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Bao X, Liu X, Dou R, Xu S, Liu D, Luo J, Gong X, Wong CF, Zhou B. How are N-methylcarbamates encapsulated by β-cyclodextrin: insight into the binding mechanism. Phys Chem Chem Phys 2023; 25:13923-13932. [PMID: 37184134 DOI: 10.1039/d3cp01252b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Guest molecules containing chromophore groups encapsulated by β-cyclodextrin (β-CD) generate circular dichroism (CD) signals, which enables a preliminary prediction of their binding modes. However, the accurate determination of the representative binding conformation (RC) remains a challenging task due to the complex conformational space of these host-guest systems. Here, we combine a molecular dynamics/quantum mechanics/continuum solvent model (MD/QM/CSM) with induced circular dichroism (ICD) data (N. L. Pacioni, A. B. Pierini and A. V. Veglia, Spectrochim. Acta A Mol. Biomol. Spectrosc., 2013, 103, 319-324.) to explore the binding mechanism of β-CD with four N-methylcarbamate molecules: promecarb (PC), bendiocarb (BC), carbaryl (CY) and carbofuran (CF). In aqueous solution, their stability decreases as: PC > BC > CY > CF. Comparing the ECD spectra computed from TD-DFT with the ICD data can help eliminate many common binding configurations and identify the RC. The host-guest binding affinities (BAs) estimated using a ONIOM2(B971:PM6)/SMD model reproduce the measured binding trend, reveal the competition between the non-covalent interaction and solvent effect and explain the large difference in their binding modes. We also examine the fluctuations in the computed BA using similar structures.
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Affiliation(s)
- Xiaofang Bao
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xiao Liu
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Ran Dou
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Sen Xu
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Dabin Liu
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Jun Luo
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xuedong Gong
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Chung F Wong
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri-Saint Louis, One University Boulevard, Saint Louis, MO 63121, USA
| | - Baojing Zhou
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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Why 2,6-di-methyl-β-cyclodextrin can encapsulate OH-substituted naphthalenes better than β-cyclodextrin: Binding pose, non-covalent interaction and solvent effect. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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3
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Dou R, Chen K, Chi G, Luo J, Wong CF, Zhou B. Why heptakis(2,3-di-O-acetyl)-β-cyclodextrin can separate terbutaline enantiomers better than β-cyclodextrin: nonbonding and hydrophobic interactions. J INCL PHENOM MACRO 2021. [DOI: 10.1007/s10847-021-01072-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Oqmhula K, Hongo K, Maezono R, Ichibha T. Ab Initio Evaluation of Complexation Energies for Cyclodextrin-Drug Inclusion Complexes. ACS OMEGA 2020; 5:19371-19376. [PMID: 32803030 PMCID: PMC7424588 DOI: 10.1021/acsomega.0c01059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/14/2020] [Indexed: 05/28/2023]
Abstract
We investigated the reliability of ab initio methods to predict the binding energies of molecular encapsulation complexes. Vast possibilities for the docking conformations were screened down to a couple of geometries using a semiempirical docking simulation. For the candidates, we applied density functional theory (DFT) with several exchange-correlation (XC) functionals to evaluate the binding energy. We carefully selected and compared the functionals to elucidate the role of the characteristic factors in achieving the XC effects. It is clarified that the improper combination in XC with D3 dispersion force correction leads to overbinding. For achieving a proper combination, the exchange interaction over the longer range to avoid the overbinding was found to be important.
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Affiliation(s)
- Kenji Oqmhula
- School
of Materials Science, JAIST, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Kenta Hongo
- Research
Center for Advanced Computing Infrastructure, JAIST, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Center
for Materials Research by Information Integration, Research and Services
Division of Materials Data and Integrated System, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047, Japan
- PRESTO,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi-shi, Saitama 322-0012, Japan
| | - Ryo Maezono
- School
of Information Science, JAIST, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Tom Ichibha
- School
of Information Science, JAIST, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Feng L, Ye R, Yuan T, Zhang X, Lu GP, Zhou B. A concerted addition mechanism in [Hmim]Br-triggered thiol–ene reactions: a typical “ionic liquid effect” revealed by DFT and experimental studies. NEW J CHEM 2019. [DOI: 10.1039/c8nj05674a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The π+–π and H-bond interactions between [Hmim]Br and substrates promote a special one-step addition mechanism in thiol–ene reactions.
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Affiliation(s)
- Lin Feng
- Chemical Engineering College
- Nanjing University of Science & Technology Xiaolingwei 200
- Nanjing
- China
| | - Renlong Ye
- Chemical Engineering College
- Nanjing University of Science & Technology Xiaolingwei 200
- Nanjing
- China
| | - Tao Yuan
- Chemical Engineering College
- Nanjing University of Science & Technology Xiaolingwei 200
- Nanjing
- China
| | - Xiao Zhang
- Chemical Engineering College
- Nanjing University of Science & Technology Xiaolingwei 200
- Nanjing
- China
| | - Guo-ping Lu
- Chemical Engineering College
- Nanjing University of Science & Technology Xiaolingwei 200
- Nanjing
- China
| | - Baojing Zhou
- Chemical Engineering College
- Nanjing University of Science & Technology Xiaolingwei 200
- Nanjing
- China
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Dang P, Ye R, Meng F, Han Y, Zhou Y, Gong X, Zhou B. Microencapsulation thermodynamics of methylated β-cyclodextrins with bile salt: enthalpy, entropy, and solvent effect. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-017-0716-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Bani-Yaseen AD. Computational molecular perspectives on the interaction of propranolol with β-cyclodextrin in solution: Towards the drug-receptor mechanism of interaction. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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