Challenges and Advances in Computational Chemistry and Physics – serie

Computational Studies of RNA and DNA includes, in an integrated way, modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes, as well as pitfalls of the computational techniques are discussed.The systems and problems considered include:- Basic principles of nucleic acid structure and structural databases- Introduction to key molecular modelling tools and methods- Application of atomistic simulations to a wide variety of DNA and RNA systems - Accurate QM calculations of base pairing, stacking and cation binding- Charge transfer, excited states and NMR parameters- Calculating mechanical properties of nucleic acids- Mesoscopic simulation of DNA, chromatin modellingThis book is ideally suited to academics and researchers in organic and computational chemistry, structural molecular biology and biophysics as well as biochemistry, and particularly those interested in the molecular modelling of nucleic acids.Besides the state-of-the-art science, the book also provides extensive introductory information for non-specialists and students to enter and understand this field.

Non-Linear Optical Properties of Matter: From Molecules to Condensed Phases attempts to draw together both theory and application in this field. As such it will be of interest to both experimentalists and theoreticians alike. Divided into two parts, Part 1 is concerned with the theory and computing of non-linear optical (NLO) properties while Part 2 reviews the latest developments in experimentation.Part 1: Surveys the current advances in the computation of the NLO properties of molecules, crystalline solids and nano-particles. It examines the methods employed to compute the properties of both microscopic and macroscopic forms of matter.Part 2: Covers the recent advances on the NLO properties of organometallic compounds, rotaxanes, glasses, Langmuir-Blodget films, gold and silver nano-particles etc. Strategies to develop novel NLO materials are also discussed along with the Hyper-Rayleigh scattering technique.

Hydrogen Bonding – New Insights is an extensive text which takes numerous examples from experimental studies and uses these to illustrate theoretical investigations to allow a greater understanding of hydrogen bonding phenomenon. The most important topics in recent studies are considered including: Intra-molecular H-bondsDifferences between H-bond and van der Waals interactions from one side and covalent bonds from the otherBader theory to analyze H-bondingInfluence of weak H-bonds upon structure and function of biological moleculesH-bonds in crystal structuresWith contributions from some of the foremost experts in this field this volume provides an invaluable resource for all members of the academic community looking for a comprehensive text on hydrogen bonding. It will be of particular interest to physical and theoretical chemists, spectroscopists, crystallographers and those involved with chemical physics.

"Molecular Materials with Specific Interactions: Modeling and Design" has a very interdisciplinary character and is intended to provide basic information as well as the details of theory and examples of its application to experimentalists and theoreticians interested in modeling molecular properties and putting into practice rational design of new materials. One of the first requirements to initiate the molecular modeling of molecular materials is an accurate and realistic description of the electronic structure, intermolecular interactions and chemical reactions at microscopic and macroscopic scale. Therefore the first four chapters contain an extensive introduction into the latest theories of intermolecular interactions, functional density techniques, microscopic and mezoscopic modeling techniques as well as first-principle molecular dynamics. In the following chapters, techniques bridging microscopic and mezoscopic modeling scales are presented. The authors then illustrate various successful applications of molecular design of new materials, drugs, biocatalysts, etc. before presenting challenging topics in molecular materials design.

Comprehensive theoretical and experimental analysis of UV-radiation and low energy electron induced phenomena in nucleic acid bases (NABs) and base assemblies are presented in this book. NABs are highly photostable; the absorbed energy is dissipated in the form of ultrafast nonradiative decay. This book highlights the possible mechanisms of these phenomena which is important for all living species and discusses technical challenges in exploration of these processes. This volume will be of particular interest for those involved in understanding the photophysical/photochemical properties of nucleic acids. All chapters are written by the world's leading experts, both from the experimental and computational areas.

Since the inception of this volume, the world's nancial climate has radically changed. Theemphasishasshiftedfromboomingeconomiesandeconomicgrowth totherealityofrecessionanddiminishingoutlook. Witheconomicdownturncomes opportunity,inallareasofchemistryfromresearchanddevelopmentthroughto productregistrationandriskassessment,replacementsarebeingsoughtforcostly time-consumingprocesses. Leadingamongstthereplacementsaremodelswithtrue predictivecapability. Ofthesecomputationalmodelsarepreferred. This volume addresses a broad need within various areas of the "chemical industries", from pharmaceuticals and pesticides to personal products to provide computationalmethodstopredicttheeffects,activitiesandpropertiesofmolecules. Itaddressestheuseofmodelstodesignnewmoleculesandassesstheirfateand effectsbothtotheenvironmentandtohumanhealth. Thereisanemphasisrunning throughoutthisvolumetoproducerobustmodelssuitableforpurpose. Thevolume aimstoallowthereaderto nddataanddescriptorsanddevelop,discoverandutilise validmodels. Gdansk, ' Poland TomaszPuzyn Jackson,MS,USA JerzyLeszczynski Liverpool,UK MarkT. D.Cronin May2009 CONTENTS Part I Theory of QSAR 1 QuantitativeStructure-ActivityRelationships(QSARs)- ApplicationsandMethodology...3 Mark T. D. Cronin 1. 1. Introduction...3 1. 2. PurposeofQSAR...4 1. 3. ApplicationsofQSAR...4 1. 4. Methods...5 1. 5. TheCornerstonesofSuccessfulPredictiveModels ...7 1. 6. AValidated(Q)SARoraValidPrediction? ...9 1. 7. UsinginSilicoTechniques ...9 1. 8. NewAreasforinSilicoModels...11 1. 9. Conclusions...11 References ...11 2 TheUseofQuantumMechanicsDerivedDescriptorsin ComputationalToxicology...13 Steven J. Enoch 2. 1. Introduction...13 2. 2. TheSchrodingerEquation...15 2. 3. Hartree-FockTheory...17 2. 4. Semi-EmpiricalMethods:AM1andRM1...18 2. 5. ABInitio:DensityFunctionalTheory...19 2. 6. QSARforNon-ReactiveMechanismsofAcute(Aquatic) Toxicity...19 2. 7. QSARsforReactiveToxicityMechanisms...21 2. 7. 1. AquaticToxicityandSkinSensitisation...21 2. 7. 2. QSARsforMutagenicity ...24 2. 8. FutureDirectionsandOutlook...25 2. 9. Conclusions...26 References ...26 vii viii Contents 3 MolecularDescriptors...29 Viviana Consonni and Roberto Todeschini 3. 1. Introduction...29 3. 1. 1. De nitions...29 3. 1. 2. History...31 3. 1. 3. Theoreticalvs.ExperimentalDescriptors...33 3. 2. MolecularRepresentation ...35 3. 3. TopologicalIndexes...38 3. 3. 1. MolecularGraphs...38 3. 3. 2. De nitionandCalculationofTopologicalIndexes(TIs) 39 3. 3. 3. Graph-TheoreticalMatrixes...42 3. 3. 4. ConnectivityIndexes ...48 3. 3. 5. CharacteristicPolynomial ...50 3. 3. 6. SpectralIndexes ...53 3. 4. AutocorrelationDescriptors ...

Trends in Computational Nanomechanics reviews recent advances in analytical and computational modeling frameworks to describe the mechanics of materials on scales ranging from the atomistic, through the microstructure or transitional, and up to the continuum. The book presents new approaches in the theory of nanosystems, recent developments in theoretical and computational methods for studying problems in which multiple length and/or time scales must be simultaneously resolved, as well as example applications in nanomechanics.This title will be a useful tool of reference for professionals, graduates and undergraduates interested in Computational Chemistry and Physics, Materials Science, Nanotechnology.

“Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics.This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes.This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.

“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 reviews various aspects of molecular spectroscopy and its application in materials science, chemistry, physics, medicine, the arts and the earth sciences. Written by an international group of recognized experts, it examines how complementary applications of diverse spectroscopic methods can be used to study the structure and properties of different materials. The chapters cover the whole spectrum of topics related to theoretical and computational methods, as well as the practical application of spectroscopic techniques to study the structure and dynamics of molecular systems, solid-state crystalline and amorphous materials, surfaces and interfaces, and biological systems. As such, the book offers an invaluable resource for all researchers and postgraduate students interested in the latest developments in the theory, experimentation, measurement and application of various advanced spectroscopic methods for the study of materials.

This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery.The book offers an invaluable resource for graduate and postgraduate students, as well as forresearchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.

This book presents recently developed computational approaches for the study of reactive materials under extreme physical and thermodynamic conditions. It delves into cutting edge developments in simulation methods for reactive materials, including quantum calculations spanning nanometer length scales and picosecond timescales, to reactive force fields, coarse-grained approaches, and machine learning methods spanning microns and nanoseconds and beyond. These methods are discussed in the context of a broad range of fields, including prebiotic chemistry in impacting comets, studies of planetary interiors, high pressure synthesis of new compounds, and detonations of energetic materials. The book presents a pedagogical approach for these state-of-the-art approaches, compiled into a single source for the first time. Ultimately, the volume aims to make valuable research tools accessible to experimentalists and theoreticians alike for any number of scientific efforts, spanning many different types of compounds and reactive conditions.

This book focuses on the electronic properties of transition metals in coordination environments. These properties are responsible for the unique and intricate activity of transition metal sites in bio- and inorganic catalysis, but also pose challenges for both theoretical and experimental studies. Written by an international group of recognized experts, the book reviews recent advances in computational modeling and discusses their interplay using experiments. It covers a broad range of topics, including advanced computational methods for transition metal systems; spectroscopic, electrochemical and catalytic properties of transition metals in coordination environments; metalloenzymes and biomimetic compounds; and spin-related phenomena. As such, the book offers an invaluable resource for all researchers and postgraduate students interested in both fundamental and application-oriented research in the field of transition metal systems.

This book reviews various aspects of molecular spectroscopy and its application in materials science, chemistry, physics, medicine, the arts and the earth sciences. Written by an international group of recognized experts, it examines how complementary applications of diverse spectroscopic methods can be used to study the structure and properties of different materials. The chapters cover the whole spectrum of topics related to theoretical and computational methods, as well as the practical application of spectroscopic techniques to study the structure and dynamics of molecular systems, solid-state crystalline and amorphous materials, surfaces and interfaces, and biological systems. As such, the book offers an invaluable resource for all researchers and postgraduate students interested in the latest developments in the theory, experimentation, measurement and application of various advanced spectroscopic methods for the study of materials.

This book provides a comprehensive review of both traditional and cutting-edge methodologies that are currently used in computational toxicology and specifically features its application in regulatory decision making. The authors from various government agencies such as FDA, NCATS and NIEHS industry, and academic institutes share their real-world experience and discuss most current practices in computational toxicology and potential applications in regulatory science. Among the topics covered are molecular modeling and molecular dynamics simulations, machine learning methods for toxicity analysis, network-based approaches for the assessment of drug toxicity and toxicogenomic analyses. Offering a valuable reference guide to computational toxicology and potential applications in regulatory science, this book will appeal to chemists, toxicologists, drug discovery and development researchers as well as to regulatory scientists, government reviewers and graduate students interested in thisfield.

This book provides a comprehensive review of both traditional and cutting-edge methodologies that are currently used in computational toxicology and specifically features its application in regulatory decision making. The authors from various government agencies such as FDA, NCATS and NIEHS industry, and academic institutes share their real-world experience and discuss most current practices in computational toxicology and potential applications in regulatory science. Among the topics covered are molecular modeling and molecular dynamics simulations, machine learning methods for toxicity analysis, network-based approaches for the assessment of drug toxicity and toxicogenomic analyses. Offering a valuable reference guide to computational toxicology and potential applications in regulatory science, this book will appeal to chemists, toxicologists, drug discovery and development researchers as well as to regulatory scientists, government reviewers and graduate students interested in thisfield.

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, 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 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 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 contributed volume overviews recently presented approaches for carrying out QSPR/QSAR analysis by using a simplifying molecular input-line entry system (SMILES) to represent the molecular structure. In contrast to traditional SMILES, quasi-SMILES is a sequence of special symbols-codes that reflect molecular features and codes of experimental conditions. SMILES and quasi-SMILES serve as a basis to develop QSPR/QSAR as well Nano-QSPR/QSAR via the Monte Carlo calculation that provides the so-called optimal descriptors for QSPR/QSAR models.  The book presents a reliable technology for developing Nano-QSPR/QSAR while it also includes the description of the algorithms of the Monte Carlo optimization. It discusses the theory and practice of the technique of variational authodecoders (VAEs) based on SMILES and analyses in detail the index of ideality of correlation (IIC) and the correlation intensity index (CII) which are new criteria for the predictive potential of the model. The mathematical apparatus used is simple so that students of relevant specializations can easily follow. This volume is a valuable contribution to the field and will be of great interest to developers of models of physicochemical properties and biological activity, chemical technologists, and toxicologists involved in the area of drug design.

This contributed volume overviews recently presented approaches for carrying out QSPR/QSAR analysis by using a simplifying molecular input-line entry system (SMILES) to represent the molecular structure. In contrast to traditional SMILES, quasi-SMILES is a sequence of special symbols-codes that reflect molecular features and codes of experimental conditions. SMILES and quasi-SMILES serve as a basis to develop QSPR/QSAR as well Nano-QSPR/QSAR via the Monte Carlo calculation that provides the so-called optimal descriptors for QSPR/QSAR models.  The book presents a reliable technology for developing Nano-QSPR/QSAR while it also includes the description of the algorithms of the Monte Carlo optimization. It discusses the theory and practice of the technique of variational authodecoders (VAEs) based on SMILES and analyses in detail the index of ideality of correlation (IIC) and the correlation intensity index (CII) which are new criteria for the predictive potential of the model. The mathematical apparatus used is simple so that students of relevant specializations can easily follow. This volume is a valuable contribution to the field and will be of great interest to developers of models of physicochemical properties and biological activity, chemical technologists, and toxicologists involved in the area of drug design.

This book summarizes the state-of-the-art advances in the area of computational modelling of molecule-based magnets. Nowadays, various computational tools based on DFT, ab initio methods and other techniques are gaining attention in molecular nanomagnets and are successfully used to solve several outstanding problems in this area. This contributed volume discusses the theoretical foundation of the modelling of molecular magnets, starting from fitting the experimental magnetic data of very large molecules to the theory of pseudo-spin Hamiltonian approach and spin-phonon relaxations mechanisms, while it also presents examples of contemporary applications of both transition metal and lanthanide molecular magnets. In addition, the transport characteristics of molecules when placed at an interface and how these assemble on surfaces are also reviewed. This book is a great tool for researchers working in the fields of molecular magnetism and computational/theoretical chemistry and will also benefit graduate students specializing in physical-inorganic chemistry and molecular modelling.Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This book summarizes the state-of-the-art advances in the area of computational modelling of molecule-based magnets. Nowadays, various computational tools based on DFT, ab initio methods and other techniques are gaining attention in molecular nanomagnets and are successfully used to solve several outstanding problems in this area. This contributed volume discusses the theoretical foundation of the modelling of molecular magnets, starting from fitting the experimental magnetic data of very large molecules to the theory of pseudo-spin Hamiltonian approach and spin-phonon relaxations mechanisms, while it also presents examples of contemporary applications of both transition metal and lanthanide molecular magnets. In addition, the transport characteristics of molecules when placed at an interface and how these assemble on surfaces are also reviewed. This book is a great tool for researchers working in the fields of molecular magnetism and computational/theoretical chemistry and will also benefit graduate students specializing in physical-inorganic chemistry and molecular modelling.Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This contributed volume offers a comprehensive discussion on how to design and discover pharmaceuticals using computational modeling techniques. The different chapters deal with the classical and most advanced techniques, theories, protocols, databases, and tools employed in computer-aided drug design (CADD) covering diverse therapeutic classes. Multiple components of Structure-Based Drug Discovery (SBDD) along with its workflow and associated challenges are presented while potential leads for Alzheimer’s disease (AD), antiviral agents, anti-human immunodeficiency virus (HIV) drugs, and leads for Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) disease are discussed in detail. Computational toxicological aspects in drug design and discovery, screening adverse effects, and existing or future in silico tools are highlighted, while a novel in silico tool, RASAR, which can be a major technique for small to big datasets when not much experimental data are present, is presented. The book also introduces the reader to the major drug databases covering drug molecules, chemicals, therapeutic targets, metabolomics, and peptides, which are great resources for drug discovery employing drug repurposing, high throughput, and virtual screening. This volume is a great tool for graduates, researchers, academics, and industrial scientists working in the fields of cheminformatics, bioinformatics, computational biology, and chemistry.

This contributed volume offers a comprehensive discussion on how to design and discover pharmaceuticals using computational modeling techniques. The different chapters deal with the classical and most advanced techniques, theories, protocols, databases, and tools employed in computer-aided drug design (CADD) covering diverse therapeutic classes. Multiple components of Structure-Based Drug Discovery (SBDD) along with its workflow and associated challenges are presented while potential leads for Alzheimer’s disease (AD), antiviral agents, anti-human immunodeficiency virus (HIV) drugs, and leads for Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) disease are discussed in detail. Computational toxicological aspects in drug design and discovery, screening adverse effects, and existing or future in silico tools are highlighted, while a novel in silico tool, RASAR, which can be a major technique for small to big datasets when not much experimental data are present, is presented. The book also introduces the reader to the major drug databases covering drug molecules, chemicals, therapeutic targets, metabolomics, and peptides, which are great resources for drug discovery employing drug repurposing, high throughput, and virtual screening. This volume is a great tool for graduates, researchers, academics, and industrial scientists working in the fields of cheminformatics, bioinformatics, computational biology, and chemistry.

Machine learning and artificial intelligence have propelled research across various molecular science disciplines thanks to the rapid progress in computing hardware, algorithms, and data accumulation. This book presents recent machine learning applications in the broad research field of molecular sciences. Written by an international group of renowned experts, this edited volume covers both the machine learning methodologies and state-of-the-art machine learning applications in a wide range of topics in molecular sciences, from electronic structure theory to nuclear dynamics of small molecules, to the design and synthesis of large organic and biological molecules. This book is a valuable resource for researchers and students interested in applying machine learning in the research of molecular sciences.

Machine learning and artificial intelligence have propelled research across various molecular science disciplines thanks to the rapid progress in computing hardware, algorithms, and data accumulation. This book presents recent machine learning applications in the broad research field of molecular sciences. Written by an international group of renowned experts, this edited volume covers both the machine learning methodologies and state-of-the-art machine learning applications in a wide range of topics in molecular sciences, from electronic structure theory to nuclear dynamics of small molecules, to the design and synthesis of large organic and biological molecules. This book is a valuable resource for researchers and students interested in applying machine learning in the research of molecular sciences.

This contributed volume presents chapters integrating experimental and computational advances in materials research and discusses how the potential release of emerging materials would impact the environment. With increasing populations, there is a growing pressure on resources and the environment to provide food, water, and energy. Innovative materials and novel technologies, such as nanocomposite and multifunctional materials, additive manufacturing, and remediation technologies, are constantly being developed to meet these demands. As technologies mature some potentially harmful materials will find their way into the environment. Depending on their environmental persistence, such as “forever chemicals” per- and polyfluoroalkyl substances (PFAS), some of the emerging materials may become a major environmental challenge. This book covers a broad spectrum of topics related to the recent advances and future directions in emerging materials research, molecular simulations, machine learning and QSAR approaches for environmental contaminants, advanced materials for water purification, remediation technologies of PFAS, and life-cycle assessment of materials. It offers an invaluable resource for postgraduate students and researchers in academia, industry, and different laboratories interested in the field.