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Scarperi A, Barcaro G, Pajzderska A, Martini F, Carignani E, Geppi M. Structural Refinement of Carbimazole by NMR Crystallography. Molecules 2021; 26:molecules26154577. [PMID: 34361730 PMCID: PMC8347463 DOI: 10.3390/molecules26154577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
The characterization of the three-dimensional structure of solids is of major importance, especially in the pharmaceutical field. In the present work, NMR crystallography methods are applied with the aim to refine the crystal structure of carbimazole, an active pharmaceutical ingredient used for the treatment of hyperthyroidism and Grave’s disease. Starting from previously reported X-ray diffraction data, two refined structures were obtained by geometry optimization methods. Experimental 1H and 13C isotropic chemical shift measured by the suitable 1H and 13C high-resolution solid state NMR techniques were compared with DFT-GIPAW calculated values, allowing the quality of the obtained structure to be experimentally checked. The refined structure was further validated through the analysis of 1H-1H and 1H-13C 2D NMR correlation experiments. The final structure differs from that previously obtained from X-ray diffraction data mostly for the position of hydrogen atoms.
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Affiliation(s)
- Andrea Scarperi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
| | - Giovanni Barcaro
- Institute For Chemical And Physical Processes, Italian National Council for Research, CNR/IPCF, Via G. Moruzzi 1, 56124 Pisa, Italy;
| | - Aleksandra Pajzderska
- Department of Radiospectroscopy, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614 Poznan, Poland;
| | - Francesca Martini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
- Center for Instrument Sharing, University of Pisa (CISUP), 56126 Pisa, Italy
| | - Elisa Carignani
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
- Institute for the Chemistry of OrganoMetallic Compounds, Italian National Council for Research, CNR/ICCOM, Via G. Moruzzi 1, 56124 Pisa, Italy
- Correspondence: (E.C.); (M.G.); Tel.: +39-050-2219353 (E.C.); +39-050-2219289 (M.G.)
| | - Marco Geppi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
- Center for Instrument Sharing, University of Pisa (CISUP), 56126 Pisa, Italy
- Institute for the Chemistry of OrganoMetallic Compounds, Italian National Council for Research, CNR/ICCOM, Via G. Moruzzi 1, 56124 Pisa, Italy
- Correspondence: (E.C.); (M.G.); Tel.: +39-050-2219353 (E.C.); +39-050-2219289 (M.G.)
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2
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Wang L, Elliott AB, Moore SD, Beran GJO, Hartman JD, Harper JK. Modeling Small Structural and Environmental Differences in Solids with 15 N NMR Chemical Shift Tensors. Chemphyschem 2021; 22:1008-1017. [PMID: 33604988 DOI: 10.1002/cphc.202000985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/28/2021] [Indexed: 11/09/2022]
Abstract
The ability to theoretically predict accurate NMR chemical shifts in solids is increasingly important due to the role such shifts play in selecting among proposed model structures. Herein, two theoretical methods are evaluated for their ability to assign 15 N shifts from guanosine dihydrate to one of the two independent molecules present in the lattice. The NMR data consist of 15 N shift tensors from 10 resonances. Analysis using periodic boundary or fragment methods consider a benchmark dataset to estimate errors and predict uncertainties of 5.6 and 6.2 ppm, respectively. Despite this high accuracy, only one of the five sites were confidently assigned to a specific molecule of the asymmetric unit. This limitation is not due to negligible differences in experimental data, as most sites exhibit differences of >6.0 ppm between pairs of resonances representing a given position. Instead, the theoretical methods are insufficiently accurate to make assignments at most positions.
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Affiliation(s)
- Luther Wang
- Department of Chemistry and Biochemistry, Brigham Young University, 84602, Provo, UT, USA
| | - Alexander B Elliott
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, 32816, Orlando, FL, USA
| | - Sean D Moore
- Burnett School of Biomedical Sciences, University of Central Florida, 4110 Libra Drive, 32816, Orlando, FL, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, 92521, Riverside, CA, USA
| | - Joshua D Hartman
- Department of Chemistry, Mt. San Jacinto College, 92583, San Jacinto, CA, USA
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, 84602, Provo, UT, USA
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4
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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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5
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Grüne M, Luxenhofer R, Iuga D, Brown SP, Pöppler AC. 14N–1H HMQC solid-state NMR as a powerful tool to study amorphous formulations – an exemplary study of paclitaxel loaded polymer micelles. J Mater Chem B 2020; 8:6827-6836. [DOI: 10.1039/d0tb00614a] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
14N–1H HMQC experiments are powerful experiments to characterize amorphous drug–polymer formulations of paclitaxel yielding well-separated signals in the 14N dimension as well as information on the symmetry of 14N and 14N–1H interactions.
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Affiliation(s)
- Marvin Grüne
- Institute of Organic Chemistry
- University of Würzburg
- 97074 Würzburg
- Germany
| | - Robert Luxenhofer
- Lehrstuhl für Chemische Technologie der Materialsynthese
- University of Würzburg
- 97070 Würzburg
- Germany
| | - Dinu Iuga
- Department of Physics
- University of Warwick
- Coventry
- UK
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6
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Engel EA, Anelli A, Hofstetter A, Paruzzo F, Emsley L, Ceriotti M. A Bayesian approach to NMR crystal structure determination. Phys Chem Chem Phys 2019; 21:23385-23400. [PMID: 31631196 DOI: 10.1039/c9cp04489b] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is particularly well suited to determine the structure of molecules and materials in powdered form. Structure determination usually proceeds by finding the best match between experimentally observed NMR chemical shifts and those of candidate structures. Chemical shifts for the candidate configurations have traditionally been computed by electronic-structure methods, and more recently predicted by machine learning. However, the reliability of the determination depends on the errors in the predicted shifts. Here we propose a Bayesian framework for determining the confidence in the identification of the experimental crystal structure, based on knowledge of the typical errors in the electronic structure methods. We demonstrate the approach on the determination of the structures of six organic molecular crystals. We critically assess the reliability of the structure determinations, facilitated by the introduction of a visualization of the similarity between candidate configurations in terms of their chemical shifts and their structures. We also show that the commonly used values for the errors in calculated 13C shifts are underestimated, and that more accurate, self-consistently determined uncertainties make it possible to use 13C shifts to improve the accuracy of structure determinations. Finally, we extend the recently-developed ShiftML model to render it more efficient, accurate, and, most importantly, to evaluate the uncertainties in its predictions. By quantifying the confidence in structure determinations based on ShiftML predictions we further substantiate that it provides a valid replacement for first-principles calculations in NMR crystallography.
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Affiliation(s)
- Edgar A Engel
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
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7
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Hofstetter A, Balodis M, Paruzzo FM, Widdifield CM, Stevanato G, Pinon AC, Bygrave PJ, Day GM, Emsley L. Rapid Structure Determination of Molecular Solids Using Chemical Shifts Directed by Unambiguous Prior Constraints. J Am Chem Soc 2019; 141:16624-16634. [PMID: 31117663 PMCID: PMC7540916 DOI: 10.1021/jacs.9b03908] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
NMR-based crystallography approaches involving the combination of crystal structure prediction methods, ab initio calculated chemical shifts and solid-state NMR experiments are powerful methods for crystal structure determination of microcrystalline powders. However, currently structural information obtained from solid-state NMR is usually included only after a set of candidate crystal structures has already been independently generated, starting from a set of single-molecule conformations. Here, we show with the case of ampicillin that this can lead to failure of structure determination. We propose a crystal structure determination method that includes experimental constraints during conformer selection. In order to overcome the problem that experimental measurements on the crystalline samples are not obviously translatable to restrict the single-molecule conformational space, we propose constraints based on the analysis of absent cross-peaks in solid-state NMR correlation experiments. We show that these absences provide unambiguous structural constraints on both the crystal structure and the gas-phase conformations, and therefore can be used for unambiguous selection. The approach is parametrized on the crystal structure determination of flutamide, flufenamic acid, and cocaine, where we reduce the computational cost by around 50%. Most importantly, the method is then shown to correctly determine the crystal structure of ampicillin, which would have failed using current methods because it adopts a high-energy conformer in its crystal structure. The average positional RMSE on the NMR powder structure is ⟨rav⟩ = 0.176 Å, which corresponds to an average equivalent displacement parameter Ueq = 0.0103 Å2.
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Affiliation(s)
- Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Martins Balodis
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Cory M Widdifield
- Department of Chemistry, Mathematics and Science Center , Oakland University , 146 Library Drive , Rochester , Michigan 48309-4479 , United States
| | - Gabriele Stevanato
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Arthur C Pinon
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Peter J Bygrave
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Graeme M Day
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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8
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Paruzzo FM, Hofstetter A, Musil F, De S, Ceriotti M, Emsley L. Chemical shifts in molecular solids by machine learning. Nat Commun 2018; 9:4501. [PMID: 30374021 PMCID: PMC6206069 DOI: 10.1038/s41467-018-06972-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/26/2018] [Indexed: 02/02/2023] Open
Abstract
Due to their strong dependence on local atonic environments, NMR chemical shifts are among the most powerful tools for strucutre elucidation of powdered solids or amorphous materials. Unfortunately, using them for structure determination depends on the ability to calculate them, which comes at the cost of high accuracy first-principles calculations. Machine learning has recently emerged as a way to overcome the need for quantum chemical calculations, but for chemical shifts in solids it is hindered by the chemical and combinatorial space spanned by molecular solids, the strong dependency of chemical shifts on their environment, and the lack of an experimental database of shifts. We propose a machine learning method based on local environments to accurately predict chemical shifts of molecular solids and their polymorphs to within DFT accuracy. We also demonstrate that the trained model is able to determine, based on the match between experimentally measured and ML-predicted shifts, the structures of cocaine and the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butylpyrazol-1-yl]benzoic acid. Solid-state nuclear magnetic resonance combined with quantum chemical shift predictions is limited by high computational cost. Here, the authors use machine learning based on local atomic environments to predict experimental chemical shifts in molecular solids with accuracy similar to density functional theory.
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Affiliation(s)
- Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Félix Musil
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Sandip De
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michele Ceriotti
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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9
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Zimmer GC, Pagliari AB, Bender CR, Salbego PRS, Orlando T, Hörner M, Zanatta N, Bonacorso HG, Martins MAP. Insights on conformation in the solid state: a case study – s-cis and/or s-trans crystallization of 5(3)-aryl-3(5)-carboxyethyl-1-tert-butylpyrazoles. CrystEngComm 2018. [DOI: 10.1039/c8ce00984h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformation adopted by COOEt group in solid state were influenced by supramolecular environment and intramolecular interaction for 1,3- and 1,5-regioisomers, respectively.
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Affiliation(s)
- Geórgia C. Zimmer
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Anderson B. Pagliari
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Caroline R. Bender
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Paulo R. S. Salbego
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Tainára Orlando
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Manfredo Hörner
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Nilo Zanatta
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Helio G. Bonacorso
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Marcos A. P. Martins
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
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10
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Soss SE, Flynn PF, Iuliucci RJ, Young RP, Mueller LJ, Hartman J, Beran GJO, Harper JK. Measuring and Modeling Highly Accurate
15
N Chemical Shift Tensors in a Peptide. Chemphyschem 2017; 18:2225-2232. [DOI: 10.1002/cphc.201700357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/08/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Sarah E. Soss
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Peter F. Flynn
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Robbie J. Iuliucci
- Department of Chemistry Washington and Jefferson College 60 Lincoln Street Washington PA 15301 USA
| | - Robert P. Young
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - Joshua Hartman
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - James K. Harper
- Department of Chemistry University of Central Florida 4111 Libra Drive Orlando FL 32816 USA
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11
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Pinon A, Rossini AJ, Widdifield CM, Gajan D, Emsley L. Polymorphs of Theophylline Characterized by DNP Enhanced Solid-State NMR. Mol Pharm 2015; 12:4146-53. [PMID: 26393368 PMCID: PMC4699642 DOI: 10.1021/acs.molpharmaceut.5b00610] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/15/2015] [Accepted: 09/22/2015] [Indexed: 11/29/2022]
Abstract
We show how dynamic nuclear polarization (DNP) enhanced solid-state NMR spectroscopy can be used to characterize polymorphs and solvates of organic solids. We applied DNP to three polymorphs and one hydrated form of the asthma drug molecule theophylline. For some forms of theophylline, sample grinding and impregnation with the radical-containing solution, which are necessary to prepare the samples for DNP, were found to induce polymorphic transitions or desolvation between some forms. We present protocols for sample preparation for solid-state magic-angle spinning (MAS) DNP experiments that avoid the polymorphic phase transitions in theophylline. These protocols include cryogrinding, grinding under inert atmosphere, and the appropriate choice of the impregnating liquid. By applying these procedures, we subsequently demonstrate that two-dimensional correlation experiments, such as (1)H-(13)C and (1)H-(15)N HETCOR or (13)C-(13)C INADEQUATE, can be obtained at natural isotopic abundance in reasonable times, thus enabling more advanced structural characterization of polymorphs.
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Affiliation(s)
- Arthur
C. Pinon
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - Aaron J. Rossini
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - Cory M. Widdifield
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - David Gajan
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
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12
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Baisch U, Vella-Zarb L. Towards understanding P-gp resistance: a case study of the antitumour drug cabazitaxel. CrystEngComm 2014. [DOI: 10.1039/c4ce01279h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A structural and Hirshfeld surface study of five forms of the antitumour drug cabazitaxel suggests key factors contributing to its poor affinity to P-gp.
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Affiliation(s)
- U. Baisch
- Crystal Engineering Laboratory
- Department of Chemistry
- University of Malta
- , Malta
- School of Chemistry
| | - L. Vella-Zarb
- Crystal Engineering Laboratory
- Department of Chemistry
- University of Malta
- , Malta
- School of Chemistry
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13
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Baias M, Dumez JN, Svensson PH, Schantz S, Day GM, Emsley L. De novo determination of the crystal structure of a large drug molecule by crystal structure prediction-based powder NMR crystallography. J Am Chem Soc 2013; 135:17501-7. [PMID: 24168679 DOI: 10.1021/ja4088874] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of form 4 of the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butyl-pyrazol-1-yl]benzoic acid is determined using a protocol for NMR powder crystallography at natural isotopic abundance combining solid-state (1)H NMR spectroscopy, crystal structure prediction, and density functional theory chemical shift calculations. This is the first example of NMR crystal structure determination for a molecular compound of previously unknown structure, and at 422 g/mol this is the largest compound to which this method has been applied so far.
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Affiliation(s)
- Maria Baias
- Centre de RMN à Très Hauts Champs, CNRS/ENS-Lyon/UCB Lyon 1, Université de Lyon , 5 rue de la Doua, 69100 Villeurbanne, France
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14
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Harper JK, Tishler D, Richardson D, Lokvam J, Pendrill R, Widmalm G. Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl α-l-Rhamnofuranoside. J Phys Chem A 2013; 117:5534-41. [DOI: 10.1021/jp4036666] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- James K. Harper
- Department of Chemistry, University of Central Florida, 4000
Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Derek Tishler
- Department of Physics, University of Central Florida, Orlando,
Florida 32816, United States
| | - David Richardson
- Department of Chemistry, University of Central Florida, 4000
Central Florida Boulevard, Orlando, Florida 32816, United States
| | - John Lokvam
- Department of Biology, University of California Berkeley, Berkeley,
California 94720, United States
| | - Robert Pendrill
- Department of Organic
Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic
Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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15
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Baias M, Widdifield CM, Dumez JN, Thompson HPG, Cooper TG, Salager E, Bassil S, Stein RS, Lesage A, Day GM, Emsley L. Powder crystallography of pharmaceutical materials by combined crystal structure prediction and solid-state 1H NMR spectroscopy. Phys Chem Chem Phys 2013; 15:8069-80. [PMID: 23503809 DOI: 10.1039/c3cp41095a] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A protocol for the ab initio crystal structure determination of powdered solids at natural isotopic abundance by combining solid-state NMR spectroscopy, crystal structure prediction, and DFT chemical shift calculations was evaluated to determine the crystal structures of four small drug molecules: cocaine, flutamide, flufenamic acid, and theophylline. For cocaine, flutamide and flufenamic acid, we find that the assigned (1)H isotropic chemical shifts provide sufficient discrimination to determine the correct structures from a set of predicted structures using the root-mean-square deviation (rmsd) between experimentally determined and calculated chemical shifts. In most cases unassigned shifts could not be used to determine the structures. This method requires no prior knowledge of the crystal structure, and was used to determine the correct crystal structure to within an atomic rmsd of less than 0.12 Å with respect to the known reference structure. For theophylline, the NMR spectra are too simple to allow for unambiguous structure selection.
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Affiliation(s)
- Maria Baias
- Université de Lyon, (CNRS/ENS-Lyon/UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
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16
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Vella-Zarb L, Baisch U, Dinnebier RE. Small molecule, big difference: the role of water in the crystallization of paclitaxel. J Pharm Sci 2012. [PMID: 23203212 DOI: 10.1002/jps.23404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Paclitaxel is an important antineoplastic drug, which is used widely in the treatment of many forms of cancer. The crystal structures of the anhydrous form and the hemihydrate were determined from laboratory X-ray powder diffraction data, whereas the dihydrate was solved from single-crystal synchrotron diffraction data. Intermolecular spaces allow for the inclusion of loosely bound water molecules, which are then lost easily upon heating. All three forms were found to crystallize in the orthorhombic spacegroup P2(1)2(1)2(1), with Z' = 2. The unit cell parameters were found to be a = 9.6530(3) Å, b = 28.1196(8) Å, c = 33.5378(14) Å, and V = 9103.5(5) Å for the anhydrous form (363 K); a = 9.6890(2) Å, b = 28.0760(4) Å, c = 33.6166(8) Å, and V = 9144.7(3) Å(3) for the hemihydrate (333 K); and a = 9.512(6) Å, b = 28.064(16) Å, c = 33.08(2) Å, and V = 8829.0(9) Å(3) for the dihydrate (120 K). Water loss occurs in two steps between 120 K ≤ t ≤ 363 K. The thermal stability of the hydrates and accompanying unit cell changes were observed in situ via temperature-resolved X-ray powder diffraction and thermogravimetric analysis.
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Affiliation(s)
- Liana Vella-Zarb
- Max Planck Institute for Solid State Research, Stuttgart D-70569, Germany
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17
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Wang WD, Gao X, Strohmeier M, Wang W, Bai S, Dybowski C. Solid-State NMR Studies of Form I of Atorvastatin Calcium. J Phys Chem B 2012; 116:3641-9. [DOI: 10.1021/jp212074a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei David Wang
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xudong Gao
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Mark Strohmeier
- Product Development, GlaxoSmithKline, Inc., 709 Swedeland Road, King of
Prussia, Pennsylvania 19406, United States
| | - Wei Wang
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Shi Bai
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
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18
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Liu W, Wang WD, Wang W, Bai S, Dybowski C. Influence of Structure on the Spectroscopic Properties of the Polymorphs of Piroxicam. J Phys Chem B 2010; 114:16641-9. [DOI: 10.1021/jp1084444] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Wei Liu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Wei David Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Wei Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shi Bai
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Cecil Dybowski
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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19
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Liu W, Wang WD, Wang W, Bai S, Dybowski C. Measurement of the principal values of the chemical-shift tensors of overlapping protonated and unprotonated carbons with the 2D-SUPER technique and dipolar dephasing (DD-SUPER). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 206:177-181. [PMID: 20667754 DOI: 10.1016/j.jmr.2010.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 06/27/2010] [Accepted: 07/02/2010] [Indexed: 05/29/2023]
Abstract
A modified 2D-SUPER technique is demonstrated to allow independent measurement of the principal values of the chemical-shift tensors of overlapping protonated and unprotonated carbons. The insertion of a dipolar-dephasing period into the sequence causes loss of signal from protonated carbons. The spectrum obtained with this modification allows one to determine the principal values of the unprotonated carbons with high precision. Subsequent fitting of the usual 2D-SUPER spectrum, with the chemical-shift parameters of the unprotonated carbons fixed, gives the parameters of the overlapped resonances of the protonated carbons. As an example, we report the determination of the (13)C chemical-shift parameters of the carbons of form II of piroxicam. The experimental results are compared with those obtained from calculations using the DFT/GIAO method. Potential applications of this method are discussed.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu 730000, China
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20
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Rode JE, Dobrowolski JC, Sadlej J. Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers. J Mol Model 2010; 17:961-70. [PMID: 20623308 PMCID: PMC3094660 DOI: 10.1007/s00894-010-0783-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 06/11/2010] [Indexed: 11/04/2022]
Abstract
The conformational landscape of phenylisoserine (PhIS) was studied. Trial structures were generated by allowing for all combinations of single-bond rotamers. Based on the B3LYP/aug-cc-pVDZ calculations 54 conformers were found to be stable in the gas phase. The six most stable conformers were further optimized at the B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVDZ levels for which characteristic intramolecular hydrogen bond types were classified. To estimate the influence of water on PhIS conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 51 neutral and six zwitterionic conformers to be stable in water solution. According to DFT calculations, the conformer equilibrium in the gas phase is dominated by one conformer, whereas the MP2 calculations suggest three PhIS structures to be significantly populated. Comparison of DFT and MP2 energies of all 57 structures stable in water indicates that, in practice, one zwitterionic and one neutral conformer determine the equilibrium in water. Based on the AIM calculations, we found that for the neutral conformers in vacuum and in water, d(H...B) is linearly correlated with Laplacian at the H-bond critical point. Phenylisoserine (PhIS) is an active side chain of cytotoxic Paclitaxel medicine. The conformational landscape of phenylisoserine was studied. One zwitterionic and one neutralconformer determine the equilibrium in water whereas in the gas phase the MP2 calculations suggest three PhIS structures to be significantly populated. ![]()
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Affiliation(s)
- Joanna E Rode
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
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21
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Salager E, Day GM, Stein RS, Pickard CJ, Elena B, Emsley L. Powder crystallography by combined crystal structure prediction and high-resolution 1H solid-state NMR spectroscopy. J Am Chem Soc 2010; 132:2564-6. [PMID: 20136091 DOI: 10.1021/ja909449k] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A fast method for crystal structure determination using crystal structure prediction and solid-state (1)H NMR is presented. This technique does not need any prior knowledge except the chemical formula; resonance assignment is not necessary. Starting from an ensemble of predicted crystal structures for powdered thymol, comparison between experimental and calculated (1)H solid-state isotropic NMR chemical shifts is sufficient to determine which predicted structure corresponds to the powder under study. The same approach using proton-proton spin-diffusion data is successful and can be used for cross-validation.
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Affiliation(s)
- Elodie Salager
- Université de Lyon, Centre de RMN à très hauts champs, CNRS/ENS Lyon/UCBL, 5 rue de la Doua, 69100 Villeurbanne, France
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22
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Webber AL, Elena B, Griffin JM, Yates JR, Pham TN, Mauri F, Pickard CJ, Gil AM, Stein R, Lesage A, Emsley L, Brown SP. Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations. Phys Chem Chem Phys 2010; 12:6970-83. [PMID: 20480118 DOI: 10.1039/c001290d] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A disaccharide is a challenging case for high-resolution (1)H solid-state NMR because of the 24 distinct protons (14 aliphatic and 10 OH) having (1)H chemical shifts that all fall within a narrow range of approximately 3 to 7 ppm. High-resolution (1)H (500 MHz) double-quantum (DQ) combined rotation and multiple pulse sequence (CRAMPS) solid-state NMR spectra of beta-maltose monohydrate are presented. (1)H-(1)H DQ-SQ CRAMPS spectra are presented together with (1)H (DQ)-(13)C correlation spectra obtained with a new pulse sequence that correlates a high-resolution (1)H DQ dimension with a (13)C single quantum (SQ) dimension using the refocused INEPT pulse-sequence element to transfer magnetization via one-bond (13)C-(1)H J couplings. Compared to the observation of only a single broad peak in a (1)H DQ spectrum recorded at 30 kHz magic-angle spinning (MAS), the use of DUMBO (1)H homonuclear decoupling in the (1)H DQ CRAMPS experiment allows the resolution of distinct DQ correlation peaks which, in combination with first-principles chemical shift calculations based on the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach, enables the assignment of the (1)H resonances to the 24 distinct protons. We believe this to be the first experimental solid-state NMR determination of the hydroxyl OH (1)H chemical shifts for a simple sugar. Variable-temperature (1)H-(1)H DQ CRAMPS spectra reveal small increases in the (1)H chemical shifts of the OH resonances upon decreasing the temperature from 348 K to 248 K.
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Affiliation(s)
- Amy L Webber
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
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23
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Halling MD, Orendt AM, Strohmeier M, Solum MS, Tsefrikas VM, Hirao T, Scott LT, Pugmire RJ, Grant DM. Solid-state 13C NMR investigations of 4,7-dihydro-1H-tricyclopenta[def,jkl,pqr]triphenylene (sumanene) and indeno[1,2,3-cd]fluoranthene: Buckminsterfullerene moieties. Phys Chem Chem Phys 2010; 12:7934-41. [DOI: 10.1039/c001903h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Salager E, Stein RS, Pickard CJ, Elena B, Emsley L. Powder NMR crystallography of thymol. Phys Chem Chem Phys 2009; 11:2610-21. [PMID: 19421517 DOI: 10.1039/b821018g] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A protocol for the structure determination of powdered solids at natural abundance by NMR is presented and illustrated for the case of the small drug molecule thymol. The procedure uses proton spin-diffusion data from two-dimensional NMR experiments in combination with periodic DFT refinements incorporating (1)H and (13)C NMR chemical shifts. For thymol, the method yields a crystal structure for the powdered sample, which differs by an atomic root-mean-square-deviation (all atoms except methyl group protons) of only 0.07 A from the single crystal X-ray diffraction structure with DFT-optimized proton positions.
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Affiliation(s)
- Elodie Salager
- Université de Lyon, (CNRS/ENS-Lyon/UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100, Villeurbanne, France
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25
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Lesage A. Recent advances in solid-state NMR spectroscopy of spin I = 1/2 nuclei. Phys Chem Chem Phys 2009; 11:6876-91. [DOI: 10.1039/b907733m] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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27
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Bernard GM, Feindel KW, Wasylishen RE, Cameron TS. Solid-state phosphorus-31 NMR spectroscopy of a multiple-spin system: an investigation of a rhodium-triphosphine complex. Phys Chem Chem Phys 2008; 10:5552-63. [PMID: 18956090 DOI: 10.1039/b803596b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphorus-31 NMR spectra of solid [tris(dimethylphenylphosphine)](2,5-norbornadiene) rhodium(I) hexafluorophosphate have been acquired at several applied magnetic field strengths. The phosphorus nuclei of the three phosphine ligands are spin-spin coupled to each other and to 103Rh, resulting in complex NMR spectra; however, the three phosphorus chemical shift (CS) tensors were determined through the analysis of NMR spectra of slow magic angle spinning and stationary samples. Spectra of spinning samples in rotational resonance and two-dimensional 31P NMR spectra were particularly useful for determining the magnitudes of the indirect spin-spin couplings, and to probe their signs. Despite being in similar environments, the three phosphorus nuclei of the phosphine ligands have distinct CS tensors. In particular, the spans of these tensors, delta11-delta33, range from 80 to 176 ppm. The phosphorus CS tensors have been assigned to specific sites determined by X-ray crystallography, based on a combination of the experimental results and the results of quantum chemical calculations of the phosphorus shielding and 2J(31P,31P) values. The effect of coordination of dimethylphenylphosphine with rhodium has been investigated by comparing calculated phosphorus CS tensors for the uncoordinated ligand with those obtained for the ligands in the complex.
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Affiliation(s)
- Guy M Bernard
- Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton AB, Canada T6G 2G2
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