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Gunaga SS, Bryce DL. Modulation of Rotational Dynamics in Halogen-Bonded Cocrystalline Solids. J Am Chem Soc 2023; 145:19005-19017. [PMID: 37586107 DOI: 10.1021/jacs.3c06343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Dynamic processes are responsible for the functionality of a range of materials, biomolecules, and catalysts. We report a detailed systematic study of the modulation of methyl rotational dynamics via the direct and the indirect influence of noncovalent halogen bonds. For this purpose, a novel series of cocrystalline architectures featuring halogen bonds (XB) to tetramethylpyrazine (TMP) is designed and prepared using gas-phase, solution, and solid-state mechanochemical methods. Single-crystal X-ray diffraction reveals the capacity of molecular bromine as well as weak chloro-XB donors to act as robust directional structure-directing elements. Methyl rotational barriers (Ea) measured using variable-temperature deuterium solid-state NMR range from 3.75 ± 0.04 kJ mol-1 in 1,3,5-trichloro-2,4,6-trifluorobenzene·TMP to 7.08 ± 0.15 kJ mol-1 in 1,4-dichlorotetrafluorobenzene·TMP. Ea data for a larger series of TMP cocrystals featuring chloro-, bromo-, and iodo-XB donors are shown to be governed by a combination of steric and electronic factors. The average number of carbon-carbon close contacts to the methyl group is found to be a key steric metric capable of rationalizing the observed trends within each of the Cl, Br, and I series. Differences between each series are accounted for by considering the strength of the σ-hole on the XB donor. One possible route to modulating dynamics is therefore via designer cocrystals of variable stoichiometry, maintaining the core chemical features of interest between a given donor and acceptor while simultaneously modifying the number of carbon close contacts affecting dynamics. These principles may provide design opportunities to modulate more complex geared or cascade dynamics involving larger functional groups.
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Affiliation(s)
- Shubha S Gunaga
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5 Canada
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5 Canada
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Kuznetsov V. Stereochemistry of Simple Molecules inside Nanotubes and Fullerenes: Unusual Behavior of Usual Systems. Molecules 2020; 25:molecules25102437. [PMID: 32456128 PMCID: PMC7287839 DOI: 10.3390/molecules25102437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Over the past three decades, carbon nanotubes and fullerenes have become remarkable objects for starting the implementation of new models and technologies in different branches of science. To a great extent, this is defined by the unique electronic and spatial properties of nanocavities due to the ramified π-electron systems. This provides an opportunity for the formation of endohedral complexes containing non-covalently bonded atoms or molecules inside fullerenes and nanotubes. The guest species are exposed to the force field of the nanocavity, which can be described as a combination of electronic and steric requirements. Its action significantly changes conformational properties of even relatively simple molecules, including ethane and its analogs, as well as compounds with C-O, C-S, B-B, B-O, B-N, N-N, Al-Al, Si-Si and Ge-Ge bonds. Besides that, the cavity of the host molecule dramatically alters the stereochemical characteristics of cyclic and heterocyclic systems, affects the energy of pyramidal nitrogen inversion in amines, changes the relative stability of cis and trans isomers and, in the case of chiral nanotubes, strongly influences the properties of R- and S- enantiomers. The present review aims at primary compilation of such unusual stereochemical effects and initial evaluation of the nature of the force field inside nanotubes and fullerenes.
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Affiliation(s)
- Valerij Kuznetsov
- Ufa State Aviation Technical University, K. Marksa, 12, Ufa 450008, Russia;
- Ufa State Petroleum Technological University, Kosmonavtov, 1, Ufa 450062, Russia
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Szell PMJ, Zablotny S, Bryce DL. Halogen bonding as a supramolecular dynamics catalyst. Nat Commun 2019; 10:916. [PMID: 30796220 PMCID: PMC6385366 DOI: 10.1038/s41467-019-08878-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/04/2019] [Indexed: 01/23/2023] Open
Abstract
Dynamic processes have many implications in functional molecules, including catalysts, enzymes, host-guest complexes, and molecular machines. Here, we demonstrate via deuterium NMR relaxation experiments how halogen bonding directly impacts the dynamics in solid 2,3,5,6-tetramethylpyrazine cocrystals, catalyzing the methyl group rotation. On average, we observe a reduction of 56% in the rotational activation energy of the methyl groups in the halogen bonded cocrystals, contrasting the reduction of 36% in the hydrogen bonded cocrystals, with respect to pure 2,3,5,6-tetramethylpyrazine. Density functional theory calculations attribute this superior catalytic ability of the halogen bond to the simultaneous destabilization of the staggered conformation and stabilization of the gauche conformation, overall reducing the rotational energy barrier. Furthermore, the calculations suggest that the catalytic ability of the halogen bond may be tuneable, with stronger halogen bond donors acting as superior dynamics catalysts. Thus, halogen bonding may play a role in both assembly and promoting dynamical processes. The halogen bond is well known for its ability to assemble supramolecules. Here, using NMR experiments, the authors reveal the role of these bonds in dynamic processes, finding that the halogen bond directly catalyzes dynamical rotation in solid cocrystals by reducing the associated energy barrier.
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Affiliation(s)
- Patrick M J Szell
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Scott Zablotny
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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Beckmann PA, Ford J, Malachowski WP, McGhie AR, Moore CE, Rheingold AL, Sloan GJ, Szewczyk ST. Proton Spin-Lattice Relaxation in Organic Molecular Solids: Polymorphism and the Dependence on Sample Preparation. Chemphyschem 2018; 19:2423-2436. [PMID: 29956438 DOI: 10.1002/cphc.201800237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Indexed: 11/07/2022]
Abstract
We report solid-state nuclear magnetic resonance 1 H spin-lattice relaxation, single-crystal X-ray diffraction, powder X-ray diffraction, field emission scanning electron microscopy, and differential scanning calorimetry in solid samples of 2-ethylanthracene (EA) and 2-ethylanthraquinone (EAQ) that have been physically purified in different ways from the same commercial starting compounds. The solid-state 1 H spin-lattice relaxation is always non-exponential at high temperatures as expected when CH3 rotation is responsible for the relaxation. The 1 H spin-lattice relaxation experiments are very sensitive to the "several-molecule" (clusters) structure of these van der Waals molecular solids. In the three differently prepared samples of EAQ, the relaxation also becomes very non-exponential at low temperatures. This is very unusual and the decay of the nuclear magnetization can be fitted with both a stretched exponential and a double exponential. This unusual result correlates with the powder X-ray diffractometry results and suggests that the anomalous relaxation is due to crystallites of two (or more) different polymorphs (concomitant polymorphism).
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Affiliation(s)
- Peter A Beckmann
- Department of Physics, Bryn Mawr College, Bryn Mawr, Pennsylvania, USA
| | - Jamie Ford
- Nanoscale Characterization Facility Singh Center for Nanotechnology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Andrew R McGhie
- Laboratory for Research on the Structure of Matter, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Curtis E Moore
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Arnold L Rheingold
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Gilbert J Sloan
- Laboratory for Research on the Structure of Matter, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Steven T Szewczyk
- Department of Materials Science and Engineering School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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T. RR, Smith JC, Krishnan M. Hidden Regularity and Universal Classification of Fast Side Chain Motions in Proteins. J Am Chem Soc 2014; 136:8590-605. [DOI: 10.1021/ja5024783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rajitha Rajeshwar T.
- Center
for Computational Natural Sciences and Bioinformatics, International
Institute of Information Technology, Gachibowli, Hyderabad 500 032, India
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Molecular and Cellular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Marimuthu Krishnan
- Center
for Computational Natural Sciences and Bioinformatics, International
Institute of Information Technology, Gachibowli, Hyderabad 500 032, India
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Wang X, Mallory FB, Mallory CW, Odhner HR, Beckmann PA. Solid state ¹H spin-lattice relaxation and isolated-molecule and cluster electronic structure calculations in organic molecular solids: the relationship between structure and methyl group and t-butyl group rotation. J Chem Phys 2014; 140:194304. [PMID: 24852535 DOI: 10.1063/1.4874157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report ab initio density functional theory electronic structure calculations of rotational barriers for t-butyl groups and their constituent methyl groups both in the isolated molecules and in central molecules in clusters built from the X-ray structure in four t-butyl aromatic compounds. The X-ray structures have been reported previously. We also report and interpret the temperature dependence of the solid state (1)H nuclear magnetic resonance spin-lattice relaxation rate at 8.50, 22.5, and 53.0 MHz in one of the four compounds. Such experiments for the other three have been reported previously. We compare the computed barriers for methyl group and t-butyl group rotation in a central target molecule in the cluster with the activation energies determined from fitting the (1)H NMR spin-lattice relaxation data. We formulate a dynamical model for the superposition of t-butyl group rotation and the rotation of the t-butyl group's constituent methyl groups. The four compounds are 2,7-di-t-butylpyrene, 1,4-di-t-butylbenzene, 2,6-di-t-butylnaphthalene, and 3-t-butylchrysene. We comment on the unusual ground state orientation of the t-butyl groups in the crystal of the pyrene and we comment on the unusually high rotational barrier of these t-butyl groups.
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Affiliation(s)
- Xianlong Wang
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, 4 North Jianshe Rd., 2nd Section, Chengdu 610054, China
| | - Frank B Mallory
- Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
| | - Clelia W Mallory
- Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
| | - Hosanna R Odhner
- Department of Physics, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
| | - Peter A Beckmann
- Department of Physics, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
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Glass DC, Krishnan M, Smith JC, Baudry J. Three entropic classes of side chain in a globular protein. J Phys Chem B 2013; 117:3127-34. [PMID: 23421556 DOI: 10.1021/jp400564q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relationship between the NMR methyl group axial order parameter and the side chain conformational entropy is investigated in inhibitor-bound and apo human HIV protease using molecular dynamics simulation. Three distinct entropic classes of methyl-bearing side chains, determined by the topological distance of the methyl group from the protein backbone (i.e., the number of χ-bonds between the Cα and the carbon of the CH3 group), are revealed by atomistic trajectory analyses performed in the local frame of reference of individual methyl probes. The results demonstrate that topologically equivalent methyl groups experience similar nonbonded microenvironments regardless of the type of residues to which they are attached. Similarly, methyl groups that belong to the same side chain but that are not topologically equivalent exhibit different thermodynamic and dynamic properties. The two-parameter classification (based upon entropy and methyl axial order parameter) of side chains described here permits improved estimates of the conformational entropies of proteins from NMR motional parameters.
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Affiliation(s)
- Dennis C Glass
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309, United States
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