Jerzy Leszczynski

Manoj Shukla

Practical Aspects of Computational Chemistry I: An Overview of the Last Two Decades and Current Trends gathers the advances made within the last 20 years by well-known experts in the area of theoretical and computational chemistry and physics. The title itself reflects the celebration of the twentieth anniversary of the “Conference on Current Trends in Computational Chemistry (CCTCC)” to which all authors have participated and contributed to its success. This volume poses (and answers) important questions of interest to the computational chemistry community and beyond. What is the historical background of the “Structural Chemistry”? Is there any way to avoid the problem of intruder state in the multi-reference formulation? What is the recent progress on multi-reference coupled cluster theory? Starting with a historical account of structural chemistry, the book focuses on the recent advances made in promising theories such as many body Brillouin-Wigner theory, multireference state-specific coupled cluster theory, relativistic effect in chemistry, linear and nonlinear optical properties of molecules, solution to Kohn-Sham problem, electronic structure of solid state materials, development of model core potential, quantum Monte Carlo method, nano and molecular electronics, dynamics of photodimerization and excited states, intermolecular interactions, hydrogen bonding and non-hydrogen bonding interactions, conformational flexibility, metal cations in zeolite catalyst and interaction of nucleic acid bases with minerals. Practical Aspects of Computational Chemistry I: An Overview of the Last Two Decades and Current Trends is aimed at theoretical and computational chemists, physical chemists, materials scientists, and particularly those who are eager to apply computational chemistry methods to problem of chemical and physical importance. This book will provide valuable information to undergraduate, graduate, and PhD students as well as to established researchers.

An Overview of the Last Two Decades and Current Trends

Practical Aspects of Computational Chemistry I

The gap between experimental objects and models for calculations in chemistry is being bridged. The size of experimental nano-objects is decreasing, while reliable calculations are feasible for larger and larger molecular systems. The results of these calculations for isolated molecules are becoming more relevant for experiments. However, there are still significant challenges for computational methods. This series of books presents reviews of current advances in computational methodologies and applications. Chapter 1 of this volume provides an overview of the theoretical and numerical aspects in the development of the polarizable continuum model (PCM). Chapter 2 demonstrates a multiplicative scheme used to estimate the properties of two- and three-dimensional clusters from the properties of their one-dimensional components. Chapter 3 discusses the application of ab initio methods for a reliable evaluation of the characteristics of hydrogen-bonded and van der Waals complexes. Ab initio quantum-chemical methods are popular among researchers investigating various aspects of DNA. The properties of DNA base polyads linked by base-base hydrogen bonds are reviewed in Chapter 4, while Chapter 5 reviews the primary radiation-induced defects in nucleic acid building blocks, and how DNA can be influenced by chemical and environmental effects. Finally, Chapter 6 discusses available experimental data of DNA bases, base pairs, and their complexes with water.

Reviews of Current Trends

Computational Chemistry

The contributions collected in this volume complement volume 1 of this series, disclosing results of current developments in methodologies and applications of computational chemistry methods. The covered topics include fundamentals and applications of propagator calculations, as well as recent developments in the computationally efficient and accurate SAC-CI method, which allows calculation of various electronic states at the same time. SAC-CI studies of excited states of large molecular systems like porphyrins are reviewed, and its application to investigations of surface phenomena is discussed. The book also features a review of recent work on quantum Monte Carlo simulations. Furthermore, the book discusses the application of computational methods to biomolecules and, in particular, the application of the DFT methods to prediction of molecular structures and the IR spectrum of the DNA bases, as well as currently developed force field parameters and their application in molecular dynamics calculations of,biologically important molecules. Lastly, there is a review of a quantum chemistry course which prepares students at the Department of Chemistry of ETH Zurich to perform their own ab initio studies.

"Practical Aspects of Computational Chemistry" presents contributions on a range of aspects of Computational Chemistry applied to a variety of research fields. The chapters focus on recent theoretical developments which have been used to investigate structures and properties of large systems with minimal computational resources. Studies include those in the gas phase, various solvents, various aspects of computational multiscale modeling, Monte Carlo simulations, chirality, the multiple minima problem for protein folding, the nature of binding in different species and dihydrogen bonds, carbon nanotubes and hydrogen storage, adsorption and decomposition of organophosphorus compounds, X-ray crystallography, proton transfer, structure-activity relationships, a description of the REACH programs of the European Union for chemical regulatory purposes, reactions of nucleic acid bases with endogenous and exogenous reactive oxygen species and different aspects of nucleic acid bases, base pairs and base tetrads.

Methods, Concepts and Applications

Practical Aspects of Computational Chemistry

The gap between experimental objects and models for calculations in chemistry is being bridged. The size of experimental nano-objects is decreasing, while reliable calculations are feasible for larger and larger molecular systems. The results of these calculations for isolated molecules are becoming more relevant for experiments. However, there are still significant challenges for computational methods. This series of books presents reviews of current advances in computational methodologies and applications. Chapter 1 of this volume provides an overview of the theoretical and numerical aspects in the development of the polarizable continuum model (PCM). Chapter 2 demonstrates a multiplicative scheme used to estimate the properties of two- and three-dimensional clusters from the properties of their one-dimensional components. Chapter 3 discusses the application of ab initio methods for a reliable evaluation of the characteristics of hydrogen-bonded and van der Waals complexes. Ab initio quantum-chemical methods are popular among researchers investigating various aspects of DNA. The properties of DNA base polyads linked by base-base hydrogen bonds are reviewed in Chapter 4, while Chapter 5 reviews the primary radiation-induced defects in nucleic acid building blocks, and how DNA can be influenced by chemical and environmental effects. Finally, Chapter 6 discusses available experimental data of DNA bases, base pairs, and their complexes with water. Contents:Computational Modelling of the Solvent Effects on Molecular Properties: An Overview of the Polarizable Continuum Model (PCM) Approach (R Cammi et al.)Electronic and Nonlinear Optical Properties of 2-Methyl-4-Nitroaniline Clusters (M Guillaume et al.)Ab Initio Calculations of the Intermolecular Nuclear Spin-Spin Coupling Constants (M Pecul & J Sadlej)Base Polyad Motifs in Nucleic Acids — Biological Significance, Occurrence in Three-Dimensional Experimental Structures and Computational Studies (M Meyer & J Sühnel)Model Calculations of Radiation Induced Damage in DNA Constituents Using Density Functional Theory (D M Close)Excited States of Nucleic Acid Bases (M K Shukla & J Leszczynski) Readership: Graduate students and researchers in computational chemistry. Keywords:Computational Chemistry

Computational Chemistry: Reviews of Current Trends

Manoj K. Shukla

Theoretical and Computational Chemistry research has made unparalleled advancements in understanding every expanding area of science and technology. This volume presents the state-of-the-art research and progress made by eminent researchers in the area of theoretical computational chemistry and physics. The title mirrors the name of the annual international conference “Conference on Current Trends on Computational Chemistry” (CCTCC) which has become a popular discussion ground for eminent Theoretical and Computational Chemists and has been honored by the presence of several Nobel Laureates. Practical Aspects of Computational Chemistry III is aimed at theoretical and computational chemists, physical chemists, material scientists and those who are eager to apply computational chemistry methods to problems of chemical and physical importance. The book is a valuable resource for undergraduate, graduate and PhD students as well as established researchers.

Practical Aspects of Computational Chemistry III

A presentation of developments in the methodologies and applications of computational chemistry methods. The topics covered include fundamentals and applications of multireference Brillouin-Wigner coupled-cluster theory, and quantum-chemical modelling ofthe interaction of solute and solvent.

This handbook is a guide to current methods of computational chemistry, explaining their limitations and advantages and providing examples of their applications. The first part outlines methods, the balance of volumes present numerous important applications.

Handbook of Computational Chemistry

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.

A Comprehensive Theoretical and Experimental Analysis

Radiation Induced Molecular Phenomena in Nucleic Acids

Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends gathers the discussion of advances made within the last 20 years by well-known experts in the area of theoretical and computational chemistry and physics. The title reflects the celebration of the twentieth anniversary of the “Conference on Current Trends in Computational Chemistry (CCTCC)” to success of which all authors contributed. Starting with the recent development of modeling of solvation effect using the Polarizable Continuum Model (PCM) at the Coupled-Cluster level and the effects of extreme pressure on the molecular properties within the PCM framework, this volume focuses on the association/dissociation of ion pairs in binary solvent mixtures, application of graph theory to determine the all possible structures and temperature-dependent distribution of water cluster, generalized-ensemble algorithms for the complex molecular simulation, QM/MD based investigation of formation of different nanostructures under nonequilibrium conditions, quantum mechanical study of chemical reactivity of carbon nanotube, covalent functionalization of single walled-carbon nanotube, designing of functional materials, importance of long-range dispersion interaction to study nanomaterials, recent advances in QSPR/QSAR analysis of nitrocompounds, prediction of physico-chemical properties of energetic materials, electronic structure and properties of 3d transition metal dimers, the s-bond activation reactions by transition metal complexes, theoretical modeling of environmental mercury depletion reaction, organolithium chemistry and computational modeling of low-energy electron induced DNA damage. Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends is aimed at theoretical and computational chemists, physical chemists, materials scientists, and particularly those who are eager to apply computational chemistry methods to problems of chemical and physical importance. This book provides valuable information to undergraduate, graduate, and PhD students as well as to established researchers. Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends is aimed at theoretical and computational chemists, physical chemists, materials scientists, and particularly those who are eager to apply computational chemistry methods to problems of chemical and physical importance. This book provides valuable information to undergraduate, graduate, and PhD students as well as to established researchers.

Practical Aspects of Computational Chemistry II

Tomasz Puzyn

Mark T. Cronin

This book presents an interdisciplinary overview on the most recent advances in QSAR studies. The first part consists of a comprehensive review of QSAR methodology. The second part highlights the interdisciplinary aspects and new areas of QSAR modelling.

Methods and Applications

Recent Advances in QSAR Studies

This volume presents a balanced blend of methodological and applied contributions. It supplements well the first three volumes of the series, revealing results of current research in computational chemistry. It also reviews the topographical features of several molecular scalar fields. A brief discussion of topographical concepts is followed by examples of their application to several branches of chemistry. The size of a basis set applied in a calculation determines the amount of computer resources necessary for a particular task. The details of a common strategy — the ab initio model potential method — which could be used to minimize such a task are revealed in the subsequent contribution. Such an approach is applied to atoms, molecules and solids. Two chapters are devoted to the prediction of solvent effects in biological systems. These effects are significant for interactions of nucleic acid bases and crucial for an evaluation of the free energies that govern the associations of macromolecules in aqueous solutions. A chapter on the developments and applications of the multireference Moller–Plesset method could be used as a reference in theoretical studies of systems where both the dynamical and nondynamical correlation effects should be accounted for. This technique is an efficient tool in such investigations. An explosive application of computational techniques — studies of detonation initiation and sensitivity in energetic compounds — is discussed in detail in the last chapter. The computational treatment of such unstable compounds allows the prediction of their crucial properties without being subject to their destructive forces. Contents:Topography of Atomic and Molecular Scalar Fields (S R Gadre)The Ab Initio Model Potential Method: A Common Strategy for Effective Core Potential and Embedded Cluster Calculations (L Seijo & Z Barandiaran)Continuum Models of Macromolecular Association in Aqueous Solution (M A Olson)Interactions of Nucleic Acid Bases: The Role of Solvent (M Orozco et al.)Recent Advances in Multireference Møller–Plesset Method (K Hirao et al.)Detonation Initiation and Sensitivity in Energetic Compounds: Some Computational Treatments (P Politzer & H E Alper) Readership: Graduate students and researchers in computational chemistry. Keywords:Continuum Model;Protein-Protein Association;Protein-Nucleic Acid Binding;Free Energy of Complex Formation;Molecular Recognition;Poisson-Boltzmann Equation;Dielectric Models;Solvation;Hydrophobic Effect;Protein Reorganization;ECP;AIMP;Core Potential;Embedding Potential;Model Potential;Ab Initio;Embedded Cluster;Relativistic;Impurity;Doped Crystal

There are strong indications that, in the 21st century, computational chemistry will be a prime research tool not only for the basic sciences but also for the life and materials sciences. Recent developments in nanotechnology allow us to detect a layer of single atoms. Researchers are able not only to image but also to manipulate molecules and atoms. It does not take much imagination to realize that before performing such a task on a real system it is much easier and faster to study models on computers. That is the aim of this volume ? it provides up-to-date reviews which cover representative areas of computational chemistry.In Chapter 1, Y Ishikawa and M J Vilkas provide a review of multireference Moller?Plesset (MR?MP) perturbation theory. Fifteen years ago Roberto Car of Princeton University and Michele Parrinello of Max Planck Institute introduced a method that revolutionized electronic structure calculations for molecules, liquids and solids. Ursula Rothlisberger, a former member of Parrinello's group, reviews the formation of the method in its most common implementations in Chapter 2. In the third chapter, Isaac B Bersuker describes the general theory of the combined quantum mechanics?molecular mechanics (QM/MM) approach. In Chapter 4, Marcel Allavena and David White present a review of applications of computational chemistry to proton transfer, the primary process for acid-base chemistry on zeolites. Chapter 5 is a review by S Roszak and J Leszczynski of recent data on the clusters formed from the charged ion and weakly interacting ligands. The last chapter, contributed by Carlos R Handy, is devoted to recent developments in the incorporation of continuous wavelet transform analysis into quantum operator theory.

Veera M. Boddu

Jeffery A. Steevens

Reddy Damavarapu

This book offers a comprehensive account of energetic materials, including their synthesis, computational modeling, applications, associated degradation mechanisms, environmental consequences and fate and transport. This multi-author contributed volume describes how armed forces around the world are moving their attention from legacy explosive compounds, which are heat and shock sensitive (thus posing greater challenges in terms of handling and storage), to the insensitive munitions compounds/formulations such as insensitive munitions explosive (IMX) and the Picatinny Arsenal Explosive (PAX) series of compounds. The description of energetic materials focuses on explosives, pyrotechnic compositions, and propellants. The contributors go on to explain how modern generation energetic compounds must be insensitive to shock and heat but at the same time yield more energy upon explosion. Nanoinspired and/or co-crystallized energetic materials offer another route to generate next-generation energetic materials, and this authoritative book bridges a large gap in the literature by providing a comprehensive analysis of these compounds. Additionally, it includes a valuable overview of energetic materials, a detailed discussion of recent advances on future energetic compounds, nanotechnology in energetic materials, environmental contamination and toxicity, assessment of munitions lethality, the application quantitative structure–activity relationship (QSAR) in design of energetics and the fate and transport of munition compounds in the environment.

From Cradle to Grave

Energetic Materials

This book is the first to provide a comprehensive review of recent progress and challenges in the risk assessment of nanomaterials by empirical and computational techniques.

Innovative Merge of Computational Approaches and Experimental Techniques

Towards Efficient Designing of Safe Nanomaterials

The contributions collected in this volume complement volume 1 of this series, disclosing results of current developments in methodologies and applications of computational chemistry methods. The covered topics include fundamentals and applications of propagator calculations, as well as recent developments in the computationally efficient and accurate SAC-CI method, which allows calculation of various electronic states at the same time. SAC-CI studies of excited states of large molecular systems like porphyrins are reviewed, and its application to investigations of surface phenomena is discussed. The book also features a review of recent work on quantum Monte Carlo simulations. Furthermore, the book discusses the application of computational methods to biomolecules and, in particular, the application of the DFT methods to prediction of molecular structures and the IR spectrum of the DNA bases, as well as currently developed force field parameters and their application in molecular dynamics calculations of biologically important molecules. Lastly, there is a review of a quantum chemistry course which prepares students at the Department of Chemistry of ETH Zurich to perform their own ab initio studies. Contents:The Electron Propagator Picture of Molecular Electronic Structure (J V Ortiz)SAC-CI Method: Theoretical Aspects and Some Recent Topics (H Nakatsuji)Quantum Monte Carlo and Electronic Structure (R N Barnett & W A Lester, Jr.)Molecular Structure and Infrared Spectra of the DNA Bases and Their Derivatives: Theory and Experiment (M J Nowak et al.)Derivation and Assessment of a New Set of Ab Initio Potentials and Its Application to Molecular Dynamics Simulations of Biological Molecules in Vacuo, in Crystal and in Aqueous Solution (M Aida)Practical Exercises in Ab Initio Quantum Chemistry — the World Wide Web as a Teaching Environment (H P Lüthi et al.) Readership: Computational and other chemists, and physicists. keywords:

Manthos G. Papadopoulos

Andrzej J. Sadlej

This book assembles both theory and application in this field, to interest experimentalists and theoreticians alike. Part 1 is concerned with the theory and computing of non-linear optical (NLO) properties while Part 2 reviews the latest developments in experimentation. This book will be invaluable to researchers and students in academia and industry, particularlrly to anyone involved in materials science, theoretical and computational chemistry, chemical physics, and molecular physics.

From molecules to condensed phases

Non-Linear Optical Properties of Matter

' Vast progress in the area of computational chemistry has been achieved in the last decade. Theoretical methods such as quantum mechanics, molecular dynamics and statistical mechanics have been successfully used to characterize chemical systems and to design new materials, drugs and chemicals. The reviews presented in this volume discuss the current advances in computational methodologies and their applications. The areas covered include materials science, nanotechnology, inorganic and biological systems. The major thrust of the book is to bring timely overviews of new findings and methods applied in the rapidly changing field of computational chemistry. Contents:Molecular Electronics with Gaussian98/03 (J J Palacios et al.)Molecular Dynamics Simulations of Single Molecule Atomic Force Microscope Experiments (W Nowak & P E Marszalek)Molecular Dynamics Simulations of a Molecular Electronics Device: The NanoCell (J Seminario et al.)Computation of Excited State Potential Energy Surfaces via Linear Response Theories Based on State Specific Multi-Reference Coupled Electron-Pair Approximation Like Methods (S Chattopadhyay et al.)Modelling of Anisotropic Exchange Coupling in Rare-Earth–Transition-Metal Pairs: Applications to Yb3+-Mn2+ and Yb3+-Cr3+ Halide Clusters and Implications to the Light Up-Conversion (M Atanasov et al.)Is a Dihydrogen Bond a Unique Phenomenon? (S J Grabowski & J Leszczynski) Readership: Graduate students and researchers in computational chemistry. Keywords:Computational Chemistry;Quantum Chemistry;Molecular Dynamics;Coupled Clusters Methods;Hydrogen Bonding;Molecular ElectronicsKey Features:Provides timely overviews of new findings and applications in a rapidly changing fieldIncludes reviews from well-known experts in the field, as well as current research data from the authors' groupsReviews:“This book is also an excellent source of information not only for advanced specialists, but also for graduate as well as undergraduate students.”Professor W A Sokalski Wroclaw University of Technology “The contents of the book is quite well-balanced; there is a good mix of both somewhat general topics and topics that are of wide current interest. It will be useful and interesting for chemists, physicists and materials scientists.”Professor Kang Hway Chuan National University of Singapore '

Jerzy Leszczynski

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