This volume presents the current status of software development in the field of computational and theoretical chemistry and gives an overview of the emerging trends. The challenges of maintaining the legacy codes and their adaptation to the rapidly growing hardware capabilities and the new programming environments are surveyed in a series of topical reviews written by the core developers and maintainers of the popular quantum chemistry and molecular dynamics programs. Special emphasis is given to new computational methodologies and practical aspects of their implementation and application in the computational chemistry codes. Modularity of the computational chemistry software is an emerging concept that enables to bypass the development and maintenance bottleneck of the legacy software and to customize the software using the best available computational procedures implemented in the form of self-contained modules. Perspectives on modular design of the computer programs for modeling molecular electronic structure, non-adiabatic dynamics, kinetics, as well as for data visualization are presented by the researchers actively working in the field of software development and application. This volume is of interest to quantum and computational chemists as well as experimental chemists actively using and developing computational software for their research. Chapters "MLatom 2: An Integrative Platform for Atomistic Machine Learning" and "Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol" are available open access under a CC BY 4.0 License via link.springer.com.

This book focuses on the modern development of techniques for analysis of the hierarchical structure of polymers from both the experimental and theoretical points of view. Starting with molecular and crystal symmetry, the author explains fundamental and professional methods, such as wide- and small-angle X-ray scattering, neutron diffraction, electron diffraction, FTIR and Raman spectroscopy, NMR, and synchrotron radiation. In addition, the author explains another indispensable method, computer simulation, which includes energy calculation, lattice dynamics, molecular dynamics, and quantum chemistry. These various methods are described in a systematic way so that the reader can utilize them for the purpose of 3D structure analysis of polymers. Not only such analytical knowledge but also the preparation techniques of samples necessary for these measurements and the methods of analyzing the experimental data collected in this way are given in a concrete manner. Examples are offered to help master the principles of how to clarify the static structures and dynamic structural changes in the phase transitions of various kinds of crystalline polymers that are revealed by these novel methods. The examples are quite useful for readers who want to apply these techniques in finding practical solutions to concrete problems that are encountered in their own research. The principal audience for this book is made up of young professional researchers including those working in industry, but it can also be used as an excellent reference for graduate-level students. This book is the first volume of a two-volume set with Structural Science of Crystalline Polymers: A Microscopically Viewed Structure-Property Relationship being the second volume by the same author.

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.

This book offers a clearly written and highly accessible account of two different aspects of carbohydrate chemistry. Carbohydrates are an essential component of life and have many important biological functions, but the details of how carbohydrates interact with other biomolecules to mediate biological signalling remain unclear. Firstly, this thesis details innovative methods to mine protein structural data to uncover new features of carbohydrate-based interactions. It also explains these findings using physical chemistry, specifically CH-pi interactions associated with the properties of the interacting partners. Carbohydrates are also critical for tissue growth and development, yet are underexploited in the materials science that underpins much of regenerative medicine. As such, the second part of this thesis describes a diverse array of techniques ranging from synthetic chemistry and enzymatic synthesis to prepare a wide variety of carbohydrates, and materials chemistry to prepare glycosylated hydrogels, to cell biology to determine the effects on cellular development for tissue engineering applications.

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.

This detailed book provides an overview of various classes of computational techniques, including machine learning techniques, commonly used for evaluating kinetic parameters of biological systems. Focusing on three distinct situations, the volume covers the prediction of the kinetics of enzymatic reactions, the prediction of the kinetics of protein-protein or protein-ligand interactions (binding rates, dissociation rates, binding affinities), and the prediction of relatively large set of kinetic rates of reactions usually found in quantitative models of large biological networks. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that leads to successful results. Authoritative and practical, Computational Methods for Estimating the Kinetic Parameters of Biological Systems will be of great interest for researchers working through the challenge of identifying the best type of algorithm and who would like to use or develop a computational method for the estimation of kinetic parameters.

There have been several recent breakthroughs in the supramolecular domain: larger molecular components are being synthesized; 2D layers involving multiple recognition sites; crystals with intricate building blocks are being designed; more components are being used in assembly and self-assembly "algorithms" (some having molecular weights as high as 15,000); and there is an increasing versatility in applications. The difficulty in characterizing and obtaining structural information on such large assemblies has increased to such a level that no single technique is now adequate. Various methods have now been upgraded and are being combined: X-ray diffraction (structures with hundreds of independent atoms), NMR, AFM/STM (manipulation of a single molecule), FAB/MS, time-resolved techniques up to the picosecond range, new computational approaches, and others. The present book aims to shed light on the most recent developments in both the synthesis of novel assemblies and on current methods for their characterization.

MICHAEL T. POPE AND ACHIM MULLER Department of Chemistry, Georgetown University, Washington, DC 20057-2222, U.S.A.; Department of Chemistry, University of Bielefeld, D-4BOO Bielefeld 1, F.R.G. Polyoxometalates, from their discovery and early development in the final decades of the 19th century to their current significance in disciplines as diverse as chemistry, mathematics, and medicine, continue to display surprisingly novel structures, unexpected reactivities and applications, and to attract increasing attention worldwide. Most of the contributors to the present volume participated in the workshop held at the Center for Interdisciplinary Research at the University of Bielefeld, July 15-17, 1992. The choice of topics illustrates some of the variety of directions and fields in which polyoxometalates can play an important role. Although many of the leading polyoxometalate research groups are represented here, we regret that time constraints, financial limitations, and in some cases difficulties of communication did not allow us to include significant and imp- tant work from other groups outside Europe and North America. In the following we briefly review the current status of the field of po- oxometalates.

Beautifully illustrated and engagingly written, Twelve Lectures in Quantum Mechanics presents theoretical physics with a breathtaking array of examples and anecdotes. Basdevant's style is clear and stimulating, in the manner of a brisk lecture that can be followed with ease and enjoyment. Here is a sample of the book's style, from the opening of Chapter 1: "If one were to ask a passer-by to quote a great formula of physics, chances are that the answer would be 'E = mc2'.... There is no way around it: all physics is quantum, from elementary particles, to stellar physics and the Big Bang, not to mention semiconductors and solar cells."

The Fourth International Congress in Quantum Chemistry under the auspices of the International Academy of Molecular Quantum Science in Menton, France was arranged at Uppsala University, Uppsala, Sweden, during the period June 14 - 19, 1982, in close collaboration with the University of Florida. The previous congresses were held in Menton 1973, New Orleans 1976, and Kyoto 1979, and the 1985 congress is tentatively planned to be held in the province of Quebec, Canada. The Congress consisted of six symposia in various areas of quantum chemistry, solid-state theory, and quantum bi ology. The meeting was attended by about 450 scientists from 45 different nations, and a total of more than 300 scientific papers were presented. Even the poster contri butions were given some plenary time. These proceedings contain the text of the plenary lec tures as well as the chairmen's introductions, whereas the contributed papers will be published in the International Journal of Quantum Chemistry, (John Wiley & Sons, New York) in the regular January - April 1983 issues."

This textbook provides a simple approach to understand the various complex aspects of stereochemistry. It deals with basic static stereochemistry and gives an overview of the different isomeric forms and nomenclatures. With simple writing style and many examples, this book covers the topics such as stereochemistry of hydrocarbons, alkenes, cycloalkenes, optically active compounds, trivalent carbon, fused, bridged and caged rings and related compounds. This textbook also covers the additional topics such as optical rotatory dispersion and circular dichroism, steroechemistry of elimination reactions, substitution reactions, rearrangement reactions and pericyclic reactions. The book includes pedagogical features like end-of-chapter problems and key concepts to help students in self-learning. The textbook is extremely useful for the senior undergraduate and postgraduate students pursuing course in chemistry, especially organic chemistry. Besides, this book will also be a useful reference book for professionals working in various chemical industries, biotechnology, bioscience and pharmacy.

Focusing on spectroscopic properties of molecular systems, Quantum Modeling of Molecular Materials presents the state-of-the-art methods in theoretical chemistry that are used to determine molecular properties relevant to different spectroscopies. This timely reference gives a basic presentation of response theory and its application to the simulation of spectroscopic properties of molecular materials. This in-depth presentation of time-dependent response theory and its applications in spectroscopy provides an important advance towards a modern vision of theoretical tools for researchers in academia and industry and postgraduate students.

From the beginnings of modern chemistry, molecular structure has been a lively area of research and speculation. For more than half a century spectroscopy and other methods have been available to characterize the structures and shapes of molecules, particularly those that are rigid. However, most molecules are at least to some degree non-rigid and this non-rigidity plays an important role in such diverse areas as biological activity, energy transfer, and chemical reactivity. In addition, the large-amplitude vibrations present in non-rigid molecules give rise to unusual low-energy vibrational level patterns which have a dramatic effect on the thermodynamic properties of these systems. Only in recent years has a coherent picture of the energetics and dynamics of the conformational changes inherent in non-rigid (and semi-rigid) molecules begun to emerge. Advances have been made in a number of different experimental areas: vibrational (infrared and Raman) spectroscopy, rotational (microwave) spectroscopy, electron diffraction, and, most recently, laser techniques probing both the ground and excited electronic states. Theoretically, the proliferation of powerful computers coupled with scientific insight has allowed both empirical and ab initio methods to increase our understanding of the forces responsible for the structures and energies of non-rigid systems. The development of theory (group theoretical methods and potential energy surfaces) to understand the unique characteristics of the spectra of these floppy molecules has also been necessary to reach our present level of understanding. The thirty chapters in this volume contributed by the key speakers at the Workshop are divided over the various areas. Both vibrational and rotational spectroscopy have been effective at determining the potential energy surfaces for non-rigid molecules, often in a complementary manner. Recent laser fluorescence work has extended these types of studies to electronic excited states. Electronic diffraction methods provide radial distribution functions from which both molecular structures and compositions of conformational mixtures can be found. Ab initio calculations have progressed substantially over the past few years, and, when carried out at a sufficiently high level, can accurately reproduce (or predict ahead of time) experimental findings. Much of the controversy of the ARW related to the question of when an ab initio is reliable. Since the computer programs are readily available, many poor calculations have been carried out. However, excellent results can be obtained from computations when properly done. A similar situation exists for experimental analyses. The complexities of non-rigid molecules are many, but major strides have been taken to understand their structures and conformational processes.

This book explains how peptide-based drug design works, what steps are needed to develop a peptide-based therapeutic, and challenges in synthesis as well as regulatory issues. It covers the design concept of peptide therapeutics from fundamental principles using structural biology and computational approaches. The chapters are arranged in a linear fashion. A fresh graduate or a scientist who works on small molecules can use this to follow the design and development of peptide therapeutics to use as understanding the basic concepts. Each chapter is written by experts from academia as well as industry. Rather than covering extensive literature, the book provides concepts of design, synthesis, delivery, as well as regulatory affairs and manufacturing of peptides in a systematic way with examples in each case. The book can be used as a reference for a pharmaceutical or biomedical scientist or graduate student who wants to pursue their career in peptide therapeutics. Some chapters will be written as a combination of basic principles and protocol so that scientists can adopt these methods to their research work. The examples provided can be used to perform peptide formulation considerations for the designed peptides. The book has nine chapters, and each chapter can be read as an independent unit on a particular concept.

The 14th Jerusalem Symposium continued the tradition of the pleasant and exciting meetings which once a year gather distinguished scientists, the world's most renowned experts in specific fields of quantum chemistry and biochemistry, in the impressive surroundings of the Israel Academy of Sciences and Humanities. The subject discussed this year - Intermolecular forces - is one of the utmost interest for all molecular sciences. I wish to thank all those who made this meeting possible and contributed toits success: the Baron Edmond de Rothschild whose continuous generosity guarantees the perenniality of our venture, t e Israel Academy of Sciences and in particular its Vice-President, Pr fes sor Yoshua Jortner for his devoted contribution to the organization and holding of this meeting, the high authorities of the Hebrew Uni versity of Jerusalem and in particular the Rector Meshulamfor their constant support and Dr. Pierre Claverie for his efficient help in the preparation of the program. Mrs Abigail Hyam and Mrs MyriamYogev must be thanked for their contribution to the efficiency and success of the local arrangements. Bernard Pullman ix B.Pullman ed.}, IntermolecularForces, ix. Copyright (c)1981byD.ReidelPublishingCompany. INTERMOLECULAR FORCES: WHAT CAN BE LEARNED FROM AB INITIO CALCULATIONS? Advan der Avoird Institute of Theoretical Chemistry, University of Nijmegen, Toernooiveld, Nijmegen, The Netherlands. 1. INTRODUCTION Various experiments, suc as elastic or rotationally inelastic molecular beamscattering(1,2 and spectroscopic studies of so-cafled Van der Waals molecules(3,4), have been designed especially to provide information about the Van der Waals interactions between molecules."

The Twenty Fourth Jerusalem Symposium reflected the high standards of these distinguished scientific meetings, which convene once a year at the Israel Academy of Sciences and Humanities in Jerusalem to discuss a specific topic in the broad area of quantum chemistry and biochemistry. The topic at this year's Jerusalem Symposium was mode selective chemistry, which constitutes a truly interdisciplinary subject of central interest in the areas of chemical physics, photochemistry and photobiology. The main theme of the Symposium was built around the exploration of the possibility and conditions for non-statistical reaction dynamics in molecules, van der Waals molecules, clusters and condensed phases. The main issues addressed photoselective and coherent excitation modes, bottlenecks for intramolecular vibrational energy redistribution, the consequences of the internal structure of many-atom systems and of rotational vibrational level structure for intramolecular dynamics, bond selective photodissociation, ultrafast chemical clocks for energy disposal, coherent control of photochemical reactions and nonstatistical unimolecular reaction dynamics. The interdisciplinary nature of this research area was deliberated by intensive and extensive interactions between theory and experiment. This volume provides a record of the invited lectures at the Symposium."

This book highlights the recent advances and state of the art in the use of functionalized nanostructured environments on catalysis. Nanoconfinements considered include well-defined molecular cages, imprinted self-assembled supramolecules, polymers made by living or controlled polymerization, metallorganic frameworks, carbon nanotubes, mesoporous inorganic solids, and hybrids thereof. Advantages of nanoconfinement of catalysts discussed include higher activities, improved selectivities, catalyst stabilization, cooperativity effects, simplified protocols for cascade syntheses, better catalyst recovery, and recyclability. The multiple applications that these materials offer are revolutionizing industrial sectors such as energy, electronics, sensors, biomedicine, and separation technology.

This essential volume explores a variety of tools and protocols of structure-based (homology modeling, molecular docking, molecular dynamics, protein-protein interaction network) and ligand-based (pharmacophore mapping, quantitative structure-activity relationships or QSARs) drug design for ranking and prioritization of candidate molecules in search of effective treatment strategy against coronaviruses. Beginning with an introductory section that discusses coronavirus interactions with humanity and COVID-19 in particular, the book then continues with sections on tools and methodologies, literature reports and case studies, as well as online tools and databases that can be used for computational anti-coronavirus drug research. Written for the Methods in Pharmacology and Toxicology series, chapters include the kind of practical detail and implementation advice that ensures high quality results in the lab. Comprehensive and timely, In Silico Modeling of Drugs Against Coronaviruses: Computational Tools and Protocols is an ideal reference for researchers working on the development of novel anti-coronavirus drugs for SARS-CoV-2 and for coronaviruses that will likely appear in the future.

The seventh Jerusalem Symposium has tried to penetrate into a field of research towards which the efforts of a large number of the most variegated modern techniques are conversing: molecular and quantum pharmacology. The hope to elucidate the mode of action of drugs, to establish correlations between the electronic and con formational structures of drugs and their mode of action and level of activity, to derive from these data the nature of the cellular receptors and an understanding of the interaction of the drugs with those receptors - is a strong stimulus to enlarge and deepen the research efforts with the ultimate view to rationalize the design of more efficient and more specific drugs. The Symposium represents an attempt to survey the progress made so far in this respect and the methods and efforts employed in order to arrive at even greater achievements. The presentation of this Symposium differs somewhat from that of the preceding ones. Owing to the political events which disturbed the peace in the Middle East and therefore the normal activities of commerce and industry in Israel at least temporarily, the printing and distribution of this volume were entrusted to the Reidel Publishing Company. We wish to thank them for their very efficient col1aboration and for all their efforts to publish this volume with a minimum delay."

Chemistry as an exact science.- Computational bottlenecks in molecular orbital calculations.- Variational transition state theory calculations of concerted hydrogen atom tunneling in water clusters and formaldehyde / water clusters.- Double many-body expansion potential energy surface for O4(3A), dynamics of the O(3P) + O3(1A1) reaction, and second virial coefficients of molecular oxygen.- The self-consistent reaction field model for molecular computations in solution.- New symmetry theorems and similarity rules for transition structures.- A topological analysis of macromolecular folding patterns.- Molecular mechanics.- Predicting the three-dimensional structure of proteins by homology-based model building.- Understanding chemical reactivity through the intersecting-state model.- The states of an electron pair and photochemical reactivity.- Ab-initio modelling of chemical reactivity using MC-SCF and VB methods.- The supra-supra mechanism of forbidden and allowed cycloaddition reactions: an analysis a VB model.- Excited state proton transfer reactions.- An exploratory study to correlate experimental and theoretical acidities of organic molecules.- Molecules with "volcanic" ground hypersurfaces. Structure, stability and energetics.- Molecular hydrogen as a ligand in transition metal complexes.- Molecular orbital studies of reductive elimination reactions.- Laboratory projects in computational organic chemistry.

"The Theory of Atomic Spectra," surrrrnanzlllg all that was then known about the quantum theory of free atoms; and in 1961, J.S. Griffith published "The Theory of Transition Metal Ions," in which he combined the ideas in Condon and Shortley's book with those of Bethe, Schlapp, Penney and Van Vleck. All this work, however, was done by physicists, and the results were reported in a way which was more accessable to physicists than to chemists. In the meantime, Carl J. Ballhausen had been studying quantum theory with W. Moffitt at Harvard; and in 1962 (almost simultaneously with Griffith) he published his extremely important book, "Introduction to Ligand Field Theory." This influential book was written from the standpoint of a chemist, and it became the standard work from which chemists learned the quantum theory of transition metal complexes. While it treated in detail the group theoretical aspects of crystal field theory, Carl J. Ballhausen's book also emphasized the limitations of the theory. As he pointed out, it is often not sufficient to treat the central metal ion as free (apart from the influence of the charges on the surrounding ligands): - In many cases hybridization of metal and ligand orbitals is significant. Thus, in general. a molecular orbital treatment is needed to describe transition metal complexes. However, much of the group theory developed In connection with crystal field theory can also be used in the molecular orbital treatment.

This overview compiles the on-going research in Europe to enlarge and deepen the understanding of the reaction mechanisms and pathways associated with the combustion of an increased range of fuels. Focus is given to the formation of a large number of hazardous minor pollutants and the inability of current combustion models to predict the formation of minor products such as alkenes, dienes, aromatics, aldehydes and soot nano-particles which have a deleterious impact on both the environment and on human health. Cleaner Combustion describes, at a fundamental level, the reactive chemistry of minor pollutants within extensively validated detailed mechanisms for traditional fuels, but also innovative surrogates, describing the complex chemistry of new environmentally important bio-fuels. Divided into five sections, a broad yet detailed coverage of related research is provided. Beginning with the development of detailed kinetic mechanisms, chapters go on to explore techniques to obtain reliable experimental data, soot and polycyclic aromatic hydrocarbons, mechanism reduction and uncertainty analysis, and elementary reactions. This comprehensive coverage of current research provides a solid foundation for researchers, managers, policy makers and industry operators working in or developing this innovative and globally relevant field.

In recent years, ever more electronic devices have started to exploit the advantages of organic semiconductors. The work reported in this thesis focuses on analyzing theoretically the energy level alignment of different metal/organic interfaces, necessary to tailor devices with good performance. Traditional methods based on density functional theory (DFT), are not appropriate for analyzing them because they underestimate the organic energy gap and fail to correctly describe the van der Waals forces. Since the size of these systems prohibits the use of more accurate methods, corrections to those DFT drawbacks are desirable. In this work a combination of a standard DFT calculation with the inclusion of the charging energy (U) of the molecule, calculated from first principles, is presented. Regarding the dispersion forces, incorrect long range interaction is substituted by a van der Waals potential. With these corrections, the C60, benzene, pentacene, TTF and TCNQ/Au(111) interfaces are analyzed, both for single molecules and for a monolayer. The results validate the induced density of interface states model.

In 1980. a distinguished group of scientists gathered In Washington. D. C. for an International Symposium on Aging and Cancer. Among the recommendations of this Symposium was to convene a future meeting to discuss the molecular basis for Interrelationships between aging and cancer when the appropriate scientific knowledge was available. That same year. the 13th Jerusalem Symposium on Quantum Chemistry and Biochemistry entitled .Carcl nogenesls: Fundamental Mechanisms and Environmental Effects.. was held. attended by some 50 International authorities In this field. At this meeting. It became clear that the fundamental process of carcinogenesis 15 Intimately associated with differentiation. which must also be mechanistically related to aging. It was therefore proposed that the next Jerusalem Symposium on Cancer could provide the appropriate forum for the study on the Interrelationship among cancer. aging and differentiation. The Impressive advances In our knowledge of the nature of the genome through molecular genetic and physical chemical techniques have now provided the opportunity to examine the Interrelationships between these complex biolo gical processes. Through the Isolation. cloning and rearranging of genes we are able to dissect and manipulate the genome In a fashion that was unanticipated only a decade ago. At the same time. the Increase In longevity and the Increased numbers of Individuals entering the last decades of life where cancer Incidences are highest raise the profound and practical question of whether aging and cancer are linked through common mechanisms."

Theoretical investigations of atoms and molecules interacting with pulsed or continuous wave lasers up to atomic field strengths on the order of 10 DEGREES16 W/cm are leading to an understanding of many challenging experimental discoveries. This book deals with the basics of femtosecond physics and goes up to the latest applications of new phenomena. The book presents an introduction to laser physics with mode-locking and pulsed laser operation. The solution of the time-dependent Schrodinger equation is discussed both analytically and numerically. The basis for the non-perturbative treatment of laser-matter interaction in the book is the numerical solution of the time-dependent Schrodinger equation. The light field is treated classically, and different possible gauges are discussed. Physical phenomena, ranging from Rabi-oscillations in two-level systems to the ionization of atoms, the generation of high harmonics, the ionization and dissociation of molecules as well as the control of chemical reactions are presented and discussed on a fundamental level. In this way the theoretical background for state of the art experiments with strong and short laser pulses is given. The text is augmented by more than thirty exercises, whose worked-out solutions are given in the last chapter. Some detailed calculations are performed in the appendices. Furthermore, each chapter ends with references to more specialized literature."