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.

Algebraic Methods in Quantum Chemistry and Physics provides straightforward presentations of selected topics in theoretical chemistry and physics, including Lie algebras and their applications, harmonic oscillators, bilinear oscillators, perturbation theory, numerical solutions of the Schrödinger equation, and parameterizations of the time-evolution operator.
The mathematical tools described in this book are presented in a manner that clearly illustrates their application to problems arising in theoretical chemistry and physics. The application techniques are carefully explained with step-by-step instructions that are easy to follow, and the results are organized to facilitate both manual and numerical calculations.

Algebraic Methods in Quantum Chemistry and Physics demonstrates how to obtain useful analytical results with elementary algebra and calculus and an understanding of basic quantum chemistry and physics.

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 handbook form, this reference monograph provides both experimental and theoretical data describing thermodynamic properties of groups of isomers of different classes, particularly for organic compound reactions. Data have been derived through chemical equilibria studies, statistical thermodynamics, and to some degree, calorimetry. Data based on equilibria studies are also valuable as a cross-check to thermodynamic functions derived purely from calorimetric measurements.

This edited, multi-author book gathers selected, peer-reviewed contributions based on papers presented at the 23rd International Workshop on Quantum Systems in Chemistry, Physics, and Biology (QSCP-XXIII), held in Mopani Camp, The Kruger National Park, South Africa, in September 2018. The content is primarily intended for scholars, researchers, and graduate students working at universities and scientific institutes who are interested in the structure, properties, dynamics, and spectroscopy of atoms, molecules, biological systems, and condensed matter.

This textbook introduces the reader to quantum theory and quantum chemistry. The textbook is meant for 2nd - 3rd year bachelor students of chemistry or physics, but also for students of related disciplines like materials science, pharmacy, and bioinformatics. At first, quantum theory is introduced, starting with experimental results that made it inevitable to go beyond classical physics. Subsequently, the Schroedinger equation is discussed in some detail. Some few examples for which the Schroedinger equation can be solved exactly are treated with special emphasis on relating the results to real systems and interpreting the mathematical results in terms of experimental observations. Ultimately, approximate methods are presented that are used when applying quantum theory in the field of quantum chemistry for the study of real systems like atoms, molecules, and crystals. Both the foundations for the different methods and a broader range of examples of their applications are presented. The textbook assumes no prior knowledge in quantum theory. Moreover, special emphasis is put on interpreting the mathematical results and less on an exact mathematical derivations of those. Finally, each chapter closes with a number of questions and exercises that help in focusing on the main results of the chapter. Many of the exercises include answers.

This volume highlights the recent advances and state of art in the experimental and theoretical studies of organometallic magnets. A plethora of organic ligands such as Mannich-base derivatives, redox-active chromophores, cyanides, Schiff base among others are used to coordinate to 3d transition metals, 4f lanthanides and 5f actinides to design the molecular magnets. Deep analysis of the coordination sphere symmetry, electronic distribution, luminescence are investigated to perform magneto-structural correlation leading to a better understanding of the magnetic properties. Furthermore, the rationalization of the magnetic behavior can be reached using ab initio calculations. The multiple applications that these molecular magnets offer could revolutionize the high-density data storage, spintronics and quantum computing technologies. This volume provides a discussion of these topics from leading international experts and will be a useful reference for researchers working in this field.

A clear, simple, graphic-led introduction to quantum physics. Are you short of time but hungry for knowledge? This beginner's quantum physics book proves that sometimes less is more. Bold graphics and easy-to-understand explanations make it the most accessible guide to quantum physics on the market. Understanding Quantum Physics Has Never Been Easier This illuminating reference book introduces you to the greatest physicists of the 20th and 21st centuries such as Albert Einstein, Neils Bohr, Erwin Schrödinger, Richard Feynman, and more! It's the perfect gift for anyone interested in physics or science in general and life-long learners. This book about quantum physics offers you: - Simple, easy-to-understand graphics that help to convey information in a visual way - Clear, authoritative text that explains 100 key concepts - Introduction to theoretical ideas and their everyday applications This smart but powerful guide cuts through the jargon and gives you the facts in a clear, visual way. Step inside the strange and fascinating world of subatomic physics that at times seems to conflict with common sense. Unlock the mysteries of more than 100 key ideas, from quantum mechanics basics to the uncertainty principle and quantum tunnelling. Each pared-back, single-page entry demystifies the groundbreaking ideas in modern science. From Schrödinger's Cat and quantum teleportation to atoms and gravity, Simply Quantum Physics is the ultimate jargon-free overview of the subject. Whether you're a physics student or just an interested layman, this indispensable guide is packed with everything you need to quickly and easily understand the basics. Complete the Series: Part of DK Book's exciting, brand-new reference series for those who are time-poor, but keen to learn more. Discover the mysteries of more key philosophical ideas in Simply Philosophy.

This book presents a number of studies on the molecular dynamics of cement-based materials. It introduces a practical molecular model of cement-hydrate, delineates the relationship between molecular structure and nanoscale properties, reveals the transport mechanism of cement-hydrate, and provides useful methods for material design. Based on the molecular model presented here, the book subsequently sheds light on nanotechnology applications in the design of construction and building materials. As such, it offers a valuable asset for researchers, scientists, and engineers in the field of construction and building materials.

This book presents a variety of techniques for tackling phenomena that are not amenable to the conventional approach based on the concept of probabilities. The methods described rely on the use of path integration, thermal Green functions, time-temperature propagators, Liouville operators, second quantization, and field correlators at finite density and temperature. Also exploring the statistical mechanics of unstable quantum systems, the book is intended as a supplementary or reference text for use in one-semester graduate courses on Quantum Mechanics, Thermodynamics, Electromagnetism, and Mathematical Methods in Physics.

This book provides a graduate-level introduction to three powerful and closely related techniques in condensed matter physics: memory functions, projection operators, and the defect technique. Memory functions appear in the formalism of the generalized master equations that express the time evolution of probabilities via equations non-local in time, projection operators allow the extraction of parts of quantities, such as the diagonal parts of density matrices in statistical mechanics, and the defect technique allows solution of transport equations in which the translational invariance is broken in small regions, such as when crystals are doped with impurities. These three methods combined form an immensely useful toolkit for investigations in such disparate areas of physics as excitation in molecular crystals, sensitized luminescence, charge transport, non-equilibrium statistical physics, vibrational relaxation, granular materials, NMR, and even theoretical ecology. This book explains the three techniques and their interrelated nature, along with plenty of illustrative examples. Graduate students beginning to embark on a research project in condensed matter physics will find this book to be a most fruitful source of theoretical training.

Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.

E = mc2 and the Periodic Table . . .
RELATIVISTIC EFFECTS IN CHEMISTRY
This century's most famous equation, Einstein's special theory of relativity, transformed our comprehension of the nature of time and matter. Today, making use of the theory in a relativistic analysis of heavy molecules, that is, computing the properties and nature of electrons, is the work of chemists intent on exploring the mysteries of minute particles.
The first work of its kind, Relativistic Effects in Chemistry details the computational and analytical methods used in studying the relativistic effects in chemical bonding as well as the spectroscopic properties of molecules containing very heavy atoms. The first of two independent volumes, Part A: Theory and Techniques describes the basic techniques of relativistic quantum chemistry. Its systematic five-part format begins with a detailed exposition of Einstein's special theory of relativity, the significance of relativity in chemistry, and the nature of relativistic effects, especially with molecules containing both main group atoms and transition metal atoms.
Chapter 3 discusses the fundamentals of relativistic quantum mechanics starting from the Klein-Gordon equation through such advanced constructs as the Breit-Pauli and Dirac multielectron Hamiltonian. Modern computational techniques, of importance with problems involving very heavy molecules, are outlined in Chapter 4. These include the relativistic effective core potentials, ab initio CASSCF, CI, and RCI techniques. Chapter 5 describes relativistic symmetry using the double group symmetry of molecules and the classification of relativistic electronic states and is of special importanceto chemists or spectroscopists interested in computing or analyzing electronic states of molecules containing very heavy atoms.
An exceptional introduction to one of chemistry's foremost analytical techniques, Relativistic Effects in Chemistry is also evidence of the still unending reverberations of Einstein's revolutionary theory.

This concise book introduces and discusses the basic theory of conical intersections with applications in atomic, molecular and condensed matter physics. Conical intersections are linked to the energy of quantum systems. They can occur in any physical system characterized by both slow and fast degrees of freedom - such as e.g. the fast electrons and slow nuclei of a vibrating and rotating molecule - and are important when studying the evolution of quantum systems controlled by classical parameters. Furthermore, they play a relevant role for understanding the topological properties of condensed matter systems. Conical intersections are associated with many interesting features, such as a breakdown of the Born-Oppenheimer approximation and the appearance of nontrivial artificial gauge structures, similar to the Aharonov-Bohm effect. Some applications presented in this book include - Molecular Systems: some molecules in nonlinear nuclear configurations undergo Jahn-Teller distortions under which the molecule lower their symmetry if the electronic states belong to a degenerate irreducible representation of the molecular point group. - Solid State Physics: different types of Berry phases associated with conical intersections can be used to detect topologically nontrivial states of matter, such as topological insulators, Weyl semi-metals, as well as Majorana fermions in superconductors. - Cold Atoms: the motion of cold atoms in slowly varying inhomogeneous laser fields is governed by artificial gauge fields that arise when averaging over the fast internal degrees of freedom of the atoms. These gauge fields can be Abelian or non-Abelian, which opens up the possibility to create analogs to various relativistic effects at low speed.

This book sheds new light on the dynamical behaviour of electron spins in molecules containing two unpaired electrons (i.e. a radical pair). The quantum dynamics of these spins are made complicated by the interaction between the electrons and the many nuclear spins of the molecule; they are intractable using analytical techniques, and a naive numerical diagonalization is not remotely possible using current computational resources. Hence, this book presents a new method for obtaining the exact quantum-mechanical dynamics of radical pairs with a modest number of nuclear spins. Readers will learn how a calculation that would take 13 years using conventional wavepacket propagation can now be done in 1 day, and will also discover a new semiclassical method for approximating the dynamics in the presence of many nuclear spins. The new methods covered in this book are shown to provide significant insights into three topical and diverse areas: charge recombination in molecular wires (which can be used in artificially mimicking photosynthesis), magnetoelectroluminescence in organic light-emitting diodes, and avian magnetoreception (how birds sense the Earth's magnetic field in order to navigate).

On-surface synthesis is appearing as an extremely promising strategy to create organic nanoarchitectures with atomic precision. Molecular building blocks holding adequate functional groups are dosed onto surfaces that support or even drive their covalent linkage. The surface confinement and the frequent lack of solvents (most commonly being performed under vacuum conditions) create a completely new scenario fully complementary to conventional chemistry. In a pedagogical way and based on the most recent developments, this volume presents our current understanding in the field, addressing fundamental reaction mechanisms, synthetic strategies to influence the reactions according to our needs, as well as the ultimate growth and characterization of functional materials. Verging on chemistry, physics and materials science, the book is aimed at students and researchers interested in nanochemistry, surface science, supramolecular materials and molecular devices. Chapters "Mechanistic insights into surface-supported chemical reactions", "Reactivity on and of Graphene Layers: Scanning Probe Microscopy Reviels" and "Bottom-up fabrication of atomically precise graphene nanoribbons" of this book are available open access under a CC BY 4.0 license at link.springer.com

Problem-solving is one of the most challenging aspects students encounter in general chemistry courses, leading to frustration and failure. Consequently, many students become less motivated to take additional chemistry courses after the first year. This book tackles this issue head on and provides innovative, intuitive, and systematic strategies to tackle any type of calculations encountered in chemistry. The material begins with the basic theories, equations, and concepts of the underlying chemistry, followed by worked examples with carefully explained step-by-step solutions to showcase the ways in which the problems can be presented. The second edition contains additional problems at the end of each chapter with varying degrees of difficulty, and many of the original examples have been revised.

Molecular self-assembly is a widespread phenomenon in both chemistry and biochemistry. Yet it was not until the rise of supramolecular chemistry that attention has increasingly been given to the designed self-assembly of a variety of synthetic molecules and ions. To a large extent, success in this area has reflected knowledge gained from nature. However, an increased awareness of the latent steric and electronic information implanted in individual molecular components has also contributed to this success. Whilst not yet approaching the sophistication of biological assemblies, synthetic systems of increasing subtlety and considerable aesthetic appeal have been created. Self-Assembly in Supramolecular Systems surveys highlights of the progress made in the creation of discrete synthetic assemblies and provides a foundation for new workers in the area, as well as background reading for experienced supramolecular chemists.

This book introduces basic concepts of mathematical physics to chemists. Many textbooks and monographs of mathematical physics may appear daunting to them. Unlike other, related books, however, this one contains a practical selection of material, particularly for graduate and undergraduate students majoring in chemistry. The book first describes quantum mechanics and electromagnetism, with the relation between the two being emphasized. Although quantum mechanics covers a broad field in modern physics, the author focuses on a hydrogen(like) atom and a harmonic oscillator with regard to the operator method. This approach helps chemists understand the basic concepts of quantum mechanics aided by their intuitive understanding without abstract argument, as chemists tend to think of natural phenomena and other factors intuitively rather than only logically. The study of light propagation, reflection, and transmission in dielectric media is of fundamental importance. This book explains these processes on the basis of Maxwell equations. The latter half of the volume deals with mathematical physics in terms of vectors and their transformation in a vector space. Finally, as an example of chemical applications, quantum chemical treatment of methane is introduced, including a basic but essential explanation of Green functions and group theory. Methodology developed by the author will also prove to be useful to physicists.

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

This book is intended as an introductory lecture in material physics, in which the modern computational group theory and the electronic structure calculation are in collaboration. The first part explains how to use computer algebra for applications in solid-state simulation, based on the GAP computer algebra package. Computer algebra enables us to easily obtain various group theoretical properties, such as the representations, character tables, and subgroups. Furthermore it offers a new perspective on material design, which could be executed in a mathematically rigorous and systematic way. The second part then analyzes the relation between the structural symmetry and the electronic structure in C60 (as an example of a system without periodicity). The principal object of the study was to illustrate the hierarchical change in the quantum-physical properties of the molecule, which correlates to the reduction in the symmetry (as it descends down in the ladder of subgroups). The book also presents the computation of the vibrational modes of the C60 by means of the computer algebra. In order to serve the common interests of researchers, the details of the computations (the required initial data and the small programs developed for the purpose) are explained in as much detail as possible.

This thesis focuses on the nanomanufacturing of graphene-a newly discovered, two-dimensional material with extraordinary properties-in order to realize its numerous potential applications. Combining experimental implementation with theoretical modelling, it investigates three classes of graphene nanostructure fabrication using particle beam irradiation: (i) doping of graphene using low energy nitrogen irradiation; (ii) joining of graphene sheets with laser and C, N, and Ar ion beam irradiation; and (iii) fabrication of graphene nanopores by means of focused ion beam and electron beam irradiation. The feasibility of the nanomanufacture of graphene using particle beam irradiation is demonstrated by various experimental methods, and the mechanisms involved under different types of beam irradiation are revealed using theoretical calculations. Further, the book analyzes the mechanical and electrical properties of the fabricated graphene nanostructures by means of atomic simulations to predict the application potentials of the proposed methods. The findings help promote the implementation of graphene-structure applications in industry.

This book describes the latest developments in the new research discipline of X-ray nanochemistry, which uses nanomaterials to enhance the effectiveness of X-ray irradiation. Nanomaterials now can be synthesized in such a way as to meet the demand for complex functions that enhance the X-ray effect. Innovative methods of delivering the X-rays, which can interact with those nanomaterials much more strongly than energetic electrons and gamma rays, also create new opportunities to enhance the X-ray effect. As a result, new concepts are conceived and new developments are made in the last decade, which are discussed and summarized in this book. This book will help define the discipline and encourage more students and scientists to work in this discipline. These efforts will eventually lead to formation of a full set of physical, chemical and materials principles for this new research field.

This book presents a collection of invited research and review contributions on recent advances in (mainly) theoretical condensed matter physics, theoretical chemistry, and theoretical physics. The volume celebrates the 90th birthday of N.H. March (Emeritus Professor, Oxford University, UK), a prominent figure in all of these fields. Given the broad range of interests in the research activity of Professor March, who collaborated with a number of eminent scientists in physics and chemistry, the volume embraces quite diverse topics in physics and chemistry, at various dimensions and energy scales. One thread connecting all these topics is correlation in aggregated states of matter, ranging from nuclear physics to molecules, clusters, disordered condensed phases such as the liquid state, and solid state physics, and the various phase transitions, both structural and electronic, occurring therein. A final chapter leaps to an even larger scale of matter aggregation, namely the universe and gravitation. A further no less important common thread is methodological, with the application of theoretical physics and chemistry, particularly density functional theory and statistical field theory, to both nuclear and condensed matter.