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  • Computational Chemistry and Molecular Modeling  (5)
  • 1995-1999  (5)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 57 (1996), S. 183-198 
    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 virial field V(r) is defined by the local statement of the quantum mechanical virial theorem, as the trace of the Schrödinger stress tensor. This field defines the electronic potential energy density of an electron at r and integrates to minus twice the electronic kinetic energy. It is the most short-ranged description possible of the local electronic potential energy and it exhibits the same transferable behavior over bounded regions of real space (corresponding to the functional groups of chemistry) as does ρ(r). This article establishes a structural homeomorphism between -V(r) and ρ(r), showing that the two fields are homeomorphic over all of the nuclear configuration space. The stable or unstable structure defined by the gradient vector field Δρ(r; X) for any configuration X of the nuclei can be placed in a one-to-one correspondence with a structure defined by the field -ΔV(r; X′). In particular, a molecular graph for ρ(r) defining a molecular structure is mirrored by a corresponding virial graph for V(r) and the lines of maximum density linking bonded nuclei in the former field are matched by a set of lines of maximally negative potential energy density in the latter. The homeomorphism is also geometrically faithful, an equilibrium geometry in general, exhibiting equivalent structures in the two fields. The demonstration that the virial field, whose integrated value equals twice the total energy, is essentially just a locally scaled version of the electron density is suggestive of possible new approaches in density functional theory. © 1996 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 454-464 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a computational method for prediction of the conformation of a ligand when bound to a macromolecular receptor. The method is intended for use in systems in which the approximate location of the binding site is known and no large-scale rearrangements of the receptor are expected upon formation of the complex. The ligand is initially placed in the vicinity of the binding site and the atomic motions of the ligand and binding site are explicitly simulated, with solvent represented by an implicit solvation model and using a grid representation for the bulk of the receptor protein. These two approximations make the method computationally efficient and yet maintain accuracy close to that of an all-atom calculation. For the benzamidine/trypsin system, we ran 100 independent simulations, in many of which the ligand settled into the low-energy conformation observed in the crystal structure of the complex. The energy of these conformations was lower than and well-separated from that of others sampled. Extensions of this method are also discussed. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 4 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 56 (1995), S. 409-419 
    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: Two different macrospopic pieces of copper have different external potentials and, because of the unique functional relationship between the electron density and the external potential as demanded by density functional theory, should possess different electron density distributions. Experimentally, however, an atom in the bulk exhibits the same electron density in both samples and they possess identical sets of intensive properties. Density functional theory does not account for the fundamental observation underlying the theory of atoms in molecules: that what are apparently identical distributions of charge can be observed for an atom or a grouping of atoms in systems with different external potentials and that these atoms contribute essentially identical amounts to the energies and all other properties of the systems in which they occur. It is shown that, unlike the external potential, the kinetic energy density and the potential energy density, defined by the virial of the Ehrenfest force acting on electron density, are short-range functions. As recorded in the first article on atoms in molecules, they exhibit a local dependence on the electron density that causes them to faithfully mimic the transferability of the atomic charge distributions from one system to another. The electron, the kinetic energy, and the virial densities are all determined directly by the one-electron density matrix, a function termed near-sighted by Professor Kohn. It is this near-sighted property of the one-matrix that underlies the working hypothesis of chemistry - that of a functional group exhibiting a characteristic set of properties. The observations obtained from the theory of atoms in molecules and the atomic theorems it determines demonstrate the existence of a local relationship between the electron density and all properties of a system. © 1995 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 60 (1996), S. 373-379 
    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: It is shown how the electron charge and current distributions, which Professor McWeeny describes as fundamental property densities, may be used to determine the atomic and group contributions to magnetic response properties. © 1996 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 527-533 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simple expressions for the forces due to dihedral-angle interactions are derived using first principles of mechanics. The expressions require significantly fewer numerical operations than those generally used in the literature and provide insight into the physics of dihedral-angle interactions. It is also shown that the scalar virial due to angle-dependent interactions is zero. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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