A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents

A novel hybrid quantum mechanical (QM)/molecular mechanical (MM) approach that employs the real‐space grids for the QM subsystem is proposed for investigating chemical reactions in an aqueous condensed phase. All of the Hamiltonian matrix elements including electric fields formed by the point charges on MM waters is represented in the real space. Details of the practical implementations are presented. The solute polarization, solvation structure, and the solvation energy of a water are computed, and the results are compared with those obtained by experiments and other QM/MM approaches that used the LCAO basis. It is shown that the real‐space grid QM/MM method is adequate and superior for the description of the polarization of QM water in a water solution as well as in the gas phase. Solvation structures of classical water solvents are also properly reproduced by this method. Further, parallelization of the code is implemented on a distributed memory architecture, and it is demonstrated that the real‐space grid approach is suitable for the high‐performance parallel computing due to the localization of Hamiltonian operations in the real space. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1252–1261, 2001

[1]  I. Tuñón,et al.  Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. I. Proton transfer in strongly H-bonded complexes , 1997 .

[2]  E. Whalley A relation between the strengths of the orientation polarization and the infrared absorption of the OH stretching vibrations of ice , 1978 .

[3]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[4]  Kari Laasonen,et al.  ‘‘Ab initio’’ liquid water , 1993 .

[5]  T. H. Dunning Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[6]  J. Gao,et al.  A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.

[7]  Ab initio molecular dynamics study of dilute hydrofluoric acid , 1996 .

[8]  Hideaki Takahashi,et al.  A Density Functional Study for Hydrogen Bond Energy by Employing Real Space Grids , 2000 .

[9]  C. Coulson,et al.  Interactions of H2O molecules in ice I. The dipole moment of an H2O molecule in ice , 1966, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[10]  Alan K. Soper,et al.  A new determination of the structure of water at 25°C , 1986 .

[11]  Jacopo Tomasi,et al.  Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent , 1994 .

[12]  Tomoya Ono,et al.  Timesaving Double-Grid Method for Real-Space Electronic-Structure Calculations , 1999 .

[13]  R. Parr Density-functional theory of atoms and molecules , 1989 .

[14]  M. Parrinello,et al.  Water dimer properties in the gradient-corrected density functional theory , 1992 .

[15]  Leonard Kleinman,et al.  Efficacious Form for Model Pseudopotentials , 1982 .

[16]  Arai,et al.  Density-functional molecular dynamics with real-space finite difference. , 1995, Physical review. B, Condensed matter.

[17]  J. Rivail,et al.  Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes , 1997 .

[18]  H. A. Levy,et al.  Liquid Water: Molecular Correlation Functions from X‐Ray Diffraction , 1971 .

[19]  Wu,et al.  Higher-order finite-difference pseudopotential method: An application to diatomic molecules. , 1994, Physical review. B, Condensed matter.

[20]  Michiel Sprik,et al.  Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient‐corrected density functionals , 1996 .

[21]  P. P. Ewald Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .

[22]  Y. Saad,et al.  Finite-difference-pseudopotential method: Electronic structure calculations without a basis. , 1994, Physical review letters.

[23]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[24]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[25]  R. Car,et al.  A microscopic model for surface-induced diamond-to-graphite transitions , 1996, Nature.

[26]  Michele Parrinello,et al.  Structural, electronic, and bonding properties of liquid water from first principles , 1999 .

[27]  Martins,et al.  Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.

[28]  Laurence S. Rothman,et al.  Dipole moment of water from Stark measurements of H2O, HDO, and D2O , 1973 .

[29]  Wu,et al.  Ab initio molecular-dynamics simulations of Si clusters using the higher-order finite-difference-pseudopotential method. , 1994, Physical review. B, Condensed matter.

[30]  Alan K. Soper,et al.  Site–site pair correlation functions of water from 25 to 400 °C: Revised analysis of new and old diffraction data , 1997 .

[31]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[32]  John A Pople Quantum Chemical Models (Nobel Lecture). , 1999, Angewandte Chemie.

[33]  Claude Millot,et al.  A coupled density functional‐molecular mechanics Monte Carlo simulation method: The water molecule in liquid water , 1996 .

[34]  P. Hohenberg,et al.  Inhomogeneous Electron Gas , 1964 .

[35]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[36]  W. Kohn,et al.  Self-Consistent Equations Including Exchange and Correlation Effects , 1965 .

[37]  T. Kerdcharoen,et al.  What Is the Solvation Number of Na + in Ammonia? An Ab Initio QM/MM Molecular Dynamics Study , 2000 .

[38]  A. Zunger,et al.  Self-interaction correction to density-functional approximations for many-electron systems , 1981 .

[39]  F. Grozema,et al.  Combined Quantum Mechanical and Molecular Mechanical Methods , 1999 .