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  • 1
    Electronic Resource
    Electronic Resource
    Shape group studies of molecular similarity and regioselectivity in chemical reactions (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 608-619 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The study of the qualitative and quantitative product distribution in a chemical reaction, in particular regioselectivity, is of fundamental importance. Recently, it has been shown that the regioselectivity of some Diels-Alder cycloadditions can be explained by analyzing the interrelations between electron density contours and molecular electrostatic potentials. This problem is related to a central topic of modern theoretical chemistry and biochemistry: the analysis of molecular shape. This work deals with a rigorous, algebraic method to analyze these surfaces. The procedure is based on the computation of the shape groups (symmetry-independent homology groups of algebraic topology) of the molecular surface, using either a fully analytical algorithm requiring no visual inspection, or a precise method for processing pictorial information if the latter is available. The method provides a concise description of the molecular contour surface, that can replace the usually intuitive, and somewhat subjective, visual characterization of density and electrostatic potential contours. The method is illustrated for the case of Diels-Alder reactions by considering a number of monosubstituted dienes. Extensions of the analysis to dienophiles, as well as other types of reactions are also discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090606
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  • 2
    Electronic Resource
    Electronic Resource
    Shape groups of the electronic isodensity surfaces for small molecules: Shapes of 10-electron hydrides (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1172-1183 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented in the form of a comprehensive package of computer programs, GSHAPE, and applied to a series of 10-electron hydrides to critically evaluate the methodology. Attention is paid to the effects of nuclear geometry and the size of basis on the molecular shape. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend on two continuous parameters: a density value defining the density contour and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is calculated at the ab initio level using basis sets ranging from STO-3G to 6-31G**. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visualization of the results is one option of our program using Application Visualization Software (AVS). For a given molecule, in a given nuclear geometry, the technique provides a 2-D shape map, displaying the distribution of the shape gruops as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, a variety of 2-D shape maps are discussed. © John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540141007
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  • 3
    Electronic Resource
    Electronic Resource
    Shape analysis of hydrogen-bonded networks in solvation clusters (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 633-643 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is developed and applied to characterize the global shape of the hydrogen-bonded networks formed in solvent and solute-solvent clusters. The methodology combines elements of geometry and topology of molecular chains, and it provides a description of the compactness and complexity of the entanglements formed by the network of hydrogen bonds between solute and solvent molecules. This approach complements others in the literature, where the hydrogen bonding is described in terms of the spatial distribution of bonds, their energetics and lifetimes, or the length hydrogen-bonded walks in space. The results of the present technique do not depend too strongly on the details of the molecular geometry. Therefore, one can assess the extent to which large-scale architecture is modified by rearrangements in the nuclear configuration, information which is important in molecular dynamics when estimating the persistence of essential structural features along dynamic trajectories. In this article we discuss the methodology and illustrate its application to the study of water clusters and solvated clusters of acetic acid. Expected qualitative features in the change of shape descriptors in actual reorganizations of hydrogen-bonding patterns are discussed briefly. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150607
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  • 4
    Electronic Resource
    Electronic Resource
    Shape characterization of some molecular model surfaces (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 554-563 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algebraic method is proposed to represent and to characterize in a concise way the shape of an arbitrarily asymmetrical surface composed from spherical pieces. These surfaces include, among others, the well-known van der Waals surfaces. The procedure is based on the computation of a hierarchy of homology groups (“shape groups”) of algebraic topology, for a family of objects defined by the original surface. The technique uses the same input information as that necessary to produce a graphical display of the molecular surface. However, the actual figure is not necessary for the computation of the shape groups. Only a classification of the points on the surface, according to their position with respect to the intersection of two or more spheres, is needed. The result is a purely algebraic characterization that can be obtained and stored by a computer, and that may prove to be useful when comparing shapes of different molecules. Illustrative examples are provided for different molecules, as well as for different conformations of the same molecule.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090513
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  • 5
    Electronic Resource
    Electronic Resource
    A topological analysis of molecular electrostatic potential on van der Waals surfaces for histamine and 4-substituted derivatives as H2-receptor agonists (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 705-716 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular electrostatic potential is an important property for characterizing chemical reactivity and the interactions between biomolecules. A joint description of the molecular electrostatics and the molecular shape in 3-space is more complete than the one provided by only the electrostatics. The characterization of the interrelations between the shape features of a formal “molecular surface” and electrostatic potential is of importance in assessing the degree of similarity within a family of molecules. In this work, we have applied a recently developed topological technique to characterize these aspects of the molecular shape. The approach allows one to calculate simple and concise shape codes which can be used for rationalizing structure-activity correlations. These shape codes are related to topological invariants which characterize the topological structure given to the molecular surface by the electrostatic potential. In this work the molecules of interest are a series of four agonists of the H2-receptor of histamine with very different pharmacological activities. We have analyzed the electrostatics on the fused-sphere (van der Waals) surfaces of these compounds for a number of conformations. Some structural properties and the shape descriptions have been found to correlate with the activity. The results are discussed in the context of the current H2-receptor models.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120608
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  • 6
    Electronic Resource
    Electronic Resource
    Genetic algorithms: A robust scheme for geometry optimizations and global minimum structure problems (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 729-742 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Genetic Algorithm for Geometry Optimizations (GALGO) program has been developed to study the efficiency of this method of finding global minimum structures. Using a semiempirical tight-binding potential, the behavior of different genetic algorithm (GA) operators has been tested for the linear chain isomer of a C8 cluster. An optimum set of parameters for the GA operators is proposed for this problem and afterward is used to obtain the global minimum structure of rare-gas atomic clusters of up to 13 atoms using the 12-6 Lennard-Jones interatomic pair potential. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540160609
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  • 7
    Electronic Resource
    Electronic Resource
    The electronic structure of weakly bound systems. I. Rare-gas bimolecular cations (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 758-767 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general perspective is presented of bimolecular positive ions formed from two rare gases that share a positive charge. These species, which are important in ionospheric processes, arise when neutral van der Waals species are ionized. A general theoretical program based on standard theoretical techniques (e.g., various configuration interaction and Møller-Plesset techniques and quadratic configuration interaction) is outlined, and results for the geometry, stability, and vibrational frequencies for a set of rare gas dimers, AB+, are presented. Specifically, the molecules HeHe+, HeNe+, HeAr+, NeNe+, NeAr+, and ArAr+ are considered; the equilibrium geometry of the ground electronic state is determined at several levels of approximation. Then binding energies are calculated in several ways, and these binding energies are compared to experimental and other sophisticated theoretical results. In general, the agreement with experiment is good, within a few kcal/mol. Harmonic vibrational frequencies at the MP2 level are also computed. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540160611
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  • 8
    Electronic Resource
    Electronic Resource
    The electronic structure of weakly bound systems. II. NeX+ and ArX+(X = H2O, HCl, and HF) bimolecular cations (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 768-776 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The theoretical framework developed and tested in our previous study of weakly bound systems is applied to a sequence of bimolecular cations: (NeX)+ and (ArX)+, where X = HF, H2O, and HCl. The equilibrium structure, binding energies, and vibrational frequencies for this sequence of bimolecular cations are computed using several post-Hartree-Fock methods and triple zeta basis sets. In all cases, the absolute minima in the potential energy surface involves a hydrogen bond. The existence and stability of the aforementioned systems are established with binding energies ranging from 0.1 eV to 1.0 eV. The stability for the systems is explained in terms of the possible dissociative channels and changes in the electron density of the constituent monomers. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540160612
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  • 9
    Electronic Resource
    Electronic Resource
    Validity of the Hammond postulate and constraints on general one-dimensional reaction barriers (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 728-744 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Hammond postulate is a useful, qualitative tool that interrelates structural similarities between reactants, transition structures, and products with the exo- or endothermicity of reactions. It applies to most chemical reactions, although several exceptions are known. In this study the following problem is addressed: is it possible to formulate conditions for the validity of the quantitative Hammond postulate in terms of simple physical quantities characteristic to the molecules involved? A detailed analysis is given for the conditions of validity of the postulate, in terms of bounds on the internal forces and force constants of nuclear arrangements encountered along a reaction path. We have determined a broad class of constraints on barrier shapes that must be satisfied in order to obtain a critical situation that violates the Hammond postulate: a reactant-like transition structure (“transition state”) for endothermic reactions, and a product-like one for exothermic reactions. The general constraints are formulated in terms of physically meaningful quantities: (i) energy differences, (ii) restrictions on slopes (e.g., an upper bound on internal forces), and (iii) restrictions on curvatures (e.g., upper bounds on force constants) along potential curves.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090704
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  • 10
    Electronic Resource
    Electronic Resource
    A complete shape characterization for molecular charge densities represented by Gaussian-type functions (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 220-230 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented, tested and applied for a family of AB2 molecules. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend continuously on two parameters: a density value defining the density contour, and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is modeled by means of Gaussian-type functions. The method employs an explicit form of the charge density function in order to compute the curvature properties for the molecular surfaces analytically, from which the shape groups are derived by the algorithm. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visual inspection of the results of the shape analysis is a possible option. For a given molecule, in a given nuclear configuration, the technique provides a two-dimensional shape map, displaying the distribution of shape groups as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis of shape maps automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, several two-dimensional shape maps for simple systems are discussed. The changes induced in these maps by a change in the nuclear geometry, as well as by the changes of the nuclear charge, are also analyzed. The method is applicable to large biomolecules of interest if charge density information is available.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120212
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