Jiali Gao, Mark A. Thompson's Combined Quantum Mechanical and Molecular Mechanical Methods PDF

By Jiali Gao, Mark A. Thompson

ISBN-10: 0841216959

ISBN-13: 9780841216952

ISBN-10: 0841235902

ISBN-13: 9780841235908

content material: Quantum mechanical-molecular mechanical coupled potentials / Kenneth M. Merz, Jr. --
Quantum mechanical-molecular mechanical techniques for learning chemical reactions in proteins and answer / 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 tools / Iris Antes and Walter Thiel --
a mode of hybrid quantum-classical calculations for big organometallic-metallobiochemical structures : functions to iron picket-fence porphyrin and diet B12 / Isaac B. Bersuker, Max ok. 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 features 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 process : digital constitution and semiclassical dynamics : purposes to difficulties in photochemistry / Michael J. Bearpark, Barry R. Smith, Fernando Bernardi, Massimo Olivucci, and Michael A. Robb --
Density sensible concept ab initio molecular dynamics and mixed density practical thought and molecular dynamics simulations / Dongqing Wei and Dennis R. Salahub --
Generalized molecular mechanics together with quantum digital constitution version of polar solvents : an outline / Hyung J. Kim, Badry D. Bursulaya, Jonggu Jeon, and Dominic A. Zichi --
RISM-SCF research of solvent impact 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 strategy / 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 structures / 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 website of human carbonic anhydrase II : a try case examine / Ursula Röthlisberger --
program of linear-scaling digital constitution easy methods to the research of polarization of proteins and DNA in answer / Darrin M. York --
intriguing eco-friendly fluorescent protein / Volkhard Helms, Erik F.Y. Hom, T.P. Straatsma, J. Andrew McCammon, and Peter Langhoff.

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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.  A Priori Evaluation of Aqueous Polarization Effects through Monte Carlo QM­MM Simulations, Science 1992, 258, 631.

Davis, M. ; McCammon, J.  M .  Phys. Chem. 1992, 96, 6428.  Lett. 1992, 198, 74. ; ACS Symposium Series; American Chemical Society: Washington, DC, 1998. ch002 (72) (73) (74) (75) (76) (77) (78) (79) Gao, J.  Comput. Chem. 1997, 18, 1061.  Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis, Science 1989, 244, 1069.  On the Nature of Phosphate Ester Hydrolysis in Aqueous Solution: Associative Versus Dissociative Mechanisms, J. Phys. Chem. 1997, submitted. Frisch, M .  M . ; Johnson, B.

39 obtained by including contributions from the orbital basis correction and density­fit basis correction terms in addition to the Hellman­Feynman force. The DFT code has been conveniently modified and interfaced with the C H A R M M package for M D simulations (34). ch003 Computational Details To demonstrate the utility of the combined M and D F T / M M method for the study of solvent effects, and the computational accuracy on the predicted geometry and electronic polarization for water in aqueous solution, we have carried out both statistical mechanical Monte Carlo and molecular dynamics simulations.

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Combined Quantum Mechanical and Molecular Mechanical Methods by Jiali Gao, Mark A. Thompson


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