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  • 1
    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
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 102 (1999), S. 279-284 
    ISSN: 1432-2234
    Keywords: Key words: Catchment regions ; Potential energy surfaces ; Molecular conformation analysis ; Fundamental group of reaction mechanisms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. A simple proof is presented for a fundamental topological property of catchment regions of potential energy hypersurfaces: each catchment region C(λ,i), representing a chemical species and its conformational range on the potential energy hypersurface, is simply k-connected for each dimension k=1,2,…3N−6−λ, where λ is the index of the catchment region. The consequences of this property on the structure of the fundamental group of reaction mechanisms (the one-dimensional homotopy group of reaction paths) is discussed.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-2234
    Keywords: Bromine, optimized Gaussian basis for ∼ ; HBr
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract An optimum (15 s 12 p 2 d ) Gaussian basis set was obtained for the Bromine atom by minimizing the open shell energy functional. In the minimization procedure the method of conjugate gradients was applied. The optimum (15 s 12 p 2 d ) basis set was contracted to an [8 s 6 p 2 d ] “double zeta” quality basis set and this contracted set was tested on the HBr molecule.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 53 (1979), S. 183-192 
    ISSN: 1432-2234
    Keywords: Universal Gaussian basis sets for first-row atoms ; First-row atoms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Analysis of various optimum and non-optimum Gaussian basis sets for firstrow elements have indicated that with a minimum increase of the basis set size and without loss of accuracy of the calculated total energy, a single “universal” Gaussian basis set may replace individually optimized Gaussian basis sets for a series of atoms. Such a universal Gaussian basis set may substantially reduce the computational work required for the calculation of molecular integrals in ab initio MO calculations.
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  • 5
    ISSN: 1432-2234
    Keywords: Biopolymer constituents, protonation of ∼
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Side-chain proton affinities for a series of peptide-forming amino acids have been calculated using ab initio Hartree-Fock-Roothaan SCF method; the order of proton affinities is Arg 〉 His 〉 Ser ≈ Tyr ≫ Lys. Protonation of some side-chains in a protein may introduce new energy levels in the band gaps thus fundamentally altering the conduction properties of the proteins.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-2234
    Keywords: Potential energy surfaces ; Reaction paths ; Transition states
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Special properties of the Riemannian metric for energy hypersurfaces, defined within the framework of the Born-Oppenheimer approximation, are utilized in devising a partitioning scheme for domains of nuclear coordinates. The chemically important coordinate domains are distinguished from domains of lesser importance by their curvature properties. Conditions are derived for the stability of minimum energy reaction paths, and the effects of instability regions are investigated. Instability domains along minimum energy paths may allow small vibrational perturbations to alter the outcome of the chemical reaction.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1432-2234
    Keywords: Protonated cytosine ; Protonated thymine ; Tautomeric forms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Proton affinities of several of the tautomeric forms of cytosine and thymine have been calculated using theab initio Hartree-Fock-Roothaan SCF method. Several of the most stable protonated forms may be obtained by direct protonation from one of the two most stable neutral forms. The calculated total energies do not exclude the possibility of the coexistence of several protonated forms in acidic solutions.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1432-2234
    Keywords: Reaction mechanism ; group theory of reaction mechanism ; reaction topology ; potential surfaces ; reaction path ; synthesis planning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The family of all possible reaction mechanisms on a potential surface has an algebraic structure with potential applications in quantum chemical molecular design and synthesis planning. Transformation properties and equivalence relations of reaction paths on potential energy hypersurfaces lead to a topological definition of reaction mechanisms. The family of all fundamental reaction mechanisms on the hypersurface has a group structure,the fundamental group of an appropriately defined topological space. Isomorphism and homomorphism relations between fundamental groups of reaction mechanisms are used to characterize the chemically important topological properties of various subsets of a hypersurface, or those of different excited state hypersurfaces.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-2234
    Keywords: Reaction mechanisms ; synthesis planning ; molecular design ; potential surfaces ; reaction path
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A countable set of distinguished fundamental reaction mechanisms on a potential surface serves as the set of generators for the fundamental group of reaction mechanisms. The effects of a change in the upper limit for energy on such groups are described with the aid of a lower semilattice, introduced into the family of all fundamental groups of reaction mechanisms, supported by the given potential energy surface. The algebraic structure of all reaction paths is described with the aid of groupoids and various subgroupoids and semigroups derived from them.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-2234
    Keywords: Potential-defying chemical species ; vibrational stabilization ; potential surfaces ; zero-point energy ; tunneling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Local and global topological criteria for the existence or non-existence of “potential defying” chemical species are investigated. The number and type of chemical structures which are not indicated by the qualitative features of potential surfaces and which owe their existence to an interplay of vibrational stabilization and destabilization in various domains of potential surfaces are related to topological invariants of compact manifolds. The topological analysis implies that potential defying species (including both stable and transition structures) never occur alone, but several of them occur simultaneously. Conditions are given for the minimum number of potential defying species of various types.
    Type of Medium: Electronic Resource
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