This book describes the forcefields/interatomic potentials that are used in the atomistic-scale and molecular dynamics simulations. It covers mechanisms, salient features, formulations, important aspects and case studies of various forcefields utilized for characterizing various materials (such as nuclear materials and nanomaterials) and applications. This book gives many help to students and researchers who are studying the forcefield potentials and introduces various applications of atomistic-scale simulations to professors who are researching molecular dynamics.

The NATO Advanced Study Institute on "Quantum Chemistry of Polymers; Solid State Aspects" lIIas held at the MARITIM Congress Hotel Braunlage/Harz in the Federal Republic of Germany from July 25 - August 5, 1983. We lIIish to express our deep gratitude to the NATO Scientific Affairs Division, the main sponsor of the Institute, and to the National Foundation for Cancer Research, Bethesda, Maryland for their substantial support. We sincerely thank Dr. Craig Sinclair, Director of the NATO Advanced Study Institutes program as lIIell as the IIIhole Advanced Study Institute/Advanced Research Workshop Advisory Board of the NATO Scientific Affairs Division, IIIho have honored us by holding their external annual meeting during this School in Braunlage. We are very much indebted also to Dr. Mario Di Lullo, Director of the Advanced Research Workshop program of the NATO Scientific Affairs Division IIIho together lIIith Dr. Sinclair has given a very informative lecture about the NATO ASI/ARW programs. Special thanks are due to Mr. Franklin Salisbury, Executive Director of the National Foundation for Cancer Research, to Mrs. Tamara Salisbury, Deputy Director of the National Foundation for Cancer Research and to Dr. Mary Hennen Aldridge, President of the National Foundation for Cancer Research, IIIho also honored the School lIIith their presence.

This volume contains nine contributions, from leading scientists, which embrace the fundamentals of various aspects of the conceptual development of quantum chemistry. Topics dealt with include the behaviour of molecules in magnetic fields, the long-standing problem of the decoupling of nuclear from electron motion in molecules, the status of density functional theory, and the string model of chemical reactions. Insights into basic concepts are also presented, such as the nature of chemical bonding and molecular structure and the quantum mechanical problem of the phase space. Trends in the mathematical base of quantum chemistry, such as the methods of hyperspherical harmonics and of the wavelet transform are discussed. This work should be useful for researchers and graduate students of quantum and theoretical chemistry, quantum mechanics and chemical physics.

The first book in the newly created book series, Computer-Aided Drug Discovery and Design, focuses on the computational aspects of early drug discovery, drug target identification, and validation. It revises current classical paradigms in target and phenotypic-based drug design with still ingrained approximations and concepts and discusses the research in the new network approach concept that include kinetic selectivity and metabolic analysis. Many often-overlooked approximations and concepts in drug discovery are fully covered. Drug Target Selection and Validation includes both introductory sections and research-based sections to be of use to both students and research scientists in drug discovery, design, kinetics and metabolic analysis. Pharmaceutical scientists, pharmaceutics, drug developers, pharmacologists, biomedical researchers in computer science, medicinal chemists, and precision medicine developers benefit from the information provided. The book concludes with a chapter on chemical and structural databases.

Over the last twenty years, developments of the ab initio metho dologies and of the computing capacities have progressively turned quantum chemistry into a predictive tool for molecular systems involving only light elements. The situation appears less advanced for systems containing transition metal elements where specific difficulties arise, like those 1inked to the quasi-degeneracy of the lowest atomic states. Correlation effects, which are important only for quantitative accuracy in the treatment of molecules made of light elements, need sometimes to be considered even for a qualitative des cription of transition metals systems (like the multiple metal-metal bond). The treatment of atoms of a high atomic number has necessited the development of model potential methods. These difficulties ex acerbate for systems containing several trans ition atoms a correct description of the dichromium molecule Crz still represents a challenge to quantum chemists. Yet many advances have been made recently in the theoretical treatment of these systems, despite the fact that our understanding still remains disparate with a variety of models and methodologies used more or less successfully (one-electron models, explicitly correlated ab initio methods, density functional formalisms). For these reasons, a NATO Advanced Research Workshop was organized to review in detail the state-of-the-art techniques and at the same time the most common applications. These encompass many fields including the spectroscopy of diatomics and small aggregates, structure and reactivity problems in organometallic chemistry, the cluster surface analogy with its implications for heterogeneous catalysis and the description of extended structures."

This volume contains the proceedings of the NATO Advanced Research Workshop on "Atomic and Molecular Wires". It was sponsored by the Ministry of Scientific Affairs Division special program on Nanoscale Science with the support of the CNRS and the Max Planck Institute. Scientists working or interested in the properties of wires at a subnanoscale were brought together in Les Houches (France) from 6 to 10 May 1996. Subnanoscale wires can be fabricated either by surface physicists (atomic wires) or by synthetic chemists (molecular wires). Both communities present their foremost advances using, for example, STM to assemble atomic lines atom for atom, to fabricate a mask for such a line or using the wide range of chemical synthesis techniques to obtain long, rigid and conjugated oligomers. Interconnecting such tiny wires to sources (voltage, current) continues to demand a great technological effort. But nanolithography associated with microfabrication or STM are now clearly identified paths for measuring the electrical resistance of an atomic or a molecular wire. The first measurements have been reported on Xe , benzene, C ' di(phenylene-ethynylene) showing 2 60 the need for a deeper understanding of transport phenomena through subnanowires. Such transport phenomena like tunnel (off-resonance) transport and Coulomb blockade have been discussed by theorists with an emphasis on the exponential decrease of the tunnel current with the wire length versus the ballistic regime of transport.

During the last twenty years, the multiplicity of potential carbon structures has consistently posed a formidable challenge to theoretical and computational physicists. Several different methods are currently being used to study the structure and the properties of such systems. These methods include simulations based on empirical potentials, tight-binding calculations and density functional theory (DFT). A combination of these methods is needed to make significant progress in the carbon field.

This volume provides the reader with a survey of state-of-the-art theoretical and computational contributions featuring novel carbon systems (excluding nanotubes). The chapters are authored by leading researchers who are all actively involved with different aspects of carbon structure and property elucidation. Consequently, a variety of methods are presented to the reader. The editors have successfully compiled an informative book that:

Showcases the latest results in carbon materials
Demonstrates how different theoretical methods are combined
Explains how new carbon structures are predicted

"Computer-Based Modeling of Novel Carbon Systems and Their Properties" is aimed at advanced undergraduates, graduates, and researchers with an interest in computational nanomaterials."

This book explores recent progress in RNA secondary, tertiary structure prediction, and its application from an expansive point of view. Because of advancements in experimental protocols and devices, the integration of new types of data as well as new analysis techniques is necessary, and this volume discusses additional topics that are closely related to RNA structure prediction, such as the detection of structure-disrupting mutations, high-throughput structure analysis, and 3D structure design. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice that leads to quality research results. Authoritative and practical, RNA Structure Prediction serves as a valuable guide for both experimental and computational RNA researchers.

In recent years the fundamental concepts and applied methodologies of molecular similarity analysis have experienced a revolutionary development. Motivated by the increased degree of understanding of elementary molecular properties on the levels ranging from fundamental quantum chemistry to the complex interactions of biomolecules, and aided by the spectacular progress in computer technology and access to computer power, the area has opened up to many new ideas and new approaches. This book covers topics in quantum similarity approaches, electron density shape analysis methods, and it provides better theoretical understanding of molecular similarity. Additionally, quantitative shape analysis, especially activity relations (QShAR) and the prediction of the pharmacological or toxicological effects of molecules in the related context of quantum QSAR (QQSAR). This volume written by the experts in the various subfields of molecular similarity, provides a collection of the most recent ideas, advances, and methodologies. It is the hope of the Editors that by representing these topics within a single volume, the readers will find a balanced overview of the status of the field. We also hope that the book will serve as a tool for selecting and assessing the best approach for various new types of problems of molecular similarity that may arise and it will provide a set of easy references for further studies and applications.

This book focuses on chemical reactions and processing under extreme conditions-how materials react with highly concentrated active species and/or in a very confined high-temperature and high-pressure volume. Those ultimate reaction environments created by a focused laser beam, discharges, ion bombardments, or microwaves provide characteristic nano- and submicron-sized products and functional nanostructures. The book explores the chemistry and processing of metals and non-metals as well as molecules that are strongly dependent on the energy deposition processes and character of the materials. Descriptions of a wide range of topics are given from the perspective of a variety of research methodologies, material preparations, and applications. The reader is led to consider and review how a high-energy source interacts with materials, and what the key factors are that determine the quality and quantity of nanoproducts and nano-processing.

This book embraces all physiochemical aspects of the structure and molecular dynamics of water, focusing on its role in biological objects, e.g. living cells and tissue, and in the formation of functionally active structures of biological molecules and their ensembles. Water is the single most abundant chemical found in all living things. It offers a detailed look into the latest modern physical methods for studying the molecular structure and dynamics of the water and provides a critical analysis of the existing literature data on the properties of water in biological objects. Water as a chemical reagent and as a medium for the formation of conditions for enzymatic catalysis is a core focus of this book. Although well suited for active researchers, the book as a whole, as well as each chapter on its own, can be used as fundamental reference material for graduate and undergraduate students throughout chemistry, physics, biophysics and biomedicine.

This textbook presents a concise comparison of catalytic and biocatalytic systems outlining their catalytic properties and peculiarities. Moreover, it presents a brief introduction to the science of catalysis and attempts to unify different catalytic systems into a single, conceptually coherent structure. In fact, molecular dynamics and complexity may occur in both catalysts and biocatalysts, with many similarities in both their structural configuration and operational mechanisms. Moreover, the interactions between the different components of the catalytic system that are important in defining the overall activity, including the nature of active sites are discussed. Each chapter includes end of chapter questions supported by an online instructor solution manual. This textbook will be useful for undergraduate and graduate chemistry and biochemistry students.

The 12th JerusaLem'Symposium was devoted to the exciting sub- ject of CataLysis in Chemistry and Biochemistry. As usuaL in these Sym- posia Theory and Experiment have been considered simuLtaneousLy in dis- cussions> invoLving renowned experts from many countries. We wish to thank aLL those who made this meeting possibLe and contributed to its success: the Baron de RothschiLd whose continuous generosity is at the source of these gatherings, the IsraeL Academy of Sciences and Humanities which offers us the cordiaL hospitaLity of its impressive and beautifuL buiLding and gardens and the Hebrew University of JerusaLem, faithfuL cosponsor of the Symposia. THE MACROMOLECULAR ELECTROSTATIC EFFECT IN BIOCHEMICAL ~EACTIVITY OF THE NUCLEIC ACIDS. BERNARD PULUIAN Institut de BioLogie Physico-Chimique, Laboratoire de Biochimie Theorique, aSSOCle au C. N. R. S. , 13, rue P. et M. Curie, Paris 75005, France. 1. INTRODUCTION The roLe of the macromoLecuLe and of its overaLL structure upon the reactivity of its reaction site(s) represents one of the fundamentaL probLems in the theory of cataLysis. The most impressive and most fre- quentLy considered exampLes occur in the fieLd of proteins where the probLem generaLLy consists of accounting for the enhancement of the reaction rate at the active site or at the coenzyme with respect to modeL systems, devoid of the macromoLecuLar superstructure. Different effects have been considered as possibLy responsibLe for the infLuence of the macromoLecuLe on such LocaLized-site reactions. I do not have the time to summarize or discuss them here.

This book is intended as an introductory text. It starts at the very fundamentals of the interaction of light and matter and progresses through the laws of light absorption, instrumentation and standards to the newer chemometric techniques. Other chapters cover colour, structural aspects of UV spectroscopy, detection in high performace liquid chromatography and flourescence.

Modern approaches to the theoretical computation and experimental determination of NMR shielding tensors are described in 29 papers based on lectures presented at the NATO ARW. All of the most popular computational methods are reviewed and recent progress is described in their application to chemical, biochemical, geochemical and materials science problems. Experimental studies on NMR shieldings in gases, liquids and solids are also included, with special emphasis placed upon the relationship between NMR shielding and geometric structure and upon tests of the accuracy of the various computational methods. Qualitative MO schemes and semi-empirical approaches are also considered in the light of the computational results. This should be a valuable book for anyone interested in how the NMR shielding tensor can be used to determine the geometric and electronic structures of molecules and solids.

This book describes a unique combination of quantum chemical methods for calculating the basic physical properties of luminescent materials, or phosphors. These solid inorganic materials containing an optically active dopant are key players in several major fields of societal interest, including energy-efficient lighting, solar cells, and medical imaging. The novel ab initio methods described in this book are especially designed to target the crowded and complex electronic excited states of lanthanide activators in inorganic solids. The book is well suited to both new and experienced researchers alike and appeals to a broad range of theoretical and experimental backgrounds. The material presented enables an adept understanding of elaborate calculations, which, in tandem with experiments, give essential insight into difficult luminescence problems and quandaries, thus fully preparing the reader for an educated search for new functional luminescent materials

Conjugated polymers suoh as polyaoetylene (CH)x polyphenylene (C6H4)x' poly thiophene (C4H2S)x' etc. , which are insulators in their pristine state, can be brought to the metallic state after "doping" with ohemioal speoies whioh oan be either eleotron donors or I aoceptors. . This doping prooess involves a oharge transfer between the dopant moleoule and the polymer ohain whioh are then supposed to be spatially olose to each other. It follows that the meohanism of doping must be oonsidered as an aotual interoalation process, which will greatly affeot the struotural oharacteristios of the starting material, as well as its morphology, as has been observed during the 2 intercalation of graphite and layered compounds . In parallel with these modifioations, the band struoture of the system changes yielding a new set of eleotronio properties. It is evident therefore that the struotural and eleotronio properties are intimately related, and must be studied simultaneously in the same system to give reliable information. A great number of studies have been devoted to the structural and electronic properties of conjugated polymers after a chemical or 2 electrochemical doping process . Most of these concern the properties of the system for a given dopant concentration. With this approach a universal pioture of the polymer/dopant system is very diffioult to obtain, as a comparison between different experiments is very hazardous. On the other hand, only a small number of measurements have been performed during the continuous electroohemioal doping of various polymers.

This book describes fundamental theory and recent advances of sum frequency generation (SFG) spectroscopy. SFG spectroscopy is widely used as a powerful tool of surface characterization, although theoretical interpretation of the obtained spectra has been a major bottleneck for most users. Recent advances in SFG theory have brought about a breakthrough in the analysis methods beyond conventional empirical ones, and molecular dynamics (MD) simulation of SFG spectroscopy allows for simultaneous understanding of observed spectra and interface structure in unprecedented detail. This book explains these recently understood theoretical aspects of SFG spectroscopy by the major developer of the theory. The theoretical topics are treated at basic levels for undergraduate students and are described in relation to computational chemistry, such as molecular modeling and MD simulation, toward close collaboration of SFG spectroscopy and computational chemistry in the near future.

This book presents the latest theoretical studies giving new predictions and interpretations on the quantum correlation in molecular dynamics induced by ultrashort laser pulses. The author quantifies the amount of correlation in terms of entanglement by employing methods developed in quantum information science, in particular applied to the photoionization of a hydrogen molecule. It is also revealed that the photoelectron-ion correlation affects the vibrational dynamics of the molecular ion and induces the attosecond-level time delay in the molecular vibration. Furthermore, the book also presents how molecular vibration can couple to photons in a plasmoic nanocavity. Physicists and chemists interested in the ultrafast molecular dynamics would be the most relevant readers. They can learn how we can employ the quantum-information-science tools to understand the correlation in the molecular dynamics and why we should consider the correlation between the photoelectron and the molecular ion to describe the ion's dynamics. They can also learn how to treat a molecule coupled to photons in a nanocavity. All the topics are related to the state-of-the-art experiments, and so, it is important to publish these results to enhance the understanding and to induce new experiments to confirm the theory presented.

This book is intended for theoretical and experimental researchers who are interested in ferroelectrics and advanced memory. After introducing readers to dielectric, perovskites, advanced memories, and ferroelectric, it explains quantum simulation. Then, using molecular orbital calculation results, it explains the ferroelectric mechanism in perovskite titanium oxides in concrete terms. Lastly, the book examines the materials designed for high-performance ferroelectrics and discusses the future of high-speed memory.

At the American Chemical Society meeting in Philadelphia, Pennsylvania, U.S.A., a symposium was organized entitled, "Comparison of Ab Initio Quantum Chemistry with Experiment: State-of-the-Art." The intent of the symposium was to bring together forefront experimen talists, who perform the types of clean, penetrating experiments that are amenable to thorough theoretical analysis, with inventive theore ticians who have developed high accuracy ab initio methods that are capable of competing favorably with experiment, to assess the current applicability of theoretical methods in chemistry. Contributions from many of those speakers (see Appendix A) plus others selected for their expertise in the subject are contained in this volume. Such a book is especially timely, since with the recent develop ment of new, more accurate and powerful ab initio methods coupled with the exceptional progress achieved in computational equipment, ab initio quantum chemistry is now often able to offer a third voice to resolve experimental discrepancies, assist essentially in the interpre tation of experiments, and frequently, provide quantitatively accurate results for molecular properties that are not available from experiment."

This book explores the philosophy and the foundations of quantum chemistry. It features chapters written by experts in the field. The contributions analyze quantum chemistry as a discipline, in particular, its relation with both chemistry and physics from the viewpoint of realism and reduction. Coverage includes such topics as quantum chemistry as an "in-between" discipline, molecular structure and quantum mechanics, quantum chemical models, and atoms and molecules in quantum chemistry. The interest of this book is twofold. First, the contributions aim to update and refresh the discussions regarding the foundations of quantum chemistry. Second, they seek to develop new philosophical perspectives that this discipline can suggest to philosophers of science. From its origins, quantum chemistry filled a problematic position in the disciplinary space. On the one hand, it is a branch of theoretical chemistry. On the other hand, it appeals essentially to theoretical tools coming from physics. This peculiar position triggered conceptual questions about its own identity. Inside this book, readers will find updated discussions on the foundations and the philosophy of this complex discipline.

The importance of molecular recognition in chemistry and biology is reflected in a recent upsurge in relevant research, promoted in particular by high-profile initiatives in this area in Europe, the USA and Japan. Although molecular recognition is necessarily microscopic in origin, its consequences are de facto macroscopic. Accordingly, a text that starts with intermolecular interactions between simple molecules and builds to a discussion of molecular recognition involving larger scale systems is timely. This book was planned with such a development in mind. The book begins with an elementary but rigorous account of the various types of forces between molecules. Chapter 2 is concerned with the hydrogen bond between pairs of simple molecules in the gas phase, with particular reference to the preferred relative orientation of the pair and the ease with which this can be distorted. This microscopic view continues in chapter 3 wherein the nature of interactions between solute molecules and solvents or between two or more solutes is examined from the experimental standpoint, with various types of spectroscopy providing the probe of the nature of the interactions. Molecular recognition is central to the catalysis of chemical reactions, especially when bonds are to be broken and formed under the severe con straint that a specific configuration is to result, as in the production of enan tiotopically pure compounds. This important topic is considered in chapter 4.

This volume provides the reader with the most up-to-date and relevant knowledge on the reactivity of metals located in zeolite materials, either in framework or extra-framework positions, and the way it is connected with the nature of the chemical environment provided by the host. Since the first report of the isomorphous substitution of titanium in the framework of zeolites giving rise to materials with unusual catalytic properties, the incorporation of many other metals have been investigated with the aim for developing catalysts with improved performance in different reactions. The continuous expansion of the field, both in the variety of metals and zeolite structures, has been accompanied by an increasing focus on the relationship between the reactivity of metal centers and their unique chemical environment. The concepts covered in this volume are of interest to people working in the field of inorganic and physical chemistry, catalysis and chemical engineering, but also for those more interested in theoretical approaches to chemical reactivity. In particular the volume is useful to postgraduate students conducting research in the design, synthesis and catalytic performance of metal-containing zeolites in both academic and application contexts.

The focus of this thesis is the computational modelling of transition metal bimetallic (nanoalloy) clusters. More specifically, the study of Pd-Pt, Ag-Pt, Au-Au and Pd-Au as a few tens of atoms in the gas phase. The author used a combination of global optimization techniques - coupled with a Gupta-type empirical many-body potential - and Density Functional Theory (DFT) calculations to study the structures, bonding and chemical ordering, as well as investigate the chemisorptions of hydrogen and carbon monoxide on bimetallic clusters. This research is highly relevant to experimental catalytic studies and has resulted in more than seven publications in international journals.