Computational Chemistry: Reviews of Current Trends (Computational Chemistry: Reviews of Current Trends, 8) PDF
Preview Computational Chemistry: Reviews of Current Trends (Computational Chemistry: Reviews of Current Trends, 8)
Computational Chemistry Reviews of Current Trends Volume 8 Computational Chemistry: Reviews of Current Trends Editor-in-Charge: Jerzy Leszczynski, Dept. of Chemistry, Jackson State University, USA Published Vol. 1: Computational Chemistry: Reviews of Current Trends Edited by Jerzy Leszczynski Vol. 2: Computational Chemistry: Reviews of Current Trends Edited by Jerzy Leszczynski Vol. 3: Computational Chemistry: Reviews of Current Trends Edited by Jerzy Leszczynski Vol. 4: Computational Chemistry: Reviews of Current Trends Edited by Jerzy Leszczynski Vol. 5: Computational Chemistry: Reviews of Current Trends Edited by Jerzy Leszczynski Vol. 6: Computational Chemistry: Reviews of Current Trends Edited by Jerzy Leszczynski Vol. 7: Computational Chemistry: Reviews of Current Trends Edited by Jerzy Leszczynski Computational Chemistry Reviews of Current Trends Volume 8 editor Jerzy Leszczynski Department of Chemistry Jackson State University USA World Scientific NEW JERSEY • LONDON • SINGAPORE • SHANGHAI • HONGKONG • TAIPEI • BANGALORE Published by World Scientific Publishing Co. Pte. Ltd. 5 Toh Tuck Link, Singapore 596224 USA office: Suite 202,1060 Main Street, River Edge, NJ 07661 UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. COMPUTATIONAL CHEMISTRY: REVIEWS OF CURRENT TRENDS Volume 8 Copyright © 2003 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or mechanical, including photocopying, recording or any information storage and retrieval system now known or to be invented, without written permission from the Publisher. For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not required from the publisher. ISBN 981-238-702-1 Printed in Singapore by World Scientific Printers (S) Pte Ltd PREFACE For many years I had not doubted the most popular theory in astrophysics that our Universe is in an expanding phase. However, I have also learned how important relativity is. I have sensed mat over the years my World has been shrinking. Not only am I able to move much faster from one location to another and visit many exotic places, but also telephone lines and the Internet have tightly linked many places on the Earth. This allows me to communicate quickly with colleagues in Europe, China, or Africa and to effectively collaborate with them on joint projects. This size reduction is analogous to a continuous decrease in the dimensions of species accessible for studies and applications. Not only that "small is beautiful," but also it enforces progress and provides a new dimension to science and technology. Chemists are finally able to work with single molecules and atoms, yet not billions of them at a time. "Nano" has become a buzzword of the new century. New "nano" journals and "nano" letters and "nano" webpages have been emerging. We are constantly reading about nano wires, sensors, transistors, and nanocomputers. It seems that a gap between experimental objects and models for calculations in chemistry is being bridged. The size of experimental nanoobjects is decreasing, while reliable calculations are feasible for larger and larger moleculer systems. The results of these calculations for isolated molecules are becoming more relevant for experiments. However, there are still significant challenges for computational methods. They include the modelling of the solid state and of solvents. Many theoretical groups are involved in the development of efficient approaches to solids and solvent effects. This series presents reviews of current advances in computational methodologies and applications. The first chapter written by R. Cammi, B. Mennucci, and J. Tomasi provides an overview of their developments of the Polarizable Continuum Model (PCM). This approach has been particularly popularized after its implementation into the GAUSSIAN suite of programs. The authors reveal both the theoretical and numerical aspects of the PCM model. Also, promising extensions of the theory are discussed. Among the possible applications, examples concerning the evaluation of molecular- response properties and spectroscopic quantities are provided. Significant simplifications are necessary in order to construct a solid state model. This could be achieved using the supermolecular approach. M. Guillaume, B. Champagne, F. Castet, and L. Ducasse demonstrate a multiplicative scheme that is often used for estimations of the properties of two- and three-dimensional clusters from the properties of their one-dimensional components. They apply semiempirical methods to simulate absorption spectra V vi Preface and to evaluate linear and nonlinear responses. The chapter concludes with a comparision of theoretical predictions with experimental results and with a discussion of the reliability of the global approach. Recently significant progress has been achieved in the theoretical prediction of NMR parameters. The application of ab initio methods allows for a reliable evaluation of the characteristics of hydrogen-bonded and van der Waals complexes. The theory and methods applied to calculations of spin-spin coupling constants are discussed by M. Pecul and J. Sadlej. The authors provide a number of applications including simple complexes, model systems for nucleic acids and proteins, and weak van der Waals systems. Ab initio quantum chemical methods are quickly gaining popularity among researchers investigating various aspects of DNA. Reliable quantum mechanical techniques do not require empirical parameters; they yield results of experimental accuracy and allow for the simultaneous study of molecular structures. The size of DNA fragments feasible for such calculations is constantly increasing. DNA base polyads are among recently studied species. The chapter by M. Meyer and J. Suhnel reviews the properties of these complexes linked by base-base hydrogen bonds. Examples include many species of biological importance. Among them are telomeres, structures formed from triplet disease sequences, and tertiary interactions in RNA. Their occurrence in nucleic acid structures is discussed. Numerous results of computational studies are provided and used to establish a link between structural biology and computational chemistry. DNA can be affected by chemical and environmental effects. D. M. Close presents a review of primary radiation-induced defects in nucleic acid building blocks. The discussion includes both EPR/ENDOR experiments and the application of quantum chemical calculations of spin densities and isotropic and anisotropic hyperfine couplings that could be used to assist in making free radical assignments. DFT theory has been selected for theoretical predictions. The chapter presents examples of successes and failures of the DFT calculations in the prediction of spin densities and hyperfine couplings for radiation-induced radicals observed in nucleobases. hi addition, a discussion of unsolved problems and suggestions for future directions is also given. Experimental studies of ground state properties of DNA bases have been carried out for many years. This includes studies of their molecular structures. Although one can conclude that the ground state of these important DNA constituents is well characterized, data concerning their excited state properties is scarce. The molecular geometry of such complex systems like DNA bases cannot be determined by experimental methods. It creates a need for theoretical studies that could shed light on the properties of DNA bases in the excited state, hi the last chapter of this volume, M.K. Shukla and J. Leszczynski discuss available experimental data of DNA bases, base pairs, and their complexes with water. The discussion is enhanced by an overview of the results of recent Preface vii theoretical studies for these species. The main emphasis is on the electronic singlet excited state properties, phototautomerism of bases and base pairs, and their interaction with water molecules. I would like to thank all authors for the excellent contributions and fine collaborations. The very efficient technical assistance of Dr. Manoj K. Shukla in putting together this volume is greatly appreciated. As always, your feedback is very important to me, please feel free to e-mail your suggestions to [email protected]. Jerzy Leszczynski Jackson, MS December 2002 CONTENTS Preface v 1. Computational Modelling of the Solvent Effects on Molecular Properties: An Overview of the Polarizable Continuum Model (PCM) Approach 1 R. Cammi, B. Mennucci and J. Tomasi 2. Electronic and Nonlinear Optical Properties of 2-Methyl-4-Nitroaniline Clusters 81 M. Guillaume, B. Champagne, F. Castet and L. Ducasse 3. Ab Initio Calculations of the Intermolecular Nuclear Spin-Spin Coupling Constants 131 M. Pecul and J. Sadlej 4. Base Polyad Motifs in Nucleic Acids — Biological Significance, Occurrence in Three-Dimensional Experimental Structures and Computational Studies 161 M. Meyer and J. Siihnel 5. Model Calculations of Radiation Induced Damage in DNA Constituents Using Density Functional Theory 209 D. M. Close 6. Excited States of Nucleic Acid Bases 249 M. K. Shukla and J. Leszczynski Index 345 ix
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