On the properties of aqueous amide solutions through classical molecular dynamics simulations

References

• Sloan , E.D. 1998 . Clathrate Hydrates of Natural Gases , 2nd ed. , New York : Marcel Dekker .
   Google Scholar
• Hammerschmidt , E.G. 1934 . Ind. Eng. Chem. Res. , 26 : 851
   Google Scholar
• Carroll , J. 2003 . Natural Gas Hydrates , Amsterdam : Elsevier .
   Google Scholar
• Anderson , F.E. and Prausnitz , J.M. 1986 . Inhibition of gas hydrates by methanol . AIChE J. , 32 : 1321
   Web of Science ®Google Scholar
• Makogon , Y.F. , Makogon , T.Y. and Holditch , S.A. 2000 . Kinetics and mechanisms of gas hydrate formation and dissociation with inhibitors . Ann. NY Acad. Sci. , 912 : 777
   Web of Science ®Google Scholar
• Koh , C.A. , Westacott , R.E. , Zhang , W. , Hirachand , K. , Creek , J.L. and Soper , A.K. 2002 . Mechanisms of gas hydrate formation and inhibition . Fluid Phase Equilib. , 194 : 143
   Web of Science ®Google Scholar
• Sloan , E.D. , Subramanian , S. , Metthews , P.N. , Lederhos , J.P. and Khokar , A.A. 1998 . Quantifying hydrate formation and kinetic inhibition . Ind. Eng. Chem. Res. , 37 : 3124
   Web of Science ®Google Scholar
• Koh , C.A. 2002 . Towards a fundamental understanding of natural gas hydrates . Chem. Soc. Rev. , 31 : 157
   PubMed Web of Science ®Google Scholar
• Carver , T.J. , Drew , M.G.B. and Rodger , P.M. 1999 . Molecular dynamics calculations of N-methylpyrrolidone in liquid water . Phys. Chem. Chem. Phys. , 1 : 1807
   Web of Science ®Google Scholar
• Storr , M.T. , Taylor , P.C. , Monfort , J.P. and Rodger , P.M. 2004 . Kinetic inhibitor of hydrate crystallization . J. Am. Chem. Soc. , 126 : 1569
   PubMed Web of Science ®Google Scholar
• Storr , M.T. , Rodger , P.M. , Montfort , J.P. and Jussaume , L. 2001 . “ A mechanistic study of low dosage inhibitors of clathrate hydrate formation ” . In Foundations of Molecular Modeling and Simulation AIChE Symposium Series No 325
   Google Scholar
• Anderson , B.J. , Tester , J.W. , Borghi , G.P. , Trout , B.L. and Am , B.L. 2005 . Properties of inhibitors of methane hydrate formation via molecular dynamics simulations . J. Chem. Soc. , 127 : 17852
   PubMed Web of Science ®Google Scholar
• Kelland , M.A. , Svartaas , T.M. , Ousthus , J. and Namba , T. 2000 . A new class of kinetic hydrate inhibitor . Ann. NY Acad. Sci. , 912 : 281
   Web of Science ®Google Scholar
• Kvamme , B. , Kuznetsova , T. and Aaasoldsen , K. 2005 . Molecular dynamics simulations for selection of kinetic hydrate inhibitors . J. Mol. Graph. Modell. , 23 : 524
   PubMed Web of Science ®Google Scholar
• Smith , W. and Forester , T.R. 1996 . DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package . J. Mol. Graph. , 14 : 136
   PubMedGoogle Scholar
• Hoover , W.G. 1985 . Canonical dynamics: equilibrium phase-space distributions . Phys. Rev. , A31 : 1695
   Web of Science ®Google Scholar
• Allen , M.P. and Tildesley , D.J. 1989 . Computer Simulation of Liquids , Oxford, UK : Clarendon Press .
   Google Scholar
• Rickaert , J.P. , Ciccotti , G. and Berendsen , H.J. 1977 . Numerical-integration of cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes . J. Comput. Phys. , 23 : 327
   Web of Science ®Google Scholar
• Essmann , U.L. , Perera , M.L. , Berkowitz , T. , Darden , H. , Lee , H. and Pedersen , L.G. 1995 . A smooth particle mesh Ewald method . J. Chem. Phys. , 103 : 8577
   Web of Science ®Google Scholar
• Berendsen , H.J. , Grigera , J.R. and Straatsma , T.P. 1987 . The missing term in effective pair potentials . J. Phys. Chem. , 91 : 6269
   Web of Science ®Google Scholar
• Guissani , Y. and Guillot , B. 1993 . A computer-simulation study of the liquid-vapor coexistence curve of water . J. Chem. Phys. , 98 : 8221
   Web of Science ®Google Scholar
• Bellisent-Funel , M.C. , Tassaing , T. , Zhao , H. and Beysens , D. 1997 . The structure of supercritical heavy water as studied by neutron diffraction . J. Chem. Phys. , 107 : 2942
   Web of Science ®Google Scholar
• Jorgensen , W.L. , Maxwell , D.S. and Tirado-Rives , J. 1996 . Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids . J. Am. Chem. Soc. , 118 : 11225
   Web of Science ®Google Scholar
• Rizzo , R.C. and Jorgensen , W.L. 1999 . OPLS all-atom model for amines: Resolution of the amine hydration problem . J. Am. Chem. Soc. , 121 : 4827
   Web of Science ®Google Scholar
• McDonald , N.A. and Jorgensen , W.L. 1998 . Development of an all-atom force field for heterocycles. Properties of liquid pyrrole, furan, diazoles, and oxazoles . J. Phys. Chem. B , 102 : 8049
   Web of Science ®Google Scholar
• Kaminski , G. , Duffy , E.M. , Matsui , T. and Jorgensen , W.L. 1994 . Free-Energies of hydration and pure liquid properties of hydrocarbons from the Opls all-atom model . J. Phys. Chem. , 98 : 13077
   Web of Science ®Google Scholar
• McCallum , J.L. and Tieleman , D.P. 2003 . Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field . J. Comput. Chem. , 24 : 1930
   PubMed Web of Science ®Google Scholar
• Zhang , R. , Li , H. , Lei , Y. and Han , S. 2004 . Different weak C-H center dot center dot O contacts in N-methylacetamide-water system: Molecular dynamics simulations and NMR experimental study . J. Phys. Chem. B , 108 : 12596
   Web of Science ®Google Scholar
• Frisch , M.J. , Trucks , G.W. , Schlegel , H.B. , Scuseria , G.E. , Robb , M.A. , Cheeseman , J.R. , Zakrzewski , V.G. , Montgomery , J.A. , Stratmann , R.E. , Burant , J.C. , Dapprich , S. , Millam , J.M. , Daniels , A.D. , Kudin , K.N. , Strain , M.C. , Farkas , O. , Tomasi , J. , Barone , V. , Cossi , M. , Cammi , R. , Mennucci , B. , Pomelli , C. , Adamo , C. , Clifford , S. , Ochterski , S. , Petersson , G.A. , Ayala , P.I. , Cui , Q. , Morokuma , K. , Salvador , P. , Dannenberg , J.J. , Malick , D.K. , Rabuck , A.D. , Raghavachari , K. , Foresman , J.B. , Cioslowski , J. , Ortiz , J.V. , Baboul , A.G. , Stefanov , B.B. , Liu , G. , Liashenko , A. , Piskorz , P. , Komaromi , I. , Gomperts , R. , Martin , R.L. , Fox , D.J. , Keith , T. , Al-Laham , M.A. , Peng , C.Y. , Nanayakkara , A. , Challacombe , M. , Gill , P.M.W. , Johnson , B. , Chen , W. , Wong , M.W. , Andres , J.L. , Gonzalez , C. , Head-Gordon , M. , Replogle , E.S. and Pople , J.A. 2001 . Gaussian 98 (Revision A.11.3) , Pittsburgh PA : Gaussian, Inc. . 20019
   Google Scholar
• Becke , A.D. 1988 . Density-functional exchange-energy approximation with correct asymptotic-behavior . Phys. Rev. A , 38 : 3098
   PubMed Web of Science ®Google Scholar
• Lee , C. , Yang , W. and Parr , R.G. 1988 . Development of the Colle-Salvetti correlationenergy formula into a functional of the electron density . Phys. Rev. B , 37 : 785
   PubMed Web of Science ®Google Scholar
• Becke , A.D. 1993 . Density-functional thermochemistry .3. The role of exact exchange . J. Chem. Phys. , 98 : 5648
   Web of Science ®Google Scholar
• Besler , B.H. , Merz , K.M. and Kollman , P.A. 1990 . Atomic charges derived from semiempirical methods . J. Comput. Chem. , 11 : 431
   Web of Science ®Google Scholar
• Aparicio-Martínez , S. , Hall , K.R. and Balbuena , P.B. 2006 . Theoretical study on the properties of linear and cyclic amides in gas phase and water solution . J. Phys. Chem. A , 110 : 9183
   PubMed Web of Science ®Google Scholar
• Yeleker , H. , Guven , A. and Ozkan , R. 1999 . Hydrogen bonding and dimeric selfassociation of 2-pyrrolidinone: An ab initio study . J. Comp. Aided. Mol. Des. , 13 : 589
   PubMed Web of Science ®Google Scholar
• Huang , X. , Margulis , C.J. and Berne , B.J. 2003 . Do molecules as small as neopentane induce a hydrophobic response similar to that of large hydrophobic surfaces? . J. Phys. Chem. B , 107 : 11742
   Web of Science ®Google Scholar
• Vishnyakov , A. , Lyubartsev , A.P. and Laaksonen , A. 2001 . Molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixture . J. Phys. Chem. A , 105 : 1702
   Web of Science ®Google Scholar
• García-Martínez , A. , Teso-Villar , E. , García-Fraile , A. and Martínez-Ruiz , P. 2002 . A computational and experimental study on the relative stabilities of cis and trans isomers of N-alkylamides in gas phase and in solution . J. Phys. Chem. A , 106 : 4942
   Web of Science ®Google Scholar
• Radzicka , A. , Pedersen , L. and Wolfenden , R. 1988 . Influences of solvent water on protein folding - free-energies of solvation of cis and trans peptides are nearly identical . Biochemistry , 27 : 4538
   PubMed Web of Science ®Google Scholar
• Nandini , G. and Sathyamarayana , D.N. 2002 . Ab initio studies on geometry and vibrational spectra of N-methyl formamide and N-methylacetamide . J. Mol. Stru. Theochem , 579 : 1
   Web of Science ®Google Scholar
• Wiberg , K.B. and Rush , D.J. 2002 . Methyl rotational barriers in amides and thioamides . J. Org. Chem. , 67 : 826
   PubMed Web of Science ®Google Scholar
• Fantoni , A.C. and Caminati , W. 1996 . Rotational spectrum and ab initio calculations of N-methylformamide . J. Chem. Soc. Faraday Trans. , 92 : 343
   Google Scholar
• Chalmet , S. and Ruiz-Lopez , M.F. 1999 . Molecular dynamics simulation of formamide in water using density functional theory and classical potentials . J. Chem. Phys. , 111 : 1117
   Web of Science ®Google Scholar
• Craw , J.S. , Guest , J.M. , Cooper , M.D. , Burton , N.A. and Hillier , I.H. 1996 . Effect of hydration on the barrier to internal rotation in formamide. Quantum mechanical calculations including explicit solvent and continuum models . J. Phys. Chem. , 100 : 6304
   Web of Science ®Google Scholar
• Gao , J. 1993 . Potential of mean force for the isomerization of Dmf in aqueous-solution - a Monte-Carlo Qm/Mm simulation study . J. Am. Chem. Soc. , 115 : 2930
   Web of Science ®Google Scholar
• Jorgensen , W.L. and Swenson , C.J. 1985 . Optimized intermolecular potential functions for amides and peptides - hydration of amides . J. Am. Chem. Soc. , 107 : 1489
   Web of Science ®Google Scholar
• Soper , A.K. 2000 . The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa . Chem. Phys. , 258 : 121
   Web of Science ®Google Scholar
• Vega , C. , McBride , C. , Sanz , E. and Abascal , J.L.F. 2005 . Radial distribution functions and densities for the SPC/E, TIP4P and TIP5P models for liquid water and ices I-h, I-c, II, III, IV, V, VI, VII, VIII, IX, XI and XII . Phys. Chem. Chem. Phys. , 7 : 1450
   PubMed Web of Science ®Google Scholar
• Ataka , S. , Takeuchi , H. and Tasumi , M. 1984 . Infrared studies of the less stable Cis form of N-methylformamide and N-methylacetamide in low-temperature nitrogen matrices and vibrational analyses of the trans and Cis forms of these molecules . J. Mol. Struct. , 113 : 147
   Web of Science ®Google Scholar
• Mantz , Y.A. , Gerard , H. , Iftimie , R. and Martyna , G.Y. 2004 . Lsomerization of a peptidic fragment studied theoretically in vacuum and in explicit water solvent at finite temperature . J. Am. Chem. Soc. , 126 : 4080
   PubMed Web of Science ®Google Scholar
• Mennucci , B. and Martínez , J.M. 2005 . Insights from a quantum-mechanical and molecular dynamics study of N-methylacetamide. 1. Geometries, infrared, and ultraviolet spectra in water . J. Phys. Chem. B , 109 : 9818
   PubMed Web of Science ®Google Scholar
• Duffy , E.M. , Severance , D.L. and Jorgensen , W.L. 1992 . Solvent effects on the barrier to isomerization for a tertiary amide from ab initio and Monte-Carlo calculations . J. Am. Chem. Soc. , 114 : 7535
   Web of Science ®Google Scholar