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  • 1
    Electronic Resource
    Electronic Resource
    The effect of force-field parameters on properties of liquids: Parametrization of a simple three-site model for methanol (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 10450-10459 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A simple rigid three-site model for methanol compatible with the simple point charge (SPC) water and the GROMOS96 force field is parametrized and tested. The influence of different force-field parameters, such as the methanol geometry and the charge distribution on several properties calculated by molecular dynamics is investigated. In particular an attempt was made to obtain good agreement with experimental data for the static dielectric constant and the mixing enthalpy with water. The model is compared to other methanol models from the literature in terms of the ability to reproduce a range of experimental properties. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.481680
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  • 2
    Electronic Resource
    Electronic Resource
    Viscosity dependence and solvent effects in the photoisomerization of cis-stilbene: Insight from a molecular dynamics study with an ab initio potential-energy function (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8987-8999 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular-dynamics simulations of the photoisomerization of cis-stilbene in supercritical argon were performed. The stilbene molecule is represented by ab initio quantum chemistry, while the solvent, the interaction with solvent, and the time evolution were described by classical mechanics. Reaction rate constants are estimated and their dependence on temperature, pressure, and viscosity are investigated. Agreement with available experimental data was obtained. Our simulations strongly suggest a minimum on the excited-state potential-energy surface at a gauche conformation which is very rapidly reached after excitation, which leads to nonequilibrium barrier transitions. Specific solvent effects were identified. Implications on the current opinion on stilbene photoisomerization are discussed. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480242
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation with an ab initio potential energy function and finite element interpolation: The photoisomerization of cis-stilbene in solution (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 8773-8781 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An interpolation scheme for potential energy surfaces is presented. It employs a regular grid and finite element interpolation. The aim is the reduction of the computational expense for molecular dynamics simulation with a quantum chemical potential energy function. The methods used are described in detail. The feasibility is demonstrated and the efficiency and accuracy are evaluated for the photoisomerization of cis-stilbene in supercritical argon, using an ab initio configuration- interaction treatment for the first electronically excited state of the stilbene molecule and classical force fields for the solvent–solute interactions (quantum mechanical/molecular mechanical molecular dynamics). The number of required quantum chemical calculations of energy and gradients was substantially reduced compared to a simulation not using the interpolation scheme. On the other hand, the impact on the accuracy is insignificant. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.475397
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  • 4
    Electronic Resource
    Electronic Resource
    Validation of molecular simulation by comparison with experiment: Rotational reorientation of tryptophan in water (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 3049-3055 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics simulations aimed at analysis of the rotational reorientation of tryptophan and 3-methylindole in water have been performed. The dependence of the rotational relaxation time of tryptophan on several simulation and model parameters has been evaluated. The considerable sensitivity found for particular parameters illustrates the necessity of a detailed analysis before jumping to conclusions regarding the validity of a molecular model and force field based on comparing simulation with experimental data. The best agreement with experimental data is obtained when using the extended simple-point-charge (SPC/E) model for water together with a reaction-field correction for the long-range electrostatic interactions. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.477900
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  • 5
    Electronic Resource
    Electronic Resource
    Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 6117-6134 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Different schemes for treating the electrostatic interactions in molecular dynamics simulations are investigated: charge-group truncation with or without reaction-field correction, atomic truncation with or without reaction-field correction, and Ewald summation. When a reaction-field correction is applied, the influence of the size of the radius selected for the spherical boundary to the continuum is also considered. The different schemes are applied to simple point charge water simulations, and simulated energetic, transport, structural, and dielectric properties are compared. It is concluded that (i) the inclusion of a reaction-field correction in a charge-group truncation scheme induces significant changes in different types of properties, and that a number of properties are not identical to those observed using the Ewald scheme, (ii) when the reaction-field correction is included in an atomic truncation scheme instead, the agreement with the Ewald results is in general improved, and (iii) the increase (decrease) of the radius of the boundary to the continuum by 0.1 (nm) with respect to the cutoff radius induces in both cases a degradation of the simulated properties. Special attention is paid to the calculation of the dielectric permittivity from the simulations. Due to the finite size of the statistical ensembles considered, this property is not assumed to be isotropic, and the degree of anisotropy is used instead as a test for convergence. Since the incorporation of the reaction-field correction into an atomic truncation scheme leads, when systems of high dielectric permittivity are considered, to electrostatic interactions which implicitly contain a (physically reasonable) shifting function and properties which are comparable to those obtained using the Ewald method, this scheme is a clear improvement over a charge-group-based truncation when a reaction-field correction is used in molecular dynamics simulations of noncharged systems. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476022
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  • 6
    Electronic Resource
    Electronic Resource
    Validation of molecular dynamics simulation (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 6109-6116 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: How the results obtained by computer simulation of molecular systems can be validated is considered. The overall quality of the simulated properties of a molecular system will depend on (i) the quality of the theory or model, (ii) the accuracy of the interatomic interaction function or force field, (iii) the degree of sampling, statistics and convergence reached in the simulation, (iv) the quality of the simulation software, and (v) how competently the simulation software is used. These five validation issues are discussed and illustrated with examples. Guidelines for different members of the scientific community are formulated which are aimed at enabling and improving the validation of simulation results in the literature. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476021
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  • 7
    Electronic Resource
    Electronic Resource
    Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 3169-3174 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dielectric constants (ε) of the simple point charge (SPC) and extended simple point charge (SPC/E) models of liquid water have been determined at 277 and 300 K using a reaction field (εRF) treatment for the long-range electrostatic interaction. Consistent dielectric constants are obtained by using statistical mechanical perturbation theory, such that the properties of the system correspond to εRF=ε, and are therefore representative of a true infinite system. The dielectric constants of SPC were determined to be 55.8 and 54.0 at 277 and 300 K, respectively, while the dielectric constants of SPC/E were 68.5 and 62.3 at 277 and 300 K, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466407
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  • 8
    Electronic Resource
    Electronic Resource
    Computer simulation of a polymer electrolyte: Lithium iodide in amorphous poly(ethylene oxide) (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 4745-4756 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Systems of lithium iodide dissolved in poly(ethylene oxide), which are prototypes of polymer electrolytes used, for example, in batteries were studied by means of molecular dynamics simulations. Investigations were aimed at the molecular driving force behind the salt uptake, the mechanism of ion transport, participation of the polymer in ion transport, ion clustering, change of polymer properties by the presence of ions, and ionic conductivity. Particular attention has been given to the differences in behavior between (previously studied) neutral and ionic species dissolved in polymers. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470611
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  • 9
    Electronic Resource
    Electronic Resource
    A molecular dynamics simulation study with a combined quantum mechanical and molecular mechanical potential energy function: Solvation effects on the conformational equilibrium of dimethoxyethane (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 1722-1730 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Solvent effects on the conformational equilibria of dimethoxyethane (DME, CH3–O–CH2–CH2–O–CH3) have been studied using molecular dynamics simulation with a combined molecular mechanical and semiempirical quantum mechanical potential energy function. The potential of mean force around the central O–C–C–O dihedral angle of DME in water was determined using umbrella sampling, with the DME molecule treated by the modified intermediate neglect of diatomic differential overlap (MNDO) method and water molecules described using the extended simple point charge model. This potential of mean force shows the same bias as the gas phase potential energy surface calculated by MNDO: the heights of the barriers are underestimated and the stability of the gauche conformation with respect to the trans conformation is overestimated. However, the calculated stabilization of the gauche state by solvation is in good agreement with experimental results, suggesting a quite reasonable description of this system by the combined potential energy function. The solute–water atom pair distributions and the averaged percentage of solute–water hydrogen bonding does not change much when the central dihedral angle changes, but in the gauche conformation one water hydrogen can be hydrogen bonded with the two solute oxygen atoms simultaneously. The interactions between DME and its explicit water environment favor the gauche over the trans conformation much more than predicted by the reaction field model, although the overall relative stabilities predicted by the latter model are not so biased due to compensation of errors. The trans conformation of the outer C–O–C–C dihedral angles is most favored during the simulations, which is qualitatively different from the reaction field prediction that the trans–gauche+–gauche− would be the most stable conformer in solution. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468699
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  • 10
    Electronic Resource
    Electronic Resource
    Free energy of cavity formation in solvent: Computational, methodological, and physical aspects (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 3787-3793 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: With molecular dynamics simulation techniques, the free energy of cavity formation in water is investigated and determined at 300 K and 1 atm. Different methods are compared: Widom particle insertion, thermodynamic integration, and perturbation. It is shown that the most efficient way to get accurate results is to apply Widom particle insertion for cavities up to a thermal radius of 0.25 nm followed by a thermodynamic integration with sampling at fixed thermal radii. In order to converge the result to 2.5% at one thermal radius a simulation period in the order of 100 ps is needed. The convergence behavior for thermal radii slightly above the van der Waals radius of a water molecule (0.31 nm) is poor and thus indicates instabilities in the water shell surrounding the cavity and that the free energy is a nonsmoothly increasing function of the thermal radius. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468560
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