Computational study of methyl group dynamics in the hydroquinoneclathrate of acetonitrile

Nemkevich, Alexandra; Corry, Ben; Spackman, Mark A.

doi:10.1039/c2cp23384c

Cited by 6 publications

(2 citation statements)

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“…In earlier work based on high-resolution X-ray, synchrotron, and neutron diffraction measurements we have explored the structure and properties of clathrates formed by β-HQ and formic acid, methanol, and acetonitrile, including detailed charge density studies of the apohost and the acetonitrile clathrate . We have also investigated the effect of pressure on these clathrates , and reported molecular dynamics (MD) simulations of guest transport and dynamics. − Most recently we have shown how a combination of single-crystal synchrotron and neutron diffraction data can reveal in exquisite detail the magnitude and three-dimensional nature of the electric fields experienced by the five different urea guest molecules, and the effect on their dipole moments, in the 18-crown-6-urea (1:5) host–guest complex . Importantly, those electric fields corroborate the conclusions of Boxer and co-workers regarding the magnitude of internal electric fields in the active site of enzymes. , …”

Section: Introductionmentioning

confidence: 99%

Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO₂ Clathrate

Grosjean

Spackman

Edwards

et al. 2021

Crystal Growth & Design

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High-resolution 100 K X-ray and neutron single-crystal diffraction data of the non-stoichiometric hydroquinone-CO2 (HQ-CO2) clathrate are combined, with the aim of providing further insight into host–guest binding in hydroquinone clathrates, measuring the electrostatic nature of the cavity formed by the HQ host and, for the first time, estimating the quadrupole moment of the CO2 guest molecule via diffraction techniques. The experimental electron density reveals the cavity in the β-HQ structure to be moderately electronegative and largely featureless, but this does not mean that guest molecules are merely trapped. Calculated binding energies for a series of HQ clathrates reveal strong interactions with the host system and, in the case of CO2, a thermodynamic stability comparable to, or exceeding, that of many molecular cocrystals. The remarkable flexibility of the β-HQ host structure is explored through an analysis of its available clathrate structures at 100 K as well as calculated elastic tensors for crystals of β-HQ and the HQ-CO2 clathrate. Establishing the CO2 quadrupole moment from this analysis of the experimental diffraction data proves challenging, but the sign and estimated range of its magnitude are in agreement with spectroscopic measurements in the gas phase.

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Section: Introductionmentioning

confidence: 99%

Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO₂ Clathrate

Grosjean

Spackman

Edwards

et al. 2021

Crystal Growth & Design

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“…Quantifying these intermolecular host–guest interactions provides insight vital for understanding the interplay between molecules in more complex structures, such as the ligand binding in proteins. The simplicity of the clathrates also allows for theoretical studies on guest transport and molecular dynamics. − Racemic Dianin’s compound (4-(2,2,4-trimethylchroman-4-yl)phenol, abbreviated DC) is known to form clathrates with a wide variation of guest molecules, and it also forms a stable guest-free apohost compound isostructural to the clathrates, which allows for studying the distortions in the host crystal structures caused by the guest species. − The stability of the host structure is emphasized by the fact that synthetic modifications to the DC molecule such as thiolation of the phenolic group, removal of one of the 2-methyl groups, or replacement of the oxygen heteroatom by S or Se do not change the coordination of the host molecules. Even deprotonating the OH ring by introducing morpholine as guest molecules result in a similar packing motif .…”

Section: Introductionmentioning

confidence: 99%

Quantifying Host–Guest Interaction Energies in Clathrates of Dianin’s Compound

Eikeland

Spackman²,

Iversen

2016

Crystal Growth & Design

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The subtle intermolecular host–guest interaction energies have been quantified for 17 different clathrates of the Dianin’s compound. Energy framework analysis of the host structure reveals that, in addition to strong electrostatic forces due to H-bonding, the framework is stabilized by very strong dispersion interactions, resulting in a three-dimensional energy framework. Compared to the host framework, the host–guest interactions are rather weak, and the enclathration only perturbs the host energy framework. Larger guest molecules result in more attractive host–guest interactions, although the shape of the guest molecule is also found to be important. Easy rotation about the c-axis was found for the hexane guest molecule, while the rotation is hindered in the cases of CCl4, CCl3CN, and C(CH3)3CN. For the Dianin clathrates containing the C(CH3)3CN or the acetone guest species, attractive interaction energies between guest molecules in adjacent cavities suggest short-range ordering of the guest molecules. For the clathrates containing multiple guest molecules per cavity, intermolecular interaction energies were used to determine probable guest molecule configurations. In the same way, simple energy calculations like the ones presented here can help crystallographers solve disordered molecular structures by discarding unstable configurations.

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Simulations of Guest Transport in Clathrates of Dianin’s Compound and Hydroquinone

Nemkevich

Spackman

Corry

2013

Chemistry A European J

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Clathrates have been proposed for use in a variety of applications including gas storage, mixture separation and catalysis due to the potential for controlled guest diffusion through their porous lattices. Here molecular dynamics simulations are employed to study guest transport in clathrates of hydroquinone (HQ) and Dianin's compound (DC). Systems investigated were HQ with methanol and acetonitrile, and DC with methanol and ethanol. Simulations were set up with one guest in the pore, two guests in the pore and one vacancy in the pore and a filled pore, and free-energy barriers for movement between cavities of the pore were estimated for all cases. Comparison between these simulations indicates that guest transport most likely proceeds by molecules moving from full to empty cavities consecutively, one by one, rather than in a concerted manner. Thus, the presence of empty cavities is very important for guest transport, which becomes more energetically demanding in fully loaded systems. Flexibility of the host can assist guest transport. In the studied DC clathrates transport occurs via an intermediate conformation in which the hydroxyl group of the alcohol guest molecule participates in the hydrogen-bonded ring of the host. We also address the issue of the number of methanol guest molecules that DC accommodates, for which conflicting information exists. We found that this is likely to be temperature dependent and suggest that under some conditions the system is most likely non-stoichiometric.

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Computational study of methyl group dynamics in the hydroquinoneclathrate of acetonitrile

Cited by 6 publications

References 9 publications

Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO₂ Clathrate

Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO₂ Clathrate

Quantifying Host–Guest Interaction Energies in Clathrates of Dianin’s Compound

Simulations of Guest Transport in Clathrates of Dianin’s Compound and Hydroquinone

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Computational study of methyl group dynamics in the hydroquinoneclathrate of acetonitrile

Cited by 6 publications

References 9 publications

Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO2 Clathrate

Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO2 Clathrate

Quantifying Host–Guest Interaction Energies in Clathrates of Dianin’s Compound

Simulations of Guest Transport in Clathrates of Dianin’s Compound and Hydroquinone

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Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO₂ Clathrate

Insights into Host–Guest Binding in Hydroquinone Clathrates: Single-Crystal X-ray and Neutron Diffraction, and Complementary Computational Studies on the Hydroquinone-CO₂ Clathrate