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Holmes ST, Boley CM, Dewicki A, Gardner ZT, Vojvodin CS, Iuliucci RJ, Schurko RW. Carbon-13 chemical shift tensor measurements for nitrogen-dense compounds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:179-189. [PMID: 38230444 DOI: 10.1002/mrc.5422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
This paper reports the principal values of the 13 C chemical shift tensors for five nitrogen-dense compounds (i.e., cytosine, uracil, imidazole, guanidine hydrochloride, and aminoguanidine hydrochloride). Although these are all fundamentally important compounds, the majority do not have 13 C chemical shift tensors reported in the literature. The chemical shift tensors are obtained from 1 H→13 C cross-polarization magic-angle spinning (CP/MAS) experiments that were conducted at a high field of 18.8 T to suppress the effects of 14 N-13 C residual dipolar coupling. Quantum chemical calculations using density functional theory are used to obtain the 13 C magnetic shielding tensors for these compounds. The best agreement with experiment arises from calculations using the hybrid functional PBE0 or the double-hybrid functional PBE0-DH, along with the triple-zeta basis sets TZ2P or pc-3, respectively, and intermolecular effects modeled using large clusters of molecules with electrostatic embedding through the COSMO approach. These measurements are part of an ongoing effort to expand the catalog of accurate 13 C chemical shift tensor measurements, with the aim of creating a database that may be useful for benchmarking the accuracy of quantum chemical calculations, developing nuclear magnetic resonance (NMR) crystallography protocols, or aiding in applications involving machine learning or data mining. This work was conducted at the National High Magnetic Field Laboratory as part of a 2-week school for introducing undergraduate students to practical laboratory experience that will prepare them for scientific careers or postgraduate studies.
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Affiliation(s)
- Sean T Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - Cameron M Boley
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Angelika Dewicki
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Zachary T Gardner
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Cameron S Vojvodin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - Robbie J Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Robert W Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
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2
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Stirk AJ, Holmes ST, Souza FES, Hung I, Gan Z, Britten JF, Rey AW, Schurko RW. An unusual ionic cocrystal of ponatinib hydrochloride: characterization by single-crystal X-ray diffraction and ultra-high field NMR spectroscopy. CrystEngComm 2024; 26:1219-1233. [PMID: 38419975 PMCID: PMC10897533 DOI: 10.1039/d3ce01062g] [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: 10/24/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024]
Abstract
This study describes the discovery of a unique ionic cocrystal of the active pharmaceutical ingredient (API) ponatinib hydrochloride (pon·HCl), and characterization using single-crystal X-ray diffraction (SCXRD) and solid-state NMR (SSNMR) spectroscopy. Pon·HCl is a multicomponent crystal that features an unusual stoichiometry, with an asymmetric unit containing both monocations and dications of the ponatinib molecule, three water molecules, and three chloride ions. Structural features include (i) a charged imidazopyridazine moiety that forms a hydrogen bond between the ponatinib monocations and dications and (ii) a chloride ion that does not feature hydrogen bonds involving any organic moiety, instead being situated in a "square" arrangement with three water molecules. Multinuclear SSNMR, featuring high and ultra-high fields up to 35.2 T, provides the groundwork for structural interpretation of complex multicomponent crystals in the absence of diffraction data. A 13C CP/MAS spectrum confirms the presence of two crystallographically distinct ponatinib molecules, whereas 1D 1H and 2D 1H-1H DQ-SQ spectra identify and assign the unusually deshielded imidazopyridazine proton. 1D 35Cl spectra obtained at multiple fields confirm the presence of three distinct chloride ions, with density functional theory calculations providing key relationships between the SSNMR spectra and H⋯Cl- hydrogen bonding arrangements. A 2D 35Cl → 1H D-RINEPT spectrum confirms the spatial proximities between the chloride ions, water molecules, and amine moieties. This all suggests future application of multinuclear SSNMR at high and ultra-high fields to the study of complex API solid forms for which SCXRD data are unavailable, with potential application to heterogeneous mixtures or amorphous solid dispersions.
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Affiliation(s)
| | - Sean T Holmes
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | | | - Ivan Hung
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - Zhehong Gan
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - James F Britten
- MAX Diffraction Facility, McMaster University Hamilton ON L8S 4M1 Canada
| | - Allan W Rey
- Apotex Pharmachem Inc. Brantford ON N3T 6B8 Canada
| | - Robert W Schurko
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
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3
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Lu X, Huang C, Li M, Skomski D, Xu W, Yu L, Byrn SR, Templeton AC, Su Y. Molecular Mechanism of Crystalline-to-Amorphous Conversion of Pharmaceutical Solids from 19F Magic Angle Spinning NMR. J Phys Chem B 2020; 124:5271-5283. [PMID: 32378905 DOI: 10.1021/acs.jpcb.0c02131] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Crystalline and amorphous materials usually possess distinct physicochemical properties due to major variations in long-range and local molecular packings. Enhanced fundamental knowledge of the molecular details of crystalline-to-amorphous interconversions is necessary to correlate the intermolecular structure to material properties and functions. While crystal structures can be readily obtained by X-ray crystallography, the microstructure of amorphous materials has rarely been explored due to a lack of high-resolution techniques capable of probing local molecular structures. Moreover, there is increasing interest in understanding the molecular nature of amorphous solids in pharmaceutical sciences due to the widespread utilization of amorphous active pharmaceutical ingredients (APIs) in pharmaceutical development for solubility and bioavailability enhancement. In this study, we explore multidimensional 13C and 19F magic angle spinning (MAS) NMR spectroscopy to study the molecular packing of amorphous posaconazole (POSA) in conjunction with the crystalline counterpart. Utilizing methods integrating homonuclear and heteronuclear 1H, 13C, and 19F correlation spectroscopy and atomic 19F-to-13C distance measurements, we identified the major differences in molecular packing between crystalline and amorphous POSA. The intermolecular "head-to-head" interaction along the molecule's major axis, as well as the "head-to-tail" molecular packing perpendicular to the major axis in POSA crystals, was recapitulated by MAS NMR. Furthermore, critical intermolecular distances in the crystal lattice were determined. Most importantly, the head-to-tail contact of two neighboring molecules was found to be preserved in amorphous POSA, suggesting localized molecular order, whereas crucial interactions for head-to-head packing are absent in the amorphous form resulting in long-range disorder. Our study, likely one of the first documented examples, provides molecular-level structural details to understand the molecular mechanism of crystalline-to-amorphous conversion of fluorine-containing drug substances occurring in drug processing and development and establish a high-resolution experimental protocol for investigating amorphous materials.
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Affiliation(s)
- Xingyu Lu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chengbin Huang
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Mingyue Li
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Daniel Skomski
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lian Yu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Stephen R Byrn
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States.,Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States.,Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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4
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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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5
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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: 33] [Impact Index Per Article: 6.6] [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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6
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Cui J, Olmsted DL, Mehta AK, Asta M, Hayes SE. NMR Crystallography: Evaluation of Hydrogen Positions in Hydromagnesite by
13
C{
1
H} REDOR Solid‐State NMR and Density Functional Theory Calculation of Chemical Shielding Tensors. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jinlei Cui
- Department of Chemistry Washington University in St. Louis 1 Brookings Drive, Campus Box 1134 St. Louis MO 63130 USA
| | - David L. Olmsted
- Department of Materials Science and Engineering University of California, Berkeley Berkeley CA USA
| | - Anil K. Mehta
- Department of Chemistry Emory University Atlanta GA USA
| | - Mark Asta
- Department of Materials Science and Engineering University of California, Berkeley Berkeley CA USA
- Materials Science Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Sophia E. Hayes
- Department of Chemistry Washington University in St. Louis 1 Brookings Drive, Campus Box 1134 St. Louis MO 63130 USA
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7
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Cui J, Olmsted DL, Mehta AK, Asta M, Hayes SE. NMR Crystallography: Evaluation of Hydrogen Positions in Hydromagnesite by 13 C{ 1 H} REDOR Solid-State NMR and Density Functional Theory Calculation of Chemical Shielding Tensors. Angew Chem Int Ed Engl 2019; 58:4210-4216. [PMID: 30672073 DOI: 10.1002/anie.201813306] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/08/2019] [Indexed: 12/24/2022]
Abstract
Solid-state NMR measurements coupled with density functional theory (DFT) calculations demonstrate how hydrogen positions can be refined in a crystalline system. The precision afforded by rotational-echo double-resonance (REDOR) NMR to interrogate 13 C-1 H distances is exploited along with DFT determinations of the 13 C tensor of carbonates (CO3 2- ). Nearby 1 H nuclei perturb the axial symmetry of the carbonate sites in the hydrated carbonate mineral, hydromagnesite [4 MgCO3 ⋅Mg(OH)2 ⋅4 H2 O]. A match between the calculated structure and solid-state NMR was found by testing multiple semi-local and dispersion-corrected DFT functionals and applying them to optimize atom positions, starting from X-ray diffraction (XRD)-determined atomic coordinates. This was validated by comparing calculated to experimental 13 C{1 H} REDOR and 13 C chemical shift anisotropy (CSA) tensor values. The results show that the combination of solid-state NMR, XRD, and DFT can improve structure refinement for hydrated materials.
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Affiliation(s)
- Jinlei Cui
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1134, St. Louis, MO, 63130, USA
| | - David L Olmsted
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Mark Asta
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA.,Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sophia E Hayes
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1134, St. Louis, MO, 63130, USA
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8
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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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9
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Yang C, Zhu L, Kudla RA, Hartman JD, Al-Kaysi RO, Monaco S, Schatschneider B, Magalhães A, Beran GJO, Bardeen CJ, Mueller LJ. Crystal structure of the meta-stable intermediate in the photomechanical, crystal-to-crystal reaction of 9-tert-butyl anthracene ester. CrystEngComm 2016. [DOI: 10.1039/c6ce00742b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Islam MT, Chantler CT, Cheah MH, Tantau LJ, Tran CQ, Best SP. Structural investigation of mM Ni(II) complex isomers using transmission XAFS: the significance of model development. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1475-1491. [PMID: 26524313 DOI: 10.1107/s1600577515014976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/10/2015] [Indexed: 06/05/2023]
Abstract
High-accuracy transmission XAFS determined using the hybrid technique has been used to refine the geometries of bis(N-n-propyl-salicylaldiminato) nickel(II) (n-pr Ni) and bis(N-i-propyl-salicylaldiminato) nickel(II) (i-pr Ni) complexes which have approximately square planar and tetrahedral metal coordination. Multiple-scattering formalisms embedded in FEFF were used for XAFS modelling of the complexes. Here it is shown that an IFEFFIT-like package using weighting from experimental uncertainty converges to a well defined XAFS model. Structural refinement of (i-pr Ni) was found to yield a distorted tetrahedral geometry providing an excellent fit, χr(2) = 2.94. The structure of (n-pr Ni) is best modelled with a distorted square planar geometry, χr(2) = 3.27. This study demonstrates the insight that can be obtained from the propagation of uncertainty in XAFS analysis and the consequent confidence which can be obtained in hypothesis testing and in analysis of alternate structures ab initio. It also demonstrates the limitations of this (or any other) data set by defining the point at which signal becomes embedded in noise or amplified uncertainty, and hence can justify the use of a particular k-range for one data set or a different range for another. It is demonstrated that, with careful attention to data collection, including the correction of systematic errors with statistical analysis of uncertainty (the hybrid method), it is possible to obtain reliable structural information from dilute solutions using transmission XAFS data.
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Affiliation(s)
| | | | - Mun Hon Cheah
- ANU College of Medicine, Biology and Environment, Australian National University, Australia
| | | | - Chanh Q Tran
- School of Physics, La Trobe University, Australia
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11
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Hartman JD, Neubauer TJ, Caulkins BG, Mueller LJ, Beran GJO. Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems. JOURNAL OF BIOMOLECULAR NMR 2015; 62:327-40. [PMID: 25993979 PMCID: PMC4512207 DOI: 10.1007/s10858-015-9947-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/12/2015] [Indexed: 05/25/2023]
Abstract
Ab initio chemical shielding calculations greatly facilitate the interpretation of nuclear magnetic resonance (NMR) chemical shifts in biological systems, but the large sizes of these systems requires approximations in the chemical models used to represent them. Achieving good convergence in the predicted chemical shieldings is necessary before one can unravel how other complex structural and dynamical factors affect the NMR measurements. Here, we investigate how to balance trade-offs between using a better basis set or a larger cluster model for predicting the chemical shieldings of the substrates in two representative examples of protein-substrate systems involving different domains in tryptophan synthase: the N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F9) ligand which binds in the α active site, and the 2-aminophenol quinonoid intermediate formed in the β active site. We first demonstrate that a chemically intuitive three-layer, locally dense basis model that uses a large basis on the substrate, a medium triple-zeta basis to describe its hydrogen-bonding partners and/or surrounding van der Waals cavity, and a crude basis set for more distant atoms provides chemical shieldings in good agreement with much more expensive large basis calculations. Second, long-range quantum mechanical interactions are important, and one can accurately estimate them as a small-basis correction to larger-basis calculations on a smaller cluster. The combination of these approaches enables one to perform density functional theory NMR chemical shift calculations in protein systems that are well-converged with respect to both basis set and cluster size.
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Affiliation(s)
- Joshua D. Hartman
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Thomas J. Neubauer
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Bethany G. Caulkins
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Leonard J. Mueller
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Gregory J. O. Beran
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
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12
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Mueller LJ, Dunn MF. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase. Acc Chem Res 2013; 46:2008-17. [PMID: 23537227 DOI: 10.1021/ar3003333] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of NMR crystallography applied to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation.
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Affiliation(s)
- Leonard J. Mueller
- Department of Chemistry and ‡Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael F. Dunn
- Department of Chemistry and ‡Department of Biochemistry, University of California, Riverside, California 92521, United States
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13
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Harper JK, Tishler D, Richardson D, Lokvam J, Pendrill R, Widmalm G. Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl α-l-Rhamnofuranoside. J Phys Chem A 2013; 117:5534-41. [DOI: 10.1021/jp4036666] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- James K. Harper
- Department of Chemistry, University of Central Florida, 4000
Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Derek Tishler
- Department of Physics, University of Central Florida, Orlando,
Florida 32816, United States
| | - David Richardson
- Department of Chemistry, University of Central Florida, 4000
Central Florida Boulevard, Orlando, Florida 32816, United States
| | - John Lokvam
- Department of Biology, University of California Berkeley, Berkeley,
California 94720, United States
| | - Robert Pendrill
- Department of Organic
Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic
Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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14
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Pandit A, Ocakoglu K, Buda F, van Marle T, Holzwarth AR, de Groot HJM. Structure Determination of a Bio-Inspired Self-Assembled Light-Harvesting Antenna by Solid-State NMR and Molecular Modeling. J Phys Chem B 2013; 117:11292-8. [DOI: 10.1021/jp402210x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Anjali Pandit
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Kasim Ocakoglu
- Max-Planck-Institute for Chemical Energy Conversion (MPI-CEC) (previously
known as Max-Planck-Institute for Bioinorganic Chemistry), Stiftstrasse
34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Thomas van Marle
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Alfred R. Holzwarth
- Max-Planck-Institute for Chemical Energy Conversion (MPI-CEC) (previously
known as Max-Planck-Institute for Bioinorganic Chemistry), Stiftstrasse
34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Huub J. M. de Groot
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
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15
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Brouwer DH. Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 51-52:37-45. [PMID: 23415450 DOI: 10.1016/j.ssnmr.2013.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 06/01/2023]
Abstract
An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state (29)Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with Si-O-Si connectivity information, symmetry restraints, and fits to (29)Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in "NMR crystallography" is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information.
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Affiliation(s)
- Darren H Brouwer
- Chemistry Department, Redeemer University College, Ancaster, ON, Canada.
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Harper JK, Iuliucci R, Gruber M, Kalakewich K. Refining crystal structures with experimental 13C NMR shift tensors and lattice-including electronic structure methods. CrystEngComm 2013. [DOI: 10.1039/c3ce40108a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Brouwer DH, Langendoen KP. A graph theory approach to structure solution of network materials from two-dimensional solid-state NMR data. CrystEngComm 2013. [DOI: 10.1039/c3ce41058g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Chierotti MR, Gobetto R. NMR crystallography: the use of dipolar interactions in polymorph and co-crystal investigation. CrystEngComm 2013. [DOI: 10.1039/c3ce41026a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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19
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Bonhomme C, Gervais C, Babonneau F, Coelho C, Pourpoint F, Azaïs T, Ashbrook SE, Griffin JM, Yates JR, Mauri F, Pickard CJ. First-principles calculation of NMR parameters using the gauge including projector augmented wave method: a chemist's point of view. Chem Rev 2012; 112:5733-79. [PMID: 23113537 DOI: 10.1021/cr300108a] [Citation(s) in RCA: 326] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris, Université Pierre et Marie Curie, CNRS UMR, Collège de France, France.
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20
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Wang WD, Gao X, Strohmeier M, Wang W, Bai S, Dybowski C. Solid-State NMR Studies of Form I of Atorvastatin Calcium. J Phys Chem B 2012; 116:3641-9. [DOI: 10.1021/jp212074a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei David Wang
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xudong Gao
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Mark Strohmeier
- Product Development, GlaxoSmithKline, Inc., 709 Swedeland Road, King of
Prussia, Pennsylvania 19406, United States
| | - Wei Wang
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Shi Bai
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
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21
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Jung SH, Hwang GS, Lee SI, Ryu DH. Total synthsis of (+)-ambuic acid: α-bromination with 1,2-dibromotetrachloroethane. J Org Chem 2012; 77:2513-8. [PMID: 22280015 DOI: 10.1021/jo202357s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Total synthesis of (+)-ambuic acid has been accomplished from the readily available stereocontrolled Diels-Alder adduct of cyclopentadiene and iodo-1,4-benzoquinone monoketal through an efficient series of steps. A new method for the highly commendable synthesis of α-brominated Diels-Alder adduct is described.
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Affiliation(s)
- Sun Hee Jung
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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22
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Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. JOURNAL OF BIOMOLECULAR NMR 2011; 51:227-33. [PMID: 21938394 PMCID: PMC3204959 DOI: 10.1007/s10858-011-9565-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/29/2011] [Indexed: 05/12/2023]
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna E. Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Robert B. Gennis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
- CORRESPONDING AUTHOR:
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23
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Brouwer DH, Langendoen KP, Ferrant Q. Measurement and calculation of 13C chemical shift tensors in α-glucose and α-glucose monohydrate. CAN J CHEM 2011. [DOI: 10.1139/v11-017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 13C chemical shift tensors of two crystalline forms of glucose (α-glucose and α-glucose·H2O) were determined from one-dimensional (1D) and two-dimensional (2D) solid-state nuclear magnetic resonance (NMR) spectroscopy experiments. The experimental values determined from 1D and 2D methods are in very good agreement. Quantum chemical calculations were also carried out using the gauge-including projector augmented wave (GIPAW) method for plane-wave density functional theory (DFT) as implemented in the CAmbridge Serial Total Energy Package (CASTEP). The calculated 13C chemical shifts were found to be in excellent agreement with experimental values for crystal structures that had their hydrogen atoms optimized and after an appropriate calibration was applied to convert calculated chemical shieldings into chemical shifts. The work presented here lays an important foundation for future solid-state NMR and quantum chemical calculation investigations of the various crystalline forms of cellulose.
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Affiliation(s)
- Darren H. Brouwer
- Chemistry Department, Redeemer University College, Ancaster, ON L9K 1J4, Canada
| | - Kevin P. Langendoen
- Chemistry Department, Redeemer University College, Ancaster, ON L9K 1J4, Canada
| | - Quentin Ferrant
- Chemistry Department, Redeemer University College, Ancaster, ON L9K 1J4, Canada
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24
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Liu W, Wang WD, Wang W, Bai S, Dybowski C. Influence of Structure on the Spectroscopic Properties of the Polymorphs of Piroxicam. J Phys Chem B 2010; 114:16641-9. [DOI: 10.1021/jp1084444] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Wei Liu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Wei David Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Wei Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shi Bai
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Cecil Dybowski
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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25
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Webber AL, Elena B, Griffin JM, Yates JR, Pham TN, Mauri F, Pickard CJ, Gil AM, Stein R, Lesage A, Emsley L, Brown SP. Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations. Phys Chem Chem Phys 2010; 12:6970-83. [PMID: 20480118 DOI: 10.1039/c001290d] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A disaccharide is a challenging case for high-resolution (1)H solid-state NMR because of the 24 distinct protons (14 aliphatic and 10 OH) having (1)H chemical shifts that all fall within a narrow range of approximately 3 to 7 ppm. High-resolution (1)H (500 MHz) double-quantum (DQ) combined rotation and multiple pulse sequence (CRAMPS) solid-state NMR spectra of beta-maltose monohydrate are presented. (1)H-(1)H DQ-SQ CRAMPS spectra are presented together with (1)H (DQ)-(13)C correlation spectra obtained with a new pulse sequence that correlates a high-resolution (1)H DQ dimension with a (13)C single quantum (SQ) dimension using the refocused INEPT pulse-sequence element to transfer magnetization via one-bond (13)C-(1)H J couplings. Compared to the observation of only a single broad peak in a (1)H DQ spectrum recorded at 30 kHz magic-angle spinning (MAS), the use of DUMBO (1)H homonuclear decoupling in the (1)H DQ CRAMPS experiment allows the resolution of distinct DQ correlation peaks which, in combination with first-principles chemical shift calculations based on the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach, enables the assignment of the (1)H resonances to the 24 distinct protons. We believe this to be the first experimental solid-state NMR determination of the hydroxyl OH (1)H chemical shifts for a simple sugar. Variable-temperature (1)H-(1)H DQ CRAMPS spectra reveal small increases in the (1)H chemical shifts of the OH resonances upon decreasing the temperature from 348 K to 248 K.
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Affiliation(s)
- Amy L Webber
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
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26
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Harper JK, Doebbler JA, Jacques E, Grant DM, Von Dreele RB. A Combined Solid-State NMR and Synchrotron X-ray Diffraction Powder Study on the Structure of the Antioxidant (+)-Catechin 4.5-hydrate. J Am Chem Soc 2010; 132:2928-37. [DOI: 10.1021/ja907671p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James K. Harper
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - Jennifer A. Doebbler
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - Elisabeth Jacques
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - David M. Grant
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - Robert B. Von Dreele
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, and Argonne National Laboratory, Advanced Photon Source, 9700 South Cass Avenue, Argonne, Illinois 60439
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27
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Lesage A. Recent advances in solid-state NMR spectroscopy of spin I = 1/2 nuclei. Phys Chem Chem Phys 2009; 11:6876-91. [DOI: 10.1039/b907733m] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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28
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Vogt FG, Katrincic LM, Long ST, Mueller RL, Carlton RA, Sun YT, Johnson MN, Copley RC, Light ME. Enantiotropically-related polymorphs of {4-(4-chloro-3-fluorophenyl)-2-[4-(methyloxy)phenyl]-1,3-thiazol-5-yl} acetic acid: Crystal structures and multinuclear solid-state NMR. J Pharm Sci 2008; 97:4756-82. [DOI: 10.1002/jps.21336] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Gajda J, Olejniczak S, Bryndal I, Potrzebowski MJ. Elucidation of Structural Restraints for Phosphate Residues with Different Hydrogen Bonding and Ionization States. J Phys Chem B 2008; 112:14036-44. [DOI: 10.1021/jp807516b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Gajda
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland, and Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - S. Olejniczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland, and Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - I. Bryndal
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland, and Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - M. J. Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland, and Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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30
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Brouwer DH. A structure refinement strategy for NMR crystallography: an improved crystal structure of silica-ZSM-12 zeolite from 29Si chemical shift tensors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:136-146. [PMID: 18656402 DOI: 10.1016/j.jmr.2008.06.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 05/26/2023]
Abstract
A strategy for performing crystal structure refinements with NMR chemical shift tensors is described in detail and implemented for the zeolite silica-ZSM-12 (framework type code MTW). The 29Si chemical shift tensors were determined from a slow magic-angle spinning spectrum obtained at an ultrahigh magnetic field of 21.1T. The Si and O atomic coordinate parameters were optimized to give the best agreement between experimentally measured and ab initio calculated principal components of the 29Si chemical shift tensors, with the closest Si-O, O-O, and Si-Si distances restrained to correspond with the distributions of the distances found in a set of single-crystal X-ray diffraction (XRD) structures of high-silica zeolites. An improved structure for the silica-ZSM-12 zeolite, compared to a prior structure derived from powder XRD data, is obtained in which the agreement between the experimental and calculated 29Si chemical shift tensors is dramatically improved, the Si-O, O-O, and Si-Si distances correspond to the expected distributions, while the calculated powder XRD pattern remains in good agreement with the experimental powder XRD data. It is anticipated that this "NMR crystallography" structure refinement strategy will be an important tool for the accurate structure determination of materials that are difficult to fully characterize by traditional diffraction methods.
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Affiliation(s)
- Darren H Brouwer
- Steacie Institute for Molecular Science, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ont., Canada.
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31
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Brouwer DH. NMR Crystallography of Zeolites: Refinement of an NMR-Solved Crystal Structure Using ab Initio Calculations of 29Si Chemical Shift Tensors. J Am Chem Soc 2008; 130:6306-7. [DOI: 10.1021/ja800227f] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darren H. Brouwer
- Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa ON, K1A 0R6, Canada
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32
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Brouwer DH, Enright GD. Probing Local Structure in Zeolite Frameworks: Ultrahigh-Field NMR Measurements and Accurate First-Principles Calculations of Zeolite 29Si Magnetic Shielding Tensors. J Am Chem Soc 2008; 130:3095-105. [DOI: 10.1021/ja077430a] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darren H. Brouwer
- Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Gary D. Enright
- Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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33
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Harris RK, Hodgkinson P, Pickard CJ, Yates JR, Zorin V. Chemical shift computations on a crystallographic basis: some reflections and comments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S174-S186. [PMID: 18157842 DOI: 10.1002/mrc.2132] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Computations for chemical shifts of molecular organic compounds using the gauge-including projector augmented wave method and the NMR-CASTEP code are reviewed. The methods are briefly introduced, and some general aspects involving the sources of uncertainty in the results are explored. The limitations are outlined. Successful applications of the computations to problems of interpretation of NMR results are discussed and the range of areas in which useful information is obtained is illustrated by examples. The particular value of the computations for comparing shifts between resonances where the same chemical site is involved is emphasised. Such cases arise for shifts between different crystallographically independent molecules of the same chemical species, between polymorphs and for shift anisotropies and asymmetries.
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Affiliation(s)
- Robin K Harris
- Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, UK.
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34
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Hertkorn N, Ruecker C, Meringer M, Gugisch R, Frommberger M, Perdue EM, Witt M, Schmitt-Kopplin P. High-precision frequency measurements: indispensable tools at the core of the molecular-level analysis of complex systems. Anal Bioanal Chem 2007; 389:1311-27. [PMID: 17924102 PMCID: PMC2259236 DOI: 10.1007/s00216-007-1577-4] [Citation(s) in RCA: 225] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 08/20/2007] [Indexed: 11/30/2022]
Abstract
This perspective article provides an assessment of the state-of-the-art in the molecular-resolution analysis of complex organic materials. These materials can be divided into biomolecules in complex mixtures (which are amenable to successful separation into unambiguously defined molecular fractions) and complex nonrepetitive materials (which cannot be purified in the conventional sense because they are even more intricate). Molecular-level analyses of these complex systems critically depend on the integrated use of high-performance separation, high-resolution organic structural spectroscopy and mathematical data treatment. At present, only high-precision frequency-derived data exhibit sufficient resolution to overcome the otherwise common and detrimental effects of intrinsic averaging, which deteriorate spectral resolution to the degree of bulk-level rather than molecular-resolution analysis. High-precision frequency measurements are integral to the two most influential organic structural spectroscopic methods for the investigation of complex materials-NMR spectroscopy (which provides unsurpassed detail on close-range molecular order) and FTICR mass spectrometry (which provides unrivalled resolution)-and they can be translated into isotope-specific molecular-resolution data of unprecedented significance and richness. The quality of this standalone de novo molecular-level resolution data is of unparalleled mechanistic relevance and is sufficient to fundamentally advance our understanding of the structures and functions of complex biomolecular mixtures and nonrepetitive complex materials, such as natural organic matter (NOM), aerosols, and soil, plant and microbial extracts, all of which are currently poorly amenable to meaningful target analysis. The discrete analytical volumetric pixel space that is presently available to describe complex systems (defined by NMR, FT mass spectrometry and separation technologies) is in the range of 10(8-14) voxels, and is therefore capable of providing the necessary detail for a meaningful molecular-level analysis of very complex mixtures. Nonrepetitive complex materials exhibit mass spectral signatures in which the signal intensity often follows the number of chemically feasible isomers. This suggests that even the most strongly resolved FTICR mass spectra of complex materials represent simplified (e.g. isomer-filtered) projections of structural space.
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Affiliation(s)
- N Hertkorn
- GSF Research Center for Environment and Health, Institute of Ecological Chemistry, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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35
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Gajda J, Jeziorna A, Ciesielski W, Potrzebowski WM, Prezdo WW, Potrzebowski MJ. High-resolution solid-state NMR spectroscopy as a tool for investigation of enantioselective inclusion complexation. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2007; 31:153-61. [PMID: 17537616 DOI: 10.1016/j.ssnmr.2007.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 04/22/2007] [Accepted: 04/24/2007] [Indexed: 05/15/2023]
Abstract
In this paper, we showed the application of solid state-NMR (SS NMR) spectroscopy in structural studies of chiral compounds employing sample of (E)-1-diphenylphosphinoylpent-3-en-2-ol 1 as a model compound. Racemate of 1 was fully characterized by NMR techniques (both in liquid and solid phase) and X-ray crystallography. Theoretical calculations employing the GIAO approach were used to explain the influence of hydrogen bonding on 31P NMR shielding parameter in racemate. Enantioselective inclusion complexation (EIC) method with TADDOL as host molecule was applied to separate of enantiomers. The formation of host-guest complex and decomplexation procedure was monitored by means of the SS NMR. The liquid-state NMR, due to similarity of 13C and 31P spectral parameters was not able to distinguish racemate from enantiomer. In the solid phase, owing to distinction of hydrogen bonding and molecular packing in the crystal lattice, racemate and enantiomers were easy recognized by NMR spectroscopy.
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Affiliation(s)
- J Gajda
- Polish Academy of Sciences, Center of Molecular and Macromolecular Studies, Sienkiewicza 112, 90-363 Łódź, Poland
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36
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Ma Z, Halling MD, Solum MS, Harper JK, Orendt AM, Facelli JC, Pugmire RJ, Grant DM, Amick AW, Scott LT. Ring Current Effects in Crystals. Evidence from 13C Chemical Shift Tensors for Intermolecular Shielding in 4,7-Di-t-butylacenaphthene versus 4,7-Di-t-butylacenaphthylene. J Phys Chem A 2007; 111:2020-7. [PMID: 17388281 DOI: 10.1021/jp068400h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
13C chemical shift tensor data from 2D FIREMAT spectra are reported for 4,7-di-t-butylacenaphthene and 4,7-di-t-butylacenaphthylene. In addition, calculations of the chemical shielding tensors were completed at the B3LYP/6-311G** level of theory. While the experimental tensor data on 4,7-di-t-butylacenaphthylene are in agreement with theory and with previous data on polycyclic aromatic hydrocarbons, the experimental and theoretical data on 4,7-di-t-butylacenaphthene lack agreement. Instead, larger than usual differences are observed between the experimental chemical shift components and the chemical shielding tensor components calculated on a single molecule of 4,7-di-t-butylacenaphthene, with a root mean square (rms) error of +/-7.0 ppm. The greatest deviation is concentrated in the component perpendicular to the aromatic plane, with the largest value being a 23 ppm difference between experiment and theory for the 13CH2 carbon delta11 component. These differences are attributed to an intermolecular chemical shift that arises from the graphitelike, stacked arrangement of molecules found in the crystal structure of 4,7-di-t-butylacenaphthene. This conclusion is supported by a calculation on a trimer of molecules, which improves the agreement between experiment and theory for this component by 14 ppm and reduces the overall rms error between experiment and theory to 4.0 ppm. This intermolecular effect may be modeled with the use of nuclei independent chemical shieldings (NICS) calculations and is also observed in the isotropic 1H chemical shift of the CH2 protons as a 4.2 ppm difference between the solution value and the solid-state chemical shift measured via a 13C-1H heteronuclear correlation experiment.
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Affiliation(s)
- Zhiru Ma
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Webster A, Osifo PO, Neomagus HWJP, Grant DM. A comparison of glycans and polyglycans using solid-state NMR and X-ray powder diffraction. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2006; 30:150-61. [PMID: 16935479 DOI: 10.1016/j.ssnmr.2006.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 07/15/2006] [Accepted: 07/17/2006] [Indexed: 05/11/2023]
Abstract
Individual polyglycans and their corresponding monomers have been studied separately for several decades. Attention has focused primarily on the modifications of these polyglycans instead of the simple relationship between the polyglycans themselves and their corresponding monomers. Two polyglycans, chitin and chitosan, were examined along with their respective monomeric units, N-acetyl-D-glucosamine (GlcNAc) and (+)D-glucosamine (GlcN) using solid-state proton decoupling Magic Angle Turning (MAT) techniques and X-Ray Powder Diffraction (XRPD). A down-field shift in isotropic (13)C chemical shifts was observed for both polymers in Cross Polarization/Magic Angle Spinning (CP/MAS) spectra. An explanation of misleading peak assignments in previous NMR studies for these polyglycans was determined by comparing sideband patterns of the polymers with their corresponding monomers generated in a 2D FIve pi REplicated Magic Angle Turning (FIREMAT) experiment processed by Technique for Importing Greater Evolution Resolution (TIGER). Structural changes in the crystalline framework were supported by XRPD diffraction data.
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Affiliation(s)
- Athena Webster
- Chemistry Department, University of Utah, Salt Lake City, UT 84112, USA
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Madine J, Middleton DA. An NMR strategy for obtaining multiple conformational constraints for15N–13C spin-pair labelled organic solids. Phys Chem Chem Phys 2006; 8:5223-8. [PMID: 17203146 DOI: 10.1039/b610014g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work demonstrates a solid-state NMR strategy for extracting multiple interatomic distance and angle constraints from moderately complex solid organic compounds containing a single (13)C label and a single (15)N label. It is shown that the constraints obtained for the compound cimetidine, with the labels placed at positions directed by the standard synthetic route, are sufficient to provide reliable estimates of 5 of the 8 torsional degrees of freedom in the molecule and are consistent with a molecular conformation close to that determined by crystallography. This strategy will be useful for determining the conformations of sparsely-labelled small molecules in motionally restrained environments, such as within the binding sites of membrane-embedded receptors.
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Affiliation(s)
- Jillian Madine
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool, UKL69 7ZB.
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