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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 5020-5033 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A method is presented that uses integral equation theory to determine analytic temperature derivatives of the radial distribution functions. It is illustrated by studying the solvation thermodynamics of monatomic solutes in aqueous solution. The results agree well with the density derivative method developed previously [Yu and Karplus, J. Chem. Phys. 89, 2366 (1988)]. An expression for the solvation enthalpy is derived which allows direct comparison with experimental and isobaric–isothermal (NPT) ensemble simulation data. Satisfactory agreement with experiment is found for pure water and for the aqueous solvation of monovalent ions. Simple equations that exploit the site–site HNC closures are given for the decomposition of the potential of mean force into its enthalpic (or energetic) and entropic components. Since the extended RISM (HNC-RISM) theory yields an incorrect (trivial) value of the dielectric constant, two different ways to correct for the asymptotic behavior of the solute–solute potential of mean force are compared. They lead to similar results but the method in which the solvent dielectric constant is modified from the outset can be applied more generally.The interactions between nonpolar and between polar solutes in water are decomposed into enthalpic and entropic contributions. This is difficult to do by computer simulations because of the lack of precision in such calculations. The association of nonpolar solutes in water is found to have comparable enthalpic and entropic contributions; this result disagrees with the usual description of an entropy-dominated hydrophobic interaction. For ions, the somewhat surprising result is that the association of like-charged species is enthalpy driven while for oppositely charged ions entropic effects are dominant. The process of bringing two like-charged ions together leads to higher local charge density; the more favorable solvation enthalpy arising from this increase in charge density (q2 dependence) more than compensates for the Coulombic repulsion. For oppositely charged ions, association leads to a partial charge neutralization in which the favorable Coulombic attraction is overwhelmed by the loss of stabilizing solvation enthalpy. The entropic increase is due to the greater freedom of the surrounding water molecules resulting from the partial charge neutralization.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 2366-2379 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The free energy, energy, and entropy of solvation, relative to the pure liquid, are analyzed. By a coupling parameter integration it is shown that only averages over the solute–solvent interaction energy contribute to the free energy and that the solvent–solvent interaction term, which contributes the so-called cavity (solvent reorganization) term to the energy, is cancelled exactly by a corresponding term in the entropy. These terms exist even in the infinite dilution limit since they arise from the derivative of the free energy with respect to the solute density. Following the approach of Garisto et al. [J. Chem. Phys. 79, 6294 (1983)], the site–site Ornstein–Zernike integral equations and HNC closures are used to determine the derivatives of the distribution functions with respect to the density. This makes it possible to calculate the energetic and entropic contributions to the solvation free energy in the infinite dilution limit. The method is applied to pure solvent and to infinitely dilute aqueous solutions of cations, anions and neutral Lennard-Jones particles. The results are in agreement with numerical calculations of the thermodynamic quantities by use of finite difference values for the temperature derivatives. A simple empirical relation for the charge dependence of the solvation free energy is observed; it is shown for the case of an ion in a dipolar solvent, as typified by aqueous electrolyte solutions, that the free energy of solvation varies quadratically with the charge and is very nearly equal to one-half the solute–solvent portion of the solvation energy. Some discussion of the relation of the present results to entropy–enthalpy compensation and to computer simulations is given.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 112 (1990), S. 5706-5716 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 94 (1990), S. 4683-4688 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 113 (1991), S. 2425-2434 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 16 (1993), S. 172-194 
    ISSN: 0887-3585
    Keywords: serine protease ; active site solvation ; stochastic simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The motions of water molecules, the acyl moiety, the catalytic triad, and the oxyanion binding site of acyl-chymotrypsin were studied by means of a stochastic boundary molecular dynamics simulation. A water molecule that could provide the nucleophilic OH- for the deacylation stage of the catalysis was found to be trapped between the imidazole ring of His-57 and the carbonyl carbon of the acyl group. It makes a hydrogen bond with the Nε2 of His-57 and is heldin place through a network of hydrogen-bonded water molecules in theactive site. The water molecule was found as close as 2.8 Å to the carbonyl carbon. This appears to be due to the constraints imposed by nonbonded interaction in the active site. Configurations were found in which one hydrogen of the trapped water shared a bifurcated hydrogen bond with His-57-Nε2 and Ser-195-0γ with the water oxygen very close to the carbonyl carbon. The existence of such a water molecule suggests that large movement of the His-57 imidazole ring between positions suitable for providing general-base catalyzed assistance and for providing general-acid catalyzed assistance may notbe required during the reaction. The simulation indicates that the side chains of residues involved in catalysis (i.e., His-57, Ser-195, and Asp-102) are significantly less flexible than other side chains in the protein. The 40% reduction in rms fluctuations is consistent with a comparable reduction calculated from the temperature factors obtained in the X-ray crystal-lographic data of γ-chymotrypsin. The greater rigidity of active site residues seems to result from interconnected hydrogen bonding networks among the residues and between the residues and the solvent water in the active site. © Wiley-Liss, Inc.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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