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 ...

"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.

Advances in the Theory of Atomic and Molecular Systems, is a collection of contributions presenting recent theoretical and computational developments that provide new insights into the structure, properties, and behavior of a variety of atomic and molecular systems. This volume (subtitled Dynamics, Spectroscopy, Clusters, and Nanostructures ) deals with the topics of Quantum Dynamics and Spectroscopy, Complexes and Clusters, and Nanostructures and Complex Systems .

This volume is an invaluable resource for faculty, graduate students, and researchers interested in theoretical and computational chemistry and physics, physical chemistry and chemical physics, molecular spectroscopy, and related areas of science and engineering."

Advances in the Theory of Atomic and Molecular Systems, is a collection of contributions presenting recent theoretical and computational developments that provide new insights into the structure, properties, and behavior of a variety of atomic and molecular systems. This volume (subtitled: Conceptual and Computational Advances in Quantum Chemistry) focuses on electronic structure theory and its foundations.

This volume is an invaluable resource for faculty, graduate students, and researchers interested in theoretical and computational chemistry and physics, physical chemistry and chemical physics, molecular spectroscopy, and related areas of science and engineering.

Channels of nanotubular dimensions exist in a variety of materials (examples are carbon nanotubes and the nanotubular channels of zeolites and zeotypes) and show promise for numerous applications due to their unique properties. One of their most important properties is their capacity to adsorb molecules and these may exist in a variety of phases.

"Adsorption and Phase Behaviour in Nanochannels and Nanotubes" provides an excellent review of recent and current work on adsorption on nanometerials. It is an impressive collection of papers dealing with the adsorption and phase behaviour in nanoporous materials from both experimental and theoretical perspectives.

"Adsorption and Phase Behaviour in Nanochannels and Nanotubes" focuses on carbon nanotubes as well as zeolites and related materials.

"Mas has dicho, Sancho, de 10 que sabes (dixo Don Quixote), que hay algunos que se cansan en saber, y averiguar cosas que despues de sabidas, y averiguadas, no importa un ardite al entendimiento, ni a la memoria. " "You have said more than you know, Sancho," said Don Quixote, "for there are some who tire them selves out learning and proving things which, once learnt and proved, do not concern either 'the under standing 01' the memory a jot. " Cervantes, Don Quixote, Part II, Chapter LXXV, Of the great Adventure of Montesinos' Cave in the heart of La Mancha, which the valorous Don Quixote brought to a happy ending. This book explores a relationship between classical tessellations and three-manifolds. All of us are very familiar with the symmetrical ornamental motifs used in the decoration of walls and ceilings. Oriental palaces contain an abundance of these, and many examples taken from them will be found in the following pages. These are the so-called mosaics or symmetrical tessellations of the euclidean plane. Even though we can imagine or even create very many of them, in fact the rules governing them are quite restrictive, if our purpose is to understand the symmetric group of the tessellation, that is to say, the group consisting of the plane isometries which leave the tessel lation invariant."

The role of quantum coherence in promoting the e ciency of the initial stages of photosynthesis is an open and intriguing question. Lee, Cheng, and Fleming, Science 316, 1462 (2007) The understanding and design of functional biomaterials is one of today's grand challenge areas that has sparked an intense exchange between biology, materials sciences, electronics, and various other disciplines. Many new - velopments are underway in organic photovoltaics, molecular electronics, and biomimetic research involving, e. g. , arti cal light-harvesting systems inspired by photosynthesis, along with a host of other concepts and device applications. In fact, materials scientists may well be advised to take advantage of Nature's 3. 8 billion year head-start in designing new materials for light-harvesting and electro-optical applications. Since many of these developments reach into the molecular domain, the - derstanding of nano-structured functional materials equally necessitates f- damental aspects of molecular physics, chemistry, and biology. The elementary energy and charge transfer processes bear much similarity to the molecular phenomena that have been revealed in unprecedented detail by ultrafast op- cal spectroscopies. Indeed, these spectroscopies, which were initially developed and applied for the study of small molecular species, have already evolved into an invaluable tool to monitor ultrafast dynamics in complex biological and materials systems. The molecular-level phenomena in question are often of intrinsically quantum mechanical character, and involve tunneling, non-Born- Oppenheimer e ects, and quantum-mechanical phase coherence.

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."

The discussions and plans on all scienti?c, advisory, and political levels to realize an even larger "European Supercomputer" in Germany, where the hardware costs alone will be hundreds of millions Euro - much more than in the past - are getting closer to realization. As part of the strategy, the three national supercomputing centres HLRS (Stuttgart), NIC/JSC (Julic h) and LRZ (Munich) have formed the Gauss Centre for Supercomputing (GCS) as a new virtual organization enabled by an agreement between the Federal Ministry of Education and Research (BMBF) and the state ministries for research of Baden-Wurttem berg, Bayern, and Nordrhein-Westfalen. Already today, the GCS provides the most powerful high-performance computing - frastructure in Europe. Through GCS, HLRS participates in the European project PRACE (Partnership for Advances Computing in Europe) and - tends its reach to all European member countries. These activities aligns well with the activities of HLRS in the European HPC infrastructure project DEISA (Distributed European Infrastructure for Supercomputing Appli- tions) and in the European HPC support project HPC-Europa. Beyond that, HLRS and its partners in the GCS have agreed on a common strategy for the installation of the next generation of leading edge HPC hardware over the next ?ve years. The University of Stuttgart and the University of Karlsruhe have furth- more agreed to bundle their competences and resources.

This book covers the results obtained in the Tera op Workbench project during a four years period from 2004 to 2008. The Tera op Workbench project is a colla- ration betweenthe High PerformanceComputingCenter Stuttgart (HLRS) and NEC Deutschland GmbH (NEC-HPCE) to support users to achieve their research goals using high performance computing. The Tera op Workbench supports users of the HLRS systems to enable and - cilitate leading edge scienti c research. This is achieved by optimizing their codes and improving the process work ow which results from the integration of diff- ent modules into a "hybrid vector system". The assessment and demonstration of industrial relevance is another goal of the cooperation. The Tera op Workbench project consists of numerous individual codes, grouped together by application area and developed and maintained by researchers or c- mercial organizations. Within the project, several of the codes have shown the ab- ity to reach beyond the TFlop/s threshold of sustained performance. This created the possibility for new science and a deeper understanding of the underlying physics. The papers in this book demonstrate the value of the project for different scienti c areas.

Providing the quantum-mechanical foundations of chemical bonding, this unique textbook emphasizes key concepts such as superposition, degeneracy of states and the role of the electron spin. An initial, concise and compact presentation of the rudiments of quantum mechanics enables readers to progress through the book with a firm grounding. Experimental examples are included to illustrate how the abstract concepts are manifest in real systems.

In this volume we have collected some of the contributions made to the Twelfth European Workshop on Quantum Systems in Chemistry and Physics (QSCP-XII) in 2007. The workshop was held at Royal Holloway College, the most westerly campusof the University of London,and situated just a stone's throw from Windsor Great Park. The workshop, which ran from 30 August to 5 September, continued the series that was established by Roy McWeeny in April 1996 with a meeting held at San Miniato, near Pisa. The purpose of the QSCP workshops is to bring together, in an informal atmosphere and with the aim of fostering collaboration, those chemists and physicists who share a common ?eld of interest in the theory of the quantum many-body problem. Quantum mechanics provides a theoretical foundation for our understandingof the structure,propertiesanddynamicsof atoms, moleculesandthe solid state, in terms of their component particles: electrons and nuclei. The study of 'Quantum Systems in Chemistry and Physics' therefore underpins many of the emerging?elds in twenty-?rstcenturyscience andtechnology:nanostructure,smart materials, drug design - to name but a few. Members of the workshop were keen to discuss their research and engage in collaboration centred upon the development of fundamental and innovative theory which would lead to the exploration of new concepts. The proceedings of all of the workshops, which have been held annually since 1996, have been published both to disseminate the latest developments within the wider community and to stimulate further collaboration.

A large number of biologically relevant species are negatively charged, the- fore it is not surprising that nature has developed sophisticated receptors to recognise, detect and transformanions. For example, complex receptors such as phosphate- and sulphate-binding proteins are employed by living cells to selectively recognise these two geometrically analogous anions. In addition to their roles in biological systems, some anions also have important en- ronmental impacts. For example, cyanide, pertechnetate and chromates pose serious health problems if present in water supplies. Because of their important biological roles and potential environmental impact there is great current interest in developing molecular receptors to selectively recogniseanionsandindoingsobeabletosequester, transformor sense them. The six chapters presented in this volume provide an overview of anion recognition and the most recent advances in this fast-growing area of supramolecular chemistry are highlighted. The?rstchapterbyBatesandGaleprovidesanoverviewofthecoordination of anions by synthetic organic hosts. The different organic functional groups used to bind anions are presented and this provides an introduction to the structuraland electronicproperties that hostsmust have to recogniseanionic guests.Ontheother hand, Bayly andBeer giveadetailed accountoftheuse of metalcomplexes asanionreceptors. Besides the important structuralfeatures that metals can confer to receptors, their optical and redox properties make themattractiveforthedevelopment ofanionsensors

In the 1980's sonochemistry was considered to be a rather restricted branch of chemistry involving the ways in which ultrasound could improve synthetic procedures, predominantly in heterogeneous systems and particularly for organometallic reactions. Within a few years the subject began to expand into other disciplines including food technology, environmental protection and the extraction of natural materials. Scientific interest grew and led to the formation of the European Society of Sonochemistry in 1990 and the launch of a new journal Ultrasonics Sonochemistry in 1994. The subject continues to develop as an exciting and multi-disciplinary science with the participation of not only chemists but also physicists, engineers and biologists. The resulting cross-fertilisation of ideas has led to the rapid growth of interdisciplinary research and provided an ideal way for young researchers to expand their knowledge and appreciation of the ways in which different sciences can interact. It expands scientific knowledge through an opening of the closed doors that sometimes restrict the more specialist sciences. The journey of exploration in sonochemistry and its expansion into new fields of science and engineering is recounted in "Sonochemistry Evolution and Expansion" written by two pioneers in the field. It is unlike other texts about sonochemistry in that it follows the chronological developments in several very different applications of sonochemistry through the research experiences of the two authors Tim Mason and Mircea Vinatoru. Designed for chemists and chemical engineers Written by two experts and practitioners in the subject Volume 1 covers the historical background and evolution of sonochemistry Volume 2 explains the wider applications and expansion of the subject VOLUME 2 Applications and Developments Volume 2 contains six chapters which detail the developments of sonochemistry in fields which continue to attract considerable research and development interest from academia and industry. The topics range from the important developments in chemical synthesis through food technology and materials processing to therapeutic ultrasound. The authors have made contributions to all of these and so the content is written in a way which should be understandable to readers whose expertise may not necessarily be in the individual topic. Each of the applications and developments described help to illustrate not only the diverse nature of sonochemistry but also the unifying theme of the effects of acoustic cavitation on a wide range of procedures.

This series presents critical reviews of the present position and future trends in modern chemical research concerned with chemical structure and bonding. It contains short and concise reports, each written by the world's renowned experts. The series is still valid and useful after five or ten years. More information is available at springerlink.com along with the electronic version of the whole content.

Photochemistry (a term that broadly speaking includes photophysics) is abranchofmodernsciencethatdealswiththeinteractionoflightwithmatter and lies at the crossroadsof chemistry, physics, and biology. However, before being a branch of modern science, photochemistry was (and still is today), an extremely important natural phenomenon. When God said: "Let there be light", photochemistry began to operate, helping God to create the world as wenowknowit.Itislikelythatphotochemistrywasthesparkfortheoriginof life on Earth and played a fundamental role in the evolution of life. Through the photosynthetic process that takes place in green plants, photochemistry is responsible for the maintenance of all living organisms. In the geological past photochemistry caused the accumulation of the deposits of coal, oil, and naturalgasthat wenowuseasfuels.Photochemistryisinvolved inthecontrol ofozoneinthestratosphereandinagreatnumber ofenvironmentalprocesses thatoccurintheatmosphere,inthesea,andonthesoil.Photochemistryisthe essenceoftheprocessofvisionandcausesavarietyofbehavioralresponsesin living organisms. Photochemistry as a science is quite young; we only need to go back less than one century to ?nd its early pioneer [1]. The concept of coordination compound is also relatively young; it was established in 1892, when Alfred Werner conceived his theory of metal complexes [2]. Since then, the terms coordination compound and metal complex have been used as synonyms, even if in the last 30 years, coordination chemistry has extended its scope to the binding ofall kinds of substrates [3, 4].

Reinvigorated by advances and insights the quantum theory of irreversible processes has recently attracted growing attention.

This volume introduces the very basic concepts of semigroup dynamics of open quantum systems and reviews a variety of modern applications. Originally published as Volume 286 (1987) in Lecture in Physics, this volume has been newly typeset, revised and corrected and also expanded to include a review on recent developments.

This volume contains a representative selection of the papers presented at the 10th European Workshop on Quantum Systems in Chemistry and Physics, held at Beit al Hikma, Carthage, Tunisia, from September 1st to 7th, 2005. The workshop continued the series which initiated at San Miniato, near Pisa, Italy, in 1996. The workshop's aim was to bring together chemists and physicists with a common interest in the quantum-mechanical many-body problem, in order to foster conceptual and methodological development for the understanding of the structure, dynamics and properties of atoms, molecules, and the solid state. This underpins many of the new emerging fields of science and technology: molecular engines, nanomaterials, responsive structural materials, synthetic bio-materials, drugs, and so on.

This textbook offers an accessible approach to the subject of mathematics which divides the topic into smaller units, guiding students through questions, exercises and problems designed to slowly increase student confidence and experience. The sequence of studies is individualised according to performance and can be regarded as full tutorial course. The study guide satisfies two objectives simultaneously: firstly it enables students to make effective use of the textbook and secondly it offers advice on the improvement of study skills. Empirical studies have shown that the student's competence for using written information has improved significantly by using this study guide. The new edition includes a new chapter on Fourier integrals and Fourier transforms, numerous sections had been updated, 30 new problems with solutions had been added. The interactive study guide has seen a substantial update.

Lowe's new edition assumes little mathematical or physical sophistication and emphasizes an understanding of the techniques and results of quantum chemistry. It can serve as a primary text in quantum chemistry courses, and enables students and researchers to comprehend the current literature. This third edition has been thoroughly updated and includes numerous new exercises to facilitate self-study and solutions to selected exercises.
* Assumes little initial mathematical or physical sophistication, developing insights and abilities in the context of actual problems
* Provides thorough treatment of the simple systems basic to this subject
* Emphasizes UNDERSTANDING of the techniques and results of modern quantum chemistry
* Treats MO theory from simple Huckel through ab intio methods in current use
* Develops perturbation theory through the topics of orbital interaction as well as spectroscopic selection rules
* Presents group theory in a context of MO applications
* Includes qualitative MO theory of molecular structure, Walsh rules, Woodward-Hoffmann rules, frontier orbitals, and organic reactions
develops MO theory of periodic systems, with applications to organic polymers.

Table of contents P.L.A. Popelier: Quantum Chemical Topology: on Bonds and Potentials.- A. Soncini, P.W. Fowler, L.W. Jenneskens: Angular Momentum and Spectral Decomposition of Ring Currents: Aromaticity and the Annulene Model.- S.L. Price, L.S. Price: Modelling Intermolecular Forces for Organic Crystal Structure Prediction.- C. Millot: Molecular Dynamics Simulations and Intermolecular Forces.- S. Tsuzuki: Interactions with Aromatic Rings

Provides historical perspective as well as current data

Abundantly illustrated with figures redrawn from literature data

Covers all pertinent theory and physical chemistry

Catalytic and chemotherapeutic applications are included

Liquid crystals, polymers and polymer liquid crystals are soft condensed matter systems of major technological and scientific interest. An understanding of the macroscopic properties of these complex systems and of their many and interesting peculiarities at the molecular level can nowadays only be attained using computer simulations and statistical mechanical theories. Both in the Liquid Crystal and Polymer fields a considerable amount of simulation work has been done in the last few years with various classes of models at different special resolutions, ranging from atomistic to molecular and coarse-grained lattice models. Each of the two fields has developed its own set of tools and specialized procedures and the book aims to provide a state of the art review of the computer simulation studies of polymers and liquid crystals. This is of great importance in view of a potential cross-fertilization between these connected areas which is particularly apparent for a number of experimental systems like, e.g. polymer liquid crystals and anisotropic gels where the different fields necessarily merge. An effort has been made to assess the possibilities of a coherent description of the themes that have developed independently, and to compare and extend the theoretical and computational techniques put forward in the different areas.

Axel Christian Klixbull Jorgensen was a "Polyhistor",one of the very few in the highly specialized science of our time.His interests and contributions in ch- istry covered the whole Periodic Table.This statement demonstrates the breadth of his interests,however,it also sheds light on the constraints of chemistry which deals with a large, yet limited number of elements. It is not surprising that Jorgensen went beyond these limits,exploring the probable or plausible ch- istry of yet unknown elements and elementary particles such as quarks. Even chemistry itself did not place rigid limits on his mind,he was able to transfer his chemical concepts to scientific problems far beyond the normal such as in astrophysics. "Structure and Bonding" is intimately associated with the name C.K. J- gensen both as initiator and author over several decades.The appearance of a special edition in memory of this great scientist is a self-evident prolongation of his many contributions to the success of this series.