Continuum Solvation Models: Classical and Quantum Mechanical Implementations

[1]  M. B. Pinto,et al.  Optimized δ expansion for relativistic nuclear models , 1997, nucl-th/9709049.

[2]  David J. Giesen,et al.  General Semiempirical Quantum Mechanical Solvation Model for Nonpolar Solvation Free Energies. n-Hexadecane , 1995 .

[3]  M. Newton,et al.  The multi-configurational adiabatic electron transfer theory and its invariance under transformations of charge density basis functions , 1994 .

[4]  M. Abraham,et al.  The Honig–Flory–Huggins combinatorial entropy correction—is it valid for aqueous solutions? , 1994 .

[5]  C. Cramer,et al.  Entropic contributions to free energies of solvation , 1994 .

[6]  Christopher J. Cramer,et al.  Use of calculated quantum chemical properties as surrogates for solvatochromic parameters in structure-activity relationships , 1993 .

[7]  A. Warshel,et al.  Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .

[8]  Arieh Ben-Naim,et al.  Size dependence of the solvation free energies of large solutes , 1993 .

[9]  Timothy Clark,et al.  A numerical self-consistent reaction field (SCRF) model for ground and excited states in NDDO-based methods , 1993 .

[10]  Donald G. Truhlar,et al.  Correlation and solvation effects on heterocyclic equilibria in aqueous solution , 1993 .

[11]  Arieh Warshel,et al.  A Quantized Classical Path Approach for Calculations of Quantum Mechanical Rate Constants , 1993 .

[12]  J. Mayoral,et al.  Solvent effects on the mechanism and selectivities of asymmetric Diels-Alder reactions , 1993 .

[13]  George P. Ford,et al.  New approach to the rapid semiempirical calculation of molecular electrostatic potentials based on the am1 wave function: Comparison with ab initio hf/6‐31g* results , 1993, J. Comput. Chem..

[14]  J. Tomasi,et al.  Chemical reactions in solution: modelling of the delay of solvent synchronism (dielectric friction) along the reaction path of an SN2 reaction , 1993 .

[15]  Dan W. Urry,et al.  Molecular Machines: How Motion and Other Functions of Living Organisms Can Result from Reversible Chemical Changes , 1993 .

[16]  Donald G. Truhlar,et al.  Quantum Chemical Conformational Analysis of Glucose in Aqueous Solution , 1993 .

[17]  D. Rinaldi,et al.  Solvent effects on molecular geometries and isomerization processes: a study of push-pull ethylenes in solution , 1993 .

[18]  Jacopo Tomasi,et al.  Nonequilibrium solvation: An ab initio quantum‐mechanical method in the continuum cavity model approximation , 1993 .

[19]  Juan Jesús Pérez,et al.  Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3‐benzazepines for the D1receptor , 1993, J. Comput. Chem..

[20]  Timothy Clark,et al.  Multicenter point charge model for high‐quality molecular electrostatic potentials from AM1 calculations , 1993, J. Comput. Chem..

[21]  Werner Braun,et al.  Minimization of empirical energy functions in proteins including hydrophobic surface area effects , 1993, J. Comput. Chem..

[22]  T. Varnali,et al.  Conformational equilibria of α-substituted carbonyl compounds. Study of solvent effects , 1993 .

[23]  J. Andrew McCammon,et al.  Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation , 1993 .

[24]  F.J.Olivares del Valle,et al.  Solute-solvent interactions , 1993 .

[25]  A Monte Carlo simulation study of the aqueous hydration of d(CGCGCG) in Z form , 1993 .

[26]  R. Leung-Toung,et al.  Tautomeric equilibrium and hydrogen shifts of tetrazole in the gas phase and in solution , 1993 .

[27]  Peter A. Kollman,et al.  Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation , 1993, J. Comput. Chem..

[28]  K. Tasaki,et al.  Observations concerning the treatment of long‐range interactions in molecular dynamics simulations , 1993, J. Comput. Chem..

[29]  Alan R. Katritzky,et al.  Reconsideration of solvent effects calculated by semiempirical quantum chemical methods , 1993, J. Comput. Chem..

[30]  Randy J. Zauhar,et al.  Electrostatic solvent effects on the electronic structure of ground and excited states of molecules: Applications of a cavity model based upon a finite element method , 1993, J. Comput. Chem..

[31]  Kenneth M. Merz,et al.  Rapid approximation to molecular surface area via the use of Boolean logic and look‐up tables , 1993, J. Comput. Chem..

[32]  George R. Famini,et al.  Conformational dependence of the electrostatic potential‐derived charges of dopamine: Ramifications in molecular mechanics force field calculations in the gas phase and in aqueous solution , 1993, J. Comput. Chem..

[33]  Jacopo Tomasi,et al.  On the use of potential derived (PD) atomic charges for the evaluation of solvation free energy , 1993 .

[34]  F.J.Olivares del Valle,et al.  Polarizable continuum model calculations including electron correlation in the ab initio wavefunction , 1993 .

[35]  K. Sharp,et al.  Macroscopic models of aqueous solutions : biological and chemical applications , 1993 .

[36]  Arieh Warshel,et al.  Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs , 1993, J. Comput. Chem..

[37]  Michael J. Holst,et al.  Multigrid solution of the Poisson—Boltzmann equation , 1992, J. Comput. Chem..

[38]  I. Gould,et al.  Modelling of tautomeric equilibria of 5-hydroxyisoxazole in aqueous solution , 1993 .

[39]  F. J. Luque,et al.  Induced dipole moment and atomic charges based on average electrostatic potentials in aqueous solution , 1993 .

[40]  A new method of geometry optimization for molecules in solution in the framework of the Born-Kirkwood-Onsager approach , 1993 .

[41]  A. Klamt,et al.  COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .

[42]  Jean-Louis Rivail,et al.  Reaction field factors for a multipole distribution in a cavity surrounded by a continuum , 1993 .

[43]  Jacopo Tomasi,et al.  Evaluation of dispersion—repulsion contributions to the solvation energy. Calibration of the uniform approximation with the aid of RISM calculations , 1993 .

[44]  J. Tomasi,et al.  Molecular reactivity in solution. Modelling of the effects of the solvent and of its stochastic fluctuation on an SN2 reaction , 1992 .

[45]  E. M. Evleth,et al.  Critical analysis of electric field modeling: Formamide , 1992 .

[46]  George P. Ford,et al.  Incorporation of hydration effects within the semiempirical molecular orbital framework. AM1 and MNDO results for neutral molecules, cations, anions, and reacting systems , 1992 .

[47]  T. Fox,et al.  On the cavity model for solvent shifts of excited states. A critical appraisal , 1992 .

[48]  C. S. Ewig,et al.  Ab Initio computed molecular structures and energies of the conformers of glucose , 1992 .

[49]  William L. Jorgensen,et al.  Effects of hydration on the Claisen rearrangement of allyl vinyl ether from computer simulations , 1992 .

[50]  M. Spackman Molecular Electric Moments from X-Ray Diffraction Data , 1992 .

[51]  I. Tuñón,et al.  Molecular surface area and hydrophobic effect. , 1992, Protein engineering.

[52]  Donald G. Truhlar,et al.  AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution , 1992, J. Comput. Aided Mol. Des..

[53]  B. B. Neto,et al.  Comparative study of atomic charges derived from infrared intensities and from electrostatic potentials using AM1 and MNDO wavefunctions , 1992 .

[54]  Jonathan W. Essex,et al.  Errors in free-energy perturbation calculations due to neglecting the conformational variation of atomic charges , 1992 .

[55]  J. Andrew McCammon,et al.  Solving the finite‐difference non‐linear Poisson–Boltzmann equation , 1992 .

[56]  C. Cramer,et al.  What Causes Aqueous Acceleration of the Claisen Rearrangement , 1992 .

[57]  C.X. Wang,et al.  Improvements on the protein–dipole Langevin–dipole model , 1992 .

[58]  C. Cramer,et al.  PM3‐SM3: A general parameterization for including aqueous solvation effects in the PM3 molecular orbital model , 1992 .

[59]  Gabriel Cuevas,et al.  Recent studies of the anomeric effect , 1992 .

[60]  Donald G. Truhlar,et al.  Polarization of the nucleic acid bases in aqueous solution , 1992 .

[61]  G. R. Famini,et al.  A computational study of solvent effects on the conformation of dopamine , 1992 .

[62]  J. Tomasi,et al.  Methylamines basicity calculations: in vacuo and in solution comparative analysis , 1992 .

[63]  George P. Ford,et al.  Molecular-orbital theory of a solute in a continuum with an arbitrarily shaped boundary represented by finite surface elements , 1992 .

[64]  Ernest R. Davidson,et al.  A test of the Hirshfeld definition of atomic charges and moments , 1992 .

[65]  Arieh Warshel,et al.  A local reaction field method for fast evaluation of long‐range electrostatic interactions in molecular simulations , 1992 .

[66]  H A Scheraga,et al.  Empirical solvation models in the context of conformational energy searches: Application to bovine pancreatic trypsin inhibitor , 1992, Proteins.

[67]  F. J. Luque,et al.  A new strategy for the representation of environment effects in semi-empirical calculations based on Dewar's Hamiltonians , 1992 .

[68]  Mati Karelson,et al.  Theoretical treatment of solvent effects on electronic spectroscopy , 1992 .

[69]  D. Rinaldi,et al.  Fast geometry optimizationin self‐cosistent reaction field computations on solvated molecules , 1992 .

[70]  J. Mccammon,et al.  Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions , 1992 .

[71]  K. Merz,et al.  Analysis of a large data base of electrostatic potential derived atomic charges , 1992 .

[72]  J. Andrew McCammon,et al.  Electrostatic energy calculations by a Finite‐difference method: Rapid calculation of charge–solvent interaction energies , 1992 .

[73]  A. Holtzer The use of flory–huggins theory in interpreting partitioning of solutes between organic liquids and water , 1992, Biopolymers.

[74]  J. Mayoral,et al.  Experimental and theoretical study of the influence of the solvent on asymmetric diels—alder reactions , 1992 .

[75]  C. Cramer,et al.  An SCF Solvation Model for the Hydrophobic Effect and Absolute Free Energies of Aqueous Solvation , 1992, Science.

[76]  Intramolecular electron correlation in the self-consistent reaction field model of solvation. A MP2/6-31G** ab initio study of the NH3HCl complex , 1992 .

[77]  Barry Honig,et al.  A local dielectric constant model for solvation free energies which accounts for solute polarizability , 1992 .

[78]  A. Warshel,et al.  Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. , 1992, Protein engineering.

[79]  T. Fox,et al.  The calculation of solvatochromic shifts: the n-π* transition of acetone , 1992 .

[80]  George P. Ford,et al.  The optimized ellisoidal cavity and its application to the self‐consistent reaction field calculation of hydration energies of cations and neutral molecules , 1992 .

[81]  Arieh Warshel,et al.  Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies , 1992 .

[82]  M. V. Basilevsky,et al.  Quantum-chemical calculations of the hydration energies of organic cations and anions in the framework of a continuum solvent approximation , 1992 .

[83]  D. Chandler,et al.  Free energies of electron transfer , 1992 .

[84]  Kenneth B. Wiberg,et al.  Solvent effects. 3. Tautomeric equilibria of formamide and 2-pyridone in the gas phase and solution: an ab initio SCRF study , 1992 .

[85]  G. Diezemann,et al.  Methyl group dynamics in α-crystallized toluene as studied by deuteron spin-lattice relaxation , 1992 .

[86]  Akbar Nayeem,et al.  MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives , 1992 .

[87]  R. Longo,et al.  Reaction-field–supermolecule approach to calculation of solvent effects , 1992 .

[88]  M. Frisch,et al.  Solvent effects. 2. Medium effect on the structure, energy, charge density, and vibrational frequencies of sulfamic acid , 1992 .

[89]  B. Montgomery Pettitt,et al.  A microscopic view of protein solvation , 1992 .

[90]  M. Vincent,et al.  Tautomeric equilibria in 3- and 5-hydroxyisoxazole in the gas phase and in aqueous solution: a test of molecular dynamics and continuum models of solvation , 1992 .

[91]  Jiali Gao,et al.  Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials , 1992 .

[92]  K. Wiberg,et al.  Hartree–Fock second derivatives and electric field properties in a solvent reaction field: Theory and application , 1991 .

[93]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[94]  H. Berendsen,et al.  The electric potential of a macromolecule in a solvent: A fundamental approach , 1991 .

[95]  Iñaki Tuñón,et al.  GEPOL: An improved description of molecular surfaces II. Computing the molecular area and volume , 1991 .

[96]  B Honig,et al.  Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. , 1991, Biochemistry.

[97]  C. Cramer,et al.  General parameterized SCF model for free energies of solvation in aqueous solution , 1991 .

[98]  C. Cramer,et al.  Molecular orbital theory calculations of aqueous solvation effects on chemical equilibria , 1991 .

[99]  Jacopo Tomasi,et al.  Theoretical chemistry in solution. Some results and perspectives of the continuum methods and in particular of the polarizable continuum model , 1991 .

[100]  J. Tomasi,et al.  Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation , 1991 .

[101]  Peter A. Kollman,et al.  Free energy calculations on the relative solvation free energies of benzene, anisole and 1,2,3-trimethoxybenzene : theoretical and experimental analysis of aromatic methoxy solvation , 1991 .

[102]  Douglas A. Smith,et al.  Molecular modeling of intramolecular hydrogen bonding in simple oligoamides 2. GB/SA CH2Cl2. , 1991 .

[103]  R. Wolfenden,et al.  TESTING THE LIMITS OF PROTEIN-LIGAND BINDING DISCRIMINATION WITH TRANSITION-STATE ANALOGUE INHIBITORS , 1991 .

[104]  Kenneth B. Wiberg,et al.  Solvent effects. 1. The mediation of electrostatic effects by solvents , 1991 .

[105]  J. Tomasi,et al.  The influence of the solvent on the conformational energy differences due to the anomeric effect , 1991 .

[106]  William L. Jorgensen,et al.  OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform , 1991 .

[107]  I. N. Demetropoulos,et al.  A supermolecule study of the effect of hydration on the conformational behaviour of leucine-enkephalin , 1991, J. Comput. Aided Mol. Des..

[108]  Miquel Solà,et al.  Analysis of Solvent Effects on the Menshutkin Reaction , 1991 .

[109]  Peter A. Kollman,et al.  The overlooked bond‐stretching contribution in free energy perturbation calculations , 1991 .

[110]  B. Honig,et al.  A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .

[111]  B. Montgomery Pettitt,et al.  Convergence of the Chemical Potential in Aqueous simulations , 1991 .

[112]  Kim A. Sharp,et al.  Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method , 1991 .

[113]  Peter A. Kollman,et al.  Ion solvation in polarizable water: molecular dynamics simulations , 1991 .

[114]  H. Scheraga,et al.  Empirical solvation models can be used to differentiate native from near‐native conformations of bovine pancreatic trypsin inhibitor , 1991, Proteins.

[115]  A. Goldblum,et al.  A molecular model for an anionic opiate mu-receptor: affinity and activation of morphine conformers. , 1991, European journal of pharmacology.

[116]  Alan R. Katritzky,et al.  AM1 calculations of reaction field effects on the tautomeric equilibria of nucleic acid pyrimidine and purine bases and their 1-methyl analogs , 1991 .

[117]  Jacopo Tomasi,et al.  Electron correlation and solvation effects. I, Basic formulation and preliminary attempt to include the electron correlation in the quantum mechanical polarizable continuum model so as to study solvation phenomena , 1991 .

[118]  Anna Tempczyk,et al.  Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations , 1991 .

[119]  R. Bonaccorsi,et al.  On the ab initio geometry optimization of molecular solutes , 1991 .

[120]  Michael K. Gilson,et al.  The inclusion of electrostatic hydration energies in molecular mechanics calculations , 1991, J. Comput. Aided Mol. Des..

[121]  O. Tapia On the theory of solvent-effect representation , 1991 .

[122]  J. Andrew McCammon,et al.  Free energy difference calculations by thermodynamic integration: Difficulties in obtaining a precise value , 1991 .

[123]  Manuel F. Ruiz-López,et al.  The Self-Consistent Reaction Field Model for Molecular Computations in Solution , 1991 .

[124]  M. Zerner,et al.  GEOMETRY OPTIMISATION AT THE SEMIEMPIRICAL SELF-CONSISTENT-REACTION-FIELD LEVEL USING THE AMPAC AND MOPAC PROGRAMS , 1991 .

[125]  Bruce Tidor,et al.  Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis , 1991 .

[126]  H. Rzepa,et al.  An AM1 and PM3 molecular orbital and self-consistent reaction-field study of the aqueous solvation of glycine, alanine and proline in their neutral and zwitterionic forms , 1991 .

[127]  M. Zerner,et al.  ON THE N-PI BLUE SHIFT ACCOMPANYING SOLVATION , 1990 .

[128]  Jacopo Tomasi,et al.  A computational ab-initio model for the evaluation of thermodynamic functions for solvent transfer processes. , 1990 .

[129]  B. J. Yoon,et al.  A boundary element method for molecular electrostatics with electrolyte effects , 1990 .

[130]  Estanislao Silla,et al.  GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set , 1990 .

[131]  J. Kroon,et al.  Hydrogen-bond geometry around sugar molecules: comparison of crystal statistics with simulated aqueous solutions☆ , 1990 .

[132]  Ignacio Tinoco,et al.  Dna Dynamics in Aqueous Solution: Opening the Double Helix , 1990, Int. J. High Perform. Comput. Appl..

[133]  Wolfgang Heiden,et al.  Triangulation algorithms for the representation of molecular surface properties , 1990, J. Comput. Aided Mol. Des..

[134]  K. Dill Dominant forces in protein folding. , 1990, Biochemistry.

[135]  Peter A. Kollman,et al.  Computer modeling of the interactions of complex molecules , 1990 .

[136]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[137]  Jan Kroon,et al.  Solvent effect on the conformation of the hydroxymethyl group established by molecular dynamics simulations of methyl‐β‐D‐glucoside in water , 1990 .

[138]  Jacopo Tomasi,et al.  Theoretical determination of the gibbs energy of solution and transfer between immiscible solvents, with comments on the dynamics of phase transfer , 1990 .

[139]  Rebecca C. Wade Solvation of the active site of cytochrome P450-cam , 1990, J. Comput. Aided Mol. Des..

[140]  R. Bonaccorsi,et al.  Influence of a liquid-liquid phase boundary on the energetics of a molecular solute , 1990 .

[141]  G. Chang,et al.  Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics , 1990 .

[142]  P. Kollman,et al.  Atomic charges derived from semiempirical methods , 1990 .

[143]  Malcolm E. Davis,et al.  Electrostatics in biomolecular structure and dynamics , 1990 .

[144]  Benoît Roux,et al.  Molecular basis for the Born model of ion solvation , 1990 .

[145]  K. Dill,et al.  Partitioning of nonpolar solutes into bilayers and amorphous n-alkanes [Erratum to document cited in CA112(8):63160d] , 1990 .

[146]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[147]  R. Longo,et al.  Adenine–Thymine proton relay: Electric field and environmental effects on point mutation DNA , 1990 .

[148]  Alexander A. Rashin,et al.  Hydration phenomena, classical electrostatics, and the boundary element method , 1990 .

[149]  O. Tapia,et al.  Generalized self-consistent reaction field theory in a multicenter-multipole ab-initio LCGO framework. I. Electronic properties of the water molecule in a Monte Carlo sample of liquid water molecules studied with standard basis sets , 1990 .

[150]  M. Zerner,et al.  A theoretical treatment of solvent effects on the tautomeric equilibria of five-membered rings with two heteroatoms , 1990 .

[151]  M. Zerner,et al.  Reaction field effects on the electronic structure of carbon radical and ionic centers , 1990 .

[152]  K. Dill,et al.  Partitioning of nonpolar solutes into bilayers and amorphous n-alkanes , 1990 .

[153]  Jacopo Tomasi,et al.  An appraisal of solvation effects on chemical functional groups: The amidic and the esteric linkages , 1990 .

[154]  K. Sharp,et al.  Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.

[155]  Alan R. Katritzky,et al.  Quantitative predictions of tautomeric equilibria for 2-, 3-, and 4-substituted pyridines in both the gas phase and aqueous solution: combination of AM1 with reaction field theory , 1989 .

[156]  G. Vriend,et al.  A very fast program for visualizing protein surfaces, channels and cavities. , 1989, Journal of molecular graphics.

[157]  Jerzy Cioslowski,et al.  A new population analysis based on atomic polar tensors , 1989 .

[158]  Arieh Warshel,et al.  A surface constrained all‐atom solvent model for effective simulations of polar solutions , 1989 .

[159]  S. Creighton,et al.  Enzymes work by solvation substitution rather than by desolvation. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[160]  Heinrich R. Karfunkel,et al.  An algorithm for the representation and computation of supermolecular surfaces and volumes , 1989 .

[161]  Jacopo Tomasi,et al.  Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation , 1989 .

[162]  E. Huque The hydrophobic effect , 1989 .

[163]  W. L. Jorgensen Free energy calculations: a breakthrough for modeling organic chemistry in solution , 1989 .

[164]  Bhyravabhotla Jayaram,et al.  Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations , 1989 .

[165]  B Jayaram,et al.  The electrostatic potential of B‐DNA , 1989, Biopolymers.

[166]  Donald G. Truhlar,et al.  Generalized born fragment charge model for solvation effects as a function of reaction coordinate , 1989 .

[167]  J. A. McCammon,et al.  Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods , 1989 .

[168]  Kenji Morihashi,et al.  MNDO-effective charge model study of solvent effect on the potential energy surface of the SN2 reaction , 1989 .

[169]  J. Stewart Optimization of parameters for semiempirical methods II. Applications , 1989 .

[170]  J. Stewart Optimization of parameters for semiempirical methods I. Method , 1989 .

[171]  M. Aguilar,et al.  Solute-solvent interactions. a simple procedure for constructing the solvent cavity for retaining a molecular solute , 1989 .

[172]  A. Laaksonen,et al.  Molecular dynamics simulation of double helix Z-DNA in solution , 1989 .

[173]  M. Dewar,et al.  Mechanism of the Claisen rearrangement of allyl vinyl ethers , 1989 .

[174]  J. Rivail Solvent Effects on Potential Energy Surfaces and Chemical Kinetics , 1989 .

[175]  Alan R. Katritzky,et al.  M. O. calculations applicable to condensed phases: The combination of self-consistent reaction field theory with semi-empirical quantum-chemical methods , 1989 .

[176]  S. Harvey Treatment of electrostatic effects in macromolecular modeling , 1989, Proteins.

[177]  M Karplus,et al.  A molecular dynamics analysis of protein structural elements , 1989, Proteins.

[178]  D. Beveridge,et al.  Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.

[179]  R. Bonaccorsi,et al.  A preliminary report on a quantum-mechanical model for the energetics of a solute at the surface separating two immiscible liquid phases , 1989 .

[180]  Haruki Nakamura,et al.  Numerical Calculations of Reaction Fields of Protein-Solvent Systems , 1988 .

[181]  S. Miertus,et al.  The extended polarizable continuum model for calculation of solvent effects , 1988 .

[182]  M. Karplus,et al.  Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. A theoretical analysis. , 1988, Journal of molecular biology.

[183]  L. Curtiss,et al.  Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint , 1988 .

[184]  Trygve Helgaker,et al.  A multiconfigurational self‐consistent reaction‐field method , 1988 .

[185]  Martin Karplus,et al.  A thermodynamic analysis of solvation , 1988 .

[186]  J. Palca,et al.  NIH speeds to resolve charges of scientific error , 1988, Nature.

[187]  A. Fersht,et al.  Contribution of hydrophobic interactions to protein stability , 1988, Nature.

[188]  K. Sharp,et al.  Calculating the electrostatic potential of molecules in solution: Method and error assessment , 1988 .

[189]  M. Drummond A supertensor formalism for solute–continuum solvent interactions with an arbitrarily shaped cavity. II. Preliminary applications to model systems , 1988 .

[190]  A. Rashin Continuum electrostatics and hydration phenomena , 1988 .

[191]  R. Levy,et al.  Viewing the born model for ion hydration through a microscope , 1988 .

[192]  R. Zauhar,et al.  The rigorous computation of the molecular electric potential , 1988 .

[193]  Andrew Komornicki,et al.  Transition structures for the Claisen rearrangement , 1988 .

[194]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[195]  W. C. Still,et al.  A rapid approximation to the solvent accessible surface areas of atoms , 1988 .

[196]  B. Honig,et al.  Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.

[197]  M K Gilson,et al.  Energetics of charge–charge interactions in proteins , 1988, Proteins.

[198]  Alexander A. Rashin,et al.  A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes , 1987 .

[199]  Jacopo Tomasi,et al.  Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution. , 1987 .

[200]  Minoru Sakurai,et al.  Medium effects on the molecular electronic structure. I. The formulation of a theory for the estimation of a molecular electronic structure surrounded by an anisotropic medium , 1987 .

[201]  H. Scheraga,et al.  Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[202]  P. A. Bash,et al.  Free energy calculations by computer simulation. , 1987, Science.

[203]  B. D. Rogers,et al.  Synthesis and Claisen rearrangement of alkoxyallyl enol ethers. Evidence for a dipolar transition state , 1987 .

[204]  B. Ganem,et al.  The mechanism of rearrangement of chorismic acid and related compounds , 1987 .

[205]  Ralph G. Pearson,et al.  Ionization potentials and electron affinities in aqueous solution , 1986 .

[206]  Lennart Nilsson,et al.  Empirical energy functions for energy minimization and dynamics of nucleic acids , 1986 .

[207]  J. Warwicker,et al.  Continuum dielectric modelling of the protein-solvent system, and calculation of the long-range electrostatic field of the enzyme phosphoglycerate mutase. , 1986, Journal of theoretical biology.

[208]  R. Bonaccorsi,et al.  Structural deformations of the DNA double helix in the first stages of DNA transcription studied with a simple model , 1986 .

[209]  A. Y. Meyer Molecular mechanics and molecular shape. III. Surface area and cross‐sectional areas of organic molecules , 1986, Journal of computational chemistry.

[210]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[211]  M. Zerner,et al.  Reaction field effects on the electron distribution and chemical reactivity of molecules , 1986 .

[212]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[213]  Barry Honig,et al.  Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification , 1986, Proteins.

[214]  N. K. Rogers,et al.  The modelling of electrostatic interactions in the function of globular proteins. , 1986, Progress in biophysics and molecular biology.

[215]  R. Zauhar,et al.  A new method for computing the macromolecular electric potential. , 1985, Journal of molecular biology.

[216]  F. Richards,et al.  Electrostatic field of the large fragment of Escherichia coli DNA polymerase I. , 1985, Journal of molecular biology.

[217]  Barry Honig,et al.  Reevaluation of the Born model of ion hydration , 1985 .

[218]  G L Seibel,et al.  A molecular dynamics simulation of double-helical B-DNA including counterions and water. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[219]  G. Rose,et al.  Hydrophobicity of amino acid residues in globular proteins. , 1985, Science.

[220]  F. Weinhold,et al.  Natural population analysis , 1985 .

[221]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[222]  William L. Jorgensen,et al.  Energy profile for a nonconcerted SN2 reaction in solution , 1985 .

[223]  M. Sternberg,et al.  Electrostatic interactions in globular proteins: calculation of the pH dependence of the redox potential of cytochrome c551. , 1985, Journal of molecular biology.

[224]  Michael L. Connolly,et al.  Computation of molecular volume , 1985 .

[225]  D. Rinaldi,et al.  Liquid state quantum chemistry : A cavity model , 1985 .

[226]  Amatzya Y. Meyer,et al.  Molecular mechanics and molecular shape. Part 1. van der Waals descriptors of simple molecules , 1985 .

[227]  Eamonn F. Healy,et al.  Ground states of molecules. 68. MNDO study of the Claisen rearrangement , 1984 .

[228]  István Mayer,et al.  Comments on the quantum theory of valence and bonding: Choosing between alternative definitions , 1984 .

[229]  T. Richmond,et al.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.

[230]  Michael J. E. Sternberg,et al.  Regular representation of irregular charge distributions , 1984 .

[231]  A. Warshel,et al.  Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[232]  M J Sternberg,et al.  Electrostatic interactions in globular proteins. Different dielectric models applied to the packing of alpha-helices. , 1984, Journal of molecular biology.

[233]  R. Constanciel,et al.  Self consistent field theory of solvent effects representation by continuum models: Introduction of desolvation contribution , 1984 .

[234]  R. Contreras,et al.  Proton transfer in water polymers as a model for intime and solvent-separated ion pairs , 1984 .

[235]  R. K. Hill 8 – Chirality Transfer via Sigmatropic Rearrangements , 1984 .

[236]  R. Bonaccorsi,et al.  Ab initio evaluation of absorption and emission transitions for molecular solutes, including separate consideration of orientational and inductive solvent effects , 1983 .

[237]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[238]  M. L. Connolly Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[239]  István Mayer,et al.  Charge, bond order and valence in the AB initio SCF theory , 1983 .

[240]  Manuel F. Ruiz-López,et al.  Ab initio SCF calculations on electrostatically solvated molecules using a deformable three axes ellipsoidal cavity , 1983 .

[241]  J. Warwicker,et al.  Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. , 1982, Journal of molecular biology.

[242]  P. Claverie Intermolecular Interactions and Solvent Effects: Simplified Theoretical Methods , 1982 .

[243]  Jean-Louis Rivail,et al.  Énergie libre d’une distribution de charges électriques séparée d’un milieu diélectrique infini par une cavité ellipsoïdale quelconque, application à l’étude de la solvation des molécules , 1982 .

[244]  Anthony J. Stone,et al.  Distributed multipole analysis, or how to describe a molecular charge distribution , 1981 .

[245]  Vincenzo Mollica,et al.  Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution , 1981 .

[246]  J. Tomasi,et al.  Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .

[247]  H. Scheraga,et al.  Effect of protein-solvent interactions on protein conformation. , 1981, Annual review of biophysics and bioengineering.

[248]  O. Tapia,et al.  Solvent effects on the structure and the electronic properties of simple molecules. A MINDO/3-SCRF-MO study , 1980 .

[249]  G. Klopman,et al.  Solvatons. II. Aqueous dissociation of hydrides in the MINDOS approximation , 1980 .

[250]  O. Tapia,et al.  Local Field Representation of Surrounding Medium Effects. From Liquid Solvent to Protein Core Effects , 1980 .

[251]  Arieh Warshel,et al.  Calculations of chemical processes in solutions , 1979 .

[252]  O. Tapia Some remarks on the SCRF theory of solvent effects and the calculation of proton potentials , 1978 .

[253]  O. Tapia,et al.  Environmental effects on H-bond potentials: A SCRF MO CNDO/2 study of some model systems. , 1978, Journal of theoretical biology.

[254]  R. Wolfenden,et al.  Interaction of the peptide bond with solvent water: a vapor phase analysis. , 1978, Biochemistry.

[255]  Dj McLennan,et al.  Semi-empirical calculation of rates of SN2 Finkelstein reactions in solution by a quasi-thermodynamic cycle , 1978 .

[256]  C. Herrmann,et al.  Theoretical study of the shifts of electronic spectra from solute-solvent interaction , 1977 .

[257]  G. S. Manning Limiting laws and counterion condensation in polyelectrolyte solutions. IV. The approach to the limit and the extraordinary stability of the charge fraction. , 1977, Biophysical chemistry.

[258]  Walter Thiel,et al.  Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .

[259]  F. L. Hirshfeld Bonded-atom fragments for describing molecular charge densities , 1977 .

[260]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[261]  Peter Beak,et al.  Energies and alkylations of tautomeric heterocyclic compounds: old problems - new answers , 1977 .

[262]  Jean-Louis Rivail,et al.  A quantum chemical approach to dielectric solvent effects in molecular liquids , 1976 .

[263]  G. G. Hall,et al.  The development of quantum mechanical solvent effect models. Macroscopic electrostatic contributions , 1976 .

[264]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[265]  Samuel H. Yalkowsky,et al.  Solubility of nonelectrolytes in polar solvents. VI. Refinements in molecular surface area computations , 1976 .

[266]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[267]  Orlando Tapia,et al.  Self-consistent reaction field theory of solvent effects , 1975 .

[268]  Harold L. Friedman,et al.  Image approximation to the reaction field , 1975 .

[269]  Samuel H. Yalkowsky,et al.  Solubility of nonelectrolytes in polar solvents. V. Estimation of the solubility of aliphatic monofunctional compounds in water using a molecular surface area approach , 1975 .

[270]  C. Tanford,et al.  Empirical correlation between hydrophobic free energy and aqueous cavity surface area. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[271]  J. I. Brauman,et al.  GAS-PHASE NUCLEOPHILIC DISPLACEMENT REACTIONS , 1974 .

[272]  A. Shrake,et al.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.

[273]  Michael C. Zerner,et al.  An intermediate neglect of differential overlap technique for spectroscopy: Pyrrole and the azines , 1973 .

[274]  James J. P. Stewart,et al.  Bond indices and valency , 1973 .

[275]  Robert B. Hermann,et al.  Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area , 1972 .

[276]  P. Claverie,et al.  Calculation of the interaction energy of one molecule with its whole surrounding. I. Method and application to pure nonpolar compounds , 1972 .

[277]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[278]  Paul J. Flory,et al.  Fifteenth Spiers Memorial Lecture. Thermodynamics of polymer solutions , 1970 .

[279]  J. Pople,et al.  Approximate Self‐Consistent Molecular‐Orbital Theory. V. Intermediate Neglect of Differential Overlap , 1967 .

[280]  G. Klopman Solvations: a semi-empirical procedure for including solvation in quantum mechanical calculations of large molecules , 1967 .

[281]  P. Flory,et al.  Treatment of Liquid-Liquid Phase Equilibria. Hydrocarbon-Perfluorocarbon Mixtures , 1966 .

[282]  J. Pople,et al.  Approximate Self‐Consistent Molecular Orbital Theory. II. Calculations with Complete Neglect of Differential Overlap , 1965 .

[283]  P. Flory Statistical Thermodynamics of Liquid Mixtures , 1965 .

[284]  P. Flory,et al.  The Thermodynamic Properties of Mixtures of Small, Nonpolar Molecules , 1965 .

[285]  G. Klopman,et al.  A semiempirical treatment of molecular structures. II. Molecular terms and application to diatomic molecules , 1964 .

[286]  A. Bondi van der Waals Volumes and Radii , 1964 .

[287]  R. Pierotti,et al.  THE SOLUBILITY OF GASES IN LIQUIDS1 , 1963 .

[288]  Harold A. Scheraga,et al.  Structure of Water and Hydrophobic Bonding in Proteins. II. Model for the Thermodynamic Properties of Aqueous Solutions of Hydrocarbons , 1962 .

[289]  J. Jortner Dielectric medium effects on loosely bound electrons , 1962 .

[290]  Rudolph A. Marcus,et al.  On the Theory of Oxidation‐Reduction Reactions Involving Electron Transfer. I , 1956 .

[291]  W. P. Weijland,et al.  Reduction potentials of various aromatic hydrocarbons and their univalent anions , 1956 .

[292]  R. S. Mulliken Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[293]  H. C. Longuet-Higgins Solutions of chain molecules—A new statistical theory , 1953 .

[294]  M. Huggins The effect of size, shape, and flexibility of the solute molecules on the properties of colloidal solutions. , 1948, The Journal of physical and colloid chemistry.

[295]  H. C. Longuet-Higgins,et al.  The electronic structure of conjugated systems I. General theory , 1947, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[296]  Joel H. Hildebrand,et al.  The Entropy of Solution of Molecules of Different Size , 1947 .

[297]  P. Flory Thermodynamics of Dilute Solutions of High Polymers , 1945 .

[298]  M. Huggins Some Properties of Solutions of Long-chain Compounds. , 1942 .

[299]  P. Flory Thermodynamics of High Polymer Solutions , 1941 .

[300]  Isidor Kirshenbaum,et al.  The Vapor Pressure and Heat of Vaporization of N15 , 1941 .

[301]  M. Huggins Solutions of Long Chain Compounds , 1941 .

[302]  Kenneth S. Pitzer,et al.  The Free Energy of Hydration of Gaseous Ions, and the Absolute Potential of the Normal Calomel Electrode , 1939 .

[303]  L. Onsager Electric Moments of Molecules in Liquids , 1936 .

[304]  Robert S. Mulliken,et al.  Electronic Structures of Molecules X. Aldehydes, Ketones and Related Molecules , 1935 .

[305]  J. Kirkwood,et al.  Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions , 1934 .

[306]  Lars Onsager,et al.  Theories of Concentrated Electrolytes. , 1933 .

[307]  M. Born Volumen und Hydratationswärme der Ionen , 1920 .