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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1930-1942 
    ISSN: 0192-8651
    Keywords: molecular simulation ; periodic boundary conditions ; box shape ; lattice ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In molecular simulations with periodic boundary conditions the computational box may have five different shapes: triclinic; the hexagonal prism; two types of dodecahedrons; and the truncated octahedron. In this article, we show that every molecular simulation, formulated in one of these boxes, can be transformed into a simulation in one of the other ones. The transformation can be done in a preprocessing phase. The simulation in the new box is exactly identical to the simulation in the original one. This means that every molecular simulation may be done in the same type of box. Because the triclinic box is the easiest one to implement, we pay special attention to how to transform the other four box types into triclinic boxes. As a consequence, simulations in the often used truncated octahedron are superfluous; they may be done in a much simpler way in a triclinic box.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1930-1942, 1997
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0192-8651
    Keywords: constraints ; molecular dynamics ; Langevin dynamics ; SHAKE ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1463-1472, 1997
    Additional Material: 2 Ill.
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  • 3
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The activation energy parameters for the reaction of PdX42- (X=Cl-, Br-) in aqueous halide acid solution with thiourea (tu) and selenourea (seu) have been determined. High rates of reaction parallel low enthalpies and appreciable negative entropy of activation. The rate law in each case simplifies to kobs=k[L] where L=tu or seu, and only ligand-dependent rate constants are observed at 25°C. The ligand-dependent rate constants for the first identifiable step in the PdCl42- + X system is (9.1±0.1) × 103 M-1 sec-1 and (4.5±0.1) × 104 M-1 sec-1 for X=tu and seu, respectively, while for the PdBr42- + X system it is (2.0±0.1) × 104 M-1 sec-1 and (9.0±0.1) × 104 M-1 sec-1 for X=tu and seu, respectively.
    Additional Material: 4 Tab.
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  • 4
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Paramagnetic NMR shift reagents, Eu(fod)3 and Pr(fod)3, have been applied to study the one-ene conformations of isomeric dienones. The results obtained using various complex formation models are analysed. The preferred model suggests participation of both carbonyl oxygen Ione pairs in binding with the shift reagents. Criteria for the estimation of errors in the determination of the structure parameters of the substrate-paramagnetic reagent complexes are suggested. The data obtained using NMR shift reagents are consistent with the existence of dienone α,β-cis-isomers as s-cis-conformers only, with the carbonyl group lying out of the plane of all the other atoms of the molecule. Both s-cis and s-trans conformers occur in dienone α,β-trans-isomers.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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