Handbook of Computational Chemistry

Jerzy LeszczynskiEditor

Anna Kaczmarek-Kedziera • Tomasz Puzyn •Manthos G. Papadopoulos • Heribert Reis •Manoj K. ShuklaCo-Editors

Handbook ofComputational Chemistry

Second Edition

Volume 2

With 588 Figures and 123 Tables

123

EditorJerzy LeszczynskiDepartment of Chemistry and BiochemistryInterdisciplinary Center for NanotoxicityJackson State UniversityJackson, MS, USA

Co-EditorsAnna Kaczmarek-KedzieraFaculty of ChemistryNicolaus Copernicus UniversityTorun, Poland

Manthos G. PapadopoulosInstitute of BiologyMedicinal Chemistry and BiotechnologyNational Hellenic Research FoundationAthens, Greece

Manoj K. ShuklaUS Army Engineer Researchand Development CenterVicksburg, MS, USA

Tomasz PuzynLaboratory of Environmental ChemometricsFaculty of ChemistryUniversity of GdanskGdansk, Poland

Heribert ReisInstitute of BiologyMedicinal Chemistry and BiotechnologyNational Hellenic Research FoundationAthens, Greece

ISBN 978-3-319-27281-8 ISBN 978-3-319-27282-5 (eBook)ISBN 978-3-319-28572-6 (print and electronic bundle)DOI 10.1007/978-3-319-27282-5

Library of Congress Control Number: 2011941760

1st edition: © Springer Science+Business Media B.V. 2012© Springer International Publishing Switzerland 2017This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part ofthe material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting, reproduction on microfilms or in any other physical way, and transmission or informationstorage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodologynow known or hereafter developed.The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoes not imply, even in the absence of a specific statement, that such names are exempt from the relevantprotective laws and regulations and therefore free for general use.The publisher, the authors and the editors are safe to assume that the advice and information in this bookare believed to be true and accurate at the date of publication. Neither the publisher nor the authors orthe editors give a warranty, express or implied, with respect to the material contained herein or for anyerrors or omissions that may have been made.

Printed on acid-free paper

This Springer imprint is published by Springer NatureThe registered company is Springer International Publishing AGThe registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface

We are delighted to deliver a second, expanded, and brought up to date edition ofthe Handbook of Computational Chemistry. It is apparent that this fast-growingresearch area requires constant updates. The second edition of our book providesthe reader with current, key references to both methodologies and the results of thecomputational chemistry studies. We selected various focus areas to be covered bythe handbook, and this selection is a subjective choice of the editors since due to avast number of studies published every year, only the most representative examplesof applications could be incorporated in the five volumes of this edition.

An amazing transformation of chemistry from an exclusively experimental sci-ence to one with theoretical foundations started in the early twentieth century, whenprinciples of quantum mechanics had been established. The most notable progresshas been accomplished during the last 50 years during which time it has advancedthrough noticeable developments and applications of computational methods. Thistransformation has its roots in both theoretical breakthroughs (Heisenberg’s 1925and Schrodinger’s 1926 first papers on quantum mechanics) and the developmentof the first computer – Electronic Numerical Integrator and Computer (ENIAC) –built in 1943 for the US Department of the Army. However, it took about 20 yearsafter the creation of the ENIAC computers to deliver computational chemistrytechniques to the scientific community. Such early methods, being semiempiricalin nature, do rely on the large number of experimental parameters. Disappointedly,though such an approach unites experimental chemistry origins with new theoreticalapproaches, it proves to produce in various cases artificial computational results, andit also lacks reliable parameters for some elements. The next successful chapter forcomputational chemistry started in the 1970s with applications of nonempirical abinitio methods. The first ab initio computer code popular among non theoreticians– GAUSSIAN 70 – was developed in the 1970s by John A. Pople’s group. Itinitiated a computational chemistry revolution that fired up in the 1980s whensupercomputers became accessible to the general scientific community. Also duringthis period, density functional theory approaches gained a prominent positionamong efficient computational methods. The vital role of computational chemistryin many research areas was convincingly acknowledged in 1998 when the chemicaland physical community celebrated the Nobel Prize that was awarded to two leading

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vi Preface

computational experts. It was not by chance that Walter Kohn and John A. Poplewere recognized by the Nobel Committee for their contributions to the developmentof efficient computational methods for quantum chemistry.

Over the past years, different methods of theoretical chemistry were successfullytransformed into useful tools that could be applied in diverse areas of research,science, and technology. Owing to the fundamental methodological developmentsand continuous impressive progress in computational technologies in the last quarterof the twentieth century, several fast and user-friendly programs were developedand made accessible to a wide community of scientists. These near-automaticcomputer codes are evidence of how methods of theoretical chemistry could beapplied as both diagnostic and predictive research tools which support efforts oreven guide the direction of traditional experimental approaches. The user-friendlyfeatures of commercial codes combined with efficient visualization methods makethem accessible to researchers with almost no educational background. Generally,only a limited knowledge and a little formal experience in theoretical chemistry arerequired to use such programs and to obtain some numerical data. This might causeunexpected outcomes. Most of the methods of theoretical (quantum) chemistry havea limited range of applications, and their use by an inexperienced amateur whoperforms computational studies without understanding such constraint may lead toserious problems and mistakes. Moreover, a variety of methods of different qualitiesexist, and a user without a good background in theoretical chemistry may feel lostat the choices from usually rich menus of available programs.

The multivolume Handbook of Computational Chemistry is primarily intendedas a guide to help navigate among different computational methods currently inuse. In order to accomplish this goal, it provides a compact description of thebasis of computational chemistry along with many examples of applications ofthese methods in various areas. The handbook is designed for researchers whoare just being introduced into computational methods, as well as for those whoare searching for the best choice for a solution to a specific problem involvingtheoretical approaches.

The first two volumes briefly describe different methods used in computationalchemistry without going into exhaustive details of theory. Basic assumptionscommon to the majority of computational methods based on either quantum orstatistical mechanics are outlined. Particular attention is paid to the limits oftheir applicability. Importantly, this volume also establishes definitions of variousacronyms and terminologies used in the area of computational chemistry.

Since we assumed that the readers of this book are interested in applicationsof computational methods, a broad range of the most important applications ofcomputational chemistry is provided. The applications include descriptions ofstandard chemical calculations for model molecules under various conditions. Thehandbook provides information on prediction of various molecular properties aswell as investigations of chemical reactions.

There are two classes of species, biomolecules and nanomaterials, that are of avital interest not only to chemists but also to physicists, biologists, and materialscientists. Two volumes are devoted to description of specific computational

Preface vii

methods that are designed to investigate such species. Numerous examples ofapplications as well as descriptions of specific research problems and their solutionsfor various types of biomolecules and nanoparticles are given in volumes 3 and 4of the handbook. The reviewed topics will attract the attention of all those who arealready working or planning to start research involving computational approaches.

The fifth volume, an entirely new addition to the second edition, is devoted to thecheminformatics – both a description of techniques and discussion of applications.This is an important enhancement of the current Handbook of ComputationalChemistry since the techniques of cheminformatics are vital tools of many com-putational chemists, those in research laboratories and, especially, those working inindustry. Techniques developed allow storage, indexing, search, and comparing ofinformation on chemical compounds. Such information could be used in the well-known quantitative structure-property (activity) relationship (QSPR/QSAR) studiesfor the prediction of specific property/activity of compounds of interest. QSARtechniques have been successfully applied for over 50 years in the pharmaceuticalindustry, and at the beginning of this century they were also adopted to investigateproperties, biological activities, and toxicity of a new, unique class of compounds –nanomaterials.

We welcome all comments and suggestions related to the current version of thehandbook as well as recommendations for possible revisions in the future. Many ofthe suggestions obtained from the readers of the first edition of the handbook havebeen applied to improve the second edition, and we are grateful for all inputs andcomments. Such feedback and active participation help us to focus on areas that areimportant for the majority of our readers and improve the context of the book.

The Editors

Contents

Volume 1

Part I Theory and Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Anna Kaczmarek-Kedziera and Heribert Reis

1 Computational Chemistry: From the Hydrogen Moleculeto Nanostructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3Lucjan Piela

2 Molecular Mechanics: Principles, History, and Current Status . . . . 21Valeri Poltev

3 The Position of the Clamped Nuclei ElectronicHamiltonian in Quantum Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . 69Brian Sutcliffe and R. Guy Woolley

4 Remarks on Wave Function Theory and Methods . . . . . . . . . . . . . . . 123Dariusz Kedziera and Anna Kaczmarek-Kedziera

5 Adiabatic, Born-Oppenheimer, and Non-adiabatic Approaches . . . 173Monika Stanke

6 Directions for Use of Density Functional Theory: A ShortInstruction Manual for Chemists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225Heiko Jacobsen and Luigi Cavallo

7 Introduction to Response Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269Thomas Bondo Pedersen

8 Intermolecular Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295Alston J. Misquitta

9 Molecular Dynamics Simulation: From “Ab Initio” to“Coarse Grained” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337Chris Lorenz and Nikos L. Doltsinis

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10 Statistical Mechanics of Force-Induced Transitions ofBiopolymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397Sanjay Kumar

Part II Applications of Computational Methods toModel Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421

Anna Kaczmarek-Kedziera and Heribert Reis

11 Molecular Structure and Vibrational Spectra . . . . . . . . . . . . . . . . . . 423Jon Baker

12 Molecular Electric, Magnetic, and Optical Properties . . . . . . . . . . . 497Michał Jaszunski, Antonio Rizzo, and Kenneth Ruud

13 Weak Intermolecular Interactions: A SupermolecularApproach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 593Mark Waller and Stefan Grimme

14 Chemical Reactions: Thermochemical Calculations . . . . . . . . . . . . . 621John D. Watts

15 Calculation of Excited States: Molecular Photophysicsand Photochemistry on Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 639Luis Serrano-Andrés and Juan José Serrano-Pérez

16 Solvent Effects in Quantum Chemistry . . . . . . . . . . . . . . . . . . . . . . . . 727Gerald Monard and Jean-Louis Rivail

17 Solvent Effects on Molecular Electric Properties . . . . . . . . . . . . . . . . 741Miroslav Medved’, Šimon Budzák, Wojciech Bartkowiak,and Heribert Reis

18 Auxiliary Density Functional Theory: From Molecules toNanostructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 795Patrizia Calaminici, Aurelio Alvarez-Ibarra, DomingoCruz-Olvera, Victor-Daniel Domínguez-Soria, RobertoFlores-Moreno, Gabriel U. Gamboa, Gerald Geudtner,Annick Goursot, Daniel Mejía-Rodríguez, Dennis R. Salahub,Bernardo Zuniga-Gutierrez, and Andreas M. Köster

19 Guide to Programs for Nonrelativistic QuantumChemistry Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861Tao Zeng and Mariusz Klobukowski

20 Relativistic Methods in Computational Quantum Chemistry . . . . . 885Paweł Tecmer, Katharina Boguslawski, and Dariusz Kedziera

21 Time-Dependent Density Functional Theory: A Tool toExplore Excited States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 927Daniel Escudero, Adèle D. Laurent, and Denis Jacquemin

Contents xi

22 Molecular Aspects of Solvation Investigated UsingStatistical Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 963Norio Yoshida and Katsura Nishiyama

Volume 2

Part III Solid States and Nanomaterials . . . . . . . . . . . . . . . . . . . . . . . . . 981

Manthos Papadopoulos and Heribert Reis

23 Photoactive Semiconducting Oxides for Energy andEnvironment: Experimental and Theoretical Insights . . . . . . . . . . . . 983Malgorzata Makowska-Janusik and Abdel-Hadi Kassiba

24 Structures and Stability of Fullerenes, Metallofullerenes,and Their Derivatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1031Alexey A. Popov

25 Structures and Electric Properties of Semiconductor clusters . . . . . 1097Panaghiotis Karamanis

26 Structures, Energetics, and Spectroscopic Fingerprintsof Water Clusters n D 2 –24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1139Soohaeng Yoo and Sotiris S. Xantheas

27 Fundamental Structural, Electronic, and ChemicalProperties of Carbon Nanostructures: Graphene,Fullerenes, Carbon Nanotubes, and Their Derivatives . . . . . . . . . . . 1175Tandabany C. Dinadayalane and Jerzy Leszczynski

28 Optical Properties of Quantum Dot Nano-compositeMaterials Studied by Solid-State Theory Calculations . . . . . . . . . . . 1259Ying Fu and Hans Ågren

29 Modeling of Quasi-One-Dimensional CarbonNanostructures with Density Functional Theory . . . . . . . . . . . . . . . . 1297Veronica Barone, Oded Hod, and Juan E. Peralta

30 Variation of the Surface to Bulk Contribution to ClusterProperties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1339Antonis N. Andriotis, Zacharias G. Fthenakis, andMadhu Menon

31 Theoretical Studies of Structural and ElectronicProperties of Clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1357Michael Springborg

32 The Response of Extended Systems to Electrostatic Fields . . . . . . . . 1415Michael Springborg, Bernard Kirtman, and MohammadMolayem

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33 Modeling of Nanostructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1459Hande Toffoli, Sakir Erkoç, and Daniele Toffoli

Part IV Biomolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1515

Manoj K. Shukla

34 Quantum Cluster Theory for the Polarizable ContinuumModel (PCM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1517Roberto Cammi and Jacopo Tomasi

35 Spin-Orbit Coupling in Enzymatic Reactions and the Roleof Spin in Biochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1557Boris F. Minaev, Hans Ågren, and V. O. Minaeva

36 Protein Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1589G. Náray-Szabó, A. Perczel, A. Láng, and D. K. Menyhárd

37 Applications of Computational Methods to Simulations ofProteins Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1627Wieslaw Nowak

38 Molecular Dynamics and Advanced Sampling Simulationsof Nucleic Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1671Jeremy Curuksu, Srinivasaraghavan Kannan, andMartin Zacharias

39 Model Systems for Dynamics of  -ConjugatedBiomolecules in Excited States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1697Mario Barbatti, Matthias Ruckenbauer, Jaroslaw J. Szymczak,Bernhard Sellner, Mario Vazdar, Ivana Antol, MirjanaEckert-Maksic, and Hans Lischka

40 Low-Energy Electron (LEE)-Induced DNA Damage:Theoretical Approaches to Modeling Experiment . . . . . . . . . . . . . . . 1741Anil Kumar and Michael D. Sevilla

41 Computational Modeling of DNA and RNA Fragments . . . . . . . . . . 1803Jirí Šponer, Manoj K. Shukla, Jing Wang, andJerzy Leszczynski

42 Metal Interactions with Nucleobases, Base Pairs, andOligomer Sequences; Computational Approach . . . . . . . . . . . . . . . . . 1827Jaroslav V. Burda, Jirí Šponer, and Filip Šebesta

43 Two Photon Absorption in Biological Molecules . . . . . . . . . . . . . . . . 1875M. Alaraby Salem, Melis Gedik, and Alex Brown

Contents xiii

44 Consequences of Electron Attachment to ModifiedNucleosides Incorporated into DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . 1895Lidia Chomicz-Manka, Paweł Wityk, Łukasz Golon,Magdalena Zdrowowicz, Justyna Wiczk, Kinga Westphal,Michał Zyndul, Samanta Makurat, and Janusz Rak

45 Molecular Dynamics Simulations of Large Systems inElectronic Excited States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1917Jakub Rydzewski and Wieslaw Nowak

46 Ab Initio Investigation of Photochemical ReactionMechanisms: From Isolated Molecules to ComplexEnvironments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1943Igor Schapiro, Patrick Zakhia El-Khoury, andMassimo Olivucci

Volume 3

Part V Chemoinformatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1995

Tomasz Puzyn

47 Computer Representation of Chemical Compounds . . . . . . . . . . . . . 1997Jaroslaw Polanski and Johann Gasteiger

48 Application of Quantum Mechanics and MolecularMechanics in Chemoinformatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2041Natalia Sizochenko, Devashis Majumdar, Szczepan Roszak,and Jerzy Leszczynski

49 Molecular Descriptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2065Andrea Mauri, Viviana Consonni, and Roberto Todeschini

50 Unsupervised Learning Methods and Similarity Analysisin Chemoinformatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2095Katarzyna Odziomek, Anna Rybinska, and Tomasz Puzyn

51 Recent Developments in 3D QSAR and MolecularDocking Studies of Organic and Nanostructures . . . . . . . . . . . . . . . . 2133Bakhtiyor Rasulev

52 Ontologies in Chemoinformatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2163Janna Hastings and Christoph Steinbeck

53 Chemoinformatics Methods for Studying Biomolecules . . . . . . . . . . 2183Adam Liwo, Cezary Czaplewski, Stanisław Ołdziej,Bartłomiej Zaborowski, Dawid Jagieła, and Jooyoung Lee

xiv Contents

54 Open Source Chemoinformatics Software includingKNIME Analytics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2201Georgios Leonis, Georgia Melagraki, and Antreas Afantitis

55 Prioritization of Chemicals Based on ChemoinformaticAnalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2231Paola Gramatica

56 Predicting ADME Properties of Chemicals . . . . . . . . . . . . . . . . . . . . . 2265Hyun Kil Shin, Young-Mook Kang, and Kyoung Tai No

57 Predictive QSAR Modeling: Methods and Applications inDrug Discovery and Chemical Risk Assessment . . . . . . . . . . . . . . . . . 2303Alexander Golbraikh, Xiang Simon Wang, Hao Zhu, andAlexander Tropsha

58 Quantitative Structure–Activity Relationships ofAntimicrobial Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2341F. P. Maguna, N. B. Okulik, and Eduardo A. Castro

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2359

Editorial Board

Theory and MethodologyAnna Kaczmarek-KedzieraHeribert Reis

Applications of Computational Methods to Model SystemsAnna Kaczmarek-KedzieraHeribert Reis

Solid States and NanomaterialsManthos G. PapadopoulosHeribert Reis

BiomoleculesManoj K. Shukla

ChemoinformaticsTomasz Puzyn

xv

Contributors

Antreas Afantitis InSilicoLab LP, Athens, Greece

Novamechanics Ltd, Nicosia, Cyprus

Hans Ågren Division of Theoretical Chemistry and Biology, School of Biotech-nology, Royal Institute of Technology, Stockholm, Sweden

Organic Chemistry, Bogdam Khmelnitskii National University, Cherkassy, Ukraine

Aurelio Alvarez-Ibarra Departamento de Química, CINVESTAV, Av. InstitutoPolitécnico Nacional, México, D.F., México

Antonis N. Andriotis Department of Physics and Astronomy and Center forComputational Sciences, University of Kentucky, Lexington, KY, USA

Institute of Electronic Structure and Laser, FORTH, Heraklio, Crete, Greece

Ivana Antol Laboratory for Physical–Organic Chemistry – Division of OrganicChemistry and Biochemistry, Rudjer Boškovic Institute, Zagreb, Croatia

Jon Baker Parallel Quantum Solutions, Fayetteville, AR, USA

Mario Barbatti Institute for Theoretical Chemistry, University of Vienna, Vienna,Austria

Veronica Barone Department of Physics, Central Michigan University, MountPleasant, MI, USA

Wojciech Bartkowiak Department of Physical and Quantum Chemistry, WrocławUniversity of Technology, Wroclaw, Poland

Katharina Boguslawski Institute of Physics, Faculty of Physics, Astronomy andInformatics, Nicolaus Copernicus University, Torun, Poland

Alex Brown Department of Chemistry, University of Alberta, Edmonton, AB,Canada

Šimon Budzák Department of Chemistry, Faculty of Natural Sciences, Matej BelUniversity, Banská Bystrica, Slovak Republic

xvii

xviii Contributors

Jaroslav V. Burda Faculty of Mathematics and Physics, Charles University inPrague, Prague 2, Czech Republic

Patrizia Calaminici Departamento de Química, CINVESTAV, Av. InstitutoPolitécnico Nacional, México, D.F., México

Roberto Cammi Dipartimento di Chimica, Università di Parma, Parma, Italy

Eduardo A. Castro INIFTA, Divisin Qumica Terica, Departamento de Química,Facultad de Ciencias Exactas, La Plata, Buenos Aires, Argentina

Luigi Cavallo Physical Sciences and Engineering Division, Kaust Catalysis Cen-ter, King Abdullah University of Science and Technology (Kaust), Thuwal, SaudiArabia

Lidia Chomicz-Manka Biological Sensitizers Laboratory, Faculty of Chemistry,University of Gdansk, Gdansk, Poland

Viviana Consonni Department of Earth and Environmental Sciences, Universityof Milano-Bicocca, Milan, Italy

Domingo Cruz-Olvera Departamento de Química, CINVESTAV, Av. InstitutoPolitécnico Nacional, México, D.F., México

Jeremy Curuksu Mathematics Department, Swiss Federal Institute of Technol-ogy, Lausanne (EPFL), Switzerland

Cezary Czaplewski Faculty of Chemistry, University of Gdansk, Gdansk, Poland

Tandabany C. Dinadayalane Department of Chemistry, Clark Atlanta University,Atlanta, GA, USA

Nikos L. Doltsinis Institute for Solid State Theory and Center for MultiscaleTheory and Computation, University of Münster, Münster, Germany

Victor-Daniel Domínguez-Soria Departamento de Ciencias Básicas, UAM-A,Avenida San Pablo, México, D.F., México

Mirjana Eckert-Maksic Laboratory for Physical-Organic Chemistry – Divisionof Organic Chemistry and Biochemistry, Rudjer Boškovic Institute, Zagreb, Croatia

Patrick Zakhia El-Khoury Chemistry Department, Bowling Green State Univer-sity, Bowling Green, OH, USA

Sakir Erkoç Department of Physics, Middle East Technical University, Ankara,Turkey

Daniel Escudero CEISAM, UMR CNRS 6230, Université de Nantes, Nantes,France

Roberto Flores-Moreno Departamento de Química, CUCEI, Universidad deGuadalajara, Guadalajara Jalisco, México

Contributors xix

Zacharias G. Fthenakis Department of Physics and Astronomy and Center forComputational Sciences, University of Kentucky, Lexington, KY, USA

Institute of Electronic Structure and Laser, FORTH, Heraklio, Crete, Greece

Ying Fu Division of Theoretical Chemistry and Biology, School of Biotechnology,Royal Institute of Technology, Stockholm, Sweden

Gabriel U. Gamboa Departamento de Química, CINVESTAV, Av. InstitutoPolitécnico Nacional, México, D.F., México

Johann Gasteiger Computer-Chemie-Centrum, Universität Erlangen-Nürnberg,Erlangen, Germany

Melis Gedik Department of Chemistry, University of Alberta, Edmonton, AB,Canada

Gerald Geudtner Departamento de Química, CINVESTAV, Av. Instituto Politéc-nico Nacional, México, D.F., México

Alexander Golbraikh Laboratory for Molecular Modeling and Carolina Centerfor Exploratory Cheminformatics Research, Division of Medicinal Chemistry andNatural Products, UNC Eshelman School of Pharmacy, University of North Car-olina, Chapel Hill, NC, USA

łukasz Golon Biological Sensitizers Laboratory, Faculty of Chemistry, Universityof Gdansk, Gdansk, Poland

Annick Goursot Institut Charles Gerhardt, UMR 5253 CNRS, Ecole de Chimie deMontpellier, Montpellier, Cédex 5, France

Paola Gramatica QSAR Research Unit in Environmental Chemistry and Ecotox-icology, Department of Theoretical and Applied Sciences, University of Insubria,Varese, Italy

Stefan Grimme Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany

Janna Hastings European Bioinformatics Institute, Hinxton, UK

Oded Hod Department of Chemical Physics, School of Chemistry, The SacklerFaculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel

Heiko Jacobsen KemKom, New Orleans, LA, USA

Denis Jacquemin CEISAM, UMR CNRS 6230, Université de Nantes, Nantes,France

Institut universitaire de France, Paris, France

Dawid Jagieła Faculty of Chemistry, University of Gdansk, Gdansk, Poland

Michał Jaszunski Institute of Organic Chemistry, Polish Academy of Sciences,Warszawa, Poland

xx Contributors

Anna Kaczmarek-Kedziera Faculty of Chemistry, Nicolaus Copernicus Univer-sity, Torun, Poland

Young-Mook Kang Bioinformatics and Molecular Design Research Center, Seoul,Republic of Korea

Srinivasaraghavan Kannan Bioinformatics Institute (A*STAR), Singapore, Sin-gapore

Panaghiotis Karamanis Groupe de Chimie Théorique et Réactivité, ECP, IPREMUMR 5254, Université de Pau et de Pays de l’ Adour, PAU Cedex, France

Abdel-Hadi Kassiba Institute of Molecules and Materials of Le Mans – UMR-CNRS 6283, Université du Maine, Le Mans, France

Dariusz Kedziera Department of Chemistry and Photochemistry of Polymers,Faculty of Chemistry, Nicolaus Copernicus University, Torun, Poland

Bernard Kirtman Department of Chemistry and Biochemistry, University ofCalifornia, Santa Barbara, CA, USA

Mariusz Klobukowski Department of Chemistry, University of Alberta, Edmon-ton, AB, Canada

Andreas M. Köster Departamento de Química, CINVESTAV, Av. InstitutoPolitécnico Nacional, México, D.F., México

Anil Kumar Department of Chemistry, Oakland University, Rochester, MI, USA

Sanjay Kumar Department of Physics, Banaras Hindu University, Varanasi, India

A. Láng Laboratory of Structural Chemistry and Biology, Institute of Chemistry,Eötvös Loránd University and MTA-ELTE Protein Modelling Research Group,Budapest, Hungary

Adèle D. Laurent CEISAM, UMR CNRS 6230, Université de Nantes, Nantes,France

Jooyoung Lee Center for In Silico Protein Structure and School of ComputationalSciences, Korea Institute for Advanced Study, Seoul, Republic of Korea

Georgios Leonis Novamechanics Ltd, Nicosia, Cyprus

Jerzy Leszczynski Department of Chemistry and Biochemistry, InterdisciplinaryCenter for Nanotoxicity, Jackson State University, Jackson, MS, USA

Hans Lischka Department of Chemistry and Biochemistry, Texas Tech University,Lubbock, TX, USA

Adam Liwo Faculty of Chemistry, University of Gdansk, Gdansk, Poland

Center for In Silico Protein Structure and School of Computational Sciences, KoreaInstitute for Advanced Study, Seoul, Republic of Korea

Contributors xxi

Chris Lorenz Department of Physics, King’s College London, Strand, London,UK

F. P. Maguna Facultad de Agroindustrias, Universidad Nacional del Nordeste,Chaco, Argentina

Devashis Majumdar Department of Chemistry, Jackson State University, Jackson,MS, USA

Malgorzata Makowska-Janusik Institute of Physics, Faculty of Mathematics andNatural Science, Jan Dlugosz University in Czestochowa, Czestochowa, Poland

Samanta Makurat Biological Sensitizers Laboratory, Faculty of Chemistry, Uni-versity of Gdansk, Gdansk, Poland

Andrea Mauri Department of Earth and Environmental Sciences, University ofMilano-Bicocca, Milan, Italy

Miroslav Medved’ Department of Chemistry, Faculty of Natural Sciences, MatejBel University, Banská Bystrica, Slovak Republic

Daniel Mejía-Rodríguez Departamento de Química, CINVESTAV, Av. InstitutoPolitécnico Nacional, México, D.F., México

Georgia Melagraki InSilicoLab LP, Athens, Greece

Novamechanics Ltd, Nicosia, Cyprus

Madhu Menon Department of Physics and Astronomy and Center for Computa-tional Sciences, University of Kentucky, Lexington, KY, USA

Institute of Electronic Structure and Laser, FORTH, Heraklio, Crete, Greece

D. K. Menyhárd Laboratory of Structural Chemistry and Biology, Institute ofChemistry, Eötvös Loránd University and MTA-ELTE Protein Modelling ResearchGroup, Budapest, Hungary

Boris F. Minaev Organic Chemistry, Bogdam Khmelnitskii National University,Cherkassy, Ukraine

Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology,Stockholm, Sweden

V. O. Minaeva Organic Chemistry, Bogdam Khmelnitskii National University,Cherkassy, Ukraine

Alston J. Misquitta School of Physics, Queen Mary, University of London,London, UK

TCM Group, Cambridge, UK

Mohammad Molayem Physical and Theoretical Chemistry, University of Saar-land, Saarbrücken, Germany

xxii Contributors

Gerald Monard Theoretical Chemistry and Biochemistry Group SRSMC, Nancy-University CNRS Boulevard des Aiguillettes, Vandoeuvre-les-Nancy, France

G. Náray-Szabó Laboratory of Structural Chemistry and Biology, Institute ofChemistry, Eötvös Loránd University and MTA-ELTE Protein Modelling ResearchGroup, Budapest, Hungary

Katsura Nishiyama Faculty of Education, Shimane University, Matsue, Japan

Kyoung Tai No Bioinformatics and Molecular Design Research Center, Seoul,Republic of Korea

Department of Biotechnology, Yonsei University, Seoul, Republic of Korea

Wieslaw Nowak Institute of Physics, Faculty of Physics, Astronomy and Infor-matics, Nicolaus Copernicus University, Torun, Poland

Katarzyna Odziomek Laboratory of Environmental Chemometrics, Faculty ofChemistry, University of Gdansk, Gdansk, Poland

N. B. Okulik Facultad de Agroindustrias, Universidad Nacional del Nordeste,Chaco, Argentina

Stanisław Ołdziej Laboratory of Biopolymer Structure, Intercollegiate Faculty ofBiotechnology, University of Gdansk and Medical University of Gdansk, Gdansk,Poland

Massimo Olivucci Dipartimento di Chimica, Università di Siena, Siena, Italy

Thomas Bondo Pedersen Department of Chemistry, Centre for Theoretical andComputational Chemistry, University of Oslo, Oslo, Norway

Juan E. Peralta Department of Physics, Central Michigan University, MountPleasant, MI, USA

A. Perczel Laboratory of Structural Chemistry and Biology, Institute of Chemistry,Eötvös Loránd University and MTA-ELTE Protein Modelling Research Group,Budapest, Hungary

Lucjan Piela Department of Chemistry, University of Warsaw, Warsaw, Poland

Jaroslaw Polanski Organic Chemistry and Chemoinformatics, University of Sile-sia Institute of Chemistry, Katowice, Poland

Valeri Poltev Autonomous University of Puebla, Puebla, Mexico

Alexey A. Popov Leibniz-Institute for Solid State and Materials Research (IFWDresden), Dresden, Germany

Tomasz Puzyn Laboratory of Environmental Chemometrics, Faculty of Chemistry,University of Gdansk, Gdansk, Poland

Janusz Rak Biological Sensitizers Laboratory, Faculty of Chemistry, University ofGdansk, Gdansk, Poland

Contributors xxiii

Bakhtiyor Rasulev Center for Computationally Assisted Science and Technology,North Dakota State University, Fargo, ND, USA

Heribert Reis Institute of Biology, Medicinal Chemistry and Biotechnology,National Hellenic Research Foundation, Athens, Greece

Jean-Louis Rivail Theoretical Chemistry and Biochemistry Group SRSMC,Nancy-University CNRS Boulevard des Aiguillettes, Vandoeuvre-les-Nancy, France

Antonio Rizzo Istituto per i Processi Chimico Fisici del Consiglio Nazionale delleRicerche, Area della Ricerca di Pisa, Pisa, Italy

Szczepan Roszak Advanced Materials Engineering and Modelling Group, Facultyof Chemistry, Wroclaw University of Technology, Wroclaw, Poland

Matthias Ruckenbauer Max-Planck-Institut für Kohlenforschung, Mülheim ander Ruhr, Germany

Kenneth Ruud Centre for Theoretical and Computational Chemistry, Departmentof Chemistry, University of Tromsø, Tromsø, Norway

Anna Rybinska Laboratory of Environmental Chemometrics, Faculty of Chem-istry, University of Gdansk, Gdansk, Poland

Jakub Rydzewski Institute of Physics, Faculty of Physics, Astronomy and Infor-matics, Nicolaus Copernicus University, Torun, Poland

Dennis R. Salahub Department of Chemistry, CMS Centre for Molecular Simu-lation, IQST Institute for Quantum Science and Technology, University of Calgary,Calgary, AB, Canada

M. Alaraby Salem Department of Chemistry, University of Alberta, Edmonton,AB, Canada

Igor Schapiro Chemistry Department, Bowling Green State University, BowlingGreen, OH, USA

Filip Šebesta Faculty of Mathematics and Physics, Charles University in Prague,Prague 2, Czech Republic

Bernhard Sellner Laboratory for Physical–Organic Chemistry – Division ofOrganic Chemistry and Biochemistry, Rudjer Boškovic Institute, Zagreb, Croatia

Luis Serrano-Andrés Instituto de Ciencia Molecular, Universitat de Valéncia,Valencia, Spain

Juan José Serrano-Pérez Department of Chemistry, Imperial College LondonComputational and Structural Research Group, London, UK

Michael D. Sevilla Department of Chemistry, Oakland University, Rochester, MI,USA

xxiv Contributors

Hyun Kil Shin Department of Biotechnology, Yonsei University, Seoul, Republicof Korea

Manoj K. Shukla US Army Engineer Research and Development Center, Vicks-burg, MS, USA

Natalia Sizochenko Department of Chemistry, Jackson State University, Jackson,MS, USA

Jirí Šponer Institute of Biophysics, Academy of Sciences of the Czech Republic,Brno, Czech Republic

Michael Springborg Physical and Theoretical Chemistry, University of Saarland,Saarbrücken, Germany

School of Materials Science and Engineering, Tianjin University, Tianjin, China

Monika Stanke Institute of Physics, Faculty of Physics, Astronomy and Informat-ics, Nicholas Copernicus University, Torun, Poland

Christoph Steinbeck European Bioinformatics Institute, Hinxton, UK

Brian Sutcliffe School of Science and Technology, Nottingham Trent University,Nottingham, UK

Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles,Bruxelles, Belgium

Jaroslaw J. Szymczak Research Lab Computational Technologies and Applica-tions, University of Vienna, Vienna, Austria

Paweł Tecmer Institute of Physics, Faculty of Physics, Astronomy and Informat-ics, Nicolaus Copernicus University, Torun, Poland

Roberto Todeschini Department of Earth and Environmental Sciences, Universityof Milano-Bicocca, Milan, Italy

Daniele Toffoli Department of Chemistry, Middle East Technical University,Ankara, Turkey

Hande Toffoli Department of Physics, Middle East Technical University, Ankara,Turkey

Jacopo Tomasi Dipartimento di Chimica e Chimica Industriale, Università di Pisa,Pisa, Italy

Alexander Tropsha Division of Medicinal Chemistry and Natural Products, UNCEshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA

Mario Vazdar Department of Chemistry and Biochemistry, Texas Tech University,Lubbock, TX, USA

Contributors xxv

Mark Waller Organisch-Chemisches Institut, Westfälische Wilhelms-UniversitätMünster, Münster, Germany

Jing Wang Department of Chemistry and Biochemistry, Interdisciplinary Centerfor Nanotoxicity, Jackson State University, Jackson, MS, USA

Xiang Simon Wang Laboratory for Molecular Modeling and Carolina Center forExploratory Cheminformatics Research, Division of Medicinal Chemistry and Nat-ural Products, UNC Eshelman School of Pharmacy, University of North Carolina,Chapel Hill, NC, USA

John D. Watts Department of Chemistry and Biochemistry, Jackson State Univer-sity, Jackson, MS, USA

Kinga Westphal Biological Sensitizers Laboratory, Faculty of Chemistry, Univer-sity of Gdansk, Gdansk, Poland

Justyna Wiczk Biological Sensitizers Laboratory, Faculty of Chemistry, Univer-sity of Gdansk, Gdansk, Poland

Paweł Wityk Biological Sensitizers Laboratory, Faculty of Chemistry, Universityof Gdansk, Gdansk, Poland

R. Guy Woolley School of Science and Technology, Nottingham Trent University,Nottingham, UK

Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles,Bruxelles, Belgium

Sotiris S. Xantheas Chemical and Material Sciences Division, Pacific NorthwestNational Laboratory, Richland, WA, USA

Soohaeng Yoo Chemical and Material Sciences Division, Pacific NorthwestNational Laboratory, Richland, WA, USA

Norio Yoshida Department of Chemistry, Graduate School of Science, KyushuUniversity, Fukuoka, Japan

Bartłomiej Zaborowski Faculty of Chemistry, University of Gdansk, Gdansk,Poland

Martin Zacharias Physik-Department T38, Technische Universität München,Garching, Germany

Magdalena Zdrowowicz Biological Sensitizers Laboratory, Faculty of Chemistry,University of Gdansk, Gdansk, Poland

Tao Zeng Department of Chemistry, Carleton University, Ottawa, ON, Canada

Hao Zhu Laboratory for Molecular Modeling and Carolina Center for ExploratoryCheminformatics Research, Division of Medicinal Chemistry and Natural Products,UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill,NC, USA

xxvi Contributors

Bernardo Zuniga-Gutierrez Departamento de Ciencias Computacionales, Uni-versidad de Guadalajara, Guadalajara Jalisco, México

Michał Zyndul Biological Sensitizers Laboratory, Faculty of Chemistry, Univer-sity of Gdansk, Gdansk, Poland