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Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: I. Internal Dynamics of Cyclodextrins; y-Cyclodextrin as a Case Study
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
Stockholm University, Faculty of Science, Department of Organic Chemistry.
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2012 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 44, 13159-13171 p.Article in journal (Refereed) Published
Abstract [en]

In this work, we address the description of the dynamics of cyclodextrins in relation with nuclear magnetic resonance (NMR) relaxation data collected for hydroxymethyl groups. We define an integrated computational approach based on the definition and parametrization of a stochastic equation able to describe the relevant degrees of freedom affecting the NMR observables. The computational protocol merges molecular dynamics simulations and hydrodynamics approaches for the evaluation of most of the molecular parameters entering the stochastic description of the system. We apply the method to the interpretation of the C-13 NMR relaxation of the -CH2OH group of cyclodextrins. We use gamma-cyclodextrin as a case study. Results are in agreement with quantitative and qualitative analyses performed in the past with simpler models and molecular dynamics simulations. The element of novelty in our approach is in the treatment of the coupling of the relevant internal (glucopyranose ring twisting/tilting and hydroxymethyl group jumps) and global (molecular tumbling) degrees of freedom.

Place, publisher, year, edition, pages
2012. Vol. 116, no 44, 13159-13171 p.
National Category
Physical Chemistry
URN: urn:nbn:se:su:diva-83808DOI: 10.1021/jp306624dISI: 000310768600002OAI: diva2:577140
Swedish Research Council


Available from: 2012-12-14 Created: 2012-12-14 Last updated: 2013-01-10Bibliographically approved

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Kowalewski, JozefWidmalm, Goran
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Department of Materials and Environmental Chemistry (MMK)Department of Organic Chemistry
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ReferencesLink to record
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