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Erastova V, Evans IR, Glossop WN, Guryel S, Hodgkinson P, Kerr HE, Oganesyan VS, Softley LK, Wickins HM, Wilson MR. Unravelling Guest Dynamics in Crystalline Molecular Organics Using 2H Solid-State NMR and Molecular Dynamics Simulation. J Am Chem Soc 2024; 146:18360-18369. [PMID: 38935813 PMCID: PMC11240262 DOI: 10.1021/jacs.4c03246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024]
Abstract
2H solid-state NMR and atomistic molecular dynamics (MD) simulations are used to understand the disorder of guest solvent molecules in two cocrystal solvates of the pharmaceutical furosemide. Traditional approaches to interpreting the NMR data fail to provide a coherent model of molecular behavior and indeed give misleading kinetic data. In contrast, the direct prediction of the NMR properties from MD simulation trajectories allows the NMR data to be correctly interpreted in terms of combined jump-type and libration-type motions. Time-independent component analysis of the MD trajectories provides additional insights, particularly for motions that are invisible to NMR. This allows a coherent picture of the dynamics of molecules restricted in molecular-sized cavities to be determined.
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Affiliation(s)
- Valentina Erastova
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
- Department
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, U.K.
| | - Ivana R. Evans
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - William N. Glossop
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Songül Guryel
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Paul Hodgkinson
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Hannah E. Kerr
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | | | - Lorna K. Softley
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Helen M. Wickins
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Mark R. Wilson
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
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2
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Sasaki R, Takahashi Y, Hayashi Y, Kawauchi S. Atomistic Mechanism of Anisotropic Heat Conduction in the Liquid Crystal 4-Heptyl-4'-cyanobiphenyl: All-Atom Molecular Dynamics. J Phys Chem B 2020; 124:881-889. [PMID: 31880459 DOI: 10.1021/acs.jpcb.9b08158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
All-atom molecular dynamics simulations were performed on 4-heptyl-4'-cyanobiphenyl (7CB) to study the mechanism of heat conduction in this nematic liquid crystal atomistically. To describe 7CB properly, the AMBER-type force field was optimized for the dihedral parameter of biphenyl and the Lennard-Jones parameters. The molecular dynamics calculation using the optimized force field well reproduced the experimental values of the isotropic-nematic phase transition temperature, density, and anisotropy of the thermal conductivity. Furthermore, the contributions of convection, intramolecular interaction, and intermolecular interaction to the thermal conductivity were determined by performing thermal conductivity decomposition analysis. According to the analysis, the contributions of convection, bond stretching, and bond bending interactions were higher in the direction parallel to the nematic director than that perpendicular to the director, which is the origin of the anisotropy in the nematic phase. This result indicates that the anisotropy is caused by well-aligned covalent bonds and high mobility parallel to the director. This quantitative description of the mechanism of heat conduction of 7CB is foreseen to provide new insights toward designing highly thermally conductive liquid-crystalline materials.
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Affiliation(s)
- Ryoma Sasaki
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology , Tokyo Institute of Technology , 2-12-1-E4-6 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan.,Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI) , Tokyo Institute of Technology , 2-12-1 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan
| | - Yuki Takahashi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology , Tokyo Institute of Technology , 2-12-1-E4-6 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan
| | - Yoshihiro Hayashi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology , Tokyo Institute of Technology , 2-12-1-E4-6 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan.,Research Institute of Polymer Science and Technology (RIPST) , Tokyo Institute of Technology , 2-12-1 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan
| | - Susumu Kawauchi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology , Tokyo Institute of Technology , 2-12-1-E4-6 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan.,Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI) , Tokyo Institute of Technology , 2-12-1 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan.,Research Institute of Polymer Science and Technology (RIPST) , Tokyo Institute of Technology , 2-12-1 Ookayama , Meguro-ku, Tokyo 152-8552 , Japan
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3
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Vorobiev AK, Bogdanov AV, Yankova TS, Chumakova NA. Spin Probe Determination of Molecular Orientation Distribution and Rotational Mobility in Liquid Crystals: Model-Free Approach. J Phys Chem B 2019; 123:5875-5891. [PMID: 31251620 DOI: 10.1021/acs.jpcb.9b05431] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A model-free approach for simulation of EPR spectra of nitroxide spin probes in liquid-crystalline materials was suggested and used to obtain parameters of molecular orientation and rotational mobility. The developed method is based on experimental recording and numerical simulation of the angular dependence of EPR spectra, which is shown to be much more informative in comparison with a single EPR spectrum. Quantitative spectral simulations considering both local orientational ordering and distribution of local directors in the sample were used for discrimination of models of rotational mobility and orientational alignment. The method was applied for detailed quantitative characterization of axial, orthorhombic, and low-symmetry non-orthorhombic molecular orientation distributions. It is shown that the ordinarily used model of rotational diffusion in a mean-field potential is suitable for the description of molecular mobility and orientational ordering only for relatively low sample temperatures and low-mobility probe molecules with large sizes. In cases of high molecular mobility, the more realistic jump mechanism of molecular moves can be approximately described as quasi-librations. For ordered liquid crystals it was found that mostly the order parameters up to rank 12-14 are essential and easily determined. When well-aligned materials are described, the order parameters up to 18th rank or even higher become meaningful. Both molecular and sample biaxiality is analyzed and quantitatively characterized. The local molecular ordering and sample orientational alignment are quantitatively characterized separately.
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Affiliation(s)
- A Kh Vorobiev
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - A V Bogdanov
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - T S Yankova
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - N A Chumakova
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
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4
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Affiliation(s)
- Michael P. Allen
- Department of Physics, University of Warwick, Coventry, UK
- H. H. Wills Physics Laboratory, Royal Fort, Bristol, UK
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Boyd NJ, Wilson MR. Validating an optimized GAFF force field for liquid crystals: TNI predictions for bent-core mesogens and the first atomistic predictions of a dark conglomerate phase. Phys Chem Chem Phys 2018; 20:1485-1496. [DOI: 10.1039/c7cp07496d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atomistic simulations of bent core mesogens provide excellent TNI predictions and show the formation of a dark conglomerate phase.
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6
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Prior C, Danilāne L, Oganesyan VS. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies. Phys Chem Chem Phys 2018; 20:13461-13472. [DOI: 10.1039/c7cp08625c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prediction of motional EPR spectra of spin labelled DNA structures from fully atomistic MD simulations.
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Affiliation(s)
- C. Prior
- School of Chemistry
- University of East Anglia
- Norwich
- UK
| | - L. Danilāne
- School of Chemistry
- University of East Anglia
- Norwich
- UK
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7
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Prior C, Oganesyan VS. Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach. Chemistry 2017; 23:13192-13204. [PMID: 28741312 DOI: 10.1002/chem.201702682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Indexed: 12/17/2022]
Abstract
We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules.
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Affiliation(s)
- Christopher Prior
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
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Sims MT, Abbott LC, Cowling SJ, Goodby JW, Moore JN. Principal molecular axis and transition dipole moment orientations in liquid crystal systems: an assessment based on studies of guest anthraquinone dyes in a nematic host. Phys Chem Chem Phys 2017; 19:813-827. [DOI: 10.1039/c6cp05979a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analyses of MD simulations assess different definitions of the axes along which molecules align in a nematic host, and the effects of molecular flexibility on transition dipole moment orientations.
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Affiliation(s)
- Mark T. Sims
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | | | | | - John W. Goodby
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | - John N. Moore
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
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Sims MT, Abbott LC, Cowling SJ, Goodby JW, Moore JN. Experimental and molecular dynamics studies of anthraquinone dyes in a nematic liquid-crystal host: a rationale for observed alignment trends. Phys Chem Chem Phys 2016; 18:20651-63. [DOI: 10.1039/c6cp03823a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The experimental alignment trend of a set of anthraquinone dyes in a nematic host is rationalised by calculated molecular order parameters and transition dipole moments.
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Affiliation(s)
- Mark T. Sims
- Department of Chemistry
- The University of York
- Heslington
- UK
| | | | | | - John W. Goodby
- Department of Chemistry
- The University of York
- Heslington
- UK
| | - John N. Moore
- Department of Chemistry
- The University of York
- Heslington
- UK
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Boyd NJ, Wilson MR. Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions. Phys Chem Chem Phys 2015; 17:24851-65. [DOI: 10.1039/c5cp03702f] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Systematic optimization of the General Amber Force Field (GAFF) for mesogenic fragments leads to a dramatic improvement in the modelling of liquid crystal clearing points.
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Gopee H, Cammidge AN, Oganesyan VS. Probing columnar discotic liquid crystals by EPR spectroscopy with a rigid-core nitroxide spin probe. Angew Chem Int Ed Engl 2013; 52:8917-20. [PMID: 23873587 PMCID: PMC4499263 DOI: 10.1002/anie.201303194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Indexed: 12/04/2022]
Affiliation(s)
- Hemant Gopee
- School of Chemistry, University of East Anglia, Norwich Research ParkNorwich, NR4 7TJ (UK)
| | - Andrew N Cammidge
- School of Chemistry, University of East Anglia, Norwich Research ParkNorwich, NR4 7TJ (UK)
| | - Vasily S Oganesyan
- School of Chemistry, University of East Anglia, Norwich Research ParkNorwich, NR4 7TJ (UK)
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12
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Gopee H, Cammidge AN, Oganesyan VS. Probing Columnar Discotic Liquid Crystals by EPR Spectroscopy with a Rigid-Core Nitroxide Spin Probe. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Yan F, Earl DJ. Atomistic simulations of liquid crystal mixtures of alkoxy substituted phenylpyrimidines 2PhP and PhP14. J Chem Phys 2012; 136:124506. [DOI: 10.1063/1.3692731] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Oganesyan VS. A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein. Phys Chem Chem Phys 2011; 13:4724-37. [PMID: 21279205 DOI: 10.1039/c0cp01068e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.
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