1
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Zhao D, Zhao Y, Xu E, Liu W, Ayers PW, Liu S, Chen D. Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates. J Chem Theory Comput 2024; 20:2655-2665. [PMID: 38441881 DOI: 10.1021/acs.jctc.3c01415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Simultaneous prediction of the molecular response properties, such as polarizability and the NMR shielding constant, at a low computational cost is an unresolved issue. We propose to combine a linear-scaling generalized energy-based fragmentation (GEBF) method and deep learning (DL) with both molecular and atomic information-theoretic approach (ITA) quantities as effective descriptors. In GEBF, the total molecular polarizability can be assembled as a linear combination of the corresponding quantities calculated from a set of small embedded subsystems in GEBF. In the new GEBF-DL(ITA) protocol, one can predict subsystem polarizabilities based on the corresponding molecular wave function (thus electron density and ITA quantities) and DL model rather than calculate them from the computationally intensive coupled-perturbed Hartree-Fock or Kohn-Sham equations and finally obtain the total molecular polarizability via a linear combination equation. As a proof-of-concept application, we predict the molecular polarizabilities of large proteins and protein aggregates. GEBF-DL(ITA) is shown to be as accurate enough as GEBF, with mean absolute percentage error <1%. For the largest protein aggregate (>4000 atoms), GEBF-DL(ITA) gains a speedup ratio of 3 compared with GEBF. It is anticipated that when more advanced electronic structure methods are used, this advantage will be more appealing. Moreover, one can also predict the NMR chemical shieldings of proteins with reasonably good accuracy. Overall, the cost-efficient GEBF-DL(ITA) protocol should be a robust theoretical tool for simultaneously predicting polarizabilities and NMR shieldings of large systems.
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Affiliation(s)
- Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
| | - Yilin Zhao
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ONL8S4M1, Canada
| | - Enhua Xu
- Graduate School of System Informatics, Kobe University, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Wenqi Liu
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ONL8S4M1, Canada
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
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2
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Rahman M, Dannatt HRW, Blundell CD, Hughes LP, Blade H, Carson J, Tatman BP, Johnston ST, Brown SP. Polymorph Identification for Flexible Molecules: Linear Regression Analysis of Experimental and Calculated Solution- and Solid-State NMR Data. J Phys Chem A 2024; 128:1793-1816. [PMID: 38427685 PMCID: PMC10945485 DOI: 10.1021/acs.jpca.3c07732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
The Δδ regression approach of Blade et al. [ J. Phys. Chem. A 2020, 124(43), 8959-8977] for accurately discriminating between solid forms using a combination of experimental solution- and solid-state NMR data with density functional theory (DFT) calculation is here extended to molecules with multiple conformational degrees of freedom, using furosemide polymorphs as an exemplar. As before, the differences in measured 1H and 13C chemical shifts between solution-state NMR and solid-state magic-angle spinning (MAS) NMR (Δδexperimental) are compared to those determined by gauge-including projector augmented wave (GIPAW) calculations (Δδcalculated) by regression analysis and a t-test, allowing the correct furosemide polymorph to be precisely identified. Monte Carlo random sampling is used to calculate solution-state NMR chemical shifts, reducing computation times by avoiding the need to systematically sample the multidimensional conformational landscape that furosemide occupies in solution. The solvent conditions should be chosen to match the molecule's charge state between the solution and solid states. The Δδ regression approach indicates whether or not correlations between Δδexperimental and Δδcalculated are statistically significant; the approach is differently sensitive to the popular root mean squared error (RMSE) method, being shown to exhibit a much greater dynamic range. An alternative method for estimating solution-state NMR chemical shifts by approximating the measured solution-state dynamic 3D behavior with an ensemble of 54 furosemide crystal structures (polymorphs and cocrystals) from the Cambridge Structural Database (CSD) was also successful in this case, suggesting new avenues for this method that may overcome its current dependency on the prior determination of solution dynamic 3D structures.
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Affiliation(s)
- Mohammed Rahman
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | | | - Leslie P. Hughes
- Oral
Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Helen Blade
- Oral
Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Jake Carson
- Mathematics
Institute at Warwick, University of Warwick, Coventry CV4 7AL, U.K.
| | - Ben P. Tatman
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Steven P. Brown
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
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3
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Beran GJO. Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials. Chem Sci 2023; 14:13290-13312. [PMID: 38033897 PMCID: PMC10685338 DOI: 10.1039/d3sc03903j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
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4
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Lopatik N, De A, Paasch S, Schneemann A, Brunner E. High-field and fast-spinning 1H MAS NMR spectroscopy for the characterization of two-dimensional covalent organic frameworks. Phys Chem Chem Phys 2023; 25:30237-30245. [PMID: 37921503 DOI: 10.1039/d3cp04144a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Two-dimensional (2D) materials, like 2D covalent organic frameworks (COFs), have been attracting increasing research interest. They are usually obtained as polycrystalline powders. Solid-state NMR spectroscopy is capable of delivering structural information about such materials. Previous studies have applied, for example, 13C cross-polarization magic angle spinning (CP MAS) NMR experiments to characterize 2D COFs. Herein, we demonstrate the usefulness of high-field and fast-spinning 1H MAS NMR spectroscopy to resolve and quantify the signals of different 1H species within 2D COFs, including the edge sites and/or defects. Moreover, 1H-13C heteronuclear correlation (HETCOR) spectroscopy has also been applied and can provide improved resolution to obtain further information about stacking effects as well as edge sites/defects.
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Affiliation(s)
- Nikolaj Lopatik
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany.
| | - Ankita De
- Chair of Inorganic Chemistry I, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Silvia Paasch
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany.
| | - Andreas Schneemann
- Chair of Inorganic Chemistry I, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Eike Brunner
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany.
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5
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Cordova M, Moutzouri P, Nilsson Lill SO, Cousen A, Kearns M, Norberg ST, Svensk Ankarberg A, McCabe J, Pinon AC, Schantz S, Emsley L. Atomic-level structure determination of amorphous molecular solids by NMR. Nat Commun 2023; 14:5138. [PMID: 37612269 PMCID: PMC10447443 DOI: 10.1038/s41467-023-40853-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder leads to a high degree of overlap between measured signals, and prevents the unambiguous identification of a single modeled periodic structure as representative of the whole material. Here, we determine the atomic-level ensemble structure of the amorphous form of the drug AZD4625 by combining solid-state NMR experiments with molecular dynamics (MD) simulations and machine-learned chemical shifts. By considering the combined shifts of all 1H and 13C atomic sites in the molecule, we determine the structure of the amorphous form by identifying an ensemble of local molecular environments that are in agreement with experiment. We then extract and analyze preferred conformations and intermolecular interactions in the amorphous sample in terms of the stabilization of the amorphous form of the drug.
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Affiliation(s)
- Manuel Cordova
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pinelopi Moutzouri
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Sten O Nilsson Lill
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Alexander Cousen
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Martin Kearns
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Stefan T Norberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Anna Svensk Ankarberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - James McCabe
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Arthur C Pinon
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Staffan Schantz
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden.
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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6
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Rehman Z, Franks WT, Nguyen B, Schmidt HF, Scrivens G, Brown SP. Discovering the Solid-State Secrets of Lorlatinib by NMR Crystallography: To Hydrogen Bond or not to Hydrogen Bond. J Pharm Sci 2023; 112:1915-1928. [PMID: 36868358 DOI: 10.1016/j.xphs.2023.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023]
Abstract
Lorlatinib is an active pharmaceutical ingredient (API) used in the treatment of lung cancer. Here, an NMR crystallography analysis is presented whereby the single-crystal X-ray diffraction structure (CSD: 2205098) determination is complemented by multinuclear (1H, 13C, 14/15N, 19F) magic-angle spinning (MAS) solid-state NMR and gauge-including projector augmented wave (GIPAW) calculation of NMR chemical shifts. Lorlatinib crystallises in the P21 space group, with two distinct molecules in the asymmetric unit cell, Z' = 2. Three of the four NH2 hydrogen atoms form intermolecular hydrogen bonds, N30-H…N15 between the two distinct molecules and N30-H…O2 between two equivalent molecules. This is reflected in one of the NH21H chemical shifts being significantly lower, 4.0 ppm compared to 7.0 ppm. Two-dimensional 1H-13C, 14N-1H and 1H (double-quantum, DQ)-1H (single-quantum, SQ) MAS NMR spectra are presented. The 1H resonances are assigned and specific HH proximities corresponding to the observed DQ peaks are identified. The resolution enhancement at a 1H Larmor frequency of 1 GHz as compared to 500 or 600 MHz is demonstrated.
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Affiliation(s)
- Zainab Rehman
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | | | | | | | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
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7
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Zwitterionic or Not? Fast and Reliable Structure Determination by Combining Crystal Structure Prediction and Solid-State NMR. Molecules 2023; 28:molecules28041876. [PMID: 36838863 PMCID: PMC9966216 DOI: 10.3390/molecules28041876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
When it comes to crystal structure determination, computational approaches such as Crystal Structure Prediction (CSP) have gained more and more attention since they offer some insight on how atoms and molecules are packed in the solid state, starting from only very basic information without diffraction data. Furthermore, it is well known that the coupling of CSP with solid-state NMR (SSNMR) greatly enhances the performance and the accuracy of the predictive method, leading to the so-called CSP-NMR crystallography (CSP-NMRX). In this paper, we present the successful application of CSP-NMRX to determine the crystal structure of three structural isomers of pyridine dicarboxylic acid, namely quinolinic, dipicolinic and dinicotinic acids, which can be in a zwitterionic form, or not, in the solid state. In a first step, mono- and bidimensional SSNMR spectra, i.e., 1H Magic-Angle Spinning (MAS), 13C and 15N Cross Polarisation Magic-Angle Spinning (CPMAS), 1H Double Quantum (DQ) MAS, 1H-13C HETeronuclear CORrelation (HETCOR), were used to determine the correct molecular structure (i.e., zwitterionic or not) and the local molecular arrangement; at the end, the RMSEs between experimental and computed 1H and 13C chemical shifts allowed the selection of the correct predicted structure for each system. Interestingly, while quinolinic and dipicolinic acids are zwitterionic and non-zwitterionic, respectively, in the solid state, dinicotinic acid exhibits in its crystal structure a "zwitterionic-non-zwitterionic continuum state" in which the proton is shared between the carboxylic moiety and the pyridinic nitrogen. Very refined SSNMR experiments were carried out, i.e., 14N-1H Phase-Modulated (PM) pulse and Rotational-Echo Saturation-Pulse Double-Resonance (RESPDOR), to provide an accurate N-H distance value confirming the hybrid nature of the molecule. The CSP-NMRX method showed a remarkable match between the selected structures and the experimental ones. The correct molecular input provided by SSNMR reduced the number of CSP calculations to be performed, leading to different predicted structures, while RMSEs provided an independent parameter with respect to the computed energy for the selection of the best candidate.
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8
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Cordova M, Moutzouri P, Simões de Almeida B, Torodii D, Emsley L. Pure Isotropic Proton NMR Spectra in Solids using Deep Learning. Angew Chem Int Ed Engl 2023; 62:e202216607. [PMID: 36562545 PMCID: PMC10107932 DOI: 10.1002/anie.202216607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The resolution of proton solid-state NMR spectra is usually limited by broadening arising from dipolar interactions between spins. Magic-angle spinning alleviates this broadening by inducing coherent averaging. However, even the highest spinning rates experimentally accessible today are not able to completely remove dipolar interactions. Here, we introduce a deep learning approach to determine pure isotropic proton spectra from a two-dimensional set of magic-angle spinning spectra acquired at different spinning rates. Applying the model to 8 organic solids yields high-resolution 1 H solid-state NMR spectra with isotropic linewidths in the 50-400 Hz range.
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Affiliation(s)
- Manuel Cordova
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials MARVEL, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Pinelopi Moutzouri
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Bruno Simões de Almeida
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Daria Torodii
- Institut des Sciences et Ingénierie Chimiques, 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.,National Centre for Computational Design and Discovery of Novel Materials MARVEL, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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9
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Smith AN, Harrabi R, Halbritter T, Lee D, Aussenac F, van der Wel PCA, Hediger S, Sigurdsson ST, De Paëpe G. Fast magic angle spinning for the characterization of milligram quantities of organic and biological solids at natural isotopic abundance by 13C- 13C correlation DNP-enhanced NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 123:101850. [PMID: 36592488 DOI: 10.1016/j.ssnmr.2022.101850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
We show that multidimensional solid-state NMR 13C-13C correlation spectra of biomolecular assemblies and microcrystalline organic molecules can be acquired at natural isotopic abundance with only milligram quantities of sample. These experiments combine fast Magic Angle Spinning of the sample, low-power dipolar recoupling, and dynamic nuclear polarization performed with AsymPol biradicals, a recently introduced family of polarizing agents. Such experiments are essential for structural characterization as they provide short- and long-range distance information. This approach is demonstrated on diverse sample types, including polyglutamine fibrils implicated in Huntington's disease and microcrystalline ampicillin, a small antibiotic molecule.
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Affiliation(s)
- Adam N Smith
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000, Grenoble, France
| | - Rania Harrabi
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000, Grenoble, France
| | - Thomas Halbritter
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107, Reykjavik, Iceland
| | - Daniel Lee
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000, Grenoble, France
| | | | - Patrick C A van der Wel
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000, Grenoble, France
| | - Snorri Th Sigurdsson
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107, Reykjavik, Iceland
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000, Grenoble, France.
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10
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Szell PMJ, Rehman Z, Tatman BP, Hughes LP, Blade H, Brown SP. Exploring the Potential of Multinuclear Solid-State 1 H, 13 C, and 35 Cl Magnetic Resonance To Characterize Static and Dynamic Disorder in Pharmaceutical Hydrochlorides. Chemphyschem 2023; 24:e202200558. [PMID: 36195553 PMCID: PMC10099218 DOI: 10.1002/cphc.202200558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/30/2022] [Indexed: 02/04/2023]
Abstract
Crystallographic disorder, whether static or dynamic, can be detrimental to the physical and chemical stability, ease of crystallization and dissolution rate of an active pharmaceutical ingredient. Disorder can result in a loss of manufacturing control leading to batch-to-batch variability and can lengthen the process of structural characterization. The range of NMR active nuclei makes solid-state NMR a unique technique for gaining nucleus-specific information about crystallographic disorder. Here, we explore the use of high-field 35 Cl solid-state NMR at 23.5 T to characterize both static and dynamic crystallographic disorder: specifically, dynamic disorder occurring in duloxetine hydrochloride (1), static disorder in promethazine hydrochloride (2), and trifluoperazine dihydrochloride (3). In all structures, the presence of crystallographic disorder was confirmed by 13 C cross-polarization magic-angle spinning (CPMAS) NMR and supported by GIPAW-DFT calculations, and in the case of 3, 1 H solid-state NMR provided additional confirmation. Applying 35 Cl solid-state NMR to these compounds, we show that higher magnetic fields are beneficial for resolving the crystallographic disorder in 1 and 3, while broad spectral features were observed in 2 even at higher fields. Combining the data obtained from 1 H, 13 C, and 35 Cl NMR, we show that 3 exhibits a unique case of disorder involving the + N-H hydrogen positions of the piperazinium ring, driving the chloride anions to occupy three distinct sites.
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Affiliation(s)
| | - Zainab Rehman
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Ben P Tatman
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Leslie P Hughes
- Oral Product Development Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Helen Blade
- Oral Product Development Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
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11
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Khalaji M, Paluch P, Potrzebowski MJ, Dudek MK. Narrowing down the conformational space with solid-state NMR in crystal structure prediction of linezolid cocrystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 121:101813. [PMID: 35964358 DOI: 10.1016/j.ssnmr.2022.101813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Many solids crystallize as microcrystalline powders, thus precluding the application of single crystal X-Ray diffraction in structural elucidation. In such cases, a joint use of high-resolution solid-state NMR and crystal structure prediction (CSP) calculations can be successful. However, for molecules showing significant conformational freedom, the CSP-NMR protocol can meet serious obstacles, including ambiguities in NMR signal assignment and too wide conformational search space to be covered by computational methods in reasonable time. Here, we demonstrate a possible way of avoiding these obstacles and making as much use of the two methods as possible in difficult circumstances. In a simple case, our experiments led to crystal structure elucidation of a cocrystal of linezolid (LIN), a wide-range antibiotic, with 2,3-dihydroxybenzoic acid, while a significantly more challenging case of a cocrystal of LIN with 2,4-dihydroxybenzoic acid led to the identification of the most probable conformations of LIN inside the crystal. Having four rotatable bonds, some of which can assume many discreet values, LIN molecule poses a challenge in establishing its conformation in a solid phase. In our work, a set of 27 conformations were used in CSP calculations to yield model crystal structures to be examined against experimental solid-state NMR data, leading to a reliable identification of the most probable molecular arrangements.
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Affiliation(s)
- Mehrnaz Khalaji
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Marta K Dudek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland.
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12
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Chotera‐Ouda A, Jeziorna A, Kaźmierski S, Dolot R, Dudek MK, Potrzebowski MJ. “Crystal memory” Affects the Properties of Peptide Hydrogels – The Case of the Cyclic Tyr‐Tyr dipeptide. Chemistry 2022; 28:e202202005. [DOI: 10.1002/chem.202202005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Agata Chotera‐Ouda
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Agata Jeziorna
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
- Lodz Institute of Technology Łukasiewicz Research Network M. Sklodowskiej-Curie 19/27 90-570 Lodz Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Marta K. Dudek
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
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13
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Al-Ani A, Szell PMJ, Rehman Z, Blade H, Wheatcroft HP, Hughes LP, Brown SP, Wilson CC. Combining X-ray and NMR Crystallography to Explore the Crystallographic Disorder in Salbutamol Oxalate. CRYSTAL GROWTH & DESIGN 2022; 22:4696-4707. [PMID: 35971412 PMCID: PMC9374327 DOI: 10.1021/acs.cgd.1c01093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Salbutamol is an active pharmaceutical ingredient commonly used to treat respiratory distress and is listed by the World Health Organization as an essential medicine. Here, we establish the crystal structure of its oxalate form, salbutamol oxalate, and explore the nature of its crystallographic disorder by combined X-ray crystallography and 13C cross-polarization (CP) magic-angle spinning (MAS) solid-state NMR. The *C-OH chiral center of salbutamol (note that the crystal structures are a racemic mixture of the two enantiomers of salbutamol) is disordered over two positions, and the tert-butyl group is rotating rapidly, as revealed by 13C solid-state NMR. The impact of crystallization conditions on the disorder was investigated, finding variations in the occupancy ratio of the *C-OH chiral center between single crystals and a consistency across samples in the bulk powder. Overall, this work highlights the contrast between investigating crystallographic disorder by X-ray diffraction and solid-state NMR experiment, and gauge-including projector-augmented-wave (GIPAW) density functional theory (DFT) calculations, with their combined use, yielding an improved understanding of the nature of the crystallographic disorder between the local (i.e., as viewed by NMR) and longer-range periodic (i.e., as viewed by diffraction) scale.
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Affiliation(s)
- Aneesa
J. Al-Ani
- Centre
for Sustainable and Circular Technologies (CSCT), University of Bath, Claverton Down, Bath BA2
7AY, U.K.
| | | | - Zainab Rehman
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Helen Blade
- Oral
Product Development, Pharmaceutical Technology & Development,
Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Helen P. Wheatcroft
- Chemical
Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Leslie P. Hughes
- Oral
Product Development, Pharmaceutical Technology & Development,
Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Steven P. Brown
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Chick C. Wilson
- Centre
for Sustainable and Circular Technologies (CSCT), University of Bath, Claverton Down, Bath BA2
7AY, U.K.
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14
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Zhang Z, Su Y, Xiao H, Yang J. Selective Nuclear Magnetic Resonance Method for Enhancing Long-Range Heteronuclear Correlations in Solids. J Phys Chem Lett 2022; 13:6376-6382. [PMID: 35796704 DOI: 10.1021/acs.jpclett.2c01527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The long-range heteronuclear correlation remains a significant challenge in solid-state nuclear magnetic resonance (NMR), which is critical in the structural elucidation of biomolecular, material, and pharmaceutical solids. We propose a selective NMR method, heteronuclear selective phase-optimized recoupling (hetSPR), to selectively enhance long-range correlations of interest by utilizing characteristic chemical shifts. Compared to conventional methods, hetSPR can selectively enhance desired heteronuclear correlations (e.g., 1H-13C and 1H-19F) by factors up to 5 and largely suppress the unwanted ones. The method proves useful by enhancing the long-range correlation from an intermolecular 1H-19F distance of 4.8 Å by a factor of 2.4 in a fluorinated pharmaceutical drug, bicalutamide, under fast magic-angle spinning. It does not use selective pulses and is thus user-friendly even for nonexperts. The new method is expected to boost solid-state NMR to elucidate the structures of various solids.
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Affiliation(s)
- Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yongchao Su
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, the University of Texas at Austin, Austin, Texas 78712, United States
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Hang Xiao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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15
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Newman JA, Iuzzolino L, Tan M, Orth P, Bruhn J, Lee AY. From Powders to Single Crystals: A Crystallographer's Toolbox for Small-Molecule Structure Determination. Mol Pharm 2022; 19:2133-2141. [PMID: 35576503 PMCID: PMC10152450 DOI: 10.1021/acs.molpharmaceut.2c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the crystal structures of small-molecule compounds are often determined from single-crystal X-ray diffraction (scXRD), recent advances in three-dimensional electron diffraction (3DED) and crystal structure prediction (CSP) methods promise to expand the structure elucidation toolbox available to the crystallographer. Herein, a comparative assessment of scXRD, 3DED, and CSP in combination with powder X-ray diffraction is carried out on two former drug candidate compounds and a multicomponent crystal of a key building block in the synthesis of gefapixant citrate.
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Affiliation(s)
- Justin A. Newman
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Luca Iuzzolino
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Melissa Tan
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter Orth
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jessica Bruhn
- Nanoimaging
Services, San Diego, California 92121, United States
| | - Alfred Y. Lee
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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16
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Balodis M, Cordova M, Hofstetter A, Day GM, Emsley L. De Novo Crystal Structure Determination from Machine Learned Chemical Shifts. J Am Chem Soc 2022; 144:7215-7223. [PMID: 35416661 PMCID: PMC9052749 DOI: 10.1021/jacs.1c13733] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Determination of the three-dimensional atomic-level structure of powdered solids is one of the key goals in current chemistry. Solid-state NMR chemical shifts can be used to solve this problem, but they are limited by the high computational cost associated with crystal structure prediction methods and density functional theory chemical shift calculations. Here, we successfully determine the crystal structures of ampicillin, piroxicam, cocaine, and two polymorphs of the drug molecule AZD8329 using on-the-fly generated machine-learned isotropic chemical shifts to directly guide a Monte Carlo-based structure determination process starting from a random gas-phase conformation.
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Affiliation(s)
- Martins Balodis
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Manuel Cordova
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Graeme M Day
- School of Chemistry, University of Southampton, Highfield SO17 1BJ, Southampton, United Kingdom
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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17
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Dudek MK, Druzbicki K. Along the road to Crystal Structure Prediction (CSP) of pharmaceutical-like molecules. CrystEngComm 2022. [DOI: 10.1039/d1ce01564h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational methods used for predicting crystal structures of organic compounds are mature enough to be routinely used with many rigid and semi-rigid organic molecules. The usefulness of Crystal Structure Prediction...
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18
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Bravetti F, Bordignon S, Alig E, Eisenbeil D, Fink L, Nervi C, Gobetto R, Schmidt MU, Chierotti MR. Solid-State NMR-Driven Crystal Structure Prediction of Molecular Crystals: The Case of Mebendazole. Chemistry 2021; 28:e202103589. [PMID: 34962330 DOI: 10.1002/chem.202103589] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Indexed: 11/06/2022]
Abstract
Among all possible NMR crystallography approaches for crystal-structure determination, crystal structure prediction - NMR crystallography (CSP-NMRX) has recently turned out to be a powerful method. In the latter, the original procedure exploited solid-state NMR (SSNMR) information during the final steps of the prediction. In particular, it used the comparison of computed and experimental chemical shifts for the selection of the correct crystal packing. Still, the prediction procedure, generally carried out with DFT methods, may require important computational resources and be quite time-consuming, especially if there are no available constraints to use at the initial stage. Herein, the successful application of this combined prediction method, which exploits NMR information also in the input step to reduce the search space of the predictive algorithm, is presented. Herein, this method was applied on mebendazole, which is characterized by desmotropism. The use of SSNMR data as constraints for the selection of the right tautomer and the determination of the number of independent molecules in the unit cell led to a considerably faster process, reducing the number of calculations to be performed. In this way, the crystal packing was successfully predicted for the three known phases of mebendazole. To evaluate the quality of the predicted structures, these were compared to the experimental ones. The crystal structure of phase B of mebendazole, in particular, was determined de novo by powder diffraction and is presented for the first time in this paper.
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Affiliation(s)
- Federica Bravetti
- Department of Chemistry, Università degli Studi di Torino, via Pietro Giuria 7, 10125, Torino, Italy
| | - Simone Bordignon
- Department of Chemistry, Università degli Studi di Torino, via Pietro Giuria 7, 10125, Torino, Italy
| | - Edith Alig
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Daniel Eisenbeil
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Lothar Fink
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Carlo Nervi
- Department of Chemistry, Università degli Studi di Torino, via Pietro Giuria 7, 10125, Torino, Italy
| | - Roberto Gobetto
- Department of Chemistry, Università degli Studi di Torino, via Pietro Giuria 7, 10125, Torino, Italy
| | - Martin U Schmidt
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Michele R Chierotti
- Department of Chemistry, Università degli Studi di Torino, via Pietro Giuria 7, 10125, Torino, Italy
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19
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Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: Gibbs Sampling and Bayesian Inference Using Floating Chirality Distance Geometry Calculations. Mar Drugs 2021; 20:14. [PMID: 35049868 PMCID: PMC8781118 DOI: 10.3390/md20010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
Floating chirality restrained distance geometry (fc-rDG) calculations are used to directly evolve structures from NMR data such as NOE-derived intramolecular distances or anisotropic residual dipolar couplings (RDCs). In contrast to evaluating pre-calculated structures against NMR restraints, multiple configurations (diastereomers) and conformations are generated automatically within the experimental limits. In this report, we show that the "unphysical" rDG pseudo energies defined from NMR violations bear statistical significance, which allows assigning probabilities to configurational assignments made that are fully compatible with the method of Bayesian inference. These "diastereomeric differentiabilities" then even become almost independent of the actual values of the force constants used to model the restraints originating from NOE or RDC data.
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Affiliation(s)
- Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar-und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany;
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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20
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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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21
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Deringer VL, Bartók AP, Bernstein N, Wilkins DM, Ceriotti M, Csányi G. Gaussian Process Regression for Materials and Molecules. Chem Rev 2021; 121:10073-10141. [PMID: 34398616 PMCID: PMC8391963 DOI: 10.1021/acs.chemrev.1c00022] [Citation(s) in RCA: 197] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 12/18/2022]
Abstract
We provide an introduction to Gaussian process regression (GPR) machine-learning methods in computational materials science and chemistry. The focus of the present review is on the regression of atomistic properties: in particular, on the construction of interatomic potentials, or force fields, in the Gaussian Approximation Potential (GAP) framework; beyond this, we also discuss the fitting of arbitrary scalar, vectorial, and tensorial quantities. Methodological aspects of reference data generation, representation, and regression, as well as the question of how a data-driven model may be validated, are reviewed and critically discussed. A survey of applications to a variety of research questions in chemistry and materials science illustrates the rapid growth in the field. A vision is outlined for the development of the methodology in the years to come.
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Affiliation(s)
- Volker L. Deringer
- Department
of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Albert P. Bartók
- Department
of Physics and Warwick Centre for Predictive Modelling, School of
Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Noam Bernstein
- Center
for Computational Materials Science, U.S.
Naval Research Laboratory, Washington D.C. 20375, United States
| | - David M. Wilkins
- Atomistic
Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Michele Ceriotti
- Laboratory
of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- National
Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne, Lausanne, Switzerland
| | - Gábor Csányi
- Engineering
Laboratory, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
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22
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Moutzouri P, Simões de Almeida B, Torodii D, Emsley L. Pure Isotropic Proton Solid State NMR. J Am Chem Soc 2021; 143:9834-9841. [PMID: 34170672 DOI: 10.1021/jacs.1c03315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Resolution in proton solid state magic angle sample spinning (MAS) NMR is limited by the intrinsically imperfect nature of coherent averaging induced by either MAS or multiple pulse sequence methods. Here, we suggest that instead of optimizing and perfecting a coherent averaging scheme, we could approach the problem by parametrically mapping the error terms due to imperfect averaging in a k-space representation, in such a way that they can be removed in a multidimensional correlation leaving only the desired pure isotropic signal. We illustrate the approach here by determining pure isotropic 1H spectra from a series of MAS spectra acquired at different spinning rates. For six different organic solids, the approach is shown to produce pure isotropic 1H spectra that are significantly narrower than the MAS spectrum acquired at the fastest possible rate, with linewidths down to as little as 48 Hz. On average, we observe a 7-fold increase in resolution, and up to a factor of 20, as compared with spectra acquired at 100 kHz MAS. The approach is directly applicable to a range of solids, and we anticipate that the same underlying principle for removing errors introduced here can be applied to other problems in NMR spectroscopy.
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Affiliation(s)
- Pinelopi Moutzouri
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Bruno Simões de Almeida
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Daria Torodii
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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23
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Pawlak T, Sudgen I, Bujacz G, Iuga D, Brown SP, Potrzebowski MJ. Synergy of Solid-State NMR, Single-Crystal X-ray Diffraction, and Crystal Structure Prediction Methods: A Case Study of Teriflunomide (TFM). CRYSTAL GROWTH & DESIGN 2021; 21:3328-3343. [PMID: 34267599 PMCID: PMC8273857 DOI: 10.1021/acs.cgd.1c00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/27/2021] [Indexed: 06/13/2023]
Abstract
In this work, for the first time, we present the X-ray diffraction crystal structure and spectral properties of a new, room-temperature polymorph of teriflunomide (TFM), CSD code 1969989. As revealed by DSC, the low-temperature TFM polymorph recently reported by Gunnam et al. undergoes a reversible thermal transition at -40 °C. This reversible process is related to a change in Z' value, from 2 to 1, as observed by variable-temperature 1H-13C cross-polarization (CP) magic-angle spinning (MAS) solid-state NMR, while the crystallographic system is preserved (triclinic). Two-dimensional 13C-1H and 1H-1H double-quantum MAS NMR spectra are consistent with the new room-temperature structure, including comparison with GIPAW (gauge-including projector augmented waves) calculated NMR chemical shifts. A crystal structure prediction procedure found both experimental teriflunomide polymorphs in the energetic global minimum region. Differences between the polymorphs are seen for the torsional angle describing the orientation of the phenyl ring relative to the planarity of the TFM molecule. In the low-temperature structure, there are two torsion angles of 4.5 and 31.9° for the two Z' = 2 molecules, while in the room-temperature structure, there is disorder that is modeled with ∼50% occupancy between torsion angles of -7.8 and 28.6°. These observations are consistent with a broad energy minimum as revealed by DFT calculations. PISEMA solid-state NMR experiments show a reduction in the C-H dipolar coupling in comparison to the static limit for the aromatic CH moieties of 75% and 51% at 20 and 40 °C, respectively, that is indicative of ring flips at the higher temperature. Our study shows the power of combining experiments, namely DSC, X-ray diffraction, and MAS NMR, with DFT calculations and CSP to probe and understand the solid-state landscape, and in particular the role of dynamics, for pharmaceutical molecules.
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Affiliation(s)
- Tomasz Pawlak
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Isaac Sudgen
- Molecular
Systems Engineering Group, Centre for Process Systems Engineering,
Department of Chemical Engineering, Imperial
College London, London SW7 2AZ, U.K.
| | - Grzegorz Bujacz
- Institute
of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Dinu Iuga
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Steven P. Brown
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Marek J. Potrzebowski
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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24
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Li H, Kopiec G, Müller F, Nyßen F, Shimizu K, Ceccato M, Daasbjerg K, Plumeré N. Spectroscopic Evidence for a Covalent Sigma Au-C Bond on Au Surfaces Using 13C Isotope Labeling. JACS AU 2021; 1:362-368. [PMID: 33829214 PMCID: PMC8016281 DOI: 10.1021/jacsau.0c00108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Indexed: 05/20/2023]
Abstract
The Au-C linkage has been demonstrated as a robust interface for coupling thin organic films on Au surfaces. However, the nature of the Au-C interaction remains elusive up to now. Surface-enhanced Raman spectroscopy was previously used to assign a band at 412 cm-1 as a covalent sigma Au-C bond for films generated by spontaneous reduction of the 4-nitrobenzenediazonium salt on Au nanoparticles. However, this assignment is disputed based on our isotopic shift study. We now provide direct evidence for covalent Au-C bonds on the surface of Au nanoparticles using 13C cross-polarization/magic angle spinning solid-state NMR spectroscopy combined with isotope substitution. A 13C NMR shift at 165 ppm was identified as an aromatic carbon linked to the gold surface, while the shift at 148 ppm was attributed to C-C junctions in the arylated organic film. This demonstration of the covalent sigma Au-C bond fills the gap in metal-C bonds for organic films on surfaces, and it has great practical and theoretical significance in understanding and designing a molecular junction based on the Au-C bond.
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Affiliation(s)
- Huaiguang Li
- Center
for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
- Campus
Straubing for Biotechnology and Sustainability, Technical University Munich, Schulgasse 22, 94315 Straubing, Germany
- . (H.L.)
| | - Gabriel Kopiec
- Center
for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Frank Müller
- Center
for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Frauke Nyßen
- Center
for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Kyoko Shimizu
- Interdisciplinary
Nanoscience Center/Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Marcel Ceccato
- Interdisciplinary
Nanoscience Center/Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kim Daasbjerg
- Interdisciplinary
Nanoscience Center/Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Nicolas Plumeré
- Center
for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
- Campus
Straubing for Biotechnology and Sustainability, Technical University Munich, Schulgasse 22, 94315 Straubing, Germany
- . (N.P.)
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25
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Reggelin M, Immel S. Configurational Analysis by Residual Dipolar Couplings: Critical Assessment of "Structural Noise" from Thermal Vibrations. Angew Chem Int Ed Engl 2021; 60:3412-3416. [PMID: 33137233 PMCID: PMC7898695 DOI: 10.1002/anie.202011081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Indexed: 12/11/2022]
Abstract
The certainty of configurational assignments of natural products based on anisotropic NMR parameters, such as residual dipolar couplings (RDCs), must be amended by estimates on structural noise emerging from thermal vibrations. We show that vibrational analysis significantly affects the error margins with which RDCs can be back-calculated from molecular models, and the implications of thermal motions on the differentiability of diastereomers are derived.
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Affiliation(s)
- Michael Reggelin
- Technische Universität DarmstadtClemens Schöpf Institut für Organische Chemie und BiochemieAlarich-Weiss-Strasse 464287DarmstadtGermany
| | - Stefan Immel
- Technische Universität DarmstadtClemens Schöpf Institut für Organische Chemie und BiochemieAlarich-Weiss-Strasse 464287DarmstadtGermany
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26
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Reggelin M, Immel S. Configurational Analysis by Residual Dipolar Couplings: Critical Assessment of “Structural Noise” from Thermal Vibrations. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Reggelin
- Technische Universität Darmstadt Clemens Schöpf Institut für Organische Chemie und Biochemie Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Stefan Immel
- Technische Universität Darmstadt Clemens Schöpf Institut für Organische Chemie und Biochemie Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
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27
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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28
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Viger-Gravel J, Pinon AC, Björgvinsdóttir S, Skantze U, Svensk Ankarberg A, Von Corswant C, Schantz S, Emsley L. High Sensitivity Detection of a Solubility Limiting Surface Transformation of Drug Particles by DNP SENS. J Pharm Sci 2021; 110:2452-2456. [PMID: 33417900 DOI: 10.1016/j.xphs.2020.12.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/11/2020] [Accepted: 12/18/2020] [Indexed: 01/13/2023]
Abstract
We investigate the presence of a surface species for the active pharmaceutical ingredient (API) AZD9496 with dynamic nuclear polarization surface enhanced nuclear spectroscopy (DNP SENS). We show that using DNP we can elucidate the presence of an amorphous form of the API at the surface of crystalline particles of the salt form. The amorphous form of the API has distinguishable 13C chemical shifts when compared to the salt form under various acidic conditions. The predominant form in frozen particles of AZD9496 is the salt, and we provide evidence to suggest that the amorphous layer at the surface is mainly made up of the dissociated free form.
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Affiliation(s)
- Jasmine Viger-Gravel
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Organic Chemistry Department, School of Chemistry and Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Arthur C Pinon
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swedish NMR Center, 413 90 Gothenburg, Sweden
| | - Snædís Björgvinsdóttir
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Urban Skantze
- Advanced Drug Delivery, Pharmaceutical Science, AstraZeneca, Gothenburg, Sweden
| | - Anna Svensk Ankarberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Christian Von Corswant
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Staffan Schantz
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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29
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Backler F, Sani MA, Separovic F, Vasilyev V, Wang F. NMR Chemical Shift and Methylation of 4-Nitroimidazole: Experiment and Theory. Aust J Chem 2021. [DOI: 10.1071/ch20199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nitroimidazoles and derivatives are a class of active pharmaceutical ingredients (APIs) first introduced sixty years ago. As anti-infection agents, the structure–activity relationships of nitroimidazole compounds have been particularly difficult to study due to their low reduction potentials and unique electronic structures. In this study, we combine dynamic nuclear polarization (DNP)-enhanced solid-state (100K), solid-state (298K), and 1H-13C heteronuclear single quantum coherence (HSQC) solution-state NMR techniques (303K) with density functional theory (DFT) to study the 1H, 13C, and 15N chemical shifts of 4-nitroimidazole (4-NI) and 1-methyl-4-nitroimidazole (CH3-4NI). The 4-NI chemical shifts were observed at 119.4, 136.4, and 144.7ppm for 13C, and at 181.5, 237.4, and 363.0ppm for 15N. The measurements revealed that methylation (deprotonation) of the amino nitrogen N(1) of 4-NI had less effect (Δδ=−4.8ppm) on the N(1) chemical shift but was compensated by shielding of the N(3) (Δδ=11.6ppm) in CH3-4NI. The calculated chemical shifts using DFT for 4-NI and CH3-4NI agreed well with the experimental values (within 2%) for the imidazole carbons. However, larger discrepancies (up to 13%) were observed between the calculated and measured 15N NMR chemical shifts for the imidazole nitrogen atoms of both molecules, which indicate that effects such as imidazole ring resonant structures and molecular dynamics may also contribute to the nitrogen chemical environment.
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30
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Blade H, Blundell CD, Brown SP, Carson J, Dannatt HRW, Hughes LP, Menakath AK. Conformations in Solution and in Solid-State Polymorphs: Correlating Experimental and Calculated Nuclear Magnetic Resonance Chemical Shifts for Tolfenamic Acid. J Phys Chem A 2020; 124:8959-8977. [DOI: 10.1021/acs.jpca.0c07000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Helen Blade
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K
| | | | - Steven P. Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Jake Carson
- Department of Statistics, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Leslie P. Hughes
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K
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31
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Hope M, Zhang B, Zhu B, Halat DM, MacManus-Driscoll JL, Grey CP. Revealing the Structure and Oxygen Transport at Interfaces in Complex Oxide Heterostructures via 17O NMR Spectroscopy. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2020; 32:7921-7931. [PMID: 32982045 PMCID: PMC7513580 DOI: 10.1021/acs.chemmater.0c02698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/18/2020] [Indexed: 05/24/2023]
Abstract
Vertically aligned nanocomposite (VAN) films, comprising nanopillars of one phase embedded in a matrix of another, have shown great promise for a range of applications due to their high interfacial areas oriented perpendicular to the substrate. In particular, oxide VANs show enhanced oxide-ion conductivity in directions that are orthogonal to those found in more conventional thin-film heterostructures; however, the structure of the interfaces and its influence on conductivity remain unclear. In this work, 17O NMR spectroscopy is used to study CeO2-SrTiO3 VAN thin films: selective isotopic enrichment is combined with a lift-off technique to remove the substrate, facilitating detection of the 17O NMR signal from single atomic layer interfaces. By performing the isotopic enrichment at variable temperatures, the superior oxide-ion conductivity of the VAN films compared to the bulk materials is shown to arise from enhanced oxygen mobility at this interface; oxygen motion at the interface is further identified from 17O relaxometry experiments. The structure of this interface is solved by calculating the NMR parameters using density functional theory combined with random structure searching, allowing the chemistry underpinning the enhanced oxide-ion transport to be proposed. Finally, a comparison is made with 1% Gd-doped CeO2-SrTiO3 VAN films, for which greater NMR signal can be obtained due to paramagnetic relaxation enhancement, while the relative oxide-ion conductivities of the phases remain similar. These results highlight the information that can be obtained on interfacial structure and dynamics with solid-state NMR spectroscopy, in this and other nanostructured systems, our methodology being generally applicable to overcome sensitivity limitations in thin-film studies.
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Affiliation(s)
- Michael
A. Hope
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Bowen Zhang
- Department
of Materials Science and Metallurgy, University
of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, United Kingdom
| | - Bonan Zhu
- Department
of Materials Science and Metallurgy, University
of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, United Kingdom
| | - David M. Halat
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Judith L. MacManus-Driscoll
- Department
of Materials Science and Metallurgy, University
of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, United Kingdom
| | - Clare P. Grey
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
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32
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Dračínský M, Vícha J, Bártová K, Hodgkinson P. Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids. Chemphyschem 2020; 21:2075-2083. [PMID: 32691463 DOI: 10.1002/cphc.202000629] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/20/2020] [Indexed: 12/18/2022]
Abstract
The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH2 , CH3 , OH, SH and NH3 ) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic
| | - Jan Vícha
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic.,Centre of Polymer Systems, Tomas Bata University in Zlín, Tomáše Bati 5678, Zlín, CZ-760 01, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, DH1 3LE, Durham, UK
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33
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Ashbrook SE, Dawson DM, Gan Z, Hooper JE, Hung I, Macfarlane LE, McKay D, McLeod LK, Walton RI. Application of NMR Crystallography to Highly Disordered Templated Materials: Extensive Local Structural Disorder in the Gallophosphate GaPO-34A. Inorg Chem 2020; 59:11616-11626. [PMID: 32799506 DOI: 10.1021/acs.inorgchem.0c01450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an NMR crystallographic investigation of two as-made forms of the recently characterized gallophosphate GaPO-34A, which has an unusual framework composition with a Ga:P ratio of 7:6 and contains both hydroxide and fluoride anions and either 1-methylimidazolium or pyridinium as the structure-directing agent. We combine previously reported X-ray crystallographic data with solid-state NMR spectroscopy and periodic density functional theory (DFT) calculations to show that the structure contains at least three distinct types of disorder (occupational, compositional, and dynamic). The occupational disorder arises from the presence of six anion sites per unit cell, but a total occupancy of five of these, leading to full occupancy of four sites and partial occupancy of the fifth and sixth (which are related by symmetry). The mixture of OH and F present leads to compositional disorder on the occupied anion sites, although the occupancy of some sites by F is calculated to be energetically unfavorable and signals relating to F on these sites are not observed by NMR spectroscopy, confirming that the compositional disorder is not random. Finally, a combination of high-field 71Ga NMR spectroscopy and variable-temperature 13C and 31P NMR experiments shows that the structure directing agents are dynamic on the microsecond time scale, which can be supported by averaging the 31P chemical shifts calculated with the SDA in different orientations. This demonstrates the value of an NMR crystallographic approach, particularly in the case of highly disordered crystalline materials, where the growth of large single crystals for conventional structure determination may not be possible owing to the extent of disorder present.
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Affiliation(s)
- Sharon E Ashbrook
- School of Chemistry, EaStCHEM and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Daniel M Dawson
- School of Chemistry, EaStCHEM and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Joseph E Hooper
- School of Chemistry, EaStCHEM and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Laurie E Macfarlane
- School of Chemistry, EaStCHEM and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - David McKay
- School of Chemistry, EaStCHEM and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Lucy K McLeod
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Richard I Walton
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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34
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Vícha J, Švec P, Růžičková Z, Samsonov MA, Bártová K, Růžička A, Straka M, Dračínský M. Experimental and Theoretical Evidence of Spin‐Orbit Heavy Atom on the Light Atom
1
H NMR Chemical Shifts Induced through H⋅⋅⋅I
−
Hydrogen Bond. Chemistry 2020; 26:8698-8702. [DOI: 10.1002/chem.202001532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Jan Vícha
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
- Centre of Polymer SystemsTomas Bata University in Zlín Tomáše Bati 5678 Zlín 760 01 Czech Republic
| | - Petr Švec
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Maksim A. Samsonov
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
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35
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Dudek MK, Paluch P, Pindelska E. Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:322-335. [PMID: 32831253 DOI: 10.1107/s205252062000373x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/12/2020] [Indexed: 06/11/2023]
Abstract
This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z' = 1 polymorph (form II), crystallize in P21/c and P1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z' = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.
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Affiliation(s)
- Marta K Dudek
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Piotr Paluch
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Edyta Pindelska
- Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, Warsaw, 02097, Poland
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36
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Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides. Int J Mol Sci 2020; 21:ijms21082700. [PMID: 32295042 PMCID: PMC7215618 DOI: 10.3390/ijms21082700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
Reliable values of the solid-state NMR (SSNMR) parameters together with precise structural data specific for a given amino acid site in an oligopeptide are needed for the proper interpretation of measurements aiming at an understanding of oligopeptides' function. The periodic density functional theory (DFT)-based computations of geometries and SSNMR chemical shielding tensors (CSTs) of solids are shown to be accurate enough to support the SSNMR investigations of suitably chosen models of oriented samples of oligopeptides. This finding is based on a thorough comparison between the DFT and experimental data for a set of tripeptides with both 13Cα and 15Namid CSTs available from the single-crystal SSNMR measurements and covering the three most common secondary structural elements of polypeptides. Thus, the ground is laid for a quantitative description of local spectral parameters of crystalline oligopeptides, as demonstrated for the backbone 15Namid nuclei of samarosporin I, which is a pentadecapeptide (composed of five classical and ten nonproteinogenic amino acids) featuring a strong antimicrobial activity.
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37
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Dudek MK, Paluch P, Śniechowska J, Nartowski KP, Day GM, Potrzebowski MJ. Crystal structure determination of an elusive methanol solvate – hydrate of catechin using crystal structure prediction and NMR crystallography. CrystEngComm 2020. [DOI: 10.1039/d0ce00452a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A useful short-cut was developed to limit the number of molecular conformations that need to be regarded in crystal structure prediction calculations, which led to the crystal structure determination of new methanol solvate – hydrate of catechin.
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Affiliation(s)
- Marta K. Dudek
- Centre of Molecular and Macromolecular Studies of Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies of Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Justyna Śniechowska
- Centre of Molecular and Macromolecular Studies of Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Karol P. Nartowski
- Department of Drug Form Technology
- Wroclaw Medical University
- 50-556 Wroclaw
- Poland
| | - Graeme M. Day
- Computational Systems Chemistry
- School of Chemistry
- University of Southampton
- UK
| | - Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies of Polish Academy of Sciences
- 90-363 Lodz
- Poland
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38
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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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