Fragment Molecular Orbital Method
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Fragmentation Toward Accurate Calculations On Complex Molecular Systems
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Author : Mark S. Gordon
language : en
Publisher: John Wiley & Sons
Release Date : 2017-10-23
Fragmentation Toward Accurate Calculations On Complex Molecular Systems written by Mark S. Gordon and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-23 with Science categories.
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.
The Fragment Molecular Orbital Method
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Author : Dmitri Fedorov
language : en
Publisher: CRC Press
Release Date : 2009-05-14
The Fragment Molecular Orbital Method written by Dmitri Fedorov and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-05-14 with Science categories.
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
Recent Advances Of The Fragment Molecular Orbital Method
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Author : Yuji Mochizuki
language : en
Publisher: Springer Nature
Release Date : 2021-01-04
Recent Advances Of The Fragment Molecular Orbital Method written by Yuji Mochizuki and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-01-04 with Science categories.
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.
Fragment Molecular Orbital Method
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Author :
language : en
Publisher:
Release Date : 2020
Fragment Molecular Orbital Method written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with categories.
Complete Guide To The Fragment Molecular Orbital Method In Gamess From One Atom To A Million At Your Service
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Author : Dmitri G Fedorov
language : en
Publisher: World Scientific
Release Date : 2023-02-17
Complete Guide To The Fragment Molecular Orbital Method In Gamess From One Atom To A Million At Your Service written by Dmitri G Fedorov and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-02-17 with Science categories.
The fragment molecular orbital (FMO) method is a fast linear-scaling quantum-mechanical method employed by chemists and physicists all over the world. It provides a wealth of properties of fragments from quantum-chemical calculations, a bottomless treasure pit for data mining and machine learning. However, there is no user-friendly description of its usage in the widely employed quantum-chemical open-source software GAMESS, nor is there any book covering the usage of GAMESS in general. This leaves very many interested users to their own devices to get through a variety of problems with very cryptic descriptions of keywords in the program manual and no guide whatsoever as to what options should be set for particular scientific tasks. This book is the panacea to many frustrations.The main focus of the book is to build a solid bridge connecting FMO users to GAMESS, by giving a helpful introduction of various FMO methods as needed for particular problems found in computational chemistry, and describing in detail how to do these simulations and understand the results from the output of the program. The book also covers parallelization strategies for attaining high parallel efficiency in massively parallel computations, and provides means to analyze performance and design a solution for overcoming performance bottlenecks. A special section is devoted to dealing with problems in executing GAMESS, arising from computational environment and user errors. Finally, 14 carefully selected types of applications are discussed in detail, describing the input keywords and explaining where to find the main results in the text-based output.
Computer Simulation Of Biomolecular Systems
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Author : W.F. van Gunsteren
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-11-27
Computer Simulation Of Biomolecular Systems written by W.F. van Gunsteren and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-27 with Technology & Engineering categories.
The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...
Frontier Orbitals And Reaction Paths
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Author : Kenichi Fukui
language : en
Publisher: World Scientific
Release Date : 1997
Frontier Orbitals And Reaction Paths written by Kenichi Fukui and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 1997 with Science categories.
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.
An Introduction To Molecular Orbitals
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Author : Yves Jean
language : en
Publisher: Oxford University Press on Demand
Release Date : 1993
An Introduction To Molecular Orbitals written by Yves Jean and has been published by Oxford University Press on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 1993 with Science categories.
This text for advanced undergraduate and graduate students guides the reader through a smooth progression from the most elementary ideas of molecular orbital theory to an understanding of the electronic structure, geometry, and reactivity of large molecules. It starts with simple molecules and proceeds to relatively large organometallic complexes. The slant is theoretical, but in the last chapter the authors strengthen the link between theory and experiment. Focusing on basic concepts, the authors take a qualitative approach, which enables this text to fill a void in the undergraduate curriculum. The book is intended as a core or supplementary text in an advanced chemistry course.
Linear Scaling Techniques In Computational Chemistry And Physics
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Author : Robert Zaleśny
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-03-21
Linear Scaling Techniques In Computational Chemistry And Physics written by Robert Zaleśny and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-03-21 with Science categories.
"Linear-Scaling Techniques in Computational Chemistry and Physics" summarizes recent progresses in linear-scaling techniques and their applications in chemistry and physics. In order to meet the needs of a broad community of chemists and physicists, the book focuses on recent advances that extended the scope of possible exploitations of the theory. The first chapter provides an overview of the present state of the linear-scaling methodologies and their applications, outlining hot topics in this field, and pointing to expected developments in the near future. This general introduction is then followed by several review chapters written by experts who substantially contributed to recent developments in this field. The purpose of this book is to review, in a systematic manner, recent developments in linear-scaling methods and their applications in computational chemistry and physics. Great emphasis is put on the theoretical aspects of linear-scaling methods. This book serves as a handbook for theoreticians, who are involved in the development of new efficient computational methods as well as for scientists, who are using the tools of computational chemistry and physics in their research.
Orbital Interaction Theory Of Organic Chemistry
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Author : Arvi Rauk
language : en
Publisher: John Wiley & Sons
Release Date : 2004-04-07
Orbital Interaction Theory Of Organic Chemistry written by Arvi Rauk and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004-04-07 with Science categories.
A practical introduction to orbital interaction theory and its applications in modern organic chemistry Orbital interaction theory is a conceptual construct that lies at the very heart of modern organic chemistry. Comprising a comprehensive set of principles for explaining chemical reactivity, orbital interaction theory originates in a rigorous theory of electronic structure that also provides the basis for the powerful computational models and techniques with which chemists seek to describe and exploit the structures and thermodynamic and kinetic stabilities of molecules. Orbital Interaction Theory of Organic Chemistry, Second Edition introduces students to the fascinating world of organic chemistry at the mechanistic level with a thoroughly self-contained, well-integrated exposition of orbital interaction theory and its applications in modern organic chemistry. Professor Rauk reviews the concepts of symmetry and orbital theory, and explains reactivity in common functional groups and reactive intermediates in terms of orbital interaction theory. Aided by numerous examples and worked problems, he guides readers through basic chemistry concepts, such as acid and base strength, nucleophilicity, electrophilicity, and thermal stability (in terms of orbital interactions), and describes various computational models for describing those interactions. Updated and expanded, this latest edition of Orbital Interaction Theory of Organic Chemistry includes a completely new chapter on organometallics, increased coverage of density functional theory, many new application examples, and worked problems. The text is complemented by an interactive computer program that displays orbitals graphically and is available through a link to a Web site. Orbital Interaction Theory of Organic Chemistry, Second Edition is an excellent text for advanced-level undergraduate and graduate students in organic chemistry. It is also a valuable working resource for professional chemists seeking guidance on interpreting the quantitative data produced by modern computational chemists.