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Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches

Binding affinity and intermolecular interactions are essential characteristics that could be used to comprehend molecular recognition between molecules in supramolecular host-guest systems. This work presented a molecular docking simulation and density functional theory (DFT) calculation at the B3LY...

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Main Authors:	Mustafa, Siti Fatimah Zaharah, Arsad, Siti Rosilah, Mohamad, Habsah, Abdallah, Hassan H., Maarof, Hasmerya
Format:	Article
Published:	Springer Science+Business Media, LLC, part of Springer Nature 2021
Subjects:	QD Chemistry
Online Access:	http://eprints.utm.my/id/eprint/94095/ http://dx.doi.org/10.1007/s11224-020-01708-4
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spelling	my.utm.940952022-02-28T13:31:50Z http://eprints.utm.my/id/eprint/94095/ Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches Mustafa, Siti Fatimah Zaharah Arsad, Siti Rosilah Mohamad, Habsah Abdallah, Hassan H. Maarof, Hasmerya QD Chemistry Binding affinity and intermolecular interactions are essential characteristics that could be used to comprehend molecular recognition between molecules in supramolecular host-guest systems. This work presented a molecular docking simulation and density functional theory (DFT) calculation at the B3LYP-631g(d) level of theory on dillapiole and its derivatives (guest compounds) complexation with cucurbit[7]uril (host compound). The supramolecular host-guest inclusion complex binding energies, − 4.46 to − 5.47 kcal mol−1 and − 0.53 to − 15.38 kcal mol−1 for docking and DFT calculation, respectively, were calculated, and the intermolecular interactions such as the hydrogen bonding, electrostatic, dispersion, and pi-alkyl formation involved were observed. The negative binding energies of D1-CB [7], D2-CB [7], D3-CB [7], D4-CB [7], D5-CB [7], D6-CB [7], and D-CB [7], computed from both the theoretical approaches, suggested the possible inclusion of the guests inside the cucurbit[7]uril cavity, enabling the formation of stable inclusion compounds. However, the significant difference in the binding energy values from the DFT calculation demonstrated a clustered preference in terms of the complex stabilisation, with D2-CB [7], D3-CB [7], D5-CB [7], and D6-CB [7] dominantly favourable, while D1-CB [7], D4-CB [7], and D were inclusion complexes with the least favourable. Encapsulation of the guests’ structural frame as a whole or a part and steric constraint associated with the guests’ substituents positioning in addition to the intermolecular interactions were also noted to induce stabilisation in the binding energy, thus reflecting a preferable inclusion complex. Besides, the theoretical calculations on the rationalisation of the selected guests’ energy barrier were found to correlate well with experimental works of hydroboration oxidation synthesis to produce alcohol derivatives of dillapiole. Springer Science+Business Media, LLC, part of Springer Nature 2021-06 Article PeerReviewed Mustafa, Siti Fatimah Zaharah and Arsad, Siti Rosilah and Mohamad, Habsah and Abdallah, Hassan H. and Maarof, Hasmerya (2021) Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches. Structural Chemistry, 32 (3). pp. 1151-1161. ISSN 1040-0400 http://dx.doi.org/10.1007/s11224-020-01708-4 DOI:10.1007/s11224-020-01708-4
institution	Universiti Teknologi Malaysia
building	UTM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Teknologi Malaysia
content_source	UTM Institutional Repository
url_provider	http://eprints.utm.my/
topic	QD Chemistry
spellingShingle	QD Chemistry Mustafa, Siti Fatimah Zaharah Arsad, Siti Rosilah Mohamad, Habsah Abdallah, Hassan H. Maarof, Hasmerya Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches
description	Binding affinity and intermolecular interactions are essential characteristics that could be used to comprehend molecular recognition between molecules in supramolecular host-guest systems. This work presented a molecular docking simulation and density functional theory (DFT) calculation at the B3LYP-631g(d) level of theory on dillapiole and its derivatives (guest compounds) complexation with cucurbit[7]uril (host compound). The supramolecular host-guest inclusion complex binding energies, − 4.46 to − 5.47 kcal mol−1 and − 0.53 to − 15.38 kcal mol−1 for docking and DFT calculation, respectively, were calculated, and the intermolecular interactions such as the hydrogen bonding, electrostatic, dispersion, and pi-alkyl formation involved were observed. The negative binding energies of D1-CB [7], D2-CB [7], D3-CB [7], D4-CB [7], D5-CB [7], D6-CB [7], and D-CB [7], computed from both the theoretical approaches, suggested the possible inclusion of the guests inside the cucurbit[7]uril cavity, enabling the formation of stable inclusion compounds. However, the significant difference in the binding energy values from the DFT calculation demonstrated a clustered preference in terms of the complex stabilisation, with D2-CB [7], D3-CB [7], D5-CB [7], and D6-CB [7] dominantly favourable, while D1-CB [7], D4-CB [7], and D were inclusion complexes with the least favourable. Encapsulation of the guests’ structural frame as a whole or a part and steric constraint associated with the guests’ substituents positioning in addition to the intermolecular interactions were also noted to induce stabilisation in the binding energy, thus reflecting a preferable inclusion complex. Besides, the theoretical calculations on the rationalisation of the selected guests’ energy barrier were found to correlate well with experimental works of hydroboration oxidation synthesis to produce alcohol derivatives of dillapiole.
format	Article
author	Mustafa, Siti Fatimah Zaharah Arsad, Siti Rosilah Mohamad, Habsah Abdallah, Hassan H. Maarof, Hasmerya
author_facet	Mustafa, Siti Fatimah Zaharah Arsad, Siti Rosilah Mohamad, Habsah Abdallah, Hassan H. Maarof, Hasmerya
author_sort	Mustafa, Siti Fatimah Zaharah
title	Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches
title_short	Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches
title_full	Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches
title_fullStr	Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches
title_full_unstemmed	Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches
title_sort	host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches
publisher	Springer Science+Business Media, LLC, part of Springer Nature
publishDate	2021
url	http://eprints.utm.my/id/eprint/94095/ http://dx.doi.org/10.1007/s11224-020-01708-4
_version_	1726791480286117888
score	13.244109

Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches

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