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Wang L, Elliott AB, Moore SD, Beran GJO, Hartman JD, Harper JK. Modeling Small Structural and Environmental Differences in Solids with 15 N NMR Chemical Shift Tensors. Chemphyschem 2021; 22:1008-1017. [PMID: 33604988 DOI: 10.1002/cphc.202000985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/28/2021] [Indexed: 11/09/2022]
Abstract
The ability to theoretically predict accurate NMR chemical shifts in solids is increasingly important due to the role such shifts play in selecting among proposed model structures. Herein, two theoretical methods are evaluated for their ability to assign 15 N shifts from guanosine dihydrate to one of the two independent molecules present in the lattice. The NMR data consist of 15 N shift tensors from 10 resonances. Analysis using periodic boundary or fragment methods consider a benchmark dataset to estimate errors and predict uncertainties of 5.6 and 6.2 ppm, respectively. Despite this high accuracy, only one of the five sites were confidently assigned to a specific molecule of the asymmetric unit. This limitation is not due to negligible differences in experimental data, as most sites exhibit differences of >6.0 ppm between pairs of resonances representing a given position. Instead, the theoretical methods are insufficiently accurate to make assignments at most positions.
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Affiliation(s)
- Luther Wang
- Department of Chemistry and Biochemistry, Brigham Young University, 84602, Provo, UT, USA
| | - Alexander B Elliott
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, 32816, Orlando, FL, USA
| | - Sean D Moore
- Burnett School of Biomedical Sciences, University of Central Florida, 4110 Libra Drive, 32816, Orlando, FL, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, 92521, Riverside, CA, USA
| | - Joshua D Hartman
- Department of Chemistry, Mt. San Jacinto College, 92583, San Jacinto, CA, USA
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, 84602, Provo, UT, USA
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2
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Hernandes IS, Da Silva HC, Dos Santos HF, De Almeida WB. Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of 1H NMR Chemical Shifts. J Phys Chem B 2021; 125:3321-3342. [PMID: 33760611 DOI: 10.1021/acs.jpcb.1c00609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloroquine (CQ) and hydroxychloroquine (HCQ) have been standard antimalarial drugs since the early 1950s, and very recently, the possibility of their use for the treatment of COVID-19 patients has been considered. To understand the drug mode of action at the submicroscopic level (atoms and molecules), molecular modeling studies with the aid of computational chemistry methods have been of great help. A fundamental step in such theoretical investigations is the knowledge of the predominant drug molecular structure in solution, which is the real environment for the interaction with biological targets. Our strategy to access this valuable information is to perform density functional theory (DFT) calculations of 1H NMR chemical shifts for several plausible molecular conformers and then find the best match with experimental NMR profile in solution (since it is extremely sensitive to conformational changes). Through this procedure, after optimizing 30 trial distinct molecular structures (ωB97x-D/6-31G(d,p)-PCM level of calculation), which may be considered representative conformations, we concluded that the global minimum (named M24), stabilized by an intramolecular N-H hydrogen bond, is not likely to be observed in water, chloroform, and dimethyl sulfoxide (DMSO) solution. Among fully optimized conformations (named M1 to M30, and MD1 and MD2), we found M12 (having no intramolecular H-bond) as the most probable structure of CQ and HCQ in water solution, which is a good approximate starting geometry in drug-receptor interaction simulations. On the other hand, the preferred CQ and HCQ structure in chloroform (and CQ in DMSO-d6) solution was assigned as M8, showing the solvent effects on conformational preferences. We believe that the analysis of 1H NMR data in solution can establish the connection between the macro level (experimental) and the sub-micro level (theoretical), which is not so apparent to us and appears to be more appropriate than the thermodynamic stability criterion in conformational analysis studies.
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Affiliation(s)
- Isabel S Hernandes
- Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Outeiro de São João Batista s/n, Campus do Valonguinho, Centro, Niterói 24020-141, Rio de Janeiro, Brazil
| | - Haroldo C Da Silva
- Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Outeiro de São João Batista s/n, Campus do Valonguinho, Centro, Niterói 24020-141, Rio de Janeiro, Brazil
| | - Hélio F Dos Santos
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora 36036-330, Minas Gerais, Brazil
| | - Wagner B De Almeida
- Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Outeiro de São João Batista s/n, Campus do Valonguinho, Centro, Niterói 24020-141, Rio de Janeiro, Brazil
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3
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Holmes ST, Vojvodin CS, Schurko RW. Dispersion-Corrected DFT Methods for Applications in Nuclear Magnetic Resonance Crystallography. J Phys Chem A 2020; 124:10312-10323. [DOI: 10.1021/acs.jpca.0c06372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Cameron S. Vojvodin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Robert W. Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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Wong YTA, Babcock TK, Chen S, Lucier BEG, Huang Y. CO Guest Interactions in SDB-Based Metal-Organic Frameworks: A Solid-State Nuclear Magnetic Resonance Investigation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15640-15649. [PMID: 30512953 DOI: 10.1021/acs.langmuir.8b02205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Metal-organic frameworks (MOFs) are promising materials for greener carbon monoxide (CO) capture and separation processes. SDB-based (SDB = 4,4'-sulfonyldibenzoate) MOFs are particularly attractive due to their remarkable gas adsorption capacity under humid conditions. However, to the best of our knowledge, their CO adsorption abilities have yet to be investigated. In this report, CO-loaded PbSDB and CdSDB were characterized using variable-temperature (VT) 13C solid-state nuclear magnetic resonance (SSNMR) spectroscopy. These MOFs readily captured CO, with the adsorbed CO exhibiting dynamics as indicated by the temperature-dependent changes in the SSNMR spectra. Spectral simulations revealed that the CO simultaneously undergoes a localized wobbling about the adsorption site and a nonlocalized hopping between adjacent adsorption sites. The wobbling and hopping angles were also found to be temperature-dependent. From the appearance of the VT spectra and the extracted motional data, the CO adsorption mechanism was concluded to be analogous to that of CO2. To gain a better understanding on the gas adsorption properties of these MOFs and their CO capture abilities, we subsequently compared the motional data to those reported for CO2 in SDB-based MOFs and CO in MOF-74, respectively. A significant contrast in adsorption strength was observed in both cases because of the different physical properties of the guests (i.e., CO vs CO2) and the MOF frameworks (i.e., SDB-based MOFs vs MOFs with open metal sites). Our results demonstrate that SSNMR spectroscopy can be employed to probe variations in binding behavior.
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Affiliation(s)
- Y T Angel Wong
- Department of Chemistry , The University of Western Ontario , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
| | - Troy K Babcock
- Department of Chemistry , The University of Western Ontario , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
| | - Shoushun Chen
- Department of Chemistry , The University of Western Ontario , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
| | - Bryan E G Lucier
- Department of Chemistry , The University of Western Ontario , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
| | - Yining Huang
- Department of Chemistry , The University of Western Ontario , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
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Hartman JD, Beran GJO. Accurate 13-C and 15-N molecular crystal chemical shielding tensors from fragment-based electronic structure theory. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 96:10-18. [PMID: 30273904 DOI: 10.1016/j.ssnmr.2018.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Standard nuclear magnetic resonance (NMR) spectroscopy experiments measure isotropic chemical shifts, but measuring the chemical shielding anisotropy (CSA) tensor can provide additional insights into solid state chemical structures. Interpreting the principal components of these tensors is facilitated by first-principles chemical shielding tensor predictions. Here, the ability to predict molecular crystal CSA tensor components for 13C and 15N nuclei with fragment-based electronic structure techniques is explored. Similar to what has been found previously for isotropic chemical shifts, the benchmarking demonstrates that fragment-based techniques can accurately reproduce CSA tensor components. The use of hybrid density functionals like PBE0 or B3LYP provide higher accuracy than generalized gradient approximation functionals like PBE. Unlike for planewave density functional techniques, hybrid density functionals can be employed routinely with modest computational cost in fragment approaches. Finally, good consistency between the regression parameters used to map either isotropic shieldings or CSA tensor components is demonstrated, providing further evidence for the quality of the models and highlighting that models trained for isotropic shifts can also be applied to CSA tensor components.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, CA, 92521, USA.
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Widdifield CM, Nilsson Lill SO, Broo A, Lindkvist M, Pettersen A, Svensk Ankarberg A, Aldred P, Schantz S, Emsley L. Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease. Phys Chem Chem Phys 2018. [PMID: 28621371 DOI: 10.1039/c7cp02349a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured 13C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR (1H, 13C, 15N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct 13C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental 13C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of 13C shift tensors and the observation of residual dipolar coupling between 13C and 14N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD16 = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD16 = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.
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Affiliation(s)
- Cory M Widdifield
- Institut des Sciences Analytiques (CNRS/ENS de Lyon/UCB Lyon 1), Centre de RMN à Très Hauts Champs, Université de Lyon, 69100 Villeurbanne, France
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8
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Wong YTA, Landmann J, Finze M, Bryce DL. Dynamic Disorder and Electronic Structures of Electron-Precise Dianionic Diboranes: Insights from Solid-State Multinuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2017; 139:8200-8211. [PMID: 28548827 DOI: 10.1021/jacs.7b01783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The J(11B,11B) coupling constants of various salts of the electron-precise hexacyanodiborane(6) dianion, [B2(CN)6]2-, were obtained using 11B double-quantum-filtered (DQF) J-resolved solid-state nuclear magnetic resonance (SSNMR) spectroscopy. Our results show that the magnitude of the DQF J splitting is influenced by both the crystallographic symmetry of the system and the presence of dynamics. The splittings are amplified by a factor of 3 as compared to the corresponding theoretical J coupling constants for cases where (1) there is an absence of dynamics but the boron pairs are crystallographically equivalent or (2) the boron pairs are crystallographically inequivalent but are rendered magnetically equivalent on the time scale of the experiment due to dynamic disorder, which was identified by 11B and 13C SSNMR experiments. Consequently, molecular motions need to be taken into consideration when interpreting the results of DQF J-resolved experiments, and conversely, these experiments may be used to identify dynamic disorder. Variable-temperature NMR data support the notion of three different motional processes with correlation times ranging from 102 to 106 s-1 over the temperature range of 248-306 K. When molecular motion and crystallographic symmetry are both accounted for, the J(11B,11B) coupling constants for various [B2(CN)6]2- salts were measured to range from 29.4 to 35.8 Hz, and their electronic origins were determined using natural localized molecular orbital and natural bond orbital analyses. The coupling constants were found to strongly correlate to the hybridization states of the boron orbitals that form the B-B bonds and to the strength of the B-B bonds. This study provides a novel tool to study dynamics in ordered and disordered solids and provides new perspectives on electron-precise dianionic diboranes featuring two-center-two-electron bonds in the context of related compounds featuring multiply and singly bonded boron spin pairs.
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Affiliation(s)
- Y T Angel Wong
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa , Ottawa, Ontario, Canada K1N6N5
| | - Johannes Landmann
- Institut für Anorganische Chemie, Institut für nachhaltige Chemie & Katalyse mit Bor (ICB), Julius-Maximilians-Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Maik Finze
- Institut für Anorganische Chemie, Institut für nachhaltige Chemie & Katalyse mit Bor (ICB), Julius-Maximilians-Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa , Ottawa, Ontario, Canada K1N6N5
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Soss SE, Flynn PF, Iuliucci RJ, Young RP, Mueller LJ, Hartman J, Beran GJO, Harper JK. Measuring and Modeling Highly Accurate
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N Chemical Shift Tensors in a Peptide. Chemphyschem 2017; 18:2225-2232. [DOI: 10.1002/cphc.201700357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/08/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Sarah E. Soss
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Peter F. Flynn
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Robbie J. Iuliucci
- Department of Chemistry Washington and Jefferson College 60 Lincoln Street Washington PA 15301 USA
| | - Robert P. Young
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - Joshua Hartman
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - James K. Harper
- Department of Chemistry University of Central Florida 4111 Libra Drive Orlando FL 32816 USA
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Holmes ST, Iuliucci RJ, Mueller KT, Dybowski C. Semi-empirical refinements of crystal structures using 17O quadrupolar-coupling tensors. J Chem Phys 2017; 146:064201. [DOI: 10.1063/1.4975170] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Robbie J. Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, USA
| | - Karl T. Mueller
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Hartman J, Day GM, Beran GJO. Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions. CRYSTAL GROWTH & DESIGN 2016; 16:6479-6493. [PMID: 27829821 PMCID: PMC5095663 DOI: 10.1021/acs.cgd.6b01157] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/09/2016] [Indexed: 05/10/2023]
Abstract
Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.
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Affiliation(s)
- Joshua
D. Hartman
- Department
of Chemistry, University of California, Riverside, California 92521 United States
| | - Graeme M. Day
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Gregory J. O. Beran
- Department
of Chemistry, University of California, Riverside, California 92521 United States
- E-mail:
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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