Fragmentation Toward Accurate Calculations On Complex Molecular Systems

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Answering the need to facilitate quantum-chemical calculations of systems with thousands of atoms, Kazuo Kitaura and his coworkers developed the Fragment Molecular Orbital (FMO) method in 1999. Today, the FMO method can be applied to the study of whole proteins and protein-ligand interactions, and is extremely effective in calculating the propertie

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.

London dispersion interactions are responsible for numerous phenomena in physics, chemistry and biology. Recent years have seen the development of new, physically well-founded models, and dispersion-corrected density functional theory (DFT) is now a hot topic of research. This book is an overview of current understanding of the physical origin and modelling of London dispersion forces manifested at an atomic level. It covers a wide range of system, from small intermolecular complexes, to organic molecules and crystalline solids, through to biological macromolecules and nanostructures. In presenting a broad overview of the of the physical foundations of dispersion forces, the book provides theoretical, physical and synthetic chemists, as well as solid-state physicists, with a systematic understanding of the origins and consequences of these ubiquitous interactions. The presentation is designed to be accessible to anyone with intermediate undergraduate mathematics, physics and chemistry.

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.

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.