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Combined Quantum Mechanical and Molecular Mechanical Methods

Combined Quantum Mechanical and Molecular Mechanical Methods
Author: Jiali Gao
Publisher:
Total Pages: 328
Release: 1998
Genre: Medical
ISBN:

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Combined quantum mechanical and molecular mechanical methods (QM/MM) is one of the most promising approaches for quantum mechanical calculations of chemical processes in solution and in enzymes. This book provides an in-depth survey of the methods and applications of these combined techniques in chemistry and biochemistry.


Combining Quantum Mechanics and Molecular Mechanics. Some Recent Progresses in QM/MM Methods

Combining Quantum Mechanics and Molecular Mechanics. Some Recent Progresses in QM/MM Methods
Author:
Publisher: Academic Press
Total Pages: 433
Release: 2010-06-14
Genre: Science
ISBN: 0123808995

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Advances in Quantum Chemistry presents surveys of current developments in this rapidly developing field. With invited reviews written by leading international researchers, each presenting new results, it provides a single vehicle for following progress in this interdisciplinary area. Publishes articles, invited reviews and proceedings of major international conferences and workshops Written by leading international researchers in quantum and theoretical chemistry Highlights important interdisciplinary developments


Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems – Recent Developments and Advanced Applications

Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems – Recent Developments and Advanced Applications
Author: Thomas S. Hofer
Publisher: Frontiers Media SA
Total Pages: 188
Release: 2018-11-28
Genre:
ISBN: 2889456269

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The QM/MM method, short for quantum mechanical/molecular mechanical, is a highly versatile approach for the study of chemical phenomena, combining the accuracy of quantum chemistry to describe the region of interest with the efficiency of molecular mechanical potentials to represent the remaining part of the system. Originally conceived in the 1970s by the influential work of the the Nobel laureates Martin Karplus, Michael Levitt and Arieh Warshel, QM/MM techniques have evolved into one of the most accurate and general approaches to investigate the properties of chemical systems via computational methods. Whereas the first applications have been focused on studies of organic and biomolecular systems, a large variety of QM/MM implementations have been developed over the last decades, extending the range of applicability to address research questions relevant for both solution and solid-state chemistry as well. Despite approaching their 50th anniversary in 2022, the formulation of improved QM/MM methods is still an active field of research, with the aim to (i) extend the applicability to address an even broader range of research questions in chemistry and related disciplines, and (ii) further push the accuracy achieved in the QM/MM description beyond that of established formulations. While being a highly successful approach on its own, the combination of the QM/MM strategy with other established theoretical techniques greatly extends the capabilities of the computational approaches. For instance the integration of a suitable QM/MM technique into the highly successful Monte-Carlo and molecular dynamics simulation protocols enables the description of the chemical systems on the basis of an ensemble that is in part constructed on a quantum-mechanical basis. This eBook presents the contributions of a recent Research Topic published in Frontiers in Chemistry, that highlight novel approaches as well as advanced applications of QM/MM method to a broad variety of targets. In total 2 review articles and 10 original research contributions from 48 authors are presented, covering 12 different countries on four continents. The range of research questions addressed by the individual contributions provide a lucid overview on the versatility of the QM/MM method, and demonstrate the general applicability and accuracy that can be achieved for different problems in chemical sciences. Together with the development of improved algorithms to enhance the capabilities of quantum chemical methods and the continuous advancement in the capacities of computational resources, it can be expected that the impact of QM/MM methods in chemical sciences will be further increased already in the near future.


Development and Application of Combined Quantum Mechanical and Molecular Mechanical Methods

Development and Application of Combined Quantum Mechanical and Molecular Mechanical Methods
Author: Rui Lai
Publisher:
Total Pages: 64
Release: 2014
Genre:
ISBN:

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Compromising of computational cost and accuracy, combined quantum mechanical and molecular mechanical (QM/MM) methods are practical methods for studying large molecular systems. The use of induced dipole polarizable force fields can significantly improve the accuracy of MM and QM/MM methods. However, induced dipole models tend to overestimate the polarization energy at short interaction distances. Damping functions can be applied to reduce the over polarization. MM-MM damping schemes have been developed to correct the overestimated polarization between MM atoms; QM-MM damping scheme has not been developed. In this thesis, a QM-MM damping scheme is developed for the damping of the MM dipole polarizability when the MM atoms are in short interacting distance with QM atoms. With this damping scheme, the induced dipole polarization energies in QM/MM calculation can reproduce the values from accurate QM calculations. A general protocol for applying QM/MM methods to study enzyme catalysis is established, and applied to compute the activation free energy of the hydrogen abstraction reaction of camphor catalyzed by cytochrome enzyme P450cam. The estimated activation free energy is in good agreement with the experiments and the results obtained from other QM/MM methods.


Molecular Dynamics

Molecular Dynamics
Author: Perla Balbuena
Publisher: Elsevier
Total Pages: 971
Release: 1999-04-22
Genre: Science
ISBN: 0080536840

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The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering. Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD). Features of this book: • Presents advances in methodologies, introduces quantum methods and lists new techniques for classical MD • Deals with complex systems: biomolecules, aqueous solutions, ice and clathrates, liquid crystals, polymers • Provides chemical reactions, interfaces, catalysis, surface phenomena and solids Although the book is not formally divided into methods and applications, the chapters are arranged starting with those that discuss new algorithms, methods and techniques, followed by several important applications.


Methods of Molecular Quantum Mechanics

Methods of Molecular Quantum Mechanics
Author: Valerio Magnasco
Publisher: John Wiley & Sons
Total Pages: 299
Release: 2009-10-29
Genre: Science
ISBN: 0470684542

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Methods of Molecular Quantum Mechanics This advanced text introduces to the advanced undergraduate and graduate student the mathematical foundations of the methods needed to carry out practical applications in electronic molecular quantum mechanics, a necessary preliminary step before using commercial programmes to carry out quantum chemistry calculations. Major features of the book include: Consistent use of the system of atomic units, essential for simplifying all mathematical formulae Introductory use of density matrix techniques for interpreting properties of many-body systems An introduction to valence bond methods with an explanation of the origin of the chemical bond A unified presentation of basic elements of atomic and molecular interactions The book is intended for advanced undergraduate and first-year graduate students in chemical physics, theoretical and quantum chemistry. In addition, it is relevant to students from physics and from engineering sub-disciplines such as chemical engineering and materials sciences.


Elementary Methods of Molecular Quantum Mechanics

Elementary Methods of Molecular Quantum Mechanics
Author: Valerio Magnasco
Publisher: Elsevier
Total Pages: 750
Release: 2006-12-20
Genre: Science
ISBN: 008046680X

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Elementary Methods of Molecular Quantum Mechanics shows the methods of molecular quantum mechanics for graduate University students of Chemistry and Physics. This readable book teaches in detail the mathematical methods needed to do working applications in molecular quantum mechanics, as a preliminary step before using commercial programmes doing quantum chemistry calculations.This book aims to bridge the gap between the classic Coulson’s Valence, where application of wave mechanical principles to valence theory is presented in a fully non-mathematical way, and McWeeny’s Methods of Molecular Quantum Mechanics, where recent advances in the application of quantum mechanical methods to molecular problems are presented at a research level in a full mathematical way. Many examples and mathematical points are given as problems at the end of each chapter, with a hint for their solution. Solutions are then worked out in detail in the last section of each Chapter. * Uses clear and simplified examples to demonstrate the methods of molecular quantum mechanics * Simplifies all mathematical formulae for the reader* Provides educational training in basic methodology


Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions

Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions
Author:
Publisher: Academic Press
Total Pages: 331
Release: 2015-11-16
Genre: Science
ISBN: 0128020180

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Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions continues the tradition of the Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins, with each thematically organized volume guest edited by leading experts in a broad range of protein-related topics. Describes advances in application of powerful techniques in the biosciences Provides cutting-edge developments in protein chemistry and structural biology Chapters are written by authorities in their field Targeted to a wide audience of researchers, specialists, and students