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  • Articles  (5)
  • Atomic, Molecular and Optical Physics  (5)
  • 1990-1994  (5)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 40 (1991), S. 49-59 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects of the solvent on the stability of the zwitterion in the active site of papain is investigated with numerical methods. The solvent is represented by a homogeneous dielectric continuum surrounding a cavity, defined by a fragment of the protein enclosed by a surface obtained following Connolly's method. The discretisized boundary surface is used to solve the Poisson equation in its integral form by means of a numerical approximation based on the boundary element method (BEM), resulting in a set of surface polarization charges. The solvent effect on the proton transfer in papain is studied on the basis of MO-SCF-direct reaction field (DRF) calculations of the energy and charge distribution of the fragment in the field of the surface charges. The role of Asp-158 in the proton transfer in the active site of papain is reevaluated in the presence of the solvent. It is concluded that the effect of the negative charge of Asp-158 is nearly completely screened by the solvent.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 40 (1991), S. 687-702 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This article describes the computation of the tunnel current in a scanning tunneling microscope (STM). The calculation accounts for the three-dimensional scattering taking place simultaneously in the first atomic layers of the sample and in the apex of the probing tip. The model is built with the following ingredients: (a) the tip is represented by a cluster of atoms attached to an otherwise planar, free-electron metal surface, and (b) the analyzed sample is a planar free-electron metal with a local potential corrugation induced by an isolated molecule or adatom. The potential barrier includes the strong bending effect due to the image-charge formation occurring as the tunneling electron crosses the gap between the tip and the sample. The specific theoretical approach designed to solve this scattering problem exploits the fast Fourier transform algorithm to construct a transfer matrix in a mixed real- and momentum-spaces representation. The total current is obtained by summing the contributions of all scattered waves traveling in the barrier between the tip and the sample, and it is studied in this article for various positions of the tip relative to the adsorbed atomic cluster. The theory is used here to simulate the scan of a model-aluminum atom on a free-electron metal substrate using electrons focused by a single-atom tungsten tip.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 48 (1993), S. 451-466 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently we presented an extension of the direct reaction field (DRF) method, in which a quantum system and a set of point charges and interacting polarizabilities are embedded in a continuum that is characterized by a dielectric constant ∊ and a finite ionic strength. The reaction field of the continuum is found by solving the (linearized) Poisson-Boltzmann equation by a boundary element method for the complete charge distribution in a cavity of arbitrary size and form. Like many other authors, we found that the results depend critically on the choice of the size of the cavity, in the sense that the continuum contribution to the solvation energy decreases rapidly with the relative cavity size. The literature gives no clues for the definition of the cavity size beyond “physical intuition” or implicit fitting to experimental or otherwise desired results. From theoretical considerations, a number of limitations on the position of the boundary are derived. With a boundary defined within these limitations, the experimental hydration energies cannot be reproduced, mainly because of the neglected specific interactions. In addition, we found that the description of the solute's electronic states also depends on the solvation model. We suggest that one or more explicit solvent layers are needed to obtain reliable solvation and excitation energies. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 38 (1990), S. 181-189 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The direct reaction field (DRF) method, developed to incorporate the effects of a (large) semiclassical environment into the Hamiltonian of a quantum mechanical system, is briefly reviewed. It is shown that the DRF method behaves - at least - like a supermolecule SCF calculation. With the water dimer as an example, the similarity with the SCF procedure is demonstrated, and an application to the interaction between the active site of papain and the remaining 3000 or so atoms of this protein shows the inadequacy of dielectric constant models and the necessity of including atomic polarizabilities in model force fields.
    Additional Material: 3 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 45 (1993), S. 637-647 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a new numerical method for solving the Schrödinger equation in the case of scattering or tunneling states. As an example, we study a model of the scanning tunneling microscope. The method uses a finite-element approximation of the wave function in the region of the scattering potential. From the wave function that we obtain, we derive the tunnel current density. © 1993 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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