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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
    Manifold theory of multidimensional potential surfaces (1981)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 20 (1981), S. 185-196 
    Details
    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: Local coordinate systems are introduced into open sets of topological spaces, defined for the nuclear configuration space R of polyatomic nuclear systems. The open sets are directly related to common chemical concepts, such as chemical structure, reaction mechanism, and stability of reaction paths. A topological model of molecules and chemical reactions is a generalization of the geometrical model, and is particularly suitable to account for the nonrigid nature of chemical structures. The coordinate neighborhoods defined on R and on its submanifolds represent the extent and natural limits for partial analyses of multidimensional potential surfaces.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560200716
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  • 3
    Electronic Resource
    Electronic Resource
    Level set topology of the nuclear charge space and the electronic energy functional (1982)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 22 (1982), S. 101-114 
    Details
    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: Electronic energy level set topologies in the abstract nuclear charge space Z of molecular systems are defined and analyzed. Two theorems, one on the general convexity of level sets in Z, another on homotopies of boundaries of level sets, induced by nuclear geometry variations in the nuclear configuration space R, are proven. The applications of the two theorems are illustrated by examples of various molecules and ions.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560220111
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  • 4
    Electronic Resource
    Electronic Resource
    Nuclear charges and molecular total energies: A rule on nested reaction globes (1986)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 29 (1986), S. 333-343 
    Details
    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 simple convexity relation for the nuclear charges of isoelectronic molecules implies some energy relations and topological constraints on their respective reaction globes. These energy relations take the form of a “rule on nested reaction globes.” These reaction globes and their special cases of conformational globes describe the interrelations within families of chemical reactions and conformational changes, respectively. The nuclear charge relations lead to constraints on the relative positioning of reaction globes. These relative positions provide a concise description of energy relations for families of reactions. Conditions are given for a special case, when one reaction globe is completely enclosed by another. The general conclusions are illustrated by results of ab initio potential surface calculations on the conformational problem of 1,4-disubstituted 2-butenes.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560290307
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  • 5
    Electronic Resource
    Electronic Resource
    The metric properties of the reduced nuclear configuration space (1984)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 26 (1984), S. 983-985 
    Details
    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 proof is given for the triangle inequality of distance function d in the reduced nuclear configuration space M, used in the differentiable manifold model of potential-energy hypersurfaces [P. G. Mezey, Int. J. Quantum Chem. Quantum Chem. Symp. 17, 137 (1983)]. This result completes the proof that M is indeed a metric space with metric d.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560260603
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  • 6
    Electronic Resource
    Electronic Resource
    Dependence of MO shapes on a continuous measure of delocalization (1988)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 34 (1988), S. 1-13 
    Details
    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: Whereas localization of orbitals has long been a tool for a semiclassical interpretation of chemical properties, it is in fact electron delocalization that is a fundamental property of quantum mechanical molecules. A mathematically well-defined measure is suggested for the degree of delocalization of molecular orbitals. It is shown that an orbital set of maximum delocalization exists for which the degree of delocalization depends on the charge distribution of the molecule. Hartree-Fock canonical orbitals are definitely more localized than the most uniformaly distributed MO's giving an equivalent description of the molecule. The changes in the geometrical shape of molecular orbitals are studied passing (quasi-) continuously from the strongly localized description towards the most delocalized picture. In the case of charge-inhomogeneities even the most delocalized orbitals remain rather compact. The degree of maximum delocalization may be correlated with chemical properties such as reactivity. The shape distortion of MO's under the perturbing effect of other ions and small molecules is investigated in several examples.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560340804
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  • 7
    Electronic Resource
    Electronic Resource
    Network relations on potential surfaces as aids to computer-based quantum-chemical synthesis planning (1984)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 26 (1984), S. 675-681 
    Details
    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: Current computer hardware developments, in particular, vector processing and parallel processing, are likely to open the door for new applications in quantum chemistry. One applied field that is expected to evolve is a computer-based approach to quantum-chemical synthesis design. Whereas some of the computational difficulties still appear formidable, there are reasons to be optimistic: besides the direct impact of computer hardware developments on existing methods, new theoretical approaches such as density functional theory and numerical molecular wave functions may also become feasible. The topological model of energy hypersurfaces, reaction topology, and quantumchemical manifold theory of reacting systems form a possible framework for a global analysis of a set of all reactions involving a fixed set of nuclei and a fixed number of electrons. The apparent bottleneck for the application of the topological method is the actual computation of the catchment regions (open sets) of reaction topology Tc. In this study some properties of catchment region boundaries are described which lead to computational simplifications. Whereas the ultimate goal of the proposed analysis is to serve as an aid in future quantum-chemical synthesis planning, nonetheless, the boundary networks and sum rules developed in this study may also be of some immediate interest in local surface analysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560260859
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  • 8
    Electronic Resource
    Electronic Resource
    Reflection properties of reaction paths in the reduced nuclear configuration space (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 32 (1987), S. 191-198 
    Details
    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: Chemical reactions and conformational changes of N-atom systems can be described as displacements in a (3N-6)-dimensional metric configuration space M provided with a global metric. Although space M has a metric, it is not in general a vector space; it is a topological space. In contrast to the commonly used internal configuration spaces based on bond length/bond angle internal coordinates, and having no global metrics, within space M each internal configuration of the nuclei of the molecule corresponds to one and only one point of the space. This property of M is advantageous when analyzing chemical reactions. The global metric of M ensures that differences between any two internal configurations can be interpreted as a distance in this space that allows one to provide M with coordinate systems by turning M into a manifold with boundary. Certain formal reaction paths show some counterintuitive behavior within this space: they may undergo a formal reflection at some points of M. A condition, the tangent criterion, is used for the diagnosis of such reaction paths and for the determination of special nuclear configurations where such reflections occur.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560320722
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  • 9
    Electronic Resource
    Electronic Resource
    A method for the characterization of molecular conformations (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 32 (1987), S. 133-147 
    Details
    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: In the course of conformational motions of molecules the changes in shapes of electronic charge distributions follow that of the nuclear framework. However, this coupling between the changes in the nuclear geometry and electron density may depend on the actual nuclear displacement; the coupling may be weak or strong for a given conformational motion. It is of some interest to analyze how faithfully the charge density variations follow the nuclear displacements in a family of conformational rearrangements. In certain cases small conformational changes may induce large changes in the shape of charge density distributions, while in other cases large and qualitatively important conformational changes may involve qualitatively inessential distortions in the shape of electron distributions. In this article we describe a new classification of conformations based on those domains of nuclear configuration space within which the „shape groups“ (symmetry independent homology groups) of the electric charge density remain invariant. Such an analysis might be valuable when seeking correlations between molecular structure and certain biological or biochemical activities.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560320817
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  • 10
    Electronic Resource
    Electronic Resource
    On the inhibition of alcohol dehydrogenase: Shape group analysis of molecular electrostatic potential on van der Waals surfaces for some pyrazole derivatives (1991)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 40 (1991), S. 269-288 
    Details
    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 assessment of molecular similarity between molecules is a fundamental task in computer-aided drug design. In this work, we have applied a combined analysis of steric and electrostatic properties of a series of inhibitors of liver alcohol dehydrogenase (LADH) to rationalize their action. The methodology is based on a topological characterization of the distribution of molecular electrostatic potential (MEP) on the fused-sphere van der Waals surface of a molecule. The topological description can be rendered in the form of two-dimensional diagrams that allow a quick visual or algorithmic analysis of the most relevant shape features of a molecule. By using the representations mentioned above (topological information as a function of the MEP), one can correlate this “structural” information with the values of inhibition constants KI for compounds with different levels of inhibitory activity. This approach allows one to have quantitative measures of similarity for related molecules and to eventually propose compounds that may exhibit a desired activity. The compounds analyzed in this work are a series of substituted derivatives of pyrazole, which span a relatively wide range of inhibitory powers. We have studied the role of the nature of the substituent, as well as its substitutional position, on the molecular shape and correlated these findings with the activity of each compound. Some consequences on the mechanism of inhibition of LADH are also discussed.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560400725
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