Intramolecular H-bond properties in Solvated Cyclodextrins Elucidated by SAXS and molecular Dynamics simulation

Bakó, I. and Wacha, András Ferenc and Pothoczki, Szilvia (2025) Intramolecular H-bond properties in Solvated Cyclodextrins Elucidated by SAXS and molecular Dynamics simulation. JOURNAL OF MOLECULAR LIQUIDS, 421. No. 126922. ISSN 0167-7322

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Abstract

The structural rigidity of cyclodextrin (CD) molecules, which plays a leading role in their ability to form inclusion complexes, is largely due to the hydrogen bonds (HBs) formed within the CD molecule. To describe these intramolecular HB properties we performed Molecular Dynamics (MD) simulations for α-, β-, and γ-CD molecules in an aqueous environment. We scrutinized the role of tumbling phenomenon, that is, the glucopyranose (Glcp) units may rotate around the glycosidic bonds, in formation of intramolecular HBs. As a first step the tumbling of Glcp units were characterized and different water model were applied to monitor their effects on the ratio of rotated cases. The results show that this ratio can highly depend on the applied water model. Small-angle X-ray diffraction experiments were performed. A comparison of the molecular shape factors obtained from MD simulations and SAXS experiments reveals a low probability of tumbling of Glcp units. This result corresponds with the calculated average probability of rotated Glcp unit from MD simulation for α-CD and β-CD. However, it significantly deviates in the case of γ-CD.

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