This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2019. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to computer science with a special emphasis on industrially relevant applications. Presenting findings of one of Europe's leading systems, this volume covers a wide variety of applications that deliver a high level of sustained performance. The book covers the main methods in high-performance computing. Its outstanding results in achieving the best performance for production codes are of particular interest for both scientists and engineers. The book comes with a wealth of color illustrations and tables of results.

This book addresses the construction and application of the major types of basis sets for computational chemistry calculations. In addition to a general introduction, it includes mathematical basics and a discussion of errors arising from incomplete or inappropriate basis sets. The different chapters introduce local orbitals and orbital localization as well as Slater-type orbitals and review basis sets for special applications, such as those for correlated methods, solid-state calculations, heavy atoms and time-dependent adaptable Gaussian bases for quantum dynamics simulations. This detailed review of the purpose of basis sets, their design, applications, possible problems and available solutions provides graduate students and beginning researchers with information not easily obtained from the available textbooks and offers valuable supporting material for any quantum chemistry or computational chemistry course at the graduate and/or undergraduate level. This book is also useful as a guide for researchers who are new to computational chemistry but are willing to extend their research tools by applying such methods.

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

This book discusses recent advances in theoretical-computational studies on the biosynthesis of melanin pigment (melanogenesis). These advances are being driven by the development of high-performance computers, new experimental findings, and extensive work on medical applications involving the control of pigmentation and the treatment of challenging dermatological diseases. Understanding the elementary processes involved in chemical reactions at the atomic scale is important in biochemical reaction design for effective control of the pigmentary system. Accordingly, the book focuses on the elementary steps involved in melanogenesis, which crucially affect the composition of the resulting melanin pigment by means of competitive reactions. The book also addresses reactions analogous to melanogenesis, with a focus on o-quinone reactions, which are especially important for understanding melanogenesis-associated cytotoxicity.

This book presents a comprehensive overview of the fundamental concept, design, working protocols, and diverse photo-chemicals aspects of different solar cell systems with promising prospects, using computational and experimental techniques. It presents and demonstrates the art of designing and developing various solar cell systems through practical examples. Compared to most existing books in the market, which usually analyze existing solar cell approaches this volume provides a more comprehensive view on the field. Thus, it offers an in-depth discussion of the basic concepts of solar cell design and their development, leading to higher power conversion efficiencies. The book will appeal to readers who are interested in both fundamental and application-oriented research while it will also be an excellent tool for graduates, researchers, and professionals working in the field of photovoltaics and solar cell systems.

This textbook facilitates students' ability to apply fundamental principles and concepts in classical thermodynamics to solve challenging problems relevant to industry and everyday life. It also introduces the reader to the fundamentals of statistical mechanics, including understanding how the microscopic properties of atoms and molecules, and their associated intermolecular interactions, can be accounted for to calculate various average properties of macroscopic systems. The author emphasizes application of the fundamental principles outlined above to the calculation of a variety of thermodynamic properties, to the estimation of conversion efficiencies for work production by heat interactions, and to the solution of practical thermodynamic problems related to the behavior of non-ideal pure fluids and fluid mixtures, including phase equilibria and chemical reaction equilibria. The book contains detailed solutions to many challenging sample problems in classical thermodynamics and statistical mechanics that will help the reader crystallize the material taught. Class-tested and perfected over 30 years of use by nine-time Best Teaching Award recipient Professor Daniel Blankschtein of the Department of Chemical Engineering at MIT, the book is ideal for students of Chemical and Mechanical Engineering, Chemistry, and Materials Science, who will benefit greatly from in-depth discussions and pedagogical explanations of key concepts. Distills critical concepts, methods, and applications from leading full-length textbooks, along with the author's own deep understanding of the material taught, into a concise yet rigorous graduate and advanced undergraduate text; Enriches the standard curriculum with succinct, problem-based learning strategies derived from the content of 50 lectures given over the years in the Department of Chemical Engineering at MIT; Reinforces concepts covered with detailed solutions to illuminating and challenging homework problems.

This book covers intentional design aspects for combinations of drugs, single-molecule hybrids with potential or actual multiple actions, pro-drugs which could yield multiple activity outcomes, and future possibilities. The approach of the book is interdisciplinary, and it provides greater understanding of the complex interplay of factors involved in the medicinal chemistry design and laboratory development of multiply active antibacterials. The scope of the book appeals to readers who are researching in the field of antibacterials using the approach of medicinal chemistry design and drug development.

In simple language, without mathematics, this book explains the strange and exciting ideas that make the subatomic world so different from the world of the every day. It offers the general reader access to one of the greatest discoveries in the history of physics and one of the oustanding intellectual achievements of the twentieth century.

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 book is designed to serve as a textbook for core courses offered to postgraduate students enrolled in chemistry. This book can also be used as a core or supplementary text for nuclear chemistry courses offered to students of chemical engineering. The book covers various topics of nuclear chemistry like Shell model, fission/fusion reaction, natural radioactive equilibrium series, nuclear reactions carried by various types of accelerators. In addition, it describes the law of decay of radioactivity, type of decay, and interaction of radiation with matter. It explains the difference between ionization counter, scintillation counter and solid state detector. This book also consists of end-of-book problems to help readers aid self-learning. The detailed coverage and pedagogical tools make this an ideal textbook for postgraduate students and researchers enrolled in various chemistry and engineering courses. This book will also be beneficial for industry professionals in the allied fields.

This book explores the potential of quantum crystallography. The field accompanied the major milestones of x-ray diffraction and it has undergone a rapid evolution in the past few years. For this reason, some reflections are necessary in order to scrutinize the next steps and anticipate the future developments. After a short survey of the historical background and in depth description of the state of the art, some examples are provided of current and future applications of the know-how in this discipline. This implies attracting readership of both experts in the field and neophytes. The former will test their own views with the one exposed in the book; the newcomers, instead, will learn both what has been done and what could be done with quantum crystallography.

Valence bond theory is one of two commonly used methods in molecular quantum mechanics, the other is molecular orbital theory. This book focuses on the first of these methods, ab initio valence bond theory. The book is split into two parts. Part I gives simple examples of two-electron calculations and the necessary theory to extend these to larger systems. Part II gives a set of case studies of related molecule sets designed to show the nature of the valence bond description of molecular structure. It also highlights the stability of this description to varying basis sets. There are references to the CRUNCH computer program for molecular structure calculations which is currently available in the public domain. The book will be of primary interest to researchers and students working on electronic theory and computation in chemistry and chemical physics.

This book deals with a central topic at the interface of chemistry and physics-the understanding of how the transformation of matter takes place at the atomic level. Building on the laws of physics, the book focuses on the theoretical framework for predicting the outcome of chemical reactions. The style is highly systematic with attention to basic concepts and clarity of presentation. The emphasis is on concepts and insights obtained via analytical theories rather than computational and numerical aspects. Molecular reaction dynamics is about the detailed atomic-level description of chemical reactions. Based on quantum mechanics and statistical mechanics, the dynamics of uni- and bi-molecular elementary reactions are described. The book features a comprehensive presentation of transition-state theory which plays an important role in practice, and a detailed discussion of basic theories of reaction dynamics in condensed phases. Examples and end-of-chapter problems are included in order to illustrate the theory and its connection to chemical problems. The second edition includes updated descriptions of adiabatic and non-adiabatic electron-nuclear dynamics, an expanded discussion of classical two-body models of chemical reactions, including the Langevin model, additional material on quantum tunnelling and its implementation in Transition-State Theory, and a more thorough description of the Born and Onsager models for solvation.

This volume summarises recent developments and highlights new techniques which will define possible future directions for small molecule X-ray crystallography. It provides an insight into how specific aspects of crystallography are developing and shows how they may interact or integrate with other areas of science. The development of more sophisticated equipment and the massive rise in computing power has made it possible to solve the three-dimensional structure of an organic molecule within hours if not minutes. This successful trajectory has resulted in the ability to study ever more complex molecules and use smaller and smaller crystals. The structural parameters for over a million organic and organometallic compounds are now archived in the most commonly used database and this wealth of information creates a new set of problems for future generations of scientists. The volume provides some insight into how users of crystallographic structural data banks can navigate their way through a world where "big data" has become the norm. The coupling of crystallography to quantum chemical calculations provides detailed information about electron distributions in crystals affording a much more detailed analysis of bonding than has been possible previously. In quantum crystallography, quantum mechanical wavefunctions are used to extract information about bonding and properties from the measured X-ray structure factors. The advent of quantum crystallography has resulted in form and structure factors derived from quantum mechanics which have been used in advanced refinement and wavefunction fitting. This volume describes how quantum mechanically derived atomic form factors and structure factors are constructed to allow the improved description of the diffraction experiment. It further discusses recent developments in this field and illustrates their applications with a wide range of examples. This volume will be of interest to chemists and crystallographers with an interest in the synthesis, characterisation and physical and catalytic properties of solid-state materials. It will also be relevant for the community of computational chemists who study chemical systems. Postgraduate students entering the field will benefit from a historical introduction to the way in which scientists have used the data derived from crystallography to develop new structural and bonding models.

This volume summarises recent developments and possible future directions for small molecule X-ray crystallography. It reviews specific areas of crystallography which are rapidly developing and places them in a historical context. The interdisciplinary nature of the technique is emphasised throughout. It introduces and describes the chemical crystallographic and synchrotron facilities which have been at the cutting edge of the subject in recent decades. The introduction of new computer-based algorithms has proved to be very influential and stimulated and accelerated the growth of new areas of science. The challenges which will arise from the acquisition of ever larger databases are considered and the potential impact of artificial intelligence techniques stressed. Recent advances in the refinement and analysis of X-ray crystal structures are highlighted. In addition the recent developments in time resolved single crystal X-ray crystallography are discussed. Recent years have demonstrated how this technique has provided important mechanistic information on solid-state reactions and complements information from traditional spectroscopic measurements. The volume highlights how the prospect of being able to routinely "watch" chemical processes as they occur provides an exciting possibility for the future. Recent advances in X-ray sources and detectors that have also contributed to the possibility of dynamic single-crystal X-ray diffraction methods are presented. The coupling of crystallography and quantum chemical calculations provides detailed information about electron distributions in crystals and has resulted in a more detailed understanding of chemical bonding. The volume will be of interest to chemists and crystallographers with an interest in the synthesis, characterisation and physical and catalytic properties of solid-state materials. Postgraduate students entering the field will benefit from a historical introduction to the subject and a description of those techniques which are currently used. Since X-ray crystallography is used so widely in modern chemistry it will serve to alert senior chemists to those developments which will become routine in coming decades. It will also be of interest to the broad community of computational chemists who study chemical systems.

This graduate level text presents the first comprehensive overview of modern chemical valency and bonding theory, written by internationally recognised experts in the field. The authors build on the foundation of Lewis- and Pauling-like localized structural and hybridization concepts to present a book that is directly based on current ab-initio computational technology. The presentation is highly visual and intuitive throughout, based on the recognizable and transferable graphical forms of natural bond orbitals (NBOs) and their spatial overlaps in the molecular environment. The book shows applications to a broad range of molecular and supramolecular species of organic, inorganic and bioorganic interest. Hundreds of orbital illustrations help to convey the essence of modern NBO concepts for those with no extensive background in the mathematical machinery of the Schroedinger equation. This book will appeal to those studying chemical bonding in relation to chemistry, chemical engineering, biochemistry and physics.

This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.

This book deals with the basic principles and techniques of nonequilibrium statistical mechanics. The importance of this subject is growing rapidly in view of the advances being made, both experimentally and theoretically, in statistical physics, chemical physics, biological physics, complex systems and several other areas. The presentation of topics is quite self-contained, and the choice of topics enables the student to form a coherent picture of the subject. The approach is unique in that classical mechanical formulation takes center stage. The book is of particular interest to advanced undergraduate and graduate students in engineering departments.

This book provides advanced undergraduate and graduate students with an overview of the fundamentals of cold and ultracold chemistry. Beginning with definitions of what cold and ultracold temperatures mean in chemistry, the book then takes the student through the essentials of scattering theory (classical and quantum mechanical), light-matter interaction, reaction dynamics and Rydberg physics. The author aims to show the reader the richness of the topic while motivating students to understand the fundamentals of these intriguing reactions and underlying connecting relationships. Including material which was previously only found in specialized review articles, this book provides students working in the fields of ultracold gases, chemical physics and physical chemistry with the tools they need to immerse themselves in the realm of cold and ultracold chemistry. This book opens up the exciting chemical laws which govern chemistry at low temperatures to the next generation of researchers.

This book focuses on the computational modeling of organometallic reactivity. In recent years, computational methods, particularly those based on Density Functional Theory (DFT) have been fully incorporated into the toolbox of organometallic chemists' methods. Nowadays, energy profiles of multistep processes are routinely calculated, and detailed mechanistic pictures of the reactions arise from these calculations. This type of analysis is increasingly performed even by experimentalists themselves. The volume aims to connect established computational organometallics with the more recent theoretical and methodological developments applied to this field. This would allow broadening of the simulation scope toward emergent organometallic areas (as ligand design or photoactivated processes), to narrow the gap between calculations and experiments (microkinetic models) and even to discover new reactions (automated methods). Given the broad interest and extensive application that computational methods have reached within the organometallic community, this new volume will attract the interest of both experimental and computational organometallic chemists.

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 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.

This book covers the role of water in global atmospheric phenomena, focussing on the physical processes involving water molecules and water microparticles. It presents the reader with a detailed look at some of the most important types of global atmospheric phenomena involving water, such as water circulation, atmospheric electricity and the greenhouse effect. Beginning with the cycle of water evaporation and condensation, and the important roles played by the nucleation and growth processes of water microdroplets, the book discusses atmospheric electricity as a secondary phenomenon of water circulation in the atmosphere, comprising a chain of processes involving water molecules and water microdroplets. Finally, the book discusses aspects of the molecular spectroscopy of greenhouse atmospheric components, showing how water molecules and water microdroplets give the main contribution to atmospheric emission in the infrared spectrum range. Featuring numerous didactic schematics and appendices detailing all necessary unit conversion factors, this book is useful to both active researchers and doctoral students working in the fields of atmospheric physics, climate science and molecular spectroscopy.

The Science and Business of Drug Discovery is written for those who want to learn about the biopharmaceutical industry and its products whatever their level of technical knowledge. Its aim is to demystify the jargon used in drug development, but in a way that avoids over simplification and the resulting loss of key information. Each of the twenty chapters is illustrated with figures and tables which clarify some of the more technical points being made. Also included is a drug discovery case history which draws the relevant material together into a single chapter. In recognizing that it is difficult to navigate through the many external resources dealing with drug development, the book has been written to guide the reader towards the most appropriate information sources, including those listed in the two appendices. The following topics are covered: Different types of drugs: from small molecules to stem cells Background to chemistry of small and large molecules Historical background to drug discovery, pharmacology and biotechnology The drug discovery pipeline: from target discovery to marketed medicine Commercial aspects of drug discovery Challenges to the biopharmaceutical industry and its responses Material of specific interest to technology transfer executives, recruiters and pharmaceutical translators

This book covers recent advances of the fragment molecular orbital (FMO) method, consisting of 5 parts and a total of 30 chapters written by FMO experts. The FMO method is a promising way to calculate large-scale molecular systems such as proteins in a quantum mechanical framework. The highly efficient parallelism deserves being considered the principal advantage of FMO calculations. Additionally, the FMO method can be employed as an analysis tool by using the inter-fragment (pairwise) interaction energies, among others, and this feature has been utilized well in biophysical and pharmaceutical chemistry. In recent years, the methodological developments of FMO have been remarkable, and both reliability and applicability have been enhanced, in particular, for non-bio problems. The current trend of the parallel computing facility is of the many-core type, and adaptation to modern computer environments has been explored as well. In this book, a historical review of FMO and comparison to other methods are provided in Part I (two chapters) and major FMO programs (GAMESS-US, ABINIT-MP, PAICS and OpenFMO) are described in Part II (four chapters). dedicated to pharmaceutical activities (twelve chapters). A variety of new applications with methodological breakthroughs are introduced in Part IV (six chapters). Finally, computer and information science-oriented topics including massively parallel computation and machine learning are addressed in Part V (six chapters). Many color figures and illustrations are included. Readers can refer to this book in its entirety as a practical textbook of the FMO method or read only the chapters of greatest interest to them.