A CFF 91-based Continuum Solvation Model: Solvation Free Energies of Small Organic Molecules and Conformations of the Alanine Dipeptide in Solution

References

• Warshel , A. and Russel , S. 1984 . Calculation of electrostatic interactions in biological systems and in solution . Quart. Rev. Biophys. , 17 : 283
   PubMed Web of Science ®Google Scholar
• Beveridge , D. L. and DiCapua , F. M. 1989 . Free energy via molecular simulation: applications to chemical and biomolecular systems . Annu. Rev. Biophys. Chem. , 18 : 431
   PubMedGoogle Scholar
• Straatsma , T. P. and McCammon , J. A. 1992 . Computational Alchemy . Annu. Rev. Phys. Chem. , 43 : 407
   Web of Science ®Google Scholar
• Rashin , A. A. 1993 . Aspects of protein energetics and dynamics . Progr. Biophys. Mol. Biol. , 60 : 73
   PubMed Web of Science ®Google Scholar
• Miertus , S. , Scrocco , E. and Tomasi , J. 1981 . Electrostatic interaction of a solute with continuum. A direct utilitization of ab initio molecular potentials for the prevision of solvent effects . Chem. Phys. , 55 : 117
   Web of Science ®Google Scholar
• Field , M. J. , Bash , P. A. and Karplus , M. 1990 . A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations . J. Comput. Chem. , 11 : 700
   Web of Science ®Google Scholar
• Gao , J. , Luque , F. J. and Orozco , M. 1993 . Induced dipole moment and atomic charges based on average electrostatic potentials in aqueous solutions . J. Chem. Phys. , 98 : 2975
   Web of Science ®Google Scholar
• Ford , G. P. and Wang , B. 1992 . Incorporation of hydration effects within the semiempirical molecular orbital framework. AM1 and MNDO results for neutral molecules, cations, anions, and reacting systems . J. Amer. Chem. Soc. , 114 : 10563
   Web of Science ®Google Scholar
• Baldridge , K. , Fine , R. and Hagler , A. J. Comput. Chem. , (in press)
   Google Scholar
• Rashin , A. , Bukatin , M. , Andzelm , J. and Hagler , A. Biophysical Chemistry , (in press)
   Google Scholar
• Bom , M. 1920 . Volumes and heats of hydration of ions . Z. Phys. , 1 : 45
   Google Scholar
• Tanford , C. and Kirkwood , J. G. 1957 . Theory of protein titration curves. I. General equations for impenetrable spheres . J. Amer. Chem. Soc. , 79 : 5333
   Web of Science ®Google Scholar
• Gilson , M. K. , Rashin , A. , Fine , R. and Honig , B. 1985 . On the calculation of electrostatic interactions in proteins . J. Mot. Biol. , 183 : 503
   PubMed Web of Science ®Google Scholar
• Warwicker , J. and Watson , H. C. 1982 . Calculation of the electric potential in the active cleft due to α-Helix dipoles . J. Mol. Biol. , 157 : 671
   PubMed Web of Science ®Google Scholar
• Klapper , I. , Hangstrom , R. , Fine , R. , Sharp , K. and Honig , B. 1986 . Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino acid modification . Proteins , 1 : 47
   PubMedGoogle Scholar
• Gilson , M. K. , Sharp , K. A. and Honig , B. 1987 . Calculating the electrostatic potential of molecules in solution: Method and errors assessment . J. Comp. Chem. , 9 : 327
   Web of Science ®Google Scholar
• Nicholls , A. and Honig , B. 1991 . A Rapid Finite Difference Algorithm, Utilizing Successive Over-Relaxation to Solve the Poisson-Boltzmann Equation . J. Comp. Chem. , 12 : 435
   Web of Science ®Google Scholar
• Sharp , K. , Jean-Charles , A. and Honig , B. 1992 . A local dielectric constant model for solvation free energies which accounts for solute polarizability . J. Phys. Chem. , 96 : 3822
   Web of Science ®Google Scholar
• Davis , M. E. and McCammon , J. A. 1990 . Electrostatics in Biomolecular Structure and Dynamics . Chem. Rev. , 10 : 386
   Google Scholar
• Rashin , A. A. 1989 . Hydration phenomena, classical electrostatics, and the boundary element method . J. Phys. Chem. , 93 : 4664
   Google Scholar
• Juffer , A. H. , Botta , E. F.F. , van Keulen , B. A.M. , van der Ploeg , A. and Berendsen , H. J.C. 1991 . The electric potential of a macromolecule in a solvent: a fundamental approach . J. Comp. Phys. , 97 : 144
   Web of Science ®Google Scholar
• Zauhar , R. J. and Morgan , R. S. 1988 . The rigorous computation of the molecular electric potential . J. Comp. Chem. , 9 : 171
   Web of Science ®Google Scholar
• You , T. J. and Harvey , S. C. 1993 . Finite element approach to the electrostatics of the macromolecules with arbitrary geometries . J. Comp. Chem. , 14 : 484
   Web of Science ®Google Scholar
• Still , W. C. , Tempczyk , A. , Hawley , R. C. and Hendrickson , T. 1990 . Semianalytical treatment of solvation for molecular mechanics and dynamics . J. Amer. Chem. Soc. , 112 : 6129
   Web of Science ®Google Scholar
• Cabani , S. , Gianni , P. , Mollica , V. and Lepori , L. 1981 . Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution . J. Solution Chem. , 10 : 563
   Web of Science ®Google Scholar
• Ben-Naim , A. and Marcus , Y. 1984 . Solvation thermodynamics of nonionic solutions . J. Chem. Phys. , 81 : 2016
   Web of Science ®Google Scholar
• Radzicka , A. and Wolfenden , R. 1988 . Comparing the polarities of the amino acids: side chain distribution coefficients betweenthe vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution . Biochemistry , 27 : 1664
   Web of Science ®Google Scholar
• Tanford , C. H. 1980 . The Hydrophobic Effect , NY : Wiley .
   Google Scholar
• Ben-Naim , A. 1987 . Solvation Thermodynamics , NY : Plenum Press .
   Google Scholar
• Cramer , C. J. and Truhlar , D. G. 1992 . AM1-SM2 and PM3-SM3 parametrized SCF solvation models for free energies in aqueous solution . J. Comput.-Aided Mol. Des. , 6 : 629
   PubMed Web of Science ®Google Scholar
• Sitkoff , D. , Sharp , K. A. and Honig , B. 1994 . Accurate calculation of hydration free energies using macroscopic solvent models . J. Phys. Chem. , 98 : 1978
   Web of Science ®Google Scholar
• Shrake , A. and Rupley , J. A. 1973 . Environment and exposure to solvent of protein atoms. Lisozyme and insuline . J. Molec. Biol. , 79 : 351
   PubMed Web of Science ®Google Scholar
• Richards , F. M. 1977 . Areas, volumes, packing, and protein structure . Ann. Rev. Biophys. Bioeng. , 6 : 151
   PubMedGoogle Scholar
• Ben-Naim , A. and Mazo , R. M. 1993 . Size dependence of the solvation energies of large solutes . J. Phys. Chem. , 97 : 10829
   Web of Science ®Google Scholar
• Schmidt , A. B. Excluded volume effect in solvation thermodynamics: simple Lennard-Jones model . Biophys Chem , (in press)
   Web of Science ®Google Scholar
• Wesson , L. and Eisenberg , D. 1992 . Atomic solvation parameters applied to molecular dynamics of proteins in solution . Protein Science , 1 : 227
   PubMed Web of Science ®Google Scholar
• Schiffer , C. A. , Caldwell , J. W. , Collman , P. A. and Stroud , R. M. 1993 . Protein structure prediction with a combined solvation free energy-molecular mechanics force field . Molecular Simulaton , 10 : 121
   Web of Science ®Google Scholar
• 1993 . DISCOVER User Guide , 92121 San Diego, CA : Biosym Technologies .
   Google Scholar
• Jackson , J. D. 1962 . Classical Electrodynamics , NY : Wiley .
   Google Scholar
• Bottcher , C. J.F. 1973 . Theory of Electric Polarization, , 2nd ed. , NY : Elsevier .
   Google Scholar
• Nicholls , A. and Honig , B. (unpublished results)
   Google Scholar
• Meyer , A. Y. 1988 . Molecular mechanics and molecular shape. V. On the computation of the bare surface area of molecules . J. Comp. Chem. , 9 : 18
   Web of Science ®Google Scholar
• Hagler , A. T. , Osguthorpe , D. J. and Robson , B. 1980 . Monte Carlo simulation of water behavior around the dipeptide N-acetylalanyl-N-nethylamide . Science , 208 : 599
   PubMed Web of Science ®Google Scholar
• Mezei , M. , Mehotra , P. K. and Beveridge , D. L. 1985 . Monte Carlo determination of the free energy and internal energy of hydration for Ala dipeptide at 25 C . J. Amer. Chem. Soc. , 107 : 2239
   Web of Science ®Google Scholar
• Pettitt , B. M. and Karplus , M. 1985 . The potential of mean force surface for the alanine dipeptide in aqueous solution: a theoretical approach . Chem. Phys. Lett. , 121 : 94
   Web of Science ®Google Scholar
• Anderson , A. G. and Hermans , J. 1988 . Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations . Proteins , 3 : 262
   PubMed Web of Science ®Google Scholar
• Lazaridis , T. , Tobias , D. J. , Brooks , C. L. III and Paulaitis , M. E. 1991 . Reaction paths and free energy profiles for conformational transitions . J. Chem. Phys. , 95 : 7612
   Web of Science ®Google Scholar
• Smith , P. E. , Pettitt , B. M. and Karplus , M. 1993 . Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potentialenergy surface . J. Phys. Chem. , 97 : 6907
   Web of Science ®Google Scholar
• Head-Gordon , T. , Head-Gordon , M. , Frisch , M. J. , Brooks , C. L. III and Pople , J. A. 1991 . Theoretical study of blocked glycine and alanine peptide analogues . J. Amer. Chem. Soc. , 113 : 5989
   Web of Science ®Google Scholar
• Bohm , H.-J. and Brode , S. 1991 . Ab initio SCF calculations on low-energy conformers of N-acetyl-N-methylalaninamide and N-acetyl-N-methylglycinamide . J. Amer. Chem. Soc. , 113 : 7129
   Web of Science ®Google Scholar
• Avignon , M. , Garrigou-Lagrange , C. and Bothorel , P. 1973 . Conformational analysis of dipeptides in aqueous solution. II. Molecular structure of lycine and alanine dipeptides by depolarized Rayleigh scattering and laser Raman spectroscopy . Biopolymers , 12 : 1651
   PubMed Web of Science ®Google Scholar
• Madison , V. and Kopple , K. D. 1980 . Solvent-dependent conformational distributions of some peptides . J. Amer. Chem. Soc. , 102 : 4855
   Web of Science ®Google Scholar
• Wiberg , K. B. and Rablen , P. R. 1993 . Comparison of atomic charges derived via different procedures . J. Comp. Chem. , 14 : 1504
   Web of Science ®Google Scholar
• Chipot , C. , Angyan , J. G. , Ferenczy , G. G. and Scheraga , H. A. 1993 . Transferable net atomic charges from a distributed multipole analysis for the description of electrostatic properties. A case study of saturated hydrocarbons . J. Phys. Chem. , 97 : 6628
   Web of Science ®Google Scholar
• Chipot , C. , Maigret , B. , Rivail , J.-L. and Scheraga , H. A. 1992 . Modelling amino acid side chains. 1. Determination of net atomic charges from ab initio self-consistent-field molecular electrostatic properties . J. Phys. Chem. , 96 : 10276
   Web of Science ®Google Scholar
• 1992 . J. Phys. Chem. , 96 : 10276
   Web of Science ®Google Scholar
• Hermann , R. B. 1977 . Use of solvent cavity area and number of packed solvent molecules around a solute in regard to hydrocarbon solubility and hydrophobic interactions . Proc. Natl. Acad. Sci. USA , 74 : 4144
   PubMed Web of Science ®Google Scholar
• Sharp , K. A. , Nicholls , A. , Fine , R. M. and Honig , B. 1992 . Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects . Science , 252 : 106
   Web of Science ®Google Scholar
• Nicholls , A. , Sharp , K. A. and Honig , B. 1991 . Protein folding and association: insights from interfacial and thermodynamic properties of hydrocarbones . Proteins , 11 : 281
   PubMed Web of Science ®Google Scholar
• Gilson , M. , Davis , M. , Luty , B. and McCammon , J. A. 1993 . Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation . J. Phys. Chem. , 97 : 3591
   Web of Science ®Google Scholar