Theoretical and Computational Chemistry Series – serie

This is currently the only book available on the development of knowledge-based, and related, expert systems in chemistry and toxicology. Written by a pioneer in the field, it shows how computers can work with qualitative information where precise numerical methods are not satisfactory. An underlying theme is the current concern in society about the conflicts between basing decisions on reasoned judgements and wanting precise decisions and measurable effectiveness. As well as explaining how the computer programs work, the book provides insights into how personal and political factors influence scientific progress. The introduction of regulations such as REACH in Europe and modifications to UN and OECD Guidelines on assessment of chemical hazard mean that the use of toxicity prediction is at a turning point. They put a heavy burden on the chemical industry but, for the first time, allow for the use of computer prediction to support or replace in vivo and in vitro experiments. There is increasing recognition among scientists and regulators that qualitative computer methods have much to offer and that in some circumstances they may be more reliable and informative than quantitative methods. This excellent introduction to a field where employment opportunities are growing is aimed at students, scientists and academics with a knowledge of chemistry.

London dispersion interactions are responsible for numerous phenomena in physics, chemistry and biology. Recent years have seen the development of new, physically well-founded models, and dispersion-corrected density functional theory (DFT) is now a hot topic of research. This book is an overview of current understanding of the physical origin and modelling of London dispersion forces manifested at an atomic level. It covers a wide range of system, from small intermolecular complexes, to organic molecules and crystalline solids, through to biological macromolecules and nanostructures. In presenting a broad overview of the of the physical foundations of dispersion forces, the book provides theoretical, physical and synthetic chemists, as well as solid-state physicists, with a systematic understanding of the origins and consequences of these ubiquitous interactions. The presentation is designed to be accessible to anyone with intermediate undergraduate mathematics, physics and chemistry.

Covering computational tools in drug design using techniques from chemoinformatics, molecular modelling and computational chemistry, this book explores these methodologies and applications of in silico medicinal chemistry. The first part of the book covers molecular representation methods in computing in terms of chemical structure, together with guides on common structure file formats. The second part examines commonly used classes of molecular descriptors. The third part provides a guide to statistical learning methods using chemical structure data, covering topics such as similarity searching, clustering and diversity selection, virtual library design, ligand docking and de novo design. The final part of the book summarises the application of methods to the different stages of drug discovery, from target ID, through hit finding and hit-to-lead, to lead optimisation. This book is a practical introduction to the subject for researchers new to the fields of chemoinformatics, molecular modelling and computational chemistry.

The simulation of enzymatic processes is a well-established field within computational chemistry, as demonstrated by the 2013 Nobel Prize in Chemistry. It has been attracting increasing attention in recent years due to the potential applications in the development of new drugs or new environmental-friendly catalysts. Featuring contributions from renowned authors, including Nobel Laureate Arieh Warshel, this book explores the theories, methodologies and applications in simulations of enzyme reactions. It is the first book offering a comprehensive perspective of the field by examining several different methodological approaches and discussing their applicability and limitations. The book provides the basic knowledge for postgraduate students and researchers in chemistry, biochemistry and biophysics, who want a deeper understanding of complex biological process at the molecular level.

Exploring current themes in modern computational and membrane protein biophysics, this book presents a comprehensive account of the fundamental principles underlying different methods and techniques used to describe the intriguing mechanisms by which membrane proteins function. The book discusses the experimental approaches employed to study these proteins, with chapters reviewing recent crucial structural advances that have allowed computational biophysicists to discern how these molecular machines work. The book then explores what computational methods are available to researchers and what these have taught us about three key families of membrane proteins: ion channels, transporters and receptors. The book is ideal for researchers in computational chemistry and computational biophysics.

Recent years have seen tremendous progress in research on cold and controlled molecular collisions, both in theory and in experiment. The advent of techniques to prepare cold and ultracold molecules and ions, to store them in optical lattices or in charged quasicristalline structures, and to use them in crossed or merged beam experiments have opened many new possibilities to study the most fundamental aspects of molecular interactions. At the same time, theoretical work has made progress in tackling these problems and accurately describing quantum effects in complex systems, and in proposing viable options to control chemical reactions at ultralow energies. Through tutorials on both the theoretical and experimental aspects of research in cold and ultracold molecular collisions, this book provides advanced undergraduate students, graduate students and researchers with the foundations needed to understand this exciting field.

Over the past few decades, experimental excited state chemistry has moved into the femtochemistry era, where time resolution is short enough to resolve nuclear dynamics. Recently, the time resolution has moved into the attosecond domain, where electronic motion can be resolved as well. Theoretical chemistry is becoming an essential partner in such experimental investigations; not only for the interpretation of the results, but also to suggest new experiments.This book provides an integrated approach. The three main facets of excited-state theoretical chemistry; namely, mechanism, which focuses on the shape of the potential surface along the reaction path, multi-state electronic structure methods, and non-adiabatic dynamics, have been brought together into one volume. Theoretical Chemistry for Electronic Excited States is aimed at both theorists and experimentalists, involved in theoretical chemistry, in electronic structure computations and in molecular dynamics. The book will provide both with the knowledge and understanding to discover ways to work together more closely through its unified approach.

Attosecond science is a new and rapidly developing research area in which molecular dynamics are studied at the timescale of a few attoseconds. Within the past decade, attosecond pump–probe spectroscopy has emerged as a powerful experimental technique that permits electron dynamics to be followed on their natural timescales. With the development of this technology, physical chemists have been able to observe and control molecular dynamics on attosecond timescales. From these observations it has been suggested that attosecond to few-femtosecond timescale charge migration may induce what has been called “post-Born-Oppenheimer dynamics”, where the nuclei respond to rapidly time-dependent force fields resulting from transient localization of the electrons. These real-time observations have spurred exciting new advances in the theoretical work to both explain and predict these novel dynamics.This book presents an overview of current theoretical work relevant to attosecond science written by theoreticians who are presently at the forefront of its development. It is a valuable reference work for anyone working in the field of attosecond science as well as those studying the subject.

Self-propelled objects (particles, droplets) are autonomous agents that can convert energy from the environment into motion. These motions include nonlinear behaviour such as oscillations, synchronization, bifurcation, and pattern formation. In recent years, there has been much interest in self-propelled objects for their potential role in mass transport or their use as carriers in confined spaces. An improved understanding of self-organized motion has even allowed researchers to design objects for specific motion.This book gives an overview of the principles of self-propelled motion in chemical objects (particles, droplets) far from their thermodynamic equilibrium, at various spatial scales. Theoretical aspects, the characteristics of the motion and the design procedures of such systems are discussed from the viewpoint of nonlinear dynamics and examples of applications for these nonlinear systems are provided.This book is suitable for researchers and graduate students interested in physical and theoretical chemistry as well as soft matter.

As analysis, in terms of detection limits and technological innovation, in chemical and biological fields has developed so computational techniques have advanced enabling greater understanding of the data. Indeed, it is now possible to simulate spectral data to an excellent level of accuracy, allowing chemists and biologists access to robust and reliable analytical methodologies both experimentally and theoretically. This work will serve as a definitive overview of the field of computational simulation as applied to analytical chemistry and biology, drawing on recent advances as well as describing essential, established theory. Computational approaches provide additional depth to biochemical problems, as well as offering alternative explanations to atomic scale phenomena. Highlighting the innovative and wide-ranging breakthroughs made by leaders in computational spectrum prediction and the application of computational methodologies to analytical science, this book is for graduates and postgraduate researchers showing how computational analytical methods have become accessible across disciplines. Contributed chapters originate from a group of internationally-recognised leaders in the field, each applying computational techniques to develop our understanding of and supplement the data obtained from experimental analytical science.

There have been significant developments in the use of knowledge-based expert systems in chemistry since the first edition of this book was published in 2009. This new edition has been thoroughly revised and updated to reflect the advances.The underlying theme of the book is still the need for computer systems that work with uncertain or qualitative data to support decision-making based on reasoned judgements. With the continuing evolution of regulations for the assessment of chemical hazards, and changes in thinking about how scientific decisions should be made, that need is ever greater. Knowledge-based expert systems are well established in chemistry, especially in relation to toxicology, and they are used routinely to support regulatory submissions. The effectiveness and continued acceptance of computer prediction depends on our ability to assess the trustworthiness of predictions and the validity of the models on which they are based.Written by a pioneer in the field, this book provides an essential reference for anyone interested in the uses of artificial intelligence for decision making in chemistry.

Hydrogen bonded systems play an important role in all aspects of science but particularly chemistry and biology. Notably, the helical structure of DNA is heavily reliant on the hydrogens bonds between the DNA base pairs. Although the area of hydrogen bonding is one that is well established, our understanding has continued to develop as the power of both computational and experimental techniques has improved. Understanding Hydrogen Bonds presents an up-to-date overview of our theoretical and experimental understanding of the hydrogen bond. Well-established and novel approaches are discussed, including quantum theory of ‘atoms in molecules’ (QTAIM); the electron localization function (ELF) method and Car–Parinnello molecular dynamics; the natural bond orbital (NBO) approach; and X-ray and neutron diffraction and spectroscopy. The mechanism of hydrogen bond formation is described and comparisons are made between hydrogen bonds and other types of interaction. The author also takes a look at new types of interaction that may be classified as hydrogen bonds with a focus on those with multicentre proton acceptors or with multicentre proton donors.Understanding Hydrogen Bonds is a valuable reference for experimentalists and theoreticians interested in updating their understanding of the types of hydrogen bonds, their role in chemistry and biology, and how they can be studied.

Progress in the application of machine learning (ML) to the physical and life sciences has been rapid. A decade ago, the method was mainly of interest to those in computer science departments, but more recently ML tools have been developed that show significant potential across wide areas of science. There is a growing consensus that ML software, and related areas of artificial intelligence, may, in due course, become as fundamental to scientific research as computers themselves.Yet a perception remains that ML is obscure or esoteric, that only computer scientists can really understand it, and that few meaningful applications in scientific research exist. This book challenges that view.With contributions from leading research groups, it presents in-depth examples to illustrate how ML can be applied to real chemical problems. Through these examples, the reader can both gain a feel for what ML can and cannot (so far) achieve, and also identify characteristics that might make a problem in physical science amenable to a ML approach.This text is a valuable resource for scientists who are intrigued by the power of machine learning and want to learn more about how it can be applied in their own field.

Quantum tunnelling is one of the strangest phenomena in chemistry, where we see the wave nature of atoms acting in “impossible” ways. By letting molecules pass through the kinetic barrier instead of over it, this effect can lead to chemical reactions even close to the absolute zero, to atypical spectroscopic observations, to bizarre selectivity, or to colossal isotopic effects. Quantum mechanical tunnelling observations might be infrequent in chemistry, but it permeates through all its disciplines producing remarkable chemical outcomes. For that reason, the 21st century has seen a great increase in theoretical and experimental findings involving molecular tunnelling effects, as well as in novel techniques that permit their accurate predictions and analysis. Including experimental, computational and theoretical chapters, from the physical and organic to the biochemistry fields, from the applied to the academic arenas, this new book provides a broad and conceptual perspective on tunnelling reactions and how to study them. Quantum Tunnelling in Molecules is the obligatory stop for both the specialist and those new to this world.

Since the early 20th century, X-ray and electron scattering has provided a powerful means by which the location of atoms can be identified in gas-phase molecules and condensed matter with sub-atomic spatial resolution. Scattering techniques can also provide valuable observables of the fundamental properties of electrons in matter such as an electron’s spin and its energy. In recent years, significant technological developments in both X-ray and electron scattering have paved the way to time-resolved analogues capable of capturing real-time snapshots of transient structures undergoing a photochemical reaction. Structural Dynamics with X-ray and Electron Scattering is a two-part book that firstly introduces the fundamental background to scattering theory and photochemical phenomena of interest. The second part discusses the latest advances and research results from the application of ultrafast scattering techniques to imaging the structure and dynamics of gas-phase molecules and condensed matter. This book aims to provide a unifying platform for X-ray and electron scattering.

Packing problems, which are concerned with optimal arrangements of objects in space, are cross-disciplinary in nature and are encountered in mathematics, physics, chemistry, biology, engineering, and architecture. Such problems form a subject of interest in its own right, providing intriguing intellectual challenges, but are also at the heart of many material properties of condensed matter. In view of this, a series of international conferences on packing problems was launched in 2012 to provide a platform for soft-matter researchers to disseminate their findings. To continue the spirit of this conference series, this international community of researchers has also been invited to contribute reviews of their research to this book. Covering topics on models of ordered and disordered packings, mechanical behaviour of packings, and applications in soft matter and biology, this book provides a broad and authoritative overview of current research.

The cost of drug development is increasing, and investment returns are decreasing. The number of drugs approved by FDA is in decline in terms of the number of new molecular entities (NMEs). Amongst the reasons noted for this are the adverse side effects and reduced efficiency of many of the potential compounds. This is a problem both for the pharmaceutical industry and for those suffering from diseases for which there are no or few available treatments.Advances in computational chemistry, computer science, structural biology and molecular biology have all contributed to improved drug design strategies and reduced the time taken for drug discovery. By interfacing cheminformatics and bioinformatics with systems biology we can create a powerful tool for understanding the mechanisms of patho-physiological systems and identifying lead molecules for various diseases. This integration of drug design approaches can also play a crucial role in the prediction and rationalization of drug effects and side effects, improving safety and efficacy and leading to better approval rates.Addressing the lack of knowledge on the fundamental aspects of the various computational tools for drug discovery, this book is a compilation of recent bioinformatics and cheminformatics approaches, and their integration with systems biology. Written primarily for researchers and academics in chem- and bioinformatics, it may also be a useful resource for advanced-level students.

Electric-field-mediated chemistry is an emerging topic that is rapidly growing and fanning out in many directions. It involves theoretical and experimental aspects, as well as intense interplay between them, including breakthrough achievements such as the proof-of-principle that a Diels–Alder reaction, which involves two simultaneous C–C bond making events, can be catalysed or inhibited simply by changing the direction of an oriented external-electric field (OEEF). This productive interplay between the theoretical and experimental branches of chemistry is continuing, and gradually defining a new sub-field wherein various sources of electric fields, whether external or built-in and designed, or even surface induced fields (plasmons), are brought to bear on chemical reactions, molecular structures, and nano-systems, leading to control of reactivity, selectivity, chirality, molecular orientations, changes in structure, and in dynamics.Written by leaders in the field, Effects of Electric Fields on Structure and Reactivity is the first book on this exciting topic. Starting with an overview of the theory behind – and demonstrations of the effect of – electric fields on structure and reactivity, this accessible reference work aims to encourage those new to the field to consider harnessing these effects in their own work. Covering applications and recent theoretical developments, it is a useful resource for theoretical chemists and experimentalists alike.

Over the past decade, great strides have been taken in developing methodologies that can treat more and more complex nano- and nano-bio systems embedded in complex environments. Multiscale Dynamics Simulations covers methods including DFT/MM-MD, DFTB and semi-empirical QM/MM-MD, DFT/MMPOL as well as Machine-learning approaches to all of the above. Focusing on key methodological breakthroughs in the field, this book provides newcomers with a comprehensive menu of multiscale modelling options so that they can better chart their course in the nano/bio world.

Written chemical formulas, such as C2H6O, can tell us the constituent atoms a molecule contains but they cannot differentiate between the possible geometrical arrangements (isomers) of these models. Yet the chemical properties of different isomers can vary hugely. Therefore, to understand the world of chemistry we need to ask what kind of isomers can be produced from a given atomic composition, how are isomers converted into each other, how do they decompose into smaller pieces, and how can they be made from smaller pieces? The answers to these questions will help us to discover new chemistry and new molecules. A potential energy surface (PES) describes a system, such as a molecule, based on geometrical parameters. The mathematical properties of the PES can be used to calculate probable isomer structures as well as how they are formed and how they might behave.Exploration on Quantum Chemical Potential Energy Surfaces focuses on the PES search based on quantum chemical calculations. It describes how to explore the chemical world on PES, discusses fundamental methods and specific techniques developed for efficient exploration on PES, and demonstrates several examples of the PES search for chemical structures and reaction routes.

Over the last decade, there has been a significant shift from traditional mechanistic and empirical modelling into statistical and data-driven modelling for applications in reaction engineering. In particular, the integration of machine learning and first-principle models has demonstrated significant potential and success in the discovery of (bio)chemical kinetics, prediction and optimisation of complex reactions, and scale-up of industrial reactors. Summarising the latest research and illustrating the current frontiers in applications of hybrid modelling for chemical and biochemical reaction engineering, Machine Learning and Hybrid Modelling for Reaction Engineering fills a gap in the methodology development of hybrid models. With a systematic explanation of the fundamental theory of hybrid model construction, time-varying parameter estimation, model structure identification and uncertainty analysis, this book is a great resource for both chemical engineers looking to use the latest computational techniques in their research and computational chemists interested in new applications for their work.

Ions are ubiquitous in chemical, technological, ecological and biological processes. Characterizing their role in these processes in the first place requires the evaluation of the thermodynamic parameters associated with the solvation of a given ion. However, due to the constraint of electroneutrality, the involvement of surface effects and the ambiguous connection between microscopic and macroscopic descriptions, the determination of single-ion solvation properties via both experimental and theoretical approaches has turned out to be a very difficult and highly controversial problem. This unique book provides an up-to-date, compact and consistent account of the research field of single-ion solvation thermodynamics that has over one hundred years of history and still remains largely unsolved. By reviewing the various approaches employed to date, establishing the relevant connections between single-ion thermodynamics and electrochemistry, resolving conceptual ambiguities, and giving an exhaustive data compilation (in the context of alkali and halide hydration), this book provides a consistent synthesis, in depth understanding and clarification of a large and sometimes very confusing research field. The book is primarily aimed at researchers (professors, postgraduates, graduates, and industrial researchers) concerned with processes involving ionic solvation properties (these are ubiquitous, eg. in physical/organic/analytical chemistry, electrochemistry, biochemistry, pharmacology, geology, and ecology). Because of the concept definitions and data compilations it contains, it is also a useful reference book to have in a university library. Finally, it may be of general interest to anyone wanting to learn more about ions and solvation. Key features: - discusses both experimental and theoretical approaches, and establishes the connection between them - provides both an account of the past research (covering over one hundred years) and a discussion of current directions (in particular on the theoretical side) - involves a comprehensive reference list of over 2000 citations - employs a very consistent notation (including table of symbols and unambiguous definitions of all introduced quantities) - provides a discussion and clarification of ambiguous concepts (ie. concepts that have not been defined clearly, or have been defined differently by different authors, leading to confusion in past literature) - encompasses an exhaustive data compilation (in the restricted context of alkali and halide hydration), along with recommended values (after critical analysis of this literature data) - is illustrated by a number of synoptic colour figures, that will help the reader to grasp the connections between different concepts in one single picture

This book aims to understand the main aspects of non-covalent chemistry (mainly in the gas phase) and specifically compares the experimental and theoretical data available for non-covalent complexes and subsequent problems associated with this comparison. The book is authored by an experimentalist (KMD) and theorist (PH), and their main philosophy in writing together is that any book on non-covalent interactions cannot be limited either to theory or experiment. Both approaches are nowadays so closely connected that one cannot exist without the other and vice versa and their mutual connection provides the consistent description of non-covalent processes in our world. This book will be of great assistance to researchers engaged in both theoretical and experimental aspects of non-covalent bonding and in macro- and supermolecular chemistry.

Nanoscience is one of the most exciting areas of modern physical science as it encompasses a range of techniques rather than a single discipline. It stretches across the whole spectrum of science including: medicine and health, physics, engineering and chemistry. Providing a deep understanding of the behaviour of matter at the scale of individual atoms and molecules, it provides a crucial step towards future applications of nanotechnology. The remarkable improvements in both theoretical methods and computational techniques make it possible for modern computational nanoscience to achieve a new level of chemical accuracy. It is now a discipline capable of leading and guiding experimental efforts rather than just following others. Computational Nanoscience addresses modern challenges in computational science, within the context of the rapidly evolving field of nanotechnology. It satisfies the need for a comprehensive, yet concise and up-to-date, survey of new developments and applications presented by the world's leading academics. It documents major, recent advances in scientific computation, mathematical models and theory development that specifically target the applications in nanotechnology. Suitable for theoreticians, researchers and students, the book shows readers what computational nanoscience can achieve, and how it may be applied in their own work. The twelve chapters cover topics including the concepts behind recent breakthroughs, the development of cutting edge simulation tools, and the variety of new applications.

Computational Quantum Chemistry presents computational electronic structure theory as practised in terms of ab initio waveform methods and density functional approaches. Getting a full grasp of the field can often prove difficult, since essential topics fall outside of the scope of conventional chemistry education. This professional reference book provides a comprehensive introduction to the field. Postgraduate students and experienced researchers alike will appreciate Joseph McDouall's engaging writing style. The book is divided into five chapters, each providing a major aspect of the field. Electronic structure methods, the computation of molecular properties, methods for analysing the output from computations and the importance of relativistic effects on molecular properties are also discussed. Links to the websites of widely used software packages are provided so that the reader can gain first hand experience of using the techniques described in the book.

The reaction rate constant plays an essential role a wide range of processes in biology, chemistry and physics. Calculating the reaction rate constant provides considerable understanding to a reaction and this book presents the latest thinking in modern rate computational theory.The editors have more than 30 years’ experience in researching the theoretical computation of chemical reaction rate constants by global dynamics and transition state theories and have brought together a global pool of expertise discussing these in a variety of contexts and across all phases. This thorough treatment of the subject provides an essential handbook to students and researchers entering the field and a comprehensive reference to established practitioners across the sciences, providing better tools to determining reaction rate constants.