By Jiali Gao, Mark A. Thompson
content material: Quantum mechanical-molecular mechanical coupled potentials / Kenneth M. Merz, Jr. --
Quantum mechanical-molecular mechanical ways for learning chemical reactions in proteins and resolution / Jörg Bentzien, Jan Florián, Timothy M. Glennon, and Arieh Warshel --
The geometry of water in liquid water from hybrid ab initio-Monte Carlo and density functional-molecular dynamics simulations / Cristobal Alhambra, Kyoungrim Byun, and Jiali Gao --
at the therapy of hyperlink atoms in hybrid equipment / Iris Antes and Walter Thiel --
a style of hybrid quantum-classical calculations for giant organometallic-metallobiochemical structures : functions to iron picket-fence porphyrin and diet B12 / Isaac B. Bersuker, Max okay. Leong, James E. Boggs, and Robert S. Pearlman --
a strategy for quantum molecular modeling of constitution and reactivity at solid-liquid interfaces / Eugene V. Stefanovich and Thanh N. Truong --
Dual-level tools for digital constitution calculations of capability power services that use quantum mechanics because the reduce point / José C. Corchado and Donald G. Truhlar --
A mixed Car-Parrinello quantum mechanical-molecular mechanical implementation for ab initio molecular dynamics simulations of prolonged structures / Tom ok. Woo, Peter M. Margl, Liqun Deng, and Tom Ziegler --
The molecular mechanics valence bond procedure : digital constitution and semiclassical dynamics : functions to difficulties in photochemistry / Michael J. Bearpark, Barry R. Smith, Fernando Bernardi, Massimo Olivucci, and Michael A. Robb --
Density useful conception ab initio molecular dynamics and mixed density sensible concept and molecular dynamics simulations / Dongqing Wei and Dennis R. Salahub --
Generalized molecular mechanics together with quantum digital constitution version of polar solvents : an summary / Hyung J. Kim, Badry D. Bursulaya, Jonggu Jeon, and Dominic A. Zichi --
RISM-SCF learn of solvent influence on digital constitution and chemical response in resolution : temperature dependence of pKw / Fumio Hirata, Hirofumi Sato, Seiichiro Ten-no, and Shigeki Kato --
common solvation types / Gregory D. Hawkins, Tianhai Zhu, Jiabo Li, Candee C. Chambers, David J. Giesen, Daniel A. Liotard, Christopher J. Cramer, and Donald G. Truhlar --
Quantum mechanical-molecular mechanical calculations of (hyper- )polarizabilities with the direct response box method / Piet Th. van Duijnen, Marcel Swart, and Ferdinand Grozema --
The neighborhood self-consistent box rules and purposes to mixed quantum mechanical-molecular mechanical computations on biomacromolecular platforms / Xavier Assfeld, Nicolas Ferré, and Jean-Louis Rivail --
Investigating enzyme response mechanisms with quantum mechanical-molecular mechanical plus molecular dynamics calculations / Peter L. Cummins and Jill E. Gready --
Ab initio and hybrid molecular dynamics simulations of the energetic web site of human carbonic anhydrase II : a try out case learn / Ursula Röthlisberger --
program of linear-scaling digital constitution ways to the examine of polarization of proteins and DNA in resolution / Darrin M. York --
fascinating eco-friendly fluorescent protein / Volkhard Helms, Erik F.Y. Hom, T.P. Straatsma, J. Andrew McCammon, and Peter Langhoff.
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Content material: Quantum mechanical-molecular mechanical coupled potentials / Kenneth M. Merz, Jr. -- Quantum mechanical-molecular mechanical methods for learning chemical reactions in proteins and resolution / Jörg Bentzien, Jan Florián, Timothy M. Glennon, and Arieh Warshel -- The geometry of water in liquid water from hybrid ab initio-Monte Carlo and density functional-molecular dynamics simulations / Cristobal Alhambra, Kyoungrim Byun, and Jiali Gao -- at the remedy of hyperlink atoms in hybrid tools / Iris Antes and Walter Thiel -- a mode of hybrid quantum-classical calculations for big organometallic-metallobiochemical platforms : purposes to iron picket-fence porphyrin and diet B12 / Isaac B.
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Extra resources for Combined Quantum Mechanical and Molecular Mechanical Methods
Incorporation of Reaction Field Effects into Density Functional Calculations for Molecules of Arbitrary Shape in Solution, Biophys. Chem. 1994, 57, 375. Bash, P. ; Kollman, P. Free Energy Calculations by Computer Simulation, Science 1987, 236, 564. Bash, P. ; Petsko, G. ; Karplus, M. Computer Simulation and Analysis of the Reaction Pathway of Triosephosphate Isomerase, Biochemistry 1991, 30, 5826. Field, M . ; Bash, P. Comp. Chem. 1990, 11, 700. Phys. Chem. 1992, 96, 537. ; ACS Symposium Series; American Chemical Society: Washington, DC, 1998.
John Wiley & Sons: Chichester, 1997. Lee, F. ; Chu, . Comp. Chem. 1993, 14, 161. Calculations of Solvation Free Energies in Chemistry and Biology, In ACS Symposium Series: Structure and Reactivity in Aqueous Solution. ; 1994. Hybrid ab initio Quantum Mechanics/Molecular Mechanics (QM(ai)/MM) Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin, J. Phys. Chem. 1997, submitted. Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches, Chem.
36 intramolecular bond flexibility and/or electric polarization (411). The new development can potentially further extend the applicability of molecular dynamics and Monte Carlo simulations to phenomena that involve large environmental changes, such as water near interfaces, supercritical fluids, and salt solutions. A n important property charactering a flexible water model is the average geometry of water in the liquid state. However, there is a tremendous ambiguity from various flexible water models (Table I).
Combined Quantum Mechanical and Molecular Mechanical Methods by Jiali Gao, Mark A. Thompson