Quantum and theoretical chemistry Books

Book SynopsisReflecting the growing volume of published work in this field, researchers will find this book an invaluable source of information on current methods and applications.Table of ContentsChapter 1: Computer-Aided Drug Design 2003-2005; Chapter 2: Modelling Biological Systems; Chapter 3: Polarizabilities, Hyperpolarizabilities and Analogous Magnetic Properties; Chapter 4: Applications of Density Functional Theory to Heterogeneous Catalysis; Chapter 5: Numerical Methods in Chemistry; Chapter 6: Determination of Structure in Electronic Structure Calculations; Chapter 7: Simulation of Liquids; Chapter 8: Combinatorial Enumeration in Chemistry; Chapter 9: Many-Body Perturbation Theory and its Application to the Molecular Structure Problem

Read more less

Book SynopsisReflecting the growing volume of published work in this field, researchers will find this book an invaluable source of information on current methods and applications.Table of ContentsFront matter; Preface; Contents; Electric multipoles, polarizabilities and hyperpolarizabilities; Atomic structure computations; Atoms in molecules; Modelling biological systems; Relativistic pseudopotential calculations, 1993ûJune 1999; Density-functional theory; Many-body perturbation theory and its application to the molecular electronic structure problem; New development on the quantum theory of large molecules and polymers;

Read more less

Book SynopsisReflecting the growing volume of published work in this field, researchers will find this book an invaluable source of information on current methods and applications.Table of ContentsFront matter; Preface; Contents; Simulation of the liquid state; Enumeration in chemistry; Density functional theory; Numerical methods for the solution of 1D, 2D and 3D differential equations arising in chemical problems; Computer-aided drug design 2000-2001; Electric multipoles, polarizabilities, hyperpolarizabilities and analogous magnetic properties; Many-body perturbation theory and its application to the molecular electronic structure problem; Quantum topological atoms

Read more less

Book SynopsisReflecting the growing volume of published work in this field, researchers will find this book an invaluable source of information on current methods and applications.Trade Review"... a first class account ..." * Aslib Book Guide, Vol 66, No 5, May 2001 *"... a timely and detailed overview of the recent literature ..." * Journal of the American Chemical Society, Vol 123, No 39, 2001, p 9725-9726 *"... the 12 reporters have done a good job of providing an informative and useful guide to recent literature, as well as an overview of the relevant theory." * Chemistry and Industry, No 24, 17 December 2001, p 806 *Table of ContentsCalculations of the Vibration-Rotation Spectra of Small Molecules; Computer-aided Drug Design 2001-2003; Density Functional Theory; Combinatorial Enumeration in Chemistry; Photo-reduction and -oxidation; Simulation of the Liquid State; Numerical Methods in Chemistry; Many-body Perturbation Theory and Its Application to the Molecular Structure Problem

Read more less

Book SynopsisMolecular self-assembly is a widespread phenomenon in both chemistry and biochemistry. Yet it was not until the rise of supramolecular chemistry that attention has increasingly been given to the designed self-assembly of a variety of synthetic molecules and ions. To a large extent, success in this area has reflected knowledge gained from nature. However, an increased awareness of the latent steric and electronic information implanted in individual molecular components has also contributed to this success. Whilst not yet approaching the sophistication of biological assemblies, synthetic systems of increasing subtlety and considerable aesthetic appeal have been created. Self-Assembly in Supramolecular Systems surveys highlights of the progress made in the creation of discrete synthetic assemblies and provides a foundation for new workers in the area, as well as background reading for experienced supramolecular chemists.Trade Review"... useful and interesting reading to research workers in the field and to post-graduate and other advanced students." * Aslib Book Guide, Vol 66, No 5, May 2001 *"... a welcome addition. ... clearly written, well-documented ..." * Chemistry in Britain, June 2001, p 61 *"... a valuable introduction to the field for students and new investigators as well as a concise resource for practitioners of self-assembly." * Journal of Natural Products, 2001, Vol 64, p 691 *"... an excellent introduction to this field ... should certainly appeal to the novice at an advanced level and may even serve as a basis for an introductory course on self-processes." * Journal of the American Chemical Society, Vol 123, No 35, 2001, p 8647 *"... clearly written, well-documented and relatively easy to read given the great complexity of most of the species it discusses." * Chemistry in Britain, June 2001, p 61 *Table of ContentsSelf-assembly: What Does it Mean?; Intermolecular Interactions: The Glue of Supramolecular Chemistry; Hydrogen-bonded and π-Stacked Systems; Rotaxanes; Catenanes; Metal-directed Synthesis - Rotaxanes, Catenanes, Helicates and Knots; Further Metal-containing Systems; Subject Index.

Read more less

Book SynopsisChemometrics in Analytical Spectroscopy provides students and practising analysts with a tutorial guide to the use and application of the more commonly encountered techniques used in processing and interpreting analytical spectroscopic data. In detail the book covers the basic elements of univariate and multivariate data analysis, the acquisition of digital data and signal enhancement by filtering and smoothing, feature selection and extraction, pattern recognition, exploratory data analysis by clustering, and common algorithms in use for multivariate calibration techniques. An appendix is included which serves as an introduction or refresher in matrix algebra. The extensive use of worked examples throughout gives Chemometrics in Analytical Spectroscopy special relevance in teaching and introducing chemometrics to undergraduates and post-graduates undertaking analytical science courses. It assumes only a very moderate level of mathematics, making the material far more accessible than oTrade Review"a worthwhile addition to the bookshelf of any chemist"."Dr Adams has succeeded in providing a text which is focused on analytical spectroscopy and that gently guides the reader through the concepts with out recourse to too much matrix algebra.""...A very good introductory text for those wishing to understand the workings of chemometrics techniques."Table of ContentsDescriptive Statistics: The Acquisition and Enhancement of Data: Feature Selection and Extraction: Pattern Recognition I - Unsupervised Analysis: Pattern Recognition II - Supervised Learning: Calibration and Regression Analysis: Matrix Tools and Operations: Subject Index.

Read more less

Book SynopsisMolecular Physical Chemistry: A Concise Introduction focuses on two main aspects of physical chemistry: thermodynamics and reaction dynamics. By looking at the properties of the atoms and molecules that constitute matter, it makes use of results from modern experiments conducted on small numbers of molecules. These molecular properties allow the behaviour of larger groups of molecules to be predicted. This is in contrast to conventional approaches which are based upon how the subjects have developed historically. It attempts to show how some basic concepts can be easily applied to give verifiable results in simple systems before extending them to more complicated scenarios. The text is intended as an aid to understanding these central topics of physical chemistry, rather than an introduction to them, and some familiarity with them is assumed throughout. Worked examples and problems are given at the end of each chapter. Molecular Physical Chemistry: A Concise Introduction will be welcomTrade ReviewI can see this book forming the basis of a "eureka" moment for an undergraduate, where all suddenly falls into place, a light bulb suddenly appears above the reader's head, and the topic goes from being a chore to a pleasure.It will form the basis for a number of lecture courses within a few years. * Chemistry and Industry, Issue 10, 16 May 2005 (Pete Biggs) *Will be of greatest value to undergraduates in their second and subsequent years of study. We need books like this that emphasise understanding. * Education in Chemistry, January 2006 (Mike Pilling) *Table of ContentsSome basic ideas and examples; Partition functions; Thermodynamics; Applications; Reactions; Answers to problems; Some useful constants and relations; Subject index.

Read more less

Book SynopsisWhy do molecules adopt particular shapes? What determines the physical and chemical properties of a material? Molecular Modelling and Bonding answers these questions by introducing the ideas behind molecular and quantum mechanics, using a largely non-mathematical approach. Atomic and molecular orbitals, computational chemistry and bonding in solids are also discussed. A Case Study, Molecular Modelling in Drug Design, explores ways in which computer modelling, in conjunction with experimental techniques, is used to design new drugs. The accompanying CD-ROM illustrates applications of molecular and quantum mechanics, and includes many of the structures and orbitals illustrated in the text. It provides the programs necessary to view orbitals and 3D structures. The Molecular World series provides an integrated introduction to all branches of chemistry for both students wishing to specialise and those wishing to gain a broad understanding of chemistry and its relevance to the everyday worldTrade Review"... well presented, readable and, most importantly, offers an accessible, non-mathematical overview of this increasingly important branch of modern chemistry ... high quality images and an extremely effective supporting CD-ROM ... the quality of the presentation and the depth of the material covered suggest that it will be useful to chemistry students both at the start of their degrees and beyond the second year of most degree programmes." * Education in Chemistry, November 2003 *Table of ContentsIntroduction; Molecular Mechanics; Quantum Chemistry of Atoms; Molecular Orbitals; Polyatomic Molecules; Symmetry and Molecular Orbital Calculations; Calculations in Practice; Bonding in Solids; Case Study: Molecular Modelling in Rational Drug Design.

Read more less

Book SynopsisConnects fundamental knowledge of multivalent interactions with current practice and state-of-the-art applications Multivalency is a widespread phenomenon, with applications spanning supramolecular chemistry, materials chemistry, pharmaceutical chemistry and biochemistry. This advanced textbook provides students and junior scientists with an excellent introduction to the fundamentals of multivalent interactions, whilst expanding the knowledge of experienced researchers in the field. Multivalency: Concepts, Research & Applications is divided into three parts. Part one provides background knowledge on various aspects of multivalency and cooperativity and presents practical methods for their study. Fundamental aspects such as thermodynamics, kinetics and the principle of effective molarity are described, and characterisation methods, experimental methodologies and data treatment methods are also discussed. Parts two and three provide an overview of current sTable of ContentsList of Contributors xi Foreword xv Preface xvii Part I General Introduction to Multivalent Interactions 1 1 Additivity of Energy Contributions in Multivalent Complexes 3Hans-Jorg Schneider 1.1 Introduction 3 1.2 Additivity of Single Interactions – Examples 3 1.3 Limitations of Additivity 7 1.3.1 Free Energy Values ΔG Instead of Enthalpic and Entropic Values ΔH, TΔS 7 1.3.2 Mismatch as Limitation of Additivity 9 1.3.3 Medium Effects as Limiting Factor 12 1.3.4 Strain and Induced Fit 12 1.4 Cooperativity 13 1.5 Allostery 14 1.6 Conclusions 17 References 18 2 Models and Methods in Multivalent Systems 23Jurriaan Huskens 2.1 Introduction 23 2.1.1 General Introduction 23 2.1.2 Multivalent versus Cooperative Interactions 24 2.2 Numerical Data Analysis 25 2.2.1 Model Simulations Using a Spreadsheet Approach 26 2.2.2 Setting Up and Assessing Titrations 30 2.2.3 Using Spreadsheet Simulations to Fit Experimental Data to a Model 36 2.3 Models for Multivalent Systems 41 2.3.1 The Simplest Multivalent System: A 1:1 Complex with Two Interaction Sites 41 2.3.2 Multivalent Binding at Surfaces 46 2.4 Special Multivalent Systems 53 2.4.1 Increasing the Valency of Interfacial Assemblies: Dendrimers, Oligomers, and Polymers 53 2.4.2 Heterotropic Interactions 58 2.4.3 Kinetics and Dynamics 63 2.5 Conclusions 68 Acknowledgments 68 References 68 3 Design Principles for Super Selectivity using Multivalent Interactions 75Tine Curk, Jure Dobnikar, and Daan Frenkel 3.1 Introduction 75 3.1.1 Background: Ultra-sensitive Response 75 3.2 Super Selectivity: An Emergent Property of Multivalency 78 3.3 Multivalent Polymer Adsorption 84 3.4 Which Systems are Super Selective? 86 3.4.1 Rigid Geometry Interactions 86 3.4.2 Disordered Multivalency 87 3.5 Design Principles for Super-Selective Targeting 90 3.6 Summary: It is interesting, but is it useful? 93 Appendix 3.A: What Is Effective Molarity? 95 Acknowledgements 98 References 98 4 Multivalency in Biosystems 103Jens Dernedde 4.1 Introduction 103 4.2 Cell–Cell Adhesion 104 4.2.1 Homotypic Interactions, Cadherins Keep Cells Together 105 4.2.2 Selectins, Heterotypic Cell Adhesion to Fight Infections 106 4.2.3 Bacterial Adhesion by FimH 108 4.3 Phase Transition, Multivalent Intracellular Assemblies 109 4.4 Multivalency in the Fluid Phase, Pathogen Opsonization 111 4.5 Conclusion 113 Acknowledgment 113 References 114 Part II Multivalent Systems in Chemistry 121 5 Multivalency in Cyclodextrin/Polymer Systems 123Akihito Hashidzume and Akira Harada 5.1 Introduction 123 5.2 General Perspectives of Multivalency in Cyclodextrin/Polymer Systems 125 5.3 Typical Examples of Multivalency in Cyclodextrin/Polymer Systems 126 5.3.1 Formation of Polymer Aggregates from Cyclodextrin-Polymers and Guest-Polymers 126 5.3.2 Selectivity of Interaction Enhanced by Multivalency 127 5.3.3 Self-Healable Hydrogels Based on Multivalency 134 5.4 Summary and Outlook 136 Acknowledgments 136 References 138 6 Cucurbit[n-uril-Mediated Multiple Interactions 143Zehuan Huang and Xi Zhang 6.1 Introduction to Cucurbit[n-uril Chemistry 143 6.2 Heteroternary Complexes 143 6.3 Homoternary Complexes 146 6.4 Conclusions 150 References 150 7 Multivalency as a Design Criterion in Catalyst Development 153Paolo Scrimin, Maria A. Cardona, Carlos M. Leon Prieto, and Leonard J. Prins 7.1 Introduction 153 7.2 Formation of Enzyme-Like Catalytic Pockets 154 7.3 Cooperativity Between Functional Groups 157 7.4 Mechanistic Effects 161 7.5 The Dendritic Effect in Multivalent Nanozymes 164 7.5.1 Peptide-Based Dendrimers for the Cleavage of Phosphodiesters 166 7.5.2 Catalytic 3D SAMs on Au NPs 168 7.6 Multivalent Catalysts and Multivalent Substrates 170 7.7 Conclusions 172 Acknowledgements 174 References 174 8 Multivalent Molecular Recognition on the Surface of Bilayer Vesicles 177Jens Voskuhl, Ulrike Kauscher, and Bart Jan Ravoo 8.1 Introduction 177 8.2 Molecular Recognition of Vesicles 179 8.2.1 Metal Coordination 180 8.2.2 Light Responsive Interactions 184 8.2.3 Hydrogen Bonding and Electrostatic Interactions 185 8.3 Biomimetic Vesicles 188 8.3.1 Vesicles as Multivalent Platforms 188 8.3.2 Membrane Fusion 193 8.4 Vesicle-based Supramolecular Materials 196 8.4.1 Hydrogels 196 8.4.2 Immobilization of Vesicles 198 8.4.3 Nanoparticles and Nanocontainers 198 8.5 Conclusion 201 Acknowledgment 201 References 201 Part III Multivalent Systems in Biology 205 9 Blocking Pathogens by Multivalent Inhibitors 207Sumati Bhatia, Benjamin Ziem, and Rainer Haag 9.1 Introduction 207 9.2 Design of Multivalent Ligand Architectures 209 9.3 Multivalent Carbohydrate Ligands 212 9.4 Scaffold Architecture 215 9.4.1 Linear and Dendritic Scaffolds 215 9.4.2 Multivalent Gold Nanoparticles 218 9.4.3 2D Platforms 220 9.5 Nano-and Microgels for Pathogen Inhibition 222 9.6 Conclusion 223 Acknowledgments 224 References 224 10 Multivalent Protein Recognition Using Synthetic Receptors 229Akash Gupta, Moumita Ray, and Vincent M. Rotello 10.1 Introduction 229 10.2 Structural Properties of Protein Surfaces 229 10.2.1 Protein–Protein Interfacial Areas 229 10.2.2 Chemical Nature of the Protein–Protein Interface 230 10.2.3 “Hot Spots” 230 10.2.4 O-Ring Structure 232 10.3 Synthetic Receptors for Protein Surface Recognition 232 10.3.1 Porphyrin Scaffolds for Protein Surface Recognition 232 10.3.2 Protein Surface Recognition Using Molecular Tweezers 238 10.3.3 Calixarene Scaffolds for Protein Surface Recognition 240 10.3.4 Recognition of Protein Surfaces Using Nanoparticles 243 10.3.4.1 Nanoparticles as Protein Mimics 244 10.3.4.2 Regulating the Structure and Function of Proteins Using Nanoparticles 246 10.3.4.3 Nanoparticle-based Protein Sensors 250 10.4 Future Perspective and Challenges 254 Acknowledgment 257 References 257 11 Multivalent Calixarenes for the Targeting of Biomacromolecules 263Francesco Sansone and Alessandro Casnati 11.1 Introduction 263 11.2 Binding to Proteins and Enzymes 266 11.3 Recognition of Carbohydrate Binding Proteins (Lectins) 273 11.4 Binding Polyphosphates, Oligonucleotides and Nucleic Acids 279 11.5 Conclusions 284 Acknowledgements 285 References 285 12 Cucurbit[n]uril Assemblies for Biomolecular Applications 291Emanuela Cavatorta, Luc Brunsveld, Jurriaan Huskens, and Pascal Jonkheijm 12.1 Introduction 291 12.2 Molecular Recognition Properties of CB[n- 293 12.2.1 Interactions with the Carbonyl Portals of CB[n- 293 12.2.2 Release of High Energy Water Molecules from the CB[n- Cavity 295 12.2.3 Enthalpy-driven Hydrophobic Effect for CB[n- 295 12.2.4 Enthalpy-driven Hydrophobic Effect for CB[8- Heteroternary Complexes 297 12.3 Control Over the Binding Affinity with CB[n- 299 12.4 CB[n] Recognition of Amino Acids, Peptides, and Proteins 301 12.5 CB[n] for Bioanalytical and Biomedical Applications 305 12.5.1 CB[n]-mediated Assembly of Bioactive Polymers and Hydrogels 305 12.5.2 CB[n]-mediated Assembly of Bioactive Nanoparticles 307 12.5.3 CB[n]-mediated Assembly on Bioactive Surfaces 313 12.6 Conclusions and Outlook 317 Acknowledgment 319 References 319 13 Multivalent Lectin–Glycan Interactions in the Immune System 325Joao T. Monteiro and Bernd Lepenies 13.1 Introduction 325 13.2 Targeting Innate Immunity to Shape Adaptive Immunity 327 13.3 C-type Lectin Receptors 328 13.3.1 Multivalent Glycoconjugates Targeting DC-SIGN 331 13.3.2 Multivalent Glycoconjugates Targeting Other CLRs 331 13.4 Galectins 332 13.5 Siglecs 334 13.6 Conclusions 335 Acknowledgment 335 References 335 14 Blocking Disease Linked Lectins with Multivalent Carbohydrates 345Marjon Stel and Roland J. Pieters 14.1 Introduction 345 14.2 Haemagglutinin 347 14.3 LecA 349 14.4 LecB 354 14.5 Galectins 358 14.6 Concanavalin A 362 14.7 Cholera Toxin 366 14.8 Propeller Lectins 367 14.9 Conclusion 371 Acknowledgements 371 References 371 Index 381

Read more less

Book SynopsisSurface tension provides a thermodynamic avenue for analyzing systems in equilibrium and formulating phenomenological explanations for the behavior of constituent molecules in the surface region. While there are extensive experimental observations and established ideas regarding desorption of ions from the surfaces of aqueous salt solutions, a more successful discussion of the theory has recently emerged, which allows the quantitative calculation of the distribution of ions in the surface region. Surface Tension and Related Thermodynamic Quantities of Aqueous Electrolyte Solutions provides a detailed and systematic analysis of the properties of ions at the air/water interface.Unifying older and newer theories and measurements, this book emphasizes the contributions of simple ions to surface tension behavior, and the practical consequences. It begins with a general discussion on Gibbs surface thermodynamics, offering a guide to his theoretical insight and formulation oTable of ContentsIntroduction to Thermodynamic Consideration of Fluid/Fluid. Basic Thermodynamic Relations for the Analysis of Fluid/Fluid Interface. Surface Tension of Pure Water at Air/Water and Oil/Water Interfaces. Surface Tension of Solutions. Surface Tension of Simple Salt Solutions. Adsorption of Ions at Air/Water Interface. Surface Tension of Solutions and Temperature. Adsorption from Mixed Electrolyte Solutions. Aqueous Solutions of Zwitterionic Amino Acids. Appendix. Index.

Read more less

Book Synopsis

Read more less

Book SynopsisNational forests are required to take significant steps to incorporate climate change in management and planning, including the development of options that facilitate adaptation of natural resources to potentially deleterious effects of an altered climate. Despite uncertainties about the timing and magnitude of climate change effects, sufficient information exists to begin the adaptation process, a form of risk management. This book provides a guidebook for developing adaptation options in responding to climate change in national forests and discusses a climate project tool as an aid for climate change adaptation.

Read more less

Book SynopsisLondon dispersion interactions are responsible for numerous phenomena in physics, chemistry and biology. Recent years have seen the development of new, physically well-founded models, and dispersion-corrected density functional theory (DFT) is now a hot topic of research. This book is an overview of current understanding of the physical origin and modelling of London dispersion forces manifested at an atomic level. It covers a wide range of system, from small intermolecular complexes, to organic molecules and crystalline solids, through to biological macromolecules and nanostructures. In presenting a broad overview of the of the physical foundations of dispersion forces, the book provides theoretical, physical and synthetic chemists, as well as solid-state physicists, with a systematic understanding of the origins and consequences of these ubiquitous interactions. The presentation is designed to be accessible to anyone with intermediate undergraduate mathematics, physics and chemistry.Table of ContentsIntroduction; Basic Concepts from Toy Models; Macroscopic Lifshitz Approach; Supermolecular Wavefunction Methods; Intermolecular Perturbation Theory; Adiabatic Connection, Fluctuation–Dissipation Approach: RPA and Related Correlation Energy Methods; Dispersion Energy From Groundstate Electron “Densities” ρ( r⃗), ∇ρ( r⃗), τ( r⃗), etc.: Explicit Functionals; Dispersion Energies via Division Into Atoms or Larger Units; Some Chemical Effects of Dispersion Interactions; Periodic Solids; Low-dimensional Systems: Nanolayers, Nanotubes, Nanowires, etc.; Interaction of Molecules with Surfaces and Layers; Summary of Recommended Methods; Many-electron Quantum Mechanics; Linear Response and the Fluctuation–Dissipation Theorem; Basics of Groundstate Density Functional Theory; Some Useful Mathematics; Partitioning Into Atoms; Polarisation Approximation: Higher-order and Many-body Contributions

Read more less

Book SynopsisChemical Modelling covers a wide range of disciplines and this Specialist Periodical Report is the first stop for any materials scientist, biochemist, chemist or molecular physicist wishing to acquaint themselves with major developments and current opinion in the applications and theory of chemical modelling. The topics covered are wide ranging with authors writing on clusters to modelling nanotubes and dynamics. Containing both comprehensive and critical reviews, this volume is an essential resource and convenient reference for any research group active in the field or chemical sciences library.Table of ContentsPreface; Toward accurate coarse-graining approaches for protein and membrane simulations; Chemical bonding in solids: recovering chemical concepts in the realm of infinite periodic structures; Vibrational quantum dynamics at metallic surfaces; Theoretical studues of supercapcitors; Nanotubes with well-defined structure: imogolites; Application of DFT modeling in Fischer-Tropsch synthesis over Co-based catalysts; Structure prediction and its applications in computational materials design; Ab initio global optimization of clusters; Nitrogen- and phosphine-binding ligands in interaction with gold atoms, clusters, nanoparticles and surfaces

Read more less

Book SynopsisCovering computational tools in drug design using techniques from chemoinformatics, molecular modelling and computational chemistry, this book explores these methodologies and applications of in silico medicinal chemistry. The first part of the book covers molecular representation methods in computing in terms of chemical structure, together with guides on common structure file formats. The second part examines commonly used classes of molecular descriptors. The third part provides a guide to statistical learning methods using chemical structure data, covering topics such as similarity searching, clustering and diversity selection, virtual library design, ligand docking and de novo design. The final part of the book summarises the application of methods to the different stages of drug discovery, from target ID, through hit finding and hit-to-lead, to lead optimisation. This book is a practical introduction to the subject for researchers new to the fields of chemoinformatics, molecular modelling and computational chemistry.Table of ContentsIntroduction; Chemistry and Graph Theory; Structure Representation; Molecular Similarity; Molecular Property Descriptors; Topological Descriptors; Topographical Descriptors; Statistical Learning; Similarity Searching; Bioisosteres and Scaffolds; Clustering and Diversity; Quantitative Structure–Activity Relationships; Protein–Ligand Docking; De Novo Molecular Design; Applications in Medicinal Chemistry; Summary and Outlook.

Read more less

Book SynopsisThe simulation of enzymatic processes is a well-established field within computational chemistry, as demonstrated by the 2013 Nobel Prize in Chemistry. It has been attracting increasing attention in recent years due to the potential applications in the development of new drugs or new environmental-friendly catalysts. Featuring contributions from renowned authors, including Nobel Laureate Arieh Warshel, this book explores the theories, methodologies and applications in simulations of enzyme reactions. It is the first book offering a comprehensive perspective of the field by examining several different methodological approaches and discussing their applicability and limitations. The book provides the basic knowledge for postgraduate students and researchers in chemistry, biochemistry and biophysics, who want a deeper understanding of complex biological process at the molecular level.Table of ContentsPerspective on Computer Modelling of Enzymatic Reactions; Fundamentals of Enzymatic Catalysis: Determination of Rate Constants; A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applications; Electron Transfer Reactions in Enzymes: Seven Things that Might Break Down in Vanilla Marcus Theory and How to Fix Them if They Do; Kinetic Isotope Effects; Free Energy Calculation Methods and Rare Event Sampling Techniques for Biomolecular Simulations; Methods to Trace Conformational Transitions; Key Concepts and Applications of ONIOM Methods; First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics; Nuclear Quantum Effects in Enzymatic Reactions; QM/MM Methods for Simulating Enzyme Reactions; Ribozymes; Effects of Water and Non-aqueous Solvents on Enzyme Activity; Modelling Reactivity in Metalloproteins: Hydrogen Peroxide Decomposition by Haem Enzymes; Enzyme Design

Read more less

Book SynopsisRecent years have seen tremendous progress in research on cold and controlled molecular collisions, both in theory and in experiment. The advent of techniques to prepare cold and ultracold molecules and ions, to store them in optical lattices or in charged quasicristalline structures, and to use them in crossed or merged beam experiments have opened many new possibilities to study the most fundamental aspects of molecular interactions. At the same time, theoretical work has made progress in tackling these problems and accurately describing quantum effects in complex systems, and in proposing viable options to control chemical reactions at ultralow energies. Through tutorials on both the theoretical and experimental aspects of research in cold and ultracold molecular collisions, this book provides advanced undergraduate students, graduate students and researchers with the foundations needed to understand this exciting field.Table of ContentsLow temperature chemistry in uniform supersonic flows; Cold molecular collisions: quantum scattering calculations and their relevance in astrophysical applications; Low energy scattering in crossed molecular beams; Long-range interactions between ultracold atoms and molecules; Interactions of Atoms and Molecules in Cold Chemistry; Effects of External Magnetic Fields on Cold Molecular Collisions; Role of resonances at ultracold temperatures; Experiments with Large Superfluid Helium Nanodroplets; Molecular impurities interacting with a many-particle environment: from ultracold gases to helium nanodroplets; Cold ion chemistry; Controlling a quantum gas of polar molecules in an optical lattice; Ultracold collisions of molecules; Coherent Control of Cold Collisions

Read more less

Book SynopsisThe rapid development of efficient computational tools has allowed researchers to tackle biological problems and to predict, analyse and monitor, at an atomic level, molecular recognition processes. This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research. Chapters from internationally renowned leaders in the field introduce concepts and discuss the impact of technological advances in computer hardware and software in explaining and predicting phenomena involving biomolecules, from small molecules to macromolecular systems. Important topics from the understanding of biomolecules to the modification of their functions are addressed, as well as examples of the application of tools in drug discovery, glycobiology, protein design and molecular recognition. Not only are the cutting-the-edge methods addressed, but also their limitations and possible future development. For anyone wishing to learn how computational chemistry and molecular modelling can provide information not easily accessible through other experimental methods, this book will be a valuable resource. It will be of interest to postgraduates and researchers in the biological and chemical sciences, medicinal and pharmaceutical chemistry, and theoretical chemistry.Table of ContentsComputational Chemistry and Molecular Modelling Basics; Molecular Dynamics Computer Simulations of Biological Systems; Designing Chemical Tools with Computational Chemistry; Computational Design of Protein Function; Computational Enzymology: Modelling Biological Catalysts; Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions; Molecular Modelling of Nucleic Acids; Uncovering GPCR and G Protein Function by Protein Structure Network Analysis; Current Challenges in the Computational Modelling of Molecular Recognition Processes; Novel Insights into Membrane Transport from Computational Methodologies; Application of Molecular Modelling to Speed-up the Lead Discovery Process; Molecular Modelling and Simulations Applied to Challenging Drug Discovery Targets; The Polypharmacology Gap Between Chemical Biology and Drug Discovery

Read more less

Book SynopsisOver the past few decades, experimental excited state chemistry has moved into the femtochemistry era, where time resolution is short enough to resolve nuclear dynamics. Recently, the time resolution has moved into the attosecond domain, where electronic motion can be resolved as well. Theoretical chemistry is becoming an essential partner in such experimental investigations; not only for the interpretation of the results, but also to suggest new experiments. This book provides an integrated approach. The three main facets of excited-state theoretical chemistry; namely, mechanism, which focuses on the shape of the potential surface along the reaction path, multi-state electronic structure methods, and non-adiabatic dynamics, have been brought together into one volume. Theoretical Chemistry for Electronic Excited States is aimed at both theorists and experimentalists, involved in theoretical chemistry, in electronic structure computations and in molecular dynamics. The book will provide both with the knowledge and understanding to discover ways to work together more closely through its unified approach.Table of ContentsIntroduction and Motivation; Conceptual Development Centred on the Shapes and Topological Features of Potential Surfaces; Electronic Structure Methods for the Computation of Electronic States; The Dynamics of Nuclear Motion; Applications and Case Studies in Nonadiabatic Chemistry; Conclusion and Future Developments

Read more less

Book SynopsisAttosecond science is a new and rapidly developing research area in which molecular dynamics are studied at the timescale of a few attoseconds. Within the past decade, attosecond pump–probe spectroscopy has emerged as a powerful experimental technique that permits electron dynamics to be followed on their natural timescales. With the development of this technology, physical chemists have been able to observe and control molecular dynamics on attosecond timescales. From these observations it has been suggested that attosecond to few-femtosecond timescale charge migration may induce what has been called “post-Born-Oppenheimer dynamics”, where the nuclei respond to rapidly time-dependent force fields resulting from transient localization of the electrons. These real-time observations have spurred exciting new advances in the theoretical work to both explain and predict these novel dynamics. This book presents an overview of current theoretical work relevant to attosecond science written by theoreticians who are presently at the forefront of its development. It is a valuable reference work for anyone working in the field of attosecond science as well as those studying the subject.Table of ContentsIntroduction; Low-dimensional Models for Simulating Attosecond Processes in Atoms and Molecules; First-principles Many-electron Dynamics Using the B-spline Algebraic Diagrammatic Construction Approach; Ultrafast Electron Dynamics as a Route to Explore Chemical Processes; Time-dependent Multiconfigurational Theories of Electronic and Nuclear Dynamics of Molecules in Intense Laser Fields; Light-induced Conical Intersections; Theoretical Methods for Attosecond Coupled Electron-nuclear Dynamics In Molecular Photoionization; How Nuclear Motion Affects Coherent Electron Dynamics in Molecules; Attophotochemistry: Coherent Electronic Dynamics and Nuclear Motion; General Trajectory Surface Hopping Method for Ultrafast Nonadiabatic Dynamics; Time-dependent Restricted-active-space Self-consistent-field Theory for Electron Dynamics on the Attosecond Timescale; Real-time and Real-space Time-dependent Density-functional Theory Approach to Attosecond Dynamics; Elements of Structure Retrieval in Ultrafast Electron and Laser-induced Electron Diffraction from Aligned Polyatomic Molecules

Read more less

Book SynopsisSelf-propelled objects (particles, droplets) are autonomous agents that can convert energy from the environment into motion. These motions include nonlinear behaviour such as oscillations, synchronization, bifurcation, and pattern formation. In recent years, there has been much interest in self-propelled objects for their potential role in mass transport or their use as carriers in confined spaces. An improved understanding of self-organized motion has even allowed researchers to design objects for specific motion. This book gives an overview of the principles of self-propelled motion in chemical objects (particles, droplets) far from their thermodynamic equilibrium, at various spatial scales. Theoretical aspects, the characteristics of the motion and the design procedures of such systems are discussed from the viewpoint of nonlinear dynamics and examples of applications for these nonlinear systems are provided. This book is suitable for researchers and graduate students interested in physical and theoretical chemistry as well as soft matter.Table of ContentsTheoretical and Experimental Design of Self-propelled Objects Based on Nonlinearity;Mathematical Model and Analyses on Spontaneous Motion of Camphor Particle; Coupled Convective Instabilities: Autonomous Motion and Deformation of an Oil Drop on a Liquid Surface; Dynamical Deformation of Interfaces Induced by Aggregate Formation; Synthetic Approaches to Control Self-propelled Motion of Micrometre-sized Oil Droplets in Aqueous Solution; Physical Chemistry of Energy Conversion in Self-propelled Droplets Induced by Dewetting Effect; Tactic Droplets at the Liquid–Air Interface; Chemotactic Droplets Serving as ‘Chemo-Taxis’; Collective Behaviour of Self-propelled Objects on a Water Surface; Chemo-mechanical Effects for Information Processing with Camphor Particles Moving on a Water Surface; Collective Behaviour of Artificial Microswimmers in Response to Environmental Conditions; Nonlinear Dynamics of Active Deformable Particles; Active Particles Propelled by Chemical Reactions; Theory of Active Particles and Drops Driven by Chemical Reactions: The Role of Hydrodynamics on Selfpropulsion and Collective Behaviours

Read more less

Book SynopsisThe prediction of crystal structures from first principles has been one of the grand challenges for computational methods in chemistry and materials science. The goal of being able to reliably predict crystal structures at an atomistic level of detail, given only the chemical composition as input, presents several challenges. A solution to the crystal structure prediction challenge requires advances in several areas of computational chemistry. Theoretical chemists have naturally been drawn to these challenges from an academic perspective, while the development of methods for solving the problem of crystal structure prediction has also been motivated by a growing range of applications where reliable structure prediction is sought and could guide experimentation. Crystal structure predictions have been used to study organic molecules such as polymorphism of pharmaceutical molecules, where changes in crystal form can lead to changes in important physical and chemical properties, which must be strictly controlled in a pharmaceutical product, or inorganic materials where the discovery and computational design of new materials with targeted properties, such as porosity, electronic or mechanical properties are necessary. However, the communities addressing methods and applications in organic and inorganic crystal structure prediction have largely remained separate, due to the different approaches that have been used in these two areas. The community as a whole will benefit from the cross-fertilisation of ideas and methods in this volume, as well as from bringing theoreticians together with interested experimentalists. The volume will appeal to researchers from computational chemistry, informatics, physics (applying solid state electronic structure methods) and materials science in the development of methods. Applications of the methods also cover several fields, including crystallography, crystal engineering, mineralogy and pharmaceutical materials. This volume gathers key researchers representing the full scientific scope of the topic, including the developers of methods and software, those developing the application of the methods and interested experimentalists who may benefit from advances in predictive computational methods. In this volume the topics covered include: Structure searching methods Crystal structure evaluation: calculating relative stabilities and other criteria Applications of crystal structure prediction – organic molecular structures Applications of crystal structure prediction – inorganic and network structuresTable of ContentsStructure searching methods; Crystal structure evaluation: calculating relative stabilities and other criteria; Applications of crystal structure prediction – organic molecular structures; Applications of crystal structure prediction – inorganic and network structures

Read more less

Book SynopsisThe quantum mechanical properties of small molecules provide the basis for our quantitative understanding of chemistry and a testing ground for new theories of molecular structure and reactivity. With modern methods, small molecular systems can be investigated in extraordinary detail by high-resolution spectroscopic techniques in the frequency or the time domains, and by complementary theoretical and computational advances. This combination of cutting-edge approaches provides rigorous tests of our understanding of quantum phenomena in chemistry. The chemical properties of small molecules continue to present rich challenges at the chemistry/physics interface since these molecules exhibit properties in isolation, and interact with their environments, in ways that are not yet fully understood. The coupled electronic and nuclear motions may lead to complex structural or dynamical features that can now be observed experimentally. From a theoretical point of view, these features can only be explained if the quantum nature of the atomic nuclei is considered together with the possible couplings between nuclear and electronic degrees of freedom. New developments, from both the theoretical and experimental side, are urgently needed if the properties of small molecules are to be optimally exploited in future technological, engineering and biological applications of outstanding importance. This Faraday Discussion will address the quantum dynamical properties of small molecules, both in isolation where extraordinarily detailed and precise measurements and calculations are now emerging, and when embedded in complex media such as molecular clusters, quantum fluids and bulk liquids. The Discussion will appeal to researchers working on both isolated and confined molecular systems. This volume covers four main themes: Precise Characterisation of Isolated Molecules Quantum Dynamics of Isolated Molecules Molecules in Confinement in Liquid Solvents Molecules in Confinement in Clusters, Quantum Solvents and MatricesTable of ContentsPrecise Characterisation of Isolated Molecules; Quantum Dynamics of Isolated Molecules; Molecules in Confinement in Liquid Solvents; Molecules in Confinement in Clusters, Quantum Solvents and Matrices

Read more less

Book SynopsisChemical modelling covers a wide range of disciplines and this book is the first stop for any materials scientist, biochemist, chemist or molecular physicist wishing to acquaint themselves with major developments in the applications and theory of chemical modelling. Containing both comprehensive and critical reviews, it is a convenient reference to the current literature. Coverage includes, but is not limited to, boron clusters, molecular modeling of inclusion complexes, modelling of circular dichroism for DNA and proteins, and the interface effect of nanocomposites as electrode materials for Li/Na ion batteries.Table of ContentsModeling Nanoparticle Aggregation; Paths of Chemical Reactions and their Networks: From Geometry Optimization to Automated Search and Systematic Analysis; Charge Transport through Nanocontacts; Activation of Small Molecules by Transition-metal Complexes; Modeling Electronic Excitations/Formation of Trap States in Semiconducting Nanocrystals

Read more less

Book SynopsisThere have been significant developments in the use of knowledge-based expert systems in chemistry since the first edition of this book was published in 2009. This new edition has been thoroughly revised and updated to reflect the advances. The underlying theme of the book is still the need for computer systems that work with uncertain or qualitative data to support decision-making based on reasoned judgements. With the continuing evolution of regulations for the assessment of chemical hazards, and changes in thinking about how scientific decisions should be made, that need is ever greater. Knowledge-based expert systems are well established in chemistry, especially in relation to toxicology, and they are used routinely to support regulatory submissions. The effectiveness and continued acceptance of computer prediction depends on our ability to assess the trustworthiness of predictions and the validity of the models on which they are based. Written by a pioneer in the field, this book provides an essential reference for anyone interested in the uses of artificial intelligence for decision making in chemistry.Table of ContentsArtificial Intelligence – Making Use of Reasoning; Synthesis Planning by Computer;Other Programs to Support Chemical Synthesis Planning; International Repercussions of the Harvard LHASA Project; Current Interest in Synthesis Planning by Computer; Structure Representation; Structure, Substructure and Superstructure Searching; Protons That Come and Go; Aromaticity and Stereochemistry; DEREK – Predicting Toxicity; Other Alert-based Toxicity Prediction Systems; Rule Discovery; The 2D–3D Debate; Making Use of Reasoning: Derek for Windows; Predicting Metabolism; Relative Reasoning; Predicting Biodegradation; Other Applications and Potential Applications of Knowledge-based Prediction in Chemistry; Combining Predictions; The Adverse Outcome Pathways Approach; Evaluation of Knowledge-based Systems; Validation of Computer Predictions; Artificial Intelligence Developments in Other Fields; A Subjective View of the Future

Read more less

Book SynopsisHydrogen bonded systems play an important role in all aspects of science but particularly chemistry and biology. Notably, the helical structure of DNA is heavily reliant on the hydrogens bonds between the DNA base pairs. Although the area of hydrogen bonding is one that is well established, our understanding has continued to develop as the power of both computational and experimental techniques has improved. Understanding Hydrogen Bonds presents an up-to-date overview of our theoretical and experimental understanding of the hydrogen bond. Well-established and novel approaches are discussed, including quantum theory of ‘atoms in molecules’ (QTAIM); the electron localization function (ELF) method and Car–Parinnello molecular dynamics; the natural bond orbital (NBO) approach; and X-ray and neutron diffraction and spectroscopy. The mechanism of hydrogen bond formation is described and comparisons are made between hydrogen bonds and other types of interaction. The author also takes a look at new types of interaction that may be classified as hydrogen bonds with a focus on those with multicentre proton acceptors or with multicentre proton donors. Understanding Hydrogen Bonds is a valuable reference for experimentalists and theoreticians interested in updating their understanding of the types of hydrogen bonds, their role in chemistry and biology, and how they can be studied.Table of ContentsHydrogen bond – definition, criteria of existence and its various types; Counterparts of the hydrogen bond; Theoretical approaches;Experimental methods and techniques; Mechanisms of the hydrogen bond formation, red-shifting and blue-shifting hydrogen bonds; From weak interactions to covalent bonds: weak, moderate and strong hydrogen bonds; Intramolecular hydrogen bonds; At the border of hydrogen bond definition – interactions possessing some of its characteristics; Perspectives and conclusions.

Read more less

Book SynopsisQuantum tunnelling is one of the strangest phenomena in chemistry, where we see the wave nature of atoms acting in “impossible” ways. By letting molecules pass through the kinetic barrier instead of over it, this effect can lead to chemical reactions even close to the absolute zero, to atypical spectroscopic observations, to bizarre selectivity, or to colossal isotopic effects. Quantum mechanical tunnelling observations might be infrequent in chemistry, but it permeates through all its disciplines producing remarkable chemical outcomes. For that reason, the 21st century has seen a great increase in theoretical and experimental findings involving molecular tunnelling effects, as well as in novel techniques that permit their accurate predictions and analysis. Including experimental, computational and theoretical chapters, from the physical and organic to the biochemistry fields, from the applied to the academic arenas, this new book provides a broad and conceptual perspective on tunnelling reactions and how to study them. Quantum Tunnelling in Molecules is the obligatory stop for both the specialist and those new to this world.Table of ContentsDirect observation of tunnelling reactions by matrix isolation spectroscopy; Heavy atom tunnelling in organic transformations; Tunnelling instability in molecular systems: an exercise in computational chemistry prediction power; Proton tunnelling and proton-coupled electron transfer in biological systems: theory and experimental analysis; From tunnelling control to controlling tunnelling; From nuclear fluxes during tunnelling to electronic fluxes during charge migration; Tunnelling and parity violation in chiral and achiral molecules: theory and high resolution spectroscopy; Instanton theory to calculate tunnelling rates and tunnelling splittings; Semiclassical multidimensional tunnelling calculations; Evaluation of tunnelling splittings by direct diagonalization methods. An overview.; Quantum-dynamical calculation of rate constants in polyatomic reactions employing the quantum transition state concept; Eigenstate approaches for high resolution spectroscopy of tunnelling in small molecular systems; The tunnelling flight time

Read more less

Book SynopsisDensity functional theory (DFT) is today’s most widely used method for practical computational electronic structure calculations across chemistry, physics and materials science. It is not only the first choice for running simulations, but it has also delivered an alternative view-point for thinking about the electronic structure of an enormous range of molecular and solid state systems. Fuelled by a rapid increase in computational power and the advent of linear scaling technologies the systems to which DFT may be applied have become ever larger, more complex and more diverse. This rapid growth in the range of problems that may be subjected to computational study has often highlighted new challenges for DFT methodologies in terms of accuracy, speed and scope, spurring many new developments in the field. This Faraday Discussions volume is for chemists, physicists, materials scientists and applied mathematicians who develop new density-functional methods and rely on this approach as a key tool in their research. By discussing the latest cutting edge developments and their relative merits this volume should help bring these new methods to practical application quickly and effectively. It focuses on the following four themes: New density-functional approximations and beyond Challenges for large scale simulation Strong correlation in density-functional theory New approaches to study excited states in density-functional theoryTable of ContentsNew density-functional approximations and beyond; Challenges for large scale simulation; Strong correlation in density-functional theory; New approaches to study excited states in density-functional theory

Read more less