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Working Mechanism for a Redox Switchable Molecular Machine Based on Cyclodextrin: A Free Energy Profile Approach
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
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2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 19, 6561-6566 p.Article in journal (Refereed) Published
Abstract [en]

This paper reports the working mechanism for a redox-responsive bistable [2]rotaxane incorporating an alpha-cyclodextrin (alpha-CD) ring (J. Am. Chem. Soc. 2008, 130, 11294-11296), based on free energy profiles obtained from all-atom molecular dynamics simulations. Employing an umbrella sampling technique, the free energy profiles (potential of mean force, PMF) were calculated for the shuttling motion of the alpha-CD ring between a tetrathiafulvalene (TTF) recognition site and a triazole (TZ) unit on the dumbbell of the rotaxane for three oxidation states (0, +1, +2) of the TTF unit. These calculated free energy profiles verified the experimentally observed binding preference for each state. Analysis of the free energy components reveals that, for these alpha-CD-based rotaxanes with charged TTF units, the real driving force for the shuttling in the oxidized states is actually the interactions between water and the rotaxane components, which overwhelms the attractive interactions between the alpha-CD ring and the charged dumbbell. In this work, we put forward a feasible approach to correctly describe the complexation behavior of CD with charged species, that is, free energy profiles obtained from all-atom molecular dynamics simulation.

Place, publisher, year, edition, pages
2010. Vol. 114, no 19, 6561-6566 p.
National Category
Physical Chemistry
URN: urn:nbn:se:kth:diva-27876DOI: 10.1021/jp102834kISI: 000277499700038ScopusID: 2-s2.0-77952514332OAI: diva2:384587
QC 20110110Available from: 2011-01-10 Created: 2011-01-03 Last updated: 2011-05-13Bibliographically approved
In thesis
1. Molecular Dynamics Simulations of Biomimetic Carbohydrate Materials
Open this publication in new window or tab >>Molecular Dynamics Simulations of Biomimetic Carbohydrate Materials
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The present thesis honors contemporary molecular dynamics simulation methodologies which provide powerful means to predict data, interpret observations and widen our understanding of the dynamics, structures and interactions of carbohydrate systems. With this as starting point my thesis work embarked on several cutting edge problems summarized as follows.

In my first work the thermal response in crystal cellulose Iβ was studied with special emphasis on the temperature dependence of the crystal unit cell parameters and the organization of the hydrogen bonding network. The favorable comparison with available experimental data, like the phase transition temperature, the X-ray diffraction crystal structures of cellulose Iβ at room and high temperatures, and temperature dependent IR spectra supported our conclusions on the good performance of the GLYCAM06 force field for the description of cellulose crystals, and that a cautious parameterization of the non-bonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.

The adsorption properties of xyloglucans on the cellulose Iβ surface were investigated in my second paper. In our simulations, the interaction energies between xyloglucan and cellulose in water were found to be considerably lower than those in vacuo. The van der Waals interactions played a prevailing role over the electrostatic interactions in the adsorption. Though the variation in one side chain did not have much influence on the interaction energy and the binding affinity, it did affect the structural properties of the adsorbed xyloglucans.

The interaction of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 was studied in the third paper. The effect of the charge state of the “nucleophile helper” residue Asp87 on the PttXET16-34 active site structure was emphasized. The results indicate that the catalysis is optimal when the catalytic nucleophile is deprotonated, while the “helper” residue and general acid/base residue are both protonated.

In my forth paper, the working mechanism for a redox-responsive bistable [2]rotaxane based on an α-cyclodextrin ring was investigated. The umbrella sampling technique was employed to calculate the free energy profiles for the shuttling motion of the α-cyclodextrin ring between two recognition sites on the dumbbell of the rotaxane. The calculated free energy profiles verified the binding preferences observed experimentally. The driving force for the shuttling movement of the α-cyclodextrin ring was revealed by the analysis of the free energy components.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2011. viii, 66 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2011:12
molecular dynamics simulation, carbohydrate, cellulose, xyloglucan, cyclodextrin
National Category
Biochemistry and Molecular Biology
urn:nbn:se:kth:diva-33439 (URN)978-91-7415-966-0 (ISBN)
Public defence
2011-05-31, FB42, AlbaNova, Roslagstullsbacken 21, Stockholm, 14:00 (English)
Swedish e‐Science Research Center
QC 20110513Available from: 2011-05-13 Created: 2011-05-06 Last updated: 2012-05-24Bibliographically approved

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