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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 648-659 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations of chemical shifts have been carried out using “locally dense” basis sets for the resonant atom of interest, and smaller, attenuated sets on other atoms in the molecule. For carbon, calculations involving a 6-311G(d) triply split valence set with polarization on the resonant atom and 3-21G atomic bases on other heavy atoms result in good agreement with experiment, and are virtually identical to those found employing the larger basis on all atoms. For species such as nitrogen, oxygen, and fluorine where standard balanced basis sets do not agree well with experiment, use of attenuated sets fail as well. The use of locally dense basis sets permits calculations previously impractical, and the successful application to carbon suggests that the chemical shift is most dependent on the local basis set, and less so on whether or not a balanced or unbalanced calculation is being carried out.
    Additional Material: 5 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 850-855 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics simulations out to 100 ps have been carried out at 300 K in vacuo on the repeating pentapeptide, (VPGVG), of the elastin fiber. The structure employed in the simulation is a β-spiral (helical structure) with 2.7 pentamers per turn and with a 9.45 Å rise per turn and 21.6 Å rise per turn in the relaxed and extended states, respectively. Large amplitude backbone torsion angle fluctuations are observed in the relaxed state, and significant damping is observed upon extension, particularly in the suspended segments of the β-spiral structure. Accordingly the entropy change an extension was computed and found to be a substantial -1.1 entropy units per residue. The various energy components are compared for relaxed and extended states and the relevance of the results to the molecular mechanism of entropic elasticity is discussed.
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  • 3
    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 proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anions is proposed and applied to CH3-, NH2-, OH-, and CN-.
    Additional Material: 8 Tab.
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  • 4
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy profiles were calculated for τ1, the C—C—C=O torsion, and τ2, the C—C—C—C torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4-21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ1, τ2) = (0, -60), (0, 180), (120, 180), (120, -60), and the maxima (0, 0), (180, 180), and (60, -60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a C—H bond trans to a C—C bond (C—Hs) is consistently shorter than a C—H bond (C—Ha) trans to another C—H bond. Specifically, for X—C(α) (= O)—C(β)—C(γ)—C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2-pentanone: (1) C(δ)—Hs 〈 C(δ)—Ha in all the conformers in which the δ-methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)-methyl and the ester groups, the bonding pattern is affected by a C—H⃛O=C interaction. (2) In the most stable conformers, (0, 60), C(β)—Ha 〈 C(β)—Hs, and C(γ)—Ha 〈 C(γ)—Hs, regardless of X. (3) The average C—C bonds in the τ2 = 180° conformers are consistently shorter than those with τ2 = 60° (compared at τ1 constant). In the most stable conformations (τ1 = 0°, τ2 = 60° or 180°), the bonding sequence is consistently C(α)—C(β) 〈 C(β)—C(γ) 〈 C(γ)—C(δ); whereas, when τ1 = 120°, C(α)—C(β) 〈 C(β)—C(γ) 〉 C(γ)—C(δ).
    Additional Material: 5 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 520-532 
    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 method for preparing compact orbital and auxiliary basis sets for LCAO-LSD calculations has been developed. The method has been applied to construct basis sets for first row transition metal atoms from Sc to Zn for the 3dn-14s1 and 3dn-24s2 configurations. The properties of different expansion patterns have been tested in atomic calculations for the chromium atom.
    Additional Material: 1 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 598-609 
    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 many applications of the distance matrix, D(G), and the Wiener branching index, W(G), in chemistry are briefly outlined. W(G) is defined as one half the sum of all the entries in D(G). A recursion formula is developed enabling W(G) to be evaluated for any molecule whose graph G exists in the form of a tree. This formula, which represents the first general recursion formula for trees of any kind, is valid irrespective of the valence of the vertices of G or of the degree of branching in G. Several closed expressions giving W(G) for special classes of tree molecules are derived from the general formula. One illustrative worked example is also presented. Finally, it is shown how the presence of an arbitrary number of heteroatoms in tree-like molecules can readily be accommodated within our general formula by appropriately weighting the vertices and edges of G.
    Additional Material: 10 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 772-777 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force constants for both anomers of glucose are evaluated using CNDO/Force method.
    Additional Material: 1 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1104-1108 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Myelin basic protein (MBP) is the major extrinsic protein of the myelin sheath in the central nervous system. We have examined the predicted structure of segments of MBP using the molecular mechanics program ECEPP83 developed by Scheraga and coworkers as modified by Chuman, Momany, and Schafer. We have focused upon segments containing the Pro-Pro-Pro sequence (residues 100-102), which have been predicted from standard algorithms to exist in a hairpin loop connecting anti-parallel beta-strands. Both the shorter (98-105, 99-105, and 100-105) and longer segments (87-109, 87-118, and 87-120) have been examined. These results indicate potential for a chain reversal in this region. The shorter segments have been studied by others using NMR techniques and the results are compared.
    Additional Material: 5 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 158-170 
    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 report herein, the implementation of a second-order Moller-Plesset perturbation theory (MP2) program on the IBM LCAP parallel supercomputers. The LCAP systems comprise IBM 308X hosts and 10 FPS-X64 attached processing units (APs). The APs are interconnected by a 512 Mbyte shared memory which allows rapid interprocessor communication. All the computationally demanding steps of the MP2 procedure execute efficiently in parallel. Parallel computation of two-electron integrals is accomplished by distributing the loop over shell blocks among the APs. Parallel Fock matrix formation is achieved by having each AP evaluate the contribution of its own integral sublist to the total Fock matrix. The contributions are added together on the host, and the sum diagonalized either on the host or on a single AP. The parallel implementations of the integral transformation and the MP2 calculation are less straightforward. In each case, the use of the shared memory is essential for an efficient implementation. Details of the implementations and performance data are given.
    Additional Material: 5 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 112-117 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Practical methods of generating reliable and economic basis sets for relativistic self-consistent fields (RSCF) calculations are developed. Large component basis sets are generated from constrained optimizations of exponents in the nonrelativistic atomic calculations for light atoms. For heavy atoms, large component basis sets for inner core orbitals are generated by fitting numerical atomic spinors of Dirac-Hartree-Fock calculations with appropriate number of Slater-type functions. Small component basis sets are obtained by using the kinetic balance condition and other computational criteria. With judicious selections of the basis sets, virtual orbitals in RSCF calculations become very similar to those in nonrelativistic calculations, implying that relativistic virtual orbitals can be used in electron correlation calculations in the same manner as the conventional nonrelativistic virtual orbitals. It is also evident that the Koopmans' theorem is also valid in RSCF results.
    Additional Material: 8 Tab.
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