An effective force field for molecular dynamics simulations of dimethyl sulfone

A rigid five-site united atom model for dimethyl sulfone (DMSO2) compatible with the GROMOS force field is parametrized and tested. The parameters were optimized with respect to experimental quantities such as liquid density, heat of vaporization, shear viscosity and excess free energy. Good agreement with pure component properties is achieved except for the static dielectric permittivity which is calculated too low. Together with the SPC model for water the new DMSO2 model was used to study aqueous mixtures at low concentrations and compared to aqueous mixtures of DMSO. It is concluded that interaction parameters for sulfoxide oxygen are not directly transferable to sulfonyl oxygen.

[1]  Arnold Weissberger,et al.  Organic solvents;: Physical properties and methods of purification , 1970 .

[2]  J. R. Peterson,et al.  Spectroscopy and electrochemistry of selected lanthanides in molten dimethyl sulfone , 1983 .

[3]  F. Makino,et al.  The Microwave Spectrum of Dimethyl Sulfone , 1972 .

[4]  Ming-Jing Hwang,et al.  Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds , 2001, J. Comput. Chem..

[5]  H. Fujihara,et al.  Hydrogen Bonding and Complexing Properties of R2SO2 and R2SO , 2006 .

[6]  Wilfred F van Gunsteren,et al.  Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.

[7]  K. J. Ivin,et al.  Studies in the thermochemistry of sulphones. Part 3.—Fusion and vaporization heats of sulphones of the type RSO2CH3 , 1961 .

[8]  Water hydrogen-bond dynamics close to hydrophobic and hydrophilic groups , 1996 .

[9]  Aatto Laaksonen,et al.  Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide−Water Mixture , 2001 .

[10]  Wilfred F. van Gunsteren,et al.  A generalized reaction field method for molecular dynamics simulations , 1995 .

[11]  G. Richmond,et al.  Adsorption of organosulfur species at aqueous surfaces: molecular bonding and orientation. , 2005, The journal of physical chemistry. B.

[12]  R. Zhou Free energy landscape of protein folding in water: Explicit vs. implicit solvent , 2003, Proteins.

[13]  W. Greenlee,et al.  Sulfones as peptide bond isosteres , 1991 .

[14]  G. Fischer Numerical data and functional relationships in science and technology , 1987 .

[15]  S. Patai,et al.  The Chemistry of sulphones and sulphoxides , 1988 .

[16]  K. Machida,et al.  Vibrational spectra of dimethyl sulphone and dimethyl sulphone-d6 , 1971 .

[17]  W. Strecker,et al.  Versuche zur Konstitutions-Bestimmung anorganischer Verbindungen auf spektrochemischem Wege , 1926 .

[18]  E. Clark Sulfolane and Sulfones , 2000 .

[19]  Andrew E. Torda,et al.  The GROMOS biomolecular simulation program package , 1999 .

[20]  Markus Christen,et al.  The GROMOS software for biomolecular simulation: GROMOS05 , 2005, J. Comput. Chem..

[21]  B. Berne,et al.  Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Chris Oostenbrink,et al.  An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures , 2004 .

[23]  J. Murray,et al.  Why are dimethyl sulfoxide and dimethyl sulfone such good solvents? , 2008, Journal of molecular modeling.

[24]  M. Skaf Molecular Dynamics Study of Dielectric Properties of Water−Dimethyl Sulfoxide Mixtures , 1999 .

[25]  Wilfred F van Gunsteren,et al.  GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. , 2011, Journal of chemical theory and computation.

[26]  James S. Chickos,et al.  Phase Transition Enthalpy Measurements of Organic and Organometallic Compounds. Sublimation, Vaporization and Fusion Enthalpies From 1880 to 2010 , 2010 .

[27]  Faraday Discuss , 1985 .

[28]  E. Castner,et al.  Aqueous dimethyl sulfoxide solutions: Inter- and intra-molecular dynamics , 2002 .

[29]  H. Niclas,et al.  Das Lösungsmittel Dimethylsulfoxid , 1967 .

[30]  S. Papson,et al.  “Model” , 1981 .

[31]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[32]  A. Gavezzotti,et al.  Empirical intermolecular potentials for organic crystals: the `6‐exp' approximation revisited , 1993 .

[33]  M. Ramos,et al.  Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases , 2006 .

[34]  G. F. Doebbler,et al.  Neutron Inelastic Scattering and X‐Ray Studies of Aqueous Solutions of Dimethylsulphoxide and Dimethylsulphone , 1969 .

[35]  J. Bergman,et al.  Thionations using a P4S10-pyridine complex in solvents such as acetonitrile and dimethyl sulfone. , 2011, The Journal of organic chemistry.

[36]  M. Neumann The dielectric constant of water. Computer simulations with the MCY potential , 1985 .

[37]  Remo Guidieri Res , 1995, RES: Anthropology and Aesthetics.

[38]  B. Bagchi,et al.  Theoretical and computational analysis of static and dynamic anomalies in water-DMSO binary mixture at low DMSO concentrations. , 2011, The journal of physical chemistry. B.

[39]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[40]  Andreas P. Eichenberger,et al.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7 , 2011, European Biophysics Journal.

[41]  M. Berkowitz,et al.  Local structural order and molecular associations in water-DMSO mixtures. Molecular dynamics study , 1992 .

[42]  R. Sowada Darstellung, Eigenschaften und Verwendung von Dimethylsulfon , 2010 .

[43]  A. Soper,et al.  Orientation of Water Molecules around Small Polar and Nonpolar Groups in Solution: A Neutron Diffraction and Computer Simulation Study , 1996 .

[44]  W. R. Feairheller,et al.  The vibrational spectra of sulfones , 1964 .

[45]  I. Hargittai,et al.  An electron diffraction study of the molecular geometry of dimethyl sulphone , 1974 .

[46]  M. Zahniser,et al.  Uptake of gas phase sulfur species methanesulfonic acid, dimethylsulfoxide, and dimethyl sulfone by aqueous surfaces , 1994 .

[47]  S. Yalkowsky,et al.  Freeze-drying above room temperature. , 1999, Journal of pharmaceutical sciences.

[48]  J. Straub,et al.  A molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization. , 2003, Journal of the American Chemical Society.

[49]  Barbara Kirchner,et al.  Solvent effects on electronic properties from Wannier functions in a dimethyl sulfoxide/water mixture. , 2004, The Journal of chemical physics.

[50]  G. Kell,et al.  Precise representation of volume properties of water at one atmosphere , 1967 .

[51]  David S. Baker,et al.  Practical aspects of lyophilization using non-aqueous co-solvent systems. , 2002, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[52]  Masayoshi Okubo,et al.  Makromol Chem-Macromol Symp , 1990 .

[53]  Wilfred F van Gunsteren,et al.  On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase. , 2011, Journal of chemical theory and computation.

[54]  S. Puranik,et al.  Dielectric study of dimethyl sulfoxide–water mixtures using the time-domain technique , 1992 .

[55]  Jeffrey J. Potoff,et al.  Development of an optimized intermolecular potential for sulfur dioxide. , 2011, The journal of physical chemistry. B.

[56]  Fu-Ming Lee Use of organic sulfones as the extractive distillation solvent for aromatics recovery , 1986 .

[57]  C. Reichardt Solvents and Solvent Effects in Organic Chemistry , 1988 .

[58]  G. Geiseler,et al.  Schwingungsverhalten von dimethylsulfid, dimethylsulfoxid, dimethylsulfon und den entsprechenden perdeuterierten verbindungen: 1. Mitt. schwingungsspektren , 1972 .

[59]  R. C. Weast CRC Handbook of Chemistry and Physics , 1973 .

[60]  Peter A. Lee,et al.  INTRACELLULAR DIMETHYLSULFOXIDE (DMSO) IN UNICELLULAR MARINE ALGAE: SPECULATIONS ON ITS ORIGIN AND POSSIBLE BIOLOGICAL ROLE , 1999 .

[61]  C. Nielsen,et al.  Infrared spectra and ab initio calculations of matrix isolated dimethyl sulfone and its water complex , 2002 .

[62]  Philippe Ungerer,et al.  Thermodynamic study of binary systems containing sulphur dioxide: Measurements and molecular modelling , 2011 .

[63]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[64]  L. Mcgann,et al.  Cryoprotection by dimethyl sulfoxide and dimethyl sulfone. , 1987, Cryobiology.

[65]  A. Mark,et al.  On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperature protein unfolding simulations. , 2000, Biophysical journal.

[66]  E. Westrum,et al.  Dimethyl sulfoxide and dimethyl sulfone. Heat capacities, enthalpies of fusion, and thermodynamic properties , 1970 .

[67]  W. V. Gunsteren,et al.  A molecular dynamics computer simulation study of the hydration of bis(methylsulphonyl)methane in water , 1985 .

[68]  M. Skaf,et al.  Molecular association between water and dimethyl sulfoxide in solution: A molecular dynamics simulation study , 1999 .

[69]  Wilfred F. van Gunsteren,et al.  The effect of force-field parameters on properties of liquids: Parametrization of a simple three-site model for methanol , 2000 .

[70]  A. Soper Neutron scattering studies of solvent structure in systems of chemical and biological importance , 1996 .

[71]  W. Hughes Use of dapsone in the prevention and treatment of Pneumocystis carinii pneumonia: a review. , 1998, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[72]  J. Hutter,et al.  The structure of a DMSO-water mixture from Car-Parrinello simulations , 2002 .

[73]  W. V. van Gunsteren,et al.  Acetonitrile revisited: a molecular dynamics study of the liquid phase , 2006 .

[74]  S. Feller,et al.  A Flexible All-Atom Model of Dimethyl Sulfoxide for Molecular Dynamics Simulations , 2002 .

[75]  R. Bechmann,et al.  Numerical data and functional relationships in science and technology , 1969 .

[76]  Charles A Laughton,et al.  Evaluation of molecular modelling methods to predict the sequence-selectivity of DNA minor groove binding ligands. , 2009, Physical chemistry chemical physics : PCCP.

[77]  W. M. Haynes CRC Handbook of Chemistry and Physics , 1990 .

[78]  Alexander D. MacKerell,et al.  Computational Biochemistry and Biophysics , 2001 .

[79]  J. Pereira‐Ramos,et al.  Electrochemical behaviour of some transition metal oxides in molten dimethylsulphone at 150°C , 1986 .

[80]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[81]  Barbara Kirchner,et al.  The secret of dimethyl sulfoxide-water mixtures. A quantum chemical study of 1DMSO-nwater clusters. , 2002, Journal of the American Chemical Society.

[82]  Yi Fan,et al.  Molecular mechanics calculations (MM3) on sulfones , 1993, J. Comput. Chem..

[83]  D. Seebach,et al.  Synthesis of?[SCH2]-,?[SOCH2]-, and?[SO2CH2]-Peptide Isosters , 1995 .