Download or read book Quantum Mechanical Molecular Mechanical Approaches for the Investigation of Chemical Systems Recent Developments and Advanced Applications written by Thomas S. Hofer and published by Frontiers Media SA. This book was released on 2018-11-28 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Quantum Mechanical Molecular Mechanical Approaches for the Investigation of Chemical Systems Recent Developments and Advanced Applications written by and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computer Simulations in Molecular Biology written by Hiqmet Kamberaj and published by Springer Nature. This book was released on 2023-07-31 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers a range of topics in quantum mechanics and molecular dynamics simulation, including computational modeling and machine learning approaches. The book also provides a Python GUI and tutorials for simulating molecular biological systems and presents case studies of quantum mechanics simulations for predicting electronic properties. Its pedagogical formatting makes it easy for students to understand and follow and has been praised for providing clear and detailed explanations of complex topics. This book is ideal for graduate students and researchers in theoretical and computational biophysics, physics, chemistry, and materials science, as well as postgraduates in applied mathematics, computer science, and bioinformatics.

Download or read book Computational Approaches to Study the Impact of Mutations on Disease and Drug Resistance written by Nir Ben-Tal and published by Frontiers Media SA. This book was released on 2022-01-27 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Quantum Dynamics written by Fabien Gatti and published by Springer Science & Business Media. This book was released on 2014-04-09 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book "Molecular Quantum Dynamics" offers them an accessible introduction. Although the calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.

Download or read book Combining Quantum Mechanics and Molecular Mechanics Some Recent Progresses in QM MM Methods written by and published by Academic Press. This book was released on 2010-06-14 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Challenges in Computational Enzymology written by Vicent Moliner and published by Frontiers Media SA. This book was released on 2019-12-31 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Methods of Molecular Quantum Mechanics written by Valerio Magnasco and published by John Wiley & Sons. This book was released on 2009-12-21 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Applications of Quantum Dynamics in Chemistry written by Fabien Gatti and published by Springer. This book was released on 2017-09-05 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains the usage and application of Molecular Quantum Dynamics, the methodology where both the electrons and the nuclei in a molecule are treated with quantum mechanical calculations. This volume of Lecture Notes in Chemistry addresses graduate students and postdocs in the field of theoretical chemistry, as well as postgraduate students, researchers and teachers from neighboring fields, such as quantum physics, biochemistry, biophysics, or anyone else who is interested in this rising method in theoretical chemistry, and who wants to gain experience in the opportunities it can offer. It can also be useful for teachers interested in illustrative examples of time-dependent quantum mechanics as animations of realistic wave packets have been designed to assist in visualization. Assuming a basic knowledge about quantum mechanics, the authors link their explanations to recent experimental investigations where Molecular Quantum Dynamics proved successful and necessary for the understanding of the experimental results. Examples including reactive scattering, photochemistry, tunneling, femto- and attosecond chemistry and spectroscopy, cold chemistry or crossed-beam experiments illustrate the power of the method. The book restricts complicated formalism to the necessary and in a self-contained and clearly explained way, offering the reader an introduction to, and instructions for, practical exercises. Continuative explanation and math are optionally supplemented for the interested reader. The reader learns how to apply example simulations with the MCTDH program package (Multi Configuration Time Dependent Hartree calculations). Readers can thus obtain the tools to run their own simulations and apply them to their problems. Selected scripts and program code from the examples are made available as supplementary material. This book bridges the gap between the existing textbooks on fundamental theoretical chemistry and research monographs focusing on sophisticated applications. It is a must-read for everyone who wants to gain a sound understanding of Molecular Quantum Dynamics simulations and to obtain basic experience in running their own simulations.

Download or read book Multi scale Quantum Models for Biocatalysis written by Darrin M. York and published by Springer Science & Business Media. This book was released on 2009-05-30 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.

Download or read book Advances in Quantum Methods and Applications in Chemistry Physics and Biology written by Matti Hotokka and published by Springer Science & Business Media. This book was released on 2013-09-13 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Quantum Methods and Applications in Chemistry, Physics, and Biology includes peer-reviewed contributions based on carefully selected presentations given at the 17th International Workshop on Quantum Systems in Chemistry, Physics, and Biology. New trends and state-of-the-art developments in the quantum theory of atomic and molecular systems, and condensed matter (including biological systems and nanostructures) are described by academics of international distinction.

Download or read book Elementary Methods of Molecular Quantum Mechanics written by Valerio Magnasco and published by Elsevier Science Limited. This book was released on 2007 with total page 729 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Energy and Water Development Appropriations for 2014 written by United States. Congress. House. Committee on Appropriations. Subcommittee on Energy and Water Development and published by . This book was released on 2013 with total page 892 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Advances in Quantum Chemistry written by John R. Sabin and published by Academic Press. This book was released on 2011-09-06 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: Approx.500 pagesApprox.500 pages

Download or read book Development and Application of Statistical and Quantum Mechanical Methods for Modelling Molecular Ensembles written by Ellen Therese Swann and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The development of new quantum chemical methods requires extensive benchmarking to establish the accuracy and limitations of a method. Current benchmarking practices in computational chemistry use test sets that are subject to human biases and as such can be fundamentally flawed. This work presents a thorough benchmark of diffusion Monte Carlo (DMC) for a range of systems and properties as well as a novel method for developing new, unbiased test sets using multivariate statistical techniques. Firstly, the hydrogen abstraction of methanol is used as a test system to develop a more efficient protocol that minimises the computational cost of DMC without compromising accuracy. This protocol is then applied to three test sets of reaction energies, including 43 radical stabilisation energies, 14 Diels-Alder reactions and 76 barrier heights of hydrogen and non-hydrogen transfer reactions. The average mean absolute error for all three databases is just 0.9 kcal/mol. The accuracy of the explicitly correlated trial wavefunction used in DMC is demonstrated using the ionisation potentials and electron affinities of first- and second-row atoms. A multi-determinant trial wavefunction reduces the errors for systems with strong multi-configuration character, as well as for predominantly single-reference systems. It is shown that the use of pseudopotentials in place of all-electron basis sets slightly increases the error for these systems. DMC is then tested with a set of eighteen challenging reactions. Incorporating more determinants in the trial wavefunction reduced the errors for most systems but results are highly dependent on the active space used in the CISD wavefunction. The accuracy of multi-determinant DMC for strongly multi-reference systems is tested for the isomerisation of diazene. In this case no method was capable of reducing the error of the strongly-correlated rotational transition state. Finally, an improved method for selecting test sets is presented using multivariate statistical techniques. Bias-free test sets are constructed by selecting archetypes and prototypes based on numerical representations of molecules. Descriptors based on the one-, two- and three-dimensional structures of a molecule are tested. These new test sets are then used to benchmark a number of methods.

Download or read book New Methods in Computational Quantum Mechanics Volume 93 written by Ilya Prigogine and published by Wiley-Interscience. This book was released on 1996-04-25 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of quantum chemistry for the quantitative prediction of molecular properties has long been frustrated by the technical difficulty of carrying out the needed computations. In the last decade there have been substantial advances in the formalism and computer hardware needed to carry out accurate calculations of molecular properties efficiently. These advances have been sufficient to make quantum chemical calculations a reliable tool for the quantitative interpretation of chemical phenomena and a guide to laboratory experiments. However, the success of these recent developments in computational quantum chemistry is not well known outside the community of practitioners. In order to make the larger community of chemical physicists aware of the current state of the subject, this self-contained volume of Advances in Chemical Physics surveys a number of the recent accomplishments in computational quantum chemistry. This stand-alone work presents the cutting edge of research in computational quantum mechanics. Supplemented with more than 150 illustrations, it provides evaluations of a broad range of methods, including: * Quantum Monte Carlo methods in chemistry * Monte Carlo methods for real-time path integration * The Redfield equation in condensed-phase quantum dynamics * Path-integral centroid methods in quantum statistical mechanics and dynamics * Multiconfigurational perturbation theory-applications in electronic spectroscopy * Electronic structure calculations for molecules containing transition metals * And more Contributors to New Methods in Computational Quantum Mechanics KERSTIN ANDERSSON, Department of Theoretical Chemistry, Chemical Center, Sweden DAVID M. CEPERLEY, National Center for Supercomputing Applications and Department of Physics, University of Illinois at Urbana-Champaign, Illinois MICHAEL A. COLLINS, Research School of Chemistry, Australian National University, Canberra, Australia REINHOLD EGGER, Fakultät für Physik, Universität Freiburg, Freiburg, Germany ANTHONY K. FELTS, Department of Chemistry, Columbia University, New York RICHARD A. FRIESNER, Department of Chemistry, Columbia University, New York MARKUS P. FÜLSCHER, Department of Theoretical Chemistry, Chemical Center, Sweden K. M. HO, Ames Laboratory and Department of Physics, Iowa State University, Ames, Iowa C. H. MAK, Department of Chemistry, University of Southern California, Los Angeles, California PER-ÅKE Malmqvist, Department of Theoretical Chemistry, Chemical Center, Sweden MANUELA MERCHán, Departamento de Química Física, Universitat de Valéncia, Spain LUBOS MITAS, National Center for Supercomputing Applications and Materials Research Laboratory, University of Illinois at Urbana-Champaign, Illinois STEFANO OSS, Dipartimento di Fisica, Università di Trento and Istituto Nazionale di Fisica della Materia, Unità di Trento, Italy KRISTINE PIERLOOT, Department of Chemistry, University of Leuven, Belgium W. THOMAS POLLARD, Department of Chemistry, Columbia University, New York BJÖRN O. ROOS, Department of Theoretical Chemistry, Chemical Center, Sweden LUIS SERRANO-ANDRÉS, Department of Theoretical Chemistry, Chemical Center, Sweden PER E. M. SIEGBAHN, Department of Physics, University of Stockholm, Stockholm, Sweden WALTER THIEL, Institut für Organische Chemie, Universität Zürich, Zürich, Switzerland GREGORY A. VOTH, Department of Chemistry, University of Pennsylvania, Pennsylvania C. Z. Wang, Ames Laboratory and Department of Physics, Iowa State University, Ames, Iowa

Download or read book Computational Methods for the Description of Intermolecular Interactions and Molecular Motion in Confining Environments written by Heribert Reis and published by Frontiers Media SA. This book was released on 2022-06-23 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: