QM/MM simulations of carbohydrates

Abdul Mueed Muslim, Jonathan P. McNamara, Hoda Abdel-Aal, Ian H. Hillier, Richard A. Bryce

    Research output: Chapter in Book/Report/Conference proceedingChapter

    Abstract

    Hybrid quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics simulations were used to investigate disaccharide conformation in aqueous solution. In vacuo and aqueous solution conformational free energy surfaces were constructed from potential of mean force calculations, using weighted histogram analysis of combined QM/MM molecular dynamics simulations of 8.5 ns and 13.5 ns respectively. Calculations indicated die presence of direct and water-bridged intersaccharide hydrogen bonds, the latter consistent with a broad range of ψ/Ψ. To improve the accuracy of the description of carbohydrates by semi-empirical QM methods, we also detail our work on reparameterization of the PM3 Hamiltonian. This is based on fitting to 1,2-ethanediol structures and energies. Application of the resulting model, PM3CARB-1, to modeling of glucose is discussed. Improvement in energetic ranking of 4C1, and 1C4 conformations was found. QM/MM dynamics simulations of a disaccharide using PM3CARB-1 did not exhibit transitions from 4C1 to 1C4 structures. © 2006 American Chemical Society.
    Original languageEnglish
    Title of host publicationACS Symposium Series|ACS Symp. Ser.
    Pages186-202
    Number of pages16
    Volume930
    Publication statusPublished - 2006

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