We introduce a molecular dynamics/quantum mechanics/continuum solvent model (MD/QM/CSM) approach to investigate binding mechanisms of host-guest systems. The representative conformations of host, guest, and their complex generated from MD simulations at the molecular-mechanics level are used for binding free energy calculations based on a QM/CSM model. We use this approach to explore the binding mechanisms of β-cyclodextrin (β-CD) and 2, 6-di-methyl-β-CD (DM-β-CD) with various guest molecules. Our results suggest that solvent effects play a more important role in determining the relative binding affinities of DM-β-CD than those of β-CD mainly because the former is more flexible than the latter.
Bibliographical noteFunding Information:
BZ gratefully acknowledges the financial support from ‘the Fundamental Research Funds for the Central Universities ’, No. 30915011314 as well as that from the Key Laboratory of Soft Chemistry and Functional Materials, Ministry of Education, Nanjing University of Science and Technology , Nanjing 210094, China. This project is also funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions. Support from a University of Missouri Research Board Award is acknowledged. We appreciate useful comments from Dr. Norman Hamer to improve the manuscript.
© 2016 Elsevier B.V. All rights reserved.
All Science Journal Classification (ASJC) codes
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry