Molecular Orbital Calculations for Biological Systems is a hands-on guide to computational quantum chemistry and its applications in organic chemistry, biochemistry, and molecular biology. With improvements in software, molecular modeling techniques are now becoming widely available; they are increasingly used to complement experimental results, saving significant amounts of lab time. Common applications include pharmaceutical research and development; for example, ab initio and semi-empirical methods are playing important roles in peptide investigations and in drug design. The opening chapters provide an introduction for the non-quantum chemist to the basic quantum chemistry methods, ab initio, semi-empirical, and density functionals, as well as to one of the main families of computer programs, the Gaussian series. The second part then describes current research which applies quantum chemistry methods to such biological systems as amino acids, peptides, and anti-cancer drugs. Throughout the authors seek to encourage biochemists to discover aspects of their own research which might benefit from computational work. They also show that the methods are accessible to researchers from a wide range of mathematical backgrounds. Combining concise introductions with practical advice, this volume will be an invaluable tool for research on biological systems.

A collection of selected papers on the Frontier Orbital Theory, with introductory notes. It provides the basic concept and formulation of the theory, and the physical and chemical significance of the frontier orbital interactions in chemistry, together with many practical applications. The formulation of the Intrinsic Reaction Coordinate and applications to some simple systems are also presented. The aim of this volume is to show by what forces chemical reactions are driven and to demonstrate how the regio- and stereo-selectivities are determined in chemical reactions. Students and senior investigators will gain insight into the nature of chemical reactions and find out how quantum chemical calculations are connected with chemical intuition.

This is a hands-on guide for the growing number of researchers in organic chemistry, biochemistry and molecular biology who would like to augment their experiments with theoretical calculations. Given the current availability of sophisticated software, non-quantum chemistry practitioners can obtain accurate computational results and save significant amounts of laboratory time. This book teaches the use of quantum chemical computer programs while side-stepping the complex mathematical details.

This volume describes in detail the technique of molecular orbital calculations for biochemistry. The level of presentation will be accessible to biochemists, and biophysicists.

This book covers recent advances of the fragment molecular orbital (FMO) method, consisting of 5 parts and a total of 30 chapters written by FMO experts. The FMO method is a promising way to calculate large-scale molecular systems such as proteins in a quantum mechanical framework. The highly efficient parallelism deserves being considered the principal advantage of FMO calculations. Additionally, the FMO method can be employed as an analysis tool by using the inter-fragment (pairwise) interaction energies, among others, and this feature has been utilized well in biophysical and pharmaceutical chemistry. In recent years, the methodological developments of FMO have been remarkable, and both reliability and applicability have been enhanced, in particular, for non-bio problems. The current trend of the parallel computing facility is of the many-core type, and adaptation to modern computer environments has been explored as well. In this book, a historical review of FMO and comparison to other methods are provided in Part I (two chapters) and major FMO programs (GAMESS-US, ABINIT-MP, PAICS and OpenFMO) are described in Part II (four chapters). dedicated to pharmaceutical activities (twelve chapters). A variety of new applications with methodological breakthroughs are introduced in Part IV (six chapters). Finally, computer and information science-oriented topics including massively parallel computation and machine learning are addressed in Part V (six chapters). Many color figures and illustrations are included. Readers can refer to this book in its entirety as a practical textbook of the FMO method or read only the chapters of greatest interest to them.