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  • 1
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dielectric properties (static dielectric constant ε0, Debye relaxation time τD and distance dependent Kirkwood G-factor Gk(R)) of commonly used three-site water models (the "simple point charge" models SPC and SPC/E, as well as the "transferable intermolecular potentials with three point charges" TIP3P and its CHARMM modified variant TIP3Pmod) were evaluated from 2 ns molecular dynamics simulations using the Ewald summation method to compute the electrostatic interactions. The results for SPC (ε0=65±5, τD=7.6±0.8 ps) and SPC/E (ε0=68±6, τD=12.1±1.3 ps) are in good agreement with the literature; for TIP3P (TIP3Pmod) we obtained a dielectric constant ε0=97±7 (97±6) and a Debye relaxation time τD=7.3±0.7 ps (6.9±0.6 ps). The surprisingly large differences in ε0 were rationalized by an investigation of the relationship between the force field parameters and the dielectric properties. Based on simulations of hybrid SPC/TIP3P models, the HOH bond angle was identified as the determining factor of the dielectric constant. By contrast, τD was shown to depend mainly on the OH bond length and the partial charges; the HOH angle is of secondary importance. The role of the HOH angle is clarified by a comparison of the orientational correlation functions of the water models. © 1998 American Institute of Physics.
    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 115 (2001), S. 10780-10792 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dielectric self-consistent field method (DSCF) provides a continuum electrostatics tool to study the effects which the use of modified electrostatic interactions has on the properties of a solute–solvent system in molecular dynamics or Monte Carlo simulations with explicit solvent. The theoretical foundation and the implementation of the method are described. Results of calculations for small solutes, water and a spherical ion, are presented. The properties studied include the electrostatic contribution to the solvation free energy and solute–solvent orientational correlation functions. The information obtained in this manner turns out to be complementary and provides a broader basis for a critical comparison of widely used modified electrostatic interactions. We also compute the potential-of-mean-force for a pair of spherical ions of opposite charge. Among the modified electrostatic interactions compared [spherical truncation, a shifted potential, a generalized reaction field, and Ewald summation (EW)], EW is found to give the most consistent results compared with the true 1/r Coulomb potential. The paper concludes with a comparison of DSCF to related continuum electrostatic based approaches, such as numerical solutions of the Poisson–Boltzmann equation and the method of Langevin dipoles.© 2001 American Institute of Physics.
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 6953-6955 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Use of atom based truncation schemes in thermodynamic integration leads to hydration free energies of water that depend strongly on the cut-off radius. By contrast, Ewald summation, a reaction field technique, and group based truncation of the potential give the same result (6.5±0.1 kcal/mole), independently of the cut-off radius and system size. © 2000 American Institute of Physics.
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  • 4
    ISSN: 0887-3585
    Keywords: hemodynamic integration ; RISM theory ; alchemical path ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred to as “component analysis,” is meaningful, even though it is a function of the integration path. Moreover, it is shown that the path dependence can be used to determine the relation of the contribution of a given interaction to the state of the system.To illustrate these conclusions, a simple transformation(Cl- to Br- in aqueous solution) is analyzed by use of the Reference Interaction Site Model-Hypernetted Chain Closure integral equation approach; it avoids the calculational difficulties of macromolecular simulation while retaining their conceptual complexity. The difference in the solvation free energy between chloride and bromide is calculated, and the contributions of the Lennard-Jones and electrostatic terms in the potential function are analyzed by the use of suitably chosen integration paths. The model is also used to examine the path dependence of individual contributions to the double free energy differences (ΔΔG or ΔΔA) that are often employed in free energy simulations of biological systems. The alchemical path, as contrasted with the experimental path, is shown to be appropriate for interpreting the effects of mutations on ligand binding and protein stability. The formulation is used to obtain a better understanding of the success of the Poisson-Boltzmann continuum approach for determining the solvation properties of polar and ionic systems. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 10793-10807 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dielectric self-consistent field (DSCF) method is used to study finite range corrections for the electrostatic contribution to solvation free energies. Detailed results obtained from calculations using Ewald summation (EW) and a generalized reaction field (GRF) technique are reported for the solvation of a spherical ion, glycine and an alanine octapeptide in an ideal α-helical conformation. For the peptide EW calculations are carried out with both conducting ("tinfoil") dielectric boundary conditions and adjusted dielectric boundary conditions. The emphasis of this work is on solutes without net charge, but with a large dipole moment. It is shown that in this case—similarly to ionic solvation—the self-energy correction needs to be modified by a thermodynamic correction that accounts for the dielectric constant of the solvent. An analytical expression for this term is worked out. The results obtained for glycine and the alanine octapeptide demonstrate that its use improves the system-size independence of solvation free energies calculated with EW compared with just the self energy correction; the GRF results are less satisfactory. We further show the connection between finite range corrections and artifacts in the total electrostatic energy of a system resulting from the use of modified electrostatic interactions. The direct comparison of EW with GRF shows that at present EW is the best method to use in simulations with explicit solvent and periodic boundary conditions.© 2001 American Institute of Physics.
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  • 6
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dielectric self-consistent field method, a novel tool to study solvated systems based on continuum electrostatics, is introduced. It permits the qualitative and even semiquantitative calculation of orientational correlation functions, i.e., it gives insights into the orientational structure of a solute–solvent system. Further, modified Coulomb potentials and periodic boundary conditions can easily be integrated. One possible application is rapid, yet detailed methodological studies of the effects resulting from the various modified electrostatic interactions that are used regularly in computer simulations with explicit solvent molecules. As an example, we report the distance dependent Kirkwood g-factor and ion–dipole correlation functions of a solvated glycine zwitterion obtained with a simple cutoff, a shifted potential, two reaction field techniques, and Ewald summation. For the reaction fields and Ewald summation, conducting and adjusted dielectric boundary conditions are compared. © 1999 American Institute of Physics.
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 5145-5154 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The role of Jacobian factors in free energy simulations is described. They provide a simple interpretation of "moment of inertia correction'' and "dynamic stretch free energy'' terms in such simulations. Since the relevant Jacobian factors can often be evaluated analytically by use of the configurational partition function of a polyatomic molecule, it is possible to subtract them from the simulation results when they make unphysical contributions. An important case arises in alchemical simulations that use a single topology method and introduce dummy particles to have the same number of atoms in the initial and final state. The more general utility of the Jacobian factors for simulations of complex systems is briefly discussed. © 1996 American Institute of Physics.
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