Free Energy Changes in Solution

[1]  Alexander Tropsha,et al.  Energetic decomposition of the α-helix-coil equilibrium of a dynamic model system , 1998 .

[2]  W. L. Jorgensen,et al.  ELUCIDATION OF TRANSITION STRUCTURES AND SOLVENT EFFECTS FOR EPOXIDATION BY DIMETHYLDIOXIRANE , 1997 .

[3]  M L Lamb,et al.  Computational approaches to molecular recognition. , 1997, Current opinion in chemical biology.

[4]  W. L. Jorgensen,et al.  Computational Investigations of Carbenium Ion Reactions Relevant to Sterol Biosynthesis , 1997 .

[5]  Charles L. Brooks,et al.  A reexamination of the hydrophobic effect: Exploring the role of the solvent model in computing the methane–methane potential of mean force , 1997 .

[6]  W. L. Jorgensen,et al.  Energetics of Cation-Olefin Addition in the Gas Phase and in Solution , 1997 .

[7]  J. Fraser Stoddart,et al.  π–π INTERACTIONS IN SELF‐ASSEMBLY , 1997 .

[8]  Peter A. Kollman,et al.  Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes , 1997, J. Comput. Chem..

[9]  J. Briggs,et al.  Absolute Configuration of Bromochlorofluoromethane from Molecular Dynamics Simulation of Its Enantioselective Complexation by Cryptophane-C , 1997 .

[10]  F. V. Veggel.  Molecular Dynamics and FEP Monte Carlo Studies of Calix[4]arene-Derived Complexes of Eu3+: The Role of the Counterions Investigated , 1997 .

[11]  M. Gilson,et al.  The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.

[12]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[13]  Peter A. Kollman,et al.  Benzene Dimer: A Good Model for π−π Interactions in Proteins? A Comparison between the Benzene and the Toluene Dimers in the Gas Phase and in an Aqueous Solution , 1996 .

[14]  W. L. Jorgensen,et al.  SCRF/Monte Carlo Study of Solvent Effects on a Polar [2+2] Cycloaddition , 1996 .

[15]  P. Kollman.  Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules , 1996 .

[16]  W. L. Jorgensen,et al.  Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate Rearrangement , 1996 .

[17]  T. Furlani,et al.  Hydrophobic and Hydrogen-Bonding Effects on the Rate of Diels−Alder Reactions in Aqueous Solution , 1996 .

[18]  F. J. Luque,et al.  TAUTOMERISM AND PROTONATION OF GUANINE AND CYTOSINE. IMPLICATIONS IN THE FORMATION OF HYDROGEN-BONDED COMPLEXES , 1996 .

[19]  Francesc X. Avilés,et al.  Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions , 1996 .

[20]  P. Kollman,et al.  Application of Free Energy Perturbation Calculations to the “Tennis Ball” Dimer: Why Is CF4 Not Encapsulated by This Host? , 1996 .

[21]  Alan E. Mark,et al.  Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State , 1996 .

[22]  Bruce Ganem,et al.  The Mechanism of the Claisen Rearrangement: Déjà Vu All Over Again , 1996 .

[23]  A. Varnek,et al.  Solvent and counterion effects on Na+Cs+ complexation selectivity by conformationally locked calix[4]-bis-crown ligands: Molecular Dynamics and Free Energy Perturbation studies in water and methanol, acetonitrile and chloroform solutions , 1996 .

[24]  D. L. Veenstra,et al.  Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability. , 1996, Protein engineering.

[25]  D. A. Dougherty,et al.  Cation-π Interactions in Chemistry and Biology: A New View of Benzene, Phe, Tyr, and Trp , 1996, Science.

[26]  William L. Jorgensen,et al.  Free Energies of Hydration for Organic Molecules from Monte Carlo Simulations , 1995 .

[27]  William L. Jorgensen,et al.  Importance of Polarization for Dipolar Solutes in Low-Dielectric Media: 1,2-Dichloroethane and Water in Cyclohexane , 1995 .

[28]  H. Zipse.  The Addition of Water to Ethylene and trans-Butene Radical Cation. Model Systems for the Reaction of Alkene Radical Cations with Nucleophiles , 1995 .

[29]  G. Wipff,et al.  Complexation of alkali cations by calix[4]crown ionophores: Conformation and solvent dependent Na+/Cs+ binding selectivity and extraction: MD simulations in the gas phase, in water and at the chloroform-water interface , 1995 .

[30]  W. L. Jorgensen,et al.  ELUCIDATION OF TRANSITION STRUCTURES AND SOLVENT EFFECTS FOR THE MISLOW-EVANS REARRANGEMENT OF ALLYLIC SULFOXIDES , 1995 .

[31]  Hendrik Zipse,et al.  A Quantum Mechanical and Statistical Mechanical Exploration of the Thermal Decarboxylation of Kemp's Other Acid (Benzisoxazole-3-carboxylic Acid). The Influence of Solvation on the Transition State Geometries and Kinetic Isotope Effects of a Reaction with an Awesome Solvent Effect , 1995 .

[32]  G. Hummer,et al.  The hydration free energy of water , 1995, chem-ph/9507004.

[33]  B. Berne,et al.  Molecular Dynamics Calculation of the Effect of Solvent Polarizability on the Hydrophobic Interaction , 1995 .

[34]  M. Murcko,et al.  Solvent Effects on 1,2-Dihaloethane Gauche/Trans Ratios , 1995 .

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

[36]  Peter A. Kollman,et al.  Investigation of Structure, Dynamics, and Solvation in 1-Octanol and Its Water-Saturated Solution: Molecular Dynamics and Free-Energy Perturbation Studies , 1995 .

[37]  H. Schaefer,et al.  Energy Difference between the Classical and the Nonclassical 2-Norbornyl Cation in Solution. A Combined ab Initio-Monte Carlo Aqueous Solution Study , 1995 .

[38]  Jonathan W. Essex,et al.  Generalized alteration of structure and parameters: A new method for free‐energy perturbations in systems containing flexible degrees of freedom , 1995, J. Comput. Chem..

[39]  P. Kollman,et al.  QUANTITATION AND NATURE OF THE MACROCYCLIC EFFECT : K+ COMPLEXATION WITH 18-CROWN-6 AND PENTAGLYME , 1995 .

[40]  W. L. Jorgensen,et al.  Investigations into the stereochemistry of cyclophane-steroid complexes via Monte Carlo simulations , 1995 .

[41]  William L. Jorgensen,et al.  Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model , 1994 .

[42]  Jiali Gao,et al.  POLARIZATION EFFECTS ON THE TAUTOMERIC EQUILIBRIA OF 2- AND 4-HYDROXYPYRIDINE IN AQUEOUS AND ORGANIC SOLUTION , 1994 .

[43]  J. Hermans,et al.  310 HELIX VERSUS ALPHA -HELIX : A MOLECULAR DYNAMICS STUDY OF CONFORMATIONAL PREFERENCES OF AIB AND ALANINE , 1994 .

[44]  H. Zipse.  The SRN2 Pathway-A Mechanistic Alternative for Radicals in Polar Media?** , 1994 .

[45]  W. L. Jorgensen,et al.  Structure and Binding for Complexes of Rebek's Acridine Diacid with Pyrazine, Quinoxaline, and Pyridine from Monte Carlo Simulations with an All-Atom Force Field , 1994 .

[46]  A. Mark,et al.  Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations , 1994 .

[47]  W. L. Jorgensen,et al.  Solvent Effects on the Ring Opening of Cyclopropanones to Oxyallyls: A Combined ab Initio and Monte Carlo Study , 1994 .

[48]  B. Berne,et al.  The Aqueous Solvation of Water: A Comparison of Continuum Methods with Molecular Dynamics , 1994, chem-ph/9403006.

[49]  W. L. Jorgensen,et al.  Monte-Carlo Results for the Effect of Solvation on the Anomeric Equilibrium for 2-Methoxytetrahydropyran , 1994 .

[50]  P. Rossky,et al.  Molecular Simulation of a Chemical Reaction in Supercritical Water , 1994 .

[51]  M. Márquez,et al.  The energy components of the anomeric effect for 2-methoxytetrahydropyran. An experimental comparison of the gas phase and solutions , 1994 .

[52]  Jiali Gao,et al.  Combined QM/MM Simulation Study of the Claisen Rearrangement of Allyl Vinyl Ether in Aqueous Solution , 1994 .

[53]  L. Troxler,et al.  Conformation and Dynamics of 18-Crown-6, Cryptand 222, and Their Cation Complexes in Acetonitrile Studied by Molecular Dynamics Simulations , 1994 .

[54]  Garland R. Marshall,et al.  α/310‐Helix transitions in α‐methylalanine homopeptides: Conformational transition pathway and potential of mean force , 1994 .

[55]  Garland R. Marshall,et al.  Free energy profile of a 310- to .alpha.-helical transition of an oligopeptide in various solvents , 1993 .

[56]  William L. Jorgensen,et al.  Molecular dynamics and Monte Carlo simulations favor the .alpha.-helical form for alanine-based peptides in water , 1993 .

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

[58]  Peter A. Kollman,et al.  FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .

[59]  Jiali Gao,et al.  A two-dimensional energy surface for a type II SN2 reaction in aqueous solution , 1993 .

[60]  Kenneth M. Merz,et al.  Theoretical investigation of the CO2 + OH- → HCO3- reaction in the gas and aqueous phases , 1993 .

[61]  Heather A. Carlson,et al.  Accuracy of free energies of hydration for organic molecules from 6‐31g*‐derived partial charges , 1993, J. Comput. Chem..

[62]  D A Dougherty,et al.  A mechanism for ion selectivity in potassium channels: computational studies of cation-pi interactions. , 1993, Science.

[63]  Jiali Gao.  Supercritical hydration of organic compounds. The potential of mean force for benzene dimer in supercritical water , 1993 .

[64]  P A Kollman,et al.  Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches , 1993, Proteins.

[65]  C. Brooks,et al.  Constant-temperature free energy surfaces for physical and chemical processes , 1993 .

[66]  J. Hermans.  Molecular dynamics simulations of helix and turn propensities in model peptides , 1993 .

[67]  W F van Gunsteren,et al.  Can the stability of protein mutants be predicted by free energy calculations? , 1993, Protein engineering.

[68]  W. L. Jorgensen,et al.  Modeling the complexation of substituted benzenes by a cyclophane host in water. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[69]  J. Madura,et al.  Molecular recognition : effect of rotational isomers on host-guest binding , 1993 .

[70]  William L. Jorgensen,et al.  Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions , 1993, J. Comput. Chem..

[71]  Shoshana J. Wodak,et al.  Molecular dynamics study of methane hydration and methane association in a polarizable water phase , 1993 .

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

[73]  G. Millhauser,et al.  Short alanine-based peptides may form 310-helices and not α-helices in aqueous solution , 1992, Nature.

[74]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[75]  William J. Dunn,et al.  Relative log P and solution structure for small organic solutes in the chloroform/water system using monte carlo methods , 1992 .

[76]  Jonathan W. Essex,et al.  Theoretical determination of partition coefficients , 1992 .

[77]  P. Kollman,et al.  Molecular dynamics studies of calixspherand complexes with alkali metal cations: calculation of the absolute and relative free energies of binding of cations to a calixspherand , 1992 .

[78]  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 .

[79]  W F van Gunsteren,et al.  On the interpretation of biochemical data by molecular dynamics computer simulation. , 1992, European journal of biochemistry.

[80]  William L. Jorgensen,et al.  Solvent effects on a Diels-Alder reaction from computer simulations , 1991 .

[81]  Jiali Gao,et al.  A priori computation of a solvent-enhanced SN2 reaction profile in water : the Menshutkin reaction , 1991 .

[82]  R. Levy,et al.  Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water , 1991 .

[83]  M Karplus,et al.  Simulation analysis of the stability mutant R96H of T4 lysozyme. , 1991, Biochemistry.

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

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

[86]  Peter A. Kollman,et al.  A theoretical examination of solvatochromism and solute-solvent structuring in simple alkyl carbonyl compounds. Simulations using statistical mechanical free energy perturbation methods , 1990 .

[87]  C. Reynolds.  Theoretical electrode potentials and conformational energies of benzoquinones and naphthoquinones in aqueous solution , 1990 .

[88]  W. L. Jorgensen,et al.  Origin of the strong binding of adenine to a molecular tweezer , 1990 .

[89]  Christopher A. Hunter,et al.  The nature of .pi.-.pi. interactions , 1990 .

[90]  P A Kollman,et al.  The calculated free energy effects of 5‐methyl cytosine on the B to Z transition in DNA , 1990, Biopolymers.

[91]  William L. Jorgensen,et al.  Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene , 1990 .

[92]  Charles L. Brooks,et al.  The thermodynamics of solvophobic effects: A molecular‐dynamics study of n‐butane in carbon tetrachloride and water , 1990 .

[93]  William L. Jorgensen,et al.  Relative partition coefficients for organic solutes from fluid simulations , 1990 .

[94]  William L. Jorgensen,et al.  Importance of secondary interactions in triply hydrogen bonded complexes: guanine-cytosine vs uracil-2,6-diaminopyridine , 1990 .

[95]  Peter A. Kollman,et al.  The lag between the Hamiltonian and the system configuration in free energy perturbation calculations , 1989 .

[96]  T. P. Straatsma,et al.  Treatment of rotational isomers in free energy calculations. II. Molecular dynamics simulation study of 18‐crown‐6 in aqueous solution as an example of systems with large numbers of rotational isomeric states , 1989 .

[97]  R. Levy,et al.  Solvent effects on optical absorption spectra: the 1A1 .fwdarw. 1A2 transition of formaldehyde in water , 1989 .

[98]  William L. Jorgensen,et al.  A priori pKa calculations and the hydration of organic anions , 1989 .

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

[100]  William L. Jorgensen,et al.  Free energy of TIP4P water and the free energies of hydration of CH4 and Cl- from statistical perturbation theory , 1989 .

[101]  William L. Jorgensen,et al.  Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water , 1988 .

[102]  J. Hermans,et al.  Excess free energy of liquids from molecular dynamics simulations. Application to water models. , 1988, Journal of the American Chemical Society.

[103]  W. Richards,et al.  Computed redox potentials and the design of bioreductive agents , 1988, Nature.

[104]  Martin J. Field,et al.  Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential , 1987 .

[105]  William L. Jorgensen,et al.  Use of statistical perturbation theory for computing solvent effects on molecular conformation: butane in water , 1987 .

[106]  W. L. Jorgensen,et al.  A priori calculations of pKa's for organic compounds in water. The pKa of ethane , 1987 .

[107]  Peter A. Kollman,et al.  A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy perturbation methods , 1987 .

[108]  Mihaly Mezei,et al.  Grand-canonical ensemble Monte Carlo study of dense liquid Lennard-Jones, soft spheres and water , 1987 .

[109]  M. Mezei.  The finite difference thermodynamic integration, tested on calculating the hydration free energy difference between acetone and dimethylamine in water , 1987 .

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

[111]  William L. Jorgensen,et al.  Ab initio and Monte Carlo calculations for a nucleophilic addition reaction in the gas phase and in aqueous solution , 1986 .

[112]  P. Rossky,et al.  Molecular conformational equilibria in liquids , 1986 .

[113]  J A McCammon,et al.  Theoretical calculation of relative binding affinity in host-guest systems. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[114]  W. L. Jorgensen,et al.  Monte Carlo simulation of differences in free energies of hydration , 1985 .

[115]  Scott F. Smith,et al.  Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution , 1985 .

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

[117]  Scott F. Smith,et al.  SN2 reaction profiles in the gas phase and aqueous solution , 1984 .

[118]  J. Andrew McCammon,et al.  Sodium chloride ion pair interaction in water: computer simulation , 1984 .

[119]  William L. Jorgensen,et al.  Theoretical studies of medium effects on conformational equilibria , 1983 .

[120]  M. Mezei.  Excess free energy of different water models computed by Monte Carlo methods , 1982 .

[121]  B. Berne,et al.  Hydrophobic effect on chain folding. The trans to gauche isomerization of n-butane in water , 1982 .

[122]  William L. Jorgensen,et al.  Monte Carlo simulation of n‐butane in water. Conformational evidence for the hydrophobic effect , 1982 .

[123]  M Karplus,et al.  Dynamical theory of activated processes in globular proteins. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[124]  W. L. Jorgensen,et al.  Sampling methods for Monte Carlo simulations of n‐butane in dilute solution , 1981 .

[125]  W. L. Jorgensen,et al.  Structures and properties of organic liquids: n-butane and 1,2-dichloroethane and their conformation equilibriums , 1981 .

[126]  Bruce J. Berne,et al.  A Monte Carlo simulation of the hydrophobic interaction , 1979 .

[127]  K. Nakanishi,et al.  Monte Carlo studies on the hydrophobic hydration in dilute aqueous solutions of nonpolar molecules , 1979 .

[128]  Bruce J. Berne,et al.  A molecular dynamics and Monte Carlo study of solvent effects on the conformational equilibrium of n‐butane in CCl4a),b) , 1979 .

[129]  M. Mezei,et al.  Ab initio calculation of the free energy of liquid water , 1978 .

[130]  D. Chandler,et al.  Theory of the hydrophobic effect , 1977 .

[131]  Charles H. Bennett,et al.  Efficient estimation of free energy differences from Monte Carlo data , 1976 .

[132]  G. Torrie,et al.  Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid , 1974 .

[133]  D. N. Card,et al.  Monte Carlo Estimation of the Free Energy by Multistage Sampling , 1972 .

[134]  R. Zwanzig.  High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[135]  J. Kirkwood.  Statistical Mechanics of Fluid Mixtures , 1935 .

[136]  J. Briggs,et al.  Structure-based drug design: computational advances. , 1997, Annual review of pharmacology and toxicology.

[137]  A. Casnati,et al.  Alkaline earth and uranyl cation complexes of a calix[4]arene-tetraamide: MD and FEP simulations in aqueous and acetonitrile solutions and X-ray structure of its Sr(Picrate)2 complex , 1996 .

[138]  D. Hartsough,et al.  Potential of mean force calculations on the SN1 fragmentation of tert-butyl chloride , 1995 .

[139]  Jiali Gao.  AN AUTOMATED PROCEDURE FOR SIMULATING CHEMICAL REACTIONS IN SOLUTION. APPLICATION TO THE DECARBOXYLATION OF 3-CARBOXYBENZISOXAZOLE IN WATER , 1995 .

[140]  K. Merz,et al.  Molecular Recognition of K+ and Na+ by Valinomycin in Methanol , 1995 .

[141]  G. Marshall,et al.  .alpha.-Helical versus 310-Helical Conformation of Alanine-Based Peptides in Aqueous Solution: An Electron Spin Resonance Investigation , 1995 .

[142]  H. Zipse.  Open-Shell Analogs of Closed Shell Reaction Paths. The SRN2' case , 1994 .

[143]  W. Richards,et al.  Calculation of the tautomer ratio of histamine in aqueous solution using free energy perturbation methods : an in-depth study , 1994 .

[144]  P. Kollman,et al.  Molecular dynamics and free energy calculations on the peculiar bimodal alkali ion selectivity of an 8-subunit cavitand , 1994 .

[145]  William L. Jorgensen,et al.  Investigation of solvent effects on pericyclic reactions by computer simulations , 1994 .

[146]  Charles L. Brooks,et al.  Simulations of peptide conformational dynamics and thermodynamics , 1993 .

[147]  W. L. Jorgensen,et al.  Urea: Potential Functions, log P, and Free Energy of Hydration , 1993 .

[148]  William L. Jorgensen,et al.  Monte Carlo simulations yield absolute free energies of binding for guanine—cytosine and adenine—uracil base pairs in chloroform , 1991 .

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

[150]  James Andrew McCammon,et al.  Ligand-receptor interactions , 1984, Comput. Chem..

[151]  H. Berendsen,et al.  THERMODYNAMICS OF CAVITY FORMATION IN WATER - A MOLECULAR-DYNAMICS STUDY , 1982 .

[152]  Mihaly Mezei,et al.  Monte Carlo computer simulation study of the hydrophobic effect. Potential of mean force for [(CH4)2]aq at 25 and 50 °C , 1982 .

[153]  R. Bell,et al.  The electrostatic energy of dipole molecules in different media , 1931 .