variations of the Levels or Composition of a Modifier in the Infusion Solution, 93 4.3.3 Lipid Concentration in the Infusion Solution, 97 4.4 Variables in Ionization, 98 4.4.1 Source Temperature, 98 4.4.2 Spray Voltage, 99 4.4.3 Injection/Eluent Flow Rate, 100 4.5 Variables in Building-Block monitoring with MS/MS Scanning, 102 4.5.1 Precursor-Ion Scanning of a Fragment Ion Whose m/z Serves as a Variable, 102 4.5.2 Neutral-Loss Scanning of a Neutral Fragment Whose Mass Serves as a Variable, 102 4.5.3 Fragments Associated with the Building Blocks are the Variables in Product-Ion MS Analysis, 103 4.6 Variables in Collision, 104 4.6.1 Collision Energy, 104 4.6.2 Collision-Gas Pressure, 104 4.6.3 Collision Gas Type, 108 4.7 Variables in Separation, 108 4.7.1 Charge Properties in Intrasource Separation, 108 4.7.2 Elution Time in LC Separation, 111 4.7.3 Matrix Properties in Selective Ionization by MALDI, 112 4.7.4 Drift Time (or Collision Cross Section) in Ion-Mobility Separation, 112 4.8 Conclusion, 114 References, 114 5 Bioinformatics in Lipidomics 121 5.1 Introduction, 121 5.2 Lipid Libraries and Databases, 122 5.2.1 Lipid MAPS Structure Database, 122 5.2.2 Building-Block Concept-Based Theoretical Databases, 123 5.2.3 LipidBlast – in silico Tandem Mass Spectral Library, 129 5.2.4 METLIN Database, 130 5.2.5 Human Metabolome Database, 131 5.2.6 LipidBank Database, 131 5.3 Bioinformatics Tools in Automated Lipid Data Processing, 132 5.3.1 LC-MS Spectral Processing, 132 5.3.2 Biostatistical Analyses and Visualization, 134 5.3.3 Annotation for Structure of Lipid Species, 135 5.3.4 Software Packages for Common Data Processing, 136 5.3.4.1 XCMS, 136 5.3.4.2 MZmine 2, 136 5.3.4.3 A Practical Approach for Determination of Mass Spectral Baselines, 137 5.3.4.4 LipidView, 137 5.3.4.5 LipidSearch, 137 5.3.4.6 SimLipid, 138 5.3.4.7 MultiQuant, 139 5.3.4.8 Software Packages for Shotgun Lipidomics, 139 5.4 Bioinformatics for Lipid Network/Pathway Analysis and Modeling, 139 5.4.1 Reconstruction of Lipid Network/Pathway, 139 5.4.2 Simulation of Lipidomics Data for Interpretation of Biosynthesis Pathways, 140 5.4.3 Modeling of Spatial Distributions and Biophysical 5.5 Integration of "Omics", 143 5.5.1 Integration of Lipidomics with Other Omics, 143 5.5.2 Lipidomics Guides Genomics Analysis, 144 References, 145 Part II Characterization of Lipids 151 6 Introduction 153 6.1 Structural Characterization for Lipid Identification, 153 6.2 Pattern Recognition for Lipid Identification, 157 6.2.1 Principles of Pattern Recognition, 157 6.2.2 Examples, 159 6.2.2.1 Choline Lysoglycerophospholipid, 159 6.2.2.2 Sphingomyelin, 161 6.2.2.3 Triacylglycerol, 164 6.2.3 Summary, 169 References, 170 7 Fragmentation Patterns of Glycerophospholipids 173 7.1 Introduction, 173 7.2 Choline Glycerophospholipid, 175 7.2.1 Positive Ion Mode, 175 7.2.1.1 Protonated Species, 175 7.2.1.2 Alkaline Adducts, 175 7.2.2 Negative-Ion Mode, 178 7.3 Ethanolamine Glycerophospholipid, 180 7.3.1 Positive-Ion Mode, 180 7.3.1.1 Protonated Species, 180 7.3.1.2 Alkaline Adducts, 180 7.3.2 Negative-Ion Mode, 182 7.3.2.1 Deprotonated Species, 182 7.3.2.2 Derivatized Species, 183 7.4 Phosphatidylinositol and Phosphatidylinositides, 184 7.4.1 Positive-Ion Mode, 184 7.4.2 Negative-Ion Mode, 184 7.5 Phosphatidylserine, 185 7.5.1 Positive-Ion Mode, 185 7.5.2 Negative-Ion Mode, 186 7.6 Phosphatidylglycerol, 186 7.6.1 Positive-Ion Mode, 186 7.6.2 Negative-Ion Mode, 186 7.7 Phosphatidic Acid, 187 7.7.1 Positive-Ion Mode, 187 7.7.2 Negative-Ion Mode, 188 7.8 Cardiolipin, 188 7.9 Lysoglycerophospholipids, 190 7.9.1 Choline Lysoglycerophospholipids, 190 7.9.2 Ethanolamine Lysoglycerophospholipids, 191 7.9.3 Anionic Lysoglycerophospholipids, 193 7.10 Other Glycerophospholipids, 193 7.10.1 N-Acyl Phosphatidylethanolamine, 193 7.10.2 N-Acyl Phosphatidylserine, 194 7.10.3 Acyl Phosphatidylglycerol, 194 7.10.4 Bis(monoacylglycero)phosphate, 194 7.10.5 Cyclic Phosphatidic Acid, 196 References, 196 8 Fragmentation Patterns of Sphingolipids 201 8.1 Introduction, 201 8.2 Ceramide, 202 8.2.1 Positive-Ion Mode, 202 8.2.2 Negative-Ion Mode, 203 8.3 Sphingomyelin, 205 8.3.1 Positive-Ion Mode, 205 8.3.2 Negative-Ion Mode, 205 8.4 Cerebroside, 205 8.4.1 Positive-Ion Mode, 205 8.4.2 Negative-Ion Mode, 207 8.5 Sulfatide, 208 8.6 Oligoglycosylceramide and Gangliosides, 208 8.7 Inositol Phosphorylceramide, 210 8.8 Sphingolipid Metabolites, 210 8.8.1 Sphingoid Bases, 210 8.8.2 Sphingoid-1-Phosphate, 212 8.8.3 Lysosphingomyelin, 212 8.8.4 Psychosine, 213 References, 213 9 Fragmentation Patterns of Glycerolipids 217 9.1 Introduction, 217 9.2 Monoglyceride, 218 9.3 Diglyceride, 218 9.4 Triglyceride, 222 9.5 Hexosyl Diacylglycerol, 223 9.6 Other Glycolipids, 224 References, 226 10 Fragmentation Patterns of Fatty Acids and Modified Fatty Acids 229 10.1 Introduction, 229 10.2 Nonesterified Fatty Acid, 230 10.2.1 Underivatized Nonesterified Fatty Acid, 230 10.2.1.1 Positive-Ion Mode, 230 10.2.1.2 Negative-Ion Mode, 230 10.2.2 Derivatized Nonesterified Fatty Acid, 233 10.2.2.1 Off-Line Derivatization, 233 10.2.2.2 Online Derivatization (Ozonolysis), 234 10.3 Modified Fatty Acid, 234 10.4 Fatty Acidomics, 238 References, 241 11 Fragmentation Patterns of other Bioactive Lipid Metabolites 243 11.1 Introduction, 243 11.2 Acylcarnitine, 244 11.3 Acyl CoA, 245 11.4 Endocannabinoids, 246 11.4.1 N-Acyl Ethanolamine, 247 11.4.2 2-Acyl Glycerol, 247 11.4.3 N-Acyl Amino Acid, 247 11.5 4-Hydroxyalkenal, 248 11.6 Chlorinated Lipids, 251 11.7 Sterols and Oxysterols, 251 11.8 Fatty Acid–Hydroxy Fatty Acids, 252 References, 253 12 Imaging Mass Spectrometry of Lipids 259 12.1 Introduction, 259 12.1.1 Samples Suitable for MS Imaging of Lipids, 260 12.1.2 Sample Processing/Preparation, 260 12.1.3 Matrix Application, 261 12.1.3.1 Matrix Application, 261 12.1.3.2 Matrix Application Methods, 262 12.1.4 Data Processing, 263 12.1.4.1 Biomap, 263 12.1.4.2 FlexImaging, 264 12.1.4.3 MALDI Imaging Team Imaging Computing System (MITICS), 264 12.1.4.4 DataCube Explorer, 264 12.1.4.5 imzML, 264 12.2 MALDI-MS Imaging, 264 12.3 Secondary-Ion Mass Spectrometry Imaging, 267 12.4 DESI-MS Imaging, 268 12.5 Ion-Mobility Imaging, 270 12.6 Advantages and Drawbacks of Imaging Mass Spectrometry for Analysis of Lipids, 270 12.6.1 Advantages, 270 12.6.2 Limitations, 272 References, 272 Part III Quantification of Lipids in Lipidomics 281 13 Sample Preparation 283 13.1 Introduction, 283 13.2 Sampling, Storage, and Related Concerns, 284 13.2.1 Sampling, 284 13.2.2 Sample Storage Prior to Extraction, 286 13.2.3 Minimizing Autoxidation, 287 13.3 Principles and Methods of Lipid Extraction, 288 13.3.1 Principles of Lipid Extraction, 289 13.3.2 Internal Standards, 292 13.3.3 Lipid Extraction Methods, 295 13.3.3.1 Folch Extraction, 295 13.3.3.2 Bligh–Dyer Extraction, 296 13.3.3.3 MTBE Extraction, 297 13.3.3.4 BUME Extraction, 298 13.3.3.5 Extraction of Plant Samples, 298 13.3.3.6 Special Cases, 298 13.3.4 Contaminants and Artifacts in Extraction, 299 13.3.5 Storage of Lipid Extracts, 300 References, 300 14 Quantification of Individual Lipid Species in Lipidomics 305 14.1 Introduction, 305 14.2 Principles of Quantifying Lipid Species by Mass Spectrometry, 308 14.3 Methods for Quantification in Lipidomics, 312 14.3.1 Tandem Mass Spectrometry-Based Method, 312 14.3.2 Two-Step Quantification Approach Used in MDMS-SL, 317 14.3.3 Selected Ion Monitoring Method, 321 14.3.4 Selected Reaction Monitoring Method, 324 14.3.5 High Mass Accuracy Mass Spectrometry Approach, 327 References, 329 15 Factors Affecting Accurate Quantification of Lipids 335 15.1 Introduction, 335 15.2 Lipid Aggregation, 336 15.3 Linear Dynamic Range of Quantification, 337 15.4 Nuts and Bolts of Tandem Mass Spectrometry for Quantification of Lipids, 339 15.5 Ion Suppression, 341 15.6 Spectral Baseline, 343 15.7 The Effects of Isotopes, 344 15.8 Minimal Number of Internal Standards for Quantification, 347 15.9 In-Source Fragmentation, 349 15.10 Quality of Solvents, 350 15.11 Miscellaneous in Quantitative Analysis of Lipids, 350 References, 350 16 Data Quality Control and Interpretation 353 16.1 Introduction, 353 16.2 Data Quality Control, 354 16.3 Recognition of Lipid Metabolism Pathways for Data Interpretation, 355 16.3.1 Sphingolipid Metabolic Pathway Network, 356 16.3.2 Network of Glycerophospholipid Biosynthesis Pathways, 356 16.3.3 Glycerolipid Metabolism, 359 16.3.4 Interrelationship between Different Lipid Categories, 360 16.4 Recognition of Lipid Functions for Data Interpretation, 360 16.4.1 Lipids Serve as Cellular Membrane Components, 360 16.4.2 Lipids Serve as Cellular Energy Storage Depots, 363 16.4.3 Lipids Serve as Signaling Molecules, 365 16.4.4 Lipids Play Other Cellular Roles, 366 16.5 Recognizing the Complication of Sample Inhomogeneity and Cellular Compartments in Data Interpretation, 368 16.6 Integration of "Omics" for Data Supporting, 369 References, 370 Part IV Applications of Lipidomics in Biomedical and Biological Research 377 17 Lipidomics for Health and Disease 379 17.1 Introduction, 379 17.2 Diabetes and Obesity, 380 17.3 Cardiovascular Diseases, 382 17.4 Nonalcohol Fatty Liver Disease, 383 17.5 Alzheimer’s disease, 385 17.6 Psychosis, 387 17.7 Cancer, 388 17.8 Lipidomics in Nutrition, 390 17.8.1 Lipidomics in Determination of the Effects of Specific Diets or Challenge Tests, 391 17.8.2 Lipidomics to Control Food Quality, 392 References, 393 18 Plant Lipidomics 405 18.1 Introduction, 405 18.2 Characterization of Lipids Special to Plant Lipidome, 406 18.2.1 Galactolipids, 407 18.2.2 Sphingolipids, 408 18.2.3 Sterols and Derivatives, 410 18.2.4 Sulfolipids, 410 18.2.5 Lipid A and Intermediates, 411 18.3 Lipidomics for Plant Biology, 411 18.3.1 Stress-Induced Changes of Plant Lipidomes, 411 18.3.1.1 Lipid Alterations in Plants Induced by Temperature Changes, 411 18.3.1.2 Wounding-Induced Alterations in Plastidic Lipids, 415 18.3.1.3 Phosphorus Deficiency-Resulted Changes of Glycerophospholipids and Galactolipids, 416 18.3.2 Changes of Plant Lipidomes during Development, 416 18.3.2.1 Alterations in Lipids during Development of Cotton Fibers, 416 18.3.2.2 Changes of Lipids during Potato Tuber Aging and Sprouting, 417 18.3.3 Characterization of Gene Function by Lipidomics, 417 18.3.3.1 Role of Fatty Acid Desaturases and DHAP Reductase in Systemic Acquired Resistance, 417 18.3.3.2 Roles of Phospholipases in Response to Freezing, 419 18.3.3.3 Role of PLDζ in Phosphorus Deficiency-Induced Lipid Changes, 419 18.3.4 Lipidomics Facilitates Improvement of Genetically Modified Food Quality, 420 References, 421 19 Lipidomics on Yeast and Mycobacterium Tuberculosis 427 19.1 Introduction, 427 19.2 Yeast Lipidomics, 428 19.2.1 Protocol for Analysis of Yeast Lipidomes by Mass Spectrometry, 428 19.2.2 Quantitative Analysis of Yeast Lipidome, 430 19.2.3 Comparative Lipidomics Studies on Different Yeast Strains, 431 19.2.4 Lipidomics of Yeast for Lipid Biosynthesis and Function, 432 19.2.5 Determining the Effects of Growth Conditions on Yeast Lipidomes, 435 19.3 Mycobacterium Tuberculosis Lipidomics, 436 References, 438 20 Lipidomics on Cell Organelle and Subcellular Membranes 443 20.1 Introduction, 443 20.2 Golgi, 444 20.3 Lipid Droplets, 445 20.4 Lipid Rafts, 447 20.5 Mitochondrion, 449 20.6 Nucleus, 452 20.7 Conclusion, 453 References, 454 Index 459

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Book SynopsisThe current volume continues the tradition of providing significant and interesting procedures, which should prove worthwhile to many synthetic chemists working in increasingly diverse areas. Following precedent, there is no specific or central theme to this volume.

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Book SynopsisColour is a sensation and as such it is a subjective and incommunicable quantity. Colour measurement is possible because we can create a correspondence between colour sensations and the light radiations that stimulate them. This correspondence concerns the physics of light radiation, the physiology of the visual process and the psychology of vision. Historically, in parallel to standard colorimetry, systems for colour ordering have been developed that allow colour specifications in a very practical and concrete way, based on the direct vision of material colour samples arranged in colour atlases. Colour-ordering systems are sources of knowledge of colour vision, which integrate standard colorimetry. Standard Colorimetry: Definitions, Algorithms and Software: Describes physiology and psychophysics useful to understand colorimetry Considers all the photometric and colorimetric systems standardized by CIE (XYZ, CIELAB, CIELUV, LMSTable of ContentsSociety of Dyers and Colourists xv Preface xvii 1 Generalities on Colour and Colorimetry 1 1.1 Colour 1 1.2 Colorimetry 2 References 4 Bibliography 4 2 Optics for Colour Stimulus 5 2.1 Introduction 5 2.2 Electromagnetic Waves 7 2.3 Photons 11 2.4 Radiometric and Actinometric Quantities 11 2.5 Inverse Square Law 14 2.6 Photometric Quantities 14 2.7 Retinal Illumination 16 References 16 Bibliography 16 3 Colour and Light–Matter Interaction 17 3.1 Introduction 17 3.1.1 Luminous Colours 17 3.1.2 Non]luminous Colours 18 3.1.3 Light Phenomena and Body Appearance 18 3.2 Light Sources 19 3.3 Planckian Radiator 20 3.4 Light Regular Reflection and Refraction 21 3.4.1 Snell’s Laws 22 3.4.2 Fresnel’s Laws 23 3.5 Light Scattering 24 3.5.1 Lambertian Diffusion 25 3.5.2 Light Scattering on a Rough Surface 25 3.5.3 Light Scattering in an Optically Heterogeneous Medium 26 3.6 Light Absorption and Colour Synthesis 28 3.6.1 Simple Subtractive Synthesis 28 3.6.2 Complex Subtractive Synthesis 28 3.7 Fluorescence 29 3.8 Transparent Media 30 3.8.1 Internal Transmittance of a Medium 30 3.8.2 Total Transmittance and Total Reflectance 32 3.9 Turbid Media 33 3.9.1 Two]Flux Model of Kubelka–Munk 34 3.9.2 Saunderson’s Equation 36 3.9.3 Colorant Characterization and Formulation 38 3.10 Ulbricht’s Integration Sphere 41 References 43 Bibliography 44 4 Perceptual Phenomenology of Light and Colour 45 4.1 Introduction 45 4.2 Perceived Colours, Categorization and Language 46 4.3 Light Dispersion and Light Mixing 47 4.3.1 Newton’s Prism Experiment, Colour Wheel and Colour Attributes 48 4.3.2 Maxwell’s Disk Experiment 50 4.4 Unique Hues, Colour Opponencies and Degree of Resemblance 52 4.5 Colour Similitude 55 4.6 Unrelated and Related Colours 56 4.6.1 Relative Attributes 56 4.7 Colour Interactions 57 References 65 5 Visual System 67 5.1 Introduction 67 5.2 Eye Anatomy and Optical Image Formation 68 5.3 Eye and Pre]retina Physics 72 5.4 Anatomy of the Retina 74 5.4.1 Retina Layers 76 5.4.2 Fovea 77 5.4.3 Foveola 78 5.4.4 Extra Fovea 78 5.4.5 Macula Lutea 79 5.4.6 Rod and Cone Distribution 79 5.5 From the Retina to the Brain 80 5.5.1 Scotopic Vision 80 5.5.2 Photopic Trichromatic Vision 81 5.5.3 Rushton’s Univariance Principle and Photoreceptor Activation 82 5.5.4 Horizontal Cells 83 5.5.5 Bipolar Cells 83 5.5.6 Amacrine Cells 84 5.5.7 Ganglion Cells and Visual Pathways 84 5.5.8 From the Ganglion Cells to the Visual Cortex 85 5.6 Visual System and Colorimetry 87 Bibliography 88 References 88 6 Colour]Vision Psychophysics 91 6.1 Introduction 91 6.1.1 Psychophysics and Physiology 91 6.1.2 Visual Judgement 92 6.1.3 Modes of Colour Appearance and Viewing Situations 93 6.1.4 Colour Stimuli 95 6.1.5 Colour]Attribute Matching 98 6.1.6 Visual Detection Threshold and Sensitivity 99 6.1.7 Scaling of Colour Attributes 100 6.2 Adaptation 103 6.2.1 Brightness Adaptation 105 6.2.2 Threshold in Dark Adaptation 106 6.3 Absolute Thresholds in Human Vision 108 6.4 Absolute Threshold and Spectral Sensitivity in Scotopic and Photopic Visions 108 6.4.1 Silent Substitution Method 109 6.5 Luminous Efficiency Function 113 6.5.1 Abney Additivity Law and Luminance 114 6.6 Light Adaptation and Sensitivity 116 6.7 Weber’s and Fechner’s Laws 118 6.7.1 Contrast Sensitivity 119 6.7.2 Fechner’s Scaling 119 6.8 Stevens’ Law 119 6.8.1 Brightness Scaling and Stevens’ Law 119 6.9 Fechner’s and Stevens’ Psychophysics 121 6.10 Wavelength Discrimination 121 6.11 Saturation Discrimination and Least Colorimetric Purity 123 6.12 Rushton’s Univariance Principle and Scotopic Vision 124 6.13 Tristimulus Space 125 6.13.1 Rushton’s Univariance Principle and Grassmann’s Laws in Photopic Vision 126 6.13.2 Metamerism 130 6.13.3 Chromaticity 131 6.13.4 Reference Frames in Tristimulus Space 132 6.13.5 Measurement of the Colour-Matching Functions in the RGB Reference Frame 134 6.13.6 Luminance and Exner-Schrödinger’s ‘Helligkeit’ Equation 139 6.13.7 Dichromats and Fundamental Reference Frame 141 6.13.8 Newton’s Centre]of]Gravity Rule and Chromaticity]Diagram Properties 145 6.14 Lightness Scales 149 6.15 Helmholtz-Kohlrausch Effect 150 6.16 Colour Opponencies and Chromatic Valence 153 6.17 MacAdam’s Chromatic Discrimination Ellipses 155 6.18 Perceived Colour Difference 156 6.19 Abney’s and Bezold-Brücke’s Phenomena 161 6.20 Chromatic Adaptation and Colour Constancy 164 6.20.1 Asymmetric Colour Matching 165 6.20.2 Empirical Data 166 6.20.3 Von Kries’s Coefficient Law 166 6.20.4 Retinex 168 6.21 Colour]Vision Psychophysics and Colorimetry 170 References 171 7 CIE Standard Photometry 177 7.1 Introduction 177 7.2 History of the Basic Photometric Unit 180 7.3 CIE 1924 Spectral Luminous Efficiency Function 180 7.4 CIE 1924 and CIE 1988 Standard Photometric Photopic Observers 181 7.5 Photometric and Radiometric Quantities 182 7.6 CIE 1951 Standard Scotopic Photometric Observer 185 7.7 CIE 2005 Photopic Photometric Observer with 10° Visual Field 185 7.8 CIE Fundamental Photopic Photometric Observer with 2°/10° Visual Field 185 7.8.1 Photopic Spectral Luminous Efficiency Functions for the 2° Fundamental Observer 186 7.8.2 Photopic Spectral Luminous Efficiency Functions for the 10° Fundamental Observer 186 References 186 8 Light Sources and Illuminants for Colorimetry 189 8.1 Introduction 189 8.2 Equal]Energy Illuminant 190 8.3 Blackbody Illuminant 191 8.4 CIE Daylights 193 8.5 CIE Indoor Daylights 195 8.6 CIE Standard Illuminants 196 8.7 CIE Light Sources: A, B and C 197 8.8 CIE Sources for Colorimetry 198 8.9 CIE Illuminants: B, C and D 199 8.10 Fluorescent Lamps 199 8.10.1 Typical Fluorescent Lamps 199 8.10.2 New Set of Fluorescent Lamps 200 8.11 Gas]Discharge Lamps 204 8.12 Light]Emitting Diodes 205 References 208 9 CIE Standard Psychophysical Observers and Systems 209 9.1 Introduction 209 9.2 CIE 1931 Standard Colorimetric System and Observer 210 9.2.1 CIE 1931 RGB Reference Frame and WDW Chromaticity]Coordinates Normalization 211 9.2.2 CIE 1931 XYZ Reference Frame 214 9.3 CIE 1964 (Supplementary) Standard Colorimetric Observer/System (10°]Standard Colorimetric Observer) 218 9.4 CIE 1989 Standard Deviate Observer/System 221 9.5 Vos’ 1978 Modified Observer for 2° Visual Field 221 9.5.1 Smith–Pokorny’s Cone Fundamentals 223 9.5.2 Vos’ 1978 2° Fundamental Observer Data and MacLeod–Boynton’s Chromaticity Diagram 223 9.6 CIE Standard Stockman]Sharpe’s ‘Physiologically Relevant’ Fundamentals and XYZ Reference Frame 224 9.6.1 XFYFZF and XF,10YF,10ZF,10 Reference Frames 226 9.6.2 MacLeod-Boynton’s Tristimulus Space and Chromaticity Diagram 229 9.7 CIE Colorimetric Specification of Primary and Secondary Light Sources 232 References 234 10 Chromaticity Diagram from Newton to the CIE 1931 Standard System 237 10.1 Introduction 237 10.2 Newton and the Centre of Gravity Rule 237 10.3 Material Colours and Impalpable Colours in the Eighteenth Century 243 10.4 Physiological Intuitions and the Centre of Gravity Rule – Young, Grassmann, Helmholtz, Maxwell and Schrödinger 245 10.5 Conclusion 251 References 251 11 CIE Standard Psychometric Systems 253 11.1 Introduction to Psychometric Systems in Colour Vision 253 11.2 CIE Lightness L* 254 11.3 Psychometric Chromaticity Diagrams and Related Colour Spaces 255 11.3.1 CIE 1960 (u, v) UCS Psychometric Chromaticity Diagram 255 11.3.2 CIE 1964 (U*, V*, W*) Uniform Colour Space – CIEUVW Colour Space 257 11.3.3 CIE 1976 (u′, v′) UCS Psychometric Chromaticity Diagram 257 11.3.4 CIE 1976 (L*, u*, v*) Colour Space – CIELUV Colour Space 259 11.3.5 CIE 1976 (L*, a*, b*) Colour Space – CIELAB Colour Space 261 11.4 Colour Difference Specification 264 11.4.1 Colour Difference Data 264 11.4.2 CIE 1976 Colour]Difference Formulae 265 11.4.3 CMC(l : c) Colour]Difference Formula 266 11.4.4 CIE 1994 Colour]Difference Formula 267 11.4.5 CIEDE2000 Total Colour]Difference Formula 268 11.4.6 Small Colour Differences in OSA]UCS Space 270 11.4.7 Metamerism Indices 270 11.4.8 Daylight]Simulator Evaluation and ‘Special Metamerism Index: Change in Illuminant’ 273 11.5 Conclusion 276 References 276 12 Instruments and Colorimetric Computation 279 12.1 Introduction 279 12.2 Reflection and Transmission Optical]Modulation 282 12.2.1 Absolute Quantities of Optical]Modulation 282 12.2.2 Relative Quantities of Optical]Modulation 283 12.3 Spectroradiometric and Spectrophotometric Measurements 296 12.3.1 Introduction to the Spectrometer 296 12.3.2 Instrumental Convolution 303 12.3.3 Deconvolution 308 12.4 Colorimetric Calculations 309 12.4.1 CIE Colour Specification 309 12.4.2 Relative Colour Specification 310 12.4.3 Deconvolution 312 12.4.4 Interpolation 313 12.4.5 Extrapolation 315 12.5 Uncertainty in Colorimetric Measurements 315 12.5.1 Laws of Propagation of Uncertainty 317 12.5.2 Uncertainty Computation 318 12.6 Physical Standards for Colour]Instrument Calibration 320 References 322 13 Basic Instrumentation for Radiometry, Photometry and Colorimetry 325 13.1 Introduction 325 13.2 Lighting Cabinet 327 13.3 Visual Comparison Colorimeter 329 13.4 Instruments with Power Spectral Weighting Measurement 330 13.4.1 Photometric Instruments 330 13.4.2 Colorimetric Instruments 332 13.5 Instruments for Measurements with Spectral Analysis 336 13.5.1 Spectroradiometer 336 13.5.2 Spectrophotometer 337 13.5.3 Multiangle Spectrophotometers 337 13.5.4 Fibre]Optic]Reflectance Spectroscopy (FORS) 338 13.6 Glossmeter 341 13.7 Imaging Instruments 343 13.7.1 Imaging Photometer 343 13.7.2 Colorimetric Camera 344 13.7.3 Multispectral and Hyperspectral Camera 344 References 346 14 Colour]Order Systems and Atlases 349 14.1 Introduction 349 14.2 Colour Solid, Optimal Colours and Full Colours 351 14.2.1 MacAdam’s Limit 354 14.3 Ostwald’s Colour]Order System and Atlas 354 14.3.1 Ostwald’s Hue Circle with Temperate Scale 355 14.3.2 Ostwald’s Semichrome 356 14.3.3 Ostwald’s Blackness, Whiteness and Purity 357 14.3.4 Ostwald’s Atlas 358 14.4 Munsell’s Colour]Order System and Atlas 360 14.4.1 Munsell’s Instruments 362 14.4.2 Chromatic Tuning Fork 362 14.4.3 Munsell’s Value and Grey Scale 364 14.4.4 Munsell’s Hue 365 14.4.5 Munsell’s Value in Coloured Scales 367 14.4.6 Colour Sphere and Munsell’s Colour Specification 367 14.4.7 Munsell’s Chroma 369 14.4.8 Colour Tree 369 14.4.9 Munsell’s System and CIE Chromaticity Specification 369 14.4.10 Helmholtz-Kohlrausch’s Effect and Abney’s Hue Shift Phenomenon in the Munsell Atlas 371 14.4.11 Munsell’s Colour Atlas 371 14.5 DIN 6264’s Colour]Order System and Atlas 372 14.6 OSA]UCS’s Colour]Order System and Atlas 374 14.6.1 OSA]UCS’s Lightness 376 14.6.2 OSA]UCS’s (g, j) Coordinates 377 14.6.3 OSA]UCS’s Colour Difference Formula 379 14.6.4 OSA]UCS’s Metrics 379 14.7 NCS’s Colour]Order System and Atlas 380 14.7.1 NCS’s Axioms 381 14.7.2 NCS’s Hue, Chromaticness and Nuance 382 14.7.3 Production of the NCS System and Visual Situation 384 14.7.4 Psychophysics and Psychometrics for NCS 384 14.7.5 Luminance Factor and NCS’s Whiteness Scale 385 14.7.6 NCS’s Atlas 387 References 387 15 Additive Colour Synthesis in Images 391 15.1 Introduction 391 15.2 Video Colour Image 392 15.2.1 RGB Colorimetry 395 15.2.2 Video Signal and γ Correction 397 15.2.3 Tristimulus Space and YIQ Reference Frame 401 15.2.4 sRGB System 404 15.2.5 Prints in the sRGB System 406 15.2.6 Camera, Photo]Site and Pixel 406 15.2.7 Spectral Sensitivities of Digital Cameras 409 15.3 Principles of Halftone Printing 412 15.4 Towards the Colorimetry of Appearance 419 References 420 16 Software (Software developed by Gabriele Simone) 423 16.1 Introduction to the Software 423 16.1.1 Software Installation 423 16.1.2 Data Files 425 16.2 Monitor 429 16.2.1 Monitor Setup 429 16.2.2 Visual Evaluation of Gamma (γ) 430 16.3 Colour]Vision Tests 432 16.4 Visual Contrast Phenomena 440 16.4.1 Simultaneous Brightness Contrast and Crispening 440 16.4.2 Simultaneous Brightness Contrast in Colour Scales 441 16.4.3 Brightness and Chromatic Contrast 442 16.4.4 After Image 442 16.5 Colour Atlases 443 16.5.1 Ostwald’s Atlas 444 16.5.2 Munsell’s Atlas 444 16.5.3 DIN’s Atlas 444 16.5.4 OSA]UCS’ Atlas 446 16.5.5 NCS’ Atlas 447 16.6 CIE 1976 CIELUV and CIELAB Systems 448 16.7 Cone Activation and Tristimulus 450 16.8 CIE Colorimetry 451 16.8.1 CIE Colour Specification 452 16.8.2 CIE Systems 456 16.8.3 Chromaticity Diagrams 459 16.8.4 Fundamental Observers 462 16.8.5 Dominant Wavelength and Purity 463 16.8.6 Tristimulus Space Transformations 463 16.8.7 Colour]Difference Formulae ΔE 464 16.8.8 CIE 1974 Colour Rendering Index Ra 465 16.9 Black Body and Daylight Spectra and Other CIE Illuminant Spectra 470 16.10 Additive Colour Synthesis 471 16.10.1 RGB Monitor, Additive Colour Mixture 472 16.10.2 Halftone CMY Printing 472 16.11 Subtractive Colorant Mixing 474 16.11.1 Two Pigment Mixture 475 16.11.2 Four Pigment Mixture 475 16.12 Spectral Data View and Download – Illuminant-Observer Weights 478 16.13 Save File Opening 478 References 480 Index 481

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Book SynopsisForensic Chemistry: Fundamentals and Applications presents a new approach to the study of applications of chemistry to forensic science. It is edited by one of the leading forensic scientists with each chapter written by international experts specializing in their respective fields, and presents the applications of chemistry, especially analytical chemistry, to various topics that make up the forensic scientists toolkit. This comprehensive, textbook includes in-depth coverage of the major topics in forensic chemistry including: illicit drugs, fibers, fire and explosive residues, soils, glass and paints, the chemistry of fingerprint recovery on porous surfaces, the chemistry of firearms analysis, as well as two chapters on the key tools of forensic science, microscopy and chemometrics. Each topic is explored at an advanced college level, with an emphasis, throughout the text, on the use of chemical tools in evidence analysis. Forensic Chemistry: Fundamentals aTable of ContentsAbout the editor, xii Contributors, xiii Series preface, xv Preface, xvi 1 Drugs of abuse, 1Niamh Nic Daéid 1.1 Introduction, 1 1.2 Law and legislation, 2 1.3 Sampling, 4 1.3.1 Random sampling and representative sampling, 6 1.3.2 Arbitrary sampling, 7 1.3.3 Statistical sampling methods, 8 1.4 Specific drug types, 9 1.4.1 Cannabis, 9 1.4.2 Heroin, 14 1.4.3 Cocaine, 22 1.4.4 Amphetamine]type stimulants, 27 1.4.5 New psychoactive substances, 33 1.5 Conclusions, 36 Acknowledgements, 36 References, 36 2 Textiles, 40Max Houck 2.1 Introduction, 40 2.2 A science of reconstruction, 40 2.2.1 Classification, 41 2.2.2 Comparison, 42 2.2.3 Transfer and persistence, 43 2.3 Textiles, 43 2.3.1 Information, 44 2.3.2 Morphology, 45 2.4 Natural fibers, 48 2.4.1 Animal fibers, 48 2.4.2 Plant fibers, 51 2.5 Manufactured fibers, 52 2.6 Yarns and fabrics, 55 2.6.1 Fabric construction, 56 2.6.2 Finishes, 59 2.7 Fiber types, 59 2.7.1 Acetate, 59 2.7.2 Acrylic, 59 2.7.3 Aramids, 60 2.7.4 Modacrylic, 60 2.7.5 Nylon, 61 2.7.6 Olefins (polypropylene and polyethylene), 61 2.7.7 Polyester, 62 2.7.8 Rayon, 62 2.7.9 Spandex, 65 2.7.10 Triacetate, 66 2.7.11 Bicomponent fibers, 66 2.8 Chemistry, 67 2.8.1 General analysis, 67 2.8.2 Instrumental analysis, 68 2.8.3 Color, 69 2.8.4 Raman spectroscopy, 70 2.8.5 Interpretation, 71 2.9 The future, 72 References, 72 3 Paint and coatings examination, 75Paul Kirkbride 3.1 Introduction, 75 3.2 Paint chemistry, 76 3.2.1 Binders, 76 3.2.2 Dyes and pigments, 86 3.2.3 Additives, 89 3.3 Automotive paint application, 91 3.4 Forensic examination of paint, 92 3.4.1 General considerations, 92 3.4.2 Microscopy, 95 3.4.3 Vibrational spectrometry, 96 3.4.4 SEM]EDX and XRF, 106 3.4.5 Pyrolytic techniques, 111 3.4.6 Color analysis, 116 3.5 Paint evidence evaluation and expert opinion, 120 References, 128 Contents vii 4 Forensic fire debris analysis, 135Reta Newman 4.1 Introduction, 135 4.2 Process overview, 135 4.3 Sample collection, 136 4.4 Ignitable liquid classification, 137 4.5 Petroleum]based ignitable liquids, 144 4.6 Non]petroleum]based ignitable liquids, 160 4.7 Sample preparation, 161 4.8 Sample analysis and data interpretation, 166 4.9 Summary, 172 References, 173 5 Explosives, 175John Goodpaster 5.1 The nature of an explosion, 175 5.1.1 Types of explosions, 175 5.1.2 Explosive effects, 176 5.2 Physical and chemical properties of explosives, 180 5.2.1 Low explosives, 181 5.2.2 High explosives, 186 5.3 Protocols for the forensic examination of explosives and explosive devices, 192 5.3.1 Recognition of evidence, 192 5.3.2 Portable technology and on]scene analysis, 193 5.3.3 In the laboratory, 194 5.4 Chemical analysis of explosives, 200 5.4.1 Consensus standards (TWGFEX), 201 5.4.2 Chemical tests, 203 5.4.3 X]ray techniques, 204 5.4.4 Spectroscopy, 207 5.4.5 Separations, 212 5.4.6 Gas chromatography, 213 5.4.7 Mass spectrometry, 215 5.4.8 Provenance and attribution determinations, 219 5.5 Ongoing research, 221 Acknowledgements, 222 References, 222 Further reading, 226 6 Analysis of glass evidence, 228Jose Almirall and Tatiana Trejos 6.1 Introduction to glass examinations and comparisons, 228 6.2 Glass, the material, 231 6.2.1 Physical and chemical properties, 231 6.2.2 Manufacturing, 233 6.2.3 Fractures and their significance, 236 6.2.4 Forensic considerations: Transfer and persistence of glass, 238 6.3 A brief history of glass examinations, 241 6.4 Glass examinations and comparison, standard laboratory practices, 242 6.4.1 Physical measurements, 243 6.4.2 Optical measurements, 244 6.4.3 Chemical measurements: elemental analysis, 247 6.5 Interpretation of glass evidence examinations and comparisons, 256 6.5.1 Defining the match criteria, 256 6.5.2 Descriptive statistics, 256 6.5.3 Match criteria for refractive index measurements, 257 6.5.4 Informing power of analytical methods, forming the opinion, 260 6.5.5 Report writing and testimony, 262 6.6 Case examples, 263 6.6.1 Case 1: Hit]and]run case, 263 6.6.2 Case 2: Multiple transfer of glass in breaking]and]entry case, 264 6.7 Conclusions, 265 References, 266 7 The forensic comparison of soil and geologic microtraces, 273Richard E. Bisbing 7.1 Soil and geologic microtraces as trace evidence, 273 7.2 Comparison process, 274 7.3 Developing expertise, 278 7.4 Genesis of soil, 279 7.5 Genesis of geologic microtraces, 284 7.6 Collecting questioned samples of unknown origin, 287 7.7 Collecting soil samples of known origin, 288 7.8 Initial comparisons, 290 7.9 Color comparison, 290 7.10 Texture comparison, 293 7.11 Mineral comparison, 297 7.12 Modal analysis, 301 7.13 Automated instrumental modal analysis, 308 7.14 Ecological constituents, 310 7.15 Anthropogenic constituents, 312 7.16 Reporting comparison results, 312 7.17 Future directions and research, 314 Acknowledgments, 314 References, 315 Further reading, 316 8 Chemical analysis for the scientific examination of questioned documents, 318Gerald M. LaPorte 8.1 Static approach, 320 8.2 Dynamic approach, 324 8.3 Ink composition, 324 8.4 Examinations, 328 8.4.1 Physical examinations, 329 8.4.2 Optical examinations, 332 8.4.3 Chemical examinations, 333 8.4.4 Paper examinations, 339 8.5 Questioned documents, crime scenes and evidential considerations, 342 8.5.1 How was the questioned document produced?, 342 8.5.2 What evidence can be used to associate a questioned document with the crime scene and/or victim?, 343 8.5.3 Are there other forensic examinations that can be performed?, 345 8.5.4 Demonstrating that a suspect altered a document, 346 8.6 Interpreting results and rendering conclusions, 347 References, 350 9 Chemical methods for the detection of latent fingermarks, 354Amanda A. Frick, Patrick Fritz, and Simon W. Lewis 9.1 Introduction, 354 9.2 Sources of latent fingermark residue, 355 9.2.1 Aqueous components, 356 9.2.2 Lipid components, 357 9.2.3 Sources of compositional variation, 359 9.3 Chemical processing of latent fingermarks, 361 9.3.1 Amino acid sensitive reagents, 361 9.3.2 Reagents based on colloidal metals, 370 9.3.3 Lipid]sensitive reagents, 377 9.3.4 Other techniques, 383 9.4 Experimental considerations for latent fingermark chemistry research, 384 9.5 Conclusions and future directions, 387 Acknowledgements, 388 References, 388 Further reading, 398 10 Chemical methods in firearms analysis, 400Walter F. Rowe 10.1 Introduction, 400 10.2 Basic firearms examination, 400 10.2.1 Cleaning bullets and cartridges, 402 10.2.2 Analysis of bullet lead, 404 10.2.3 Serial number restoration, 406 10.3 Shooting incident reconstruction, 408 10.3.1 Muzzle]to]target determinations, 411 10.3.2 Firearm primers, 416 10.3.3 Collection of gunshot residue, 425 10.4 Conclusion, 433 References, 433 11 Forensic microscopy, 439Christopher S. Palenik 11.1 The microscope as a tool, 439 11.2 Motivation, 440 11.2.1 Intimidation, 442 11.2.2 Limitations, 442 11.3 Scale, 442 11.3.1 Scale and magnification, 443 11.3.2 Noting scale, 443 11.3.3 Analytical volume and limits of detection, 443 11.4 Finding, 445 11.4.1 Spatial resolution, 445 11.4.2 Recovery resolution, 447 11.4.3 Stereomicroscope, 447 11.5 Preparing, 448 11.5.1 Preservation and documentation, 448 11.5.2 Isolation, 450 11.5.3 Mounting, 451 11.6 Looking, 455 11.6.1 Light microscopy, 456 11.6.2 Scanning electron microscopy, 457 11.7 Analyzing, 458 11.7.1 Polarized light microscopy, 458 11.7.2 Energy dispersive X]ray spectroscopy, 462 11.7.3 FTIR and Raman spectroscopy, 464 11.7.4 Other methods, 465 11.8 Thinking, 465 11.9 Thanking, 467 References, 467 12 Chemometrics, 469Ruth Smith 12.1 Introduction, 469 12.2 Chromatograms and spectra as multivariate data, 470 12.3 Data preprocessing, 470 12.3.1 Baseline correction, 471 12.3.2 Smoothing, 473 12.3.3 Retention]time alignment, 473 12.3.4 Normalization and scaling, 475 12.4 Unsupervised pattern recognition, 477 12.4.1 Hierarchical cluster analysis, 478 12.4.2 Principal components analysis, 480 12.5 Supervised pattern recognition procedures, 485 12.5.1 k]Nearest neighbors, 486 12.5.2 Discriminant analysis, 487 12.5.3 Soft independent modeling of class analogy, 492 12.5.4 Model validation, 493 12.6 Applications of chemometric procedures in forensic science, 494 12.6.1 Fire debris and explosives, 495 12.6.2 Controlled substances and counterfeit medicines, 496 12.6.3 Trace evidence, 497 12.6.4 Impression evidence, 499 12.7 Conclusions, 499 Acknowledgements, 500 References, 500 Index, 504

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Book SynopsisStereoelectronic Effects illustrates the utility of stereoelectronic concepts using structure and reactivity of organic molecules An advanced textbook that provides an up-to-date overview of the field, starting from the fundamental principles Presents a large selection of modern examples of stereoelectronic effects in organic reactivity Shows practical applications of stereoelectronic effects in asymmetric catalysis, photochemical processes, bioorganic chemistry and biochemistry, inorganic and organometallic reactivity, supramolecular chemistry and materials science Trade Review"This book is highly recommended to every chemist and particularly to every student to work through this book. The higher understanding thus obtained in many chemical fields will be beneficial throughout every phase of chemical education and work. It should furthermore be perfectly suitable as accompanying book for an advanced course on this topic." (Angewandte, 1 February 2017)Table of ContentsAcknowledgement ix Supplementory Material x 1 Introduction 1 1.1 Stereoelectronic effects – orbital interactions in control of structure and reactivity 1 1.2 Orbital interactions in theoretical chemistry 3 1.3 The birth of stereoelectronic concepts in organic chemistry 4 References 6 2 Direct Effects of Orbital Overlap on Reactivity 8 2.1 Bond formation without bond breaking: types of overlap in two-orbital interactions 9 2.1.1 Factors controlling σ-bond overlap 12 2.2 Bond formation coupled with bond breaking 25 2.2.1 Three-orbital interactions: stereoelectronic reasons for the preferred trajectories of intermolecular attack at a chemical bond 25 2.3 Stereoelectronics of supramolecular interactions 29 2.3.1 FMO interactions in intermolecular complexes 29 2.3.2 Expanding the palette of supramolecular interactions: from H-bonding to Li-, halogen, pnictogen, chalcogen and tetrel binding 30 References 36 3 Beyond Orbital Overlap: Additional Factors Important for Orbital Interactions. Classifying Delocalizing Interactions 42 3.1 Electronic count: two]electron, one]electron and three]electron bonds 43 3.2 Isovalent vs. sacrificial conjugation 48 3.3 Neutral, negative, and positive hyperconjugation 49 References 52 4 Computational and Theoretical Approaches for Studies of Stereoelectronic Effects 54 4.1 Quantifying orbital interactions 54 4.2 Localized orbitals from delocalized wavefunctions 56 References 60 5 General Stereoelectronic Trends – Donors, Acceptors, and Chameleons 62 5.1 Three types of delocalization: conjugation, hyperconjugation, and σ-conjugation 62 5.2 Geminal and vicinal interactions 63 5.3 Stereoelectronic main rule: antiperiplanarity 64 5.3.1 Effects of bond polarity 65 5.3.2 Polarity-induced acceptor anisotropy 68 5.4 Scales of donor and acceptor ability of orbitals: polarization, hybridization, and orbital energy effects 68 5.4.1 Donors 68 5.4.2 Acceptors 81 5.4.3 Stereoelectronic chameleons: donors masquerading as acceptors 84 5.5 Cooperativity of stereoelectronic effects and antiperiplanar lone pair hypothesis (ALPH) theory – several donors working together 91 5.6 Summary 92 References 92 6 Stereoelectronic Effects with Donor and Acceptor Separated by a Single Bond Bridge: The Broad Spectrum of Orbital Contributions to Conformational Analysis 97 6.1 σ/σ-Interactions 99 6.1.1 Rotational barrier in ethane 99 6.1.2 Axial/equatorial equilibrium in methylcyclohexane 105 6.1.3 The gauche effect 110 6.2 σ/π-Interactions 113 6.2.1 “Eclipsed” and “staggered” conformations of alkenes – stereoelectronic misnomers 114 6.2.2 Carbonyls 117 6.2.3 Strained bonds 121 6.3 p/σ-Interactions 122 6.3.1 Primary, secondary, tertiary carbocation stabilization 122 6.3.2 Hyperconjomers of cyclohexyl cations 124 6.3.3 β-Silicon effect and related β-effects 124 6.4 n/σ-Interactions 126 6.4.1 Anomeric effects 129 6.4.2 Reverse anomeric effect 142 6.4.3 “Anomeric effects without lone pairs”: beyond the n→σ* interactions 143 6.5 n/π-Interactions 147 6.5.1 Esters and related carboxylic acid derivatives 147 6.5.2 Vinyl ethers and enamines 157 6.6 π/π-Interactions 167 6.6.1 Hyperconjugation in alkynes and its relation to the “absence” of conjugation between two triple bonds in 1,3-diynes 168 References 170 7 Stereoelectronic Effects with Donor and Acceptor Separated by a Vinyl Bridge 183 7.1 σ/σ* interactions 184 7.1.1 Cis-effect: the case of two σ-acceptors 184 7.2 σ/π interactions: allenes vs. alkenes 185 7.2.1 Neutral systems 185 7.2.2 Anions 186 7.2.3 Positive conjugation and hyperconjugation in vinyl systems 187 7.2.4 σ→π* delocalization in allenes: allenyl silanes in reactions with electrophiles 188 7.3 Vinyl halides and their carbanions (transition from σC-H→σ*C]Hal to nC→σ*C-Hal interactions) 192 7.3.1 Heteroatom-containing systems 195 7.4 Diazenes and the isomerization of azo compounds 196 7.5 Antiperiplanarity in coordinated bond-breaking and bond-forming processes: eliminations, fragmentations and additions 199 7.6 Syn-periplanarity: the second best choice 207 References 208 8 Remote Stereoelectronic Effects 214 8.1 Extended through space interactions: homoconjugation and homohyperconjugation 215 8.1.1 Homoconjugation 215 8.1.2 Homoanomeric effects 217 8.1.3 Cross-hyperconjugation 223 8.2 Double hyperconjugation and through-bond interactions 223 8.3 Combined through-bond and through-space interactions 228 8.4 Symmetry and cooperativity effects in cyclic structures 229 8.4.1 Hyperaromaticity 229 8.4.2 σ-Aromaticity 230 8.4.3 Double aromaticity 231 References 231 9 Transition State Stabilization with Stereoelectronic Effects: Stereoelectronic Control of Reaction Bottlenecks 236 9.1 Torquoselectivity 240 9.2 Diastereoselection in nucleophilic addition to carbonyl compounds and other π-systems 243 9.3 Electrophilic addition to enamines 245 9.4 Hyperconjugative assistance to alkyne bending and alkyne cycloadditions 246 9.5 Negative conjugation – donation from oxygen lone pairs to breaking bonds 248 9.6 Remote lone pairs in radical reactions: fragmentations 251 References 254 10 Stereoelectronic Effects in Reaction Design 257 10.1 Static stereoelectronics 257 10.2 Dynamic stereoelectronics 259 References 273 11 Stereoelectronic Effects in Action: The Many Doors Opened by Orbital Interactions 275 11.1 Gauche effect (σ→σ* interactions) 275 11.2 Trans-effect – the cousin of gauche effect in organometallic chemistry 283 11.3 Anomeric effects (n→σ* interactions) 284 11.3.1 Cooperativity and anticooperativity in anomeric systems 288 11.3.2 Spectrum of armed and disarmed glycosides 289 11.3.3 Restoring exo-anomeric effect in carbasugars 294 11.4 Bioorganic chemistry and enzyme reactions 311 References 316 12 Probing Stereoelectronic Effects with Spectroscopic Methods 322 12.1 Infrared spectroscopy 323 12.1.1 Bohlmann effect 323 12.1.2 Red-shifting hydrogen bonds – an intermolecular version of the Bohlmann effect 331 12.2 Nuclear magnetic resonance spectroscopy 335 12.2.1 Stereoelectronic effects on chemical shifts 335 12.2.2 Diamagnetic effects in 1 H NMR 336 12.2.3 Paramagnetic effects in 13C NMR 338 12.2.4 Through-space interactions – γ]substituent effects 340 12.2.5 Stereoelectronic effects on coupling constants 342 12.3 Conclusion 368 References 368 Index 376

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Book SynopsisEssential Statistics for the Pharmaceutical Sciences is targeted at all those involved in research in pharmacology, pharmacy or other areas of pharmaceutical science; everybody from undergraduate project students to experienced researchers should find the material they need. This book will guide all those who are not specialist statisticians in using sound statistical principles throughout the whole journey of a research project - designing the work, selecting appropriate statistical methodology and correctly interpreting the results. It deliberately avoids detailed calculation methodology. Its key features are friendliness and clarity. All methods are illustrated with realistic examples from within pharmaceutical science. This edition now includes expanded coverage of some of the topics included in the first edition and adds some new topics relevant to pharmaceutical research. a clear, accessible introduction to the key statistical techniques used Table of ContentsPreface xiii Statistical packages xix About the Website xxi PART 1: PRESENTING DATA 1 1 Data types 3 1.1 Does it really matter? 3 1.2 Interval scale data 4 1.3 Ordinal scale data 4 1.4 Nominal scale data 5 1.5 Structure of this book 6 1.6 Chapter summary 6 2 Data presentation 7 2.1 Numerical tables 8 2.2 Bar charts and histograms 9 2.3 Pie charts 14 2.4 Scatter plots 16 2.5 Pictorial symbols 21 2.6 Chapter summary 22 PART 2: INTERVAL-SCALE DATA 23 3 Descriptive statistics for interval scale data 25 3.1 Summarising data sets 25 3.2 Indicators of central tendency: Mean, median and mode 26 3.3 Describing variability – Standard deviation and coefficient of variation 33 3.4 Quartiles – Another way to describe data 36 3.5 Describing ordinal data 40 3.6 Using computer packages to generate descriptive statistics 43 3.7 Chapter summary 45 4 The normal distribution 47 4.1 What is a normal distribution? 47 4.2 Identifying data that are not normally distributed 48 4.3 Proportions of individuals within 1SD or 2SD of the mean 52 4.4 Skewness and kurtosis 54 4.5 Chapter summary 57 4.6 Appendix: Power, sample size and the problem of attempting to test for a normal distribution 58 5 Sampling from populations. The standard error of the mean 63 5.1 Samples and populations 63 5.2 From sample to population 65 5.3 Types of sampling error 65 5.4 What factors control the extent of random sampling error when estimating a population mean? 68 5.5 Estimating likely sampling error – The SEM 70 5.6 Offsetting sample size against SD 74 5.7 Chapter summary 75 6 95% Confidence Interval for the Mean and Data Transformation 77 6.1 What is a confidence interval? 78 6.2 How wide should the interval be? 78 6.3 What do we mean by ‘95%’ confidence? 79 6.4 Calculating the interval width 80 6.5 A long series of samples and 95% C.I.s 81 6.6 How sensitive is the width of the C.I. to changes in the SD, the sample size or the required level of confidence? 82 6.7 Two statements 85 6.8 One-sided 95% C.I.s 85 6.9 The 95% C.I. for the difference between two treatments 88 6.10 The need for data to follow a normal distribution and data transformation 90 6.11 Chapter summary 94 7 The two-sample t-test (1): Introducing hypothesis tests 95 7.1 The two-sample t-test – an example of an hypothesis test 96 7.2 Significance 103 7.3 The risk of a false positive finding 104 7.4 What aspects of the data will influence whether or not we obtain a significant outcome? 106 7.5 Requirements for applying a two-sample t-test 108 7.6 Performing and reporting the test 109 7.7 Chapter summary 110 8 The two]sample t-test (2): The dreaded P value 111 8.1 Measuring how significant a result is 111 8.2 P values 112 8.3 Two ways to define significance? 113 8.4 Obtaining the P value 113 8.5 P values or 95% confidence intervals? 114 8.6 Chapter summary 115 9 The two-sample t-test (3): False negatives, power and necessary sample sizes 117 9.1 What else could possibly go wrong? 118 9.2 Power 119 9.3 Calculating necessary sample size 122 9.4 Chapter summary 130 10 The two-sample t-test (4): Statistical significance, practical significance and equivalence 131 10.1 Practical significance – Is the difference big enough to matter? 131 10.2 Equivalence testing 135 10.3 Non-inferiority testing 139 10.4 P values are less informative and can be positively misleading 141 10.5 Setting equivalence limits prior to experimentation 143 10.6 Chapter summary 144 11 The two-sample t-test (5): One-sided testing 145 11.1 Looking for a change in a specified direction 146 11.2 Protection against false positives 148 11.3 Temptation! 149 11.4 Using a computer package to carry out a one-sided test 153 11.5 Chapter summary 153 12 What does a statistically significant result really tell us? 155 12.1 Interpreting statistical significance 155 12.2 Starting from extreme scepticism 159 12.3 Bayesian statistics 160 12.4 Chapter summary 161 13 The paired t-test: Comparing two related sets of measurements 163 13.1 Paired data 163 13.2 We could analyse the data by a two-sample t]test 165 13.3 Using a paired t-test instead 165 13.4 Performing a paired t-test 166 13.5 What determines whether a paired t-test will be significant? 169 13.6 Greater power of the paired t-test 170 13.7 Applicability of the test 170 13.8 Choice of experimental design 171 13.9 Requirement for applying a paired t-test 172 13.10 Sample sizes, practical significance and one-sided tests 173 13.11 Summarising the differences between paired and two-sample t-tests 175 13.12 Chapter summary 175 14 Analyses of variance: Going beyond t-tests 177 14.1 Extending the complexity of experimental designs 177 14.2 One-way analysis of variance 178 14.3 Two-way analysis of variance 188 14.4 Fixed and random factors 198 14.5 Multi-factorial experiments 204 14.6 Chapter summary 204 15 Correlation and regression – Relationships between measured values 207 15.1 Correlation analysis 208 15.2 Regression analysis 218 15.3 Multiple regression 225 15.4 Chapter summary 235 16 Analysis of Covariance 237 16.1 A clinical trial where ANCOVA would be appropriate 238 16.2 General interpretation of ANCOVA results 239 16.3 Analysis of the COPD trial results 241 16.4 Advantages of ANCOVA over a simple two]sample t]test 244 16.5 Chapter summary 249 PART 3: NOMINAL-SCALE DATA 251 17 Describing categorised data and the goodness of fit chi-square test 253 17.1 Descriptive statistics 254 17.2 Testing whether the population proportion might credibly be some pre-determined figure 258 17.3 Chapter summary 264 18 Contingency chi-square, Fisher’s and McNemar’s tests 265 18.1 Using the contingency chi]square test to compare observed proportions 266 18.2 Extent of change in proportion with an expulsion – Clinically significant? 270 18.3 Larger tables – Attendance at diabetic clinics 270 18.4 Planning experimental size 273 18.5 Fisher’s exact test 275 18.6 McNemar’s test 277 18.7 Chapter summary 279 18.8 Appendix 280 19 Relative Risk, Odds Ratio and Number Needed to Treat 283 19.1 Measures of treatment effect – Relative Risk, Odds Ratio and Number Needed to Treat 283 19.2 Similarity between Relative Risk and Odds Ratio 287 19.3 Interpreting the various measures 288 19.4 95% confidence intervals for measures of effect size 289 19.5 Chapter summary 293 20 Logistic regression 295 20.1 Modelling a binary outcome 295 20.2 Additional predictors and the problem of confounding 304 20.3 Analysis by computer package 307 20.4 Extending logistic regression beyond dichotomous outcomes 308 20.5 Chapter summary 309 20.6 Appendix 309 PART 4: ORDINAL-SCALE DATA 311 21 Ordinal and non-normally distributed data. Transformations and non-parametric tests 313 21.1 Transforming data to a normal distribution 314 21.2 The Mann–Whitney test – a non]parametric method 318 21.3 Dealing with ordinal data 323 21.4 Other non-parametric methods 325 21.5 Chapter summary 333 21.6 Appendix 334 PART 5: OTHER TOPICS 337 22 Measures of agreement 339 22.1 Answers to several questions 340 22.2 Several answers to one question – do they agree? 344 22.3 Chapter summary 358 23 Survival analysis 361 23.1 What special problems arise with survival data? 362 23.2 Kaplan–Meier survival estimation 363 23.3 Declining sample sizes in survival studies 369 23.4 Precision of sampling estimates of survival 369 23.5 Indicators of survival 371 23.6 Testing for differences in survival 374 23.7 Chapter summary 383 24 Multiple testing 385 24.1 What is it and why is it a problem? 385 24.2 Where does multiple testing arise? 386 24.3 Methods to avoid false positives 388 24.4 The role of scientific journals 392 24.5 Chapter summary 393 25 Questionnaires 395 25.1 Types of questions 396 25.2 Sample sizes and low return rates 398 25.3 Analysing the results 399 25.4 Problem number two: Confounded questionnaire data 401 25.5 Problem number three: Multiple testing with questionnaire data 401 25.6 Chapter summary 403 Index 000

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Book SynopsisThis book provides a rigorous treatment of the fundamental concepts and techniques involved in process modeling and simulation.Table of ContentsPreface xiii Notation xv 1 Introduction 1 1.1 System 1 1.1.1 Uniform System 2 1.1.2 Properties of System 2 1.1.3 Classification of System 3 1.1.4 Model 3 1.2 Process 3 1.2.1 Classification of Processes 4 1.2.2 Process Model 5 1.3 Process Modeling 6 1.3.1 Relations 7 1.3.2 Assumptions 7 1.3.3 Variables and Parameters 8 1.4 Process Simulation 9 1.4.1 Utility 9 1.4.2 Simulation Methods 10 1.5 Development of Process Model 11 1.6 Learning about Process 13 1.7 System Specification 14 Bibliography 16 Exercises 16 2 Fundamental Relations 17 2.1 Basic Form 17 2.1.1 Application 19 2.2 Mass Balance 21 2.2.1 Microscopic Balances 21 2.2.2 Equation of Change for Mass Fraction 23 2.3 Mole Balance 24 2.3.1 Microscopic Balances 24 2.3.2 Equation of Change for Mole Fraction 25 2.4 Momentum Balance 26 2.4.1 Convective Momentum Flux 27 2.4.2 Total Momentum Flux 28 2.4.3 Macroscopic Balance 29 2.4.4 Microscopic Balance 31 2.5 Energy Balance 33 2.5.1 Microscopic Balance 33 2.5.2 Macroscopic Balance 35 2.6 Equation of Change for Kinetic and Potential Energy 38 2.6.1 Microscopic Equation 38 2.6.2 Macroscopic Equation 40 2.7 Equation of Change for Temperature 41 2.7.1 Microscopic Equation 41 2.7.2 Macroscopic Equation 42 2.A Enthalpy Change from Thermodynamics 44 2.B Divergence Theorem 48 2.C General Transport Theorem 50 2.D Equations in Cartesian, Cylindrical and Spherical Coordinate Systems 53 2.D.1 Equations of Continuity 54 2.D.2 Equations of Continuity for Individual Species 54 2.D.3 Equations of Motion 55 2.D.4 Equations of Change for Temperature 56 Bibliography 57 Exercises 57 3 Constitutive Relations 59 3.1 Diffusion 59 3.1.1 Multicomponent Mixtures 60 3.2 Viscous Motion 60 3.2.1 Newtonian Fluids 61 3.2.2 Non-Newtonian Fluids 62 3.3 Thermal Conduction 63 3.4 Chemical Reaction 63 3.5 Rate of Reaction 65 3.5.1 Equations of Change for Moles 66 3.5.2 Equations of Change for Temperature 67 3.5.3 Macroscopic Equation of Change for Temperature 69 3.6 Interphase Transfer 71 3.7 Thermodynamic Relations 72 3.A Equations in Cartesian, Cylindrical and Spherical Coordinate Systems 74 3.A.1 Equations of Continuity for Binary Systems 74 3.A.2 Equations of Motion for Newtonian Fluids 75 3.A.3 Equations of Change for Temperature 76 References 77 Bibliography 77 Exercises 78 4 Model Formulation 79 4.1 Lumped-Parameter Systems 80 4.1.1 Isothermal CSTR 80 4.1.2 Flow through Eccentric Reducer 83 4.1.3 Liquid Preheater 84 4.1.4 Non-Isothermal CSTR 87 4.2 Distributed-Parameter Systems 90 4.2.1 Nicotine Patch 90 4.2.2 Fluid Flow between Inclined Parallel Plates 93 4.2.3 Tapered Fin 96 4.2.4 Continuous Microchannel Reactor 99 4.2.5 Oxygen Transport to Tissues 103 4.2.6 Dermal Heat Transfer in Cylindrical Limb 106 4.2.7 Solvent Induced Heavy Oil Recovery 108 4.2.8 Hydrogel Tablet 112 4.2.9 Neutron Diffusion 117 4.2.10 Horton Sphere 119 4.2.11 Reactions around Solid Reactant 122 4.3 Fluxes along Non-Linear Directions 127 4.3.1 Saccadic Movement of an Eye 128 4.A Initial and Boundary Conditions 131 4.A.1 Initial Condition 131 4.A.2 Boundary Condition 131 4.A.3 Periodic Condition 132 4.B Zero Derivative at the Point of Symmetry 133 4.C Equation of Motion along the Radial Direction in Cylindrical Coordinates 134 References 137 Exercises 137 5 Model Transformation 139 5.1 Transformation between Orthogonal Coordinate Systems 139 5.1.1 Scale Factors 139 5.1.2 Differential Elements 142 5.1.3 Vector Representation 143 5.1.4 Derivatives of Unit Vectors 144 5.1.5 Differential Operators 146 5.2 Transformation between Arbitrary Coordinate Systems 155 5.2.1 Transformation of Velocity 155 5.2.2 Transformation of Spatial Derivatives 156 5.2.3 Correctness of Transformation Matrices 156 5.3 Laplace Transformation 161 5.3.1 Examples 162 5.3.2 Properties of Laplace Transforms 164 5.3.3 Solution of Linear Differential Equations 168 5.4 Miscellaneous Transformations 178 5.4.1 Higher Order Derivatives 178 5.4.2 Scaling 178 5.4.3 Change of Independent Variable 179 5.4.4 Semi-Infinite Domain 179 5.4.5 Non-Autonomous to Autonomous Differential Equation 180 5.A Differential Operators in an Orthogonal Coordinate System 180 5.A.1 Gradient of a Scalar 180 5.A.2 Divergence of a Vector 181 5.A.3 Laplacian of a Scalar 184 5.A.4 Curl of a Vector 184 References 186 Bibliography 186 Exercises 186 6 Model Simplification and Approximation 189 6.1 Model Simplification 189 6.1.1 Scaling and Ordering Analysis 190 6.1.2 Linearization 193 6.2 Model Approximation 200 6.2.1 Dimensional Analysis 201 6.2.2 Model Fitting 204 6.A Linear Function 220 6.B Proof of Buckingham Pi Theorem 221 6.C Newton's Optimization Method 223 References 224 Bibliography 224 Exercises 225 7 Process Simulation 227 7.1 Algebraic Equations 227 7.1.1 Linear Algebraic Equations 227 7.1.2 Non-Linear Algebraic Equations 236 7.2 Differential Equations 241 7.2.1 Ordinary Differential Equations 242 7.2.2 Explicit Runge–Kutta Methods 242 7.2.3 Step-Size Control 246 7.2.4 Stiff Equations 247 7.3 Partial Differential Equations 253 7.3.1 Finite Difference Method 255 7.4 Differential Equations with Split Boundaries 263 7.4.1 Shooting Newton–Raphson Method 264 7.5 Periodic Differential Equations 268 7.5.1 Shooting Newton–Raphson Method 268 7.6 Programming of Derivatives 271 7.7 Miscellanea 274 7.7.1 Integration of Discrete Data 274 7.7.2 Roots of a Single Algebraic Equation 276 7.7.3 Cubic Equations 278 7.A Partial Pivoting for Matrix Inverse 281 7.B Derivation of Newton–Raphson Method 281 7.B.1 Quadratic Convergence 282 7.C General Derivation of Finite Difference Formulas 284 7.C.1 First Derivative, Centered Second Order Formula 285 7.C.2 Second Derivative, Forward Second Order Formula 286 7.C.3 Third Derivative, Mixed Fourth Order Formula 287 7.C.4 Common Finite Difference Formulas 289 References 291 Bibliography 291 Exercises 291 8 Mathematical Review 295 8.1 Order of Magnitude 295 8.2 Big-O Notation 295 8.3 Analytical Function 295 8.4 Vectors 296 8.4.1 Vector Operations 297 8.4.2 Cauchy–Schwarz Inequality 302 8.5 Matrices 302 8.5.1 Terminology 303 8.5.2 Matrix Operations 304 8.5.3 Operator Inequality 305 8.6 Tensors 306 8.6.1 Multilinearity 306 8.6.2 Coordinate-Independence 306 8.6.3 Representation of Second Order Tensor 307 8.6.4 Einstein or Index Notation 308 8.6.5 Kronecker Delta 310 8.6.6 Operations Involving Vectors and Second Order Tensors 310 8.7 Differential 318 8.7.1 Derivative 318 8.7.2 Partial Derivative and Differential 318 8.7.3 Chain Rule of Differentiation 319 8.7.4 Material and Total Derivatives 321 8.8 Taylor Series 322 8.8.1 Multivariable Taylor Series 323 8.8.2 First Order Taylor Expansion 323 8.9 L'Hôpital's Rule 326 8.10 Leibniz's Rule 326 8.11 Integration by Parts 327 8.12 Euler’s Formulas 327 8.13 Solution of Linear Ordinary Differential Equations 327 8.13.1 Single First Order Equation 327 8.13.2 Simultaneous First Order Equations 328 Bibliography 332 Index 333

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Book SynopsisWritten by the creator of Rieke metals, valuable for chemical reaction methods and efficiency, this groundbreaking book addresses a significant aspect of organic and inorganic chemistry. The author discusses synthetic methods, preparation procedures, chemical reactions, and applications for highly reactive metals and organometallic reagents.Table of ContentsPreface xvii 1 Genesis of Highly Reactive Metals 1 2 General Methods of Preparation and Properties 5 2.1 General Methods for Preparation of Highly Reactive Metals 5 2.2 Physical Characteristics of Highly Reactive Metal Powders 8 2.3 Origin of the Metals’ High Reactivity 9 References 10 3 Zinc 13 3.1 General Methods for Preparation of Rieke Zinc 13 3.2 Direct Oxidative Addition of Reactive Zinc to Functionalized Alkyl, Aryl, and Vinyl Halides 16 3.3 Reactions of Organozinc Reagents with Acid Chlorides 20 3.4 Reactions of Organozinc Reagents with α,β-Unsaturated Ketones 27 3.5 Reactions of Organozinc Reagents with Allylic and Alkynyl Halides 30 3.6 Negishi Cross-Coupling of Vinyl and Aryl Organozinc Halides 34 3.7 Intramolecular Cyclizations and Conjugate Additions Mediated by Rieke Zinc 42 3.8 The Formation and Chemistry of Secondary and Tertiary Alkylzinc Halides 44 3.9 Electrophilic Amination of Organozinc Halides 50 3.10 Reformatsky and Reformatsky-Like Reagents and Their Chemistry 52 3.11 Configurationally Stable Organozinc Reagents and Intramolecular Insertion Reactions 54 3.12 Preparation of Tertiary Amides via Aryl, Heteroaryl, and Benzyl Organozinc Reagents 55 3.13 Preparation of 5-Substituted-2-Furaldehydes 61 3.14 Preparation and Chemistry of 4-Coumarylzinc Bromide 73 3.15 Preparation and Cross-Coupling of 2-Pyridyl and 3-Pyridylzinc Bromides 77 3.16 Preparation of Functionalized α-Chloromethyl Ketones 106 3.17 Rieke Zinc as a Reducing Agent for Common Organic Functional Groups 108 3.18 Detailed Studies on the Mechanism of Organic Halide Oxidative Addition at a Zinc Metal Surface 111 3.19 Regiocontrolled Synthesis of Poly(3-Alkylthiophenes) Mediated by Rieke Zinc: A New Class of Plastic Semiconductors 133 4 Magnesium 161 4.1 General Background and Mechanistic Details of Grignard Reaction 161 4.2 General Methods for Preparation of Rieke Magnesium 165 4.3 Grignard Reagent Formation and Range of Reactivity of Magnesium 167 4.4 1,3-Diene-Magnesium Complexes and Their Chemistry 172 4.5 Regioselectivity of Reaction of Complexes with Electrophiles 173 4.6 Carbocyclization of (1,4-Diphenyl-2-butene-1,4-diyl) magnesium with Organic Dihalides 175 4.7 1,2-Dimethylenecycloalkane-Magnesium Reagents 175 4.8 Synthesis of Fused Carbocycles, β-γ-Unsaturated Ketones, and 3-Cyclopentenols from Conjugated Diene-Magnesium Reagents 178 4.9 Synthesis of Spiro-γ-Lactones and Spiro-δ-Lactones from 1,3-Diene-Magnesium Reagents 184 4.10 Synthesis of γ-Lactams from Conjugated Diene-Magnesium Reagents 190 4.11 Low-Temperature Grignard Chemistry 192 4.12 Typical Procedures for Preparation of Active Magnesium and Typical Grignard Reactions as Well as 1,3-Diene Chemistry 197 5 Copper 209 5.1 Background of Copper and Organocopper Chemistry 209 5.2 Development of Rieke Copper 210 5.3 Phosphine-Based Copper 211 5.4 Lithium 2-Thienylcyanocuprate-Based Copper 220 5.5 Copper Cyanide-Based Active Copper 224 5.6 Formal Copper Anion Preparation and Resulting Chemistry 228 5.7 Typical Experimental Details of Copper Chemistry 232 6 Indium 241 6.1 Background and Synthesis of Rieke Indium 241 6.2 Preparation of Organoindium Compounds 241 6.3 Preparation and Reactions of Indium Reformatsky Reagents 246 6.4 Experimental Details for Preparation and Reactions of Activated Indium 250 7 Nickel 255 7.1 Preparation of Rieke Nickel, Characterization of Active Nickel Powder, and Some Chemistry 255 7.2 Preparation of 3-Aryl-2-hydroxy-1-propane by Nickel-Mediated Addition of Benzylic Halides to 1,2-Diketones 261 7.3 Preparation of 3-Arylpropanenitriles by Nickel-Mediated Reaction of Benzylic Halides with Haloacetonitriles 265 7.4 Reformatsky-Type Additions of Haloacetonitriles to Aldehydes Mediated by Metallic Nickel 267 7.5 Preparation of Symmetrical 1,3-Diarylpropan-2-ones from Benzylic Halides and Alkyl Oxalyl Chlorides 269 7.6 Nickel-Mediated Coupling of Benzylic Halides and Acyl Halides to Yield Benzyl Ketones 273 7.7 Nickel-Assisted Room Temperature Generation and Diels–Alder Chemistry of o-Xylylene Intermediates 275 8 Manganese 305 8.1 Preparation of Rieke Manganese 305 8.2 Direct Formation of Aryl-, Alkyl-, and Vinylmanganese Halides Oxidative Addition of the Active Metal to the Corresponding Halide 306 8.3 Direct Formation of Organomanganese Tosylates and Mesylates and Some Cross-Coupling Reactions 316 8.4 Benzylic Manganese Halides, Sulfonates, and Phosphates: Preparation, Coupling Reactions, and Applications in New Reactions 320 8.5 Preparation and Coupling Reactions of Thienylmanganese Halides 339 8.6 Synthesis of β-Hydroxy Esters Using Active Manganese 343 8.7 Reductive Coupling of Carbonyl-Containing Compounds and Imines Using Reactive Manganese 347 8.8 Preparation of Heteroarylmanganese Reagents and Their Cross-Coupling Chemistry 355 9 Calcium 371 9.1 Preparation of Rieke Calcium 371 9.2 Oxidative Addition Reactions of Rieke Calcium with Organic Halides and Some Subsequent Reactions 372 9.3 Preparation and Reaction of Calcium Cuprate Reagents 373 9.4 Preparation and Reactions of Calcium Metallocycles 377 9.5 Synthesis of Polyphenylcarbynes Using Highly Reactive Calcium, Barium, and Strontium: A Precursor for 9.6 Chemical Modification of Halogenated Polystyrenes Using Rieke Calcium or Rieke Copper 386 10 Barium 391 10.1 Preparation of Rieke Barium 391 10.2 Oxidative Addition of Rieke Barium to Allylic Halides: Preparation of Stereochemically Homogeneous Allylic Barium Reagents 392 11 Iron 395 11.1 Preparation of Highly Reactive Iron and Some Oxidative Addition Chemistry 395 12 Palladium and Platinum 399 12.1 Preparation of Highly Reactive Palladium and Platinum and Some Oxidative Addition Chemistry 399 13 Highly Reactive Uranium and Thorium 407 13.1 Two Methods for Preparation of Highly Reactive Uranium and Thorium: Use of a Novel Reducing Agent Naphthalene Dianion 407 14 Aluminum 425 14.1 Preparation of Highly Reactive Aluminum and Reaction with Aryl Halides 425 15 Cobalt 429 15.1 Two Methods for Preparing Rieke Cobalt: Reaction with CO and Also Fischer–Tropsch Chemistry 429 16 Chromium 443 16.1 Preparation of Highly Reactive Chromium Metal and Its Reaction with CO to Yield Cr(CO)6 443 References 446 Index 447

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Book SynopsisThis book presents a guidance on a large range of decision aids for risk analysts and decision makers in industry so that vital decisions can be made in a more consistent, logical, and rigorous manner. It provide good industry practices on how risk decision making is conducted in the chemical industry from many risk information sources as well as all the elements that need to be addressed to ensure good decisions are being made. Topics Include: Identifying Risk Decisions, A Risk Decision Strategy for Process Safety, Case Studies in Risk Decision Making Failures, Guidance on Selecting Decision Aids, Templates for Decision Making in Risk-Based Process Safety, Understanding Process Hazards & Worst Possible Consequences, Management of Change as an Exercise in Risk Identification, Inherently Safer Design as an Exercise in Risk Tradeoff Analysis, Using LOPA and Risk Matrices in Risk Decisions, Using CPQRA and Safety Risk Criteria in Risk Decisions, Group Decision Making, Avoiding DecisionTable of ContentsContents v List of Tables xi List of Figures xiii Acronyms and Abbreviations xv Glossary xix Acknowledgements xxxi Preface xxxiii Introduction 35 1.1 History of Approaches to Process Safety Management 35 1.2 The Paradigm of Risk-Based Process Safety Management 36 1.2.1 Risk Based Process Safety (RBPS) Management 36 1.2.2 Risk Decisions Characteristics 39 1.3 A Risk Decision Making Method 40 1.4 Road Map and Relationship of this Book with Other Material 41 1.5 Risk Decisions during Process Life Cycle 43 1.6 Pros and cons 44 1.7 Summary 44 Key Concepts in Risk Management 47 2.1 Risk Management Process 47 2.2 Risk Identification – Risk Scenario 47 2.2.1 Risk Identification 49 2.3 Risk Analysis - Consequences and Frequency 49 2.3.1 Consequences and Impacts 50 2.3.2 Frequency 50 2.3.3 Risk Estimation 51 2.4 Risk Evaluation 56 2.4.1 Decision criteria 56 2.4.2 Qualitative, Semi-Quantitative and Quantitative Risk Criteria 59 2.4.3 Risk Reduction Factor 61 2.5 Summary 62 Understanding Process Hazards, Consequences and Risks 63 3.1 Process Hazards 63 3.1.1 Acute Toxicity 63 3.1.2 Flammability and Explosivity 67 3.1.3 Chemical Reactivity 70 3.1.4 Significant or Large Environmental Release Hazards 72 3.1.5 Other Process Hazards 72 3.2 Risk Identification 73 3.3 Consequences and Impacts 73 3.4 Frequency 74 3.5 Risk 76 Risk Decisions and Strategies 79 4.1 Objectives and attributes 79 4.1.1 Objectives 79 4.1.2 Attributes 79 4.2 Process Life Cycle and Alternatives 81 4.3 The Decision Process 82 4.3.1 Define the Problem 82 4.3.2 Evaluate the Baseline Risk 83 4.3.3 Identify the Alternatives 83 4.3.4 Screen the Alternatives 84 4.3.5 Make the Decision 84 4.4 Objectives and Outcomes 84 4.5 Tradeoffs 85 4.6 Uncertainty 87 4.7 Risk Tolerance 90 4.8 Linked Decisions 91 4.9 Decision trees 92 Decision Making 95 5.1 Defining the Decision Problem 95 5.1.1 Types of Decisions 95 5.2 Selecting a Decision Tool 97 5.2.1 Progression of Risk Analysis Tools 97 5.2.2 Factors in Decision Tool Selection 98 5.3 Assembling the Appropriate Assessment Resources 101 5.3.1 Team Members 101 5.3.2 Opening Meeting 104 5.3.2 Tools/Methods 104 5.3.3 Time 105 5.4 Define decision criteria 105 5.4.1 Process Safety Risk Criteria 105 5.4.2 Other Criteria 107 5.5 Making the decision 107 5.5.1 Characteristics of Decision Aids 107 5.5.2 Appling the Decision Tools, Aids, and Criteria 108 5.5.3 Recognizing and Dealing with Uncertainties 111 5.5.4 Recognizing the Need to Escalate the Decision 113 5.6 Finalizing decision and the approval process 114 5.7 Communicating, Documenting, and implementing the Decision 114 5.7 Summary 116 Potential Decision Traps 117 6.1 Introduction 117 6.2 Anchoring Trap 117 6.2.1 Anchoring Trap Example, Titanic 118 6.2.2 Countering the Anchoring Trap 118 6.3 Status-Quo Trap 119 6.3.1 Status Quo Examples 119 6.3.2 Countering the Status-Quo Trap 120 6.4 Sunk-cost and escalation of commitment trap 120 6.4.1 Countering the Sunk-Cost Trap 121 6.5 Confirming-Evidence Trap 121 6.5.1 Countering the Confirming Evidence Trap 122 6.6 Framing Trap 122 6.6.1 Framing Example 123 6.6.2 Countering the Framing Trap 123 6.7 Estimating and Forecasting Trap 123 6.7.1 Overconfidence 123 6.7.2 Prudence 126 6.7.3 Recallability 127 6.7.4 Countering Estimating and Forecasting Traps 127 6.8 Groupthink Trap 128 6.8.1 Groupthink Example, Flixborough, UK Explosion 128 6.8.2 Countering the Groupthink Trap 128 6.9 Summary 129 Inherently Safer Design 131 7.1 Introduction to inherently safer design 131 7.2 Inherently Safer Design Strategies 131 7.3 Hierarchy of Risk Management Controls 132 7.4 ISD examples to illustrate decision Process 133 7.4.1 Example with minimization 135 7.4.2 Example with moderation 136 7.4.3 Example with simplification 137 7.4.3 Other tradeoffs 137 Make versus buy 138 Substitution 138 7.5 Summary 138 Management of Change 139 8.1 Introduction 139 8.2 Decision Approval level 143 8.3 Examples of Decision Process Applied to Changes 144 8.3.1 Equipment Change 144 8.3.2 Procedural Change 145 8.3.3 Process Parameter Change 146 8.3.4 Organizational Change 147 8.3.5 Raw Material Change 148 8.3.6 Vendor Change 149 8.4 Summary 150 Using LOPA and Risk Matrices in Risk Decisions 151 9.1 Introduction 151 9.2 Risk Matrices 151 9.2.1 Risk Matrix Format 152 9.3 Layer of Protection Analysis 155 9.3.1 Independent Protection Layers 158 9.3.2 LOPA Format 159 9.4 Phosgene Handling Process for Risk Decision Example 159 9.4.1 Description 159 9.4.2 Risk Matrix for Phosgene Handling Example 161 9.5 Phosgene Example Decision Process Using Risk Matrix 164 9.6 Decision Process for Phosgene Example Using LOPA 165 9.7 Summary 172 Using QRA and Safety Risk Criteria in Risk Decisions 173 10.1 Introduction to CPQRA 173 10.1.1 Calculate Frequencies 173 10.1.2 Calculate Consequences 178 10.1.3 Quantitative Risk Analysis (QRA) 179 10.2 Safety Risk Criteria 179 10.2.1 Scope of Risk Criteria 179 10.2.2 Individual and Societal Risk 180 10.2.3 Continual Improvement 184 10.3 High Consequence Low Probability (HCLP) Events 185 10.4 Examples 188 10.4.1 Comparing Design Options: Bromine Handling Facility 188 10.4.2 Compliance and Continual Improvement: Organic Acid Vent System 192 10.4.3 Special Case: The Domino Effect 193 10.5 Summary 195 Decision Implementation 197 11.1 Introduction 197 11.2 Implementation 197 11.3 Documentation 197 11.3.1 Importance of a decision document 197 11.3.2 Writing recommendations 197 11.3.3 Advice of legal counsel 198 11.3.4 Contents of the decision document 199 11.3.5 Retention of the decision document 199 11.4 Revalidation 200 11.4.1 Time based 200 11.4.2 Situation based 200 11.5 Summary 201 Summary and Lessons 203 12.1 Introduction 203 12.2 Case Studies in Risk: Decision Making Failures 203 12.2.1 Failure to Define the Problem 203 12.2.2 Failure to Establish Baseline Risk and Identify Alternatives 204 12.2.3 Make the Decision - Failure to consider tradeoffs 205 12.2.4 Make the Decision - Failure to understand uncertainty 206 12.2.5 Make the Decision – Failure to do risk identification and Failure to probe risk tolerance 206 12.2.6 Make the Decision - Failure to recognize linked decisions 207 12.3 Lessons and Summary 207 References 211 Index 219

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Book SynopsisUniquely describes both the crystallography and properties of perovskite related materials. Practical applications in solar cells, microelectronics and telecommunications Interdisciplinary topic drawing on materials science, chemistry, physics, and geology Contains problems and answers to enhance knowledge retention Table of ContentsPreface xi 1 The ABX3 Perovskite Structure 1 1.1 Perovskites 1 1.2 The Cubic Perovskite Structure: SrTiO3 4 1.3 The Goldschmidt Tolerance Factor 6 1.4 ABX3 Perovskite Structure Variants 11 1.5 Cation Displacement: BaTiO3 as an Example 12 1.6 Jahn–Teller Octahedral Distortion: KCuF3 as an Example 16 1.7 Octahedral Tilting 19 1.7.1 Tilt Descriptions 19 1.7.2 Trigonal Symmetry: LaAlO3 as an Example 24 1.7.3 Orthorhombic Symmetry: GdFeO3 and CaTiO3 as Examples 26 1.8 Symmetry Relationships 30 1.9 Hybrid Organic–Inorganic Perovskites 33 1.10 Antiperovskites 34 1.10.1 Cubic and Related Structures 34 1.10.2 Other Structures 36 1.11 Structure‐Field Maps 36 1.12 Theoretical Calculations 38 References 40 Further Reading 40 2 ABX3–Related Structures 42 2.1 Double Perovskites and Related Ordered Structures 42 2.1.1 Rock‐Salt Ordered Double Perovskites 42 2.1.2 Other Ordered Perovskites 45 2.1.3 AA′3B4O12‐Related Phases 48 2.2 Anion Substituted Perovskites 51 2.2.1 Nitrides and Oxynitrides 51 2.2.2 Oxyfluorides 53 2.3 A‐Site‐Deficient Perovskite Structures 54 2.3.1 ReO3, WO3 and Related Structures 54 2.3.2 Perovskite Tungsten Bronzes 55 2.3.3 A‐Site‐Deficient Titanates, Niobates and Tantalates 55 2.4 Anion‐Deficient Phases Containing Tetrahedra 57 2.4.1 Brownmillerites 57 2.4.2 Brownmillerite Microstructures 62 2.4.3 Temperature Variation and Disorder 63 2.4.4 B‐Site Doped Brownmillerite Phases 64 2.4.5 B‐Site Doping and Oxygen Pressure 65 2.4.6 A‐Site Doped Brownmillerite Phases 65 2.4.7 Brownmillerite‐Related Phases 66 2.5 Anion‐Deficient Phases Containing Square Pyramids 69 2.5.1 Manganites 69 2.5.2 SrFeO2.5 and Related Phases 71 2.5.3 Cobaltite‐Related Phases 73 2.6 Point Defects, Microdomains and Modulated Phases 74 Further Reading 78 3 Hexagonal Perovskite–Related Structures 79 3.1 The BaNiO3 Structure 79 3.2 BaNiO3‐Related Phases Containing Trigonal Prisms 81 3.2.1 Commensurate Structures 81 3.2.2 Modulated Structures 89 3.3 Perovskites with Mixed Hexagonal/Cubic Packing: Nomenclature 92 3.4 Perovskites with Mixed Hexagonal/Cubic Packing: Stacking Sequences 95 3.5 Hexagonal Perovskites with chq and cph Stacking 98 3.5.1 (chq) Structures 98 3.5.2 (cph) Structures 99 3.5.3 cphq Intergrowth Structures 104 3.6 Hexagonal Perovskites with cphh Stacking 106 3.6.1 (cc…chh) AnBnO3n Structures 107 3.6.2 (cc…chh) AnBn−1O3n Structures 108 3.6.3 (hhcc…chhcc…c) Intergrowth Phases 110 3.6.4 (cc…ch) AnBn−1O3n Shift and Twinned Phases 112 3.7 Anion‐Deficient Phases Containing BaO2 (c′) Layers 112 3.7.1 (c…c′…ch) Structures 113 3.7.2 (c…c′…chh) Structures 113 3.7.3 (c…c′…chhh) Structures 115 3.8 Anion‐Deficient Phases with BaOX Layers 117 3.8.1 (h′) Layers 117 3.8.2 (c′c′) Layers 119 3.9 Sr4Mn3O10 and Ba6Mn5O16 120 3.10 Temperature and Pressure Variation 120 Reference 122 Further Reading 122 4 Modular Structures 123 4.1 K2NiF4 (A2BX4) and Ruddlesden–Popper Phases 123 4.1.1 The K2NiF4 (T or T/O) Structure 123 4.1.2 Ruddlesden–Popper Phases 127 4.2 The Nd2CuO4 (T′) and T* Structures 129 4.3 Dion–Jacobson and Related Phases 131 4.4 Aurivillius Phases 134 4.5 The Ca2Nb2O7‐Related Phases 136 4.6 Cuprate Superconductors and Related Phases 138 4.6.1 La2CuO4, Nd2CuO4 and YBa2Cu3O7 139 4.6.2 Layered Perovskite Structures 141 4.6.3 Structures Related to the Layered Cuprate Phases 142 4.7 Composition Variation 146 4.8 Intercalation and Exfoliation 151 Further Reading 154 5 Diffusion and Ionic Conductivity 156 5.1 Diffusion 156 5.2 Ionic Conductivity 159 5.3 Proton Conductivity 162 5.4 Oxygen Pressure Dependence and Electronic Conductivity 165 5.5 Oxide Ion Mixed Conductors 167 5.6 Proton Mixed Conductors 169 5.7 Solid Oxide Fuel Cells 172 References 174 Further Reading 174 6 Dielectric Properties 176 6.1 Insulating Perovskites 176 6.2 Dielectric Perovskites 178 6.2.1 General Properties 178 6.2.2 Colossal Dielectric Constant Materials 181 6.3 Ferroelectric/Piezoelectric Perovskites 182 6.3.1 Spontaneous Polarisation and Domains 182 6.3.2 Ferroelectric Domain Switching 185 6.3.3 Ferroelectric Hysteresis Loops 188 6.3.4 Temperature Dependence of Ferroelectricity 189 6.3.5 Pyroelectrics, Piezoelectrics and Crystal Symmetry 191 6.3.6 Strain versus Electric Field Loops 192 6.4 The Development of Ferroelectric/Piezoelectric Ceramic Bodies 193 6.4.1 Ceramic Piezoelectrics 193 6.4.2 Electrostriction 195 6.5 Antiferroelectrics 196 6.6 Ferrielectrics 199 6.7 Relaxor Ferroelectrics 200 6.7.1 Macroscopic Characteristics of Relaxor Ferroelectrics 200 6.7.2 Microstructures of Relaxor Ferroelectrics 202 6.8 Improper Ferroelectricity 206 6.9 Doping and Modification of Properties 208 6.10 Nanoparticles and Thin Films 212 References 215 Further Reading 215 7 Magnetic Properties 217 7.1 Magnetism in Perovskites 217 7.2 Paramagnetic Perovskites 219 7.3 Antiferromagnetic Perovskites 222 7.3.1 Cubic Perovskite‐Related Structures 222 7.3.2 Hexagonal Perovskites 229 7.4 Ferromagnetic Perovskites 233 7.5 Ferrimagnetic Perovskites 236 7.6 Spin Glass Behaviour 237 7.7 Canted Spins and Other Magnetic Ordering 238 7.8 Thin Films 240 7.9 Nanoparticles 243 7.10 Multiferroic Perovskites 243 References 246 Further Reading 246 8 Electronic Conductivity 247 8.1 Perovskite Band Structure: Metallic Perovskites 247 8.2 Metal–Insulator Transitions 250 8.2.1 Titanates and Related Phases 250 8.2.2 LnNiO3 252 8.2.3 Lanthanoid Manganites 253 8.2.4 Lanthanoid Cobaltites 254 8.2.5 (Sr, Ca)2RuO4 and Ca2Ru1−xCrxO4 255 8.2.6 NaOsO3 256 8.3 Perovskite Superconductors 257 8.4 Cuprate High‐Temperature Superconductors 258 8.4.1 Overview 258 8.4.2 Lanthanum Cuprate, La2CuO4 259 8.4.3 Neodymium Cuprate, Nd2CuO4 260 8.4.4 Yttrium Barium Copper Oxide, YBa2Cu3O7 261 8.4.5 Perovskite‐Related Structures and Series 263 8.4.6 The Generic Superconductivity Phase Diagram 263 8.4.7 Defects and Conductivity 265 8.5 Spin Polarisation and Half‐Metals 267 8.6 Charge Ordering and Orbital Ordering 268 8.7 Magnetoresistance 270 8.7.1 Collosal Magnetoresistance (CMR) in Manganites 270 8.7.2 Low‐Field Magnetoresistance 272 8.8 Semiconductivity in Perovskites 272 8.9 Thin Films and Surface Conductivity 275 References 275 Further Reading 275 9 Thermal and Optical Properties 277 9.1 Thermal Expansion 277 9.1.1 Normal Thermal Expansion 277 9.1.2 Thermal Contraction 280 9.1.3 Zero Thermal Expansion Materials 283 9.2 Thermoelectric Properties 284 9.3 The Magnetocaloric Effect 287 9.4 The Pyroelectric and Electrocaloric Effect 288 9.5 Transparency 289 9.6 Electrochromic Films 291 9.7 Electro‐optic Properties 293 9.7.1 Refractive Index Changes 293 9.7.2 Electro‐optic Phase Modulators 294 9.7.3 Electro‐optic Intensity Modulators 296 9.7.4 Ceramic Modulators 299 9.8 Perovskite Solar Cells 299 Reference 302 Further Reading 302 Appendix A The Bond Valence Model for Perovskites 303 Appendix B Summary of the Kröger–Vink Defect Notation 307 Index 309

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Book SynopsisFiesers'' Reagents for Organic Synthesis provides an up-to-date, A-to-Z listing of reagents cited in synthetic literature. Covers, in volume 28, chemical literature and methodologies from July 2011 - December 2012Features entries with concise descriptions, illustrations of chemical reactions, selected examples of applicationsIncludes author indexes and subject indexesOffers practical information on making/buying reagent, its usefulness, where to find complete detailsTable of ContentsPreface vii General Abbreviations viii Reference Abbreviations xii Chapter A 1 Chapter B 18 Chapter C 112 Chapter D 246 Chapter E 258 Chapter F 259 Chapter G 263 Chapter H 304 Chapter I 316 Chapter L 345 Chapter M 349 Chapter N 358 Chapter O 366 Chapter P 385 Chapter R 467 Chapter S 486 Chapter T 506 Chapter U 558 Chapter V 559 Chapter W 560 Chapter Y 562 Chapter Z 564 Author Index 571 Subject Index 665

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Book SynopsisA quick, easy-to-consult source of practical overviews on wide-ranging issues of concern for those responsible for the health and safety of workers This new and completely revised edition of the popular Handbook is an ideal, go-to resource for those who need to anticipate, recognize, evaluate, and control conditions that can cause injury or illness to employees in the workplace. Devised as a how-to guide, it offers a mix of theory and practice while adding new and timely topics to its core chapters, including prevention by design, product stewardship, statistics for safety and health, safety and health management systems, safety and health management of international operations, and EHS auditing. The new edition of Handbook of Occupational Safety and Health has been rearranged into topic sections to better categorize the flow of the chapters. Starting with a general introduction on management, it works its way up from recognition of hazards Table of ContentsContributors vii Foreword ix Part I Recognition and Control of Hazards 1 1. Recognition of Health Hazards in the Workplace 3Martin R. Horowitz and Marilyn F. Hallock 2. Information Resources for Occupational Safety and Health Professionals 37Ralph Stuart, James Stewart, and Robert Herrick 3. Ergonomics: Achieving System Balance Through Ergonomic Analysis and Control 49Graciela M. Perez 4. Evaluation of Exposure to Chemical Agents 89Jerry Lynch and Charles Chelton 5. Statistical Methods for Occupational Exposure Assessment 125David L. Johnson 6. Evaluation and Management of Exposure to Infectious Agents 147Janet M. Macher, Deborah Gold, Patricia Cruz, Jennifer L. Kyle, Timur S. Durrani, and Dennis Shusterman 7. Occupational Dermatoses 199David E. Cohen 8. Indoor Air Quality in Nonindustrial Occupational Environments 231Philip R. Morey and Richard Shaughnessy 9. Occupational Noise Exposure and Hearing Conservation 261Charles P. Lichtenwalner and Kevin Michael 10. Heat Stress 335Anne M. Venetta Richard and Ralph Collipi, Jr. 11. Radiation: Nonionizing and Ionizing Sources 359Donald L. Haes, Jr., and Mitchell S. Galanek 12. Enterprise Risk Management: An Integrated Approach 381Chris Laszcz‐Davis 13. Safety and Health in Product Stewardship 425Thomas Grumbles Part II General Control Practices 435 14. Prevention Through Design 437Frank M. Renshaw 15. How to Select and Use Personal Protective Equipment 469Richard J. Nill 16. Respiratory Protective Devices 495James S. Johnson 17. How to Establish Industrial Loss Prevention and Fire Protection 531Peter M. Bochnak 18. Philosophy and Management of Engineering Control 569Pamela Greenley and William A. Burgess 19. Environmental Health and Safety (EHS) Auditing 613Andrew McIntyre, Harmony Scofield, and Steven Trammell Part III Management Approaches 639 20. Addressing Legal Requirements and Other Compliance Obligations 641Thea Dunmire 21. Occupational Safety and Health Management 653Fred A. Manuele 22. Effective Safety and Health Management Systems: Management Roles and Responsibilities 671Fred A. Manuele 23. Safety and Health Management of International Operations 691S. Z. Mansdorf 24. The Systems Approach to Managing Occupational Health and Safety 701Victor M. Toy Index 717

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Book SynopsisExplains why modern supercritical fluid chromatography (SFC) is the leading green analytical and purification separations technology. Modern supercritical fluid chromatography (SFC) is the leading method used to analyze and purify chiral and achiral chemical compounds, many of which are pharmaceuticals, pharmaceutical candidates, and natural products including cannabis-related compounds. This book covers current SFC instrumentation as it relates to greater robustness, better reproducibility, and increased analytical sensitivity. Modern Supercritical Fluid Chromatography: Carbon Dioxide Containing Mobile Phases covers the history, instrumentation, method development and applications of SFC. The authors provided readers with an overview of analytical and preparative SFC equipment, stationary phases, and mobile phase choices. Topics covered include: Milestones of Supercritical Fluid Chromatography; Physical Properties of Supercritical Fluids; InstrumentationTable of ContentsPreface xiii 1 Historical Development of SFC 1 1.1 Physical Properties of Supercritical Fluids 1 1.2 Discovery of Supercritical Fluids (1822–1892) 6 1.3 Supercritical Fluid Chromatography (1962–1980) 8 1.4 SFC with Open Tubular Columns (1980–1992) 15 1.5 Rediscovery of pcSFC (1992–2005) 19 1.6 Modern Packed Column SFC 22 References 24 2 Carbon Dioxide as the Mobile Phase 29 2.1 Introduction to Carbon Dioxide 29 2.2 Supercritical Carbon Dioxide 32 2.3 Solvating Power of Supercritical CO2 35 2.4 Solvating Power of Modified CO2 45 2.5 Clustering of CO2 49 References 52 3 Instrumentation for Analytical Scale Packed Column SFC 55 3.1 Introduction 56 3.2 Safety Considerations 56 3.3 Fluid Supply 58 3.3.1 Carbon Dioxide and Other Compressed Gases 58 3.3.2 Mobile Phase “Modifiers” and “Additives” 59 3.4 Fluid Delivery – Pumps and Pumping Considerations 60 3.4.1 Pump Thermostating 60 3.4.2 Fluid Pressurization and Metering 60 3.4.3 Modifier Fluid Pumping 61 3.4.4 Pressure and Flow Ranges 62 3.4.5 Fluid Mixing 62 3.5 Sample Injection and Autosamplers 62 3.6 Tubing and Connections 64 3.6.1 Tubing 64 3.6.1.1 Stainless Steel Tubing 64 3.6.1.2 Polymeric Tubing 65 3.6.2 Connections 66 3.7 Column and Mobile Phase Temperature Control 66 3.8 Chromatographic Column Materials of Construction 67 3.9 Backpressure Regulation 68 3.9.1 Passive Flow Restriction 69 3.9.2 Active Backpressure Regulation 70 3.10 Waste Disposal 72 3.11 Conclusion 72 References 72 4 Detection in Packed Column SFC 77 4.1 Introduction 78 4.2 Predecompression Detection (Condensed‐Fluid‐Phase Detection) 78 4.2.1 UV/VIS Absorbance 78 4.2.2 Fluorescence Detection 81 4.2.3 Electrochemical Detection 82 4.2.4 Other Less Common Condensed Phase Detectors 83 4.2.4.1 Flow‐Cell Fourier Transform Infra‐Red Absorbance (FTIR) Detection 83 4.2.4.2 Online Nuclear Magnetic Resonance (NMR) Detection 84 4.2.4.3 Refractive Index (RI) Detection 85 4.3 Postdecompression Detection (Gas/Droplet Phase Detection) – Interfacing Approaches 85 4.3.1 Pre-BPR Flow Splitting 86 4.3.2 Total Flow Introduction (Post-BPR Detection) 88 4.3.2.1 BPR Requirements for Total‐Flow Introduction Detection 88 4.3.2.2 Total Flow Introduction with Mechanical BPR 89 4.3.2.3 Total Flow Introduction – Pressure‐Regulating‐Fluid (PRF) Interface 89 4.3.2.4 Total Flow Introduction without Active Backpressure Regulation 91 4.4 Postdecompression Detection 93 4.4.1 Flame‐Based Detectors 93 4.4.2 Evaporative Light Scattering Detection (ELSD) and Charged Aerosol Detection (Corona CAD) 97 4.4.3 Mass Spectrometric Detection 98 4.4.3.1 Interfacing and Ionization Approaches 99 4.4.3.2 Atmospheric Pressure Chemical Ionization (APCI) 100 4.4.3.3 Pneumatically Assisted Electrospray Ionization (ESI) 101 4.4.3.4 Atmospheric Pressure Photoionization (APPI) 103 4.4.4 Postdecompression Detection Using Less Common Approaches – Deposition IR 103 4.5 Concluding Remarks 103 References 104 5 Chiral Analytical Scale SFC – Method Development, Stationary Phases, and Mobile Phases 117 5.1 Introduction 117 5.2 Chiral Stationary Phases for SFC 119 5.3 Chiral SFC vs. Chiral HPLC 128 5.4 Method Development Approaches 130 5.4.1 Modifiers for Chiral SFC 132 5.4.2 Additives for Chiral SFC 133 5.4.3 Nontraditional Modifiers 135 5.4.4 Method Development Approaches 137 5.5 High Throughput Method Development 139 5.6 Summary 141 References 142 6 Achiral Analytical Scale SFC – Method Development, Stationary Phases, and Mobile Phases 147 6.1 Introduction 147 6.2 The Mixture to Be Separated 148 6.2.1 Molecular Interactions 148 6.2.2 Molecular “Handles” 149 6.3 Achiral SFC Stationary Phases 150 6.3.1 Column Safety and Compatibility 150 6.3.2 Efficiency 150 6.3.3 Retention 153 6.3.4 Selectivity 156 6.4 Mobile‐Phase Choices 157 6.4.1 Primary Mobile‐Phase Component 158 6.4.2 Secondary Mobile‐Phase Component – The “Modifier” 159 6.4.3 Tertiary Mobile‐Phase Component – “Additives” 163 6.5 Influence of Column Temperature on Efficiency and Selectivity 170 6.6 Where Do I Go from Here? Method Development Decision Tree and Summary 172 References 174 7 Instrumentation for Preparative Scale Packed Column SFC 183 7.1 Introduction 183 7.2 Safety Considerations 184 7.3 Fluid Supply 185 7.3.1 Carbon Dioxide 185 7.3.2 Mobile Phase Modifiers and Additives 187 7.3.3 Carbon Dioxide Recycling 188 7.4 Pumps and Pumping Considerations 189 7.4.1 CO2 and Modifier Fluid Pumping 189 7.4.2 Pressures and Flow Ranges 189 7.5 Sample Injection 190 7.5.1 Injection of Solutions 190 7.5.2 Extraction Type Injection 190 7.6 Chromatographic Columns 192 7.7 Detection 192 7.8 Back Pressure Regulation 193 7.9 Fraction Collection 193 7.9.1 Cyclone Collection 194 7.9.2 Open‐Bed Collection 195 7.10 Conclusion 197 References 197 8 Preparative Achiral and Chiral SFC – Method Development, Stationary Phases, and Mobile Phases 199 8.1 Introduction 200 8.1.1 Advantages and Disadvantages of SFC vs. HPLC for Purification 201 8.1.2 Cost Comparison: Preparative HPLC vs. SFC 202 8.2 Safety Considerations 202 8.3 Developing Preparative Separations 203 8.3.1 Linear Scale‐Up Calculations 209 8.3.2 Scaling Rule in Supercritical Fluid Chromatography 210 8.3.3 Metrics for Preparative Separations 213 8.3.4 Options for Increasing Purification Productivity 214 8.3.4.1 Closed‐Loop Recycling 214 8.3.4.2 Stacked Injections 214 8.3.5 Importance of Solubility on Preparative Separations 214 8.3.6 Preparative SFC Injection Options 217 8.4 Preparative Chiral SFC Purifications 220 8.4.1 Chiral Stationary Phases (CSPs) for Preparative SFC 220 8.4.2 Method Development for Chiral Purifications 222 8.4.3 Preparative SFC Examples 223 8.4.3.1 Milligram Scale Chiral Purification 223 8.4.3.2 Gram Scale Chiral Purification 224 8.4.4 Impact of Solubility on Productivity 226 8.4.5 Use of Immobilized Chiral Stationary Phase (CCP) for Solubility‐Challenged Samples 227 8.4.5.1 Immobilized CSP Example #1 227 8.4.5.2 Immobilized CSP Example #2 228 8.4.6 Coupling of Chiral and Achiral Columns for SFC Purifications 229 8.5 Preparative Achiral SFC Purifications 231 8.5.1 Introduction to Achiral SFC Purifications 231 8.5.2 Stationary Phases for Achiral Preparative SFC 232 8.5.3 Method Development for Achiral Purifications 232 8.5.4 Achiral SFC Purification Examples 234 8.5.4.1 Achiral Purification Example #1 234 8.5.4.2 Achiral Purification Example #2 234 8.5.5 Purifications Using Mass‐Directed SFC 236 8.5.6 Impurity Isolation Using Preparative SFC 237 8.5.6.1 Impurity Isolation Example 240 8.5.7 SFC as Alternative to Flash Purification 241 8.6 Best Practices for Successful SFC Purifications 244 8.6.1 Sample Filtration and Inlet Filters 244 8.6.2 Sample Purity 246 8.6.3 Salt vs. Free Base 247 8.6.4 Primary Amine Protection to Improve Enantiomer Resolution 250 8.6.5 Evaluation of Alternate Synthetic Intermediates to Improve SFC Purification Productivity 250 8.7 Summary 254 References 254 9 Impact and Promise of SFC in the Pharmaceutical Industry 267 9.1 Introduction to Pharmaceutical Industry 267 9.2 SFC in Pharmaceutical Discovery 268 9.2.1 Early Discovery Support 268 9.2.2 SFC in Medicinal Chemistry 269 9.2.2.1 Analytical SFC 270 9.2.2.2 Preparative SFC 271 9.2.3 Physiochemical Measurement by SFC 273 9.2.4 Use of SFC for Pharmacokinetic and Drug Metabolism Studies 274 9.3 SFC in Development and Manufacturing 276 9.3.1 Analytical SFC Analysis of Drug Substances and Drug Products 276 9.3.2 Preparative SFC in Development and Manufacturing 282 9.3.3 Metabolite/PKDM Studies in Development 283 9.3.4 SFC in Chemical Process Development 283 9.4 SFC for Analysis of Illegal Drugs 284 9.5 Summary 286 References 286 10 Impact of SFC in the Petroleum Industry 297 10.1 Petroleum Chemistry 297 10.1.1 Crude Refining Processes 297 10.1.2 Petrochemical Processes 298 10.2 Introduction to Petroleum Analysis 299 10.3 Historical Perspective 301 10.3.1 Hydrocarbon Analysis via FIA 301 10.3.2 SFC Replaces FIA 301 10.3.3 Hydrocarbon SFC Analysis via ASTM 5186‐91 302 10.4 Early Petroleum Applications of SFC 304 10.4.1 Samples with Broad Polymer Distribution 304 10.4.2 SFC Purification of Polycyclic Aromatic Hydrocarbons 305 10.4.3 Coal Tar Pitch 305 10.4.4 Enhanced SFC Performance 305 10.4.5 Sulfur Detection in a Petroleum Matrix 307 10.5 SFC Replacement for GC and LC 308 10.5.1 Simulated Distillation 308 10.5.2 Hydrocarbon Group‐Type Separations – PIONA Analysis 310 10.6 Biodiesel Purification 311 10.7 Multidimensional Separations 314 10.7.1 Comprehensive Two‐Dimensional SFC 314 10.7.2 SFC‐GC × GC 315 10.7.3 Comprehensive – SFC‐Twin‐Two‐Dimensional (GC × GC) 316 References 317 11 Selected SFC Applications in the Food, Polymer, and Personal Care Industries 321 11.1 Introduction 321 11.2 Selected Applications in the Foods Industry 322 11.2.1 Fats, Oils, and Fatty Acids 322 11.2.2 Tocopherols 325 11.2.3 Other Vitamins 327 11.2.4 Food Preservatives (Other Antioxidants and Antimicrobials) 330 11.2.5 Coloring Agents 330 11.2.6 Sugars 331 11.3 Selected Applications in the Field of Synthetic Polymers 332 11.3.1 Molecular Weight Distribution 332 11.3.2 Structural Characterization 334 11.3.3 “Critical Condition” Group/Block Separations of Complex Polymers Using CO2‐containing Mobile Phases 334 11.3.4 Polymer Additives 335 11.4 Selected Applications in the Personal Care Industry 337 11.4.1 Lipophilic Components of Cosmetics 337 11.4.2 Surfactants in Cleaning Mixtures 337 11.4.3 Emulsifiers in Personal Care Products 337 11.4.4 Preservatives 338 11.5 Conclusions 340 References 340 12 Analysis of Cannabis Products by Supercritical Fluid Chromatography 347 12.1 Introduction 347 12.1.1 Cannabis History 348 12.2 Analytical SFC 351 12.2.1 Introduction 351 12.2.2 Early SFC of Cannabis Products 352 12.2.3 Achiral SFC 353 12.2.4 Chiral SFC 354 12.2.5 Metabolite Analysis 357 12.3 Preparative SFC 357 12.4 Summary 360 References 361 13 The Future of SFC 365 13.1 Introduction 365 13.2 SFC Publication Record 366 13.3 SFC Research in Academia 368 13.4 SFC Conferences 368 13.5 Anticipated Technical Advances 369 13.6 Limits to SFC Expansion 370 13.7 Summary 372 References 373 Index 377

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Book SynopsisA reference on drug metabolism and metabolite safety in the development phase, this book reviews the analytical techniques and experimental designs critical for metabolite studies. It features case studies of lessons learned and real world examples, along with regulatory perspectives from the US FDA and EMA.Trade Review"Written by individuals who collectively possess hundreds of years of experience within the drug metabolism field, the wealth of information and insight contained is amazing. The purpose of the tome is to provide the reader with, �... a comprehensive overview of why and how metabolites are studied during drug development in the pharmaceutical industry� (page 13). This objective is certainly achieved in a lucid, scholarly and engaging manner. I would not hesitate to recommend this book to anyone interested in this subject and also for those who may wish to delve into this area." (ISSX Newsletter, April 2017)Table of ContentsPreface xi List of Contributors xiii 1 Introduction: History of Metabolite Safety in Drug Development 1Dennis A. Smith and Suzanne L. Iverson 1.1 People, Events, and Reaction, 1 1.2 The Rise of Industrial Drug Metabolism, 2 1.3 The Appearance of Mist, 4 1.4 The Journey Triggered by Thalidomide: Would Present Science have Made a Difference?, 5 1.5 Key Events from Thalidomide to Mist, 8 1.6 The Purpose of this Book, 13 References, 14 2 “Mist” and other Metabolite Guidelines in the Context of Industrial Drug Metabolism 17Gordon J. Dear and Angus N. R. Nedderman 2.1 A Historical Perspective, 17 2.2 The Emergence of the Regulatory Guidance Documents, 23 2.3 Impact of the Guidelines, 30 2.4 Future Directions, 32 References, 37 3 Metabolite Technology: Qualitative and Quantitative 45Gordon J. Dear and Andrew McEwen 3.1 Introduction, 45 3.2 Clinical Samples, 46 3.3 Preclinical Samples, 48 3.4 Radiolabeled Test Compounds, 51 3.5 Mass Spectrometry, 55 3.6 NMR Spectroscopy, 65 3.7 Accelerator Mass Spectrometry, 72 References, 75 Further Reading, 85 4 In Vitro Methods for Evaluation of Drug Metabolism: Identification of Active and Inactive Metabolites and the Enzymes that Generate them 87R. Scott Obach, Amit S. Kalgutkar, and Deepak K. Dalvie 4.1 Introduction, 87 4.2 In Vitro Methods for Metabolite Profiling and Identification, 88 4.2.1 In Vitro Systems We Use: Most Complex to Simplest, 88 4.2.2 Criteria for Selecting the Most Appropriate In Vitro System for In Vitro Metabolite Profiling, 92 4.3 Application of In Vitro Methods for Metabolite Profiling in Drug Discovery and Development, 96 4.3.1 In Vitro Metabolite Profiling and Identification in the Early Drug Discovery Stage, 96 4.3.2 In Vitro Metabolite Profiling and Identification in the Late Drug Discovery Stage: Selection of Candidate Compounds for Further Development, 98 4.3.3 In Vitro Metabolite Profiling and Identification in the Drug Development Stage: Support of CandidateCompounds for New Drug Registration, 101 4.4 How Well Do In Vitro Metabolite Profiles Represent In Vivo Metabolite Profiles?, 103 4.5 Pharmacologically Active Metabolites and their Identification, 104 4.5.1 When Is a Metabolite Considered Active?, 104 4.5.2 Experimental Approaches to Reveal Active Metabolites, 106 4.6 Conclusion, 108 References, 108 5 Integrated Reactive Metabolite Strategies 111J. Gerry Kenna and Richard A. Thompson 5.1 Introduction, 111 5.2 Role of RMs in Toxicity, 114 5.3 Strategies for Predicting, Assessing, and Derisking RM-Mediated Toxicity, 118 5.3.1 Assessing RM Hazard: Awareness/Avoidance, 118 5.3.2 Assessing RM Risk: Covalent Binding and Dose, 122 5.3.3 Integrated Risk Assessments: Integrating RM Assessment and In Vitro Safety Assay Endpoints, 127 5.3.4 Integrated RM Risk Assessments: Future Directions, 129 References, 131 6 Understanding Drug Metabolism in Humans: In Vivo 141Lars Weidolf and Ian D. Wilson 6.1 Introduction, 141 6.2 Preclinical Animal Studies, 142 6.2.1 Whole-Body Autoradiography and Imaging, 144 6.3 Early Human In Vivo Metabolism Studies, 146 6.3.1 Pre-FTIM Data Acquisition, 147 6.3.2 The First Clinical Studies, 149 6.3.3 Metabolite Exposure Assessment, 150 6.3.4 Exceptions to Regulatory Recommendations, 153 6.3.5 Dealing with DHMs, 153 6.3.6 The Human ADME Study, 156 6.3.7 Early Metabolite Exposure Assessment and Relevance to the Target Patient Population, 159 6.3.8 Summary, 160 6.4 The “What ifs…?”, 162 6.5 Sources of Variability in In Vivo Biotransformation Studies: Species, Strain, Age, and Sex Differences, 162 6.6 Extrahepatic Drug Metabolism (Animals and Man), 164 6.7 Nonhuman Metabolism in Humans, 166 6.8 Nonhuman Models of Human In Vivo Metabolism, 167 6.8.1 “Humanized” Transgenic Mice, 168 6.8.2 “Chimeric” Humanized Mice, 169 6.9 Alternatives to Radiolabels, 170 6.10 Conclusions, 171 References, 172 7 Topical Administration and Safety Testing of Metabolites 177Vibeke Hougaard Sunesen 7.1 Introduction, 177 7.2 Skin Structure and Function of the Epidermal Layer, 178 7.3 Skin Models, 180 7.3.1 In Vivo Studies, 181 7.3.2 Ex Vivo Skin, 182 7.3.3 In Vitro Skin Models, 182 7.4 Metabolic Capacity of Human Skin, 186 7.4.1 Phase 1 Enzymes, 186 7.4.2 Non-CYP Phase 1 Enzymes, 190 7.4.3 Phase 2 Enzymes, 193 7.5 Species Differences in Metabolic Capacity of the Skin, 196 7.6 Metabolic Capacity of Diseased Skin, 197 7.7 Soft Drug Approach, 198 7.7.1 Soft Corticosteroids, 199 7.7.2 PDE4 Inhibitors, 200 7.8 Exposure to Metabolites and Risk of Adverse Events, 202 7.8.1 Drug Interaction Potential, 204 7.8.2 Toxicities and Safety Concerns, 205 References, 206 8 In Silico Modeling of Metabolite Kinetics 213Lu Gaohua, Howard Burt, Helen Humphries, Amin Rostami-Hodjegan, and Masoud Jamei 8.1 Introduction, 213 8.1.1 Why Do We Need to Model Metabolite PK?, 213 8.1.2 Brief Review of Existing PBPK Models of Metabolites, 214 8.2 Simcyp Approach to Modeling Metabolite PBPK, 215 8.2.1 Parent/Metabolite PBPK Model Structure, 215 8.2.2 Formation/Absorption of the Metabolite, 217 8.2.3 Distribution of Metabolite, 219 8.2.4 Elimination of Metabolite, 222 8.2.5 Interaction of Metabolite, 222 8.3 Model Verifications, 223 8.3.1 Comparison of Prediction versus Observation, 223 8.3.2 What-If Simulation Examples, 223 8.4 Discussion, 230 8.4.1 Role of M&S in Handling Metabolites, 230 8.4.2 How to Deal with Multiple Metabolites, 231 8.4.3 Role of M&S of Metabolites in Regulatory Submissions, 232 8.5 Concluding Remarks, 232 8.5.1 What has been Achieved?, 232 8.5.2 Future Works, 232 Glossary, 233 Superscription, 233 Subscription, 234 References, 234 9 Introduction to Case Studies 239Suzanne L. Iverson References, 242 10 A Mass Balance and Metabolite Profiling Study of Sonidegib in Healthy Male Subjects Using Microtrace Approach 243Piet Swart, Frederic Lozac’h, and Markus Zollinger 10.1 Introduction to the Study, 243 10.2 Radioactive Dose Limitations, 245 10.3 Results, 246 10.4 Metabolite Profiling and Identification, 249 Acknowledgments, 258 References, 258 11 Dealing with Reality: When is it Necessary to Qualify and Quantify Metabolites? Some Case Studies 261Deepak K. Dalvie, R. Scott Obach, and Amit S. Kalgutkar 11.1 Introduction, 261 11.2 Case Study 1, 261 11.3 Case Study 2, 265 11.4 Case Study 3, 268 References, 271 12 The Value of Metabolite Identification and Quantification in Clinical Studies. Some Case Studies Enabling Early Assessment of Safety in Humans: GlaxoSmithKline 275Jackie Bloomer, Claire Beaumont, Gordon J. Dear, Stephanie North, and Graeme Young 12.1 GW644784: Species-Specific Metabolites, 276 12.2 Danirixin: Assessment of Victim Drug Interaction Risk Using Bile Sampling, 279 12.3 Sitamaquine: Unique, Active, and Possible Genotoxic Metabolites and Human Radiolabel Study Not Feasible, 280 12.4 SB-773812: Concerns Over Long Half-Life Metabolite and Early Employment of Accelerator Mass Spectrometry, 285 12.5 GW766994: Consideration of Steady-State Kinetics and Multiple Analytical Methodologies for an Accurate Assessment of Human Metabolism, 288 References, 290 13 The Importance of Dose- and Time-Dependent Pharmacokinetics During Early Metabolite Safety Assessment in Humans 293Laurent Leclercq, Marc Bockx, Hilde Bohets, Hans Stieltjes, Vikash Sinah, and Ellen Scheers References, 303 14 Mist and the Future 305B. Kevin Park and Dennis A. Smith 14.1 Introduction, 305 14.2 Mist and Pharmacology, 306 14.3 Reactive Metabolites, Pharmacology, and Mist, 309 14.4 Implications of Drug Bioactivation and Covalent Binding for Mist, 309 14.5 Drug Bioactivation and Drug Hepatotoxicity, 311 14.6 Drug-Conjugate Formation and Drug Hypersensitivity, 313 14.7 Drug Bioactivation, Conjugate Formation, and Drug Hypersensitivity, 315 14.8 Toward a Mist Strategy for Reactive Metabolites, 317 References, 318 Index 323

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Book SynopsisAdvances in Chemical Physics is the only series of volumes available that explores the cutting edge of research in chemical physics. This is the only series of volumes available that presents the cutting edge of research in chemical physics. Includes contributions from experts in this field of research. Contains a representative cross-section of research that questions established thinking on chemical solutions. Structured with an editorial framework that makes the book an excellent supplement to an advanced graduate class in physical chemistry or chemical physics. Table of ContentsPhase Space Approach to Solving The Schrödinger Equation: Thinking Inside the Box 1 David J. Tannor, Norio Takemoto, and Asaf Shimshovitz Entropy-Driven Phase Transitions In Colloids: From Spheres to Anisotropic Particles 35 Marjolein Dijkstra Sub-Nano Clusters: The Last Frontier of Inorganic Chemistry 73 Anastassia N. Alexandrova and Louis-S. Bouchard Supercooled Liquids and Glasses by Dielectric Relaxation Spectroscopy 101 Ranko Richert Confined Fluids: Structure, Properties and Phase Behavior 197 G. Ali Mansoori and Stuart A. Rice Theories and Quantum Chemical Calculations of Linear and Sum-Frequency Generation Spectroscopies, and Intramolecular Vibrational Redistribution and Density Matrix Treatment of Ultrafast Dynamics 295 L. Yang, Y.L. Niu, C.K. Lin, M. Hayashi, C.Y. Zhu, and S.H. Lin On The Kramers Very Low Damping Escape Rate for Point Particles and Classical Spins 393 Declan J. Byrne, William T. Coffey, William J. Dowling, Yuri P. Kalmykov, and Serguey V. Titov Author Index 461 Subject Index 499

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Book SynopsisBased on the ''240'' Conference held at the University of Chicago in September of 2012, this special volume of The Advances in Chemical Physics series celebratesscientific research contributions and careers of R. Stephen Berry, Stuart A. Rice and Joshua Jortner.In addition to continuing thechemical physics field with a forum for critical, authoritative evaluations of advances in the discipline,Volume 157explores the following topics: The Emergence and Breakdown of Complexity Dynamics at Extremes Grand Questions Regarding Biomolecular Homochirality in the Origin and Evolution of Life The book: celebratesthescientific research contributions and careers of R. Stephen Berry, Stuart A. Rice and Joshua Jortner contributes to the only series available that presents the cutting edge of research in chemical physics includes contributions from experts in this field oTable of ContentsPart I The Emergence and Breakdown of Complexity Features of Complexity 3by Ronnie Kosloff Exploring Quantum-Classical Boundary 19by Kenji Ohmori Transition from Atoms to Clusters to Condensed Matter 25by Julius Jellinek Free Energies of Staging a Scenario and Perpetual Motion Machines of the Third Kind 43by Peter Salamon, Bjarne Andresen, Karl Heinz Hoffmann, James D. Nulton, Anca M. Segall, and Forest L. Rohwer Finite-Time Thermodynamics Tools to Analyze Dissipative Processes 57by Karl Heinz Hoffmann, Bjarne Andresen, and Peter Salamon New Types of Complexity in Chemical Kinetics: Intersections, Coincidences, and Special Symmetrical Relationships 69by G. S. Yablonsky, D. Constales, and G. B. Marin Opportunities in the Area of Noise in Biological Reaction Networks 75by Aaron R. Dinner Thermodynamic Approach to Chemical Networks 85by G. Nicolis and C. Nicolis On the Emergence of Simple Structures in Complex Phenomena: Concepts and Some Numerical Examples 97by Martin Quack The Emergence of Simplicity from Complexity 119by John D. Weeks and John C. Tully Part II Dynamics at Extremes On the Way to a Theory of Solid State Synthesis: Issues and Open Questions 125by J. Christian Schön Beyond Molecular Conduction: Optical and Thermal Effects in Molecular Junctions 135by Abraham Nitzan Thermal Conductance at the Interface Between Molecules 159by David M. Leitner Laser Energy Deposition in Nanodroplets and Nuclear Fusion Driven by Coulomb Explosion 165by Andreas Heidenreich Understanding Ultraintense x-ray Interactions with Matter 183by Linda Young Time-Dependent Computational Methods for Matter Under Extreme Conditions 195by Barry I. Schneider, Klaus R. Bartschat, Xiaoxu Guan, David Feder, and Lee A. Collins Elementary Excitations in Ultracold Finite Systems 215by John Weiner Part III Grand Questions On Biomolecular Homochirality as a Quasi-Fossil of the Evolution of Life 249by Martin Quack Origins of Life 293by Sydney Leach Author Index 315 Subject Index 343

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Book SynopsisProvides a clear and accessible summary of all stages and aspects of the discovery, design, development, validation and clinical use of anticancer drugs This new edition provides an update on the current state of the art of cancer chemotherapy and clinical practice and presents new pipeline anticancer agents and promising therapeutic strategies that are emerging alongside new breakthroughs in cancer biology. Its unique approach enables students to gain an understanding of the pathological, physiological, and molecular processes governing malignancy, while also introducing the role of health professionals and scientists in the research and treatment of cancer. Invaluable for its clarity and accessibility, Cancer Chemotherapy: Basic Science to the Clinic, 2nd Edition offers complete coverage of the scientific and clinical aspects of the creation, development, and administration of drugs or drug regimens used in the treatment of the disease. Chapters look at: cancer epidemiology and histopathology; carcinogenesis; current research; tumor hypoxia; antiangiogenic and antivascular agents; protein kinase and Ras blockers; new targets associated with development such as Hedgehog and Wnt signaling; stem cells; immunotherapy and oncolytic viruses; and more. Presents a clear, accessible, and comprehensive approach to cancer chemotherapy from basic science to clinical practice Offers a major update that reflects the latest developments in personalized chemotherapy Provides in-depth coverage of advances in biomarker diagnostics Includes new chapters/sections on bioinformatics and the omic sciences'; pharmaceutical strategies used to achieve tumor-selective drug delivery; and cancer cell autophagy Combines descriptions of both clinical protocol and explanations of the drug design process in one self-contained book Features numerous diagrams and illustrations to enhance reader understanding Aimed at upper undergraduate, graduate, and medical students, Cancer Chemotherapy: Basic Science to the Clinic, 2nd Edition is also an excellent reference for health professional, especially clinicians specializing in Clinical Oncology, and their patients who want to gain an understanding of cancer and available treatment options.Table of ContentsPreface xi About the Companion Website xiii 1 Cancer Epidemiology 1 1.1 Cancer Incidence and Mortality 1 1.2 Childhood Cancer 4 1.3 Global Epidemiology 5 1.4 Cancer Survival Rates 8 1.5 Summary and Conclusions 12 Further Reading 12 2 Cancer Histopathology 13 2.1 Cancer Morphology, Phenotype, and Nomenclature 14 2.2 Apoptosis 16 2.3 Necrosis 22 2.4 Autophagy and Others 23 2.5 Summary and Conclusions 24 Further Reading 25 3 Carcinogenesis 27 3.1 Initiation 27 3.2 Promotion 29 3.3 Progression and Environmental Carcinogenesis 30 3.4 Cell Cycle 31 3.5 Summary and Conclusions 33 Further Reading 33 4 Molecular Biology of Cancer 35 4.1 Oncogenes: Disruptors and Instigators 36 4.2 Cellular Oncogenes 39 4.3 Viral Oncogenes 41 4.4 Altered Oncogenic Products 42 4.5 Biological Carcinogens 44 4.6 Tumor Suppressor Genes 46 4.7 Familial Cancers and Cancer Syndromes 50 4.8 Summary and Conclusions 52 Further Reading 52 5 Cancer Metastasis 53 5.1 Detachment from the Primary Tumor 54 5.2 Migration of Cancer Cells from Primary Tumor 55 5.3 Intravasation of Tumor Cells into Vessels 57 5.4 Metastatic Transport 60 5.5 Extravasation 61 5.6 Growth of the Metastatic Tumor Mass 63 5.6.1 Cancer Dormancy 63 5.6.2 Extracellular Matrix of the Tumor Microenvironment 64 5.6.3 Seed and Soil 65 5.7 Summary and Conclusions 66 Further Reading 67 6 Health Professionals and Cancer Treatment 69 6.1 Pathology 69 6.2 Radiology 70 6.3 Biopsies 72 6.4 Surgical Treatment 73 6.5 Oncology Pharmacy 74 6.6 Oncology Nursing 75 6.7 Artificial Intelligence and Healthcare 75 6.8 Summary and Conclusions 75 Further Reading 76 7 Principles of Cancer Chemotherapy 77 7.1 Staging, Treatment, and Monitoring 77 7.2 General Types of Chemotherapy 79 7.3 Biomarker Uses and Limitations 82 7.4 Pharmacogenetics, Pharmacogenomics, Pharmacokinetics, Pharmacodynamics, and Personalized Medicine 86 7.5 Summary and Conclusions 87 Further Reading 88 8 Cytotoxic Compounds 89 8.1 Alkylating Agents 89 8.2 Intercalating Agents 94 8.3 Topoisomerase Blockers 104 8.4 Tubulin Disruptors 109 8.5 Summary and Conclusions 113 Further Reading 113 9 Antimetabolites and Hormonal Blockers 115 9.1 Nucleic Acid Analogs 115 9.2 Folate Analogs 118 9.3 Amino Acid Blockers 120 9.4 Hormone Modulators 121 9.5 Estrogen Antagonists 124 9.6 Aromatase Inhibitors 127 9.7 Antiandrogens 127 9.8 Endocrine Therapy 128 9.9 Summary and Conclusions 129 Further Reading 130 10 Cancer Research 131 10.1 Gel Electrophoresis Methods 131 10.2 Polymerase Chain Reaction 132 10.3 Molecular Cloning 133 10.4 Enzyme-Linked Immunosorbent Assay, Immunohistochemistry, and Immunofluorescence 134 10.5 Mass Spectroscopy and Proteomics 135 10.6 Genomics, Transcriptomics, and Metabolomics 136 10.7 Microarrays 137 10.8 Cell Culture and Exogenous Expression Strategies 138 10.9 Protein Expression and Targeting 141 10.9.1 Targeting RNA. 143 10.9.2 Targeting the Genome 145 10.10 Animal Models 147 10.11 Delivery Systems 149 10.12 Resources 151 10.13 Summary and Conclusions 152 Further Reading 153 11 Clinical Trials 155 11.1 Clinical Trial Design 158 11.2 Clinical Trials Governance and Quality Assurance 161 11.3 Clinical Trial Ethics 166 11.4 Clinical Trial Study Schema 168 11.5 Measurement of Clinical Endpoints, Response, and Outcomes 169 11.6 Local and National Organization of Clinical Trials 169 11.7 Summary and Conclusions 173 Further Reading 174 12 Tumor Hypoxia 175 12.1 Effects of Hypoxia on Chemotherapy 177 12.2 Energy Reprogramming and the Warburg Effect 178 12.3 Hypoxia-Inducible Factor 181 12.4 Lactate Dehydrogenase and Carbonic Anhydrase 183 12.5 Hypoxic Vascularization and Imaging 185 12.6 Bioreductive Drugs 189 12.7 Summary and Conclusions 192 Further Reading 192 13 Antiangiogenic and Antivascular Agents 193 13.1 History of Antiangiogenic Chemotherapy 193 13.2 Endogenous Integrin Blockers 195 13.3 Matrix Metalloproteinase Inhibitors 197 13.4 Synthetic Integrin Blockers 202 13.5 The Return of Thalidomide 204 13.6 Vascular Disrupting Agents 205 13.7 Antiangiogenic Antibodies 207 13.8 Summary and Conclusions 210 Further Reading 210 14 Protein Kinase and Ras Blockers 211 14.1 Signal Transduction 211 14.2 Receptor Tyrosine Kinase Blockers 214 14.3 Nonreceptor Tyrosine Kinase Blockers 216 14.4 Receptor Serine/Threonine Kinase Blockers 220 14.5 Nonreceptor Serine/Threonine and Multiple Kinase Blockers 223 14.6 Ras and PLC Blockers 226 14.7 Summary and Conclusions 228 Further Reading 228 15 Modulating Global Gene and Protein Expression 231 15.1 Stress Protein Inhibitors 231 15.2 Proteasome Inhibitors 234 15.3 Ubiquitin Ligase Inhibitors 237 15.4 Histone Deacetylase Inhibitors 238 15.5 DNA Methylation Inhibitors 241 15.6 Summary and Conclusions 242 Further Reading 243 16 Stem Cells – Telomerase, Wnt, Hedgehog, Notch, and Galectins 245 16.1 Telomerase Blockers 246 16.2 Wnt Blockers 250 16.3 Hedgehog Blockers 252 16.4 Notch Blockers 254 16.5 Galectin Blockers 257 16.6 Summary and Conclusions 258 Further Reading 258 17 Immunotherapy and Oncolytic Viruses 261 17.1 Immunization 264 17.2 Immune Checkpoint Blockers 266 17.3 Chimeric Antigen Receptor T-Cells 268 17.4 Oncolytic Viruses 270 17.5 Summary and Conclusions 275 Further Reading 275 18 Pharmaceutical Problems in Cancer Chemotherapy 277 18.1 Manifestation of Toxicity 277 18.2 Regimen-Related Toxicity 282 18.3 Secondary Malignancies 283 18.4 Drug Resistance 284 18.4.1 Multiple Drug Resistance 284 18.4.2 Enhanced DNA Repair 286 18.4.3 Alteration of Drug Targets 287 18.5 Pharmaceutical Complications 287 18.5.1 Extravasation 288 18.5.2 Local and National Extravasation Guidelines 290 18.6 Phlebitis and Venous Irritation 290 18.7 Health and Safety 291 18.8 National Guidance on the Safe Administration of Intrathecal Chemotherapy 291 Further Reading 292 Index 295

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Book SynopsisHighlighting dynamic developments in polymer synthesis, this book focuses on the chemical techniques to synthesize and characterize biomedically relevant polymers and macromolecules. Aids researchers developing polymers and materials for biomedical applications Describes biopolymers from a synthetic perspective, which other similar books do not do Covers areas that include: cationically-charged macromolecules, pseudo-peptides, polydrugs and prodrugs, controlled radical polymerization, self-assembly, polycondensates, and polymers for surface modificationTable of ContentsList of Contributors ix Part I. Pseudo-Peptides, Polyamino acids and Polyoxazolines 1 Chapter 1 - Characterization of Polypeptides and Polypeptoides­ –Methods and Challenges 3David Huesmann and Matthias Barz Chapter 2- Poly(2-Oxazoline): The structurally Diverse Biocompatibilizing Polymer 31Rodolphe Obeid Chapter 3- Poly(2-oxazoline) Polymers – synthesis, characterization and Applications in Development of Therapeutics 51Randall W. Moreadith and Tacey X. Viegas Chapter 4- Polypeptoid Polymers: Synthesis, Characterization and Properties 77Brandon A. Chan, Sunting Xuan, Ang Li, Jessica M. Simpson and Donghui Zhang Part II - Advanced Polycondensates 121 Chapter 5 - Polyanhydrides: Synthesis and Characterization 123Rohan Ghadi, Eameema Muntimadugu Wahid Khan and Abraham J. Domb Chapter 6 - New Routes to Tailor-Made Polyesters 149Kazuki Fukushima and Tomoko Fujiwara Chapter 7 - Polyphosphoesters: An old biopolymer in a new light 191Kristin N. Bauer, Hisaschi T.C. Tee, Evandro M. Alexandrino and Frederik R. Wurm Part III. Cationically Charged Macromolecules 243 Chapter 8 - Design and Synthesis of Amphiphilic Vinyl Copolymers with Antimicrobial Activity 245Leanna L. Foster, Masato Mizutani, Yukari Oda, Edmund F. Palermo and Kenichi Kuroda Chapter 9 - Enhanced Polyethylenimine-Based Delivery of Nucleic Acids 273Jeff Sparks, Tooba Anwer and Khursheed Anwer Chapter 10 - Cationic graft copolymers for DNA engineering 297Atsushi Maruyama and Naohiko Shimada Part IV. Biorelated polymers by Controlled Radical Polymerization 313 Chapter 11 - Synthesis of (Bio)degradable Polymers by Controlled/“Living” Radical Polymerization 315Shannon R. Woodruff and Nicolay V. Tsarevsky Part V. Polydrugs and Polyprodrugs 355 Chapter 12 - Polymerized drugs – a novel approach to controlled release systems 357B. Demirdirek, J. J. Faig, R. Guliyev and K.E.Uhrich Chapter 13 - Structural design and synthesis of polymer prodrugs 391Petr Chytil, Libor Kostka and Tomáš Etrych Part VI. Biocompatibilization of Surfaces 421 Chapter 14 - Polymeric ultrathin films for surface modifications 423Henning Menzel Chapter 15 - Surface Functionalization of Biomaterials by Poly(2-oxazoline)s 457Giulia Morgese and Edmondo M. Benetti Chapter 16 - Biorelated polymer brushes by surface initiated reversible deactivation radical polymerization 487Rueben Pfukwa, Lebohang Hlalele and Bert Klumperman Part VII. Self-assembled Structures and Formulations 525 Chapter 17 - Synthesis of amphiphilic invertible polymers for biomedical applications 527A.M. Kohut, I.O. Hevus, S.A. Voronov and A.S. Voronov Chapter 18 - Bioadhesive Polymers for Drug Delivery 559Eenko Larrañeta and Ryan F. Donnelly INDEX

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Book SynopsisPROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONSEMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section ofMass Spectrometry-Based Chemical Proteomicsstarts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategieTable of ContentsPreface xv 1 Protein Analysis by Shotgun Proteomics 1 Yu Gao and John R. Yates III 1.1 Introduction 1 1.1.1 Terminology 1 1.1.2 Power of Shotgun Proteomics 1 1.1.3 Advantage of Shotgun Proteomics 2 1.2 Overview of Shotgun Proteomics 2 1.3 Sample Preparation 4 1.3.1 Protein Separation 4 1.3.1.1 Overview 4 1.3.1.2 2D‐Gel Approach 4 1.3.1.3 Separation of Membrane Protein 5 1.3.1.4 Subcellular Fractionation 5 1.3.1.5 Protein Enrichment 6 1.3.1.6 Phosphoprotein 6 1.3.1.7 Glycoprotein 6 1.3.1.8 AP–MS and Interactome 7 1.3.2 Protein Modification 8 1.3.2.1 Overview 8 1.3.2.2 Reduction of Disulfide Bond and Alkylation 8 1.3.2.3 Chemical Crosslinking 8 1.3.2.4 Proximity Labeling 9 1.3.3 Protein Digestion 9 1.4 Peptide Separation and Data Acquisition 11 1.4.1 Peptide Separation 11 1.4.1.1 Reversed Phase (RP) 11 1.4.1.2 HILIC 11 1.4.1.3 MudPIT 11 1.4.1.4 Capillary Electrophoresis 13 1.4.2 Peptide Ionization 13 1.4.3 Mass Analyzer 13 1.4.4 Peptide Fragmentation Method 15 1.4.4.1 CID/HCD 15 1.4.4.2 ETD/ECD 16 1.4.4.3 IRMPD/UVPD 16 1.4.5 Acquisition Mode 17 1.5 Informatics 17 1.5.1 Peptide Identification 18 1.5.1.1 Database Search 18 1.5.1.2 Spectral Library Search 21 1.5.1.3 De novo Sequencing 22 1.5.1.4 Peptide‐Centric Analysis 23 1.5.2 Peptide/Protein Quantitation 23 1.5.2.1 Labeled Quantitation 23 1.5.2.2 Label‐Free Quantitation 27 1.5.3 Protein Inference 29 References 31 2 Quantitative Proteomics for Analyses of Multiple Samples in Parallel with Chemical Perturbation 39 Amanda Rae Buchberger, Jillian Johnson, and Lingjun Li 2.1 Introduction 39 2.2 Relative and Absolute Label‐Free Quantitation Strategies 40 2.3 Stable Isotope‐Based Quantitative Proteomics 42 2.3.1 Relative Quantitation 42 2.3.2 Absolute Quantitation 47 2.4 Conclusion 48 2.5 Methodology 50 2.6 Notes 52 Acknowledgments 55 References 56 3 Chemoproteomic Analyses by Activity‐Based Protein Profiling 67 Bryan J. Killinger, Kristoffer R. Brandvold, Susan J. Ramos‐Hunter, and Aaron T. Wright 3.1 Introduction 67 3.2 How ABPP Works 68 3.3 ABPP Probe Design 71 3.3.1 Mechanism‐Based Probes 72 3.3.2 Reactivity‐Based Probes 74 3.3.3 Photoaffinity Probes 74 3.4 ABPP and Mass Spectrometry for Chemoproteomics 75 3.4.1 Determining ABP Target Identity 75 3.4.2 Considerations for Analyzing ABP Targets with MS 77 3.4.3 Determining the Site of ABP Labeling 78 3.4.4 Quantification of ABPP Probe Targets 80 3.4.4.1 Label‐Free Methods 80 3.4.4.2 Isotopic Methods 81 3.5 ABPP Applications and Recent Advances 83 3.5.1 Using ABPs for Functional Protein Annotation 83 3.5.2 ABPPs Applied to Microbes and Their Communities 84 3.6 ABPP Applied to Drug Discovery 88 3.7 Comparative, Competitive, and Convolution ABPP 90 3.8 Conclusions and The Outlook of ABPP 91 Acknowledgements 91 References 91 4 Activity‐Based Probes for Profiling Protein Activities 101 Kasi V. Ruddraraju and Zhong‐Yin Zhang 4.1 Introduction 101 4.2 Design of Activity‐Based Probes 102 4.2.1 The Reactive Group 102 4.2.2 The Linker 104 4.2.3 The Tag 104 4.3 Analytical Platforms for ABPP 105 4.3.1 Gel‐Based Platforms 105 4.3.2 Mass Spectrometry Platforms for ABPP 106 4.3.3 Microarray Platform for ABPP 107 4.3.4 Capillary Electrophoresis Platform for ABPP 107 4.4 Classes of Enzymes Studied by ABPP 108 4.4.1 Serine Hydrolases 108 4.4.2 Cysteine Proteases 109 4.4.3 Metallohydrolases 110 4.4.4 Glycosidases 111 4.4.5 Protein Kinases 114 4.4.6 Protein Phosphatases 116 4.5 Conclusions 119 Acknowledgment 120 References 120 5 Chemical Probes for Proteins and Networks 127 Scott Lovell, Charlotte L. Sutherell, and Edward W. Tate 5.1 Introduction 127 5.1.1 Probe Design and Validation 128 5.1.2 Application to a Proteomics Workflow 129 5.1.3 Quantitative Chemical Proteomics 131 5.2 Application of Metabolic Chemical Probes to Lipidated Protein Networks 132 5.2.1 Chemical Probes for N‐Myristoylation 133 5.2.2 Chemical Probes for Hedgehog Proteins 136 5.3 Chemical Probes for Target Identification 137 5.3.1 Identifying New Target Profiles of Sulforaphane in Breast Cancer Cells 138 5.3.2 Target Profiling of Zerumbone Using a Novel Clickable Probe 140 5.4 Protocol 143 5.4.1 Introduction 143 5.4.2 Materials 143 5.4.2.1 Chemical Tools 143 5.4.2.2 Cell Culture 143 5.4.2.3 Cell Lysis, Enrichment and Sample Preparation 144 5.4.2.4 Click Chemistry and Enrichment 144 5.4.2.5 Proteomics Sample Preparation 144 5.4.2.6 Proteomics Analysis 144 5.4.3 Method 144 5.4.3.1 HeLa Cell Culture and Preparation of Spike‐in Standard 144 5.4.3.2 Preparation of Cell Lysates for Protein Enrichment 145 5.4.3.3 Pull‐Down Experiments and Sample Preparation 145 5.4.3.4 LC–MS/MS Analysis 147 5.4.3.5 Data Analysis 147 5.4.3.6 Identification of N‐Terminal Myristoylated Peptides 151 5.5 Notes 152 References 153 6 Probing Biological Activities with Peptide and Peptidomimetic Biosensors 159 Laura J. Marholz, Tzu-Yi Yang, and Laurie L. Parker 6.1 Introduction 159 6.2 Peptide Biosensors for Assignment and Characterization of Enzymatic Reactions and Substrate Specificity 160 6.3 Screening Inhibitors and Detecting Ligand Interactions 165 6.4 Diagnostic and Clinical Applications 168 6.5 Profiling Enzymatic Activity 172 6.6 Protocol 178 Materials 179 Methods 180 6.7 Conclusion 182 References 182 7 Chemoselective Tagging to Promote Natural Product Discovery 187 Emily J. Tollefson and Erin E. Carlson 7.1 Introduction 187 7.2 Nonreversible Mass Spectrometry Tags 189 7.2.1 Azides and Alkynes 189 7.2.2 Thiols 192 7.2.3 Aminooxy 194 7.3 Reversible Enrichment Tags 195 7.3.1 Boronic Acids 195 7.3.2 Hydrazines 196 7.3.3 Silanes 196 7.3.4 Disulfides 197 7.4 Conclusions 198 7.5 Protocol for Enrichment of Carboxylic‐Acid‐Containing Natural Products 198 7.5.1 Dialkylsiloxane Resin Synthesis 198 7.5.2 Production of S. rochei Extract 200 7.5.3 Chemoselective Capture 200 7.5.4 Release of Carboxylic‐Acid‐Containing Compounds from Resin 201 References 201 8 Identification and Quantification of Newly Synthesized Proteins Using Mass‐Spectrometry Based Chemical Proteomics 207 Suttipong Suttapitugsakul, Haopeng Xiao, and Ronghu Wu 8.1 Introduction 207 8.2 Protein Labeling to Study Newly Synthesized Proteins 209 8.2.1 Radioactive Labeling 209 8.2.2 Protein Labeling with Fluorescent Probes 209 8.2.3 SILAC Labeling 210 8.2.4 Protein Labeling with Noncanonical Amino Acids 210 8.3 Global Identification of Newly Synthesized Proteins by Noncanonical Amino Acids and MS 212 8.4 Comprehensive Quantification of Newly Synthesized Proteins by MS 213 8.5 Materials 217 8.5.1 Cell Culture and AHA Labeling 217 8.5.2 Cell Lysis 218 8.5.3 Enrichment of Newly Synthesized Proteins Using Click Chemistry 218 8.5.4 On‐Bead Protein Reduction, Alkylation, and Digestion 218 8.5.5 Peptide Desalting 218 8.5.6 TMT Labeling 219 8.5.7 Peptide Fractionation 219 8.5.8 StageTips 219 8.5.9 LC–MS/MS Analysis 219 8.5.10 Database Searches and Data Filtering 220 8.6 Methods 220 8.6.1 Cell Culture with AHA Labeling 220 8.6.2 Cell Lysis and Protein Extraction 220 8.6.3 Enrichment of Newly Synthesized Proteins 220 8.6.4 On‐Bead Reduction, Alkylation, and Digestion 221 8.6.5 Peptide Desalting 221 8.6.6 TMT Labeling 222 8.6.7 Peptide Fractionation 222 8.6.8 StageTip Purification 222 8.6.9 LC–MS/MS Analysis 223 8.6.10 Database Searches, Data Filtering, and Half‐Life Calculation of Newly Synthesized Proteins 223 Acknowledgements 224 References 224 9 Tracing Endocytosis by Mass Spectrometry 231 Mayank Srivastava, Ying Zhang, Linna Wang, and W. Andy Tao 9.1 Introduction 231 9.2 Clathrin‐Mediated Endocytosis 232 9.2.1 Proteins Involved in the Formation of Clathrin‐Coated Vesicles 233 9.2.2 Molecular Mechanism for CCV Formation 234 9.2.3 Vesicle Uncoating and Fusion with Endosomal Compartments 237 9.3 Mass Spectrometry as a Tool to Study Endocytosis 237 9.3.1 Isolation of Clathrin‐Coated Vesicles and Analysis Using Mass Spectrometry 238 9.3.2 Chemical Proteomic Approaches for Studying the Endocytosis 240 9.3.2.1 Identification of Receptor by Ligand‐based–Receptor Capture (LRC) Technology 240 9.3.2.2 Studying the Entry and Trafficking of Nanoparticles Using Time‐Resolved Chemical Proteomic Approach 241 9.4 Protocols for TITAN 243 9.4.1 Materials 243 9.4.2 Dendrimer Functionalization 245 9.4.2.1 Synthesis of Masked Aldehyde Handle 245 9.4.2.2 Functionalization of Dendrimer 245 9.4.3 Internalization of Dendrimer by HeLa and MS Sample Preparation 247 9.4.4 Mass Spectrometry and Data Analysis 249 9.5 Conclusion and Future Directions 250 References 251 10 Functional Identification of Target by Expression Proteomics (FITExP) 257 Massimiliano Gaetani and Roman A. Zubarev 10.1 Introduction 257 10.2 FITExP Protocol 261 10.2.1 Cell Line(s) and Drugs/Compounds Selection 261 10.2.2 Drug Treatments of Cell Cultures 261 10.2.3 Cell Lysis and Protein Extraction 262 10.2.4 Estimation of Protein Concentration and Protein Sample Processing 263 10.2.5 Protein Digestion 263 10.2.6 Peptide TMT (Tandem Mass Tag) Labeling and Desalting 263 10.2.7 High pH Fractionation TMT 264 10.2.8 Mass Spectrometry Analysis 264 10.2.9 Data Analysis 265 References 265 11 Target Discovery Using Thermal Proteome Profiling 267 Sindhuja Sridharan, Ina Günthner, Isabelle Becher, Mikhail Savitski, and Marcus Bantscheff 11.1 Introduction 267 11.2 Thermodynamics of Ligand Binding as a Measure of Target Engagement 270 11.3 Thermal Proteome Profiling – Proteome‐wide Detection of Drug–Target Interactions 273 11.3.1 Overview 273 11.3.2 Distinguishing Direct Drug Targets from Downstream Effectors of Drug Action 273 11.4 Experimental Formats 275 11.4.1 Temperature‐Range Experiment (TPP‐TR) 275 11.4.2 Compound Concentration‐Range Experiment (TPP‐CCR) 277 11.4.3 Two‐Dimensional TPP (2D‐TPP) 278 11.5 Experimental Protocol 278 11.6 Reagents 280 11.6.1 Step 1: Compound Treatment 280 11.6.2 Step 2: Temperature Treatment 281 11.6.3 Step 3: Protein Digestion and Labeling 282 11.6.4 Step 4: Mass Spectrometric Analysis of Samples 283 11.6.5 Step 5: Peptide and Protein Identification and Quantification 283 11.6.6 Step 6: Data Handling and Analysis 284 11.7 Present Challenges with TPP 284 11.8 CETSA to TPP – Where are We Heading? 285 References 287 12 Chemical Strategies to Glycoprotein Analysis 293 Joseph L. Mertz, Christian Toonstra, and Hui Zhang 12.1 Introduction 293 12.2 Sample Preparation Strategies for Glycoproteomics 297 12.2.1 Enzymatic/Chemical Modification for Glycopeptide Enrichment 297 12.2.2 Enrichment of Glycans or Glycopeptides by Physical–Chemical Approaches 300 12.3 MS Analysis 302 12.3.1 Glycoproteomic Analysis by Mass Spectrometry 302 12.3.2 Bioinformatics and Data Analysis 304 12.4 Conclusions 306 References 307 13 Proteomic Analysis of Protein–Lipid Modifications: Significance and Application 317 Kiall F. Suazo, Garrett Schey, Chad Schaber, Audrey R. Odom John, and Mark D. Distefano 13.1 Introduction 317 13.2 Chemical Proteomic Approach to Identify Lipidated Proteins 318 13.2.1 Fatty Acylation 322 13.2.1.1 N‐Myristoylation 323 13.2.1.2 S‐Palmitoylation 325 13.2.2 Prenylation 328 13.2.3 Modification with Cholesterol and GPI Anchors 330 13.3 Protocol for Proteomic Analysis of Prenylated Proteins 331 13.3.1 Materials 332 13.3.1.1 Reagents 332 13.3.1.2 Equipment 333 13.3.1.3 Reagents and Instrument Setup 333 13.3.2 Procedure 334 13.3.2.1 Labeling with Probe 334 13.3.2.2 Isolating Parasites via Saponin Lysis 335 13.3.2.3 In‐gel Fluorescence Analysis 335 13.3.2.4 Biotinylation and Streptavidin Pull‐down 336 13.3.2.5 Sample Preparation for LC–MS/MS Analysis 337 13.3.2.6 LC–MS/MS Analysis 337 13.3.2.7 Proteomic Data Analysis Using Spectral Counting 338 13.3.3 Results 338 References 341 14 Site‐Specific Characterization of Asp‐ and Glu‐ADP‐Ribosylation by Quantitative Mass Spectrometry 349 Shuai Wang, Yajie Zhang, and Yonghao Yu 14.1 Introduction 349 14.2 Materials 353 14.2.1 Cell Culture 353 14.2.2 Generation of Stable Cell Lines Expressing shPARG 353 14.2.3 Sample Preparation for Mass Spectrometry 353 14.2.4 Mass Spectrometry Analysis 354 14.2.5 Equipment 354 14.3 Methods 354 14.3.1 Generation of shPARG‐Expressing Cell Line 354 14.3.2 SILAC Cell Culture 355 14.3.3 Cell Lysis 355 14.3.4 Reduction, Alkylation, and Precipitation of Proteins 355 14.3.5 Protein Digestion and Enrichment of the PARylated Peptides 356 14.3.6 Cleanup of the Peptide 357 14.3.7 Mass Spectrometry Analysis and Data Processing 357 14.4 Notes 357 Acknowledgements 358 References 358 15 MS‐Based Hydroxyl Radical Footprinting: Methodology and Application of Fast Photochemical Oxidation of Proteins (FPOP) 363 Ben Niu and Michael L. Gross 15.1 Introduction 363 15.1.1 General Approaches for Mapping Protein Conformations 363 15.1.2 MS‐Based Approaches 364 15.2 Generation of Hydroxyl Radicals 365 15.2.1 Fenton and Fenton‐like Chemistry 365 15.2.2 Electron-Pulse Radiolysis 368 15.2.3 High‐Voltage Electrical Discharge 370 15.2.4 Synchrotron X‐ray Radiolysis of Water 371 15.2.5 Plasma Formation of OH Radicals 372 15.2.6 Photolysis of Hydrogen Peroxide 374 15.3 Fast Photochemical Oxidation of Proteins (FPOP) 375 15.3.1 FPOP Footprints Faster than Protein Folding/Unfolding 377 15.3.2 FPOP Dosimetry 378 15.3.3 Primary Radical Lifetime and Adjustment of Radical Scavengers 379 15.3.4 Radical Lifetimes Can Be Milliseconds 381 15.3.5 Differential Scavenging and Use of a Reporter Peptide in FPOP 381 15.3.6 New Reactive Reagents for the FPOP Platform 383 15.4 Applications of FPOP 384 15.4.1 FPOP for Protein–Protein Interactions and Epitope Mapping 384 15.4.2 FPOP for Protein Aggregation/Oligomerization 387 15.4.3 FPOP for Protein Dynamics 390 15.4.4 FPOP for Protein Folding 391 15.4.5 FPOP for Characterizing Membrane Proteins 394 15.5 Conclusions 395 References 396 Index 417

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Book SynopsisVolume 85 represents the ninth single chapter volume to be produced in Organic Reactions'' 72-year history. The original authors, Drs. Shaughnessy and DeVasher, have compiled an enormous (and growing) literature and distilled it into an extraordinarily useful treatise on all aspects of the copper-catalyzed amination process. Given the myriad types of nitrogen-based nucleophiles and various ligand sets and reaction conditions, the authors have done an outstanding job of identifying the best options for various permutations of donor and acceptor. This comprehensive treatment of so many different options constitutes a dream field guide for the perplexed chemist who wants to know how best to approach the formation of a C-N bond in a target structure and whether copper or palladium catalysis is recommended.Table of Contents1. Copper-Catalyzed Amination of Aryl and Alkenyl Electrophiles 1 Kevin H. Shaughnessy, Engelbert Ciganek, and Rebecca B. DeVasher Cumulative Chapter Titles by Volume 669 Author Index, Volumes 1–85 685 Chapter and Topic Index, Volumes 1–85 691

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Book SynopsisCompeting and winning in today?s competitive marketplace requires a strategy that includes sustainability. Business leaders who embrace it and convey a strong sense of purpose behind their strategy are propelling their organizations into revenue-increasing, cost-reducing outcomes. Purposely Profitable: Embedding Sustainability into the DNA of Food Processing and other Businesses provides a proven, step-by-step methodology for integrating sustainability into the strategic plan to develop a strategy that is sustainable and aligned to a greater purpose. This book notably includes the following: A primer on Sustainability that defines Sustainable Business and presents the Business Case for Sustainability What is an organizational purpose and why is it so important in today?s competitive marketplace Step by step instructions, supported by a case study, for developing each component of the strategic plan (Purpose, Vision, Strategic Pillars, KPITable of ContentsAbout the Author, x Sustainability Primer, xi Understanding sustainability, xi The sustainable organization, xiv Business case for sustainability, xxii Introduction – Setting the Stage, xxvi Chapter 1 Finding Purpose, 1 1.1 Why a purpose?, 3 1.2 Finding purpose and developing a purpose statement, 4 Step 1: Articulating the purpose, 5 Step 2: Crafting a purpose statement, 6 Step 3: Finalizing the purpose statement, 7 Chapter 2 Creating a Shared Vision of the Future, 9 2.1 Crafting a meaningful vision statement, 11 Step 1: Setting the stage, 11 Step 2: Key word development, 12 Step 3: Key word grouping, 13 Step 4: Key word identification, 13 Step 5: Drafting a vision statement, 13 Step 6: Finalizing the vision statement, 14 2.2 Creating a shared vision, 14 2.2.1 Painting a clear picture of the future state, 15 2.2.2 Aligning daily activities to the vision, 16 Chapter 3 Getting Focused – Pillar Development, 18 3.1 The power of pillars, 19 3.1.1 Providing clear direction and focus, 19 3.1.2 Creating a culture of Sustainability, 21 3.2 Building the pillars, 22 Step 1: Pillar identification, 22 Step 2: Integrating Sustainability into the pillars, 25 Step 3: Pillar key word development, 32 Step 4: Key word grouping, 35 Step 5: Developing pillar mission statements, 36 3.3 Visually illustrating the pillars, 38 Chapter 4 Financial Objectives, 41 4.1 Understanding business objectives, 42 4.2 Setting business objectives, 44 4.2.1 Setting a Revenue objective, 45 4.2.2 Setting a Gross Margin objective, 46 4.2.3 Setting an Overhead objective, 48 Chapter 5 Measuring What Matters – KPI Development, 51 5.1 Understanding KPIs and metrics, 52 5.1.1 Leading vs lagging, 53 5.1.2 Absolute vs normalized measures, 54 5.2 Pillar KPI development, 55 Step 1: Identify what needs to be measured, 56 Step 2: Identifying KPIs vs metrics, 58 Step 3: Defining the KPI number, 62 Step 4: Building the baselines, 64 5.3 Building a dashboard, 66 Chapter 6 Setting Expectations – KPI Goal Development, 69 External benchmarking, 73 Internal benchmarking, 74 Opportunity based benchmarking, 74 6.1 Pillar goal development, 75 Step 1: Choose goal‐setting approach, 75 Step 2: Setting a commitment level (goal), 79 Step 3: Setting milestones, 83 Step 4: Assigning ownership, 86 Chapter 7 Adding Value – Program Development, 89 7.1 Program development, 92 Step 1: Gap analysis, 92 Step 2: Pareto analysis, 93 Step 3: Program identification, 94 Step 4: Program metric development, 96 Step 5: Program goal development, 97 Step 6: Action plan development, 99 Chapter 8 Getting Tactical – Strategy Execution, 102 8.1 Communicating the strategic plan, 103 8.1.1 Purpose, 104 8.1.2 Pillars, 106 8.1.3 KPIs, 107 8.1.4 Goals (aka Commitments), 107 8.1.5 Programs, 108 8.2 Cascading the strategic plan, 108 8.3 Building accountability, 109 8.4 Managing strategy execution, 112 8.4.1 Building the right team, 114 8.4.2 Being disciplined, 115 8.4.3 Locking in the gains, 116 8.5 Leveraging technology, 117 Final Thoughts: Making the Leap, 119 Tools and Resources, 126 References, 140 Index, 141

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Book SynopsisThe complete step-by-step guide to mastering the basics of Aspen Plus software Used for a wide variety of important scientific tasks, Aspen Plus software is a modeling tool used for conceptual design, optimization, and performance monitoring of chemical processes. After more than twenty years, it remains one of the most popular and powerful chemical engineering programs used both industrially and academically. Teach Yourself the Basics of Aspen Plus, Second Edition continues to deliver important fundamentals on using Aspen Plus software. The new edition focuses on the newest version of Aspen Plus and covers the newest functionalities. Lecture-style chapters set the tone for maximizing the learning experience by presenting material in a manner that emulates an actual workshop classroom environment. Important points are emphasized through encouragement of hands-on learning techniques that direct learners toward achievement in creating effective designs fluiTable of ContentsPREFACE TO THE SECOND EDITION xiii PREFACE TO THE FIRST EDITION xv ACKNOWLEDGMENTS xix ABOUT THE COMPANION WEBSITE xxi 1 INTRODUCTION TO ASPEN PLUS 1 1.1 Basic Ideas / 1 1.2 Starting Aspen Plus / 4 1.3 The Next Function / 6 1.4 The Navigation Pane / 6 1.5 The Property Environment / 8 1.6 Properties for Simulation / 11 1.7 The Simulation Environment / 13 1.8 Simulation Options / 13 1.9 Units / 14 1.10 Streams / 15 1.11 Blocks / 16 1.12 The Object Manager / 17 1.13 Model Execution / 17 1.14 Viewing Results / 18 1.15 Plotting Results / 20 References / 20 2 PROPERTIES 21 2.1 Introduction / 21 2.2 The Pure Component Databanks / 22 2.3 Property Analysis / 25 2.4 Property Estimation / 29 2.5 Workshops / 32 2.6 Workshop Notes / 33 References / 34 3 THE SIMPLE BLOCKS 35 3.1 Introduction / 35 3.2 Mixer/Splitter Blocks / 35 3.3 The Simple Separator Blocks / 37 3.4 Some Manipulator Blocks / 40 3.5 Workshops / 43 3.6 Workshop Notes / 44 4 PROCESSES WITH RECYCLE 47 4.1 Introduction / 47 4.2 Blocks with Recycle / 48 4.3 Heuristics / 51 4.4 Workshops / 51 4.5 Workshop Notes / 55 References / 56 5 FLOWSHEETING AND MODEL ANALYSIS TOOLS 57 5.1 Introduction / 57 5.2 Introduction to Fortran in Aspen Plus / 58 5.3 Basic Interpreted Fortran Capabilities / 58 5.4 The Sensitivity Function / 61 5.5 The Design Specification / 63 5.6 The Calculator Function / 65 5.7 The Transfer Function / 68 5.8 Workshops / 69 5.9 Workshop Notes / 71 References / 71 6 THE DATA REGRESSION SYSTEM (DRS) 73 6.1 Introduction / 73 6.2 Parameters of Equations of State / 74 6.3 Parameters of Activity Coefficient Equations / 76 6.4 Basic Ideas of Regression / 78 6.5 The Mathematics of Regression / 80 6.6 Practical Aspects of Regression of VLE or LLE Data / 82 6.7 VLE and LLE Data Sources / 90 6.8 Workshops / 93 6.9 Workshop Notes / 95 References / 96 7 FLASHES AND DECANTER 99 7.1 Introduction / 99 7.2 The Flash2 Block / 99 7.3 The Flash3 Block / 104 7.4 The Decanter Block / 105 7.5 Workshops / 107 7.6 Workshop Notes / 108 References / 109 8 PRESSURE CHANGERS 111 8.1 Introduction / 111 8.2 The Pump Block / 111 8.3 The Compr Block / 112 8.4 The MCompr Block / 113 8.5 Pipelines and Fittings / 114 8.6 Workshops / 115 8.7 Workshop Notes / 116 References / 116 9 HEAT EXCHANGERS 117 9.1 Introduction / 117 9.2 The Heater Block / 118 9.3 The Heatx Block / 122 9.4 The Mheatx Block / 126 9.5 Workshops / 127 9.6 Workshop Notes / 128 References / 129 10 REACTORS 131 10.1 Introduction / 131 10.2 The RStoic Block / 132 10.3 The RYield Block / 133 10.4 The REquil Block / 135 10.5 The RGibbs Block / 136 10.6 Reactions for the Rigorous Models / 138 10.7 The RCSTR Block / 143 10.8 The RPlug Block / 143 10.9 The RBatch Block / 145 10.10 Workshops / 148 10.11 Workshop Notes / 150 References / 151 11 MULTISTAGE EQUILIBRIUM SEPARATORS 153 11.1 Introduction / 153 11.2 The Basic Equations / 153 11.3 The Design Problem / 156 11.4 A Three-Product Distillation Example / 160 11.5 Preliminary Design and Rating Models / 162 11.6 Rigorous Models / 165 11.7 BatchSep / 174 11.8 Workshops / 178 11.9 Workshop Notes / 179 References / 181 12 PROCESS FLOWSHEET DEVELOPMENT 183 12.1 Introduction / 183 12.2 Heuristics / 184 12.3 An Example –The Production of Styrene / 184 12.4 A Model with Basic Blocks / 185 12.5 Properties / 185 12.6 Rigorous Flash and Decanter / 187 12.7 Analyzing the Rigorous Distillation / 188 12.8 Integrating the Rigorous Distillation into the Flowsheet / 189 12.9 The Reactor Feed / 192 12.10 Miscellaneous Considerations / 192 12.11 Workshops / 192 12.12 Workshop Notes / 195 Reference / 196 13 OPTIMIZATION 197 13.1 Introduction / 197 13.2 An Optimization Example / 198 13.3 Workshops / 202 13.4 Workshop Notes / 203 References / 205 14 COMPLEX EQUILIBRIUM STAGE SEPARATIONS 207 14.1 Introduction / 207 14.2 Energy Integration Applications / 208 14.3 Homogeneous Azeotropic Distillation / 210 14.4 Extractive Distillation / 211 14.5 Heterogeneous Operations / 214 14.6 Workshops / 215 14.7 Workshop Notes / 217 References / 219 15 EQUATION-ORIENTED SIMULATION 221 15.1 Introduction / 221 15.2 Identification of Variables / 222 15.3 Equations for EO Simulation / 223 15.4 Solving the EO Equations / 225 15.5 Comparing Calculated Variables in SM and EO Simulation / 227 15.6 Synchronization of the Equations / 228 15.7 The Equation Oriented Menu / 229 15.8 Solution of an EO Problem / 230 15.9 Reinitialization / 232 15.10 A Design Specification / 233 15.11 An SM Problem That is Difficult to Converge / 234 15.12 Sensitivity Analysis / 235 15.13 Equation-Oriented Optimization / 235 15.14 Workshops / 238 15.15 Workshop Notes / 241 References / 241 16 ELECTROLYTES 243 16.1 Introduction / 243 16.2 Electrolyte Solution Equilibria / 243 16.3 Electrolyte Solution Equilibria and the Electrolyte Wizard / 244 16.4 Electrolyte Equilibrium/Phase Equilibrium Examples / 248 References / 250 17 BEYOND THE BASICS OF ASPEN PLUS 251 INDEX 253

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Book SynopsisAddressing a cutting-edge, multidisciplinary field, this book reviews nanomaterials and their biomedical applications. It covers regeneration, implants, adhesives, and biosensors and strategies for more efficient therapy, diagnosis, and drug delivery with the use of nanotechnology.Table of ContentsList of Contributors xi Preface xiii 1 Nanomaterials for Medicine 1 Mustafa O. Guler and Ayse B. Tekinay 1.1 Introduction 1 1.2 Nanoscale Material Properties 2 1.3 Nanomaterials for Understanding Disease Pathways 2 1.4 Nanomaterials for Therapy 3 1.5 Challenges and Future Prospects 5 2 Nanosized Delivery Systems for Tissue Regeneration 7 Goksu Cinar, Didem Mumcuoglu, Ayse B. Tekinay, and Mustafa O. Guler 2.1 Introduction 7 2.2 Delivery of Protein Therapeutics with Nanocarriers for Tissue Regeneration 10 2.2.1 GFs and Cytokines 10 2.3 Gene and siRNA Delivery with Nanocarriers for Tissue Regeneration 13 2.3.1 Gene Delivery 13 2.3.2 siRNA Delivery 15 2.4 Systemic Targeting and Cellular Internalization Strategies for Tissue Regeneration 15 2.4.1 Targeted Delivery 15 2.4.2 Cellular Internalization Strategies 18 2.5 Future Perspectives 20 References 22 3 Nanomaterials for Neural Regeneration 33 Melike Sever, Busra Mammadov, Mevhibe Gecer, Mustafa O. Guler, and Ayse B. Tekinay 3.1 Introduction 33 3.1.1 Extracellular Matrix of Central Nervous System 33 3.1.2 ECM of Peripheral Nervous System 37 3.1.3 Urgent Need for Materials to Induce Regeneration in Nervous Tissue 39 3.2 Nanomaterials for Neural Regeneration 40 3.2.1 Physical Functionalization of Nanomaterials to Induce Neural Differentiation 40 3.2.2 Effects of Mechanical Stiffness on Cellular Behavior 40 3.2.3 Effects of Dimensionality on Cellular Behavior 42 3.2.4 Effects of Substrate Topography on Cell Behavior 43 3.2.5 Effects of Electrical Conductivity on Cell Behavior 44 3.3 Chemical and Biological Functionalization of Nanomaterials for Neural Differentiation 45 3.3.1 Effects of Biologically Active Molecules on Cell Behavior 45 3.3.2 Effects of Chemical Groups on Cellular Behavior 46 3.3.3 Effects of Biofunctionalization on Cellular Behavior Through ECM‐Derived Short Peptides 48 3.4 Conclusion 50 References 51 4 Therapeutic Nanomaterials for Cartilage Regeneration 59 Elif Arslan, Seher Ustun Yaylacı, Mustafa O. Guler, and Ayse B. Tekinay 4.1 Introduction 59 4.2 Current Treatment Methods for Cartilage Injuries 63 4.3 Tissue Engineering Efforts 66 4.3.1 Natural Polymers 67 4.3.2 Synthetic Polymers 69 4.3.3 Composite Materials 70 4.3.4 Physical Stimuli 71 4.4 Clinical Therapeutics for Cartilage Regeneration 72 4.5 Conclusions and Future Perspectives 73 References 78 5 Wound Healing Applications of Nanomaterials 87 Berna Senturk, Gozde Uzunalli, Rashad Mammadov, Mustafa O. Guler, and Ayse B. Tekinay 5.1 Introduction 87 5.1.1 The Structure of Healthy Mammalian Skin 88 5.1.2 The Mechanisms of Wound Healing 89 5.1.3 Repair Process in Chronic Wounds 94 5.2 Applications of Nanomaterials for the Enhancement of Wound Healing Process 95 5.2.1 Artificial Skin 96 5.2.2 Natural Nanomaterials for Wound Healing 97 5.2.3 Synthetic Nanomaterials for Wound Healing 100 5.2.4 Wound Dressings Containing Growth Factors 101 5.2.5 Biomimetic Materials 102 5.2.6 Current Challenges in the Design of Nanomaterials for Chronic Wound Management 103 5.3 Peptide Nanofiber Gels for Wound Healing 105 5.3.1 Relevance of Nanofibrous Structure of Peptide Gels for Wound Healing 106 5.3.2 Engineered PA Nanofiber Gels for Wound Healing and Insights into Various Designs 107 References 110 6 Nanomaterials for Bone Tissue Regeneration and Orthopedic Implants 119 Gulcihan Gulseren, Melis Goktas, Hakan Ceylan, Ayse B. Tekinay, and Mustafa O. Guler 6.1 Introduction 119 6.2 Bone Matrix 120 6.2.1 Organic Matrix and Bioactivity 120 6.3 Inorganic Matrix, Mineralization, and Bone Organization 122 6.3.1 Mechanical Properties and Structural Hierarchy of Bone Tissue 123 6.4 Regulation of Bone Matrix in Adult Tissue 125 6.4.1 Angiogenic Factors in Bone Remodeling 126 6.5 Strategies for Bone Tissue Regeneration 127 6.5.1 Hard Grafts for Bone Regeneration 127 6.6 Soft Grafts for Bone Regeneration 131 6.6.1 Peptide‐Based Bone Grafts 132 6.6.2 Polymer Nanocomposites as Bone Grafts 134 6.7 Future Perspectives 138 References 138 7 Nanomaterials for the Repair and Regeneration of Dental Tissues 153 Gulistan Tansık, Alper Devrim Ozkan, Mustafa O. Guler, and Ayse B. Tekinay 7.1 Introduction 153 7.2 Formation of Dental and Osseous Tissues 155 7.3 Dental Implants 156 7.3.1 Metallic Implants 158 7.3.2 Ceramic Implants 158 7.3.3 Polymeric Implants 159 7.4 Osseointegration of Dental Implants 159 7.5 Uses of Nanotechnology in the Development of Dental Implants 160 7.5.1 Enhancement of the Osseointegration Process 161 7.5.2 Pulp and Dentin Tissue Regeneration 162 7.5.3 Whole Tooth Regeneration 165 7.6 Conclusions and Future Perspectives 166 References 166 8 Nanomaterials as Tissue Adhesives 173 I. Ceren Yasa, Hakan Ceylan, Ayse B. Tekinay, and Mustafa O. Guler 8.1 Introduction 173 8.2 Tissue Adhesives Based on Synthetic Polymers 176 8.3 Naturally Derived Tissue Adhesives 180 8.4 Bioinspired Strategies 182 8.5 Nanoenabled Adhesives 186 8.6 Conclusion and Future Prospects 186 References 189 9 Advances in Nanoparticle‐Based Medical Diagnostic and Therapeutic Techniques 197 Melis Sardan, Alper Devrim Ozkan, Aygul Zengin, Ayse B. Tekinay, and Mustafa O. Guler 9.1 Introduction 197 9.2 NPs used in MRI 200 9.2.1 T1 CAs 201 9.2.2 T2 CAs 205 9.2.3 Dual Modal Contrast Agents 207 9.3 NPs used in Computed Tomography 208 9.3.1 Noble Metal‐Based NPs 209 9.3.2 Heavy Metal‐Based NPs 211 9.4 NPs used in Optical and Fluorescence Imaging 213 9.4.1 Quantum Dots 214 9.4.2 AuNPs 216 9.4.3 UCNPs 217 9.5 Theranostic Approaches and Multimodal Systems 218 9.6 Overlook and Future Directions 222 References 223 10 Biosensors for Early Disease Diagnosis 235 Ahmet E. Topal, Alper Devrim Ozkan, Aykutlu Dana, Ayse B. Tekinay, and Mustafa O. Guler 10.1 Introduction 235 10.2 Biosensor Elements 237 10.2.1 Recognition Elements 237 10.2.2 Output Type and Detection Techniques 239 10.2.3 Optical Biosensors 248 10.2.4 Electrical and Electrochemical Biosensors 250 10.2.5 Mechanical Biosensors 251 10.2.6 Other Biosensor Types 252 10.3 The Impact of Nanotechnology and Nanomaterials in Biosensor Design 253 10.4 Early Diagnosis and Biosensor‐Based Disease Detection 255 10.5 Conclusion and Future Directions 258 References 259 11 Safety of Nanomaterials 271 Nuray Gunduz, Elif Arslan, Mustafa O. Guler, and Ayse B. Tekinay 11.1 Introduction 271 11.2 Characterization, Design, and Synthesis of Nanomaterials 272 11.2.1 Chemical Identity and Physicochemical Properties 272 11.2.2 Biological Identity 275 11.3 Interactions at the Cell–Material Interface 277 11.3.1 Intracellular Activity 278 11.3.2 Cellular Uptake Mechanisms 283 11.4 Assays for Cell Viability/Proliferation 283 11.4.1 Assays for Oxidative Stress and Apoptosis Mechanisms 284 11.4.2 E valuation of Uptake and Accumulation of ENMs 284 11.4.3 Genotoxicity Assays 285 11.5 Animal Models and Long‐Term Risk Assessment 286 11.5.1 The Blood–Brain Barrier 286 11.6 Conclusions and Future Perspectives 290 References 291 Index 299

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Book SynopsisA step-by-step guide for students (and faculty) on the use of Aspen in teaching thermodynamics Easily-accessible modern computational techniques opening up new vistas in teaching thermodynamicsA range of applications of Aspen Plus in the prediction and calculation of thermodynamic properties and phase behavior using the state-of-the art methodsEncourages students to develop engineering insight by doing repetitive calculations with changes in parameters and/or modelsCalculations and application examples in a step-by-step manner designed for out-of-classroom self-studyMakes it possible to easily integrate Aspen Plus into thermodynamics courses without using in-class timeStresses the application of thermodynamics to real problemsTable of ContentsPreface vii An Introduction for Students ix 1. Getting Started with Aspen Plus® 1 Problems 9 2. Two Simple Simulations 10 Problems 34 3. Pure Component Property Analysis 36 Problems 55 4. The NIST ThermoData Engine (TDE) 56 Problems 64 5. Vapor–Liquid Equilibrium Calculations Using Activity Coefficient Models 66 5.1 Property Analysis Method 69 5.2 The Simulation Method 80 5.3 Regression of Binary VLE Data with Activity Coefficient Models 89 Problems 115 6. Vapor–Liquid Equilibrium Calculations Using an Equation of State 119 6.1 The Property Analysis Method 120 6.2 The Simulation Method 122 6.3 Regression of Binary VLE Data with an Equation of State 129 Problems 142 7. Regression of Liquid–Liquid Equilibrium (LLE) Data and Vapor–Liquid–Liquid Equilibrium (VLLE) and Predictions 144 7.1 Liquid–Liquid Data Regression 144 7.2 The Prediction of Liquid–Liquid and Vapor–Liquid–Liquid Equilibrium 158 7.3 High Pressure Vapor–Liquid–Liquid Equilibrium 167 Problems 173 8. The Property Methods Assistant and Property Estimation 175 8.1 The Property Methods Assistant 175 8.2 Property Estimation 182 8.3 Regressing Infinite Dilution Activity Coefficient Data 188 Problems 201 9. Chemical Reaction Equilibrium in Aspen Plus® 203 Problems 229 10. Shortcut Distillation Calculations 233 Problems 250 11. A Rigorous Distillation Calculation: RadFrac 252 Problems 271 12. Liquid–Liquid Extraction 272 Problems 286 13. Sensitivity Analysis: A Tool for Repetitive Calculations 287 Problems 304 14. Electrolyte Solutions 305 Problems 337 Index 339

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Book SynopsisAn introduction to the state-of-the-art of the diverse self-assembly systems Self-Assembly: From Surfactants to Nanoparticles provides an effective entry for new researchers into this exciting field while also giving the state of the art assessment of the diverse self-assembling systems for those already engaged in this research. Over the last twenty years, self-assembly has emerged as a distinct science/technology field, going well beyond the classical surfactant and block copolymer molecules, and encompassing much larger and complex molecular, biomolecular and nanoparticle systems. Within its ten chapters, each contributed by pioneers of the respective research topics, the book: Discusses the fundamental physical chemical principles that govern the formation and properties of self-assembled systems Describes important experimental techniques to characterize the properties of self-assembled systems, particularly the nature of molecuTable of ContentsList of Contributors xi Preface xv Acknowledgments xxi 1 Self-Assembly from Surfactants to Nanoparticles – Head vs. Tail 1Ramanathan Nagarajan 1.1 Introduction 1 1.2 Classical Surfactants and Block Copolymers 4 1.2.1 Tanford Model for Surfactant Micelles 4 1.2.2 de Gennes Model for Block Copolymer Micelles 11 1.2.3 Surfactant Self-Assembly Model Incorporating Tail Effects 13 1.2.4 Star Polymer Model of Block Copolymer Self-Assembly Incorporating Headgroup Effects 15 1.2.5 Mean Field Model of Block Copolymer Self-Assembly Incorporating Headgroup Effects 17 1.2.6 Tail Effects on Shape Transitions in Surfactant Aggregates 20 1.2.7 Headgroup Effects on Shape Transitions in Block Copolymer Aggregates 22 1.3 Self-Assembly of Nonclassical Amphiphiles Based on Head−Tail Competition 24 1.3.1 Dendritic Amphiphiles 25 1.3.2 DNA Amphiphiles 27 1.3.3 Peptide Amphiphiles 29 1.3.4 Protein−Polymer Conjugates 31 1.3.5 Amphiphilic Nanoparticles 34 1.4 Conclusions 37 Acknowledgments 37 References 38 2 Self-Assembly into Branches and Networks 41Alexey I. Victorov 2.1 Introduction 41 2.2 Rheology and Structure of Solutions Containing Wormlike Micelles 44 2.2.1 Viscoelasticity of Entangled Wormlike Micelles 44 2.2.2 Growth of Nonionic Micelles 50 2.2.3 Growth of Ionic Micelles 51 2.2.4 Persistence Length of an Ionic Micelle 52 2.2.5 Networks of Branched Micelles 53 2.2.6 Ion-Specific Effect on Micellar Growth and Branching 55 2.3 Branching and Equilibrium Behavior of a Spatial Network 56 2.3.1 The Entropic Network of Chains 56 2.3.2 The Shape of Micellar Branch and the Free Energy 61 2.4 Conclusions 66 Acknowledgments 69 References 69 3 Self-Assembly of Responsive Surfactants 77Timothy J. Smith and Nicholas L. Abbott 3.1 Introduction 77 3.2 Redox-Active Surfactants 77 3.2.1 Reversible Changes in Interfacial Properties 78 3.2.2 Reversible Changes in Bulk Solution Properties 82 3.2.3 Control of Biomolecule-Surfactant Assemblies 84 3.2.4 Spatial Control of Surfactant-Based Properties 87 3.3 Light-Responsive Surfactants 90 3.3.1 Interfacial Properties 90 3.3.2 Bulk Solution Properties 90 3.3.3 Biomolecule-Surfactant Interactions 91 3.3.4 Spatial Control of Surfactant-Based Properties Using Light 93 3.4 Conclusion 93 Acknowledgments 96 References 96 4 Self-Assembly and Primitive Membrane Formation: Between Stability and Dynamism 101Martin M. Hanczyc and Pierre-AlainMonnard 4.1 Introduction 101 4.2 Basis of Self-Assembly of Single-Hydrocarbon-Chain Amphiphiles 104 4.2.1 van derWaals Forces and Hydrophobic Effect 104 4.2.2 Headgroup-to-Headgroup Interactions 105 4.2.3 Interactions Between the Amphiphile Headgroups and Solute/Solvent Molecules 106 4.3 Types of Structures 106 4.3.1 Critical Aggregate Concentration 107 4.3.2 Packing Parameter 108 4.4 Self-Assembly of a Single Type of Single-Hydrocarbon-Chain Amphiphile 109 4.4.1 Single Species of Single-Hydrocarbon-Chain Amphiphile 109 4.4.2 Mixtures of Single-Hydrocarbon-Chain Amphiphiles 110 4.4.2.1 Mixtures of Amphiphiles with the Same Functional Headgroups 111 4.4.2.2 Mixtures of Single-Hydrocarbon Chain Amphiphiles and Neutral Co-surfactants 111 4.4.2.3 Mixtures of Charged Single Hydrocarbon Chain Amphiphiles 112 4.4.2.4 Mixtures of Single-Chain Amphiphiles and Lipids 113 4.4.3 Mixtures of Single-Hydrocarbon-Chain Amphiphiles and Other Molecules 114 4.4.4 Self-Assembly on Surfaces 115 4.5 Catalysis Compartmentalization with Single-Hydrocarbon-Chain Amphiphiles 116 4.5.1 Enclosed Protocell Models 118 4.5.2 Interfacial Protocell Models 120 4.5.3 Membranes as Energy Transduction Systems 124 4.5.3.1 Linking Light Energy Harvesting and Chemical Conversion 124 4.5.3.2 Formation of Chemical Gradients 125 4.5.3.3 Energy Harvesting and Its Conversion into High-Energy Bonds of Phosphate-Chemicals 125 4.6 Dynamism 126 4.7 Conclusion 128 Acknowledgments 129 References 129 5 ProgrammingMicelles with Biomolecules 137Matthew P. Thompson and Nathan C. Gianneschi 5.1 Introduction 137 5.2 Peptide-Containing Micelles 138 5.2.1 Peptide Amphiphiles 139 5.2.2 Peptide−Polymer Amphiphiles (PPAs) 141 5.3 DNA-Programmed Micelle Systems 151 5.3.1 Lipid-Like DNA Amphiphiles 154 5.3.2 DNA−Polymer Amphiphiles 159 5.4 Summary 172 References 172 6 Protein Analogous Micelles 179Lorraine Leon andMatthew Tirrell 6.1 Introduction 179 6.2 Physicochemical Properties of Peptide Amphiphiles 181 6.2.1 The Role of Secondary Structures in PAMs 182 6.2.2 The Role of Different Tails in PAMs 185 6.2.3 The Role of Multiple Headgroups in PAMs 186 6.2.4 Stabilizing Spherical Structures 187 6.2.5 Electrostatic Interactions 188 6.2.6 Mixed Micelles 188 6.2.7 Stimuli-Responsive PAMs 190 6.3 PAMs in Biomedical Applications 192 6.3.1 Tissue Engineering and RegenerativeMedicine 192 6.3.2 Diagnostic and Therapeutic PAMs 195 6.4 Conclusions 199 Acknowledgments 199 References 200 7 Self-Assembly of Protein−Polymer Conjugates 207Xuehui Dong, Aaron Huang, Allie Obermeyer, and Bradley D. Olsen 7.1 Introduction 207 7.2 Helical Protein Copolymers 209 7.3 β-Sheet Protein Copolymers 215 7.4 Cyclic Protein Copolymers 220 7.5 Coil-Like Protein Copolymers 223 7.6 Globular Protein Copolymers 229 7.7 Outlook 236 Acknowledgments 237 References 237 8 Multiscale Modeling and Simulation of DNA-Programmable Nanoparticle Assembly 257Ting Li, Rebecca J.McMurray, and Monica Olvera de la Cruz 8.1 Introduction 257 8.2 A Molecular Dynamics Study of a Scale-Accurate Coarse-Grained Model with Explicit DNA Chains 259 8.3 Thermally Active Hybridization 263 8.4 DNA-Mediated Nanoparticle Crystallization in Wulff Polyhedra 268 8.5 Conclusions 272 Acknowledgments 273 References 273 9 Harnessing Self-Healing Vesicles to Pick Up, Transport, and Drop Off Janus Particles 277Xin Yong, Emily J. Crabb, Nicholas M. Moellers, Isaac Salib, Gerald T.McFarlin, Olga Kuksenok, and Anna C. Balazs 9.1 Introduction 277 9.2 Methodology 279 9.3 Results and Discussion 285 9.3.1 Selective Pick-Up of a Single Particle 285 9.3.1.1 Symmetric Janus Particles and Pure Hydrophilic Particles 285 9.3.1.2 Asymmetric Janus Particles 288 9.3.2 Interaction between Multiple Particles and a Lipid Vesicle 291 9.3.3 Depositing Janus Particles on Patterned Surfaces 295 9.3.3.1 Step Trench 295 9.3.3.2 Wedge Trench 298 9.3.3.3 “Sticky” Stripe 301 9.4 Conclusions 303 Acknowledgments 304 References 304 10 Solution Self-Assembly of Giant Surfactants: An Exploration on Molecular Architectures 309Xue-Hui Dong, Yiwen Li, Zhiwei Lin, Xinfei Yu, Kan Yue, Hao Liu, Mingjun Huang,Wen-Bin Zhang, and Stephen Z. D. Cheng 10.1 Introduction 309 10.2 Molecular Architecture of Giant Surfactants 311 10.3 Giant Surfactants with Short Nonpolymeric Tails 312 10.4 Giant Surfactants with a Single Head and Single Polymer Tail 315 10.5 Giant Surfactants with Multiheads and Multitails 319 10.6 Giant Surfactants with Block Copolymer Tails 321 10.7 Conclusions 324 Acknowledgments 325 References 325 Index 331

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Book SynopsisChemistry as a Game of Molecular Construction: The Bond-Click Way utilizes an innovative and engaging approach to introduce students to the basic concepts and universal aspects of chemistry, with an emphasis on molecules' beauty and their importance in our lives. Offers a unique approach that portrays chemistry as a window into mankind's material-chemical essence Reveals the beauty of molecules through the click method, a teaching methodology comprised of the process of constructing molecules from building blocks Styles molecular construction in a way that reveals the universal aspect of chemistry Allows students to construct molecules, from the simple hydrogen molecule all the way to complex strands of DNA, thereby showing the overarching unity of matter Provides problems sets and solutions for each chapterTable of ContentsFOREWORD xv PREFACE xvii Comments to the Teachers/Students xvii A Conversation on the Textbook and Its Intended Readers xx LECTURE 1 MOLECULAR BLUES 1 1.1 Conversation on Contents of Lecture 1 1 1.2 The Universal Aspect of Chemistry 2 1.3 Love, Addiction, Psychological Balance, etc. 2 1.4 The Chemical Mechanism of Neurotransmission 8 1.5 Molecules of Pleasure, Wellness, and Pair Bonding 10 1.6 More Chemical Control 13 1.7 The Chemical Matter 15 1.8 Molecular Architecture and Its Emergent Properties 18 1.8.1 Diamond, Graphite, and More 18 1.8.2 And There Was Light… 19 1.9 Chirality, and the Magic by Which Molecules Recognize Others in Nature 21 1.10 Our Genetic Code Is Chemical 23 1.11 Chemistry and Its Emergent Expressions 24 1.12 References and Notes 26 1.A Appendix 29 1.A.1 Proposed Demonstrations 29 1.A.2 References for Appendix 1.A 31 1.R Retouches 31 1.R.1 More Drugs Looking like PEA 31 1.R.2 The Atomic Hypothesis 32 1.R.3 The Uncertainty Principle, The Exclusion Rule, and Valence 32 1.R.4 Units of Size 33 1.R.5 References for Retouches 33 LECTURE 2 THE CHEMICAL BOND AND THE LEGO PRINCIPLE 35 2.1 Conversation on Contents of Lecture 2 35 2.2 The Periodic Table: The Storehouse of Atoms 36 2.2.1 The Chemical Language 38 2.3 The LEGO Principle 40 2.3.1 The Covalent Bond in H2 41 2.4 The Bonding Capability of Atoms and The Law of Nirvana for Main Group Elements 44 2.4.1 The Valence Shell and Connectivity in a Family 45 2.4.2 The Octet and Duet Rules: The Law of Nirvana 46 2.5 Making Molecules Using the Available Atom Connectivity and The Law of Nirvana 48 2.5.1 Using the Table of Connectivity to Make Molecules That Attain Nirvana 50 2.5.2 Bonding in Atoms with Multiple Connectivity 53 2.6 The Principle of Conservation of the Number of Atoms in Chemical Reactions 56 2.7 Summary 57 2.8 References 59 2.A Appendix 59 2.R Retouches 60 2.R.1 Elements versus Atoms 60 2.R.2 Electron Pairing 61 2.R.3 Enzymes and Catalysis 61 2.R.4 Alchemy 62 2.R.5 References for Retouches 63 2.P Problem Set 63 LECTURE 3 ELECTRON-DEFICIENT MOLECULES, GIANT MOLECULES, AND CONNECTIVITY OF LARGE FRAGMENTS 65 3.1 Conversation on Contents of Lecture 3 65 3.2 Electron-Deficient Molecules 66 3.2.1 Electron-Deficient Free Radicals 68 3.3 The Power of Multiple Connectivity: SiO2—A Giant Molecule 69 3.3.1 SiO2—A Giant Molecule 69 3.3.2 Definitions of Terms That Follow from the SiO2 Story: Stoichiometry and Polymers 71 3.4 SiO2 and Glass Making 73 3.5 Glass Making from Water Glass 74 3.6 Must We Work So Hard to Construct Large Molecules? 75 3.6.1 Creating Larger Modular Building Blocks 75 3.6.2 Making New Molecules from the New Modular Fragments 75 3.7 Summary 80 3.8 References 81 3.A Appendix 81 3.A.1 Proposed Demonstrations 81 3.A.2 References for Appendix 3.A 82 3.R Retouches 82 3.R.1 Formal Charges 82 3.R.2 Multiple Bonds to Silicon 83 3.R.3 The Lone-Pair Bond Weakening Effect 83 3.R.4 The O2 Molecule and Its Magnetism 84 3.R.5 References for Retouches 86 3.P Problem Set 86 LECTURE 4 CONSTRUCTING MOLECULAR WORLDS OF CARBON–HYDROGEN FROM LARGE LEGO FRAGMENTS 87 4.1 Conversation on Contents of Lecture 4 87 4.2 Molecular Chains Involving Only C and H 89 4.2.1 Extended Chains 89 4.2.2 Branched Chains and Isomerism 91 4.2.3 Isomers of Octane (C8H18) 93 4.2.4 Some Applications of Alkanes 94 4.3 Molecular Rings and Cages Made From CH2 and CH Fragments 96 4.3.1 Molecular Rings Made of CH2 Fragments 96 4.3.2 Molecular Cages Made of CH Fragments 97 4.4 Molecular Planes and Cages Made from C Fragments 100 4.5 Isomers of Rings and Cages 105 4.6 Infinity of Molecular Worlds Made from C and H 106 4.7 Summary 108 4.8 References 108 4.R Retouches 108 4.R.1 Atomic Weight, Isotopes, Atomic Mass Unit, and Molecular Weights 108 4.R.2 Avogadro’s Number 109 4.R.3 The Mole Concept 110 4.R.4 Calculation of CO2 Emission by a Car 111 4.R.5 The Molecule Benzene, Kekul´e’s Dream, and Resonance Theory 112 4.R.6 Resonance Theory and Collective Bonding 114 4.R.7 References for Retouches 115 4.P Problem Set 115 LECTURE 5 CONSTRUCTING MOLECULAR WORLDS OF LIFE FROM LARGE LEGO FRAGMENTS 117 5.1 Conversation on Contents of Lecture 5 117 5.2 Alcohols, Aldehydes, Ketones, Ethers, and Amines 120 5.2.1 Alcohols 120 5.2.2 Ethers 122 5.2.3 Amines 124 5.2.4 Biogenic Amines: Our Neurotransmitters 124 5.2.5 Aldehydes, Ketones, Acids, and Esters 128 5.2.6 Fats (Lipids): Fatty Acids, Prostaglandins, Triglycerides, Cholesterol, Cortisone, etc. 130 5.2.7 Amino Acids, Peptides, Proteins, and Enzymes 136 5.3 Summary 145 5.4 References 145 5.A Appendix 146 5.A.1 The Natural Amino Acids (NAAs) 146 5.R Retouches 146 5.R.1 P450 Enzymes and Grapefruit Juice 146 5.R.2 The Discovery of O2 146 5.R.3 References for Retouches 150 5.P Problem Set 150 LECTURE 6 ELECTRON RICHNESS, DNA AND RNA MOLECULES, AND SYNTHETIC POLYMERS 153 6.1 Conversation on Contents of Lecture 6 153 6.2 Electron Richness: A Different State of Nirvana 155 6.2.1 “Who Is Who in Electron Richness” 155 6.2.2 Examples of Electron-Rich Molecules 156 6.2.3 Phosphoric and Sulfuric Acids 157 6.3 DNA and RNA Strands 159 6.3.1 Formation of DNA and RNA Strands 161 6.3.2 DNA and RNA Nucleotide-Based Drugs 161 6.4 Synthetic Polymers 164 6.4.1 Constructing Polymers Using the LEGO Principles 165 6.4.2 Polymers and Additives 171 6.5 Summary 172 6.6 References and Notes 173 6.A Appendix 174 6.A.1 Proposed Demonstrations 174 6.A.2 References for Appendix 6.A 175 6.R Retouches 175 6.R.1 To Be or Not to Be in Octet? This Is the Question 175 6.P Problem Set 177 LECTURE 7 THE 3D STRUCTURE OF MOLECULES, ELECTRONEGATIVITY, HYDROGEN BONDS, AND MOLECULAR ARCHITECTURE 179 7.1 Conversation on Contents of Lecture 7 179 7.2 3D Structures of Molecules 186 7.2.1 Selection Rules of 3D Molecular Structures 186 7.2.2 Lone Pairs Count in 3D Structure Determination 189 7.2.3 A Multiple Bond Counts as a Single Space Unit 191 7.2.4 Isomerism in Double-Bonded Molecules 192 7.2.5 Nature’s Usage of Cis and Trans Isomers 194 7.3 Handedness (Chirality) and Isomerism 195 7.3.1 Handedness (Chirality) in Nature 197 7.4 Extension of the 3D Rules to Conformations 200 7.5 The Architecture of Matter and Its Origins 202 7.5.1 The Electronegativity of Atoms 203 7.5.2 Polarity Trends in Bonds 204 7.5.3 Molecular Polarity 205 7.5.4 Intermolecular Interactions and the Hydrogen Bond 206 7.5.5 Properties of Water 207 7.5.6 H-Bonds in Proteins 208 7.6 H-Bonding and Our Genetic Code 209 7.7 Summary 213 7.8 References and Note 214 7.A Appendix 215 7.A.1 The Periodic Table of Electronegativity Values 215 7.A.2 Proposed Demonstrations for Lecture 7 215 7.A.3 References for Appendix 7.A 218 7.R Retouches 218 7.R.1 Electron Pair Repulsion 218 7.R.2 Pictorial Description of Lone Pairs 218 7.R.3 The Nature of the Double Bond 219 7.R.4 Conformations of C2H6 219 7.R.5 Other Intermolecular Forces 220 7.R.6 More on DNA 221 7.R.7 References for Retouches 225 7.P Problem Set 225 LECTURE 8 THE IONIC BOND AND IONIC MATTER 227 8.1 Conversation on Contents of Lecture 8 227 8.2 Ionic Bonds versus Covalent Bonds 232 8.2.1 The Formation of Ionic Bonds. How and When? 232 8.2.2 Construction of Ionic Bonds by “Click-Clack” 235 8.2.3 Ionic Molecules Containing Complex Ions 236 8.2.4 Why Are Ionic Materials Generally Solids? 238 8.2.5 Ionic Liquids? 240 8.2.6 Solubility and Insolubility of Ionic Materials 240 8.3 The Use of Ionic Matter in Living Organisms 242 8.3.1 Soluble Ionic Material Takes Care of Biological Communication 242 8.3.2 The Insoluble Ionic Material Makes Our Skeleton and Teeth 243 8.4 Covalent Molecules that Form Ions in Solution: Acids and Bases 244 8.4.1 Acids in Water: A Proton Transfer Reaction from the Acid to Water 244 8.4.2 Bases in Water: A Proton Transfer Reaction from Water to the Base 248 8.4.3 A Proton Transfer Reaction from Acids to Bases 249 8.4.4 A Few Facts About Our Acids and Bases 250 8.5 Summary 251 8.6 References and Notes 252 8.A Appendix 253 8.A.1 Proposed Demonstrations for Lecture 8 253 8.A.2 References for Appendix 8.A 254 8.R Retouches 255 8.R.1 Energetic Aspects of Ionic Bonding 255 8.R.2 Energy Units and Bond Energy Calculation for Ionic Bonds 257 8.R.3 Dissolution of Ionic Solids in Water 259 8.R.4 Concentration, the pH Scale, and Indicators 260 8.R.5 Symbolic Representations of Chemical Reactions Using Curved Arrows 262 8.R.6 References for Retouches 264 8.P Problem Set 264 LECTURE 9 BONDING IN TRANSITION METALS, SPECTROSCOPY, AND MOLECULAR DIMENSIONS 265 9.1 Conversation on Contents of Lecture 9 265 9.2 The 18-Electron Rule for Transition Metal Bonding 275 9.2.1 An Example of a Transition Metal Complex That Obeys the 18e Rule 276 9.2.2 Electron Counts of Ligand Contributions 277 9.3 Construction of Transition Metal Complexes That Obey the 18e Rule 279 9.4 Transition Metal Complexes with 14–16e 280 9.4.1 Comments on TM-Based Catalysts 282 9.5 3D Shapes of Transition Metal Complexes 283 9.6 Bridging Transition Metal and Organic Molecules: Bonding Capabilities of Fragments of Transition Metal Complexes 285 9.7 Summary of Transition Metal Complexes 288 9.8 Spectroscopy or How Do Chemists “Listen to Molecules”? 288 9.8.1 The Electromagnetic Radiation Spectrum 288 9.8.2 Energy Levels of Molecules as the Basis of Spectroscopy 291 9.8.3 X-Ray Crystallography and 3D Molecular Information 294 9.9 Summary of Spectroscopic Methods 297 9.10 References and Notes 297 9.A Appendix 298 9.A.1 Radii Values for Transition Metals in Covalent and Ionic Bonds 298 9.A.2 Bond Dissociation Energies and Their Usage as Building Blocks 298 9.A.3 Proposed Demonstrations for Lecture 9 300 9.A.4 References for Appendix 9.A 302 9.R Retouches 302 9.R.1 Why the 18e Rule, and Why Are Many TM Complexes Colored? 302 9.R.2 High-Spin Complexes 304 9.R.3 The Active Species of CYP 450 305 9.R.4 The “Life” of a Catalyst: The Catalytic Cycle 305 9.R.5 The Relation Between the Energy of the Photon and the Frequency of the Light 308 9.R.6 References for Retouches 308 9.P Problem Set 308 LECTURE 10 CHEMISTRY, THE TWO-FACED JANUS—THE DAMAGE IT CAUSES VERSUS ITS IMMENSE CONTRIBUTION TO MANKIND 311 10.1 Conversation on Contents of Lecture 10 311 10.2 Types of Potential Chemical Damage 316 10.2.1 The Ozone Hole 316 10.2.2 The Montreal Protocol 319 10.2.3 Climate Change 319 10.2.4 Acid Rain 321 10.2.5 More Evils and the Other Side of the Chemical Janus 322 10.3 Summary 324 10.4 References and Notes 324 10.R Retouches 325 10.R.1 The Electronic Structure of Ozone 325 10.R.2 Reference for Retouches 325 10.P Problem Set 326 LECTURE 11 CHEMISTRY IS EVERYTHING AND EVERYTHING IS CHEMISTRY 327 11.1 Conversation on Contents of Lecture 11 327 11.2 The Birth of Chemistry Is the Nascence of Mankind 328 11.3 Chemistry Is Everything 331 11.4 The Magic of Chemistry and Pathological Science 334 11.5 The Love of Chemistry 337 11.6 Summary 339 11.7 References and Notes 340 11.A Appendix 340 11.A.1 Proposed Demonstrations for Lecture 11 340 11.A.2 References for Appendix 11.A 342 EPILOGUE 343 ANSWERS TO PROBLEM SETS 345 INDEX 377

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Book SynopsisThe latest volume in this series for organic chemists in industry presents critical discussions of widely used organic reactions or particular phases of a reaction. The material is treated from a preparative viewpoint, with emphasis on limitations, interfering influences, effects of structure and the selection of experimental techniques. Numerous detailed procedures illustrate the significant modifications of each method. Includes tables that contain all possible examples of the reaction under consideration.Table of Contents1. Ring-Expanding Carbonylation of Epoxides 1John W. Kramer, John M. Rowley, and Geoffrey W. Coates 2. The Tishchenko Reaction 105Ari M. P. Koskinen and Antti O. Kataja Cumulative Chapter Titles by Volume 411 Author Index, Volumes 1–86 427 Chapter and Topic Index, Volumes 1–86 433

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Book SynopsisThe first chapter describes the manifold ways in which the latent functionality embedded in the humble heterocycle furan can be revealed by various oxidative processes.The second chapter details the fascinating cycloaddition and electrocyclization chemistry of unsaturated ketenes. The third chapter chronicles the development of a remarkable organometallic reaction of unactivated alkenes and alkynes, namely carbozincation.Table of Contents1. Oxidative Cleavage of FuransPedro Merino 1 2. Cycloaddition and Electrocyclic Reactions of Vinylketenes, Allenylketenes, and AlkynylketenesNanyan Fu and Thomas T. Tidwell 257 3. Carbozincation Reactions of Carbon–Carbon Multiple BondsGenia Sklute, Hannah Cavender, and Ilan Marek 507 Cumulative Chapter Titles by Volume 765 Author Index, Volumes 1–87 781 Chapter and Topic Index, Volumes 1–87 787

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Book SynopsisThe proposed book will be divided into three parts. The chapters in Part I provide an overview of certain aspect of process retrofitting. The focus of Part II is on computational techniques for solving process retrofit problems. Finally, Part III addresses retrofit applications from diverse process industries. Some chapters in the book are contributed by practitioners whereas others are from academia. Hence, the book includes both new developments from research and also practical considerations. Many chapters include examples with realistic data. All these feature make the book useful to industrial engineers, researchers and students.Table of ContentsList of Contributors xiii Preface xv PART I OVERVIEW 1 Introduction 3G.P. Rangaiah 1.1 Chemical Process Plants 3 1.2 Process Retrofitting and Revamping 4 1.3 Stages in Process Retrofitting/Revamping Projects 6 1.4 Conceptual Process Design for Process Retrofit/Revamp Projects 8 1.5 Research and Development in Process Retrofit/Revamp 9 1.6 Scope and Organization of this Book 12 1.7 Conclusions 16 References 17 2 Project Engineering and Management for Process Retrofitting and Revamping 19C.C.S. Reddy 2.1 Introduction 19 2.2 Key Differences between Revamp and Grassroots Designs 20 2.3 Revamp Design Methodology 20 2.4 Project/Process Engineering and Management of Revamp Projects 24 2.4.1 Revamp Objectives and Pre-Feasibility Study 24 2.4.2 Conceptual Design (Pre-FEED) 24 2.4.3 FEED (Front End Engineering Design) 31 2.4.4 Detailed Engineering, Procurement and Construction 33 2.4.5 Project Completion 35 2.5 Key Elements of Project Management 35 2.5.1 Project Schedule 39 2.5.2 Project Execution and Progress Monitoring 39 2.5.3 Project Cost Control 40 2.5.4 Risk Management 41 2.5.5 Final Project Deliverables 41 2.6 Revamp Options for Process Equipment 41 2.7 Conclusions 53 Acronyms 53 References 54 3 Process Safety in Revamp Projects 57Raman Balajee and C.C.S. Reddy 3.1 Introduction 57 3.2 Lessons from Past Process Safety Incidents 59 3.3 Preliminary Hazard Review during Conceptual Design 60 3.3.1 Risk Matrix for Qualitative Judgments 61 3.3.2 What-If and Process Safety Check Lists 62 3.3.3 Plot Plan and Layout Review 63 3.3.4 Area Classification Reviews 65 3.3.5 Pressure Relief System Considerations 66 3.3.6 Fire Safety for Revamp Projects 72 3.4 Process Hazard Analysis (PHA) 74 3.4.1 Process Plant Hazard Review using HAZOP 74 3.4.2 Failure Modes and Effects Analysis (FMEA) Tool 79 3.4.3 Instrumented Protective System Design 81 3.4.4 Fault Tree Analysis 82 3.4.5 Event Tree Analysis 84 3.4.6 Layer of Protection Analysis (LOPA) 85 3.4.7 Safety Instrumented System (SIS) Life Cycle 88 3.5 Revision of PSI and Operator Induction 88 3.6 Pre-Start-up Safety Review (PSSR) 90 3.7 Management of Change (MOC) 91 3.8 Conclusions 92 Acronyms 93 Exercises 94 References 95 PART II TECHNIQUES FOR RETROFITTING AND REVAMPING 4 Mathematical Modeling, Simulation and Optimization for Process Design 99Shivom Sharma and G.P. Rangaiah 4.1 Introduction 99 4.2 Process Modeling and Model Solution 101 4.2.1 Process Modeling 101 4.2.2 Model Solution 103 4.2.3 Model for Membrane Separation of a Gas Mixture 104 4.3 Process Simulators and Aspen Custom Modeler 107 4.4 Optimization Methods and Programs 108 4.5 Interfacing a Process Simulator with Excel 112 4.6 Application to Membrane Separation Process 113 4.7 Conclusions 116 Acronyms 116 Appendix 4A: Implementation of Membrane Model in ACM 117 Appendix 4B: Interfacing of Aspen Plus v8.4 with Excel 2013 119 Appendix 4C: Interfacing of Aspen HYSYS v8.4 with Excel 2013 122 Exercises 125 References 125 5 Process Intensification in Process Retrofitting and Revamping 129D.P. Rao 5.1 Introduction 129 5.1.1 Retrofitting and Revamping 129 5.1.2 Evolution of Chemical Industries and Process Intensification 130 5.1.3 Flow Chemistry 130 5.2 Methods of Process Intensification 130 5.2.1 Intensification of Rates 131 5.2.2 Process Integration 132 5.3 Alternatives to Conventional Separators 132 5.3.1 Rotating Packed Beds (HIGEE) 133 5.3.2 HIGEE with Split Packing 134 5.3.3 Zigzag HIGEE 135 5.3.4 Multi-rotor Zigzag HIGEE 136 5.3.5 Applications of HIGEE for Retrofitting 137 5.3.6 Podbielniak Centrifugal Extractor 138 5.3.7 Annular Centrifugal Extractor 139 5.3.8 Adsorbers 140 5.4 Alternatives to Stirred Tank Reactor (STR) 142 5.4.1 HEX Reactor 142 5.4.2 Advanced-flowTM Reactor (AFR) 143 5.4.3 Agitated Cell Reactor (ACR) 145 5.4.4 Oscillatory-flow Baffled Reactors (OBR) 146 5.4.5 Spinning Disc Reactor (SDR) 147 5.4.6 Spinning Tube-in-tube Reactor (STTR) 148 5.4.7 Stator-rotor Spinning Disc Reactor (Stator-rotor SDR) 150 5.4.8 Reactor Selection 150 5.4.9 Microchannel Devices 151 5.5 Process Integration 151 5.5.1 Heat and Mass Integration 152 5.5.2 Reactive Separations 152 5.5.3 Hybrid Separation 153 5.5.4 Conversion of Crosscurrent into Countercurrent Process 153 5.5.5 Process-specific Integration 154 5.5.6 In-line Processing 157 5.5.7 Twister® - A Supersonic Separator 158 5.6 Fundamental Issues of PI 159 5.7 Future of PI 159 5.8 Conclusions 160 Acknowledgement 160 Appendix 5A: Monographs, Reviews and Some Recent Papers 160 References 163 6 Using Process Integration Technology to Retrofit Chemical Plants for Energy Conservation and Wastewater Minimization 167Russell F. Dunn and Jarrid Scott Ristau 6.1 Introduction 167 6.1.1 Heat Integration Networks 168 6.1.2 Water Recycle Networks 169 6.2 Graphical Design Tools for Retrofitting Process for Energy Conservation by Designing Heat Exchange Networks 170 6.2.1 The Temperature–Interval Diagram (TID) 171 6.2.2 The Heat Pinch Composite Curves (Temperature–Enthalpy Diagrams) 172 6.2.3 The Enthalpy-Mapping Diagram (EMD) 174 6.2.4 Identifying Heat Integration Matches Using the TID and EMD 174 6.2.5 Graphical Tools Facilitate HEN Design for Large-scale Industrial Problems 177 6.3 Graphical Design Tools for Retrofitting Processes for Wastewater Reduction by Designing Water Recycle Networks 179 6.3.1 The Material Recycle Pinch Diagram 179 6.3.2 The Source–Sink Mapping Diagram 181 6.3.3 Suggested Guidelines for Identifying Water Recycle Matches Using the Material Recycle Pinch Diagram and Source–Sink Mapping Diagrams 181 6.4 Conclusions 182 Appendix 6A: Illustrating the Water Recycle Network Design Guidelines 183 Exercises 188 References 190 7 Heat Exchanger Network Retrofitting: Alternative Solutions via Multi-objective Optimization for Industrial Implementation 193B.K. Sreepathi and G.P. Rangaiah 7.1 Introduction 193 7.2 Heat Exchanger Networks 196 7.2.1 Structural Representation 198 7.3 HEN Improvements 199 7.4 MOO Method, HEN Model and Exchanger Reassignment Strategy 203 7.4.1 Multi-objective Optimization 203 7.4.2 HEN Model 205 7.4.3 Exchanger Reassignment Strategy (ERS) 206 7.5 Case Study 208 7.6 Results and Discussion 208 7.6.1 Simple Retrofitting 209 7.6.2 Moderate Retrofitting 211 7.6.3 Complex Retrofitting 214 7.6.4 Comparison and Discussion 216 7.7 Conclusions 218 Appendix 7A: Calculation of Nodal Temperatures 218 Exercises 221 References 221 8 Review of Optimization Techniques for Retrofitting Batch Plants 223Catherine Azzaro-Pantel 8.1 Introduction 223 8.2 Batch Plant Typical Features 224 8.3 Formulation of the Batch Plant Retrofit Problem 228 8.3.1 Design versus Retrofitting Problem 228 8.3.2 Design/Retrofit Problems: A Four-Level Framework 229 8.4 Methods and Tools for Retrofit Strategies 230 8.4.1 General Comments 230 8.4.2 Key Approaches in Batch Plant Retrofitting: Deterministic vs Stochastic Methods 238 8.4.3 New Trends in Batch Plant Retrofitting: Steps for More Sustainable Processes 242 8.5 Conclusions 243 References 244 PART III RETROFITTING AND REVAMPING APPLICATIONS 9 Retrofit of Side Stream Columns to Dividing Wall Columns, with Case Studies of Industrial Applications 251Moonyong Lee, Le Quang Minh, Nguyen Van Duc Long, and Joonho Shin 9.1 Introduction 251 9.2 Side Stream Column 254 9.2.1 Side Stream Configuration 254 9.2.2 Heuristic Rules for the Use of SSCs 256 9.2.3 Pros and Cons of SSC 257 9.2.4 Design of SSC 257 9.3 Dividing Wall Column 258 9.3.1 Introduction 258 9.3.2 Design and Optimization of DWC 259 9.4 Retrofit of an SSC to a DWC 260 9.4.1 Introduction 260 9.4.2 Design and Optimization of Retrofitted DWC 260 9.4.3 Column Modification and Hardware 263 9.5 Case Studies of Industrial Applications 266 9.5.1 Acetic Acid Purification Column 266 9.5.2 n-BuOH Refining Column 271 9.6 Other Case Studies 275 9.6.1 Ethylene Dichloride (EDC) Purification Column 275 9.6.2 Diphenyl Carbonate (DPC) Purification Column 276 9.6.3 Other SSCs 277 9.7 Conclusions 277 Acknowledgements 278 Nomenclature 278 References 279 10 Techno-economic Evaluation of Membrane Separation for Retrofitting Olefin/Paraffin Fractionators in an Ethylene Plant 285X.Z. Tan, S. Pandey, G.P. Rangaiah, and W. Niu 10.1 Introduction 285 10.2 Olefin/Paraffin Separation in an Ethylene Plant 287 10.3 Membrane Model Development 289 10.3.1 Membrane Modeling 289 10.3.2 Assumptions for Membrane Separation Simulation 291 10.4 Retrofitting a Distillation Column with a Membrane Unit 292 10.4.1 HMD Modeling and Simulation 292 10.4.2 Techno-economic Feasibility of Retrofit Operation 296 10.5 Formulation of Multi-objective–Optimization Problem 300 10.6 Results and Discussion 304 10.6.1 Case 1: HMD System for EF (Assuming Credit for Reboiler Duty) 304 10.6.2 Case 2: HMD System for EF (Assuming Reboiler Duty as Cost) 306 10.6.3 Case 3: HMD System for PF 308 10.7 Conclusions 310 Appendix 10A: Membrane Model Validation 310 Appendix 10B: Costing of HMD System 312 Exercises 315 References 315 11 Retrofit of Vacuum Systems in Process Industries 317C.C.S. Reddy and G.P. Rangaiah 11.1 Introduction 317 11.2 Vacuum-generation Methods 318 11.3 Design Principles and Utility Requirements 320 11.3.1 Suction Load of Vacuum System 320 11.3.2 Steam Jet Ejectors 323 11.3.3 Liquid Ring Vacuum Pumps 325 11.3.4 Dry Vacuum Pumps 326 11.4 Chilled-water Generation 326 11.5 Optimization of Vacuum System Operating Cost 328 11.6 Case Study 1: Retrofit of a Vacuum System in a Petroleum Refinery 332 11.6.1 Analysis of the Results 335 11.7 Case Study 2: Retrofit of a Surface Condenser of a Condensing Steam Turbine 341 11.8 Conclusions 342 Nomenclature 343 Exercises 344 References 345 12 Design, Retrofit and Revamp of Industrial Water Networks using Multi-objective Optimization Approach 347Shivom Sharma and G.P. Rangaiah 12.1 Introduction 347 12.2 Mathematical Model of a Water Network 350 12.3 Water Network in a Petroleum Refinery 352 12.4 Multi-objective Optimization Problem Formulation 352 12.5 Results and Discussion 355 12.5.1 Water Network Design 355 12.5.2 Retrofitting Selected Water Networks for Change in Environmental Regulations 358 12.5.3 Retrofitting Selected Water Networks for Increase in Hydrocarbon Load 363 12.5.4 Revamping Selected Water Networks for Change in Environmental Regulations 365 12.5.5 Revamping Selected Water Networks for Increase in Hydrocarbon Load 367 12.5.6 Comparison of Retrofitting and Revamping Solutions 369 12.6 Conclusions 369 Acknowledgement 370 Nomenclature 370 Exercises 371 References 372 13 Debottlenecking and Retrofitting of Chemical Pulp Refining Process for Paper Manufacturing – Application from Industrial Perspective 375Ajit K. Ghosh 13.1 Introduction 375 13.2 Fundamentals of Chemical Pulp Refining 376 13.2.1 Refining Effects on Various Chemical Pulp Types 377 13.2.2 Effects of Refining on Pulp and Paper Properties 378 13.3 Theories of Chemical Pulp Refining 380 13.3.1 Specific Edge Load Theory 381 13.3.2 Specific Surface Load Theory 382 13.3.3 Frequency and Intensity or Severity of Impact 382 13.3.4 The ‘C’ Factor 383 13.4 Types of Commercial Refiners 384 13.5 Laboratory and Pilot-scale Refining Investigation 384 13.6 Case Studies of Retrofitting Refining Process for Paper Mills 386 13.6.1 Case A: Retrofitting of Existing Refiners to Debottleneck Output of a Modern Paper Machine 386 13.6.2 Case B: Retrofitting of Existing Refiners of a Paper Machine to Switch from ‘Flat’ to ‘Semi-extendable’ Sack Kraft Papers 402 13.7 Conclusions 406 Exercises 407 References 408 Index 410

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Book SynopsisWritten by leading research scientists, this book integrates current knowledge of toxicology and human health through coverage of environmental toxicants, genetic / epigenetic mechanisms, and carcinogenicity. Provides information on lifestyle choices that can reduce cancer risk Offers a systematic approach to identify mutagenic, developmental and reproductive toxicants Helps readers develop new animal models and tests to assess toxic impacts of mutation and cancer on human health Explains specific cellular and molecular targets of known toxicants operating through genetic and epigenetic mechanisms Table of ContentsList of Contributors xix Part One Introduction: The Case for Concern about Mutation and Cancer Susceptibility during Critical Windows of Development and the Opportunity to Translate Toxicology into a Therapeutic Discipline 1 1 What Stressors Cause Cancer and When? 3Claude L. Hughes and Michael D. Waters 1.1 Introduction 3 1.1.1 General Information about Cancer 5 1.1.2 Stressors and Adaptive Responses 8 1.2 What Stressors Cause Cancer and When? 8 1.2.1 Mutagenic MOAs 13 1.2.1.1 DNA Repair 14 1.2.2 Epigenetic MOAs 16 1.2.3 Nongenotoxic Carcinogens, ROS, Obesity, Metabolic, Diet, Environment, Immune, Endocrine MOAs 20 1.2.4 Tumor Microenvironment MOAs 25 1.3 Relevance of Circulating Cancer Markers 26 1.4 Potential Cancer Translational Toxicology Therapies 29 1.4.1 Well-Established/Repurposed Pharmaceuticals 31 1.4.2 GRAS/GRASE, Diet, and Nutraceuticals 34 1.4.2.1 Suppression of Cell Proliferation and Induction of Cell Death 35 1.4.2.2 Anti-Inflammatory Effects: Insights from Various Diseases 36 1.4.2.3 Upregulation of Tumor Suppressor MicroRNAs 38 1.4.2.4 Regulation of Oxidative Stress 38 1.4.2.5 Activation of Signal Transduction Pathways 39 1.4.2.6 Mitigating Inherited Deleterious Mutations 40 1.4.2.7 Mitigating Adverse Epigenetic States 42 1.4.2.8 Paradigm for Study of Cancer Chemoprevention 43 1.5 Modeling and the Future 47 References 51 2 What Mutagenic Events Contribute to Human Cancer and Genetic Disease? 61Michael D. Waters 2.1 Introduction 61 2.1.1 Childhood Cancer, Developmental Defects, and Adverse Reproductive Outcomes 62 2.1.2 Newborn Screening for Genetic Disease 62 2.1.3 Diagnosis of Genetic Disease 63 2.1.4 Familial and Sporadic Cancer 65 2.2 Genetic Damage from Environmental Agents 67 2.3 Testing for Mutagenicity and Carcinogenicity 71 2.4 Predictive Toxicogenomics for Carcinogenicity 73 2.5 Germ Line Mutagenicity and Screening Tests 76 2.6 Reproductive Toxicology Assays in the Assessment of Heritable Effects 80 2.6.1 Segmented Reproductive Toxicity Study Designs 80 2.6.2 Continuous Cycle Designs 81 2.6.2.1 One-Generation Toxicity Study 81 2.6.2.2 Repeat Dose Toxicity Studies 82 2.7 Assays in Need of Further Development or Validation 82 2.7.1 Transgenic Rodent Gene Mutation Reporter Assay 82 2.7.2 Expanded Simple Tandem Repeat Assay 84 2.7.3 Spermatid Micronucleus (MN) Assay 85 2.7.4 Sperm Comet Assay 86 2.7.5 Standardization of Sperm Chromatin Quality Assays 86 2.8 New Technologies 87 2.8.1 Copy Number Variants and Human Genetic Disease 87 2.8.2 Next-Generation Whole Genome Sequencing 88 2.8.3 High-Throughput Analysis of Egg Aneuploidy in C. elegans, and Other Alternative Assay Systems 90 2.9 Endpoints Most Relevant to Human Genetic Risk 91 2.10 Worldwide Regulatory Requirements for Germ Cell Testing 94 2.11 Conclusion 95 Acknowledgments 96 References 96 3 Developmental Origins of Cancer 111Suryanarayana V. Vulimiri and John M. Rogers 3.1 Introduction 111 3.2 Current Trends in Childhood Cancer 112 3.3 Potential Mechanisms of Prenatal Cancer Induction 113 3.4 Ontogeny of Xenobiotic Metabolizing Enzymes and DNA Repair Systems 113 3.5 The Developmental Origins of Health and Disease (DOHaD) Theory 115 3.6 Epigenetic Regulation during Development 115 3.6.1 Critical Periods for Epigenetic Regulation 116 3.7 Mechanisms of Cancer in Offspring from Paternal Exposures 117 3.8 Parental Exposures Associated with Cancer in Offspring 118 3.8.1 Radiation 118 3.8.2 Diethylstilbestrol 119 3.8.3 Tobacco Smoke 120 3.8.4 Pesticides 122 3.8.5 Arsenic 123 3.9 Models for the Developmental Origins of Selected Cancers 124 3.9.1 Breast Cancer 124 3.9.2 Leukemia 127 3.10 Public Health Agencies’ Views on Prenatal Exposures and Cancer Risk 129 3.10.1 The United States Environmental Protection Agency (US EPA) 129 3.10.2 The California Environmental Protection Agency (CalEPA) 131 3.10.3 Washington State Department of Ecology (WA DoE) 133 3.11 Conclusions 134 Acknowledgment 135 References 135 4 The Mechanistic Basis of Cancer Prevention 147Bernard W. Stewart 4.1 Introduction 147 4.2 A Mechanistic Approach 147 4.2.1 Specifying Carcinogens 148 4.2.2 Cancer Risk Factors Without Carcinogen Specification 148 4.3 Preventing Cancer Attributable to Known Carcinogens 149 4.3.1 Involuntary Exposure 149 4.3.1.1 Infectious Agents 149 4.3.1.2 Occupation 150 4.3.1.3 Drugs 151 4.3.1.4 Pollution 152 4.3.1.5 Dietary Carcinogens 152 4.3.2 Tobacco Smoking 153 4.3.2.1 Measures to Limit Availability and Promotion 154 4.3.2.2 Product Labeling, Health Warnings, and Usage Restrictions 154 4.3.2.3 Smoking Cessation 155 4.3.3 Alcohol Drinking 155 4.3.4 Solar and Ultraviolet Radiation 156 4.4 Prevention Involving Complex Risk Factors 157 4.4.1 Workplace Exposures 157 4.4.2 Diet and Overweight/Obesity 157 4.5 Prevention Independent of Causative Agents or Risk Factors 158 4.5.1 Screening 158 4.5.2 Chemoprevention 159 4.6 Conclusion 160 References 160 Part Two Exposures that Could Alter the Risk of Cancer Occurrence, and Impact Its Indolent or Aggressive Behavior and Progression Over Time 171 5 Diet Factors in Cancer Risk 173Lynnette R. Ferguson 5.1 Introduction 173 5.2 Obesity 174 5.3 Macronutrients 175 5.3.1 Protein 176 5.3.2 Lipids 177 5.3.3 Carbohydrates 178 5.4 Micronutrients 181 5.4.1 Vitamins 181 5.4.2 Minerals 184 5.5 Phytochemicals 184 5.5.1 Phytoestrogens 185 5.5.2 Other Phytochemicals 186 5.6 Conclusions 188 References 188 6 Voluntary Exposures: Natural Herbals, Supplements, and Substances of Abuse – What Evidence Distinguishes Therapeutic from Adverse Responses? 199Eli P. Crapper, Kylie Wasser, Katelyn J. Foster, and Warren G. Foster 6.1 Introduction 199 6.1.1 Alcohol 200 6.1.2 Cigarette Smoking 201 6.1.3 Herbals and Supplements 202 6.1.3.1 Melatonin 202 6.1.3.2 Resveratrol 204 6.1.3.3 Dong Quai 205 6.1.3.4 Eleutherococcus 206 6.1.3.5 Saw Palmetto 206 6.1.3.6 Stinging Nettle 207 6.2 Summary and Conclusions 207 References 207 7 Voluntary Exposures: Pharmaceutical Chemicals in Prescription and Over-the-Counter Drugs – Passing the Testing Gauntlet 213Ronald D. Snyder 7.1 Introduction 213 7.2 Testing of New Drug Entities for Genotoxicity 214 7.3 Relationship between Genotoxicity Testing and Rodent Carcinogenicity 217 7.4 Can Drug-Induced Human Cancer Be Predicted? 218 7.5 What Can Rodent Carcinogenicity Tell Us about Human Cancer Risk? 220 7.6 Genotoxicity Prediction Using “Traditional” In Silico Approaches 222 7.7 Covalent versus Noncovalent DNA Interaction 223 7.8 Use of New Technologies to Predict Toxicity and Cancer Risk: High-Throughput Methods 224 7.9 Transcriptomics 225 7.10 Single-Nucleotide Polymorphisms (SNPs) 226 7.11 Conclusions 227 Appendix A 228 References 253 8 Children’s and Adult Involuntary and Occupational Exposures and Cancer 259Annamaria Colacci and Monica Vaccari 8.1 Introduction 259 8.2 Occupational Exposures and Cancer 262 8.2.1 Occupational Cancer in the Twenty-First Century 262 8.2.2 Past and Present Occupational Exposure to Asbestos 263 8.2.3 Toxicology of Fibers: What We Have Learned from the Asbestos Lesson 265 8.2.3.1 Mechanism and Mode of Action of Asbestos and Asbestos-Like Fibers in Carcinogenesis: The Role of Inflammation and Immune System to Sustain the Cancer Process 268 8.2.4 Occupational Exposures and Rare Tumors 270 8.3 Environmental Exposures and Cancer 271 8.3.1 Environmental Exposures and Disease: Is This the Pandemic of the Twenty-First Century? 271 8.3.2 The Complexity of Environmental Exposures 272 8.3.3 Environmental Impact on Early Stages of Life: Are Our Children at Risk? 274 8.3.4 Environmental Endocrine Disruptors: The Steps Set Out to Recover Our Stolen Future 277 8.3.5 From Occupational to Environmental Exposures: Asbestos and Other Chemicals of Concern 279 8.3.5.1 Asbestos 279 8.3.5.2 Arsenic and Arsenic Compounds 280 8.3.5.3 Phthalates 282 8.3.5.4 Pesticides 283 8.3.5.5 Mycotoxins 286 8.3.6 Air Pollution and Airborne Particulate Matter: The Paradigmatic Example of Environmental Mixtures 288 8.3.6.1 Characteristics of PM and PM Exposures 289 8.3.6.2 PM Exposures and Cancer 291 8.3.6.3 Possible Mechanisms of PM Toxicity 293 8.3.6.4 The Role of PM Exposures in the Fetal Origin of the Disease 294 8.4 Conclusions and Future Perspectives 296 References 299 Part Three Gene–Environment Interactions 317 9 Ethnicity, Geographic Location, and Cancer 319Fengyu Zhang 9.1 Introduction 319 9.2 Classification of Cancer 320 9.2.1 Classification by Histology 320 9.2.2 Classification by Primary Location 322 9.3 Ethnicity and Cancer 323 9.3.1 Cancer Death and Incidence 323 9.3.2 Site-Specific Cancer Incidence 326 9.3.3 Site-Specific Cancer Incidence between the United States and China 328 9.4 Geographic Location and Cancer 331 9.4.1 Mapping Human Diseases to Geographic Location 331 9.4.2 Geographic Variation and Cancer in the United States 332 9.5 Ethnicity, Geographic Location, and Lung Cancer 334 9.5.1 Ethnic Differences 334 9.5.2 Geographic Variation 335 9.5.3 Individual Risk Factors 335 9.6 Common Cancers in China 338 9.6.1 Liver Cancer 339 9.6.1.1 Geographic Variation 339 9.6.1.2 Urban Residence and Sex 340 9.6.1.3 Hepatitis B Virus Infection 340 9.6.1.4 Familial Aggregation and Genetic Variants 341 9.6.2 Gastric Cancer 342 9.6.2.1 H. pylori 342 9.6.2.2 Familial Aggregation 343 9.6.2.3 Genetic Susceptibility Factors 343 9.6.3 Esophageal Cancer 344 9.6.3.1 Geographic Variation 344 9.6.3.2 Viral Infections 344 9.6.3.3 Familial Aggregation 345 9.6.3.4 Genetic Susceptibility Factors 345 9.6.4 Lung Cancer 346 9.6.5 Genetic Susceptibility Factors 347 9.6.6 Cervical Cancer 348 9.7 Cancer Risk Factors and Prevention 348 9.7.1 Environmental Chemical Exposure 348 9.7.2 Infectious Agents 349 9.7.3 Psychosocial Stress and Social Network 349 9.7.4 The Developmental Origin of Adult-Onset Cancer 350 9.7.5 Cancer Prevention and Intervention 351 References 353 10 Dietary/Supplemental Interventions and Personal Dietary Preferences for Cancer: Translational Toxicology Therapeutic Portfolio for Cancer Risk Reduction 363Sandeep Kaur, Elaine Trujillo, and Harold Seifried 10.1 Introduction 363 10.2 Gene Expression and Epigenetics 364 10.3 Environmental Lifestyle Factors Affecting Cancer Prevention and Risk 366 10.3.1 Obesity 366 10.3.2 Weight Loss 368 10.3.3 Physical Activity 369 10.4 Dietary Patterns 370 10.5 Complementary and Integrative Oncology Interventions/Restorative Therapeutics 373 10.6 Special and Alternative Diets 377 10.7 Popular Anticancer Diets 378 10.7.1 Macrobiotic Diet 378 10.7.2 The Ketogenic Diet 382 10.7.3 Fasting Diet 383 10.8 Conclusion 384 Acknowledgment 384 References 385 11 Social Determinants of Health and the Environmental Exposures: A Promising Partnership 395Lauren Fordyce, David Berrigan, and Shobha Srinivasan 11.1 Introduction 395 11.1.1 Conceptual Model 397 11.1.2 Difference versus Disparity 398 11.2 Social Determinants of Health 399 11.2.1 Race/Ethnicity 399 11.2.2 Social Determinants of Health: “Place” and Its Correlates 402 11.2.3 Gender and Sexuality 405 11.3 Conclusions: Social Determinants of Health and Windows of Susceptibility 407 Acknowledgments 408 References 408 Part Four Categorical and Pleiotropic Nonmutagenic Modes of Action of Toxicants: Causality 415 12 Bisphenol A and Nongenotoxic Drivers of Cancer 417Natalie R. Gassman and Samuel H. Wilson 12.1 Introduction 417 12.2 Dosing 420 12.3 Receptor-mediated Signaling 421 12.4 Epigenetic Reprogramming 422 12.5 Oxidative stress 424 12.6 Inflammation and Immune Response 425 12.7 BPA-Induced Carcinogenesis 426 12.8 Fresh Opportunities in BPA Research 428 References 429 13 Toxicoepigenetics and Effects on Life Course Disease Susceptibility 439Luke Montrose, Jaclyn M. Goodrich, and Dana C. Dolinoy 13.1 Introduction to the Field of Toxicoepigenetics 439 13.1.1 The Epigenome 440 13.1.2 Epigenetic Marks are Heritable and Reversible 440 13.1.3 DNA Methylation 441 13.1.4 Histone Modifications and Chromatin Packaging 442 13.1.5 Noncoding RNAs 443 13.1.6 Key Windows for Exposure-Related Epigenetic Changes 443 13.1.7 Evaluation of Environmentally Induced Epigenetic Changes in Animal Models and Humans 444 13.2 Exposures that Influence the Epigenome 444 13.2.1 Air Pollution 445 13.2.2 Metals 447 13.2.3 Endocrine Disrupting Chemicals (EDCs) 448 13.2.4 Diet 451 13.2.5 Stress 453 13.3 Intergenerational Exposures and Epigenetic Effects 454 13.4 Special Considerations and Future Directions for the Field of Toxicoepigenetics 456 13.4.1 Tissue Specificity 456 13.4.2 The Dynamic Nature of DNA Methylation 458 13.5 Future Directions 459 13.6 Conclusions 460 Acknowledgments 461 References 461 14 Tumor-Promoting/Associated Inflammation and the Microenvironment: A State of the Science and New Horizons 473William H. Bisson, Amedeo Amedei, Lorenzo Memeo, Stefano Forte, and Dean W. Felsher 14.1 Introduction 473 14.2 The Immune System 475 14.2.1 Innate Immune Response 475 14.2.2 Adaptive Immune Response 478 14.3 Prioritized Chemicals 482 14.3.1 Bisphenol A 482 14.3.2 Polybrominated Diphenyl Ethers 483 14.3.3 4-Nonylphenol 485 14.3.4 Atrazine 485 14.3.5 Phthalates 486 14.4 Experimental Models of Carcinogenesis through Inflammation and Immune System Deregulation 487 14.5 Antioxidants and Translational Opportunities 493 14.6 Tumor Control of the Microenvironment 495 Acknowledgments 497 References 497 15 Metabolic Dysregulation in Environmental Carcinogenesis and Toxicology 511R. Brooks Robey 15.1 Introduction 511 15.2 Metabolic Reprogramming and Dysregulation in Cancer 513 15.2.1 Carbohydrate Metabolism in Cancer 515 15.2.2 Lipid Metabolism in Cancer 519 15.2.3 Protein Metabolism in Cancer 521 15.3 Moonlighting Functions 523 15.4 Cancer Metabolism in Context 523 15.4.1 The Gestalt of Intermediary Metabolism 523 15.4.2 Cancer Tissues, Cells, and Organelles as Open Systems 527 15.4.3 The Endosymbiotic Nature of Cancer 527 15.4.4 Catabolic and Anabolic Support of Cell Proliferation 528 15.4.5 Cancer Heterogeneity 529 15.4.6 Phenotypic Relationships between Cancer Cells and Their Parental Cell Origins 532 15.4.7 Evolutionary Perspectives of Metabolic Fitness and Selection in Cancer Development 533 15.5 Dual Roles for Metabolism in Both the Generation and Mitigation of Cellular Stress 536 15.5.1 Metabolism and Oxidative Stress 537 15.5.2 Metabolism and Hypoxic Stress 539 15.5.3 Nutritional Stress and Metabolism 539 15.5.4 Metabolism and Physical Stress 540 15.5.5 Metabolism and Other Forms of Cellular Stress 541 15.6 Models of Carcinogenesis 541 15.6.1 Traditional Multistage Models of Cancer Development 542 15.6.2 Role of Replicative Mutagenesis in Cancer Development 543 15.6.3 Acquired Mismatch Model of Carcinogenesis 543 15.7 Potential Metabolic Targets for Environmental Exposures 546 15.7.1 Conceptual Overview of Potential Metabolic Targets 546 15.7.2 Identification of Key Targetable Contributors to Metabolic Dysregulation and Selection 549 15.7.2.1 Glycolysis 555 15.7.2.2 Lipogenesis, Lipolysis, and the PPP 555 15.7.2.3 Citric Acid Cycle 556 15.7.2.4 Organizational or Compartmental Targets 556 15.7.2.5 Metabolite Transport Mechanisms 557 15.7.2.6 Signal Transduction Effectors 558 15.8 Metabolic Changes Associated with Exposures to Selected Agents 559 15.8.1 Selected Agents Classified by the World Health Organization’s International Agency for Research on Cancer (IARC) 559 15.8.1.1 IARC Group 1 (Carcinogenic to Humans) 560 15.8.1.2 IARC Group 2A (Probably Carcinogenic to Humans) 564 15.8.1.3 IARC Group 2B (Possibly Carcinogenic to Humans) 565 15.8.1.4 Other Agents 565 15.8.2 Environmentally Relevant Combinatorial Exposures 567 15.8.2.1 Occupational and Common Environmental Exposures 567 15.8.2.2 Environmentally Relevant Low-Dose Combinatorial Exposures 568 15.8.2.3 The Halifax Project 570 15.9 A Conceptual Overview of Traditional and Emerging Toxicological Approaches to the Problem of Cancer Metabolism: Implications for Future Research 571 15.9.1 General Experimental Considerations in the Study of Metabolism In Vitro 571 15.9.2 Systems Biology and Current Approaches to In Vitro Toxicology Screening 573 15.10 The Nosology of Cancer and Cancer Development 577 15.11 Discussion 579 Acknowledgments 583 References 583 Part Five Biomarkers for Detecting Premalignant Effects and Responses to Protective Therapies during Critical Windows of Development 607 16 Circulating Molecular and Cellular Biomarkers in Cancer 609Ilaria Chiodi, A. Ivana Scovassi, and Chiara Mondello 16.1 Introduction 609 16.2 Proteins in Body Fluids: Potential Biomarkers 610 16.2.1 Diagnostic Protein Biomarkers 612 16.2.2 Prognostic Protein Biomarkers 613 16.2.3 Protein Biomarkers of Drug Response 615 16.3 Circulating Cell-Free Nucleic Acids 615 16.3.1 Circulating Cell-Free Tumor DNA 616 16.3.1.1 Cf-DNA Integrity, Microsatellite Instability, and LOH 617 16.3.1.2 Tumor-Specific Genetic Alterations 617 16.3.1.3 Tumor Genetic Alterations and Therapy Resistance 619 16.3.1.4 Tumor Epigenetic Alterations: DNA Methylation 620 16.3.2 Circulating Cell-Free RNA 621 16.3.2.1 Circulating Cell-Free microRNA 621 16.4 Extracellular Vesicles: General Features 624 16.4.1 Classification of EVs 624 16.4.2 EVs and Cancer 625 16.4.3 EVs as Mediators of Cell-To-Cell Communication 627 16.5 Circulating Tumor Cells 628 16.5.1 Two-Step Processing of Blood Samples: Enrichment and Identification of Circulating Tumor Cells 628 16.5.1.1 CTC Number as a Cancer Biomarker 630 16.5.2 Characterization of CTCs 630 16.5.2.1 Molecular Characterization of CTCs 630 16.5.2.2 Functional Characterization of CTCs 632 16.5.3 Single CTCs versus CTC Clusters 634 16.5.4 In Hiding Before Getting Home, the Long Journey of CTCs 635 16.6 Conclusions 635 References 637 17 Global Profiling Platforms and Data Integration to Inform Systems Biology and Translational Toxicology 657Barbara A. Wetmore 17.1 Introduction 657 17.2 Global Omics Profiling Platforms 659 17.2.1 Genomics 659 17.2.2 Epigenomics 661 17.2.3 Transcriptomics 662 17.2.4 Proteomics 665 17.2.5 Metabolomics 668 17.3 High-Throughput Bioactivity Profiling 669 17.3.1 High-Throughput Bioactivity and Toxicity Screening 669 17.3.2 In Vitro–In Vivo Extrapolation 671 17.4 Biomarkers 672 17.5 Exposomics 673 17.6 Bioinformatics to Support and Data Integration and Multiomics Efforts 674 17.7 Data Integration: Multiomics and High-Dimensional Biology Efforts 676 17.8 Conclusion 679 References 679 18 Developing a Translational Toxicology Therapeutic Portfolio for Cancer Risk Reduction 691Rebecca Johnson and David Kerr 18.1 Introduction 691 18.2 The Identification of Novel Predictors of Adverse Events 693 18.2.1 Candidate Gene Studies 693 18.2.2 Genome-wide Associations 694 18.2.3 Next-Generation Sequencing 695 18.3 Proof of Principle Toxgnostics 696 18.4 Proposed Protocol 698 18.4.1 Integration within Randomized Control Trials 698 18.4.2 Biobanking and Future-Proofing Samples 699 18.4.3 Data Protection and Full Consent 702 18.4.4 The Need for a Collaborative Approach 703 18.4.5 Open Access to Results 704 18.4.6 Translation from Bench to Bedside 705 18.5 Fiscal Matters 706 18.6 The Future of Toxgnostics 706 References 707 19 Ethical Considerations in Developing Strategies for Protecting Fetuses, Neonates, Children, and Adolescents from Exposures to Hazardous Environmental Agents 711David B. Resnik and Melissa J. Mills 19.1 Introduction 711 19.2 What Is Ethics? 712 19.2.1 Some Fundamental Ethical Values 712 19.2.1.1 Benefits and Costs 712 19.2.1.2 Individual Rights and Responsibilities 713 19.2.1.3 Justice 713 19.2.2 Value Conflicts and Ethical Decision-Making 713 19.3 Ethical Considerations for Strategies Used to Protect Fetuses, Neonates, Children, and Adolescents from Exposures to Harmful Environmental Agents 715 19.3.1 Education 715 19.3.2 Testing/Screening/Monitoring 717 19.3.3 Worker Protection 720 19.3.4 Government Regulation 722 19.3.5 Taxation 725 19.3.6 Civil Liability 726 19.3.7 Criminal Liability 729 19.4 Research with Human Participants 730 19.4.1 Return of Individualized Research Results 732 19.4.2 Protecting Privacy and Confidentiality 733 19.4.3 Interventional Studies 734 19.4.4 Intentional Exposure Studies 736 19.4.5 Protecting Vulnerable Participants 739 19.5 Conclusion 742 References 742 Index 751

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Book SynopsisThe important resource that explores the twelve design principles of sustainable environmental engineering Sustainable Environmental Engineering (SEE) is to research, design, and build Environmental Engineering Infrastructure System (EEIS) in harmony with nature using life cycle cost analysis and benefit analysis and life cycle assessment and to protect human health and environments at minimal cost. The foundations of the SEE are the twelve design principles (TDPs) with three specific rules for each principle. The TDPs attempt to transform how environmental engineering could be taught by prioritizing six design hierarchies through six different dimensions. Six design hierarchies are prevention, recovery, separation, treatment, remediation, and optimization. Six dimensions are integrated system, material economy, reliability on spatial scale, resiliency on temporal scale, and cost effectiveness. In addition, the authors, two experts in the field, introduce major computer packages that aTable of ContentsPreface xv 1 Renewable Resources and Environmental Quality 1 1.1 Renewable Resources and Energy 1 1.2 Human Demand and Footprint 5 1.2.1 Human Demand 5 1.2.2 Human Footprints 6 1.2.2.1 Water Footprints 7 1.2.2.2 Gray Water System 7 1.3 Challenges and Opportunities 9 1.3.1 Excessive Nitrogen Runoff 10 1.3.2 Phosphorus Depletion 10 1.3.3 Carbon Pollution 11 1.3.4 Peak Oil 11 1.3.5 Climate Change 11 1.4 Carrying Capacity 11 1.5 Air, Water, and Soil Quality Index 13 1.5.1 Air Quality Standards 13 1.5.2 Air Quality Index 13 1.5.3 Water Quality Index 14 1.5.4 Soil Quality Index 17 1.5.4.1 F1 (Scope) 17 1.5.4.2 F2 (Frequency) 17 1.5.4.3 F3 (Amplitude) 17 1.5.4.4 Soil Quality Index (SQI) 18 1.6 Air, Water, and Soil Pollution 19 1.6.1 Air Pollution 19 1.6.2 Water Pollution 19 1.7 Life Cycle Assessment 21 1.7.1 LCA Tools 22 1.8 Environmental Laws 22 1.9 Exercise 24 1.9.1 Questions 24 1.9.2 Assignment 25 1.9.3 Problems 25 1.9.4 Projects 25 1.9.4.1 Xiongan Project 25 1.9.4.2 Community Project 26 References 26 2 Health Risk Assessment 29 2.1 Environmental Health 29 2.2 Environmental Standards 31 2.3 Health Risk Assessment 36 2.3.1 Hazard Identification 36 2.3.2 Dose–Response Curves 37 2.3.2.1 Nonlinear Dose–Response Assessment 37 2.3.2.2 Linear Dose–Response Assessment 40 2.3.3 Exposure Assessment 41 2.3.3.1 Cancer Screening Calculation for Dermal Contaminants in Water 41 2.3.3.2 Noncancer Screening Calculation for Contaminants in Residential Soil 43 2.3.4 DBP Health Advisory Concentration 44 2.3.5 Risk Characterizations 46 2.4 QSAR Analysis in HRA 46 2.4.1 Multiple Linear Regression (MLR) 48 2.4.2 Validation of QSAR Models 49 2.5 Quantification of Uncertainty 54 2.5.1 Quantification of QSAR Model’s Uncertainty 55 2.5.2 Monte Carlo Simulation 56 2.5.3 Comparison of Uncertainties of Different QSAR Models 60 2.5.4 Sensitivity Analysis by Monte Carlo Simulation 61 2.5.5 Computer Software for Quantitative Risk Assessment 62 2.6 Exercise 62 2.6.1 Questions 62 2.6.2 Calculation 62 2.6.3 Assignment 63 2.6.4 Projects 63 2.6.4.1 Xiongan Project 63 2.6.4.2 Community Project 63 References 63 3 Twelve Design Principles of Sustainable Environmental Engineering 67 3.1 Sustainability 67 3.1.1 The United Nations Sustainable Development Goals 68 3.2 Challenges and Opportunities 69 3.2.1 Challenges 69 3.2.2 Opportunities 71 3.3 Sustainable Environmental Engineering 74 3.3.1 SEE Metrics 76 3.4 SEE Design Principles 78 3.4.1 Principle 1: Integrated and Interconnected System Hierarchy 78 3.4.2 Principle 2: Reliability on Spatial Scale 79 3.4.3 Principle 3: System Resiliency on a Temporal Scale 80 3.4.3.1 Principle 4: Efficiency of Renewable Material 80 3.4.4 Principle 6: Prevention 82 3.4.5 Principle 7: Recovery 83 3.5 Principle 8: Separation 84 3.5.1 Principle 9: Treatment 85 3.5.2 Principle 10: Retrofitting and Remediation 86 3.5.3 Principle 11: Optimization through Modeling and Simulation 86 3.5.4 Principle 12: Balance Between Capital and Operating Costs 87 3.6 Implementation of the SEE Design Principles 88 3.6.1 Procedure to Implement SEE Design Principles 88 3.6.2 Integration of SEE into Undergraduate Education 89 3.7 Exercise 91 3.7.1 Questions 91 3.7.2 Calculation 91 3.7.3 Projects 92 3.7.3.1 Xiongan Project 92 3.7.3.2 Community Projects 92 3.7.3.3 Proposal Development 92 References 93 4 Integrated and Interconnected Systems 95 4.1 Principle 1 95 4.2 Challenges and Opportunities 98 4.2.1 Market Size of Solid Waste Management in China 98 4.3 Integrated Solid Waste Management 103 4.3.1 Integrated Solid Waste Management Market in China 103 4.3.2 Strategy of ISWM 103 4.3.3 LCA on Footprint of Solid Waste Recycle 109 4.3.4 ISWM Data Analysis 115 4.3.4.1 Calculations for Measuring Quantity 115 4.3.4.2 Calculations for Composition 116 4.3.5 Determining Waste Composition 117 4.3.5.1 Moisture Content 117 4.3.5.2 Calorific Value 117 4.3.5.3 Chemical Composition 117 4.3.5.4 Calorific Values 119 4.3.5.5 Data Presentation 119 4.3.6 Zero Waste 120 4.3.7 Integrated Waster Resource Management (IWRM) 124 4.3.8 Water Resource Recovery Facilities (WRRF) 127 4.4 Integrated Air Quality Management (IAQM) 131 4.5 Exercise 132 4.5.1 Questions 132 4.5.2 Calculation 133 4.5.3 Projects 133 4.5.3.1 Community Projects 133 4.5.3.2 Xiongan Projects 134 References 134 5 Reliable Systems on a Spatial Scale 135 5.1 Principle 2 135 5.1.1 Central Versus Decentralized WWTP 136 5.1.2 Best Practice for Small WWTPs 137 5.2 Integrated System Approach 137 5.2.1 The EPA Tools 137 5.2.2 Integrated Engineering Design Example 137 5.3 Scale-up of Laboratory or Pilot Design to Full-scale Plant 141 5.3.1 Minimum Requirements for Validation Testing 141 5.3.1.1 Collimated Beam Test 141 5.3.2 Correlation of UV Sensitivity of Different Challenge Microorganisms with Target Microorganisms 143 5.3.2.1 Sampling Ports 144 5.3.3 Calculating the RED 145 5.3.3.1 Flow Rate for Validation 146 5.3.4 Uncertainty in Validation 149 5.3.4.1 Calculating UIN for the Calculated Dose Approach 149 5.3.4.2 Determining the Validated Dose and Validated Operating Conditions 149 5.3.5 Collimated Beam Data Uncertainty 152 5.3.6 Electrical Energy per Order (EE/O) 153 5.4 Exercise 154 5.4.1 Questions 154 5.4.2 Calculation 154 5.4.3 Projects 155 5.4.3.1 Xiongan Design Project 155 5.4.3.2 Community Proposal Project 155 References 155 6 Resiliency on Temporal Scale 157 6.1 Principle 3 157 6.2 Challenges and Opportunities 159 6.3 Discharge Standards 159 6.4 Population Growth 160 6.5 Steady Versus Unsteady 162 6.5.1 Equalization Basin 162 6.6 Hydraulic Condition of Different Reactors 167 6.7 Chemical Kinetics 168 6.8 Group Theory Predicting Hydroxyl Radical Kinetic Constants 172 6.9 Photocatalytic Oxidation of Halogen-substituted Meta-phenols by UV/TiO2 172 6.10 Environmental Issues on Different Temporal Scales 178 6.10.1 Correlation Between Temporal and Spatial Scales in the Sustainable Design of WTPs and WWTPs 178 6.11 Exercise 181 6.11.1 Questions 181 6.11.2 Calculation 181 6.11.3 Project 181 6.11.3.1 Xiongan Project 181 6.11.3.2 Community Proposal Project 182 References 182 7 Efficiency of Renewable Materials 185 7.1 Principle 4 185 7.2 Stoichiometry 185 7.3 Avoid the Addition of Chemicals 187 7.3.1 Avoid Acid Addition 187 7.3.2 Replacing Chlorination with UV Disinfection 193 7.3.3 Anammox to Replace Nitrification/Denitrification 199 7.3.3.1 Nitrogen Forms 199 7.3.3.2 Nitrification 200 7.3.3.3 Denitrification 200 7.3.3.4 Anammox 201 7.4 Design Efficient Reactors 203 7.4.1 Cost of Different Volume Reactors 212 7.5 Exercise 213 7.5.1 Questions 213 7.5.2 Calculation 213 7.5.3 Project 213 7.5.3.1 Xiongan Project 213 7.5.3.2 Proposal Project 214 References 214 8 Efficiency of Renewable Energy 215 8.1 Principle 5 215 8.2 Challenges and Opportunities 216 8.2.1 Inefficient Combustion of Fossil Fuels 216 8.2.2 Challenges in China 217 8.3 Energy Conservation Laws 218 8.3.1 Thermodynamics Laws 218 8.3.2 The First Thermodynamic Law 221 8.3.3 The Second Thermodynamic Law 221 8.3.3.1 Energy Conversion 221 8.3.3.2 Enthalpy 222 8.3.3.3 Conservation of Energy 222 8.4 Energy Balances 223 8.4.1 Physical Framework by Thermodynamics 224 8.4.2 Exergy 225 8.5 Benchmarks for Unit Energy Consumption in WTP and WWTP 225 8.5.1 Unit Energy Consumption Values in WTP 225 8.5.2 Unit Energy Consumption Values in WWTP 225 8.6 Energy Consumption by Pump 232 8.6.1 Flow in Pipe 232 8.6.2 Pump Station 232 8.7 Solar Energy 233 8.7.1 Calculation Solar Energy 233 8.7.2 Solar-powered WWTP 235 8.8 Exercise 235 8.8.1 Questions 235 8.8.2 Calculation 236 8.8.3 Project 236 8.8.3.1 Xiongan Project 236 8.8.3.2 Community Project 236 References 236 9 Prevention 239 9.1 Principle 6 239 9.2 Challenges and Opportunities 240 9.3 Green Infrastructure 241 9.3.1 Integrated Urban Water Management Paradigm 241 9.3.2 Green Infrastructure Design Tools 242 9.3.3 Green Infrastructure Modeling Tools 242 9.4 Design Tools of Rain Harvest 244 9.4.1 Determine the Water Demand of a Public Bathroom 244 9.4.2 Determine the Roof Area and the Tank Size 247 9.4.3 Design Rainwater System by Cumulative Plot Method 250 9.4.4 Design Rainwater System Design to Achieve the Smallest Roof Area 252 9.4.4.1 Flowchart for Rainwater System 252 9.4.5 Determine Roof Area for a Rainwater Harvest Tank Without Adding City Water in the First Year 254 9.4.6 Design Rainwater Harvest Tank for Specific Roof Areas 257 9.4.7 Design a Rainwater Harvest Tank of the Optimized Size 260 9.5 Design Anaerobic Digester Reactor 262 9.6 Green Roof Design 263 9.6.1 Life Cycle Assessment 265 9.6.2 Footprint 266 9.7 Rain Garden Design 268 9.7.1 Life Cycle Assessment 270 9.7.2 Environmental Impacts of Aluminum 271 9.7.3 Cost and Benefit Analysis of Rain Garden 271 9.7.4 Water Footprint 274 9.7.5 Nitrogen and Phosphorus Footprint 274 9.8 Exercise 276 9.8.1 Questions 276 9.8.2 Calculations 276 9.8.3 Projects 276 9.8.3.1 Xiongan Project 276 9.8.3.2 Community Proposal Project 277 References 277 10 Recovery 279 10.1 Principle 7 279 10.2 Phosphorus Removal from Wastewater 280 10.2.1 Phosphorus Removal in Conventional Treatment 281 10.2.2 Chemical Phosphorus Removal 281 10.3 Phosphorus Recovery 283 10.3.1 Enhanced Phosphorus Uptake 283 10.3.2 Struvite Precipitation 284 10.4 Capital and Operation Cost of Reclaiming Water for Reuse 286 10.4.1 Building 286 10.4.2 Headwork 290 10.4.3 Oxidation 293 10.4.4 Aerobic SBR 297 10.4.5 MBR 301 10.4.6 Microfiltration 304 10.4.7 Reverse Osmosis 308 10.4.8 Filtration 311 10.4.9 Disinfection 314 10.5 Exercise 317 10.5.1 Questions 317 10.5.2 Calculations 318 10.5.3 Projects 319 10.5.3.1 Xiongan Project 319 10.5.3.2 Community Proposal Project 319 References 319 11 Separation 321 11.1 Principle 8 321 11.2 Challenges and Opportunities 323 11.3 Precipitation 324 11.4 Coagulation and Flocculation 325 11.4.1 Camp–Stein Equation 326 11.4.2 Static and Plug-flow Reactor Mixers 327 11.4.3 Power, Pressure, and Pump in Reactors 327 11.5 Membrane Filtration Systems 333 11.6 Activated Carbon Adsorption 335 11.7 Anaerobic Membrane Biological Reactor 339 11.8 Air Stripping 341 11.9 LCA Tools for WWTPs 350 11.10 Capital and O&M Costs of Membrane Filtration 353 11.11 Exercise 361 11.11.1 Questions 361 11.11.2 Calculation 361 11.11.3 Projects 361 11.11.3.1 Xiongan Project 361 11.11.3.2 Community Projects 362 References 362 12 Treatment 365 12.1 Principle 9 365 12.2 Challenges 365 12.3 Environmental Regulations 366 12.4 UV Disinfection 370 12.4.1 History 370 12.4.2 Photochemistry 370 12.4.3 UV Dose 371 12.4.4 Absorption Coefficient 372 12.4.5 Fluence 372 12.4.6 UV Dose–Response 374 12.5 Virus Sensitivity Index of UV Disinfection 376 12.5.1 Virus Sensitivity Index (VSI) 376 12.5.2 Applications of VSI 379 12.6 Bacteria Sensitivity Index (BSI) with Shoulder Effect 381 12.6.1 Bacteria Sensitivity Index (BSI) 381 12.6.2 Shoulder Broadness Index (SBI) 382 12.6.3 Transformation of H into ΔH/ΔHr 382 12.6.4 Validation of the Models 384 12.6.5 Application of the Model 384 12.6.5.1 Experimental Data of UV Disinfection of ARBs 384 12.6.5.2 Error Analysis of Predicted H Compared with the Observed H 386 12.6.5.3 Prediction of Fluence Required at 5 log I for ARBs 386 12.7 Emerging Treatment Technologies 386 12.8 Design Considerations of UV Disinfection System 389 12.8.1 UV Dose 390 12.8.2 Hydraulic Retention Time 390 12.8.3 UV Lamps 391 12.8.4 Turbidity 391 12.8.5 Typical Design Lives of Major UV Components 391 12.9 Exercise 392 12.9.1 Questions 392 12.9.2 Calculations 392 12.9.3 Projects 392 12.9.3.1 Xiongan Project 392 12.9.3.2 Community Proposal Project 392 References 392 13 Green Retrofitting and Remediation 395 13.1 Principle 10 395 13.2 Challenges of WWTP Design 395 13.2.1 Energy Efficiency of Water and Wastewater Treatment 396 13.3 Anaerobic Digestion for Biogas Production 396 13.3.1 Operation Guidelines for Wastewater Treatment Plants 397 13.4 Best Practice Benchmark 399 13.5 Green Retrofitting 400 13.5.1 Energy Auditing 400 13.5.1.1 Phototrophic System 404 13.5.1.2 Renewable Energy for WWTPs 406 13.6 Sludge Processing and Disposal 406 13.6.1 Design of Wastewater Sludge Thickeners 407 13.6.2 Suspended Solids Removal Efficiency 408 13.6.3 Anaerobic Digester Capacity 409 13.6.4 Aerobic Sludge Digestion 409 13.6.5 Retrofitting Strategies of WWTPs 410 13.7 Green Remediation 410 13.7.1 Green Remediation Metrics and Methods 411 13.7.2 Approaches to Reducing Footprints 416 13.7.2.1 Approaches to Reducing Materials and Waste Footprints 416 13.7.2.2 Approaches to Reducing Water Footprints 416 13.7.2.3 Approaches to Reducing Energy and Air Footprints 417 13.7.3 Evaluation Methods 419 13.7.3.1 Greenhouse Gas (GHG) Emissions Evaluation Fact Sheet 419 13.7.3.2 Future Land Use 420 13.7.3.3 Green Building 420 13.7.3.4 Post-remediation Site Conditions 420 13.8 Tools 421 13.9 Exercise 421 13.9.1 Questions 421 13.9.2 Calculation 421 13.9.3 Projects 422 13.9.3.1 Xiongan Project 422 13.9.3.2 Community Project Proposal 422 References 423 14 Optimization through Modeling and Simulation 425 14.1 Principle 425 14.2 Introduction 425 14.2.1 History of Landfill Leachate Quality 426 14.2.2 Leachate Characteristics 426 14.3 Challenges and Opportunities 428 14.4 Modeling of the Fenton Process 428 14.4.1 Kinetic Model of DMPO–OH EPR Signal 429 14.5 Simulation 436 14.6 Optimization 437 14.6.1 Fenton Oxidation of Landfill Leachate 437 14.6.2 Optimization Fenton Oxidation of Leachate 439 14.6.3 Optimum Operating Conditions 440 14.6.3.1 pH 440 14.6.3.2 Reaction Time 440 14.6.3.3 Effect of Reaction Time on Fenton Oxidation 440 14.6.3.4 Temperature 442 14.6.3.5 Fenton Reagent Dose 442 14.6.3.6 Generalized Fenton Dosing for Landfill Leachate Treatment 443 14.6.3.7 Total COD Removal Under Different LCOD 444 14.6.3.8 Effect of LCOD on COD Removal Efficiency 445 14.6.3.9 Effect of LCOD on Biodegradability 445 14.6.3.10 Effect of LCOD on Cost of Fenton Process Treatment for Landfill Leachate 446 14.7 Validation and Uncertainty 447 14.8 Exercise 448 14.8.1 Questions 448 14.8.2 Calculations 449 14.8.3 Projects 449 14.8.3.1 Xiongan Project 449 14.8.3.2 Community Project 449 References 450 15 Life Cycle Cost and Benefit Analysis 453 15.1 Principle 453 15.2 Challenges and Opportunities 453 15.3 Optimum Pipe Size 454 15.4 Advanced Oxidation Process Costs 461 15.4.1 UV Disinfection 461 15.5 Recovery of N and P 465 15.5.1 Yield Coefficients 466 15.5.2 Capital Cost of P Recovery Systems 469 15.5.3 Activated Sludge 469 15.5.4 Two-Stage Activated Sludge 474 15.5.5 Three-Stage Activated Sludge 477 15.5.6 Three-Stage Activated Sludge with Alum Addition 479 15.5.7 Three-Stage Activated Sludge with Alum and Tertiary Clarifier 482 15.5.8 Three-Stage Activated Sludge with Alum, Tertiary Clarifier, and Filtration 484 15.5.9 Three-Stage Activated Sludge with Tertiary Clarifier and Activated Aluminum Absorption 487 15.5.10 Three-Stage Activated Sludge with Tertiary Clarifier and Activated Absorption 489 15.6 Entrepreneur in SEE 492 15.6.1 Business Plan 493 15.6.2 Finance of Environmental Infrastructure 493 15.6.3 EEI Financing 493 15.6.4 Financial Planning 495 15.7 Innovation in SEE 495 15.7.1 Innovative Technologies 495 15.7.2 Innovative Consumer Products 495 15.7.2.1 SteriPEN 495 15.7.2.2 Drinkable Book™ 496 15.7.3 Future of SEE 496 15.8 Exercise 497 15.8.1 Questions 497 15.8.2 Calculations 497 15.8.3 Projects 497 15.8.3.1 Xiongan Project 498 15.8.3.2 Community Project Proposal 498 15.8.3.3 Course Project and Beyond 499 References 499 Index 501

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Book SynopsisSmart materials are used to develop more cost-effective and high-performance water treatment systems as well as instant and continuous ways to monitor water quality. Smart materials in water research have been extensively utilized for the treatment, remediation, and pollution prevention. Smart materials can maintain the long term water quality, availability and viability of water resource. Thus, water via smart materials can be reused, recycled, desalinized and also it can detect the biological and chemical contamination whether the source is from municipal, industrial or man-made waste. The 15 state-of-the-art review chapters contained in this book cover the recent advancements in the area of waste water, as well as the prospects about the future research and development of smart materials for the waste water applications in the municipal, industrial and manmade waste areas. Treatment techniques (nanofiltration, ultrafiltration, reverse osmosis, adsorption and nano-reactive membranTable of ContentsPreface xv Part 1 Carbon Nanomaterials 1 1 Easy and Large-Scale Synthesis of Carbon Nanotube-Based Adsorbents for the Removal of Arsenic and Organic Pollutants from Aqueous Solutions 3 Fei Yu and Jie Ma 1.1 Introduction 4 1.2 Removal of Arsenic from Aqueous Solution 5 1.3 Removal of Organic Pollutants from Aqueous Solution 22 1.4 Summary and Outlook 39 Acknowledgment 40 References 40 2 Potentialities of Graphene-Based Nanomaterials for Wastewater Treatment 47 Ana L. Cukierman, Emiliano Platero, María E. Fernandez, and Pablo R. Bonelli 2.1 Introduction 48 2.2 Graphene Synthesis Routes 49 2.3 Adsorption of Water Pollutants onto Graphene-Based Materials 52 2.4 Comparison of the Adsorption Performance of Graphene-Based Nanomaterials 72 2.5 Regeneration and Reutilization of the Graphene-Based Adsorbents 73 2.6 Conclusion 77 Acknowledgements 78 Nomenclature 78 References 79 3 Photocatalytic Activity of Nanocarbon-TiO2 Composites with Gold Nanoparticles for the Degradation of Water Pollutants 87 L.M. Pastrana-Martínez, S.A.C. Carabineiro, J.L. Figueiredo, J.L. Faria, A.M.T. Silva, and J.G. Buijnsters 3.1 Introduction 88 3.2 Experimental 90 3.3 Results and Discussion 93 3.4 Conclusions 101 Acknowledgements 102 References 102 4 Carbon Nanomaterials for Chromium (VI) Removal from Aqueous Solution 109 Pavel Kopel, Vedran Milosavljevic, Dorota Wawrzak, Amitava Moulick, Marketa Vaculovicova, Rene Kizek, and Vojtech Adam 4.1 Introduction 110 4.2 Carbon Nanomaterials for Heavy Metal Removal 111 4.3 Latest Progress in Nanocarbon Materials for Cr(VI) Treatment 113 4.4 Summary 121 Acknowledgement 121 References 121 5 Nano-Carbons from Pollutant Soot: A Cleaner Approach toward Clean Environment 127 Kumud Malika Tripathi, Nidhi Rani Gupta, and Sumit Kumar Sonkar 5.1 Introduction 127 5.2 Separation of Nano-carbon from Pollutant BC 131 5.3 Functionalization of Nano-Carbons Isolated from Pollutant BC 135 5.4 Nano-Carbons from Pollutant Soot for Wastewater Treatment 141 5.5 Conclusion 145 Acknowledgments 146 References 146 6 First-Principles Computational Design of Graphene for Gas Detection 155 Yoshitaka Fujimoto 6.1 Introduction 155 6.2 Computational Methodology 157 6.3 Nitrogen Doping and Nitrogen Vacancy Complexes in Graphene 158 6.4 Molecular Gas Adsorptions 166 6.5 Summary 174 Acknowledgments 174 References 175 Part 2 Synthetic Nanomaterials 179 7 Advanced Material for Pharmaceutical Removal from Wastewater 181 Parisa Amouzgar, May Yuan Wong, Bahman Amini Horri, and Babak Salamatinia 7.1 Introduction 182 7.2 Advanced Materials in the Removal of Pharmaceuticals from Wastewater 185 7.3 Activated Carbon (AC) 185 7.4 Modified Carbon Nanotubes (CNTs) 186 7.5 Modified Polysaccharide Matrices 188 7.6 Metal Organic Framework (MOF) 190 7.7 Reactive Composites 191 7.8 TiO2-Coated Adsorbents 192 7.9 Adsorption by Zeolite and Polymer Composites 192 7.10 Adsorption by Clay 193 7.11 Conventional Technologies for the Removal of PPCPs in WWTP 200 7.12 Membrane Filtration 201 7.13 Ozonation and Advanced Oxidation Process (AOP) 201 7.14 Electro-oxidation 202 7.15 Adsorption by Coagulation and Sedimentation 202 7.16 Conclusion 203 References 203 8 Flocculation Performances of Polymers and Nanomaterials for the Treatment of Industrial Wastewaters 213 E. Fosso-Kankeu, F. Waanders, A.F. Mulaba-Bafubiandi, and A.K. Mishra 8.1 General Introduction 214 8.2 Conventional Treatment of Water with Inorganic Coagulants 214 8.3 Development of Polymer-Based Coagulants and Mechanisms of Turbidity Removal 219 8.4 Synthesis of Nanomaterials-Based Flocculants and Utilisation in the Removal of Pollutants 223 8.5 Conclusion 227 References 228 9 Polymeric Nanospheres for Organic Waste Removal 237 Ambika and Pradeep Pratap Singh 9.1 Introduction 237 9.2 Method of Preparation of Nanospheres 239 9.3 Applications of Different Type of Nanospheres in Water Purification 241 9.4 Future Aspects 248 9.5 Conclusions 248 Acknowledgment 249 References 249 10 A Perspective of the Application of Magnetic Nanocomposites and Nanogels as Heavy Metal Sorbents for Water Purification 257 Hilda Elizabeth Reynel-Avila, Didilia Ileana Mendoza-Castillo, and Adrián Bonilla-Petriciolet 10.1 Introduction 258 10.2 Description of Magnetic Nanoparticles and Nanogels 259 10.3 Routes for the Synthesis of Magnetic Nanoparticles and Nanogels 260 10.4 Heavy Metal Removal from Aqueous Solutions Using Magnetic Nanomaterials and Nanogels 266 10.5 Desorption, Regeneration, and Final Disposal 278 10.6 Conclusions and Future Perspective 279 Acknowledgments 280 References 280 11 Role of Core–Shell Nanocomposites in Heavy Metal Removal 289 Sheenam Thatai, Parul Khurana, and Dinesh Kumar 11.1 Introduction 289 11.1.1 Types of Materials 291 11.2 Core and Shell Material: Synthesis and Properties 292 11.3 Nanocomposites Material: Synthesis and Properties 295 11.4 Nanocomposite Materials for Water Decontamination Application 297 11.5 Stability of Metal Nanoparticles and Nanocomposites Material 299 Acknowledgements 302 References 303 Part 3 Biopolymeric Nanomaterials 311 12 Adsorption of Metallic Ions Cd2+, Pb2+, and Cr3+ from Water Samples Using Brazil Nut Shell as a Low-Cost Biosorbent 313 Juliana Casarin, Aff onso Celso Gonçalves Jr, Gustavo Ferreira Coelho, Marcela Zanetti Corazza, Fernanda Midori de Oliveira, César Ricardo Teixeira Tarley, Adilson Pinheiro, Matheus Meier, and Douglas Cardoso Dragunski 12.1 Introduction 314 12.2 Materials and Methods 314 12.3 Results and Discussion 318 12.4 Conclusion 330 Acknowledgments 330 References 331 13 Cellulose: A Smart Material for Water Purification 335 Bharti Arora, Eun Ha Choi, Masaharu Shiratani, and Pankaj Attri 13.1 Introduction 336 13.2 Cellulose: Smart Material for Water Treatment 337 13.3 Conclusion 343 References 343 14 Treatment of Reactive Dyes from Water and Wastewater through Chitosan and its Derivatives 347 Mohammadtaghi Vakili, Mohd Rafatullah, Zahra Gholami and Hossein Farraji 14.1 Introduction 348 14.2 Dyes 349 14.3 Reactive Dyes 350 14.4 Dye Treatment Methods 351 14.5 Adsorption 352 14.6 Adsorbents for Dye Removal 352 14.7 Chitosan 354 14.8 Conclusions and Future Perspectives 368 Acknowledgement 369 References 369 15 Natural Algal-Based Processes as Smart Approach for Wastewater Treatment 379 D. Annie Jasmine, K.B. Malarmathi, S.C.G. Kiruba Daniel, and S. Malathi 15.1 Introduction 380 15.2 Algal Species Used in Wastewater Treatment 382 15.3 Factors Affecting the Growth of Algae 385 15.4 Microalgae and Wastewater Treatment 388 15.5 Case Study of Algal Approach in the Treatment of Municipal Wastewater 390 15.6 Biofuel from Algae Treated Wastewater 391 15.7 Conclusions 394 Acknowledgment 395 References 395 Index 399

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Book SynopsisPolymers are one of the most fascinating materials of the present era finding their applications in almost every aspects of life. Polymers are either directly available in nature or are chemically synthesized and used depending upon the targeted applications.Advances in polymer science and the introduction of new polymers have resulted in the significant development of polymers with unique properties. Different kinds of polymers have been and will be one of the key in several applications in many of the advanced pharmaceutical research being carried out over the globe. This 4-partset of books contains precisely referenced chapters, emphasizing different kinds of polymers with basic fundamentals and practicality for application in diverse pharmaceutical technologies. The volumes aim at explaining basics of polymers based materials from different resources and their chemistry along with practical applications which present a future direction in the pharmaceutical industry. EachTable of ContentsPreface xvii 1 Gellan as Novel Pharmaceutical Excipient 1Priya Vashisth, Harmeet Singh, Parul A. Pruthi and Vikas Pruthi 1.1 Introduction 1 1.2 Structural Properties of Gellan 2 1.3 Physiochemical Properties of Gellan 4 1.3.1 Gelling Features and Texture Properties 4 1.3.2 Rheology 6 1.3.3 Biosafety and Toxicological Studies 6 1.4 Pharmaceutical Applications of Gellan 7 1.4.1 Gellan-Based Pharmaceutical Formulations 7 1.4.2 Role of Gellan Excipients in Drug Delivery and Wound Healing 11 1.5 Conclusion and Future Perspectives 16 References 16 2 Application of Polymer Combinations in Extended Release Hydrophilic Matrices 23Ali Nokhodchi, Dasha Palmer, Kofi Asare-Addo, Marina Levina and Ali Rajabi-Siahboomi 2.1 Extended Release Matrices 23 2.1.1 Polymers Used in ER Matrices 24 2.1.2 Water-Soluble (Hydrophilic) Polymers 24 2.1.3 Water-Insoluble Polymers 24 2.1.4 Fatty Acids/Alcohols/Waxes 25 2.2 Polymer Combinations Used in ER matrices 25 2.2.1 Compatibility and Miscibility of Polymers 25 2.2.2 Combination of Non-Ionic Polymers 26 2.3 Combination of Non-Ionic with Ionic Polymers 27 2.4 Combinations of Ionic Polymers 27 2.5 Other Polymer Combinations 28 2.6 Effect of Dissolution Method (Media) on Drug Release from ER Matrices Containing Polymer Combinations 28 2.7 Main Mechanisms of Drug-Polymer and/or Polymer-Polymer Interaction in ER Formulations 30 2.8 Summary and Conclusions 39 References 40 3 Reagents for the Covalent Attachment of mPEG to Peptides and Proteins 51Marianela González, Victoria A. Vaillard and Santiago E. Vaillard 3.1 Introduction 51 3.2 General Considerations about PEG Reagents and PEGylation Reactions 54 3.3 PEGylation of Amino Groups 57 3.3.1 PEGylation by Urethane Linkage Formation 58 3.3.2 PEGylation by Amide Linkage Formation 60 3.3.3 PEGylation by Reductive Amination 65 3.3.4 PEGylation by Alkylation 67 3.4 PEGylation of Th iol Groups 69 3.5 Reversible PEGylation 73 3.6 Enzymatic PEGylation 76 3.7 PEGylation of Carbohydrates Residues 77 3.8 PEGylation by Click Chemistry 77 3.9 Other PEGylations 79 3.9.1 PEGylation at Arginine 79 3.9.2 PEGylation at Tirosine 79 3.9.3 PEGylation at Histidine 80 3.9.4 PEGylation at Carboxylic Groups 81 3.9.5 PEGylation with mPEG Isothiocyanate 81 3.10 Actual Trends 81 3.11 Conclusions 82 Acknowledgements 83 References 83 4 Critical Points and Phase Transitions in Polymeric Matrices for Controlled Drug Release 101A. Aguilar-de-Leyva, M.D. Campiñez, M. Casas and I. Caraballo 4.1 Introduction 101 4.2 Matrix Systems 102 4.2.1 Inert Matrices 103 4.2.2 Hydrophilic Matrices 104 4.2.3 Lipidic Matrices 104 4.3 Polymers Employed in the Manufacture of Matrix Systems 104 4.3.1 Polymers for Inert Matrices 105 4.3.2 Polymers for Hydrophilic Matrices 107 4.4 Polymer Properties Aff ecting Drug Release from Matrix Systems 111 4.4.1 Mechanical Properties 111 4.4.2 Particle Size 112 4.4.3 Viscosity 112 4.4.4 Molecular Size 113 4.4.5 Substituent Content 113 4.5 Percolation Th eory 113 4.5.1 Basic Concepts 114 4.5.2 Fundamental Equation 116 4.5.3 Percolation Models 116 4.5.4 Application of the Percolation Th eory to the Design of Controlled Release System 117 4.6 Critical Points in Matrix Systems 117 4.6.1 Critical Points in Inert Matrices 117 4.6.2 Critical Points in Hydrophilic Matrices 123 4.6.3 Critical Points in Multiparticular Matrix Systems 128 4.6.4 Critical Points in Matrix Tablets Prepared by Ultrasound-Assisted Compression 129 4.7 Case-Study: Characterization of a New Biodegradable Polyurethane PU (TEG-HMDI) as Matrix-Forming Excipient for Controlled Drug Delivery 130 4.7.1 Rheological Studies 130 4.7.2 Preparation of Matrix Tablets 131 4.7.3 Drug Release Studies 131 4.7.4 Estimation of Excipient Percolation Th reshold 131 4.8 Conclusions and Future Perspectives 133 References 135 5 Polymeric Systems in Quick Dissolving Novel Films 143Prithviraj Chakraborty, Amitava Ghosh and Debarupa D. Chakraborty 5.1 Introduction 143 5.1.1 Drug Delivery Systems for Intraoral Application 144 5.1.2 Quick Dissolving Novel Pharmaceutical Films/Wafer Dosage Form 144 5.1.3 Buccoadhesive Wafer Dosage Form Advantages over Conventional Oral Dosage Forms 146 5.2 Preparation Methods of Novel Quick Dissolving Films 146 5.2.1 Hot-Melt Extrusion Process 146 5.2.2 Solvent Casting Method 147 5.3 Polymers and Blends for Utilization in Diff erent Quick Dissolving Films 147 5.4 Polymers in Novel Quick Dissolving Films 149 5.4.1 Hydroxypropyl Cellulose (Cellulose, 2-hydroxypropyl ether) 149 5.4.2 Hydroxypropyl Methyl Cellulose (Cellulose Hydroxypropyl Methyl Ether) 150 5.4.3 Pullulan 151 5.4.4 Carboxymethyl Cellulose 152 5.4.5 Polyvinyl Pyrollidone 153 5.4.6 Sodium Alginate 154 5.4.7 Polymethacrylates 155 5.4.8 Microcrystalline Cellulose 157 5.5 Role of Plasticizers in Novel Quick Dissolving Film 158 5.6 Characterization Procedure Listed in the Literature for Fast Dissolving Films 159 5.6.1 Thickness and Weight Variation 159 5.6.2 Film Flexibility 160 5.6.3 Tensile Strength 160 5.6.4 Tear Resistance 160 5.6.5 Young’s Modulus 161 5.6.6 Folding Endurance 161 5.6.7 ATR-FTIR Spectroscopy 161 5.6.8 Thermal Analysis and Differential Scanning Calorimetry (DSC) 161 5.6.9 Disintegration Test 161 5.6.10 X-ray Diffraction Study or Crystallinity Study of Films 162 5.6.11 Morphological Study 162 5.7 Conclusion and Future Perspectives 163 References 163 6 Biomaterial Design for Human ESCs and iPSCs on Feeder-Free Culture toward Pharmaceutical Usage of Stem Cells 167Akon Higuchi, S. Suresh Kumar, Murugan A. Munusamy and Abdullah A Alarfaj 6.1 Introduction 167 6.2 Analysis of the Pluripotency of hPSCs 173 6.3 Physical Cues of Biomaterials that Guide Maintenance of PSC Pluripotency 174 6.3.1 Effect of Biomaterial Elasticity on hPSC Culture 176 6.3.2 Effect of Biomaterial Hydrophilicity on hPSC Culture 177 6.4 Two-Dimensional (2D) Culture of hPSCs on Biomaterials 180 6.4.1 hPSC Culture on ECM-Immobilized Surfaces in 2D 180 6.4.2 hPSC Culture on Oligopeptide-Immobilized Surfaces in 2D 184 6.4.3 hPSC Culture on Recombinant E-cadherin Substratum in 2D 186 6.4.4 hPSC Culture on Polysaccharide-Immobilized Surfaces in 2D 187 6.4.5 hPSC Culture on Synthetic Surfaces in 2D 189 6.5 Three-Dimensional (3D) Culture of hPSCs on Biomaterials 193 6.5.1 3D Culture of hPSCs on Microcarriers 193 6.5.2 3D Culture of hPSCs Entrapped in Hydrogels (Microcapsules) 200 6.6 hPSC Culture on PDL-Coated Dishes with the Addition of Specific Small Molecules 205 6.7 Conclusion and Future Perspective 205 Acknowledgements 206 References 206 7 New Perspectives on Herbal Nanomedicine 215Sourabh Jain, Aakanchha Jain, Vikas Jain and Dharmveer Kohli 7.1 Introduction 215 7.1.1 Novel Herbal Drug Formulations 216 7.2 Phytosomes 217 7.3 Liposomes 218 7.3.1 Classification of Liposomes by Work and Mode of Delivery 219 7.3.2 Classification of Liposomes by Size and Range of Bilayers 219 7.4 Nanoparticles 220 7.4.1 Merits of Nanoparticles as Drug Delivery Systems 222 7.5 Nanoemulsions/Microemulsions 222 7.5.1 Merits of Nanoemulsions 222 7.6 Microspheres 223 7.6.1 Classifications of Polymers Used in Microspheres 224 7.7 Microcapsules 225 7.7.1 Morphological Features of Microcapsules 225 7.8 Nanocrystals 225 7.8.1 Methods for Formulation of Nanocrystals 226 7.9 Ethosomes 227 7.10 Transfersomes 228 7.10.1 Relevant Characteristics of Transferosomes 228 7.10.2 Transferosomes as Herbal Formulation 229 7.10.3 Limitations of Transfersomes 229 7.11 Nanoscale Herbal Decoction 230 7.12 Natural Polymers in Nanodrug Delivery 230 7.13 Future Prospects 231 References 232 8 Endogenous Polymers as Biomaterials for Nanoparticulate Gene Therapy 237Giovanni K. Zorzi, Begoña Seijo and Alejandro Sanchez 8.1 Introduction 237 8.2 Polymeric Nanoparticles in Gene Th erapy: Main Characteristics of Currently Proposed Nanosystems Based on Endogenous Polymers 239 8.2.1 Strategies Based on Use of Endogenous Polymers as Biomaterials 239 8.2.2 Physicochemical Characteristics of Nanosystems Based on Endogenous Polymers 246 8.2.3 Nanoparticle Internalization 249 8.3 Specific Features of Endogenous Polymers that Can Open New Prospects in Nanoparticulate Gene Therapy 250 8.3.1 Proteins 250 8.3.2 Carbohydrates 255 8.4 Conclusion and Future Perspective 258 References 259 9. Molecularly Imprinted Polymers as Biomimetic Molecules: Synthesis and their Pharmaceutical Applications 267Mohammad Reza Ganjali, Morteza Rezapour, Farnoush Faridbod and Parviz Norouzi1 9.1 Introduction 267 9.2 Preparation of Molecularly Imprinted Polymers (MIPs) 268 9.2.1 Reaction Components 268 9.2.2 Imprinting Modes 271 9.2.3 Polymerization 274 9.2.4 Physical Forms of MIPs 275 9.2.5 Removing the Template 276 9.3 Applications of Imprinted Polymers 276 9.3.1 Imprinted Polymers in Drug Delivery 276 9.3.2 Imprinted Polymers in Separation of Pharmaceuticals 286 9.3.3 MIPs in Devices for Sensing Pharmaceutical Species 289 References 300 10 Biobased Pharmaceutical Polymer Nanocomposite: Synthesis, Chemistry and Antifungal Study 327Fahmina Zafar, Eram Sharmin, Sheikh Shreaz, Hina Zafar, Muzaff ar Ul Hassan Mir, Jawad M. Behbehani and Sharif Ahmad 10.1 Introduction 328 10.1.1 Vegetable Seed Oils(VO) 329 10.1.2 Polyesteramides (PEAs) 331 10.1.3 Zinc Oxide Nanoparticles 332 10.1.4 Green Chemistry 333 10.1.5 Microwave-Assisted Reactions 334 10.2 Experimental Protocol 335 10.2.1 Procedure for Transformation of RCO to N,N-bis(2 Hydroxyethyl)Ricinolamide (MicHERA) 335 10.2.2 Procedure for the Transformation of MicHERA to PERA/Nano-ZnO Bionanocomposite 336 10.2.3 Procedure for Transformation of MicHERA to PERA 336 10.2.4 Fungal Isolates Used and Minimum Inhibitory Concentration (MIC90) Determination 336 10.2.5 Disc Diffusion Halo Assays 337 10.2.6 Growth Curve Studies 337 10.2.7 Proton Efflux Measurements 337 10.2.8 Measurement of Intracellular pH (pHi) 338 10.3 Results 338 10.3.1 Synthesis 338 10.3.2 Minimal Inhibitory Concentration 341 10.3.3 Disc Diffusion 341 10.3.4 Growth Studies (Turbidometric Measurement) 342 10.3.5 Proton Efflux Measurements 342 10.3.6 Measurement of Intracellular pH 344 10.4 Discussion 344 10.5 Conclusion 346 Acknowledgements 347 References 347 11. Improving Matters of the Heart: Th e Use of Select Pharmaceutical Polymers in Cardiovascular Intervention 351Ashim Malhotra 11.1 Pharmaceutical Polymers Used for Drug-Eluting Stents 351 11.1.1 Introduction and Historical Perspective 351 11.1.2 Polymers Used in Drug-Eluting Stents 352 11.1.3 Polymers Used for Paclitaxel Stents 353 11.2 Pharmaceutical Polymers Used in Cardiovascular Prostheses 354 11.2.1 Introduction and Historical Perspective 354 11.2.2 Factors Affecting Selection of Polymer 356 11.2.3 Specific Polymers Used in Cardiovascular Applications 356 11.3 Pharmaceutical Polymers Used for Gene Therapy 359 11.3.1 Introduction to Cardiovascular Gene Therapy 359 11.3.2 Cardiovascular Gene Delivery Systems 359 11.3.3 Ideal Polymeric Characteristics for Use in Gene Therapy 360 11.3.4 Polymers Used in the Design of Cardiovascular Vectors 360 11.3.5 Ultrasound-Targeted Microbubble Destruction (UTMD) for Cardiovascular Gene Therapy 360 11.4 Pharmaceutical Polymers Used in Tissue Engineering 361 11.5 Injectable Biopolymers 363 11.5.1 Introduction and Historical Perspective 363 11.5.2 Cardiac Restructuring 363 11.5.3 Select Biopolymer Agents Used as Bioinjectables in Cardiovascular Intervention 364 11.6 Vascular Restructuring 365 11.7 Conclusions and Future Directions 365 Acknowledgement 366 References 366 12 Polymeric Prosthetic Systems for Site-Specifi c Drug Administration: Physical and Chemical Properties 369Marián Parisi, Verónica E. Manzano, Sabrina Flor, María H. Lissarrague, Laura Ribba1, Silvia Lucangioli, Norma B. D’Accorsoand Silvia Goyanes 12.1 Introduction 370 12.2 Polymers Used in Medical Devices: General Features 373 12.3 Risks Associated with Surgical Procedures 374 12.4 Applications in Bone Tissue Engineering 375 12.4.1 Surgical Applications of PMMA 376 12.4.2 Antibiotic Treatment Commonly Used in Orthopedic Procedure Involving PMMA Bone Cement 383 12.4.3 General Drawbacks of Antibiotic-Loaded Bone Cements 384 12.4.4 PMMA Modified Materials 386 12.5 Applications in Cardiovascular Tissue Engineering 388 12.5.1 Cardiovascular Devices 391 12.5.2 Drug Treatments Commonly Used in Cardiovascular Devices 396 12.5.3 Polyurethane Modified Materials 398 12.6 Future Perspectives 400 12.7 Conclusions 403 Acknowledgements 404 References 404 13 Prospects of Guar Gum and Its Derivatives as Biomaterials 413D. Sathya Seeli and M. Prabaharan 13.1 Introduction 413 13.2 Developments of Guar Gum and Its Derivatives 414 13.2.1 Drug Delivery Systems (DDSs) 414 13.2.2 Tissue Engineering Scaffolds 423 13.2.3 Wound Healing Materials 425 13.2.4 Biosensors 425 13.2.5 Antimicrobial Agents 428 13.3 Conclusions 429 References 429 14 Polymers for Peptide/Protein Drug Delivery 433M.T. Chevalier, J.S. Gonzalez and V.A. Alvarez 14.1 Biodegradable Polymers 433 14.2 Why Protein and Peptide Encapsulation? 434 14.3 Surface Functionalization 435 14.4 Poly Lactic Acid (PLA) 437 14.4.1 Polymer Structure and Main Characteristics 437 14.4.2 Encapsulation of Peptides/Proteins in PLA 438 14.5 Poly(lactic-co-glycolic acid) (PLGA) 440 14.5.1 Polymer Structure and Main Characteristics 440 14.5.2 Encapsulation of Peptides/Proteins in PLGA 441 14.6 Chitosan 446 14.6.1 Chitosan Structure and Main Characteristics 446 14.6.2 Encapsulation of Peptides/Proteins 447 14.6.3 Peptides and Proteins Encapsulated in Chitosan 448 14.7 Final Comments and Future Perspectives 450 References 450 15 Eco-Friendly Graft ed Polysaccharides for Pharmaceutical Formulation: Structure and Chemistry 457Sumit Mishra, Kartick Prasad Dey and Srijita Bharti 15.1 Introduction 457 15.1.1 Targeted Drug Delivery 458 15.1.2 Controlled Drug Delivery 458 15.1.3 Current Status of Controlled Drug Release Technologies 459 15.1.4 Pharmaceutical Formulation 460 15.1.5 Stages and Timeline 460 15.1.6 Types of Pharmaceutical Formulation 460 15.2 Polysaccharides 462 15.2.1 Chemistry of Polysaccharides 463 15.2.2 Grafted Polysaccharides 463 15.2.3 Drug Delivery System by Grafted Polysaccharides 464 15.2.4 Concept of Drug Delivery Matrix 465 15.2.5 Concept of Inter-Polymer Network (IPN) 466 15.2.6 ‘In-Vitro’ Drug Release Study 467 15.2.7 Mechanism of Drug Release 468 15.3 Conclusions 471 References 471 16 Pharmaceutical Natural Polymers: Structure and Chemistry 477George Dan Mogoºanu1 and Alexandru Mihai Grumezescu 16.1 Introduction 477 16.2 Natural Polymers 478 16.2.1 Polysaccharides 478 16.2.2 Peptides and Proteins 494 16.2.3 Resins and Related Compounds 497 Acknowledgments 498 References 498 Index 521 Information about the Series 529

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Book SynopsisPolymers are one of the most fascinating materials of the present era finding their applications in almost every aspects of life. Polymers are either directly available in nature or are chemically synthesized and used depending upon the targeted applications. Advances in polymer science and the introduction of new polymers have resulted in the significant development of polymers with unique properties. Different kinds of polymers have been and will be one of the key in several applications in many of the advanced pharmaceutical research being carried out over the globe. This 4-partset of books contains precisely referenced chapters, emphasizing different kinds of polymers with basic fundamentals and practicality for application in diverse pharmaceutical technologies. The volumes aim at explaining basics of polymers based materials from different resources and their chemistry along with practical applications which present a future direction in the pharmaceutical industry. EacTable of ContentsPreface xvii 1 Particle Engineering of Polymers into Multifunctional Interactive Excipients 1Sharad Mangal, Ian Larson, Felix Meiser and David AV Morton 1.1 Introduction 1 1.2 Polymers as Excipients 3 1.3 Material Properties Affecting Binder Activity 6 1.3.1 Particle Size 6 1.3.2 Deformation Mechanisms 7 1.3.3 Glass Transition Temperature (Tg) 8 1.4 Strategies for Improving Polymeric Filler-Binder Performance for Direct Compression 8 1.4.1 Interactive Mixing 12 1.4.2 Challenges to Interactive Mixing 13 1.4.3 Controlling Interparticle Cohesion 14 1.5 Preparation and Characterization of Interactive Excipients 14 1.5.1 Particle Size and Size Distribution of Excipients 15 1.5.2 Effect of L-leucine on Surface Morphology 16 1.5.3 Effect of L-leucine on Surface Composition 16 1.5.4 Effect of L-leucine on Surface Energy 17 1.5.5 Effect of L-leucine on Interparticle Cohesion 18 1.6 Performance of Interactive Excipients 18 1.6.1 Blending Ability 18 1.6.2 Effect on Flow 20 1.6.3 Binder Activity 20 1.7 Investigation of the Effect of Polymer Mechanical Properties 23 1.8 Conclusion 25 References 26 2 The Art of Making Polymeric Membranes 33K.C. Khulbe, T. Matsuura and C. Feng 2.1 Introduction 33 2.2 Types of Membranes 35 2.2.1 Porous Membranes 35 2.2.2 Nonporous Membranes 36 2.2.3 Liquid Membranes (Carrier Mediated Transport) 36 2.2.4 Asymmetric Membranes 36 2.3 Preparation of Membranes 36 2.3.1 Phase Inversion/Separation 37 2.3.2 Vapor-Induced Phase Separation (VIPS) 37 2.3.3 Thermally-Induced Phase Separation (TIPS) 37 2.3.4 Immersion Precipitation 38 2.3.5 Film/Dry Casting Technique 38 2.3.6 Track Etching 39 2.3.7 Electrospinning 39 2.3.8 Spraying 42 2.3.9 Foaming 42 2.3.10 Particle Leaching 43 2.3.11 Precipitation from the Vapor Phase 43 2.3.12 Emulsion Freeze-Drying 43 2.3.13 Sintering 44 2.3.14 Stretching 44 2.3.15 Composite/Supported 44 2.3.16 Mixed Matrix Membranes (MMMs) 45 2.3.17 Hollow Fiber Membranes 46 2.3.18 Metal-Organic Frameworks (MOFs) 48 2.4 Modification of Membranes 49 2.4.1 Modification of Polymeric Membrane by Additives/Blending 49 2.4.2 Coating 50 2.4.3 Surface Modification by Chemical Reaction 50 2.4.4 Interfacial Polymerization (IP)/Copolymerization 50 2.4.5 Plasma Polymerization/Treatment 52 2.4.6 Surface Modification by Irradiation of High Energy Particles 52 2.4.7 UV Irradiation 53 2.4.8 Ion-Beam Irradiation 53 2.4.9 Surface Modification by Heat Treatment 53 2.4.10 Graft Polymerization/Grafting 53 2.4.11 Other Techniques 53 2.5 Characterization of Membrane by Different Techniques 54 2.5.1 Conventional Physical Methods to Determine Pore Size and Pore Size Distribution 55 2.5.2 Morphology 58 2.5.3 Thermal Properties 60 2.5.4 Mechanical Properties 60 2.6 Summary 61 References 62 3 Development of Microstructuring Technologies of Polycarbonate for Establishing Advanced Cell Cultivation Systems 67Uta Fernekorn, Jörg Hampl, Frank Weise, Sukhdeep Singh, Justyna Tobola and Andreas Schober 3.1 Introduction 67 3.2 Material Properties of Polycarbonate 71 3.2.1 Physical Properties 71 3.2.2 Chemical Properties 72 3.2.3 Biological Properties 72 3.3 Use of Polycarbonate Foils in Structuration Processes 75 3.3.1 Hot Embossing 75 3.3.2 Thermoforming 77 3.4 Simulation of Microstructuring of a Polycarbonate Foil 79 3.5 Chemical Functionalization of Polycarbonate 81 3.6 Surface Micropatterning of Polycarbonate 84 3.7 Application Examples 86 3.7.1 3D Liver Cell Cultivation in Polycarbonate Scaffolds 86 3.7.2 3D Lung Cell Cultivation in Semi-Actively Perfused Systems 87 3.7.3 Guiding 3D Cocultivation of Cells by Micropatterning Techniques 87 3.8 Conclusion and Further Perspectives 88 Acknowledgements 89 References 89 4 In-Situ Gelling Thermosensitive Hydrogels for Protein Delivery Applications 95Roberta Censi, Alessandra Dubbini and Piera Di Martino 4.1 Introduction 96 4.2 Polymers for the Design of Hydrogels 97 4.2.1 Polymer Architectures 97 4.2.2 Natural, Synthetic and Hybrid Hydrogels 97 4.2.3 Crosslinking Methods 99 4.2.4 Thermogelling Polymer Hydrogels 100 4.3 Pharmaceutical Applications of Hydrogels: Protein Delivery 107 4.3.1 Strategies for Protein Release from Hydrogels 109 4.4 Application of Hydrogels for Protein Delivery in Tissue Engineering 112 4.5 Conclusions 113 References 114 5 Polymers as Formulation Excipients for Hot-Melt Extrusion Processing of Pharmaceuticals 121Kyriakos Kachrimanis and Ioannis Nikolakakis 5.1 Introduction 121 5.1.1 Overview of Hot-Melt Extrusion (HME) 121 5.1.2 Solubility/Dissolution Enhancement by Solid Dispersions 123 5.2 Polymers for HME Processing 127 5.2.1 Basic Requirements 127 5.2.2 Suitability – Examples 128 5.3 Polymer Selection for the HME Process 130 5.3.1 Thermodynamic Considerations – Drug-Polymer Solubility and Miscibility 130 5.4 Processing of HME Formulations 135 5.4.1 Physical Properties of Feeding Material – Flowability, Packing and Friction 135 5.5 Improvements in Processing 141 5.5.1 Equipment Modifications 141 5.5.2 Plasticizers 142 5.6 Conclusion and Future Perspective 144 References 144 6 Poly Lactic-Co-Glycolic Acid (PLGA) Copolymer and Its Pharmaceutical Application 151Abhijeet Pandey, Darshana S. Jain, Subhashis Chakraborty 6.1 Introduction 151 6.2 Physicochemical Properties 152 6.3 Biodegradation 153 6.4 Biocompatibiliy, Toxicty and Pharmacokinetics 154 6.5 Mechanism of Drug Release 155 6.6 PLGA-Based DDS 157 6.7 Bone Regeneration 158 6.8 Pulmonary Delivery 160 6.9 Gene Therapy 162 6.10 Tumor Trageting 162 6.11 Miscellaneous Drug Delivery Applications 164 6.12 Conclusion 165 References 165 7 Pharmaceutical Applications of Polymeric Membranes 173Stefan Ioan Voicu 7.1 Introduction 173 7.2 Obtaining Pure and Ultrapure Water for Pharmaceutical Usage 178 7.3 Wastewater Treatment for Pharmaceutics 180 7.4 Controlled Drug Delivery Devices Based on Membrane Materials 183 7.5 Molecularly Imprinted Membranes 185 7.6 Conclusions 190 References 191 8 Application of PVC in Construction of Ion-Selective Electrodes for Pharmaceutical Analysis: A Review of Polymer Electrodes for Nonsteroidal, Anti-Inflammatory Drugs 195Joanna Lenik 8.1 Introduction 195 8.2 Properties and Usage of Poly(vinyl)chloride (PVC) 197 8.3 PVC Application and Properties in Construction of Potentiometric Sensors for Drug Detection 199 8.3.1 Role of Polymer Membrane Components 202 8.4 Ion-Selective, Classic, Liquid Electrodes (ISEs) 205 8.5 Ion-Selective Solid-State Electrodes 206 8.5.1 Ion-Selective Coated-Wire Electrodes (CWE) 206 8.5.2 Ion-Selective BMSA Electrodes 207 8.5.3 Electrodes Based on Conductive Polymers (SC-ISEs ) 208 8.6 Application of Polymer-Based ISEs for Determination of Analgetic, Anti-Inflammatory and Antipyretic Drugs: Literature Review (2000-2014) 211 8.6.1 Electrodes for Determination of Narcotic Medicines 211 8.6.2 Electrode Sensitive to Dextromethorphan 211 8.6.3 Electrode Sensitive to Tramadol 212 8.6.4 Electrodes for Determination of Non-Narcotic Drugs 212 8.6.5 Salicylate Electrode 214 8.6.6 Ibuprofen Electrode 214 8.6.7 Ketoprofen Electrodes 216 8.6.8 Piroxicam Electrode 216 8.6.9 Tenoxicam Electrode 217 8.6.10 Naproxen Electrodes 217 8.6.11 Indomethacin Electrodes 217 8.6.12 Sulindac Electrode 218 8.6.13 Diclofenac Electrodes 218 8.7 Conclusion 218 References 222 9 Synthesis and Preservation of Polymer Nanoparticles for Pharmaceutical Applications 229Antonello A. Barresi, Marco Vanni, Davide Fissore and Tereza Zelenková 9.1 Introduction: Polymer Nanoparticles Production 229 9.2 Production of Polymer Nanoparticles by Solvent Displacement Using Intensive Mixers 238 9.2.1 Influence of Polymer-Solvent Type and Hydrodynamics on Particle Size 243 9.2.2 Dependence on Operating Conditions – Polymer and Drug Concentration, Solvent/Antisolvent Ratio, Processing Conditions 248 9.2.3 Process Design: Selection of Mixing Device, Scale Up and Process Transfer 256 9.3 Freeze-Drying of Nanoparticles 264 9.4 Conclusions and Perspectives 268 Acknowledgements 272 References 272 10 Pharmaceutical Applications of Maleic Anhydride/Acid Copolymers 281Irina Popescu 10.1 Introduction 281 10.2 Maleic Copolymers as Macromolecular Drugs 283 10.3 Maleic Copolymer Conjugates 285 10.3.1 Polymer-Protein Conjugates 286 10.3.2 Polymer-Drug Conjugates 288 10.4 Noncovalent Drug Delivery Systems 291 10.4.1 Enteric Coatings 291 10.4.2 Solid Dispersions 292 10.4.3 Polymeric Films and Hydrogels 293 10.4.4 Microspheres and Microcapsules 294 10.4.5 Nanoparticles 295 10.4.6 Micelles 295 10.5 Conclusion 296 References 296 11 Stimuli-Sensitive Polymeric Nanomedicines for Cancer Imaging and Therapy 311F. Perche, S. Biswas and V. P. Torchilin 11.1 Introduction 311 11.2 Pathophysiological and Physical Triggers 314 11.2.1 Acidosis 314 11.2.2 Reductive Stress 319 11.2.3 Tumor Hypoxia 320 11.2.4 Cancer Associated Extracellular Enzymes 322 11.2.5 Magneto-Responsive Polymers 324 11.2.6 Temperature-Sensitive Dendrimers 325 11.2.7 Photoresponsive Polymers 326 11.3 Stimuli-Responsive Polymers for Patient Selection and Treatment Monitoring 327 11.3.1 Selection of Patients Amenable to Nanomedicine Treatment 328 11.3.2 Selection of Patients for pH-Sensitive Nanocarriers 329 11.3.3 Selection of Patients for Redox-Sensitive Nanocarriers 329 11.3.4 Mapping of Dominant Active Pathways Using Enzyme-Sensitive Probes 330 11.3.5 Selection of Patients for Molecularly-Targeted Therapies 330 11.3.6 Evaluation of Response to Treatment 331 11.4 Conclusions and Future Perspectives 331 Acknowledgments 333 References 333 12 Artificial Intelligence Techniques Used for Modeling of Processes Involving Polymers for Pharmaceutical Applications 345Silvia Curteanu 12.1 Introduction 345 12.2 Artificial Neural Networks 347 12.2.1 Elements and Structure 347 12.2.2 Working Methodology 349 12.2.3 Variants of ANN Modeling 350 12.3 Support Vector Machines 352 12.3.1 General Aspects 352 12.3.2 SVM Modeling Methodology 353 12.4 Modeling of Processes Involving Polymers for Pharmaceutical Applications 354 12.4.1 Neural Networks Used for Modeling of Processes Involving Pharmaceutical Polymers 354 12.4.2 Support Vector Machines Used for Modeling of Processes Involving Pharmaceutical Polymers 359 12.5 Conclusion and Future Perspective 360 References 361 13 Review of Current Pharmaceutical Applications of Polysiloxanes (Silicones) 363Krystyna Mojsiewicz-Pieñkowska 13.1 Introduction 363 13.2 Variety of Polysiloxane – Structure, Synthesis, Properties 364 13.2.1 Basic Silicone Chemistry 364 13.2.2 Properties of Silicones 364 13.3 Polysiloxanes as Active Pharmaceutical Ingredient (API) 368 13.3.1 Mechanism of Action of Dimethicone and Simethicone 370 13.3.2 Current Legislative Standards Related to Oral Application of Dimethicone and Simethicone (PDMS) 370 13.3.3 Admissible Doses for Dimethicone and Simethicone (PDMS) 372 13.4 Polysiloxanes as Excipients 373 13.4.1 Skin Adhesive Patches 375 13.4.2 Carrier for Controlled-Release Drugs 375 13.5 Conclusion and Future Perspective 377 References 378 14 Polymer-Doped Nano-Optical Sensors for Pharmaceutical Analysis 383M. S. Attia and M. S. A. Abdel-Mottaleb 14.1 Introduction 383 14.1.1 Sol-Gel Process 383 14.1.2 Molecular Imprinting Nanomaterial Polymer 386 14.1.3 Poly(methyl methacrylate) Polymer (PMMA) 390 14.2 Processing 392 14.2.1 Sol-Gel Technique 392 14.2.2 Molecular Imprinted Nanomaterials 394 14.2.3 Preparation of Optical Sensor Doped in PMMA Matrix 396 14.2.4 Determination of Pharmaceutical Drug in Pharmaceutical Preparations 396 14.2.5 Determination of Pharmaceutical Drug in Serum Solution 397 14.3 Application of Optical Sensor for Pharmaceutical Drug Determination 397 14.3.1 TEOS-Doped Nano-Optical Sensor for Pharmaceutical Determinations 397 14.3.2 Molecular Imprinted Nano-Polymer 401 14.3.3 Sensor Embedded in Polymethymethacrylate 404 14.4 Conclusion 405 References 405 15 Polymer-Based Augmentation of Immunosuppressive Formulations: Application of Polymer Technology in Transplant Medicine 411Ian C. Doyle and Ashim Malhotra 15.1 Introduction 411 15.2 Polymer-Based Immunosuppressive Formulations 414 15.2.1 Sirolimus 414 15.2.2 Cyclosporine A 424 15.2.3 Tacrolimus 429 15.2.4 Mycophenolic Acid 431 15.3 Conclusion and Future Perspective 433 References 434 16 Polymeric Materials in Ocular Drug Delivery Systems 439M. E. Pina, P. Coimbra, P. Ferreira, P. Alves, A. I. Figueiredo and M. H. Gil 16.1 Introduction 439 16.2 A Brief Description of Ocular Anatomy and Physiology 440 16.2.1 Anatomy of the Human Eye 440 16.2.2 Routes of Ocular Drug Delivery 441 16.2.3 Barriers in Ocular Drug Delivery 444 16.3 Polymeric Ocular Drug Delivery Systems 445 16.3.1 Non-Biodegradable Polymeric Ocular Drug Delivery Systems 446 16.3.2 Biodegradable Polymeric Ocular Drug Delivery Systems 449 16.4 Conclusion and Future Perspective 455 References 455 Index 459

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Book SynopsisPolymers are one of the most fascinating materials of the present era finding their applications in almost every aspects of life. Polymers are either directly available in nature or are chemically synthesized and used depending upon the targeted applications.Advances in polymer science and the introduction of new polymers have resulted in the significant development of polymers with unique properties. Different kinds of polymers have been and will be one of the key in several applications in many of the advanced pharmaceutical research being carried out over the globe. This 4-partset of books contains precisely referenced chapters, emphasizing different kinds of polymers with basic fundamentals and practicality for application in diverse pharmaceutical technologies. The volumes aim at explaining basics of polymers based materials from different resources and their chemistry along with practical applications which present a future direction in the pharmaceutical industry. EachTable of ContentsPreface xix 1 Bioactive Polysaccharides of Vegetable and Microbial Origins: An Overview 1 Giuseppina Tommonaro, Annarita Poli, Paola Di Donato, Roberto Abbamondi Gennaro, Ilaria Finore and Barbara Nicolaus 1.1 Introduction 1 1.2 Anticarcinogenic Polysaccharides 3 1.3 Anti-inflammatory/Immunostimulating Polysaccharides 8 1.4 Antiviral Polysaccharides 13 1.5 Antioxidant Polysaccharides 17 1.6 Other Biotechnological Applications 21 1.7 Conclusions and Future Perspectives 23 Acknowledgments 23 Reference 24 2 Chitosan: An Emanating Polymeric Carrier for Drug Delivery 33 Priti Girotra and Shailendra Kumar Singh 2.1 Introduction 33 2.2 Preparation of Chitosan 34 2.3 Physicochemical Properties of Chitosan 35 2.4 Biological Activities of Chitosan 36 2.5 Pharmaceutical Applications of Chitosan 39 2.6 Functionalization of Chitosan 49 2.7 Conclusion and Future Perspectives 49 Reference 51 3 Fungi as Sources of Polysaccharides for Pharmaceutical and Biomedical Applications 61 Filomena Freitas, Christophe Roca and Maria A. M. Reis 3.1 Introduction 61 3.2 The Fungal Cell 62 3.3 Polysaccharides Produced by Fungi 69 3.4 Production and Extraction of Polysaccharides from Fungi 77 3.5 Fungal Polysaccharides in Biomedical and Pharmaceutical Applications 81 3.6 Commercial Exploitation of Fungal Polysaccharides in Biomedical and Pharmaceutical Applications 89 3.7 Conclusion and Future Perspective 91 Reference 91 4 Environmentally Responsive Chitosan-based Nanocarriers (CBNs) 105 Ankit Jain and Sanjay K. Jain 4.1 Introduction 105 4.2 Graft Copolymerized CBNs 107 4.3 pH-Sensitive CBNs 109 4.4 Thermosensitive CBNs 111 4.5 pH-Sensitive and Thermosensitive CBNs 112 4.6 pH- and Ionic-Sensitive CBNs 113 4.7 Photosensitive CBNs 114 4.8 Electrical-Sensitive CBNs 115 4.9 Magneto-Responsive CBNs 115 4.10 Chemo-Sensitive CBNs 115 4.11 Biodegradation of Chitosan and Its Derivatives 116 4.12 Toxicity of CBNs 120 4.13 Conclusions and Future Perspectives 120 References 120 5 Biomass Derived and Biomass Inspired Polymers in Pharmaceutical Applications 127 Elisavet D. Bartzoka, Claudia Crestini and Heiko Lange 5.1 Introduction 127 5.2 Biodegradable Polymers in Biomedical Applications – Relevant Aspects 129 5.3 Biodegradable Natural Polymers in Pharmaceutical Applications 133 5.4 Micro- and Nanocrystalline Natural Polymers and Fibrils – General Regulative Considerations 175 5.5 Concluding Remarks and Outlook 176 Reference 177 6 Modification of Cyclodextrin for Improvement of Complexation and Formulation Properties 205 Tapan K. Dash and V. Badireenath Konkimalla Abbreviations 205 6.1 Introduction 206 6.2 Cyclodextrin and Its Degradation 206 6.3 Complexation by CDs and Release 207 6.4 Modifications and Scope with Respect to Pharmaceutical Application 208 6.5 Concluding Remarks 218 Acknowledgements 218 Reference 218 7 Cellulose-, Ethylene Oxide- and Acrylic-Based Polymers in Assembled Module Technology (Dome Matrix®) 225 Camillo Benetti, Paolo Colombo and Tin Wui Wong 7.1 Dome MatrixR Technology 225 7.2 Polymers for Controlled Drug Release 228 7.3 Cellulose Derivatives 230 7.4 Acrylic Acid Polymers 232 7.5 Polymethacrylates 234 7.6 Polyethylene Oxide 236 7.7 Conclusions 237 Acknowledgments 237 Reference 237 8 Structured Biodegradable Polymers for Drug Delivery 243 Nishi Mody, Udita Agrawal, Rajeev Sharma and S. P. Vyas 8.1 Introduction 243 8.2 Classification 249 8.3 Degradation Processes in Biodegradable Polymers 254 8.4 Responsive Stimuli-Sensitive Polymers 260 8.5 Conclusion and Future Prospects 271 References 271 9 Current State of the Potential Use of Chitosan as Pharmaceutical Excipient 275 A. Raquel Madureira, Bruno Sarmento and Manuela Pintado 9.1 The World of Pharmaceutical Excipients 275 9.2 Chitosan 276 9.3 Activities Found for Chitosan 277 9.4 Properties of Chitosan 280 9.5 Applications as a Pharmaceutical Excipient 282 9.6 Conclusion 289 References 290 10 Modification of Gums: Synthesis Techniques and Pharmaceutical Benefits 299 Vikas Rana, Sunil Kamboj, Radhika Sharma and Kuldeep Singh 10.1 Introduction 299 10.2 Synthesis of Modified Gums 302 10.3 Characterization 320 10.4 Pharmaceutical Applications of Modified Gums 332 10.5 Conclusion and Future Prospective 354 Reference 355 11 Biomaterials for Functional Applications in the Oral Cavity via Contemporary Multidimensional Science 365 V. Tamara Perchyonok, Vanessa Reher, Nicolaas Basson and Sias Grobler 11.1 Introduction 365 11.2 Free Radical Formation, Antioxidants and Relevance in Health 366 11.3 Oral Diseases: Oxidative Stress and the Role of Antioxidant Defenses in the Oral Cavity 369 11.4 Biomaterials and Intelligent Design of Functional Biomaterials 371 11.5 In-Vitro Developments of Free Radical Defense Mechanisms and Drug-Delivery Systems 372 11.6 Practical In-Vitro Applications of Chitosan-Based Functional Biomaterial Prototypes in Dentistry 375 11.7 Conclusion 398 References 399 12 Role of Polymers in Ternary Drug Cyclodextrin Complexes 413 Renu Chadha, Madhu Bala, Parnika, Kunal Chadha and Maninder Karan 12.1 Introduction 413 12.2 Cyclodextrins (Cycloamyloses, Cyclomaltoses, Schardinger Dextrins) 414 12.3 Role of Biodegradable/Water-Soluble Polymers in Efficacy of Inclusion Complexes 416 12.4 Solubility, Dissolution and Bioavailability Enhancement: Case Studies 423 12.5 Conclusion 433 References 433 13 Collagen-Based Materials for Pharmaceutical Applications 439 Daniela Pamfil, Manuela Tatiana Nistor and Cornelia Vasile 13.1 Introduction 439 13.2 Collagen Structure and Its Properties 440 13.3 Preparation Methods of Collagen-Based Biomaterials 443 13.4 Pharmaceutical Applications of Collagen-Based Products 450 13.5 Concluding Remarks and Future Perspectives 462 Acknowledgments 468 References 468 14 Natural Polysaccharides as Pharmaceutical Excipients 483 Nazire Deniz Yılmaz, Gülbanu Koyundereli Çılgı and Kenan Yılmaz 14.1 Introduction 483 14.2 Natural Polysaccharides 485 14.3 Conclusion 510 Reference 510 15 Structure, Chemistry and Pharmaceutical Applications of Biodegradable Polymers 517 Mazhar Ul-Islam, Shaukat Khan, Muhammad Wajid Ullah and Joong Kon Park 15.1 Introduction 517 15.2 History of Polymers 518 15.3 Concept of Biodegradability 522 15.4 Biodegradable Polymers and Their Classification 522 15.5 Biocompatibility of Biodegradable Polymers 528 15.6 Biodegradable Polymers in Pharmaceutical Applications 530 15.7 Development of Various Biodegradable Polymer Systems for Drug Delivery 532 15.8 Future Prospects 535 Acknowledgment 536 Reference 536 16 Preparation and Properties of Biopolymers: A Critical Review 541 Selvaraj Mohana Roopan, T. V. Surendra and G. Madhumitha 16.1 Introduction 541 16.2 Nature of Biopolymers 543 16.3 Common Biopolymers 544 16.4 Biopolymers in Drug Development 545 16.5 Biobased Polymers Production 548 16.6 Properties of Biopolymers 551 Acknowledgement 553 Reference 553 17 Engineering Biodegradable Polymers to Control Their Degradation and Optimize Their Use as Delivery and Theranostic Systems 557 Ilaria Armentano, Loredana Latterini, Nicoletta Rescignano, Luigi Tarpani, Elena Fortunati and Josè Maria Kenny 17.1 Introduction 557 17.2 Nanotechnology 559 17.3 Nanostructured Biodegradable Polymers 560 17.4 Design Strategies for Fluorescent Biodegradable Polymeric Systems 566 17.5 Conclusions and Perspectives 570 Reference 570 Index 577

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Book SynopsisPolymers are one of the most fascinating materials of the present era finding their applications in almost every aspects of life. Polymers are either directly available in nature or are chemically synthesized and used depending upon the targeted applications.Advances in polymer science and the introduction of new polymers have resulted in the significant development of polymers with unique properties. Different kinds of polymers have been and will be one of the key in several applications in many of the advanced pharmaceutical research being carried out over the globe. This 4-partset of books contains precisely referenced chapters, emphasizing different kinds of polymers with basic fundamentals and practicality for application in diverse pharmaceutical technologies. The volumes aim at explaining basics of polymers based materials from different resources and their chemistry along with practical applications which present a future direction in the pharmaceutical industry. EachTable of ContentsPreface xv 1 Smart Hydrogels: Therapeutic Advancements in Hydrogel Technology for Smart Drug Delivery Applications 1 Gabriel Goetten de Lima, Diwakar Kanwar, Derek Macken, Luke Geever, Declan M. Devine and Michael J.D. Nugent 1.1 Introduction 1 1.2 Types and Properties of Smart Polymer Hydrogels 4 1.2.1 Temperature-Responsive Hydrogels 4 1.2.2 pH-Sensitive Hydrogels 5 1.2.3 Glucose-Responsive Hydrogels 7 1.2.4 Electro-Signal Sensitive Hydrogels 8 1.2.5 Light-Sensitive Hydrogels 8 1.2.6 Multi-Responsive Smart Hydrogels 10 1.3 Applications of Smart Polymer Hydrogels 11 1.4 Conclusion 11 References 13 2 Molecularly Imprinted Polymers for Pharmaceutical Applications 17 Ambareesh Kumar Singh, Neha Gupta, Juhi Srivastava, Archana Kushwaha and Meenakshi Singh 2.1 Introduction 17 2.2 Fluoroquinolone Antibiotics 19 2.3 Sulfonamides 36 2.4 Miscellaneous 41 2.5 Conclusions and Future Prospects 48 2.6 Acronyms and Abbreviations 48 References 50 3 Polymeric Stabilizers for Drug Nanocrystals 67 Leena Peltonen, Annika Tuomela and Jouni Hirvonen 3.1 Introduction 67 3.2 Methods for Nanocrystallization 68 3.2.1 Bottom-Up Technologies 69 3.2.2 Top-Down Technologies 69 3.2.3 Combination Technologies 71 3.4 Polymers for Nanocrystal Stabilization 73 3.4.1 Polymers of Natural Origin 75 3.4.2 Synthetic Polymers 77 3.5 Effect of Stabilizing Polymers on Drug Biocompatibility, Bioactivity, Membrane Permeability and Drug Absorption 79 3.6 Conclusions and Future Perspective 82 References 82 4 Polymeric Matrices for the Controlled Release of Phosphonate Active Agents for Medicinal Applications 89 Konstantinos E. Papathanasiou and Konstantinos D. Demadis 4.1 Introduction 89 4.2 Polymers in Drug Delivery 91 4.2.1 Polyesters 92 4.2.1.1 Poly(lactic acid), Poly(glycolic acid), and Their Copolymers 92 4.2.1.2 Poly(ethylene glycol) Block Copolymers 93 4.2.1.3 Poly(ortho esters) 94 4.2.1.4 Poly(anhydrides) 96 4.2.1.5 Poly(anhydride−imides) 97 4.2.1.6 Poly(anhydrite esters) 98 4.2.2 Poly(amides) 99 4.2.3 Poly(iminocarbonates) 100 4.3 Release of Phosphonate-Based Drugs 100 4.4 Conclusions/Perspectives 114 References 115 5 Hydrogels for Pharmaceutical Applications 125 Veena Koul, Sirsendu Bhowmick and Th anusha A.V. 5.1 Introduction 125 5.2 What are Hydrogels? 126 5.3 Classification of Hydrogels 126 5.4 Preparation of Hydrogels 127 5.5 Characterization of Hydrogels 128 5.6 Application of Hydrogels 131 5.6.1 Wound Dressing 131 5.6.2 Implantable Drug Delivery Systems 133 5.6.3 Tissue Engineering Substitute 134 5.6.4 Injectable Hydrogels 136 5.7 Conclusion 137 Acknowledgement 138 References 138 6 Responsive Plasmid DNA Hydrogels: A New Approach for Biomedical Applications 145 Diana Costa, Artur J.M. Valente and Joao Queiroz 6.2 DNA-Based Hydrogels 147 6.3 Controlled and Sustained Release 150 6.3.1 Photodisruption of Plasmid DNA Networks 150 6.3.2 Release of Plasmid DNA 152 6.3.3 Release of Chemotherapeutic Drugs 154 6.3.4 In Vitro Studies 155 6.4 Combination of Chemo and Gene Therapies 156 6.5 Conclusions and Future Perspectives 158 References 159 7 Bioactive and Compatible Polysaccharides Hydrogels Structure and Properties for Pharmaceutical Applications 163 Teresa Cristina F. Silva, Andressa Antunes Prado de Franca and Lucian A. Lucia 7.1 Introduction 163 7.2 Materials and Methods 164 7.2.1 Isolation of Xylans 166 7.2.1.1 Preparing Hydrogel without A Priori Grafting of Vinyl Group 166 7.2.1.2 Preparing Hydrogels for Grafting Polymerization 166 7.2.2 Hydrogel Synthesis and Characterization 166 7.2.2.1 Preparing Hydrogel without A Priori Grafting of Vinyl Group 166 7.2.2.2 Preparing Hydrogels for Grafting Polymerization 166 7.2.3 Doxorubicin Release from Xylan-Based Hydrogels 167 7.3 Results and Discussion 167 7.3.1 Hydrogel without A Priori Grafting of Vinyl Group 167 7.3.1.1 Reaction of PAA with Wood 167 7.3.1.2 Hydrogel Preparation and Characterization 168 7.3.2 Hydrogels for Grafting Polymerization 170 7.3.2.1 Morphology and Rheological Properties 172 7.3.2.2 Swelling Behavior 173 7.3.2.3 Drug Release 174 References 175 8 Molecularly Imprinted Polymers for Pharmaceutical Analysis 179 Piotr Luliński 8.1 Introduction 179 8.2 Overview of the Imprinting Process 180 8.3 Molecularly Imprinted Polymers for Separation Purposes 182 8.3.1 Bulk Imprinted Materials 182 8.3.2 Imprinted Monoliths 185 8.3.3 Imprinted Stir-Bar Sorptive Extraction 187 8.3.4 Molecularly Imprinted Microparticles and Nanostructures 188 8.3.5 Magnetic Imprinted Materials 192 8.3.6 Miscellaneous Imprinted Formats 194 8.4 Molecularly Imprinted Sensors for Drugs 195 8.5 Conclusion and Future Perspective 197 References 1979 Prolamine-Based Matrices for Biomedical Applications 203 Pradeep Kumar, Yahya E. Choonara and Viness Pillay 9.1 Introduction 203 9.2 Gliadin – Prolamine Isolated from Wheat Gluten 204 9.2.1 Gliadin Nanoparticles 205 9.2.1.1 Hydrophobicity of Gliadin 206 9.2.1.2 Solubility Parameter 207 9.2.2 Controlled Drug Release from Gliadin-Based Matrices 207 9.2.2.1 Salting-Out 207 9.2.2.2 Gliadin Films 208 9.2.2.3 Gliadin Foams 209 9.3 Zein - Prolamine Isolated from Corn Gluten Meal 209 9.3.1 Drug-Loaded Zein Particulates 210 9.3.1.1 Microsphere-Based Films and Tablets 210 9.3.1.2 Zein-Based Blends and Complexes 213 9.3.1.3 Zein-Based Nanoparticulate Systems 213 9.3.2 Biomedical Applications of Zein-Based Matrices 215 9.4 Soy Protein – Prolamine Isolated from Soybean 217 9.4.1 Soy Protein Derivatives 218 9.4.2 Soy-Based Polymer Blends 218 9.4.3 Soy-Based Crosslinked Matrices 219 9.4.4 Cold-Set Gelation of Soy Protein 221 9.5 Kafi rin – Prolamine Isolated from Sorghum 222 9.5.1 Microparticles 223 9.5.2 Compressed Matrices 224 9.6 Conclusion and Future Perspective 224 References 225 10 Hydrogels Based on Poly(2-oxazoline) S for Pharmaceutical Applications 230 Anna Zahoranova and Juraj Kronek 10.1 Hydrogels for Medical Applications 231 10.1.1 Controlled Drug Delivery and Release 232 10.1.1.1 Prolonged Effect of Drugs 232 10.1.1.2 Stimuli-Sensitive Drug Delivery 234 10.1.2 3D Cell Cultivation 236 10.1.2.1 Chemical Composition 237 10.1.2.2 Porosity and Pore Size 238 10.1.3 Tissue Engineering 238 10.1.4 Nonenzymatic Detachment of Cells 239 10.2 Poly(2-oxazoline)s in Pharmaceutical Applications 240 10.2.1 Biocompatibility of Poly(2-oxazoline)s 241 10.2.2 Biomedical Applications of Poly(2-oxazoline)s 244 10.3 Poly(2-oxazoline)-Based Hydrogels – Synthetic Strategies 245 10.3.1 Hydrogels Containing Segments of Poly(2-oxazoline)s 245 10.3.2 Crosslinked Poly(2-oxazoline)s 248 10.4 Applications of Poly(2-oxazoline)-Based Hydrogels 250 10.4.1 Controlled Delivery of Drugs 250 10.4.1.1 Hydrogels for DNA Binding 251 10.4.1.2 Hydrogels Modifi ed by Peptidic Sequences 252 10.5 Conclusions and Future Perspectives 252 Acknowledgement 253 References 254 11 Mixed Biocompatible Block Copolymer/Lipid Nanostructures as Drug Nanocarriers: Advantages and Pharmaceutical Perspectives 259 Natassa Pippa, Stergios Pispas and Costas Demetzos 11.1 Introduction 259 11.2 Drug Delivery Systems 261 11.2.1 Conventional Drug Delivery Systems 261 11.2.2 Mixed Drug Delivery Systems Employing Biocompatible Polymers 263 11.3 Mixed Biocompatible Block Copolymer/Lipid Drug Nanocarriers: The Concept through Examples 266 11.3.1 Preparation of Mixed Drug Nanocarriers 266 11.3.2 Physicochemical Characterization of Mixed Drug Nanocarriers 267 11.3.3 Th ermotropic Behavior of Mixed Drug Nanocarriers 270 11.3.4 Imaging of Mixed Drug Nanocarriers 274 11.3.5 In Vitro Drug Release from the Mixed Nanocarriers 274 11.4 Conclusion and Future Perspective 277 References 279 12 Nanoparticle Polymer-Based Engineered Nanoconstructs for Targeted Cancer Th erapeutics 287 Anand Thirunavukarasou, Sudhakar Baluchamy and Anil K. Suresh 12.1 An Overview of Metal Polymer-Based Nanoconstructs 287 12.1.1 Tumor-Specific Targeting Using Nanoparticle-Polymer Nanoconstructs 290 12.1.2 Cytotoxicity Assessments of Nanoparticle-Polymer Constructs 291 12.1.2.1 MTT and/or MTS Assay 291 12.1.2.2 Live/Dead Staining Assay 291 12.1.3 Physical Characterization Techniques to Assess the Cellular Uptake of the Nanoparticle-Polymer Constructs 292 12.1.3.1 Inductively Coupled Plasma Mass Spectroscopy (ICP-MS) for Quantitative Uptake 292 12.1.3.2 Dark Field Microscopy 292 12.1.3.3 Ultramicrotome-Based Trans-Sectional Transmission Electron Microscopy Imaging 293 12.2 Conclusions 293 Acknowledgements 294 References 294 13 Th e Importance of Dendrimers in Pharmaceutical Applications 297 Veronica Brunetti, Marisa Martinelli and Miriam C. Strumia 13.1 Introduction 297 13.1.1 What are Dendrimers? 298 13.1.2 Synthetic Methods for Dendritic Molecules 300 13.1.2.1 Divergent Synthesis 300 13.1.2.2 Convergent Synthesis 301 13.2 Properties of Dendritic Polymers Useful for Biomedical Applications 301 13.3 Current Pharmaceutical Products Prepared from Dendritic Polymer: Promising Prospects for Future Applications 303 13.3.1 Diagnostic Technologies 303 13.3.2 Dendritic Polymers in Prevention 304 13.3.3 Therapeutic Applications 307 13.4 Conclusions 310 References 310 14 Pharmaceutical Polymers: Bioactive and Synthetic Hybrid Polymers 315 Roxana Cristina Popescu and Alexandru Mihai Grumezescu 14.1 Introduction 315 14.2 General Obtainment Methods for Polymeric Microspheres and Hybrid Materials 320 14.3 Stimuli-Responsive (pH/temperature/photo) polymers 321 14.3.1 PEG 321 14.3.2 PLA and PLGA 325 14.3.3 PVP 328 14.3.4 PVA 333 14.4 Conclusions 333 Acknowledgements 334 References 334 15 Eco-friendly Polymer-Based Nanocomposites for Pharmaceutical Applications 341 Ida Idayu Muhamad, Suguna Selvakumaran, Mohd Harfi z Salehudin and Saiful Izwan Abd Razak 15.1 Introduction 342 15.1.1 Eco-friendly Polymers, the Briefs 342 15.1.2 Composite 342 15.1.3 Nanocomposites 343 15.1.4 Eco-friendly Nanocomposite 343 15.1.5 Market Trend in Eco-friendly Polymer Nanocomposites in Biomedical Application 344 15.2 Structure and Properties of Some Eco-friendly Pharmaceutical Polymers 345 15.2.1 Starch 346 15.2.2 Chitosan 347 15.2.2.1 Application of Chitosan 348 15.2.3 Alginate (E400-E404) 349 15.2.4 Polyhydroxyalkanoates (PHAs) 349 15.2.5 Poly(lactic acid) (PLA) 350 15.2.6 Gelatin 351 15.2.7 Casein Protein 351 15.2.8 Carrageenan 352 15.3 Review of Development and Application of Selected Eco-friendly Polymer-Based Nanocomposites 355 15.3.1 Eco-friendly Polymer Matrix Nanocomposites for Tissue Engineering 355 15.3.2 Polymer Nanocomposites in Drug Delivery 356 15.3.3 Nanocomposite-Based Biosensor on Eco-friendly Polymer 358 15.3.4 Polymer Nanocomposite-Based Microfluidics 359 15.4 Case Study on Carrageenan-Based Nanocomposite 360 15.4.1 Carrageenan-Based Metalic Nanocomposite 360 15.4.2 Advantageous of Metalic Nanocomposite in Pharmaceutical Applications 366 15.5 Summary 366 References 367 16 Biodegradable and Biocompatible Polymers-Based Drug Delivery Systems for Cancer Th erapy 373 Ibrahim M. El-Sherbiny, Nancy M. El-Baz and Amr H. Mohamed 16.1 Introduction 373 16.1.1 Cancer-Targeted Therapy 376 16.2 Selection Considerations of Polymers for Drug Delivery 377 16.2.1 Biodegradability 377 16.2.2 Biocompatibility 379 16.2.3 Surface Modification 379 16.3 Types of Biodegradable Polymers 381 16.3.1 Natural Biodegradable Polymers 381 16.3.1.1 Protein-Based Biodegradable Polymers 381 16.3.1.2 Polysaccharides-Based Biodegradable Polymers 382 16.3.2 Synthetic Biodegradable Polymers 384 16.3.2.1 Polyesters 384 16.4 Preparation Methods of Biodegradable Polymeric Carriers 387 16.4.1 Polymer Dispersion 388 16.4.1.1 Emulsion-Solvent Evaporation Method 388 16.4.1.2 Double Emulsion Method 389 16.4.1.3 Nanoprecipitation 389 16.4.1.4 Salting Out 389 16.4.2 Polymerization 389 16.4.2.1 Emulsion Polymerization 390 16.4.2.2 Microemulsion Polymerization 390 16.4.3 Ionic Gelation 390 16.4.4 Spray Drying 391 16.5 Recent Applications of Biodegradable Polymers-Based Targeted Drug Delivery for Cancer Therapy 391 16.5.1 Passive Cancer-Targeted Delivery 392 16.5.1.1 Stealth Liposomes and Nanoparticles 393 16.5.2 Active Cancer-Targeted Drug Delivery Systems 395 16.5.3 Stimuli-Responsive Polymeric Drug Delivery 396 16.6 Conclusion 400 References 400 Index 407

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Book SynopsisADVANCED FERMENTATION AND CELL TECHNOLOGY A comprehensive and up-to-date reference covering both conventional and novel industrial fermentation technologies and their applications Fermentation and cell culture technologies encompass more than the conventional microbial and enzyme systems used in the agri-food, biochemical, bioenergy and pharmaceutical industries. New technologies such as genetic engineering, systems biology, protein engineering, and mammalian cell and plant cell systems are expanding rapidly, as is the demand for sustainable production of bioingredients, drugs, bioenergy and biomaterials. As the growing biobased economy drives innovation, industrial practitioners, instructors, researchers, and students must keep pace with the development and application of novel fermentation processes and a variety of cell technologies. Advanced Fermentation and Cell Technology provides a balanced and comprehensive overview of the microbial, mammalian, andTable of ContentsVolume 1 Preface ix Overview on Market Size of Bioproducts and Fundamentals of Cell Technology xiii Part I 1 1 Microbial Cell Technology 1 1.1 Basic bacterial growth and mode of fermentation 1 1.2 Basic fungal growth 22 1.3 Classical strain improvements and tools 26 1.3.1 Natural selection and mutation 26 1.3.2 Recombination 30 1.4 Modern strain improvement and tools 32 1.4.1 Genome shuffling 33 1.4.2 Recombinant DNA technology 34 Summary 58 1.4.3 RNA interference (RNAi) and CRISPR/Cas technology for genome editing 59 Summary 72 1.4.4 Molecular thermodynamics and down-stream processes on bioproducts 72 Summary 83 1.4.5 Protein engineering 84 Summary 91 1.4.6 Genomics, proteomics, metagenomics, and bioinformatics 91 Summary 99 1.4.7 Systems/synthetic biology and metabolic engineering 100 Summary 106 1.4.8 Quorum sensing and quenching 106 Summary 110 1.5 Bioengineering and scale-up process 111 1.5.1 Microbial and process engineering factors affecting performance and economics 114 1.5.2 Fermenter and bioreactor systems 114 1.5.3 Mass transfer concept 116 1.5.4 Heat transfer concept 120 1.5.5 Mass and heat transfer practice 123 1.5.6 Scale-up and scale-down of fermentations 137 1.5.7 Scale-up challenges 146 Summary 150 1.6 New bioprocesses of fermentation 150 1.6.1 Growth-arrested bioprocesses 150 1.6.2 Integrated bioprocesses 154 1.6.3 Consolidated bioprocessing (CBP) 158 Summary 160 Bibliography 161 Part II 173 2 Applications of Microbial Fermentation to Food Products, Chemicals and Pharmaceuticals 173 2.1 Fermented dairy products 173 2.1.1 Basic knowledge of manufacture of dairy products 177 2.1.2 Genetic engineering of lactic acid bacteria 186 Summary 197 Bibliography 197 2.2 Fermented meat and fish products 199 2.2.1 Fermented meat products 199 2.2.2 Fermented fish products 204 Summary 207 Bibliography 208 2.3 Fermented vegetable and cereal products 209 2.3.1 Fermented vegetable products 209 2.3.2 Fermented cereal products 214 Summary 219 Bibliography 220 2.4 Organic acids 220 2.4.1 Acetic acid 221 2.4.2 Citric acid 224 2.4.3 Lactic acid 225 2.4.4 Malic acid 227 2.4.5 Fumaric acid 228 Summary 229 Bibliography 230 2.5 Fermentation-derived food and feed ingredients 231 2.5.1 Flavors and amino acids 232 Summary 247 2.5.2 Sweeteners 249 Summary 259 Bibliography 260 2.5.3 Vitamins and pigments 264 Summary 274 Bibliography 274 2.5.4 Microbial polysaccharides and biopolymers 276 Summary 291 Bibliography 293 2.6 Bacteriocins and bacteriophages 296 2.6.1 Bacteriocins 296 2.6.2 Bacteriophage 307 Summary 309 Bibliography 310 2.7 Enzymes 314 Summary 330 Bibliography 331 2.8 Biomass (SCP) and mushrooms 332 2.8.1 Biomass (SCP) 332 2.8.2 Mushrooms 343 Summary 347 Bibliography 347 2.9 Functional foods and nutraceuticals 349 2.9.1 Probiotics and prebiotics 349 2.9.2 Microbiome 364 Summary 373 Bibliography 374 2.10 Alcoholic beverages 385 2.10.1 Beer 386 2.10.2 Wine 393 Summary 400 Bibliography 401 2.11 Other fermentation chemicals 401 2.11.1 Bioethanol 402 Summary 412 Bibliography 412 2.11.2 Biobutanol 414 Summary 424 2.11.3 Biobutanediol 425 Summary 433 Bibliography 434 2.11.4 Biodiesel 438 Summary 444 Bibliography 445 2.11.5 Biomethane 446 Summary 453 Bibliography 454 2.11.6 Biohydrogen 455 Summary 465 Bibliography 465 2.12 Pharmaceuticals, growth promoters, and biopesticides 467 2.12.1 Antibiotics 467 2.12.2 Antibiotic (or antimicrobial) growth promoters (AGPs) 489 Summary 496 Bibliography 498 2.12.3 Antitumor drugs 503 Summary 531 Bibliography 532 2.12.4 Steroids 536 2.12.5 Statins 551 Summary 561 Bibliography 562 2.12.6 Biopesticides 568 Summary 575 Bibliography 575 Volume 2 Preface vii Part III 579 3 Animal Cell Technology 579 3.1 Animal cell culture 579 3.1.1 Introduction 579 3.1.2 Techniques of RNAi and CRISPR 580 3.1.3 Animal cell lines 580 3.1.4 Upstream and downstream bioprocessing 590 3.1.5 Strain development of animal cell cultures 593 3.1.6 Applications of animal cell cultures 595 3.2 Transgenic animal bioreactors 661 3.2.1 Introduction and techniques 661 3.2.2 Applications of transgenic animals 664 Summary 672 Bibliography 673 Part IV 687 4 Plant Cell Technology 687 4.1 Introduction 687 4.2 Plant tissue culture 689 4.3 Applications of plant tissue culture 697 4.3.1 Traditional plant breeding (non-recombinant DNA techniques) 698 4.3.2 General media for plant tissue culture 739 4.3.3 Bioreactor types of plant cell cultures 741 4.3.4 Modern plant breeding or Biotech/GM crops (recombinant DNA techniques) 759 Summary 781 Bibliography 782 Part V 801 5 Safety Issues of New Biotechnologies on Microbial, Animal, and Plant Cells 801 5.1 Introduction 801 5.2 Safety evaluation of novel foods and cell culture products 802 5.2.1 Genetically modified microorganisms and their products 804 5.2.2 Genetically modified animal cell cultures, animals, fishes and their products 807 5.2.3 Genetically modified plants and their products 820 Summary 830 Bibliography 831 Index 835

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Book SynopsisPresenting a wide array of information on chemical ligation one of the more powerful tools for protein and peptide synthesis this book helps readers understand key methodologies and applications that protein therapeutic synthesis, drug discovery, and molecular imaging. Moves from fundamental to applied aspects, so that novice readers can follow the entire book and apply these reactions in the lab Presents a wide array of information on chemical ligation reactions, otherwise scattered across the literature, into one source Features comprehensive and multidisciplinary coverage that goes from basics to advanced topics Helps researchers choose the right chemical ligation technique for their needsTable of ContentsList of Figures xiii List of Plates xxiii List of Contributors xxix Preface xxxiii 1 Introduction to Chemical Ligation Reactions 1Lucia De Rosa, Alessandra Romanelli, and Luca Domenico D’Andrea 1.1 Introduction 1 1.2 Chemical Ligation Chemistries 6 1.3 Imine Ligations 7 1.4 Serine/Threonine Ligation (STL) 21 1.5 Thioether Ligation 24 1.6 Thioester Ligation 25 1.7 ၖKetoacid–Hydroxylamine (KAHA) Ligation 49 1.8 Staudinger Ligation 52 1.9 Azide–Alkyne Cycloaddition 57 1.10 Diels–Alder Ligation 61 References 64 2 Protein Chemical Synthesis by SEA Ligation 89Oleg Melnyk, Claire Simonneau, and Jérôme Vicogne 2.1 Introduction 89 2.2 Essential Chemical Properties of SEA Group 93 2.3 Protein Total Synthesis Using SEA Chemistry – SEAon/off Concept 97 2.4 Chemical Synthesis of HGF/SF Subdomains for Deciphering the Functioning of HGF/SF-MET System 106 2.5 Conclusion 114 References 114 3 Development of Serine/Threonine Ligation and Its Applications 125Tianlu Li and Xuechen Li 3.1 Introduction 125 3.2 Serine/Threonine Ligation (STL) 130 3.3 Application of STL in Protein Synthesis 140 3.4 Conclusion and Outlook 154 References 154 4 Synthesis of Proteins by Native Chemical Ligation–Desulfurization Strategies 161Bhavesh Premdjee and Richard J. Payne 4.1 Introduction 161 4.2 Ligation–Desulfurization and Early Applications 162 4.3 Beyond Native Chemical Ligation at Cysteine – The Development of Thiolated Amino Acids and Their Application in Protein Synthesis 174 4.4 Ligation–Deselenization in the Chemical Synthesis of Proteins 211 4.5 Conclusions and Future Directions 216 References 218 5 Synthesis of Chemokines by Chemical Ligation 223Nydia Panitz and Annette G. Beck–Sickinger 5.1 Introduction – The Chemokine–Chemokine Receptor Multifunctional System 223 5.2 Synthesis of Chemokines by Native Chemical Ligation 224 5.3 Synthesis of Chemokines by Alternative Chemical Ligation 231 5.4 Semisynthesis of Chemokines by Expressed Protein Ligation 233 5.5 Prospects 241 References 243 6 Chemical Synthesis of Glycoproteins by the Thioester Method 251Hironobu Hojo 6.1 Introduction 251 6.2 Ligation Methods and Strategy of Glycoprotein Synthesis 252 6.3 The Synthesis of the Extracellular Ig Domain of Emmprin 254 6.4 Synthesis of Basal Structure of MUC2 256 6.5 N–Alkylcysteine–Assisted Thioesterification Method and Dendrimer Synthesis 257 6.6 Synthesis of TIM–3 260 6.7 Resynthesis of Emmprin Ig Domain 262 6.8 Conclusion 264 References 264 7 Membrane Proteins: Chemical Synthesis and Ligation 269Marc Dittman and Martin Engelhard 7.1 Introduction 269 7.2 Methods for the Synthesis and Purification of Membrane Proteins 270 7.3 Ligation and Refolding 273 7.4 Illustrative Examples 276 References 280 8 Chemoselective Modification of Proteins 285Xi Chen, Stephanie Voss, and Yao-Wen Wu 8.1 Chemical Protein Synthesis 285 8.2 Chemoselective and Bioorthogonal Reactions 287 8.3 Site-Selective Protein Modification Approaches 307 References 322 9 Stable, Versatile Conjugation Chemistries for Modifying Aldehyde-Containing Biomolecules 339Aaron E. Albers, Penelope M. Drake and David Rabuka 9.1 Introduction 339 9.2 Aldehyde as a Bioorthogonal Chemical Handle for Conjugation 339 9.3 Aldehyde Conjugation Chemistries 340 9.4 The Pictet–Spengler Ligation 341 9.5 The Hydrazinyl-Iso-Pictet–Spengler (HIPS) Ligation 341 9.6 The Trapped-Knoevenagel (thioPz) Ligation 343 9.7 Applications – Antibody–Drug Conjugates 346 9.8 Next-Generation HIPS Chemistry – AzaHIPS 348 9.9 Applications – Protein Engineering 349 9.10 Applications – Protein Labeling 349 9.11 Conclusions 351 References 351 10 Thioamide Labeling of Proteins through a Combination of Semisynthetic Methods 355Christopher R. Walters, John J. Ferrie, and E. James Petersson 10.1 Introduction 355 10.2 Thioamide Synthesis 356 10.3 Thioamide Incorporation into Peptides 357 10.4 Synthesis of Full–Sized Proteins Containing Thioamides 360 10.5 Applications 368 10.6 Conclusions 381 Acknowledgments 381 References 382 11 Macrocyclic Organo-Peptide Hybrids by Intein-Mediated Ligation: Synthesis and Applications 391John R. Frost and Rudi Fasan 11.1 Introduction 391 11.2 Macrocyclic Organo-Peptide Hybrids as Natural-Product-Inspired Macrocycles 396 11.3 Application of MOrPHs for Targeting α-Helix-Mediated Protein–Protein Interactions 406 11.4 Conclusions 410 References 410 12 Protein Ligation by HINT Domains 421Hideo Iwaï and A. Sesilja Aranko 12.1 Introduction 421 12.2 Protein Ligation by Protein Splicing 423 12.3 Naturally Occurring and Artificially Split Inteins for Protein Ligation 424 12.4 Conditional Protein Splicing 427 12.5 Inter- and Intramolecular Protein Splicing 429 12.6 Protein Ligation by Other HINT Domains 430 12.7 Bottleneck of Protein Ligation by PTS 432 12.8 Comparison with Other Enzymatic Ligation Methods 432 12.9 Perspective of Protein Ligation by HINT Domains 437 12.10 Conclusions and Future Perspectives 438 Acknowledgment 438 References 438 13 Chemical Ligation for Molecular Imaging 447Aurélien Godinat, Hacer Karatas, Ghyslain Budin, and Elena A. Dubikovskaya 13.1 Introduction 447 13.2 Chemical Ligation 448 13.3 Conclusion 470 References 473 14 Native Chemical Ligation in Structural Biology 485Lucia De Rosa, Alessandra Romanelli, and Luca Domenico D’Andrea 14.1 Introduction 485 14.2 Protein (Semi)synthesis for Molecular Structure Determination 486 14.3 Protein (Semi)Synthesis for Understanding Protein Folding, Stability, and Interactions 494 14.4 Protein (Semi)Synthesis in Enzyme Chemistry 501 References 506 Index 517

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Book SynopsisThe book consists of a brief introduction, a foreward provided by professor Danishefsky of Columbia University, and about 14 - 16 chapters, each written by one or two eminent scholars/authors describing their recent research in the area of either domino reactions or intramolecular rearrangements in carbohydrate chemistry. Three or four chapters will be reviews. The domino (cascade, tandem) reactions are always intramolecular. They are usually very fast, clean and offer highly complex structures in a one pot process. Intramolecular rearrangements offer very similar advantages and often lead to highly complex products as well. Although many recently isolated carbohydrates fulfill various sophisticated functions, their structures are often very complex. The editors cover the broadest scope of novel methodologies possible. All the synthetic and application aspects of domino/cascade reactions are explored in this book. A second theme that will be covered is intramolecular rearrangement, whiTable of ContentsForeword xiii Preface xv Acknowledgments xix List of Contributors xxi Abbreviations xxv 1 Introduction to Asymmetric Domino Reactions 1Hélène Pellissier 1.1 Introduction, 1 1.2 Asymmetric Domino Reactions using Chiral Carbohydrate Derivatives, 3 1.2.1 Stereocontrolled Domino Reactions of Chiral Carbohydrate Derivatives, 3 1.2.2 Enantioselective Domino Reactions Catalyzed by Chiral Carbohydrate Derivatives, 8 1.3 Conclusions, 12 References, 13 2 Organocatalyzed Cascade Reaction in Carbohydrate Chemistry 16Benjamin Voigt and Rainer Mahrwald 2.1 Introduction, 16 2.2 C-Glycosides, 17 2.3 Amine-Catalyzed Knoevenagel-Additions, 20 2.4 Multicomponent Reactions, 32 2.5 Amine-Catalyzed Cascade Reactions of Ketoses with 1,3-Dicarbonyl Compounds, 40 2.6 Conclusions, 44 References, 44 3 Reductive Ring-Opening in Domino Reactions of Carbohydrates 49Raquel G. Soengas, Sara M. Tomé, and Artur M. S. Silva 3.1 Introduction, 49 3.2 Bernet–Vasella Reaction, 50 3.2.1 Domino Reductive Fragmentation/Reductive Amination, 51 3.2.2 Domino Reductive Fragmentation/Barbier-Type Allylation, 52 3.2.3 Domino Reductive Fragmentation/Barbier-Type Propargylation, 57 3.2.4 Domino Reductive Fragmentation/Vinylation, 59 3.2.5 Domino Reductive Fragmentation/Alkylation, 60 3.2.6 Domino Reductive Fragmentation/Olefination, 61 3.2.7 Domino Reductive Fragmentation/Nitromethylation, 62 3.3 Reductive Ring Contraction, 64 3.3.1 Ring Opening/Ketyl-Olefin Annulation, 65 3.3.2 Ring Opening/Intramolecular Carbonyl Alkylation, 69 3.4 Conclusions, 73 References, 73 4 Domino Reactions Toward Carbohydrate Frameworks for Applications Across Biology and Medicine 76Vasco Cachatra and Amélia P. Rauter 4.1 Introduction, 76 4.2 Domino Reactions Toward Butenolides Fused to Six-Membered Ring Sugars and Thio Sugars, 77 4.3 Exploratory Chemistry for Amino Sugars’ Domino Reactions, 80 4.4 Domino Reactions Toward Sugar Ring Contraction, 84 4.4.1 Pyrano–Furano Ring Contraction, 84 4.4.2 Ring Contraction of Furans to Oxetanes, 87 4.5 Macrocyclic Bislactone Synthesis via Domino Reaction, 91 4.6 Sugar Deoxygenation by Domino Reaction, 92 4.7 Conclusions, 94 References, 94 5 Multistep Transformations of BIS-Thioenol Ether-Containing Chiral Building Blocks: New Avenues in Glycochemistry 97Daniele D’Alonzo, Giovanni Palumbo, and Annalisa Guaragna 5.1 Introduction, 97 5.2 (5,6-Dihydro-1,4-dithiin-2-yl)Methanol: Not Simply a Homologating Agent, 98 5.3 Sulfur-Assisted Multistep Processes and Their Use in the De Novo Synthesis of Glycostructures, 101 5.3.1 Three Steps in One Process: Double Approach to 4-Deoxy l-(and d-)-Hexoses, 101 5.3.2 Five Steps in One Process: The Domino Way to l-Hexoses (and Their Derivatives), 102 5.3.3 Up to Six Steps in One Process: 4′-Substituted Nucleoside Synthesis, 105 5.3.4 Eight Steps in One Process: Beyond Achmatowicz Rearrangement, 109 5.4 Concluding Remarks, 111 5.5 Acknowledgments, 111 References, 111 6 Thio-Click and Domino Approach to Carbohydrate Heterocycles 114Zbigniew J. Witczak and Roman Bielski 6.1 Introduction, 114 6.2 Classification and Reaction Mechanism, 114 6.3 Conclusions, 119 References, 120 7 Convertible Isocyanides: Application in Small Molecule Synthesis, Carbohydrate Synthesis, and Drug Discovery 121Soumava Santra, Tonja Andreana, Jean-Paul Bourgault, and Peter R. Andreana 7.1 Introduction, 121 7.2 Convertible Isocyanides, 125 7.2.1 CIC Employed in the Ugi Reaction, 125 7.2.2 Resin-Bound CICs, 167 7.2.3 CIC Employed in the Ugi–Smile Reaction, 172 7.2.4 CIC Employed in the Joulli´e–Ugi Reaction, 172 7.2.5 CIC Employed in the Passerini Reaction, 175 7.2.6 CIC Employed in the Groebke–Blackburn–Bienaym´e Reaction, 178 7.2.7 CIC Employed in the Diels–Alder Reaction, 182 7.2.8 Monosaccharide Isocyanides Employed in the Ugi and Passerini Reaction, 183 7.2.9 Methyl isocyanide in the Preparation of the Hydroxy DKP Thaxtomin A, 186 7.3 Conclusions, 187 References, 187 8 Adding Additional Rings to the Carbohydrate Core: Access via (SPIRO) Annulation Domino Processes 195Daniel B. Werz 8.1 Introduction, 195 8.2 Spiroketals via a Domino Oxidation/Rearrangement Sequence, 196 8.3 Chromans and Isochromans via Domino Carbopalladation/Carbopalladation/Cyclization Sequence, 200 References, 208 9 Introduction to Rearrangement Reactions in Carbohydrate Chemistry 209Zbigniew J. Witczak and Roman Bielski 9.1 Introduction, 209 9.2 Classification, 210 9.3 Chapman Rearrangement, 211 9.4 Hofmann Rearrangement, 211 9.5 Cope Rearrangement, 211 9.6 Ferrier Rearrangement, 212 9.7 Claisen Rearrangement, 213 9.8 Overman Rearrangement, 214 9.9 Baeyer–Villiger Rearrangement, 215 9.10 Ring Contraction, 215 9.11 Conclusions, 216 References, 217 10 Rearrangement of a Carbohydrate Backbone Discovered “En Route” to Higher-Carbon Sugars 219S³awomir Jarosz, Anna Osuch-Kwiatkowska, Agnieszka Gajewska, and Maciej Cieplak 10.1 Introduction, 219 10.2 Rearrangements Without Changing the Sugar Skeleton, 220 10.3 Rearrangements Connected with the Change of Sugar Unit(s), 221 10.4 Rearrangements Changing the Structure of a Sugar Skeleton, 224 10.5 Rearrangement of the Sugar Skeleton Discovered En Route to Higher-Carbon Sugars, 226 10.5.1 Synthesis of Higher-Carbon Sugars by the Wittig-Type Methodology, 226 10.5.2 The Acetylene/Vinyltin Methodology in the Synthesis of HCS, 227 10.5.3 The Allyltin Methodology in the Synthesis of HCS, 227 10.5.4 Rearrangement of the Structure of HCS, 230 10.5.5 Synthesis of Polyhydroxylated Carbocyclic Derivatives with Large Rings, 235 10.6 Conclusions, 237 Acknowledgments, 237 References, 237 11 Novel Levoglucosenone Derivatives 240Roman Bielski and Zbigniew J. Witczak 11.1 Introduction, 240 11.2 Additions to the Double Bond of the Enone System Leading to the Formation of New Rings, 241 11.3 Reductions of the Carbonyl Group Followed by Various Reactions of the Formed Alcohol, 241 11.4 Functionalization of the Carbonyl Group by Forming Carbon-Nitrogen Double Bonds (Oximes, Enamines, Hydrazines), 242 11.5 Additions (But Not Cycloadditions) (Particularly Michael Additions) to the Double Bond of the Enone, 243 11.6 Enzymatic Reactions of Levoglucosenone, 244 11.7 High-Tonnage Products from Levoglucosenone, 244 11.7.1 Overman and Allylic Xanthate Rearrangement, 245 11.8 Conclusions, 246 References, 247 12 The Preparation and Reactions of 3,6-Anhydro-d-Glycals 248Vikram Basava, Emi Hanawa, and Cecilia H. Marzabadi 12.1 Introduction, 248 12.2 Preparation of 3,6-Anhydro-d-Glucal Under Reductive Conditions, 250 12.3 Addition Reactions of 3,6-Anhydro-d-Glucal, 251 12.4 Preparation of 6-O-Tosyl-d-Galactal and Reduction with Lithium Aluminum Hydride, 252 12.5 Conclusions, 254 References, 254 13 Ring Expansion Methodologies of Pyranosides to Septanosides and Structures of Septanosides 256Supriya Dey, N. Vijaya Ganesh, and N. Jayaraman 13.1 Introduction, 256 13.2 Synthesis of Septanosides, 258 13.2.1 Synthesis of Septanosides via Hemiacetal Formation, 258 13.2.2 Knoevenagel Condensation, 260 13.2.3 Baeyer–Villiger Oxidation of Cyclohexanone Derivatives, 260 13.2.4 Electrophile-Induced Cyclization, 260 13.2.5 Metal-Catalyzed Cyclization, 261 13.2.6 Nicolas–Ferrier Rearrangements, 262 13.2.7 Ring Opening of Carbohydrate-Derived Cyclopropanes, 263 13.2.8 Ring Opening of Glycal-Derived 1,2-Cyclopropane, 263 13.2.9 Ring Opening of Oxyglycal Derived 1,2-Cyclopropane, 265 13.2.10 Functionalization of Oxepines, 268 13.3 Structure and Conformation of Septanosides, 269 13.3.1 Solid-State Structures and Conformations, 270 13.3.2 Solution-Phase Conformations, 273 13.4 Conclusions, 275 Acknowledgments, 276 References, 276 14 Rearrangements in Carbohydrate Templates to theWay to Peptide-Scaffold Hybrids and Functionalized Heterocycles 279Bernardo Herrad´on, Irene de Miguel, and Enrique Mann 14.1 Introduction, 279 14.2 Synthesis of the Chiral Building Blocks: Applications of the Claisen–Johnson and Overman Rearrangements, 280 14.3 Peptide–Scaffold Hybrids, 282 14.4 Sequential Reactions for the Synthesis of Polyannular Heterocycles, 284 14.5 The First Total Synthesis of Amphorogynine C, 284 Acknowledgments, 293 References, 293 15 Palladium- and Nickel-Catalyzed Stereoselective Synthesis of Glycosyl Trichloroacetamides and Their Conversion to 𝛂- and 𝛃-Urea Glycosides 297Nathaniel H. Park, Eric T. Sletten, Matthew J. McKay, and Hien M. Nguyen 15.1 Introduction, 297 15.2 Development of the Palladium(II)-Catalyzed Glycal Trichloroacetimidate Rearrangement, 300 15.3 Stereoselective Synthesis of Glycosyl Ureas from Glycal Trichloroacetimidates, 307 15.4 Development of the Stereoselective Nickel-Catalyzed Transformation of Glycosyl Trichloroacetimidates to Trichloroacetamides, 310 15.5 Transformation of Glycosyl Trichloroacetimidates into α- and β-Urea Glycosides, 317 15.6 Mechanistic Studies on the Nickel-Catalyzed Transformation of Glycosyl Trichloracetimidates, 317 15.7 Conclusions, 323 References, 323 Index 325

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