Structure and thermodynamics of α-, β-, and γ-cyclodextrin dimers. Molecular dynamics studies of the solvent effect and free binding energies

Pascal Bonnet, Carlos Jaime, Luc Morin-Allory

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61 Citations (Scopus)

Abstract

The α-, β-, and γ-cyclodextrin (CyDs) dimers were studied by molecular dynamics (MD) simulations in water as an explicit solvent. The relative stability of dimers and the involved molecular interactions were determined. Three possible starting orientations were considered for the dimers: head-to-head, head-to-tail, and tail-to-tail. MD simulations were performed over a period of 5 ns to ensure the stability of the system for both the CyD dimers and monomers. The MM-PBSA methodology was used to obtain the free binding energy of the dimers and to determine the most stable arrangement for each solvated CyD. In a vacuum, MD simulations provided the head-to-head orientation as the most stable orientation for the three CyDs, while in aqueous solution the, the head-to-tail orientation was found to be the most stable for the α-CyD dimer and the tail-to-tail orientation the most stable for the β- and γ-CyD dimers.
Original languageEnglish
Pages (from-to)8602-8609
JournalJournal of Organic Chemistry
Volume67
Issue number24
DOIs
Publication statusPublished - 29 Nov 2002

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