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 highlights a comprehensive introduction to the fundamental statistical mechanics underneath the inner workings of neural networks. The book discusses in details important concepts and techniques including the cavity method, the mean-field theory, replica techniques, the Nishimori condition, variational methods, the dynamical mean-field theory, unsupervised learning, associative memory models, perceptron models, the chaos theory of recurrent neural networks, and eigen-spectrums of neural networks, walking new learners through the theories and must-have skillsets to understand and use neural networks. The book focuses on quantitative frameworks of neural network models where the underlying mechanisms can be precisely isolated by physics of mathematical beauty and theoretical predictions. It is a good reference for students, researchers, and practitioners in the area of neural networks.

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.

"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 book focuses on theoretical and computational studies by the editor's group on the direct hydroxylation of methane, which is one of the most challenging subjects in catalyst chemistry. These studies of more than 20 years include gas-phase reactions by transition-metal oxide ions, enzymatic reactions by two types of methane monooxygenase (soluble and particulate MMO), catalytic reactions by metal-exchanged zeolites, and methane C-H activation by metal oxide surfaces. Catalyst chemistry has been mostly empirical and based on enormous experimental efforts. The subject of the title has been tackled using the orbital interaction and computations based on extended Huckel, DFT, and band structure calculations. The strength of the theoretical studies is in the synergy between theory and experiment. Therefore, the group has close contacts with experimentalists in physical chemistry, catalyst chemistry, bioinorganic chemistry, inorganic chemistry, and surface chemistry. This resulting book will be useful for the theoretical analysis and design of catalysts.

This is a comprehensive textbook addressing the unique aspects of drug development for ophthalmic use. Beginning with a perspective on anatomy and physiology of the eye, the book provides a critical appraisal of principles that underlie ocular drug product development. The coverage encompasses topical and intraocular formulations, small molecules and biologics (including protein and gene therapies), conventional formulations (including solutions, suspensions, and emulsions), novel formulations (including nanoparticles, microparticles, and hydrogels), devices, and specialty products. Critical elements such as pharmacokinetics, influence of formulation technologies and ingredients, as well as impact of disease conditions on products development are addressed. Products intended for both the front and the back of the eye are discussed with an eye towards future advances.

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.

This book presents a comprehensive overview of state-of-the-art quantum dot photodetectors, including device fabrication technologies, optical engineering/manipulation strategies, and emerging photodetectors with building blocks of novel quantum dots (e.g. perovskite) as well as their hybrid structured (e.g. 0D/2D) materials. Semiconductor quantum dots have attracted much attention due to their unique quantum confinement effect, which allows for the facile tuning of optical properties that are promising for next-generation optoelectronic applications. Among these remarkable properties are large absorption coefficient, high photosensitivity, and tunable optical spectrum from ultraviolet/visible to infrared region, all of which are very attractive and favorable for photodetection applications. The book covers both fundamental and frontier research in order to stimulate readers' interests in developing novel ideas for semiconductor photodetectors at the center of future developments in materials science, nanofabrication technology and device commercialization. The book provides a knowledge sharing platform and can be used as a reference for researchers working in the fields of photonics, materials science, and nanodevices.

Proteins are exposed to various interfacial stresses during drug product development. They are subjected to air-liquid, liquid-solid, and, sometimes, liquid-liquid interfaces throughout the development cycle-from manufacturing of drug substances to storage and drug delivery. Unlike small molecule drugs, proteins are typically unstable at interfaces where, on adsorption, they often denature and form aggregates, resulting in loss of efficacy and potential immunogenicity. This book covers both the fundamental aspects of proteins at interfaces and the quantification of interfacial behaviors of proteins. Importantly, this book introduces the industrial aspects of protein instabilities at interfaces, including the processes that introduce new interfaces, evaluation of interfacial instabilities, and mitigation strategies. The audience that this book targets encompasses scientists in the pharmaceutical and biotech industry, as well as faculty and students from academia in the surface science, pharmaceutical, and medicinal chemistry areas.

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.

This is a textbook on the theory and calculation of molecular electromagnetic and spectroscopic properties designed for a one-semester course with lectures and exercise classes. The idea of the book is to provide thorough background knowledge for the calculation of electromagnetic and spectroscopic properties of molecules with modern quantum chemical software packages.
The book covers the derivation of the molecular Hamiltonian in the presence of electromagnetic fields, and of time-independent and time-dependent perturbation theory in the form of response theory. It defines many molecular properties and spectral parameters and gives an introduction to modern computational chemistry methods.

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.

This book provides a unique and comprehensive overview of the latest advances, challenges and accomplishments in the rapidly growing field of theoretical and computational materials science. Today, an increasing number of industrial communities rely more and more on advanced atomic-scale methods to obtain reliable predictions of materials properties, complement qualitative experimental analyses and circumvent experimental difficulties. The book examines some of the latest and most advanced simulation techniques currently available, as well as up-to-date theoretical approaches adopted by a selected panel of twelve international research teams. It covers a wide range of novel and advanced materials, exploring their structural, elastic, optical, mass and electronic transport properties. The cutting-edge techniques presented appeal to physicists, applied mathematicians and engineers interested in advanced simulation methods in materials science. The book can also be used as additional literature for undergraduate and postgraduate students with majors in physics, chemistry, applied mathematics and engineering.

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."

This book provides an authoritative up-to-date summary of the chemistry and applications of polyoxometalates with emphasis on new synthetic strategies directed towards functionalized organic derivatives, self-assembly of mesoscopic composite polyoxoanions, generation of framework materials and thin oxide films, extended optical, magnetic, and electrical properties, applications in homogeneous and nanocluster-based catalysts, photocatalytic water decontamination, ribosomal crystallography, and topological aspects of large symmetrical structures.

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."

Radicals play a major role as intermediates in many chemical reactions. They contribute to transformations in the atmosphere, living organisms, chemical synthesis, combustion and detonation amongst others. This comprehensive and conclusive book discusses all these aspects. N-centered Radicals deals with NOx and NCO, relatively stable radicals whose presence in the atmosphere influences the metabolism of living organisms. Also included are NHx, NCH and N3, important in radical studies, chemical synthesis, detonation and metabolism. Until now there has been no single volume bringing together all aspects of N-centered radical chemistry, from formation, to their chemistry in aqueous environments, biological systems and the atmosphere. N-centered Radicals is essential reading for researchers in organic, physical and environmental chemistry, biology and all others examining the effects of N-centered radicals.

This book uses experimental and computational methods to rationalize and predict for the first time the relative impact sensitivities of a range of energetic materials. Using knowledge of crystal structures, vibrational properties, energy-transfer mechanisms, and experimentally measured sensitivities, it describes a model that leads to excellent correlation with experimental results in all cases. As such, the book paves the way for a new, fully ab initio approach for the design of safer energetic materials based solely on knowledge of their solid-state structures. Energetic materials (explosives, propellants, gas generators, and pyrotechnics) are defined as materials that release heat and/or gaseous products at a high rate upon stimulus by heat, impact, shock, sparks, etc. They have widespread military and civilian uses, including munitions, mining, quarrying, demolition, emergency signaling, automotive safety, and space exploration. One of their most important properties is sensitivity to accidental initiation during manufacture, transport, storage, and operation, which has important implications for their safe use.

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."

Since 1983 I have been delivering lectures at Budapest University that are mainly attended by chemistry students who have already studied quantum chem istry in the amount required by the (undergraduate) chemistry curriculum of the University, and wish to acquire deeper insight in the field, possibly in prepara tion of a master's or Ph.D. thesis in theoretical chemistry. In such a situation, I have the freedom to discuss, in detail, a limited number of topics which I feel are important for one reason or another. The exact coverage may vary from year to year, but I usually concentrate on the general principles and theorems and other basic theoretical results which I foresee will retain their importance despite the rapid development of quantum chemistry. I commonly organize my lectures by treating the subject from the begin ning, without referring explicitly to any actual previous knowledge in quantum chemistry-only some familiarity with its goals, approaches and, to a lesser ex tent, techniques is supposed. I concentrate on the formulae and their derivation, assuming the audience essentially understands the reasons for deriving these results. This book is basically derived from the material of my lectures. The spe cial feature, distinguishing it from most other textbooks, is that all results are explicitly proved or derived, and the derivations are presented completely, step by step. True understanding of a theoretical result can be achieved only if one has gone through its derivation."

This thesis demonstrates how molecular modeling techniques can be used to gain significant insights into numerous applications that are increasingly attracting research interest because of their societal importance. It presents innovative ideas that, by altering the fundamental physical phenomena occurring at the solid/liquid interface, allow the fluid transport in nanochannels to be manipulated so as to improve the performance of the practical applications. The applications explicitly considered in this thesis are the design of drag-reducing and self-cleaning surfaces; water desalination; and shale gas exploration - all of which are, to some extent, governed by nanoscale fluid transport. Overall, this thesis is useful for students and researchers entering the field who wish to understand how molecular modeling can improve the performance in a wide range of applications.

In this volume we have collected some of the contributions made to the Twelfth European Workshop on Quantum Systems in Chemistry and Physics (QSCP-XII) in 2007. The workshop was held at Royal Holloway College, the most westerly campusof the University of London,and situated just a stone's throw from Windsor Great Park. The workshop, which ran from 30 August to 5 September, continued the series that was established by Roy McWeeny in April 1996 with a meeting held at San Miniato, near Pisa. The purpose of the QSCP workshops is to bring together, in an informal atmosphere and with the aim of fostering collaboration, those chemists and physicists who share a common ?eld of interest in the theory of the quantum many-body problem. Quantum mechanics provides a theoretical foundation for our understandingof the structure,propertiesanddynamicsof atoms, moleculesandthe solid state, in terms of their component particles: electrons and nuclei. The study of 'Quantum Systems in Chemistry and Physics' therefore underpins many of the emerging?elds in twenty-?rstcenturyscience andtechnology:nanostructure,smart materials, drug design - to name but a few. Members of the workshop were keen to discuss their research and engage in collaboration centred upon the development of fundamental and innovative theory which would lead to the exploration of new concepts. The proceedings of all of the workshops, which have been held annually since 1996, have been published both to disseminate the latest developments within the wider community and to stimulate further collaboration.

This book offers an easy-to-understand introduction to the computational mass transfer (CMT) method. On the basis of the contents of the first edition, this new edition is characterized by the following additional materials. It describes the successful application of this method to the simulation of the mass transfer process in a fluidized bed, as well as recent investigations and computing methods for predictions for the multi-component mass transfer process. It also demonstrates the general issues concerning computational methods for simulating the mass transfer of the rising bubble process. This new edition has been reorganized by moving the preparatory materials for Computational Fluid Dynamics (CFD) and Computational Heat Transfer into appendices, additions of new chapters, and including three new appendices on, respectively, generalized representation of the two-equation model for the CMT, derivation of the equilibrium distribution function in the lattice-Boltzmann method, and derivation of the Navier-Stokes equation using the lattice-Boltzmann model. This book is a valuable resource for researchers and graduate students in the fields of computational methodologies for the numerical simulation of fluid dynamics, mass and/or heat transfer involved in separation processes (distillation, absorption, extraction, adsorption etc.), chemical/biochemical reactions, and other related processes.

The title of this volume implies a progression of sorts from species of molecular size to a product described on the basis of continuum prop erties. The difference in approach from the standpoint of molecular be havior, on the one hand-more the forte of chemists-and from the standpoint of large-scale properties, on the other-more the province of chemical engineers and materials scientists-represents a severe cultural divide, but one with much potential for creative input from both sides. Chapter 1 of this volume attempts a broad survey of trends toward the synthesis of large, well-defined molecular systems with interesting physical, chemical, or material properties. Review articles with more de tailed treatments are emphasized. In Chapter 2, Newkome and Moore field summarize work on synthesis of /I cascade" molecules. Next, Denti, Campagna, and Balzani describe the synthesis of assemblies with con nected metal-containing chromophore units which transmit electrons or electronic energy in defined ways. In Chapter 4 Wuest describes the con struction of hydrogen-bonded organic networks, and in Chapter 5 Michl defines a molecular-level construction set. Finally, Jaszczak points out how nature's attempts over geological time spans are emulated by recent human synthetic activity in the fullerene arena, through the appearance of various morphologies of natural graphite. The book concludes with a method for describing fractal-like mole cules, and an index based on the method for appropriate compounds described in the text."