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  • 1
    Electronic Resource
    Electronic Resource
    Comparison of compuational methods for simulating nuclear Overhauser effects in NMR spectroscopy (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 292-300 
    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: Various algorithms for solving the Solomon equations describing nuclear Overhauser effects (nOes) in NMR spectroscopy have been compared. The applicability of the eigenvalue/eigenvector and the numerical integration approaches have been investigated. The eigenvalue/eigenvector approach is not a computationally efficient means of simulating nOe experiments in which a saturating radiofrequency field is applied during the time course. For experiments in which nOes develop in the absence of an RF field, this approach should only be used in simulating a full NOESY spectrum. Integration schemes have been found to be more efficient at simulating nOe experiments in which the nOe evolves in the presence of a saturating field, at simulating a partial set of initial perturbation experiments and at simulating a few rows or columns in a NOESY spectrum. Various integration schemes were applied to a two-spin system for which an analytic solution is available and to a model B-DNA oligonucleotide hexamer. The previously unused Taylor series algorithm was found to be superior to the Euler, midpoint, and fourth-order Runge-Kutta methods with regard to integration accuracy/computation time. An adaptive step size control routine for the Taylor series integration scheme was developed. Integration schemes can be speeded up in a simple fashion by introducing a distance cutoff for the dipolar interaction. Using a cutoff of 8 Å the Taylor series algorithm was able to compute the NOESY spectrum more rapidly than the eigenvalue/eigenvector algorithm for large spin systems at short mixing times. At longer mixing times the eigenvalue/eigenvector approach becomes the more efficient scheme.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120303
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  • 2
    Electronic Resource
    Electronic Resource
    Rationalizing nuclear overhauser effect data for compounds adopting multiple-solution conformations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 155-161 
    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 is described for refining the populations of a set of multiple-solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least-squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1-O-methyl-α-L-iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton-proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150206
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular dynamics study of iduronate ring conformation (1993)
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 575-588 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular dynamics (MD) simulations of the conformation of the iduronate ring in a methyl glycoside and as the central residue in a trisaccharide have been carried out. Separate simulations were carried out with initial 1C4, 2S0, and 4C1 iduronate ring conformations. Simulations were followed by observing the time development of the Cremer-Pople ring puckering parameters θ,φ2. Starting with chair geometries gave trajectories showing only ring oscillations close to the initial geometry. Simulations were performed with a 2S0 starting geometry using explicit water and in vacuum with dielectric constants (ε) of 1 and 80, as well as with distance-dependent dielectric functions of 2r and 4r. In both the explicit water simulation and the vacuum (ε = 80) simulations, extensive pseudorotational motion was observed in which boat and twist-boat ring conformers interconvert. The overall range of φ22 variation in the trisaccharide was about half of that observed in the methyl glycoside. The Haasnoot procedure for calculating H-H coupling constants in saccharides was applied to structures obtained from MD trajectories. Using MD time averaged couplings along with experimental data allowed the relative fractions of chair and boat/twist-boat forms to be derived. © 1993 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360330407
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    Paper (German National Licenses)
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