Exploring host-guest complexation mechanisms by a molecular dynamics/quantum mechanics/continuum solvent model approach

Renlong Ye; Xuemei Nie; Yumei Zhou; Chung F. Wong; Xuedong Gong; Wei Jiang; Weihua Tang; Yan A. Wang; Thomas Heine; Baojing Zhou

doi:10.1016/j.cplett.2016.02.006

Exploring host-guest complexation mechanisms by a molecular dynamics/quantum mechanics/continuum solvent model approach

Renlong Ye, Xuemei Nie, Yumei Zhou, Chung F. Wong, Xuedong Gong, Wei Jiang, Weihua Tang, Yan A. Wang, Thomas Heine, Baojing Zhou

Department of Chemistry

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	170-177
Number of pages	8
Journal	Chemical Physics Letters
Volume	648
DOIs	https://doi.org/10.1016/j.cplett.2016.02.006
Publication status	Published - 2016 Mar 16

Bibliographical note

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© 2016 Elsevier B.V. All rights reserved.

All Science Journal Classification (ASJC) codes

Physics and Astronomy(all)
Physical and Theoretical Chemistry

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10.1016/j.cplett.2016.02.006

Cite this

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title = "Exploring host-guest complexation mechanisms by a molecular dynamics/quantum mechanics/continuum solvent model approach",

abstract = "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.",

author = "Renlong Ye and Xuemei Nie and Yumei Zhou and Wong, {Chung F.} and Xuedong Gong and Wei Jiang and Weihua Tang and Wang, {Yan A.} and Thomas Heine and Baojing Zhou",

year = "2016",

month = mar,

day = "16",

doi = "10.1016/j.cplett.2016.02.006",

language = "English",

volume = "648",

pages = "170--177",

journal = "Chemical Physics Letters",

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TY - JOUR

T1 - Exploring host-guest complexation mechanisms by a molecular dynamics/quantum mechanics/continuum solvent model approach

AU - Ye, Renlong

AU - Nie, Xuemei

AU - Zhou, Yumei

AU - Wong, Chung F.

AU - Gong, Xuedong

AU - Jiang, Wei

AU - Tang, Weihua

AU - Wang, Yan A.

AU - Heine, Thomas

AU - Zhou, Baojing

PY - 2016/3/16

Y1 - 2016/3/16

N2 - 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.

AB - 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.

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DO - 10.1016/j.cplett.2016.02.006

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SN - 0009-2614

VL - 648

SP - 170

EP - 177

JO - Chemical Physics Letters

JF - Chemical Physics Letters

ER -

Exploring host-guest complexation mechanisms by a molecular dynamics/quantum mechanics/continuum solvent model approach

Abstract

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