Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.
暂无分享,去创建一个
Noam Bernstein | Gábor Csányi | Letif Mones | Csilla Várnai | Gábor Csányi | N. Bernstein | C. Várnai | L. Mones | Letif Mones
[1] Scott F. Smith,et al. Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution , 1985 .
[2] Pär Söderhjelm,et al. On the Convergence of QM/MM Energies. , 2011, Journal of chemical theory and computation.
[3] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[4] Weber,et al. Computer simulation of local order in condensed phases of silicon. , 1985, Physical review. B, Condensed matter.
[5] K. Kremer,et al. Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.
[6] Emilio Artacho,et al. Density, structure, and dynamics of water: the effect of van der Waals interactions. , 2010, The Journal of chemical physics.
[7] P. Rossky,et al. Hydration effects on SN2 reactions: an integral equation study of free energy surfaces and corrections to transition-state theory , 1989 .
[8] A. Becke,et al. Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.
[9] Alessandro Laio,et al. An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations. , 2006, Journal of chemical theory and computation.
[10] Alessandro Laio,et al. The energy gap as a universal reaction coordinate for the simulation of chemical reactions. , 2009, The journal of physical chemistry. B.
[11] B. Berne,et al. Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals , 1993 .
[12] Sheng-Yong Yang,et al. Free Energy Profiles for the Identity SN2 Reactions Cl- + CH3Cl and NH3 + H3BNH3: A Constraint Ab Initio Molecular Dynamics Study , 2004 .
[13] Scott F. Smith,et al. SN2 reaction profiles in the gas phase and aqueous solution , 1984 .
[14] M. Basilevsky,et al. Calculation of the rate constant for the reaction chloride + chloromethane .fwdarw. ClCH3 + Cl- in the framework of the continuum medium model , 1993 .
[15] Sangyoub Lee,et al. Nonadiabatic solvation model for SN2 reactions in polar solvents , 1987 .
[16] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[17] A. Laio,et al. Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[18] Hermann Stoll,et al. Results obtained with the correlation energy density functionals of becke and Lee, Yang and Parr , 1989 .
[19] Arieh Warshel,et al. Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases. , 2006, The journal of physical chemistry. B.
[20] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[21] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[22] J. Blumberger,et al. Absolute pKa Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation. , 2011, Journal of chemical theory and computation.
[23] Klaus R. Liedl,et al. A QM/MM simulation method applied to the solution of Li+ in liquid ammonia , 1996 .
[24] Noam Bernstein,et al. Hybrid atomistic simulation methods for materials systems , 2009 .
[25] Donald G Truhlar,et al. Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. , 2007, The journal of physical chemistry. B.
[26] Parr,et al. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.
[27] Lucas Visscher,et al. Toward a Practical Method for Adaptive QM/MM Simulations. , 2009, Journal of chemical theory and computation.
[28] Eric F Darve,et al. Calculating free energies using average force , 2001 .
[29] Alessandro Laio,et al. A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. , 2005, The journal of physical chemistry. B.
[30] Arieh Warshel,et al. Exploring, refining, and validating the paradynamics QM/MM sampling. , 2012, The journal of physical chemistry. B.
[31] P. Kollman,et al. A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .
[32] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[33] Stefan Grimme,et al. Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..
[34] Michele Parrinello,et al. Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics. , 2007, Journal of chemical theory and computation.
[35] G. Ciccotti,et al. Constrained reaction coordinate dynamics for the simulation of rare events , 1989 .
[36] G. Torrie,et al. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .
[37] C. Brooks,et al. Constant‐pH molecular dynamics using continuous titration coordinates , 2004, Proteins.
[38] P. Kollman,et al. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .
[39] Noam Bernstein,et al. QM/MM simulation of liquid water with an adaptive quantum region. , 2012, Physical chemistry chemical physics : PCCP.
[40] Donald G Truhlar,et al. Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations. , 2008, Journal of chemical theory and computation.
[41] George C Schatz,et al. Dynamic QM/MM: a hybrid approach to simulating gas-liquid interactions. , 2012, Topics in current chemistry.
[42] Thomas S. Hofer,et al. Ab initio quantum mechanical charge field (QMCF) molecular dynamics: a QM/MM – MD procedure for accurate simulations of ions and complexes , 2006 .
[43] A. Warshel. A microscopic model for calculations of chemical processes in aqueous solutions , 1978 .
[44] Petr Kulhánek,et al. Evaluating boundary dependent errors in QM/MM simulations. , 2009, The journal of physical chemistry. B.
[45] Michele Parrinello,et al. Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach , 2005, Comput. Phys. Commun..
[46] Teerakiat Kerdcharoen,et al. ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase , 2002 .
[47] Arieh Warshel,et al. An empirical valence bond approach for comparing reactions in solutions and in enzymes , 1980 .
[48] L Delle Site,et al. Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir. , 2011, Physical review letters.
[49] Walter Thiel,et al. Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration". , 2005, The Journal of chemical physics.
[50] D. Case,et al. Constant pH molecular dynamics in generalized Born implicit solvent , 2004, J. Comput. Chem..
[51] Hao Hu,et al. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. , 2008, Annual review of physical chemistry.
[52] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[53] B. Leimkuhler,et al. Adaptive stochastic methods for sampling driven molecular systems. , 2011, The Journal of chemical physics.
[54] D. Truhlar,et al. Effect of nonequilibrium solvation on chemical reaction rates. Variational transition-state-theory studies of the microsolvated reaction Cl-(H2O)n + CH3Cl , 1990 .
[55] Martin J. Field,et al. Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential , 1987 .
[56] Arieh Warshel,et al. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. , 2009, The journal of physical chemistry. B.
[57] Alessandro Laio,et al. An Efficient Real Space Multigrid QM/MM Electrostatic Coupling. , 2005, Journal of chemical theory and computation.
[58] R. G. Della Valle,et al. The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode. , 2011, The Journal of chemical physics.
[59] Bernd Ensing,et al. Solvation Effects on the SN2 Reaction between CH3Cl and Cl- in Water , 2001 .
[60] A. W. Götz,et al. Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems. , 2012, Journal of chemical theory and computation.
[61] R. Zwanzig. High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .
[62] S. Creighton,et al. Simulation of free energy relationships and dynamics of SN2 reactions in aqueous solution , 1988 .
[63] A. Warshel,et al. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. , 1986, Biochemistry.
[64] P. Gumbsch,et al. Low-speed fracture instabilities in a brittle crystal , 2008, Nature.