Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models.
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Walter Thiel | Hai Lin | Soroosh Pezeshki | W. Thiel | Hai Lin | Xin Wu | Xin Wu | Soroosh Pezeshki
[1] Daniel Borgis,et al. An extended empirical valence bond model for describing proton transfer in H+(H2O)n clusters and liquid water , 1998 .
[2] C. Hadad,et al. Structural studies of the water tetramer , 2008 .
[3] M. Karplus,et al. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .
[4] Gregory A Voth,et al. Special pair dance and partner selection: elementary steps in proton transport in liquid water. , 2008, The journal of physical chemistry. B.
[5] J. VandeVondele,et al. Chasing charge localization and chemical reactivity following photoionization in liquid water. , 2011, The Journal of chemical physics.
[6] Walter Thiel,et al. Orthogonalization corrections for semiempirical methods , 2000 .
[7] T. H. Dunning. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .
[8] I. H. Hillier,et al. Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules. , 2007, Physical chemistry chemical physics : PCCP.
[9] Jessica M J Swanson,et al. Role of charge transfer in the structure and dynamics of the hydrated proton. , 2009, The journal of physical chemistry. B.
[10] Bálint Aradi,et al. The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations. , 2010, The journal of physical chemistry. B.
[11] N. Agmon,et al. The Grotthuss mechanism , 1995 .
[12] Kari Laasonen,et al. Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- ions in water , 1995 .
[13] Stefan Grimme,et al. Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..
[14] S. Nosé. A molecular dynamics method for simulations in the canonical ensemble , 1984 .
[15] Jens Ulstrup,et al. Kinetics of Proton Transport in Water , 2003 .
[16] A. Soper,et al. Quantum Differences between Heavy and Light Water. , 2008, Physical review letters.
[17] Margaret E. Johnson,et al. Tetrahedral structure or chains for liquid water. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[18] Timothy C. Berkelbach,et al. Concerted hydrogen-bond dynamics in the transport mechanism of the hydrated proton: a first-principles molecular dynamics study. , 2009, Physical review letters.
[19] H. Senn,et al. QM/MM Methods for Biological Systems , 2006 .
[20] Martin Korth,et al. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields , 2010 .
[21] S. Garofalini,et al. Dissociative water potential for molecular dynamics simulations. , 2007, The journal of physical chemistry. B.
[22] Gregory A. Voth,et al. Multistate Empirical Valence Bond Model for Proton Transport in Water , 1998 .
[23] Arieh Warshel,et al. An empirical valence bond approach for comparing reactions in solutions and in enzymes , 1980 .
[24] James R. Rustad,et al. A polarizable, dissociating molecular dynamics model for liquid water , 1993 .
[25] J. Stewart. Optimization of parameters for semiempirical methods I. Method , 1989 .
[26] B. Randolf,et al. Combining a Dissociative Water Model with a Hybrid QM/MM Approach-A Simulation Strategy for the Study of Proton Transfer Reactions in Solution. , 2012, Journal of chemical theory and computation.
[27] Dominik Marx,et al. Proton transfer 200 years after von Grotthuss: insights from ab initio simulations. , 2006, Chemphyschem : a European journal of chemical physics and physical chemistry.
[28] M. Tuckerman,et al. Connecting solvation shell structure to proton transport kinetics in hydrogen-bonded networks via population correlation functions. , 2007, Physical review letters.
[29] C. David. A variable charge central force model for water and its ionic dissociation products , 1996 .
[30] J. Stewart. Optimization of parameters for semiempirical methods II. Applications , 1989 .
[31] G. Pastore,et al. A fully polarizable and dissociable potential for water , 2003, cond-mat/0309219.
[32] Frank H. Stillinger,et al. Polarization model for water and its ionic dissociation products , 1978 .
[33] Joel F. Liebman,et al. Evaluated Gas Phase Basicities and Proton Affinities of Molecules; Heats of Formation of Protonated Molecules , 1984 .
[34] M. Plesset,et al. Note on an Approximation Treatment for Many-Electron Systems , 1934 .
[35] Jindřich Fanfrlík,et al. Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes. , 2009, Journal of chemical theory and computation.
[36] D. Truhlar,et al. QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .
[37] David J. Keffer,et al. A Reactive Molecular Dynamics Algorithm for Proton Transport in Aqueous Systems , 2010 .
[38] M. Tuckerman,et al. A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases. , 2010, The Journal of chemical physics.
[39] Tai-Sung Lee,et al. A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .
[40] F. Paesani,et al. A refined MS-EVB model for proton transport in aqueous environments. , 2012, The journal of physical chemistry. B.
[41] Car,et al. Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.
[42] J. Stewart. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.
[43] J. Kress,et al. Ab initio molecular dynamics and quasichemical study of H+(aq). , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[44] Daniel Borgis,et al. Transport and spectroscopy of the hydrated proton: A molecular dynamics study , 1999 .
[45] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[46] Aaron Lefohn,et al. A Multistate Empirical Valence Bond Approach to a Polarizable and Flexible Water Model , 2001 .
[47] Walter Thiel,et al. OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. , 2008, Physical chemistry chemical physics : PCCP.
[48] Mark E. Tuckerman,et al. An empirical valence bond model for proton transfer in water , 1998 .
[49] Walter Thiel,et al. Looking at self-consistent-charge density functional tight binding from a semiempirical perspective. , 2007, The journal of physical chemistry. A.
[50] Gregory A Voth,et al. An improved multistate empirical valence bond model for aqueous proton solvation and transport. , 2008, The journal of physical chemistry. B.
[51] Walter Thiel,et al. Beyond the MNDO model: Methodical considerations and numerical results , 1993, J. Comput. Chem..
[52] M. Parrinello,et al. The nature of the hydrated excess proton in water , 1999, Nature.
[53] Thomas Frauenheim,et al. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. , 2006, Journal of the American Chemical Society.
[54] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[55] PROTONIZABLE WATER MODEL FOR QUANTUM DYNAMICAL SIMULATIONS , 1998 .
[56] Seyit Kale,et al. Lewis-inspired representation of dissociable water in clusters and Grotthuss chains , 2012, Journal of biological physics.
[57] Helmut Bönnemann. Preface: 5th German Ferrofluid Workshop, held 25–27 June 2003, at the Max‐Planck‐Institut für Kohlenforschung, Mülheim a.d. Ruhr, Germany , 2004 .
[58] Martin Korth,et al. Empirical hydrogen-bond potential functions--an old hat reconditioned. , 2011, Chemphyschem : a European journal of chemical physics and physical chemistry.
[59] Alan K. Soper,et al. The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa , 2000 .
[60] W. Thiel,et al. Benchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost As Accurate and Robust As DFT-GGA Methods for Organic Molecules. , 2011, Journal of chemical theory and computation.
[61] 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.
[62] Jessica M J Swanson,et al. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. , 2007, The journal of physical chemistry. B.
[63] M. Dewar,et al. Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .
[64] D. Truhlar,et al. Direct dynamics calculations with NDDO (neglect of diatomic differential overlap) molecular orbital theory with specific reaction parameters , 1991 .
[65] Puja Goyal,et al. Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. , 2011, The journal of physical chemistry. B.
[66] W. Thiel,et al. Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches , 1996 .
[67] Kenneth M. Merz,et al. Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian , 2000 .
[68] Albeiro Restrepo,et al. Structural studies of the water pentamer , 2011 .
[69] Joseph C. Fogarty,et al. A reactive molecular dynamics simulation of the silica-water interface. , 2010, The Journal of chemical physics.
[70] W. Thiel,et al. Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface. , 2011, Journal of chemical theory and computation.
[71] Thomas Frauenheim,et al. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment , 2001 .
[72] Tae Hoon Choi,et al. Application of the SCC-DFTB method to H+(H2O)6, H+(H2O)21, and H+(H2O)22. , 2010, The journal of physical chemistry. B.
[73] Eamonn F. Healy,et al. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .
[74] Michael Gaus,et al. DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). , 2011, Journal of chemical theory and computation.
[75] David E. Woon,et al. Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties , 1994 .