Inclusion of thymol into cucurbiturils: density functional theory approach with dispersion correction and natural bond orbital analysis

Sin, Kye-Ryong; Kim, Chol-Jin; Ko, Sun-Gyong; Hwang, Tok-Man; Han, Yong-Nam; Pak, Yusin

doi:10.1007/s10847-022-01135-4

Cited by 4 publications

(2 citation statements)

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“…Despite the wide range of bioactivities, the number of studies on the structure of thymol available in literature is relatively scarce [9][10][11]. X-ray data show that in the crystalline state, the thymol molecules are held together through O-H•••O hydrogen bonds forming hexamers, which in turn are linked to each other by van der Waals contacts, while the crystal conformation is characterized by having the O-H group pointing away from the isopropyl fragment and the tertiary C-H bond of this fragment pointing towards the hydroxyl oxygen [9].…”

Section: Introductionmentioning

confidence: 99%

Conformational Structure, Infrared Spectra and Light-Induced Transformations of Thymol Isolated in Noble Gas Cryomatrices

2022

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The conformational space of the natural product thymol (2-isopropyl-5-methylphenol) was investigated using quantum chemical calculations at the B3LYP and MP2 levels, which revealed the existence of four types of conformers differing in the orientation of the isopropyl and hydroxyl groups. Thymol monomers were isolated in noble gas (Ar and Xe) matrices (at 15 K) and characterized by IR spectroscopy. With the support of B3LYP harmonic vibrational calculations, the two most stable trans-OH-conformers, differing in the isopropyl orientation, were identified in the cryomatrices. The two less stable cis-OH conformers were not detected as they shall undergo fast tunneling to the most stable ones. Annealing experiments in a Xe matrix up to 75 K did not lead to any conversion between the two isolated conformers, which is in accordance with the significative energy barrier computed for rotamerization of the bulky isopropyl group (~24 kJ mol−1). Vibrational excitation promoted by broadband or by narrowband irradiation, at the 2ν(OH) frequencies of the isolated conformers, did not lead to any conversion either, which was interpreted in terms of a more efficient energy transfer to the hydroxyl rotamerization (associated with a lower energy barrier and a light H-atom) than to the isopropyl rotamerization coordinate. Broadband UV irradiation experiments (λ > 200 nm) led to a prompt transformation of matrix isolated thymol, with spectroscopic evidence suggesting the formation of isomeric alkyl-substituted cyclohexadienones, Dewar isomers and open-chain conjugated ketenes. The photochemical mechanism interpretation concords with that reported for analogous phenol derivatives.

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Section: Introductionmentioning

confidence: 99%

Conformational Structure, Infrared Spectra and Light-Induced Transformations of Thymol Isolated in Noble Gas Cryomatrices

2022

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“…To date, many authors have utilized the continuum solvent model , and explicit solvent water in molecular dynamics (MD) simulations − to computationally study the behavior of CB–ligand binding systems in aqueous solution. In those studies, the essential role of solvent water has been pointed out.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[n]uril of Different Sizes

et al. 2023

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The role of water in host–ligand binding was investigated using a combination of molecular dynamics simulation and three-dimensional reference interaction site model theory. Three different hosts were selected (CB6, CB7, and CB8). Six organic molecules were used as representative ligands: dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF), acetone, 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO), cyclopentanone (CPN), and pyrrole. From the binding free energy and its components, we divided the ligands into two groups: those with relatively small molecular size (DMSO, DMF, acetone, and pyrrole) and those with relatively large molecular size (DBO and CPN). We established that the solvent water in the CB6 cavity can be completely displaced by small ligands, resulting in a greater binding affinity compared with larger CBs, except in the case of the small pyrrole ligand, due to outstanding intrinsic properties such as the relatively high hydrophobicity and low dipole moment. In the case of the large ligands, the solvent water can be displaced by DBO and CPN in both CB6 and CB7; there were similar tendencies in their binding affinities, with the greatest affinity in the CB7 complexes. However, the tendencies of the binding affinity components are completely different due to the difference between the complex structure and the solvation structure when a ligand binds with a CB structure. The binding affinities suggest that the size fit between the ligand and CB cannot guarantee the greatest binding affinity gain because the binding structure and intrinsic properties of CB and ligand equally play a crucial role.

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Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions

García-Argote,

Ruiz,

Inostroza

et al. 2024

J Mol Model

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Inclusion of thymol into cucurbiturils: density functional theory approach with dispersion correction and natural bond orbital analysis

Cited by 4 publications

References 37 publications

Conformational Structure, Infrared Spectra and Light-Induced Transformations of Thymol Isolated in Noble Gas Cryomatrices

Conformational Structure, Infrared Spectra and Light-Induced Transformations of Thymol Isolated in Noble Gas Cryomatrices

Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[n]uril of Different Sizes

Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions

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