Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models.

The semiempirical MNDO-based AM1 and PM3 methods and the orthogonalization-corrected OM1, OM2, and OM3 models were reparameterized to improve their description of bulk water and of proton transfer in water. Reference data included the gas-phase geometries and energies of the water molecule, small water clusters, the hydronium ion, and small hydronium ion-water clusters, as well as the gas-phase potential energy surface for proton transfer between the two water molecules in a Zundel ion, all calculated at the MP2/aug-cc-pVTZ level of theory. Combined QM/MM molecular dynamics simulations were carried out for bulk water and for a proton solvated in water using large cluster models. Both the authentic and reparameterized semiempirical models were employed in the simulations. The reparameterization led to significantly better results in all cases. The new set of OM3 parameters gave the best overall results for the structural and dynamic properties of water and the hydrated proton, with a small but finite barrier of 0.1-0.2 kcal/mol in the potential of mean force for proton transfer, in agreement with ab initio path-integral molecular dynamics simulations. The reparameterized OM3 model is expected to be useful for efficient modeling of proton transfer in aqueous solution.

[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 .