The Latest Developments on the Role of Dynamics in Protein Functions Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, and biology show how these advanced methods provide insights into dynamic aspects of biochemical processes. A particular focus is on intrinsically disordered proteins (IDPs), which lack a well-defined three-dimensional structure and function as dynamic ensembles. The book covers a wide spectrum of dynamics, from electronic structure-based to coarse-grained techniques via multiscaling at different levels. After an introduction to dynamics and historical overview of basic methodologies, the book addresses the following issues: Is there a quantitative relationship between enzymatic catalysis and protein dynamics? Which are the functionally relevant motions of proteins? How can structural properties and partner recognition mechanisms of IDPs be simulated? How can we speed up molecular dynamics? How can we describe conformational ensembles by the synergistic effort of computations and experiments? While dynamics is now considered essential for interpreting protein action, it is not yet an integral component in establishing structure-function relationships of proteins. Helping to reshape this classical view in biochemistry, this groundbreaking book explores advances in computational methodology and contributes to the new, ensemble way of studying proteins.

The present status of Density Functional Theory (DFT), which has evolved as the main technique for the study of matter at the atomistic level, is described in this volume. Knowing the behavior of atoms and molecules provides a sure avenue for the design of new materials with specific features and properties in many areas of science and technology. A technique based on purely first principles allowing large savings in time and money greatly benefits the specialist or designer of new materials.

The range of areas where DFT is applied has expanded and continues to do so. Any area where a molecular system is the center of attention can be studied using DFT.The scope of the 22 chapters in this book amply testifies to this.

Topological Modelling of Nanostructures and Extended Systems completes and expands upon the previously published title within this series: The Mathematics and Topology of Fullerenes (Vol. 4, 2011) by gathering the latest research and advances in materials science at nanoscale. It introduces a new speculative area and novel concepts like topochemical reactions and colored reactive topological indices and provides a better understanding of the physical-chemical behaviors of extended systems. Moreover, a charming new family of space-filling fullerenic crystals is here analyzed for the first time. Particular attention is given to the fundamental influences exercised by long-range connectivity topological mechanisms on the chemical and physical properties of carbon nanostructures. Systems consisting in graphenic layers with structural and topological defects are investigated in their electronic and magnetic behaviors also in presence of metallic particles. More specifically, the book focuses on: - Electronic Properties of low dimensional nanostructures including negatively-curved carbon surfaces; Pariser-Parr-Pople model hamiltonian approach to graphene studies; - Topochemistry and Toporeactcivity of extended sp2-nanocarbons: PAH, fullerenes, nanoribbons, Moebius-like nanoribbons, nanotubes and grapheme; - Novel class of crystal networks arising from spanning fullerenes; - Nanostructures and eigenvectors of matrices and an extended treatise of topological invariants; - Enumeration hetero-fullerenes by Polya theory. Topological Modelling of Nanostructures and Extended Systems represents a valuable resource to advances graduates and researchers working in mathematics, chemistry, physics and material science.

This reference details the theory and application of cation complexation, including the design and synthesis of various cyclic systems, these materials' use as transport systems, in complexation and selectivity studies by macrocyclic systems, and methodologies for understanding these phenomena. In a

"Relativistic Methods for Chemists," written by a highly qualified team of authors, is targeted at both experimentalists and theoreticians interested in the area of relativistic effects in atomic and molecular systems and processes and in their consequences for the interpretation of the heavy element's chemistry.

The theoretical part of the book focuses on the relativistic methods for molecular calculations discussing relativistic two-component theory, density functional theory, pseudopotentials and correlations. The experimentally oriented chapters describe the use of relativistic methods in different applications focusing on the design of new materials based on heavy element compounds, the role of the spin-orbit coupling in photochemistry and photobiology, and chirality and its relations to relativistic description of matter and radiation.

This book is written at an intermediate level in order to appeal to a broader audience than just experts working in the field of relativistic theory.

This book is an introduction to the techniques of many-body quantum theory with a large number of applications to condensed matter physics. The basic idea of the book is to provide a self-contained formulation of the theoretical framework without losing mathematical rigor, while at the same time providing physical motivation and examples. The examples are taken from applications in electron systems and transport theory.
On the formal side, the book covers an introduction to second quantization, many-body Green's function, finite temperature Feynman diagrams and bosonization. The applications include traditional transport theory in bulk as well as mesoscopic systems, where both the Landau-Buttiker formalism and recent developments in correlated transport phenomena in mesoscopic systems and nano-structures are covered. Other topics include interacting electron gases, plasmons, electron-phonon interactions, superconductivity and a final chapter on one-dimensional systems where a detailed treatment of Luttinger liquid theory and bosonization techniques is given. Having grown out of a set of lecture notes, and containing many pedagogical exercises, this book is designed as a textbook for an advanced undergraduate or graduate course, and is also well suited for self-study.

This new 5-volume set presents in a balanced yet progressive manner the fundamental and advanced concepts, principles, and models of quanta, atoms, molecules, solids, and crystal and chemical-biological interaction in cells. It also addresses the first and novel combinations and applications in modeling complex natural or designed phenomena. These new volumes by Dr. Putz embrace the best knowledge at the dawn of the twenty-first century of chemical bonding approaches while further advancing the chemical bonding approaches through the author's own progressive vision, which highlights the concept of bosonic-bondon in artificial chemistry. The author approaches the systematics of atoms-in-molecule progressive modeling, in relation to chemical reactivity indices that are rooted in the electronegativity and chemical hardness prime chemical descriptors, with a refreshing and fruitful perspective. He considers the influence of chemical bonding and extends that to chemical-biological interaction in cells and organisms toward recording the biological activity. He covers the relevant connections with chemistry and atomic/molecular structures for the constituent particles/nodes in crystals and solids, including the hot topic of the propagation of defects on graphenes. The work is rigorously, thoughtfully, and analytically presented, with a flexible, instructive, and creative physical-chemical style of presentation and should be well understood by both physical and chemical communities in the nanosciences fields. These volumes will help to stimulate the creative power of the reader interested not just in knowing and understanding nature through the eyes of quantum theory but also in using the necessary know-how to predict and drive the quantum information, coined the nano-scale systems. The multi-volume book uniquely features: A multi-level unitary approach (atoms, molecules, solids, and chemical-biological interaction in an interrelated conceptual and applicative presentation) Fresh quantum views and models of atomic stability and molecular reactivity A new theory of chemical bonding by bosonic-bondons The first path integral applications in quantum chemistry The first bondonic analysis for the graphenic topological defects The volume largely achieves the Organization for Economic and Co-operation Development's (OECD) Quantitative Structure Activity Relationship (QSAR) fifth commandment ensuring mechanistically describing the chemical-biological interaction by prime structural causes-in short, explaining biological activity by chemical reactivity.

The Schroedinger equation is the master equation of quantum chemistry. The founders of quantum mechanics realised how this equation underpins essentially the whole of chemistry. However, they recognised that its exact application was much too complicated to be solvable at the time. More than two generations of researchers were left to work out how to achieve this ambitious goal for molecular systems of ever-increasing size. This book focuses on non-mainstream methods to solve the molecular electronic Schroedinger equation. Each method is based on a set of core ideas and this volume aims to explain these ideas clearly so that they become more accessible. By bringing together these non-standard methods, the book intends to inspire graduate students, postdoctoral researchers and academics to think of novel approaches. Is there a method out there that we have not thought of yet? Can we design a new method that combines the best of all worlds?

Organic materials with extraordinary magnetic properties promise a wide range of light, flexible, and inexpensive alternatives to familiar metal-based magnets. Individual organic molecules with high magnetic moments will be the foundation for design and fabrication of these materials.This book provides a systematic understanding of the structure and properties of organic magnetic molecules. After a summary of the phenomenon of magnetism at the molecular level, it presents a survey of the challenges to theoretical description and evaluation of the magnetic character of open-shell molecules, and an overview of recently developed methods and their successes and shortfalls. Several fields of application, including very strong organic molecular magnets and photo-magnetic switches, are surveyed. Finally, discussions on metal-based materials and simultaneously semiconducting and ferromagnetic extended systems and solids point the way toward future advances.The reader will find a comprehensive discourse on current understanding of magnetic molecules, a thorough survey of computational methods of characterizing known and imagined molecules, simple rules for design of larger magnetic systems, and a guide to opportunities for progress toward organic magnets.

This study guide aims at explaining theoretical concepts encountered by practitioners applying theory to molecular science. This is a collection of short chapters, a manual, attempting to walk the reader through two types of topics: (i) those that are usually covered by standard texts but are difficult to grasp and (ii) topics not usually covered, but are essential for successful theoretical research. The main focus is on the latter. The philosophy of this book is not to cover a complete theory, but instead to provide a set of simple study cases helping to illustrate main concepts. The focus is on simplicity. Each section is made deliberately short, to enable the reader to easily grasp the contents. Sections are collated in themed chapters, and the advantage is that each section can be studied separately, as an introduction to more in-depth studies. Topics covered are related to elasticity, electrostatics, molecular dynamics and molecular spectroscopy, which form the foundation for many presently active research areas such as molecular biophysics and soft matter physics. The notes provide a uniform approach to all these areas, helping the reader to grasp the basic concepts from a common set of theoretical tools.

Stochastic Energetics by now commonly designates the emerging field that bridges the gap between stochastic dynamical processes and thermodynamics.

Triggered by the vast improvements in spatio-temporal resolution in nanotechnology, stochastic energetics develops a framework for quantifying individual realizations of a stochastic process on the mesoscopic scale of thermal fluctuations.

This is needed to answer such novel questions as:

Can one cool a drop of water by agitating an immersed nano-particle?

How does heat flow if a Brownian particle pulls a polymer chain?

Can one measure the free-energy of a system through a single realization of the associated stochastic process?

This book will take the reader gradually from the basics to the applications: Part I provides the necessary background from stochastic dynamics (Langevin, master equation), Part II introduces how stochastic energetics describes such basic notions as heat and work on the mesoscopic scale, Part III details several applications, such as control and detection processes, as well as free-energy transducers.

It aims in particular at researchers and graduate students working in the fields of nanoscience and technology.

This book provides an introduction to the classical, quantum and symmetry aspects of multipole theory, demonstrating the successes of the theory and also its unphysical aspects. It presents a transformation theory, which removes these unphysical properties. The book will be of interest to physics students wishing to advance their knowledge of multipole theory, and also a useful reference work for molecular and optical physicists, theoretical chemists working on multipole effects, solid state physicists studying the effects of electromagnetic fields on condensed matter, engineers and applied mathematicians with interests in anisotrpoic materials. An interesting recent development has been the increasing use of computer calculations in applications of multipole theory. The book should assist computational physicists and chemists wishing to work in this area to acquire the necessary background in multipole theory.

The first book to aid in the understanding of multiconfigurational quantum chemistry, Multiconfigurational Quantum Chemistry demystifies a subject that has historically been considered difficult to learn. Accessible to any reader with a background in quantum mechanics and quantum chemistry, the book contains illustrative examples showing how these methods can be used in various areas of chemistry, such as chemical reactions in ground and excited states, transition metal and other heavy element systems. The authors detail the drawbacks and limitations of DFT and coupled-cluster based methods and offer alternative, wavefunction-based methods more suitable for smaller molecules.

Surface tension provides a thermodynamic avenue for analyzing systems in equilibrium and formulating phenomenological explanations for the behavior of constituent molecules in the surface region. While there are extensive experimental observations and established ideas regarding desorption of ions from the surfaces of aqueous salt solutions, a more successful discussion of the theory has recently emerged, which allows the quantitative calculation of the distribution of ions in the surface region. Surface Tension and Related Thermodynamic Quantities of Aqueous Electrolyte Solutions provides a detailed and systematic analysis of the properties of ions at the air/water interface. Unifying older and newer theories and measurements, this book emphasizes the contributions of simple ions to surface tension behavior, and the practical consequences. It begins with a general discussion on Gibbs surface thermodynamics, offering a guide to his theoretical insight and formulation of the boundary between fluids. The text then discusses the thermodynamic formulae that are useful for practical experimental work in the analysis of fluid/fluid interfaces. Chapters cover surface tension of pure water at air/water and air/oil interfaces, surface tension of solutions and the thermodynamic quantities associated with the adsorption and desorption of solutes, and surface tension of simple salt solutions. They also address adsorption of ions at the air/water interface, surface tension of solutions and the effect of temperature, adsorption from mixed electrolyte solutions, and thermodynamic properties of zwitterionic amino acids in the surface region. Focusing on the thermodynamic properties of ions at air/fluid interfaces, this book gives scientists a quantitative, rigorous, and objectively experimental methodology they can employ in their research.

In this thesis, the author outlines the discovery of an effect common to representative examples of all Li salt-free Wittig Reactions. The implications of such a universally applicable effect are that all such Wittig reactions occur through the same mechanism. Although the Wittig reaction was first discovered in 1953, its reaction mechanism has never been definitively settled with many different variants proposed and disproved. The work in this thesis shows conclusively that for [2+2] cycloadditions all Wittig reactions occur by the same irreversible mechanism. In addition, the author also describes a new chromatography-free method for the removal of phosphine oxide from the alkene crude product of the Wittig reaction. The work in this thesis has led to several publications in high-profile journals.

This new edition is a concise introduction to the basic methods of computational physics. Readers will discover the benefits of numerical methods for solving complex mathematical problems and for the direct simulation of physical processes. The book is divided into two main parts: Deterministic methods and stochastic methods in computational physics. Based on concrete problems, the first part discusses numerical differentiation and integration, as well as the treatment of ordinary differential equations. This is extended by a brief introduction to the numerics of partial differential equations. The second part deals with the generation of random numbers, summarizes the basics of stochastics, and subsequently introduces Monte-Carlo (MC) methods. Specific emphasis is on MARKOV chain MC algorithms. The final two chapters discuss data analysis and stochastic optimization. All this is again motivated and augmented by applications from physics. In addition, the book offers a number of appendices to provide the reader with information on topics not discussed in the main text. Numerous problems with worked-out solutions, chapter introductions and summaries, together with a clear and application-oriented style support the reader. Ready to use C++ codes are provided online.

"Modern Charge-Density Analysis" focuses on state-of-the-art methods and applications of electron-density analysis. It is a field traditionally associated with understanding chemical bonding and the electrostatic properties of matter. Recently, it has also been related to predictions of properties and responses of materials (having an organic, inorganic or hybrid nature as in modern materials and bio-science, and used for functional devices or biomaterials).

"Modern Charge-Density Analysis" is inherently multidisciplinary and written for chemists, physicists, crystallographers, material scientists, and biochemists alike. It serves as a useful tool for scientists already working in the field by providing them with a unified view of the multifaceted charge-density world. Additionally, this volume facilitates the understanding of scientists and PhD students planning to enter the field by acquainting them with the most significant and promising developments in this arena.

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.

The conceptualization of a problem (modeling) and the computational solution of this problem (simulation), is the foundation of Computational Science. This coupled endeavor is unique in several respects. It allows practically any complex system to be analyzed with predictive capability by invoking the multiscale paradigm linking unit-process models at lower length (or time) scales where fundamental principles have been established to calculations at the system level.

The community of multiscale materials modeling has evolved into a multidisciplinary group with a number of identified problem areas of interest. Sidney Yip and Tomas Diaz De La Rubia, the editors of this volume, have gathered 18 contributions that showcase the conceptual advantages of modeling which, coupled with the unprecedented computing power through simulations, allow scientists to tackle the formibable problems of our society, such as the search for hydrocarbons, understanding the structure of a virus, or the intersection between simulations and real data in extreme environments.

Scientific Modeling and Simulations advocates the scientific virtues of modeling and simulation, and also encourages the cross fertilization between communities, exploitations of high-performance computing, and experiment-simulation synergies.

The contents of this book were previously published in Scientific Modeling and Simulations, Vol 15, No. 1-3, 2008.

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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 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.

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.

Predicting thermodynamic quantities for chemically realistic systems on the basis of atomistic calculations is still, even today, a nontrivial task. Nonetheless, accurate treatment of inter-particle interactions, in terms of quantum chemical first principles methods, is a prerequisite for many applications, because of the complexity of both reactants and solvents in modern molecular sciences. Currently, a straightforward calculation of thermodynamic properties from these methods is only possible for high-temperature and low- density systems. Although the enthalpy of a system can often be predicted to a good level of precision with this ideal gas approach, calculating the entropy contribution to the free energy is problematic, especially as the density of the system increases. This thesis contains a compact and coherent introduction of basic theoretical features. The foundations are then laid for the development of approaches suitable for calculation of condensed phase entropies on the basis of well-established quantum chemical methods. The main emphasis of this work is on realistic systems in solution, which is the most important environment for chemical synthesis. The presented results demonstrate how isolated molecular concepts typically employed in modern quantum chemistry can be extended for the accurate determination of thermodynamic properties by means of scale- transferring approaches.

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 introduces and explores modern developments in the well established field of Hamiltonian dynamical systems. It focuses on high degree-of-freedom systems and the transitional regimes between regular and chaotic motion. The role of nonlinear normal modes is highlighted and the importance of low-dimensional tori in the resolution of the famous FPU paradox is emphasized. Novel powerful numerical methods are used to study localization phenomena and distinguish order from strongly and weakly chaotic regimes. The emerging hierarchy of complex structures in such regimes gives rise to particularly long-lived patterns and phenomena called quasi-stationary states, which are explored in particular in the concrete setting of one-dimensional Hamiltonian lattices and physical applications in condensed matter systems. The self-contained and pedagogical approach is blended with a unique balance between mathematical rigor, physics insights and concrete applications. End of chapter exercises and (more demanding) research oriented problems provide many opportunities to deepen the reader 's insights into specific aspects of the subject matter.Addressing a broad audience of graduate students, theoretical physicists and applied mathematicians, this text combines the benefits of a reference work with those of a self-study guide for newcomers to the field.