Fragmentation Toward Accurate Calculations On Complex Molecular Systems
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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 : 2017-08-04
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 2017-08-04 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.
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.
London Dispersion Forces In Molecules Solids And Nano Structures
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Author : János Ángyán
language : en
Publisher: Royal Society of Chemistry
Release Date : 2020-04-03
London Dispersion Forces In Molecules Solids And Nano Structures written by János Ángyán and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-04-03 with Science categories.
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.
Recent Advances Of The Fragment Molecular Orbital Method
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Author : Yuji Mochizuki
language : en
Publisher:
Release Date : 2021
Recent Advances Of The Fragment Molecular Orbital Method written by Yuji Mochizuki and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with 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.
Density Functional Theory
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Author : David S. Sholl
language : en
Publisher: John Wiley & Sons
Release Date : 2011-09-20
Density Functional Theory written by David S. Sholl 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 2011-09-20 with Science categories.
Demonstrates how anyone in math, science, and engineering can master DFT calculations Density functional theory (DFT) is one of the most frequently used computational tools for studying and predicting the properties of isolated molecules, bulk solids, and material interfaces, including surfaces. Although the theoretical underpinnings of DFT are quite complicated, this book demonstrates that the basic concepts underlying the calculations are simple enough to be understood by anyone with a background in chemistry, physics, engineering, or mathematics. The authors show how the widespread availability of powerful DFT codes makes it possible for students and researchers to apply this important computational technique to a broad range of fundamental and applied problems. Density Functional Theory: A Practical Introduction offers a concise, easy-to-follow introduction to the key concepts and practical applications of DFT, focusing on plane-wave DFT. The authors have many years of experience introducing DFT to students from a variety of backgrounds. The book therefore offers several features that have proven to be helpful in enabling students to master the subject, including: Problem sets in each chapter that give readers the opportunity to test their knowledge by performing their own calculations Worked examples that demonstrate how DFT calculations are used to solve real-world problems Further readings listed in each chapter enabling readers to investigate specific topics in greater depth This text is written at a level suitable for individuals from a variety of scientific, mathematical, and engineering backgrounds. No previous experience working with DFT calculations is needed.
Mass Spectrometry By The Numbers
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Author : Daniel Leo Sweeney Ph D
language : en
Publisher: Createspace Independent Publishing Platform
Release Date : 2018-11-13
Mass Spectrometry By The Numbers written by Daniel Leo Sweeney Ph D and has been published by Createspace Independent Publishing Platform this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-13 with categories.
Using the new Rational Numbers Excel Add-In described in this book, the mathematical and graphical powers of Excel can now be applied to analyzing mass spectral data obtained using LCMS (liquid chromatography-mass spectrometry). This Excel Add-In is designed to help identify small molecules from less-than-perfect mass spectral data. All data must be accurate mass fragmentation data with a minimum accuracy of +/- 5 mDa, which has become common recently. This book is not concerned with the technical or experimental aspects of ion formation, mass selection or mass measurement; it deals primarily with the analysis of accurate mass fragmentation data of small singly-charged analytes. In this book, there are no fragmentation rules, chemical drawings of hypothetical fragment ions, or quantum mechanics. This book is also not an attempt to review the literature of computational approaches to mass spectral interpretation. This book is basically the author's perspective about a different approach that can help chemists, not just mass spectrometrists, to identify analytes quickly from LCMS data generated using electrospray ionization. When a limited set of data is basically converted into graphical representations with a few scores, it is important to understand the underlying operations and heuristic assumptions that are being made. First, there is a brief description of partitioning (Chapter 1). Three properties of atoms and combinations of atoms (mass, isotopic frequency, and valence) that are critical to mass spectrometry are described in Chapter 2. These three properties, base rates, and other considerations can then be used to find plausible subfragment masses while excluding many spurious masses (Chapters 3 and 4). In Chapter 5, combinations of plausible subfragment masses are systematically generated and checked to find mathematical partitions of the molecular weight. The best partitions are partitions of the molecular weight which also have combinations of subfragments that can explain many of the more intense fragment ions. These sets of partitions are sets of subfragment masses which are not aligned in space at this point. In Chapter 6, permutations of these combinations of subfragment masses are systematically generated and checked against truth tables to find spatial alignments of the subfragments in modular structures that are consistent with the mass spectral data. Up to this point, all operations in the Excel Add-In were done using masses (numbers); in Chapter 7, the subfragment masses are converted into formulas. Some minor adjustments to scoring are described in Chapter 8. Basic data considerations are described in Chapter 9. In Chapter 10, examples of using the Excel Add-In are described in some detail.
Ab Initio Molecular Dynamics
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Author : Dominik Marx
language : en
Publisher: Cambridge University Press
Release Date : 2009-04-30
Ab Initio Molecular Dynamics written by Dominik Marx and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-04-30 with Science categories.
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.