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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 17 (1980), S. 651-671 
    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: Ab initio MO calculations, using both minimal (STO-3G) and extended (Roos-Siegbahn) basis sets are reported for the systems methanethiol-imidazole, methanethiol-imidazole-formaldehyde, and methanethiol-imidazole-formamide, which, together with a point-change representation of a long α-helix, form models for the active site of papain. It is shown that the large electric field exerted by the helix in the active-site region is responsible for the presence of the essential residues Cys 25 and His 159 in the form of an ion pair RS- ··· ImH+, which is crucial for a recently proposed mechanism for the catalytic action of the enzyme. Also, an explanation is given for the anomalies in measured pK values for these residues. Detailed studies on the (sub)systems show that minimal basis sets lack the flexibility necessary for describing the type of proton transfer involved. We conclude that α-helices are essential parts of enzymes and that they play a significant role in the catalytic process.
    Additional Material: 8 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 8 (1974), S. 179-191 
    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: A method is given for obtaining the common molecular integrals over generalized gaussian functions: \documentclass{article}\pagestyle{empty}\begin{document}$$ \chi_i = x^{\lambda_i}_i \exp \big\{ - \big(\alpha_i x^2_i + \alpha^{\prime}_i x^{\prime 2}_i + \alpha^{\prime\prime}_i x^{\prime\prime 2}_i\big)\big\} $$\end{document}The present algorithms are expected to be more efficient than those given in earlier work by the same author.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 18 (1980), S. 575-582 
    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 paper outlines a model for calculating the localized states of a 〈 100 〈 edge dislocation in α-Fe. The model used for the calculations is based on the multiple-scattering model (SCF-X α-SW). The purpose of this research is twofold: (1) To determine changes in electronic structure of the lattice near the core region of defects in α-Fe. (2) The variations of hydrostatic pressure about an edge dislocation produce a rearrangement of the conduction electrons. The question is what electrical interaction might be expected between a dislocation and a charged solute atom. The calculations show that the electrons tend to flow away from the compression side toward the dilated regions. The electrical contribution to the binding energy of a solute atom and a dislocation in α-Fe is of the order of 0.01 Ry/electronic unit charge of the atom.
    Additional Material: 5 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 21 (1982), S. 711-716 
    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: A method within the PCILO framework for the study of periodic molecular systems involving impurities is described regarding a one-dimensional chain. The calculation of the whole system is reduced to the calculation of subsystem pairs only. By use of the first-neighbor approximation only one or two subsystem pairs must be considered for subsystems with identical or differing surroundings, respectively. The procedure described yields the ground state energies and charge distributions of the subsystems.
    Additional Material: 1 Ill.
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  • 5
    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.
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  • 6
    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.
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  • 7
    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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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 523-531 
    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 dielectric constant of a material is a macroscopic property that measures the reduction of the electrostatic forces between charged plates separated by the material, compared to a vacuum as intermediate material. It is next encountered as a scaling parameter in Coulomb's law for interacting charges, not only in the force, but also in the energy. In deriving the theory for dielectrics, the macroscopic nature is essential: Only then is the basic assumption that the dielectric material is homogeneous and isotropic a valid one. The appearance of the dielectric constant as a simple scaling factor in Coulomb's law has tempted many computational chemists to forget about the macroscopic nature of the dielectric and to apply the screened Coulomb's law between charges, supposedly in a low-dielectric medium such as proteins, in microscopic force fields. Optimization of force fields even led to distance-dependent “dielectric constants.” Another use of the dielectric constant appears in the dielectric continuum reaction field approaches for the computations of solvation energies and solvent effects. The solute is embedded in a cavity surrounded by the dielectric. Specific interactions between solvent molecules and solute are thus neglected. The cavity size and dielectric constants of interior and exterior are optimized for the model. The aim of this article is to show, by means of calculations on interacting point charges embedded in cavities surrounded by dielectrics and microscopic models of “low-dielectric” materials by explicit polarizabilities, that as far as the dielectric “constant” is concerned anything can happen, depending on the nature of the charges, the distance to the cavity boundary, the spatial arrangement of charges, and polarizabilities. Thus, a warning is issued to injudicious use of dielectric models in microscopic calculations. © 1995 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 6 (1972), S. 859-880 
    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: An outline is given of a semi-empirical scheme for molecular-orbital calculations on transition-metal complexes according to a revised INDO procedure. To judge the reliability of the results of the calculations, the charge-transfer transitions of a number of complexes have been calculated and compared with experimental data. Both for the excitation energies and for the oscillator strengths the agreement is very satisfactory. With respect to the sequence of occupied metal and ligand orbitals it was found that for closed-shell d6 and d8 systems the molecular orbitals which are mainly composed of metal d orbitals have a lower energy than the orbitals built up from ligand p orbitals. Calculations by the extended Hückel method and other similar schemes give the d orbitals as the highest occupied ones as a result of a bad approximation of the diagonal elements of the Fock matrix. The consequences for the interpretation of photo-electron spectra of transition-metal complexes are discussed.
    Additional Material: 3 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 7 (1973), S. 133-134 
    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
    Type of Medium: Electronic Resource
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