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  • 1
    Electronic Resource
    Electronic Resource
    A replica reference interaction site model theory for a polar molecular liquid sorbed in a disordered microporous material with polar chemical groups (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 8620-8633 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We develop a replica generalization of the reference interaction site model (replica RISM) integral equation theory to describe the structure and thermodynamics of quenched-annealed systems comprising polar molecular species. It provides a successful approach to realistic models of molecular liquids, and properly allows for the effect of a quenched disordered matrix on the sorbed liquid. The description can be extended to an electrolyte solution in a disordered material containing charged chemical functionalities that determine its adsorption character. The replica reference interaction site model (RISM) equations are complemented with the hypernetted chain (HNC) closure and its partial linearization (PLHNC), adequate to ionic and polar molecular liquids. In these approximations, the excess chemical potentials are derived in a closed analytical form. We extend the description to a quenched-annealed system with soft-core interaction potentials between all species, in which the liquid and matrix equilibrium distributions are characterized in general by two different temperatures. The replica RISM/PLHNC-HNC theory is applied to water sorbed in a quenched disordered microporous network of atoms associated into interconnected branched chains, with activating polar groups grafted to matrix chains. The results are in qualitative agreement with experiment for water confined in disordered materials. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1409954
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  • 2
    Electronic Resource
    Electronic Resource
    Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 2793-2805 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We modify the site–site as well as three-dimensional (3D) versions of the reference interaction site model (RISM) integral equations with the hypernetted chain (HNC) closures by adding a repulsive bridge correction (RBC). The RBC treats the overestimation of water ordering around a hydrophobic solute in the RISM/HNC approximation, and thus refines the entropic component in the hydration free energy. We build up the bridge functions on r−12 repulsive core potentials, and propose RBC expressions for both the site–site and 3D-RISM approaches. To provide fast calculation, we obtain the excess chemical potential of hydration by using the thermodynamic perturbation theory (TPT). The site–site RISM/HNC+RBC as well as 3D-RISM/HNC+RBC approaches are applied to calculate the structure and thermodynamics of hydration of rare gases and alkanes in ambient water. For both approaches, the RBC drastically improves the agreement of the hydration chemical potential with simulation data and provides its correct dependence on the solute size. For solutes of a nonspherical form, the 3D treatment yields the hydration structure in detail and better fits simulation results, whereas the site–site approach is essentially faster. The TPT approximation gives the hydration thermodynamics in good qualitative agreement with the exact results of the thermodynamic integration, and substantially reduces computational burden. The RBC–TPT approximation can improve the predictive capability of the hybrid algorithm of a generalized-ensemble Monte Carlo simulation combined with the site–site RISM theory, used to describe protein folding with due account for the water effect at the microscopic level. The RBC can be optimized for better fit to reference simulation data, and can be generalized for solute molecules with charged groups. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1305885
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  • 3
    Electronic Resource
    Electronic Resource
    Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 10391-10402 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We adapt the three-dimensional reference interaction site model (3D-RISM) to calculate the potentials of mean force for ion–molecular solution as a difference between the chemical potential of solvation of a cluster of solutes and of individual ones. The method yields the solvation structure around the cluster of solutes in detail. The solvation chemical potential is obtained for the three-dimensional hypernetted chain (3D-HNC) closure as well as for its partial linearization (3D-PLHNC approximation). The solvation chemical potential is obtained in a closed analytical form for both the 3D-HNC and 3D-PLHNC closures. The 3D-RISM integral equations are solved by using the supercell technique. A straightforward supercell treatment of ionic solute in polar molecular solvent leads to a big error in the potential of mean force as well as the solvation chemical potential, which for simple ions in water amounts to about 35 kcal/mol. We elaborated corrections to the 3D-RISM integral equations, alleviating the artifact of the supercell periodicity with an accuracy of 0.05 kcal/mol or better and restoring the long-range asymptotics of the solute–solvent correlation functions. The dielectrically consistent site–site RISM/HNC theory (DRISM/HNC) is employed for the solvent correlations to provide a proper description of the dielectric properties of solution. This allowed us to extend the description to solution at a finite salt concentration. We converge both the 3D-RISM and site–site DRISM integral equations by using the method of modified direct inversion in the iterative subspace. Owing to the proper initial guess of the correlation functions, iteration begins at once for a given temperature and full molecular charge, avoiding a gradual decrease of the temperature and increase of the site charges, which greatly reduces the computation time. We calculate and discuss the potentials of mean force for sodium chloride in ambient water at infinite dilution as well as at a finite concentration. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.481676
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  • 4
    Electronic Resource
    Electronic Resource
    Potentials of mean force of simple ions in ambient aqueous solution. II. Solvation structure from the three-dimensional reference interaction site model approach, and comparison with simulations (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 10403-10417 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We applied the three-dimensional reference interaction site model (3D-RISM) integral equation theory with the 3D hypernetted chain (3D-HNC) closure or its partial linearization (3D-PLHNC) to obtain the potentials of mean force (PMFs) and the solvation structure of sodium chloride in ambient water. The bulk solvent correlations are treated by the dielectrically consistent site–site RISM/HNC theory (DRISM/HNC) to provide a proper description of the dielectric properties of solution and to include the case of a finite salt concentration. The PMF is calculated as a difference in the solvation free energy of an ion pair and of individual ions. We obtained and analyzed in detail the PMFs and solvation structure for ion pairs of NaCl at infinite dilution and a concentration of 1 M. The results are in reasonably good agreement with molecular dynamics simulations for the same model of the solution species. Positions and orientations of water molecules in the first solvation shell around the ion pair are deduced. The short-range hydration structure of the ion pairs at infinite dilution and at moderate concentration is very similar. Ionic ordering and clustering is found in 1 M solution. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.481677
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  • 5
    Electronic Resource
    Electronic Resource
    Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 7458-7470 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We developed a self-consistent three-dimensional reference interaction site model integral equation theory with the molecular hypernetted chain closure (SC-3D-RISM/HNC) for studying thermochemistry of solvation of ionic solutes in a polar molecular solvent. It is free from the inconsistency in the positions of the ion–solvent site distribution peaks, peculiar to the conventional RISM/HNC approach and improves the predictions for the solvation thermodynamics. The SC-3D-RISM treatment can be readily generalized to the case of finite ionic concentrations, including the consistent dielectric corrections to provide a consistent description of the dielectric properties of ion–molecular solution. The proposed theory is tested for hydration of the Na+ and Cl− ions in ambient water at infinite dilution. An improved agreement of the ion hydration structure and thermodynamics with molecular simulation results is found as compared to the conventional RISM/HNC treatment. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1313388
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  • 6
    Electronic Resource
    Electronic Resource
    Hydration structure and stability of Met-enkephalin studied by a three-dimensional reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 9830-9836 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study the hydration structure and free energy of several conformations of Met-enkephalin in ambient water by employing the one-dimensional (1D) as well as three-dimensional (3D) reference interaction site model (RISM) integral equation theories, complemented by the hypernetted chain (HNC) closure with the repulsive bridge correction (RBC). The RBC contribution to the excess chemical potential of solvation is calculated by means of the thermodynamic perturbation theory (TPT), which crucially reduces computational burden and thus is especially important for a hybrid algorithm of the RISM with molecular simulation. The 3D-RISM/HNC+RBC-TPT approach provides improved prediction of the solvation thermodynamics and gives a detailed description of the solvation structure of a biomolecule. The results obtained are discussed and compared to those following from the 1D-RISM/HNC theory. The latter yields physically reasonable results for the conformational stability of biomolecules in solution, which is further improved by adding the 1D-RBC. The modified, 1D-RISM/HNC+RBC-TPT integral equation theory combined with the simulated annealing or generalized-ensemble Monte Carlo simulation methods is capable of reliable prediction of conformations of biomolecules in solution with due account for the solvent effect at the microscopic level. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1321039
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  • 7
    Electronic Resource
    Electronic Resource
    Self-consistent field, ab initio molecular orbital and three-dimensional reference interaction site model study for solvation effect on carbon monoxide in aqueous solution (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 9463-9468 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have developed a three-dimensional (3D) extension of the reference interaction site model-self-consistent field (RISM-SCF) method to treat the electronic structure of a solvated molecule. The site–site treatment of the solute–solvent correlations involving the approximation of radial averaging constitutes a bottleneck of the RISM-SCF method, and thus lacks a 3D picture of the solvation structure for complex solutes. To resolve this problem, we devised out a 3D generalization of the RISM integral equations which yields the 3D correlation functions of interaction sites of solvent molecules around a solute of arbitrary shape. In the present article, we propose a SCF combination of the ab initio molecular orbital (MO) methods and 3D-RISM approach. A benchmark result for carbon monoxide in ambient water is also presented. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.481564
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  • 8
    Electronic Resource
    Electronic Resource
    Self-consistent description of a metal–water interface by the Kohn–Sham density functional theory and the three-dimensional reference interaction site model (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 10095-10112 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have developed a self-consistent description of an interface between a metal and a molecular liquid by combination of the density functional theory in the Kohn–Sham formulation (KS DFT) for the electronic structure, and the three-dimensional generalization of the reference interaction site model (3D RISM) for the classical site distribution profiles of liquid. The electron and classical subsystems are coupled in the mean field approximation. The procedure takes account of many-body effects of dense fluid on the metal–liquid interactions by averaging the pseudopotentials of liquid molecules over the classical distributions of the liquid. The proposed approach is substantially less time-consuming as compared to a Car–Parrinello-type simulation since it replaces molecular dynamics with the integral equation theory of molecular liquids. The calculation has been performed for pure water at normal conditions in contact with the (100) face cubic centered (fcc) surface of a metal roughly modeled after copper. The results are in good agreement with the Car–Parrinello simulation for the same metal model. The shift of the Fermi level due to the presence of water conforms with experiment. The electron distribution near an adsorbed water molecule is affected by dense water, and so the metal–water attraction follows the shapes of the metal effective electrostatic potential. For the metal model employed, it is strongest at the hollow site adsorption positions, and water molecules are adsorbed mainly at the hollow and bridge site positions rather than over metal atoms. Layering of water molecules near the metal surface is found. In the first hydration layer, adsorbed water molecules are oriented in parallel to the surface or tilted with hydrogens mainly outwards the metal. This orientation at the potential of zero charge agrees with experiment. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.478883
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  • 9
    Electronic Resource
    Electronic Resource
    The structure and adsorption of the four bonding sites model for associating fluids in disordered porous media from replica Ornstein–Zernike integral equation theory (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 8651-8661 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A model for a network-forming associating fluid in which each of the particles have four sites available for bonding is considered. The model possesses liquid–gas transition in the absence of attractive long-range nonassociative interactions. We have studied the adsorption of the fluid in a disordered porous media that corresponds to an equilibrium configuration of hard spheres. The associative replica Ornstein–Zernike (ROZ) equations are solved with the Percus–Yevick (PY) and hypernetted chain (HNC) closures and with the ideal network approximation. The pair distribution functions and the structure factors have been obtained. The adsorption isotherms have been calculated using a system of hard spheres adsorbed in a hard-sphere matrix as a reference. The associative contribution to the chemical potential follows from Wertheim's thermodynamic perturbation theory, however, with monomer fraction from the solution of the ROZ equations. The liquid–vapor coexistence curve has been evaluated. We have observed shrinking of the coexistence envelope with increasing matrix density. The critical temperature and the critical density are sensitive to the density of adsorbent. Both decrease with increasing matrix density. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476295
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  • 10
    Electronic Resource
    Electronic Resource
    Extended states of a shallow donor located near a semiconductor-insulator interface (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 435-456 
    Details
    ISSN: 0020-7608
    Keywords: semiconductor-insulator interface ; shallow donor ; extended electronic states ; scattering ; photoionization cross section ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Scattering of a conduction electron by a charged shallow donor located near a semiconductor-insulator interface in the semiconductor or by a charged center embedded in the insulator is considered within the model of a hydrogenlike atom in a semi-infinite space. The interface influence is allowed for by spatial confinement of the electron envelope wave function. The impurity electrostatic image at the interface is taken into account. The problem is separable in prolate spheroidal coordinates and thus is solvable exactly. A rapidly convergent expansion is proposed for the angular eigenfunctions. The radial eigenfunctions are calculated directly by numerical integration of the radial boundary value problem. Expansions of the scattering wave function and the scattering amplitude in terms of the eigenfunctions of the problem are obtained. Using the extended and localized state wave functions, the photoionization cross section of a shallow donor near a semiconductor-insulator interface is calculated. It is presented as a superposition of the oscillator strengths of transitions to the partial extended eigenstates that constitute the scattering wave function. Near the interface, the cross section is enhanced significantly and redistributed over the direction of photoionized electron escape. The photoionization threshold follows the localized state energy varying with the donor-interface distance.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 435-456, 1998
    Additional Material: 17 Ill.
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