Since the inception of this volume, the world's nancial climate has radically changed. Theemphasishasshiftedfromboomingeconomiesandeconomicgrowth totherealityofrecessionanddiminishingoutlook. Witheconomicdownturncomes opportunity,inallareasofchemistryfromresearchanddevelopmentthroughto productregistrationandriskassessment,replacementsarebeingsoughtforcostly time-consumingprocesses. Leadingamongstthereplacementsaremodelswithtrue predictivecapability. Ofthesecomputationalmodelsarepreferred. This volume addresses a broad need within various areas of the "chemical industries", from pharmaceuticals and pesticides to personal products to provide computationalmethodstopredicttheeffects,activitiesandpropertiesofmolecules. Itaddressestheuseofmodelstodesignnewmoleculesandassesstheirfateand effectsbothtotheenvironmentandtohumanhealth. Thereisanemphasisrunning throughoutthisvolumetoproducerobustmodelssuitableforpurpose. Thevolume aimstoallowthereaderto nddataanddescriptorsanddevelop,discoverandutilise validmodels. Gdansk, ' Poland TomaszPuzyn Jackson,MS,USA JerzyLeszczynski Liverpool,UK MarkT. D. Cronin May2009 CONTENTS Part I Theory of QSAR 1 QuantitativeStructure-ActivityRelationships(QSARs)- ApplicationsandMethodology...3 Mark T. D. Cronin 1. 1. Introduction...3 1. 2. PurposeofQSAR...4 1. 3. ApplicationsofQSAR...4 1. 4. Methods...5 1. 5. TheCornerstonesofSuccessfulPredictiveModels ...7 1. 6. AValidated(Q)SARoraValidPrediction? ...9 1. 7. UsinginSilicoTechniques ...9 1. 8. NewAreasforinSilicoModels...11 1. 9. Conclusions...11 References ...11 2 TheUseofQuantumMechanicsDerivedDescriptorsin ComputationalToxicology...13 Steven J. Enoch 2. 1. Introduction...13 2. 2. TheSchrodingerEquation...15 2. 3. Hartree-FockTheory...17 2. 4. Semi-EmpiricalMethods:AM1andRM1...18 2. 5. ABInitio:DensityFunctionalTheory...19 2. 6. QSARforNon-ReactiveMechanismsofAcute(Aquatic) Toxicity...19 2. 7. QSARsforReactiveToxicityMechanisms...21 2. 7. 1. AquaticToxicityandSkinSensitisation...21 2. 7. 2. QSARsforMutagenicity ...24 2. 8. FutureDirectionsandOutlook...25 2. 9. Conclusions...26 References ...26 vii viii Contents 3 MolecularDescriptors...29 Viviana Consonni and Roberto Todeschini 3. 1. Introduction...29 3. 1. 1. De nitions...29 3. 1. 2. History...31 3. 1. 3. Theoreticalvs. ExperimentalDescriptors...33 3. 2. MolecularRepresentation ...35 3. 3. TopologicalIndexes...38 3. 3. 1. MolecularGraphs...38 3. 3. 2. De nitionandCalculationofTopologicalIndexes(TIs) 39 3. 3. 3. Graph-TheoreticalMatrixes...42 3. 3. 4. ConnectivityIndexes ...48 3. 3. 5. CharacteristicPolynomial ...50 3. 3. 6. SpectralIndexes ...53 3. 4. AutocorrelationDescriptors ...

Chemical Modelling: Applications and Theory comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature. With chemical modelling covering such a wide range of subjects, this Specialist Periodical Report serves as the first port of call to any chemist, biochemist, materials scientist or molecular physicist needing to acquaint themselves of major developments in the area. Specialist Periodical Reports provide systematic and detailed review coverage in major areas of chemical research. Compiled by teams of leading authorities in the relevant subject areas, the series creates a unique service for the active research chemist, with regular, in-depth accounts of progress in particular fields of chemistry. Subject coverage within different volumes of a given title is similar and publication is on an annual or biennial basis. Current subject areas covered are Amino Acids, Peptides and Proteins, Carbohydrate Chemistry, Catalysis, Chemical Modelling. Applications and Theory, Electron Paramagnetic Resonance, Nuclear Magnetic Resonance, Organometallic Chemistry. Organophosphorus Chemistry, Photochemistry and Spectroscopic Properties of Inorganic and Organometallic Compounds. From time to time, the series has altered according to the fluctuating degrees of activity in the various fields, but these volumes remain a superb reference point for researchers.

Channels of nanotubular dimensions exist in a variety of materials (examples are carbon nanotubes and the nanotubular channels of zeolites and zeotypes) and show promise for numerous applications due to their unique properties. One of their most important properties is their capacity to adsorb molecules and these may exist in a variety of phases.

"Adsorption and Phase Behaviour in Nanochannels and Nanotubes" provides an excellent review of recent and current work on adsorption on nanometerials. It is an impressive collection of papers dealing with the adsorption and phase behaviour in nanoporous materials from both experimental and theoretical perspectives.

"Adsorption and Phase Behaviour in Nanochannels and Nanotubes" focuses on carbon nanotubes as well as zeolites and related materials.

This book reviews some of the latest developments in the field of water treatment using multi-functional chitosan-based materials. It covers the production of chitosan beads and membranes from chitosan powder, as well as modification techniques for enhancing the material for commercial and industrial purposes. The book summarizes the results of experimental adsorption/desorption studies for elucidating the underlying reaction mechanism of heavy-metal removal from wastewater, presenting an advanced overview of an array of characterization techniques such as Fourier-transform infrared spectroscopy, thermogravimetric analysis, x-ray diffraction, and scanning electron microscopy. Additionally, it features a look at the development and application of specialized engineering software and image analysis for modelling the kinetics of adsorption. This book is ideal for scientists and engineers working in the broader field of environmental materials science. It is all well suited for chemists, as well as industrial and civil engineers, interested in wastewater treatment and mitigation of water pollution

The proposed volume provides both fundamental and detailed information about the computational and computational-experimental studies which improve our knowledge of how leaving matter functions, the different properties of drugs (including the calculation and the design of new ones), and the creation of completely new ways of treating numerical diseases. Whenever it is possible, the interplay between theory and experiment is provided. The book features computational techniques such as quantum-chemical and molecular dynamic approaches and quantitative structure-activity relationships. The initial chapters describe the state-of-the art research on the computational investigations in molecular biology, molecular pharmacy, and molecular medicine performed with the use of pure quantum-chemical techniques. The central part of the book illustrates the status of computational techniques that utilize hybrid, so called QM/MM approximations as well as the results of the QSAR studies which now are the most popular in predicting drugs' efficiency. The last chapters describe combined computational and experimental investigations.

Christopher M. Cheatum and Amnon Kohen, Relationship of Femtosecond-Picosecond Dynamics to Enzyme-Catalyzed H-Transfer. Cindy Schulenburg and Donald Hilvert, Protein Conformational Disorder and Enzyme Catalysis. A. Joshua Wand, Veronica R. Moorman and Kyle W. Harpole, A Surprising Role for Conformational Entropy in Protein Function. Travis P. Schrank, James O. Wrabl and Vincent J. Hilser, Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations. Buyong Ma and Ruth Nussinov, Structured Crowding and Its Effects on Enzyme Catalysis. Michael D. Daily, Haibo Yu, George N. Phillips Jr and Qiang Cui, Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Karunesh Arora and Charles L. Brooks III, Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Steven D. Schwartz, Protein Dynamics and the Enzymatic Reaction Coordinate.

Table of contents P.L.A. Popelier: Quantum Chemical Topology: on Bonds and Potentials.- A. Soncini, P.W. Fowler, L.W. Jenneskens: Angular Momentum and Spectral Decomposition of Ring Currents: Aromaticity and the Annulene Model.- S.L. Price, L.S. Price: Modelling Intermolecular Forces for Organic Crystal Structure Prediction.- C. Millot: Molecular Dynamics Simulations and Intermolecular Forces.- S. Tsuzuki: Interactions with Aromatic Rings

This book presents recent research on Advanced Computing in Industrial Mathematics, which is one of the most prominent interdisciplinary areas and combines mathematics, computer science, scientific computations, engineering, physics, chemistry, medicine, etc. Further, the book presents the tools of Industrial Mathematics, which are based on mathematical models, and the corresponding computer codes, which are used to perform virtual experiments to obtain new data or to better understand the existing experimental results. The book gathers the peer-reviewed papers presented during the 10th Annual Meeting of the Bulgarian Section of SIAM (BGSIAM) from December 21 to 22, 2015 in Sofia, Bulgaria.

First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes, by A. Jaramillo-Botero, R. Nielsen, R. Abrol, J. Su, T. Pascal, J. Mueller and W. A. Goddard.- Dynamic QM/MM: A Hybrid Approach to Simulating Gas Liquid Interactions, by S. Yockel and G. C. Schatz.- Multiscale Modelling in Computational Heterogeneous Catalysis, by F. J. Keil.- Real-World Predictions from Ab Initio Molecular Dynamics Simulations, by B. Kirchner, P. J. di Dio and J. Hutter.- Nanoscale Wetting Under Electric Field from Molecular Simulations, by C. D. Daub, D. Bratko and A. Luzar.- Molecular Simulations of Retention in Chromatographic Systems: Use of Biased Monte Carlo Techniques to Access Multiple Time and Length Scales, by J. L. Rafferty, J. I. Siepmann, M. R. Schure.- Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields, by G. Guevara-Carrion, H. Hasse and J. Vrabec.- Multiscale Approaches and Perspectives to Modeling Aqueous Electrolytes and Polyelectrolytes, by L. Delle Site, C. Holm and N. F. A. van der Vegt.- Coarse-Grained Modeling for Macromolecular Chemistry, by H. A. Karimi-Varzaneh and F. Muller-Plathe.-"

The series Structure and Bonding publishes critical reviews on topics of research concerned with chemical structure and bonding. The scope of the series spans the entire Periodic Table and addresses structure and bonding issues associated with all of the elements. It also focuses attention on new and developing areas of modern structural and theoretical chemistry such as nanostructures, molecular electronics, designed molecular solids, surfaces, metal clusters and supramolecular structures. Physical and spectroscopic techniques used to determine, examine and model structures fall within the purview of Structure and Bonding to the extent that the focus is on the scientific results obtained and not on specialist information concerning the techniques themselves. Issues associated with the development of bonding models and generalizations that illuminate the reactivity pathways and rates of chemical processes are also relevant. The individual volumes in the series are thematic. The goal of each volume is to give the reader, whether at a university or in industry, a comprehensive overview of an area where new insights are emerging that are of interest to a larger scientific audience. Thus each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years should be presented using selected examples to illustrate the principles discussed. A description of the physical basis of the experimental techniques that have been used to provide the primary data may also be appropriate, if it has not been covered in detail elsewhere. The coverage need not be exhaustive in data, but should rather be conceptual, concentrating on the new principles being developed that will allow the reader, who is not a specialist in the area covered, to understand the data presented. Discussion of possible future research directions in the area is welcomed. Review articles for the individual volumes are invited by the volume editors

Chemical Modelling: Applications and Theory comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature, incorporating sufficient historical perspective for the non-specialist to gain an understanding. With chemical modelling covering such a wide range of subjects, this Specialist Periodical Report serves as the first port of call to any chemist, biochemist, materials scientist or molecular physicist needing to acquaint themselves with major developments in the area.

Brillouin-Wigner Methods for Many-Body Systems gives an introduction to many-body methods in electronic structure theory for the graduate student and post-doctoral researcher. It provides researchers in many-body physics and theoretical chemistry with an account of Brillouin-Wigner methodology as it has been developed in recent years to handle the multireference correlation problem. Moreover, the frontiers of this research field are defined.

This volume is of interest to atomic and molecular physicists, physical chemists and chemical physicists, quantum chemists and condensed matter theorists, computational chemists and applied mathematicians.

Frustrated Lewis Pairs: From Dihydrogen Activation to Asymmetric Catalysis, by Dianjun Chen, Jurgen Klankermayer

Coexistence of Lewis Acid and Base Functions: A Generalized View of the Frustrated Lewis Pair Concept with Novel Implications for Reactivity, by Heinz Berke, Yanfeng Jiang, Xianghua Yang, Chunfang Jiang, Subrata Chakraborty, Anne Landwehr

New Organoboranes in "Frustrated Lewis Pair" Chemistry, by Zhenpin Lu, Hongyan Ye, Huadong Wang

Paracyclophane Derivatives in Frustrated Lewis Pair Chemistry, by Lutz Greb, Jan Paradies

Novel Al-Based FLP Systems, by Werner Uhl, Ernst-Ulrich Wurthwein

N-Heterocyclic Carbenes in FLP Chemistry, by Eugene L. Kolychev, Eileen Theuergarten, Matthias Tamm

Carbon-Based Frustrated Lewis Pairs, by Shabana Khan, Manuel Alcarazo

Selective C-H Activations Using Frustrated Lewis Pairs. Applications in Organic Synthesis, by Paul Knochel, Konstantin Karaghiosoff, Sophia Manolikakes

FLP-Mediated Activations and Reductions of CO2 and CO, by Andrew E. Ashley, Dermot O Hare

Radical Frustrated Lewis Pairs, by Timothy H. Warren and Gerhard Erker

Polymerization by Classical and Frustrated Lewis Pairs, by Eugene Y.-X. Chen

Frustrated Lewis Pairs Beyond the Main Group: Transition Metal-Containing Systems, by D. Wass

Reactions of Phosphine-Boranes and Related Frustrated Lewis Pairs with Transition Metal Complexes, by Abderrahmane Amgoune, Ghenwa Bouhadir, Didier Bourissou"

This volume records the proceedings of a Forum attended by many leading researchers working in the field of Electron Density, Density Matrix and Density Functional Theory held at the Coseners' House, Abingdon-on-Thames, Oxfordshire, UK in early summer 2002.
It has long been recognized that "All the necessary information required for the energy and for calculating the properties of molecules is embodied in the first- and second-order density matrices." The wave function contains much more information than is required to yield the energy or other property. But the density matrices must correspond to some physically acceptable wave function. Coleman, one of the distinguished participants in the Forum, has dubbed this "Coulson's challenge." His paper describing recent work on the N-representability problem is included in this volume. McWeeny discusses some unsolved problems in density matrix theory and density functional theory; and Bader discusses the use of the electron density in explaining the structure and properties of atoms and molecules.
Density Functional Theory is widely used in studies of molecular and solid state systems. Yet the theoretical apparatus for this approach remains under active development. Theophilou describes a new formulation of density functional theory. Gross and his coworkers present a time-dependent theory for molecules in strong laser pulses. Nagy considers pair density functional theory, while Ludena and his colleagues examine functional N-representability in density matrix and density functional theory.
The meeting concluded with a Forum, ably chaired by B.T. Sutcliffe, in which the latest research and results were discussed. A record of thisForum is included in this volume.
This book will be of value to researchers and research students in theoretical chemistry and theoretical physics whose work involves the theoretical study of atoms, molecules and the solid state. It will be of interest to quantum chemists and solid state physicists, to materials scientists and applied mathematicians.

This book fills a gap in knowledge between chemistry- and physics-trained researchers about the properties of macroscopic (bulk) material. Although many good textbooks are available on solid-state (or condensed matter) physics, they generally treat simple systems such as simple metals and crystals consisting of atoms. On the other hand, textbooks on solid-state chemistry often avoid descriptions of theoretical background even at the simplest level. This book gives coherent descriptions from intermolecular interaction up to properties of condensed matter ranging from isotropic liquids to molecular crystals. By omitting details of specific systems for which comprehensive monographs are available-on liquid crystals and molecular conductors, for instance-this book highlights the effects of molecular properties, i.e., the presence of the shape and its deformation on the structure and properties of molecular systems.

Hydrogen bonds represent type of molecular interaction that determines the structure and function of a large variety of molecular systems. The elementary dynamics of hydrogen bonds and related proton transfer reactions, both occurring in the ultra fast time domain between 10-14 and 10-11s, form a research topic of high current interest.
In this book addressing scientists and graduate students in physics, chemistry and biology, the ultra fast dynamics of hydrogen bonds and proton transfer in the condensed phase are reviewed by leading scientists, documenting the state of the art in this exciting field from the viewpoint of theory and experiment. The nonequilibrium behavior of hydrogen-bonded liquids and intramolecular hydrogen bonds as well as photo induced hydrogen and proton transfer are covered in 7 chapters, making reference to the most recent literature.

This thesis examines various aspects of excess excitation energy dissipation via dynamic changes in molecular structure, vibrational modes and solvation. The computational work is carefully described and the results are compared to experimental data obtained using femtosecond spectroscopy and x-ray scattering. The level of agreement between theory and experiment is impressive and provides both a convincing validation of the method and significant new insights into the chemical dynamics and molecular determinants of the experimental data. Hence, the method presented in the thesis has the potential to become a very important contribution to the rapidly growing field of femtosecond x-ray science, a trend reflected in the several free-electron x-ray lasers (XFELs) currently being built around the world. Light-induced chemical processes are accompanied by molecular motion of electrons and nuclei on the femtosecond time scale. Uncovering these dynamics is central to our understanding of the chemical reaction on a fundamental level. Asmus O. Dohn has implemented a highly efficient QM/MM Direct Dynamics method for predicting the solvation dynamics of transition metal complexes in solution.

The series Topics in Heterocyclic Chemistry presents critical reviews on present and future trends in the research of heterocyclic compounds. Overall the scope is to cover topics dealing with all areas within heterocyclic chemistry, both experimental and theoretical, of interest to the general heterocyclic chemistry community. The series consists of topic related volumes edited by renowned editors with contributions of experts in the field.

Provides historical perspective as well as current data

Abundantly illustrated with figures redrawn from literature data

Covers all pertinent theory and physical chemistry

Catalytic and chemotherapeutic applications are included

This text is designed as a practical introduction to quantum chemistry. Quantum chemistry is applied to explain and predict molecular spectroscopy and the electronic structure of atoms and molecules. In addition, the text provides a practical guide to using molecular mechanics and electronic structure computations including ab initio, semi-empirical, and density functional methods. The use of electronic structure computations is a timely subject as its applications in both theoretical and experimental chemical research is increasingly prevalent. This text is written in a format that fosters mastery of the subject both in competency in the mathematics and in obtaining a conceptual understanding of quantum mechanics. The chemistry student's interest is maintained early on in the text where quantum mechanics is developed by applying it to molecular spectroscopy and through conceptual questions labeled as Chemical Connection. Questions throughout the text labeled as Chemical Connection and Points of Further Understanding focus on conceptual understanding and consequences of quantum mechanics. If an Instructor chooses, these questions can be used as a basis for classroom discussion encouraging cooperative learning techniques. This text provides a solid foundation from which students can readily build further knowledge of quantum chemistry in more advanced courses. In cases where this is a final course in quantum chemistry, this text provides the student not only with an appreciation of the importance of quantum mechanics to chemistry, but also with a practical guide to using electronic structure computations.

Chemical Modelling: Applications and Theory comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature. With chemical modelling covering such a wide range of subjects, this Specialist Periodical Report serves as the first port of call to any chemist, biochemist, materials scientist or molecular physicist needing to acquaint themselves of major developments in the area. Specialist Periodical Reports provide systematic and detailed review coverage in major areas of chemical research. Compiled by teams of leading authorities in the relevant subject areas, the series creates a unique service for the active research chemist, with regular, in-depth accounts of progress in particular fields of chemistry. Subject coverage within different volumes of a given title is similar and publication is on an annual or biennial basis. Current subject areas covered are Amino Acids, Peptides and Proteins, Carbohydrate Chemistry, Catalysis, Chemical Modelling. Applications and Theory, Electron Paramagnetic Resonance, Nuclear Magnetic Resonance, Organometallic Chemistry. Organophosphorus Chemistry, Photochemistry and Spectroscopic Properties of Inorganic and Organometallic Compounds. From time to time, the series has altered according to the fluctuating degrees of activity in the various fields, but these volumes remain a superb reference point for researchers.

Computational methods have become an indispensible tool for elucidating the mechanism of organometallic reactions. This snapshot of state-of-the-art computational studies provides an overview of the vast field of computational organometallic chemistry. Authors from Asia, Europe and the US have been selected to contribute a chapter on their specialist areas. Topics addressed include: DFT studies on zirconium-mediated reactions, force field methods in organometallic chemistry, hydrogenation of -systems, oxidative functionalization of unactivated C-H bonds and olefins, the osmylation reaction, and cobalt carbonyl clusters. The breadth and depth of the contributions demonstrate not only the crucial role that computational methods play in the study of a wide range of organometallic reactions, but also attest the robust health of the field, which continues to benefit from, as well as inspire novel experimental studies.

This book, a consecutive contribution to the series Challenges and Advances in Computational Chemistry and Physics, focuses on understanding the photoinduced processes in biological systems. Understanding and fine control of light fate in molecules is vital for the progress of society and environmental safety. Light induced changes of various physico-chemical and spectroscopic properties in nucleic acids and proteins is the basis of fundamental biological events such as vision, DNA photodamage or photosensing. The investigation of these processes is challenging to both theoretical and experimental studies. This volume encompasses the quantum mechanics/molecular mechanics theory in several subfields, including: advanced computational methods for nucleic acids and proteins systems; dynamics, spectroscopic and physico-chemical properties of biological photoreceptors; DNA photodamage. This book is of interest to readers in both fundamental and application-oriented research by overviewing recent achievements in computational modeling of excited states in nucleic acids and proteins.

The series Structure and Bonding publishes critical reviews on topics of research concerned with chemical structure and bonding. The scope of the series spans the entire Periodic Table and addresses structure and bonding issues associated with all of the elements. It also focuses attention on new and developing areas of modern structural and theoretical chemistry such as nanostructures, molecular electronics, designed molecular solids, surfaces, metal clusters and supramolecular structures. Physical and spectroscopic techniques used to determine, examine and model structures fall within the purview of Structure and Bonding to the extent that the focus is on the scientific results obtained and not on specialist information concerning the techniques themselves. Issues associated with the development of bonding models and generalizations that illuminate the reactivity pathways and rates of chemical processes are also relevant. The individual volumes in the series are thematic. The goal of each volume is to give the reader, whether at a university or in industry, a comprehensive overview of an area where new insights are emerging that are of interest to a larger scientific audience. Thus each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years should be presented using selected examples to illustrate the principles discussed. A description of the physical basis of the experimental techniques that have been used to provide the primary data may also be appropriate, if it has not been covered in detail elsewhere. The coverage need not be exhaustive in data, but should rather be conceptual, concentrating on the new principles being developed that will allow the reader, who is not a specialist in the area covered, to understand the data presented. Discussion of possible future research directions in the area is welcomed. Review articles for the individual volumes are invited by the volume editors. Readership: research scientists at universities or in industry, graduate students Special offer For all customers who have a standing order to the print version of Structure and Bonding, we offer free access to the electronic volumes of the Series published in the current year via SpringerLink.