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Liu Y, Ndukwe IE, Reibarkh M, Martin GE, Williamson RT. Prediction of anisotropic NMR data without knowledge of alignment medium structure by surface decomposition. Phys Chem Chem Phys 2022; 24:20164-20182. [PMID: 35996986 DOI: 10.1039/d2cp02621j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prediction of anisotropic NMR data directly from solute-medium interaction is of significant theoretical and practical interest, particularly for structure elucidation, configurational analysis and conformational studies of complex organic molecules and natural products. Current prediction methods require an explicit structural model of the alignment medium: a requirement either impossible or impractical on a scale necessary for small organic molecules. Here we formulate a comprehensive mathematical framework for a parametrization protocol that deconvolutes an arbitrary surface of the medium into several simple local landscapes that are distributed over the medium's surface by specific orientational order parameters. The shapes and order parameters of these local landscapes are determined via fitting that maximizes the congruence between experimentally determined anisotropic NMR measurables and their predicted counterparts, thus avoiding the need for an a priori knowledge of the global medium morphology. This method achieves substantial improvements in the accuracy of predicted anisotropic NMR values compared to current methods, as demonstrated herein with sixteen natural products. Furthermore, because this formalism extracts structural commonalities of the medium by combining anisotropic NMR data from different compounds, its robustness and accuracy are expected to improve as more experimental data become available for further re-optimization of fitting parameters.
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Affiliation(s)
- Yizhou Liu
- Analytical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT, 06340, USA.
| | - Ikenna E Ndukwe
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Gary E Martin
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - R Thomas Williamson
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
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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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3
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Singer PM, Asthagiri D, Chen Z, Valiya Parambathu A, Hirasaki GJ, Chapman WG. Role of internal motions and molecular geometry on the NMR relaxation of hydrocarbons. J Chem Phys 2018; 148:164507. [DOI: 10.1063/1.5023240] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- P. M. Singer
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - D. Asthagiri
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - Z. Chen
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - A. Valiya Parambathu
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - G. J. Hirasaki
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - W. G. Chapman
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St., Houston, Texas 77005, USA
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4
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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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6
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Weber ACJ, Burnell EE, Meerts WL, de Lange CA, Dong RY, Muccioli L, Pizzirusso A, Zannoni C. Communication: Molecular dynamics and 1H NMR of n-hexane in liquid crystals. J Chem Phys 2015; 143:011103. [DOI: 10.1063/1.4923253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Frank AO, Freudenberger JC, Shaytan AK, Kessler H, Luy B. Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:213-217. [PMID: 25612077 DOI: 10.1002/mrc.4181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/23/2014] [Accepted: 10/11/2014] [Indexed: 06/04/2023]
Abstract
Residual dipolar couplings are highly useful NMR parameters for calculating and refining molecular structures, dynamics, and interactions. For some applications, however, it is inevitable that the preferred orientation of a molecule in an alignment medium is calculated a priori. Several methods have been developed to predict molecular orientations and residual dipolar couplings. Being beneficial for macromolecules and selected small-molecule applications, such approaches lack sufficient accuracy for a large number of organic compounds for which the fine structure and eventually the flexibility of all involved molecules have to be considered or are limited to specific, well-studied liquid crystals. We introduce a simplified model for detailed all-atom molecular dynamics calculations with a polymer strand lined up along the principal axis as a new approach to simulate the preferred orientation of small to medium-sized solutes in polymer-based, gel-type alignment media. As is shown by a first example of strychnine in a polystyrene/CDCl3 gel, the simulations potentially enable the accurate prediction of residual dipolar couplings taking into account structural details and dynamic averaging effects of both the polymer and the solute.
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Affiliation(s)
- Andreas O Frank
- Institute for Advanced Study at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
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Burnell EE, Weber ACJ, Dong RY, Meerts WL, de Lange CA. A model-free temperature-dependent conformational study ofn-pentane in nematic liquid crystals. J Chem Phys 2015; 142:024904. [DOI: 10.1063/1.4904822] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- E. Elliott Burnell
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Adrian C. J. Weber
- Chemistry Department, Brandon University, 270-18th Street, Brandon, Manitoba R7A 6A9, Canada
| | - Ronald Y. Dong
- Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia V6T 1Z1, Canada
| | - W. Leo Meerts
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
- Laser Centre, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Cornelis A. de Lange
- Laser Centre, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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Pizzirusso A, Di Pietro ME, De Luca G, Celebre G, Longeri M, Muccioli L, Zannoni C. Order and Conformation of Biphenyl in Cyanobiphenyl Liquid Crystals: A Combined Atomistic Molecular Dynamics and1H NMR Study. Chemphyschem 2014; 15:1356-67. [DOI: 10.1002/cphc.201400082] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Indexed: 11/07/2022]
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Palermo MF, Pizzirusso A, Muccioli L, Zannoni C. An atomistic description of the nematic and smectic phases of 4-n-octyl-4′ cyanobiphenyl (8CB). J Chem Phys 2013; 138:204901. [DOI: 10.1063/1.4804270] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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