Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment

Dimethyl phosphate (DMP) anion has been used extensively as a model compound to simulate the properties of phosphate group. A 35-point DMP anion potential model is constructed based on the atom-bond electronegativity equalization fluctuating charge molecular force field (ABEEM/MM), and it is employed to study the properties of gas-phase DMP anion and DMP-(H2O)n (n = 1–3) clusters. The ABEEM/MM model reproduces well the properties obtained by available experiments and QM calculations, including charge distributions, geometries, and conformational energies of gas-phase DMP-water complexes. Furthermore, molecular dynamics simulation on the DMP anion in aqueous solution based on the ABEEM/MM shows that a remarkable first hydration shell around the nonesterified oxygen atom of DMP anion is formed with a coordination number of 5.2. It is also found that two hydrogen atoms of one water molecule form two hydrogen bonds with two nonesterified oxygen atoms of DMP anion simultaneously. This work could be used as a starting point for us to establish the ABEEM/MM nucleic acid force field.

[1]  K. Jordan,et al.  Comparison of models with distributed polarizable sites for describing water clusters , 2007 .

[2]  J. Tomasi,et al.  A quantum mechanical polarizable continuum model for the calculation of resonance Raman spectra in condensed phase , 2007 .

[3]  C. Cramer,et al.  Polarization Effects in Aqueous and Nonaqueous Solutions. , 2007, Journal of chemical theory and computation.

[4]  Martin Karplus,et al.  Molecular dynamics simulations of biomolecules. , 2002, Nature structural biology.

[5]  J. Pranata,et al.  Reexamination of the conformations of dimethyl phosphate anion in water , 1995 .

[6]  Xin Li,et al.  Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study. , 2005, The Journal of chemical physics.

[7]  Asbjørn Holt,et al.  Induction correction model for rotation of two or three dihedral angles , 2008, J. Comput. Chem..

[8]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[9]  MD simulations using distributed multipole electrostatics: Structural and spectroscopic properties of CO- and methane-containing clathrates , 2008 .

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

[11]  G. Pastore,et al.  A flexible atomic and polarizable potential for water Application to small clusters , 2008 .

[12]  Christophe Chipot,et al.  Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations. , 2007, Journal of chemical theory and computation.

[13]  Chang-Sheng Wang,et al.  Atom-Bond Electronegativity Equalization Method and its Applications Based on Density Functional Theory , 2003 .

[14]  A. Warshel,et al.  Conformational Flexibility of Phosphate, Phosphonate, and Phosphorothioate Methyl Esters in Aqueous Solution , 1998 .

[15]  Carmay Lim,et al.  Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions , 2009, J. Comput. Chem..

[16]  Alexander D. MacKerell,et al.  Reevaluation of stereoelectronic contributions to the conformational properties of the phosphodiester and N3'-phosphoramidate moieties of nucleic acids. , 2001, Journal of the American Chemical Society.

[17]  Bhyravabhotla Jayaram,et al.  Conformational preferences of phosphodiester torsion angles in dimethyl phosphate anion in free space and water: quasi-harmonic Monte Carlo and hydration shell calculations , 1988 .

[18]  Jay W Ponder,et al.  Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. , 2007, Journal of chemical theory and computation.

[19]  B. Jena,et al.  Ca2+–dimethylphosphate complex formation: Providing insight into Ca2+‐mediated local dehydration and membrane fusion in cells , 2008, Cell biology international.

[20]  J. Leszczynski,et al.  A comparison of the B3LYP and MP2 methods in the calculation of phosphate complexes , 2000 .

[21]  G. Thomas,et al.  Vibrational analysis of nucleic acids. I. The phosphodiester group in dimethyl phosphate model compounds: (CH3O)2PO2-, (CD3O)2PO2-, and (13CH3O)2PO2-. , 1994, Biophysical journal.

[22]  Zhong-Zhi Yang,et al.  Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters. , 2004, The Journal of chemical physics.

[23]  A. Sarai,et al.  Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion , 1999 .

[24]  Hans Ågren,et al.  Recipe of Polarized One-Electron Potential Optimization for Development of Polarizable Force Fields. , 2007, Journal of chemical theory and computation.

[25]  Terry R. Stouch,et al.  Ab initio studies of lipid model species. 1. Dimethyl phosphate and methyl propyl phosphate anions , 1993 .

[26]  Asbjørn Holt,et al.  Inclusion of the quadrupole moment when describing polarization. The effect of the dipole‐quadrupole polarizability , 2008, J. Comput. Chem..

[27]  J. Leszczynski,et al.  THEORETICAL STUDY OF COMPLEXATION OF PHOSPHODIESTER LINKAGE WITH ALKALI AND ALKALINE-EARTH CATIONS , 1999 .

[28]  Xin Li,et al.  Molecular dynamics simulations of LiCl association and NaCl association in water by means of ABEEM/MM , 2008 .

[29]  Zhong-Zhi Yang,et al.  An investigation of alkane conformations based on the ABEEM/MM model , 2005 .

[30]  Alexander D. MacKerell,et al.  Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. , 2007, Journal of chemical theory and computation.

[31]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[32]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[33]  M. Mezei,et al.  Conformational stability of dimethyl phosphate anion in water: liquid-state free energy simulations , 1988 .

[34]  Qiang Zhang,et al.  Study of peptide conformation in terms of the ABEEM/MM method , 2006, J. Comput. Chem..

[35]  Donald G Truhlar,et al.  Charge Model 4 and Intramolecular Charge Polarization. , 2007, Journal of chemical theory and computation.

[36]  M. Mezei,et al.  Monte Carlo study of the aqueous hydration of dimethylphosphate conformations , 1987 .

[37]  F. Gygi,et al.  Conformational dynamics of the dimethyl phosphate anion in solution , 2001 .

[38]  Douglas J. Tobias,et al.  Electronic Polarization and Hydration of the Dimethyl phosphate Anion: An ab Initio Molecular Dynamics Study , 2001 .

[39]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .

[40]  S. Hanlon,et al.  Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration. , 1975, Biochemistry.

[41]  Leonor Saiz,et al.  Computer simulation studies of model biological membranes. , 2002, Accounts of chemical research.

[42]  Richard Lavery,et al.  Simulations of nucleic acids and their complexes. , 2002, Accounts of chemical research.

[43]  Ping Qian,et al.  A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics. , 2006, The Journal of chemical physics.

[44]  Martin J. Field,et al.  A chemical potential equalization model for treating polarization in molecular mechanical force fields , 2000 .

[45]  William L Jorgensen,et al.  Special Issue on Polarization. , 2007, Journal of chemical theory and computation.

[46]  Zhong-Zhi Yang,et al.  Atomic Charge Calculation of Metallobiomolecules in Terms of the ABEEM Method. , 2007, Journal of chemical theory and computation.

[47]  K. Schulten,et al.  Modeling Induction Phenomena in Intermolecular Interactions with an Ab Initio Force Field. , 2007, Journal of chemical theory and computation.

[48]  A. Petrov,et al.  Calculations of Magnesium−Nucleic Acid Site Binding in Solution , 2004 .

[49]  Xin Li,et al.  Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics. , 2005, The journal of physical chemistry. A.

[50]  Asbjørn Holt,et al.  An intramolecular induction correction model of the molecular dipole moment , 2008, J. Comput. Chem..

[51]  Thomas Simonson,et al.  Free energy simulations come of age: protein-ligand recognition. , 2002, Accounts of chemical research.

[52]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

[53]  C. Cramer,et al.  Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges. , 2007, Journal of chemical theory and computation.

[54]  John SantaLucia,et al.  AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA. , 2007, Journal of chemical theory and computation.

[55]  G. Folkers,et al.  Dimethyl Phosphate: Stereoelectronic versus Environmental Effects , 1999 .

[56]  Zhong-Zhi Yang,et al.  Atom–bond electronegativity equalization method. II. Lone-pair electron model , 1999 .

[57]  Xin Li,et al.  Ion solvation in water from molecular dynamics simulation with the ABEEM/MM force field. , 2005, The journal of physical chemistry. A.

[58]  Jan Florián,et al.  IR AND RAMAN SPECTRA, CONFORMATIONAL FLEXIBILITY, AND SCALED QUANTUM MECHANICAL FORCE FIELDS OF SODIUM DIMETHYL PHOSPHATE AND DIMETHYL PHOSPHATE ANION , 1996 .

[59]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[60]  Anton S. Petrov,et al.  Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium , 2005 .

[61]  Chris Oostenbrink,et al.  An improved nucleic acid parameter set for the GROMOS force field , 2005, J. Comput. Chem..

[62]  Zhong-Zhi Yang,et al.  Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics. II. A Seven-Site Fluctuating Charge and Flexible Body Water Potential Function for Liquid Water , 2004 .

[63]  M. Plesset,et al.  Note on an Approximation Treatment for Many-Electron Systems , 1934 .

[64]  Zhong-Zhi Yang,et al.  STUDY ON COMPLEXES OF TRYPSIN AND ITS INHIBITORS BY MEANS OF ATOM-BOND ELECTRONEGATIVITY EQUALIZATION METHOD FUSED INTO MOLECULAR MECHANICS (ABEEM/MM) , 2007 .

[65]  Jiali Gao,et al.  The Design of a Next Generation Force Field: The X-POL Potential. , 2007, Journal of chemical theory and computation.

[66]  Chang-Sheng Wang,et al.  Atom−Bond Electronegativity Equalization Method. 1. Calculation of the Charge Distribution in Large Molecules , 1997 .

[67]  W. V. van Gunsteren,et al.  On the Calculation of Atomic Forces in Classical Simulation Using the Charge-on-Spring Method To Explicitly Treat Electronic Polarization. , 2007, Journal of chemical theory and computation.

[68]  S. F. Boys,et al.  The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors , 1970 .

[69]  The importance of multipole moments when describing water and hydrated amino acid cluster geometry , 2008 .

[70]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[71]  G. Thomas,et al.  Vibrational Analysis of Nucleic Acids. 2. Ab Initio Calculation of the Molecular Force Field and Normal Modes of Dimethyl Phosphate , 1995 .