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Dynamic simulation, with Chem

M. Odelius, M. Kadi, J. Davidsson, and A. N. Tarnovsky, Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations. J. Chem. Phys. 121(5), 2208-2214 (2004). [Pg.286]

Leonov AI (1994) On a self-consistent molecular modelling of linear relaxation phenomena in polymer melts and concentrated solutions. J Rheol 38( 1) 1—11 Liu B, Diinweg B (2003) Translational diffusion of polymer chains with excluded volume and hydrodynamic interactions by Brownian dynamics simulation. J Chem Phys 118(17) 8061-8072... [Pg.246]

Mosey NJ, Hu A, Woo TK, Ab initio molecular dynamics simulations with a HOMO-LUMO gap biasing potential to accelerate rare reaction events, Chem Phys Lett, 373, 498—505 (2003)... [Pg.270]

Vorobjec YN, Hermans J (1990) ES/IS estimation of conformational free energy by combining dynamic simulations with explicit solvent with an implicit solvent continuum model, Biophys Chem, 78 195-205... [Pg.336]

A. T. Briinger and M. Karplus, Acc. Chem. Res., 24, 54 (1991). Molecular Dynamics Simulations with Experimental Restraints. [Pg.170]

R. Eggenberger, S. Gerber, H. Huber, D. Searles, and M. Welker, Use of Molecular Dynamics Simulations with Ab Initio SCF Calculations for the Determination of the Deuterium Quadrupole Coupling Constant in Liquid Water and Bond Lengths in Ice, J. Comp. Chem., 14 (1993), 1553-1560. [Pg.321]

Gilson, M. K., McCammon, J. A. and Madura, J. D. (1995). Molecular Dynamics Simulation with a Continuum Electrostatic Model of the Solvent. J. Comput. Chem., 16, 1081-1095. [Pg.895]

Gilson, M., J. McCammon and J. Madura. (1994). Molecular dynamics simulation with continuum solvent. J. Comp. Chem. ... [Pg.231]

Donnamaria, M.C., Howard, E.I., and Grigera, J.R. Interaction of water with a,a-trehalose in solution — molecular dynamics simulation approach, /. Chem. Soc. Faraday Trans., 90, 2731, 1994. [Pg.162]

Qian, X.L., Schlick, T. Efficient multiple-time-step integrators with distance-based force spHtting for particle-mesh-Ewald molecular dynamics simulations, J. Chem. Phys. 2002,116,5971-83. [Pg.27]

Lamoureux, G., and B. Roux, Modeling induced polarization with classical Drude oscillators Theory and molecular dynamics simulation algorithm. . Chem. Phys., 2003.119(6), 3025-3039. [Pg.229]

Reddy G, Chang R, Yethiraj A (2(X)6) Adsorption and dynamics of a single polyelectrolyte chain near a planar charged surfaces molecular dynamics simulation with explicit solvent. J Chem Theory Comput 2 630-636. doi 10.1021/ct050267u... [Pg.1655]

Goetz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC (2012) Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. generalized born. J Chem Theory Comput 8(5) 1542-1555. doi 10.1021/ct200909j... [Pg.532]

Jaeqx S, Oomens J, Cimas A, Gaigeot M-P, Rijs AM (2014) Gas-phase peptide structures unraveled by far-IR spectroscopy combining IR-UV ion-dip experiments with Bom-Oppenheimer molecular dynamics simulations. Angew Chem hit Ed Engl 53(14) 3663-3666... [Pg.38]

M.K. Gilson, J.A. McCammon, and J.D. Madura. Molecular dynamics simulations with a continuum electrostatic model of the solvent, J. Comput. Chem., 9 (1995) 1081. [Pg.567]

Chang, R., Yethiraj, A. Strongly charged flexible polyelectrolytes in poor solvents molecular dynamics simulations with explicit solvent. J. Chem. Phys. 118, 6634 (2003). doi 10.1063/1.1558312... [Pg.83]

G. Corongiu and E. Clementi,/. Chem. Phys., 98, 4984 (1993). Molecular-Dynamics Simulations with a Flexible and Polarizable Potential - Density of States for Liquid Water at Different Temperatures. [Pg.288]

Deng, Y., and Roux, B. 2009. Computations of standard binding free energies with molecular dynamics simulations. /. Phys. Chem., 113, 2234-2246. [Pg.87]

Belhadj,M., Alper, H.A., Levy, R.M. Molecular dynamics simulations of wa ter with Ewald summation for the long-range electrostatic interactions. Chem. Phys. Lett. 179 (1991) 13-20. [Pg.32]

J. D. Weeks, D. Chandler, H. C. Andersen. Role of repulsive forces in determining the equilibrium structure of simple liquids. J Chem Phys 54 5237, 1971. R. L. Rowley, M. W. Schuck, J. Perry. A direct method for determination of chemical potential with molecular dynamics simulations. 2. Mixtures. Mol Phys 55 125, 1995. [Pg.797]

Yu HB, Geerke DP, Liu HY, van Gunsteren WE (2006) Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. J Comput Chem 27(13) 1494-1504... [Pg.250]

Lu ZY, Zhang YK (2008) Interfacing ab initio quantum mechanical method with classical Drude os-illator polarizable model for molecular dynamics simulation of chemical reactions. J Chem Theory Comput 4(8) 1237-1248... [Pg.251]

Archontis, G. Simonson, T. Dielectric relaxation in an enzyme active site molecular dynamics simulations intepreted with a macroscopic continuum model, J. Am. Chem. Soc. 2001,123, 11047-11056. [Pg.494]

Tieleman, D. P. and Berendsen, H. J. C. (1996). Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters, J. Chem. Phys., 105, 4871 —4880. [Pg.105]

Zhang, Z., Bhide, S.Y., Berkowitz, M.L. Molecular dynamics simulations of bilayers containing mixtures of sphingomyelin with cholesterol and phosphatidylcholine with cholesterol. J. Phys. Chem. B 2007, 111, 12888-97. [Pg.19]

Lin Y, Liao Q, Jin X. Molecular dynamics simulations of dendritic polyelectrolytes with flexible spacers in salt free solution. J Phys Chem B 2007 111 5819-5828. [Pg.301]

Hirata, M., Guilbaud, R, Dobler, M., Tachimori, S. 2003. Molecular dynamics simulations for the complexexation of Ln3+ and XJO ions with tridentate ligands diglycol-amide (DGA). Phys. Chem. Chem. Phys. 5 691-695. [Pg.46]

Straatsma, T. P., McCammon, J. A. (1989), Treatment of Rotational Isomers in Free Energy Calculations. II. Molecular Dynamics Simulation of 18-Crown-6 in Aqueous Solution as an Example of Systems with Large Numbers of Rotational Isomeric States, J. Chem. Phys. 91, 3631-3637. [Pg.346]

K. Ando and S. Kato, Dielectric relaxation dynamics of water and methanol solutions associated with the ionization of /V,/V-dimcltiylanilinc theoretical analyses, J. Chem. Phys., 95 (1991) 5966-82 D. K. Phelps, M. J. Weaver and B. M. Ladanyi, Solvent dynamic effects in electron transfer molecular dynamics simulations of reactions in methanol, Chem. Phys., 176 (1993) 575-88 M. S. Skaf and B. M. Ladanyi, Molecular dynamics simulation of solvation dynamics in methanol-water mixtures, J. Phys. Chem., 100 (1996) 18258-68 D. Aheme, V. Tran and B. J. Schwartz, Nonlinear, nonpolar solvation dynamics in water the roles of elec-trostriction and solvent translation in the breakdown of linear response, J. Phys. Chem. B, 104 (2000) 5382-94. [Pg.385]

Desheng L, Jian G, Yuanhua C et al (2011) Molecular dynamics simulations and MM/ GBSA methods to investigate binding mechanisms of aminomethylpyrimidine inhibitors with DPP-IV. Bioorg Med Chem Lett 21(22) 6630-6635... [Pg.112]

Tapia O, Velasquez I (1997) Molecular Dynamics Simulations of DNA with Protein s Consistent GROMOS Force Field and the Role of Counterions Symmetry, J Am Chem Soc, 119 5934... [Pg.333]

Tsui V, Case DA (2002) Molecular dynamic simulations of nucleic acids with a generalized born solvation model, J Am Chem Soc, 122 2489-2498... [Pg.337]

Diaz, N., Suarez, D., and Merz, K.M., Jr. (2001) Molecular dynamics simulation of the mononuclear zinc-P-lactomase from Bacciluscereus complexed with benzylpenicillin and quantum chemical study of the reaction mechanism, /. Am. Chem. Soc. 123, 9867-9879. [Pg.196]

A. Nyberg and T. Schlick, ]. Chem. Phys., 95, 4986 (1991). A Computational Investigation of Dynamic Properties with the Implicit-Euler Scheme for Molecular Dynamics Simulation. [Pg.66]

Figure 7.44. Molecular dynamics simulation of the ion bombardment of a Ag crystal surface with a 15 keV Ga+ beam, and a 15 keV Cgo atomic cluster beattL The Cgo beam results in a larger crater and more material removed from the surface. In contrast, the Ga+ beam results in a destructive effect at greater sample depths, without successful sputtering of the sample. Reproduced with permission from Winograd, N. Anal. Chem. 2005, 77, 142A. Copyright 2005 American Chemical Society. Figure 7.44. Molecular dynamics simulation of the ion bombardment of a Ag crystal surface with a 15 keV Ga+ beam, and a 15 keV Cgo atomic cluster beattL The Cgo beam results in a larger crater and more material removed from the surface. In contrast, the Ga+ beam results in a destructive effect at greater sample depths, without successful sputtering of the sample. Reproduced with permission from Winograd, N. Anal. Chem. 2005, 77, 142A. Copyright 2005 American Chemical Society.
Spezia R, Nicolas C, Archirel P, Boutin A. (2004) Molecular dynamics simulations of the Ag or Na cation with an excess electron in bulk water. J Chem Phys 120 5261-5268. [Pg.56]


See other pages where Dynamic simulation, with Chem is mentioned: [Pg.136]    [Pg.251]    [Pg.730]    [Pg.60]    [Pg.30]    [Pg.38]   
See also in sourсe #XX -- [ Pg.3 , Pg.303 ]




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