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Szell PMJ, Nilsson Lill SO, Blade H, Brown SP, Hughes LP. A toolbox for improving the workflow of NMR crystallography. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 116:101761. [PMID: 34736104 DOI: 10.1016/j.ssnmr.2021.101761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
NMR crystallography is a powerful tool with applications in structural characterization and crystal structure verification, to name two. However, applying this tool presents several challenges, especially for industrial users, in terms of consistency, workflow, time consumption, and the requirement for a high level of understanding of experimental solid-state NMR and GIPAW-DFT calculations. Here, we have developed a series of fully parameterized scripts for use in Materials Studio and TopSpin, based on the .magres file format, with a focus on organic molecules (e.g. pharmaceuticals), improving efficiency, robustness, and workflow. We separate these tools into three major categories: performing the DFT calculations, extracting & visualizing the results, and crystallographic modelling. These scripts will rapidly submit fully parameterized CASTEP jobs, extract data from the calculations, assist in visualizing the results, and expedite the process of structural modelling. Accompanied with these tools is a description on their functionality, documentation on how to get started and use the scripts, and links to video tutorials for guiding new users. Through the use of these tools, we hope to facilitate NMR crystallography and to harmonize the process across users.
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Affiliation(s)
| | - Sten O Nilsson Lill
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Helen Blade
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
| | - Leslie P Hughes
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK.
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2
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Widdifield CM, Nilsson Lill SO, Broo A, Lindkvist M, Pettersen A, Svensk Ankarberg A, Aldred P, Schantz S, Emsley L. Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease. Phys Chem Chem Phys 2018. [PMID: 28621371 DOI: 10.1039/c7cp02349a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured 13C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR (1H, 13C, 15N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct 13C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental 13C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of 13C shift tensors and the observation of residual dipolar coupling between 13C and 14N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD16 = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD16 = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.
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Affiliation(s)
- Cory M Widdifield
- Institut des 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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3
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Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate. J Pharm Biomed Anal 2017; 138:22-28. [DOI: 10.1016/j.jpba.2017.01.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 11/19/2022]
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4
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Rezende CA, San Gil RAS, Borré LB, Pires JR, Vaiss VS, Resende JALC, Leitão AA, De Alencastro RB, Leal KZ. Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs. J Pharm Sci 2015; 105:2648-2655. [PMID: 26372719 DOI: 10.1002/jps.24641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/29/2015] [Accepted: 08/19/2015] [Indexed: 11/06/2022]
Abstract
The experiments of carvedilol form II, form III, and hydrate by (13)C and (15)N cross-polarization magic-angle spinning (CP MAS) are reported. The GIPAW (gauge-including projector-augmented wave) method from DFT (density functional theory) calculations was used to simulate (13)C and (15)N chemical shifts. A very good agreement was found for the comparison between the global results of experimental and calculated nuclear magnetic resonance (NMR) chemical shifts for carvedilol polymorphs. This work aims a comprehensive understanding of carvedilol crystalline forms employing solution and solid-state NMR as well as DFT calculations.
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Affiliation(s)
- Carlos A Rezende
- Universidade Federal Fluminense, Instituto de Química, Niteroi CEP24020-150, Brazil
| | - Rosane A S San Gil
- Universidade Federal do Rio de Janeiro, Instituto de Quimica, Rio de Janeiro CEP21941-900, Brazil.
| | - Leandro B Borré
- Universidade Federal do Rio de Janeiro, Instituto de Quimica, Rio de Janeiro CEP21941-900, Brazil
| | - José Ricardo Pires
- Universidade Federal do Rio de Janeiro, Instituto de Bioquímica Medica, Rio de Janeiro CEP21941-902, Brazil
| | - Viviane S Vaiss
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora CEP36036-330, Brazil
| | | | - Alexandre A Leitão
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora CEP36036-330, Brazil
| | - Ricardo B De Alencastro
- Universidade Federal do Rio de Janeiro, Instituto de Quimica, Rio de Janeiro CEP21941-900, Brazil
| | - Katia Z Leal
- Universidade Federal Fluminense, Instituto de Química, Niteroi CEP24020-150, Brazil
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5
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Filip X, Filip C. Can the conformation of flexible hydroxyl groups be constrained by simple NMR crystallography approaches? The case of the quercetin solid forms. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 65:21-28. [PMID: 25465481 DOI: 10.1016/j.ssnmr.2014.10.006] [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: 07/24/2014] [Revised: 10/08/2014] [Accepted: 10/23/2014] [Indexed: 06/04/2023]
Abstract
Hydrogen atoms in systems with many flexible hydroxyl side-groups are difficult to be exactly located from experimental X-Ray diffraction and/or solid-state NMR data, thus often leading to wrong conclusions with respect to the hydrogen bonding network established in crystal lattice. A simple computational method is proposed in the present work to tackle this problem, which may be readily incorporated in conventional NMR crystallography protocols. The method is based on ranking all possible conformations of the flexible hydroxyls according to their lattice energy in crystalline environments. Its effectiveness is investigated on two distinct solid forms of quercetin, for which only two out of the five hydroxyl side-groups can be well constrained from experimental/theoretical data. For this purpose, first-principle quantum-mechanical computations were combined with calculations at the molecular mechanics (MM) level of theory, and previous ss-NMR and X-Ray diffraction data. To assess accuracy in ranking the identified conformers, tests have been performed first on quercetin dihydrate, for which an X-Ray single-crystal structure is available. The possibility of applying this method in a real NMR crystallography context has been investigated finally on anhydrous quercetin, for which only powder X-Ray crystal structure has been reported so far.
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Affiliation(s)
- Xenia Filip
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania
| | - Claudiu Filip
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania.
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6
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Lucier BEG, Johnston KE, Xu W, Hanson JC, Senanayake SD, Yao S, Bourassa MW, Srebro M, Autschbach J, Schurko RW. Unravelling the Structure of Magnus’ Pink Salt. J Am Chem Soc 2014; 136:1333-51. [DOI: 10.1021/ja4076277] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bryan E. G. Lucier
- Department
of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Karen E. Johnston
- Department
of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Wenqian Xu
- Department
of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Jonathan C. Hanson
- Department
of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Sanjaya D. Senanayake
- Department
of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Siyu Yao
- Center for Computational Science & Engineering, and PKU Green Chemistry Centre, Peking University, Beijing 100871, China
| | - Megan W. Bourassa
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Monika Srebro
- Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
- Department
of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Jochen Autschbach
- Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Robert W. Schurko
- Department
of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
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7
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Miclaus M, Grosu IG, Filip X, Tripon C, Filip C. Optimizing structure determination from powders of crystalline organic solids with high molecular flexibility: the case of lisinopril dihydrate. CrystEngComm 2014. [DOI: 10.1039/c3ce41890a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Czernek J, Brus J. Theoretical predictions of the two-dimensional solid-state NMR spectra: A case study of the 13C–1H correlations in metergoline. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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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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10
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Filip X, Grosu IG, Miclăuş M, Filip C. NMR crystallography methods to probe complex hydrogen bonding networks: application to structure elucidation of anhydrous quercetin. CrystEngComm 2013. [DOI: 10.1039/c3ce40299a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Bonhomme C, Gervais C, Babonneau F, Coelho C, Pourpoint F, Azaïs T, Ashbrook SE, Griffin JM, Yates JR, Mauri F, Pickard CJ. First-principles calculation of NMR parameters using the gauge including projector augmented wave method: a chemist's point of view. Chem Rev 2012; 112:5733-79. [PMID: 23113537 DOI: 10.1021/cr300108a] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris, Université Pierre et Marie Curie, CNRS UMR, Collège de France, France.
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12
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Ośmiałowski B, Kolehmainen E, Ikonen S, Ahonen K, Löfman M. NMR crystallography of 2-acylamino-6-[1H]-pyridones: Solid-state NMR, GIPAW computational, and single crystal X-ray diffraction studies. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.10.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Marjo CE, Bhadbhade M, Hook JM, Rich AM. Polymorphism and a Metastable Solvate of Duloxetine Hydrochloride. Mol Pharm 2011; 8:2454-64. [DOI: 10.1021/mp200455u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Christopher E. Marjo
- Mark Wainwright
Analytical Centre, Room G61, Chemical
Sciences Building (F10), University of New South Wales, Kensington, New South Wales, Australia 2052
| | - Mohan Bhadbhade
- Mark Wainwright
Analytical Centre, Room G61, Chemical
Sciences Building (F10), University of New South Wales, Kensington, New South Wales, Australia 2052
| | - James M. Hook
- Mark Wainwright
Analytical Centre, Room G61, Chemical
Sciences Building (F10), University of New South Wales, Kensington, New South Wales, Australia 2052
| | - Anne M. Rich
- Mark Wainwright
Analytical Centre, Room G61, Chemical
Sciences Building (F10), University of New South Wales, Kensington, New South Wales, Australia 2052
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14
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Filip X, Borodi G, Filip C. Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling. Phys Chem Chem Phys 2011; 13:17978-86. [DOI: 10.1039/c1cp21878f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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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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16
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Khan M, Enkelmann V, Brunklaus G. Crystal Engineering of Pharmaceutical Co-crystals: Application of Methyl Paraben as Molecular Hook. J Am Chem Soc 2010; 132:5254-63. [DOI: 10.1021/ja100146f] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mujeeb Khan
- Max-Planck-Institut für Polymerforschung, Postfach 31 48, D-55021 Mainz, Germany
| | - Volker Enkelmann
- Max-Planck-Institut für Polymerforschung, Postfach 31 48, D-55021 Mainz, Germany
| | - Gunther Brunklaus
- Max-Planck-Institut für Polymerforschung, Postfach 31 48, D-55021 Mainz, Germany
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17
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Harris RK. Applications of solid-state NMR to pharmaceutical polymorphism and related matters. J Pharm Pharmacol 2010; 59:225-39. [PMID: 17270076 DOI: 10.1211/jpp.59.2.0009] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Abstract
Magic-angle spinning NMR is now making a significant contribution to our understanding of the structure of polymorphs and solvates of pharmaceutical significance. This personal review article discusses a range of applications, with particular emphasis on information about crystallography, for which NMR can address problems that cannot be readily solved by diffraction techniques (such as dynamic disorder and non-stoichiometric hydration). Unlike diffractograms, NMR spectra yield immediate chemical information. Moreover, heterogeneous samples can be investigated and amorphous content provides no significant barrier to studies. Furthermore, NMR can be an effective technique for quantitation (down to the level of ca. 1%). Additional strength is being derived from computation of chemical shifts in solids, using a code that takes account of the spatial repetition inherent in crystalline materials.
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Affiliation(s)
- Robin K Harris
- Department of Chemistry, University of Durham, South Road, Durham, DH1 3LE, UK.
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18
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Harper JK, Doebbler JA, Jacques E, Grant DM, Von Dreele RB. A Combined Solid-State NMR and Synchrotron X-ray Diffraction Powder Study on the Structure of the Antioxidant (+)-Catechin 4.5-hydrate. J Am Chem Soc 2010; 132:2928-37. [DOI: 10.1021/ja907671p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James K. Harper
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - Jennifer A. Doebbler
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - Elisabeth Jacques
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - David M. Grant
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - Robert B. Von Dreele
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
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19
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Hammond R, Jeck S, Ma C, Pencheva K, Roberts K, Auffret T. An examination of binding motifs associated with inter-particle interactions between facetted nano-crystals of acetylsalicylic acid and ascorbic acid through the application of molecular grid-based search methods. J Pharm Sci 2009; 98:4589-602. [DOI: 10.1002/jps.21758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Zheng A, Liu SB, Deng F. 13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models. J Comput Chem 2009; 30:222-35. [DOI: 10.1002/jcc.21118] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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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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22
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Brouwer DH. A structure refinement strategy for NMR crystallography: an improved crystal structure of silica-ZSM-12 zeolite from 29Si chemical shift tensors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:136-146. [PMID: 18656402 DOI: 10.1016/j.jmr.2008.06.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 05/26/2023]
Abstract
A strategy for performing crystal structure refinements with NMR chemical shift tensors is described in detail and implemented for the zeolite silica-ZSM-12 (framework type code MTW). The 29Si chemical shift tensors were determined from a slow magic-angle spinning spectrum obtained at an ultrahigh magnetic field of 21.1T. The Si and O atomic coordinate parameters were optimized to give the best agreement between experimentally measured and ab initio calculated principal components of the 29Si chemical shift tensors, with the closest Si-O, O-O, and Si-Si distances restrained to correspond with the distributions of the distances found in a set of single-crystal X-ray diffraction (XRD) structures of high-silica zeolites. An improved structure for the silica-ZSM-12 zeolite, compared to a prior structure derived from powder XRD data, is obtained in which the agreement between the experimental and calculated 29Si chemical shift tensors is dramatically improved, the Si-O, O-O, and Si-Si distances correspond to the expected distributions, while the calculated powder XRD pattern remains in good agreement with the experimental powder XRD data. It is anticipated that this "NMR crystallography" structure refinement strategy will be an important tool for the accurate structure determination of materials that are difficult to fully characterize by traditional diffraction methods.
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Affiliation(s)
- Darren H Brouwer
- Steacie Institute for Molecular Science, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ont., Canada.
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23
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Olejniczak S, Mikuła-Pacholczyk J, Hughes CE, Potrzebowski MJ. 15N and 13C High-Resolution Solid-State NMR Study of the Polymorphism of the l-Enantiomer of N-Benzoylphenylalanine. J Phys Chem B 2008; 112:1586-93. [DOI: 10.1021/jp073428u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Olejniczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Justyna Mikuła-Pacholczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Colan E. Hughes
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
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Uldry AC, Griffin JM, Yates JR, Pérez-Torralba M, Santa María MD, Webber AL, Beaumont MLL, Samoson A, Claramunt RM, Pickard CJ, Brown SP. Quantifying Weak Hydrogen Bonding in Uracil and 4-Cyano-4‘-ethynylbiphenyl: A Combined Computational and Experimental Investigation of NMR Chemical Shifts in the Solid State. J Am Chem Soc 2008; 130:945-54. [DOI: 10.1021/ja075892i] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anne-Christine Uldry
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - John M. Griffin
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Jonathan R. Yates
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Marta Pérez-Torralba
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - M. Dolores Santa María
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Amy L. Webber
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Maximus L. L. Beaumont
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Ago Samoson
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Rosa María Claramunt
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Chris J. Pickard
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Steven P. Brown
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
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Harris RK, Hodgkinson P, Pickard CJ, Yates JR, Zorin V. Chemical shift computations on a crystallographic basis: some reflections and comments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S174-S186. [PMID: 18157842 DOI: 10.1002/mrc.2132] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Computations for chemical shifts of molecular organic compounds using the gauge-including projector augmented wave method and the NMR-CASTEP code are reviewed. The methods are briefly introduced, and some general aspects involving the sources of uncertainty in the results are explored. The limitations are outlined. Successful applications of the computations to problems of interpretation of NMR results are discussed and the range of areas in which useful information is obtained is illustrated by examples. The particular value of the computations for comparing shifts between resonances where the same chemical site is involved is emphasised. Such cases arise for shifts between different crystallographically independent molecules of the same chemical species, between polymorphs and for shift anisotropies and asymmetries.
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Affiliation(s)
- Robin K Harris
- Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, UK.
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Othman A, Evans JSO, Evans IR, Harris RK, Hodgkinson P. Structural Study of Polymorphs and Solvates of Finasteride. J Pharm Sci 2007; 96:1380-97. [PMID: 17455354 DOI: 10.1002/jps.20940] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
NMR and XRD data are reported for several new forms of finasteride, including the results of complete structure determinations for three solvates. Form III of finasteride, hitherto only mentioned in the patent literature, and a new anhydrous form designated Form X, have been found in mixtures of polymorphs and their (13)C NMR chemical shifts obtained. The results demonstrate that the crystallographic asymmetric units contain three molecules and one molecule, respectively. Attempts to reproduce "Form H1", as described in a patent, resulted in a new IPA solvate hydrate. The previously-reported acetic acid, dioxane, and ethyl acetate solvates have been further characterised, and new THF and diethyl ether solvates prepared and characterised. The crystal structures of the dioxane, IPA, and THF solvates have been determined by single-crystal X-ray diffraction. All the solvates (except the acetic acid case) are found to be hemihydrates, to have a finasteride: solvent molar ratio of 2:1 and to have a common structure. The solvate molecules are highly disordered and sited in channels in the structure. The powder XRD patterns are characteristic of the common structure. These solvates may be distinguished by the characteristic CPMAS (13)C signals from the solvent molecules, but the resonances of the host finasteride structures differ only marginally, and powder XRD patterns are almost indistinguishable. Magic-angle spinning (MAS) proton spectra give sharp lines for the solvent peaks, confirming their high degree of mobility. This is further shown in one case by direct polarisation (13)C spectra. Mobility of the tert-butyl group is also implied. Thermal characteristics have been studied and TGA used (in conjunction with solution-state proton NMR) to estimate molar ratios.
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Affiliation(s)
- Abdullah Othman
- Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, UK
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27
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Mifsud N, Elena B, Pickard CJ, Lesage A, Emsley L. Assigning powders to crystal structures by high-resolution (1)H-(1)H double quantum and (1)H-(13)C J-INEPT solid-state NMR spectroscopy and first principles computation. A case study of penicillin G. Phys Chem Chem Phys 2006; 8:3418-22. [PMID: 16855720 DOI: 10.1039/b605227d] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show how powder samples at natural isotopic abundance can be assigned to crystal structures by using high-resolution proton and carbon-13 solid-state NMR spectra in combination with first principles calculations. Homonuclear proton double-quantum spectra in combination with through-bond proton-carbon HSQC spectra are used to assign the NMR spectra. We then show that the proton chemical shifts can be included in the process of assigning the spectra to a crystal structure using first principles calculations. The method is demonstrated on the K salt of penicillin G.
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Affiliation(s)
- Nicolas Mifsud
- Laboratoire de Chimie (UMR 5182 ENS/CNRS), Laboratoire de Recherche Conventionné du CEA (DSV 23V/DSM 0432), Ecole Normale Supérieure de Lyon, 46, Allée d'Italie, 69364 Lyon, France
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