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Chaloupecká E, Tyrpekl V, Bártová K, Nishiyama Y, Dračínský M. NMR crystallography of amino acids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 130:101921. [PMID: 38422809 DOI: 10.1016/j.ssnmr.2024.101921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Václav Tyrpekl
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic
| | | | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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2
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Banerjee S, Chaykina D, Stigter R, Colombi G, Eijt SWH, Dam B, de Wijs GA, Kentgens APM. Exploring Multi-Anion Chemistry in Yttrium Oxyhydrides: Solid-State NMR Studies and DFT Calculations. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:14303-14316. [PMID: 37529664 PMCID: PMC10388355 DOI: 10.1021/acs.jpcc.3c02680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/30/2023] [Indexed: 08/03/2023]
Abstract
Rare earth oxyhydrides REOxH(3-2x), with RE = Y, Sc, or Gd and a cationic FCC lattice, are reversibly photochromic in nature. It is known that structural details and anion (O2-:H-) composition dictate the efficiency of the photochromic behavior. The mechanism behind the photochromism is, however, not yet understood. In this study, we use 1H, 2H, 17O, and 89Y solid-state NMR spectroscopy and density functional theory (DFT) calculations to study the various yttrium, hydrogen, and oxygen local environments, anion oxidation states, and hydride ion dynamics. DFT models of YOxH(3-2x) with both anion-ordered and anion-disordered sublattices are constructed for a range of compositions and show a good correlation with the experimental NMR parameters. Two-dimensional 17O-1H and 89Y-1H NMR correlation experiments reveal heterogeneities in the samples, which appear to consist of hydride-rich (x ≈ 0.25) and hydride-poor domains (x ≈ 1) rather than a single composition with homogeneous anion mixing. The compositional variation (as indicated by the different x values in YOxH(3-2x)) is determined by comparing static 1H NMR line widths with calculated 1H-1H dipolar couplings of yttrium oxyhydride models. The 1D 17O MAS spectrum demonstrates the presence of a small percentage of hydroxide (OH-) ions. DFT modeling indicates a reaction between the protons of hydroxides and hydrides to form molecular hydrogen (H+ + H- → H2). 1H MAS NMR indicates the presence of a mobile component that, based on this finding, is attributed to trapped molecular H2 in the lattice.
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Affiliation(s)
- Shrestha Banerjee
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Diana Chaykina
- Materials
for Energy Conversion and Storage, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands
| | - Rens Stigter
- Fundamental
Aspects of Materials and Energy, Department of Radiation Science and
Technology, Faculty of Applied Sciences, Delft University of Technology, Mekelweg 15, NL-2629 JB Delft, The Netherlands
| | - Giorgio Colombi
- Materials
for Energy Conversion and Storage, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands
| | - Stephan W. H. Eijt
- Fundamental
Aspects of Materials and Energy, Department of Radiation Science and
Technology, Faculty of Applied Sciences, Delft University of Technology, Mekelweg 15, NL-2629 JB Delft, The Netherlands
| | - Bernard Dam
- Materials
for Energy Conversion and Storage, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands
| | - Gilles A. de Wijs
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Arno P. M. Kentgens
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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3
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Shen J, Terskikh V, Struppe J, Hassan A, Monette M, Hung I, Gan Z, Brinkmann A, Wu G. Solid-state 17O NMR study of α-d-glucose: exploring new frontiers in isotopic labeling, sensitivity enhancement, and NMR crystallography. Chem Sci 2022; 13:2591-2603. [PMID: 35340864 PMCID: PMC8890099 DOI: 10.1039/d1sc06060k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/31/2021] [Indexed: 01/03/2023] Open
Abstract
We report the first “total synthesis” of 17O-labeled d-glucose and its solid-state 17O NMR characterization with unprecedented sensitivity and resolution.
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Affiliation(s)
- Jiahui Shen
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Victor Terskikh
- Metrology, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Alia Hassan
- Bruker Switzerland AG, Fällanden, Switzerland
| | - Martine Monette
- Bruker Biospin Ltd., 2800 High Point Drive, Suite 206, Milton, Ontario L9T 6P4, Canada
| | - Ivan Hung
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Zhehong Gan
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Andreas Brinkmann
- Metrology, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
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4
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Kawamura I, Seki H, Tajima S, Makino Y, Shigeta A, Okitsu T, Wada A, Naito A, Sudo Y. Structure of a retinal chromophore of dark-adapted middle rhodopsin as studied by solid-state nuclear magnetic resonance spectroscopy. Biophys Physicobiol 2021; 18:177-185. [PMID: 34434690 PMCID: PMC8354847 DOI: 10.2142/biophysico.bppb-v18.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
Abstract
Middle rhodopsin (MR) found from the archaeon Haloquadratum walsbyi is evolutionarily located between two different types of rhodopsins, bacteriorhodopsin (BR) and sensory rhodopsin II (SRII). Some isomers of the chromophore retinal and the photochemical reaction of MR are markedly different from those of BR and SRII. In this study, to obtain the structural information regarding its active center (i.e., retinal), we subjected MR embedded in lipid bilayers to solid-state magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy. The analysis of the isotropic 13C chemical shifts of the retinal chromophore revealed the presence of three types of retinal configurations of dark-adapted MR: (13-trans, 15-anti (all-trans)), (13-cis, 15-syn), and 11-cis isomers. The higher field resonance of the 20-C methyl carbon in the all-trans retinal suggested that Trp182 in MR has an orientation that is different from that in other microbial rhodopsins, owing to the changes in steric hindrance associated with the 20-C methyl group in retinal. 13Cζ signals of Tyr185 in MR for all-trans and 13-cis, 15-syn isomers were discretely observed, representing the difference in the hydrogen bond strength of Tyr185. Further, 15N NMR analysis of the protonated Schiff base corresponding to the all-trans and 13-cis, 15-syn isomers in MR showed a strong electrostatic interaction with the counter ion. Therefore, the resulting structural information exhibited the property of stable retinal conformations of dark-adapted MR.
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Affiliation(s)
- Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan.,Graduate School of Engineering Science, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan
| | - Hayato Seki
- Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan
| | - Seiya Tajima
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan
| | - Yoshiteru Makino
- Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan.,Present address: Graduate School of Medicine, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Arisu Shigeta
- Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan
| | - Takashi Okitsu
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, Hyogo 658-8558, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, Hyogo 658-8558, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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5
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Transue WJ, Dai Y, Riu MLY, Wu G, Cummins CC. 31P NMR Chemical Shift Tensors: Windows into Ruthenium Phosphinidene Complex Electronic Structures. Inorg Chem 2021; 60:9254-9258. [PMID: 34152768 DOI: 10.1021/acs.inorgchem.1c01099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A series of octamethylcalix[4]pyrrole/ruthenium phosphinidene complexes (Na2[1=PR]) can be accessed by phosphinidene transfer from the corresponding RPA (A = C14H10, anthracene) compounds (R = tBu, iPr, OEt, NH2, NMe2, NEt2, NiPr2, NA, dimethylpiperidino). Isolation of the tert-butyl and dimethylamino derivatives allowed comparative studies of their 31P nuclear shielding tensors by magic-angle-spinning solid-state nuclear magnetic resonance spectroscopy. Density functional theory and natural chemical shielding analyses reveal the relationship between the 31P chemical shift tensor and the local ruthenium/phosphorus electronic structure. The general trend observed in the 31P isotropic chemical shifts for the ruthenium phosphinidene complexes was controlled by the degree of deshielding in the δ11 principal tensor component, which can be linked to the σRuP/πRuP* energy gap. A "δ22-δ33 crossover" effect for R = tBu was also observed, which was caused by different degrees of deshielding associated with polarizations of the σPR and σPR* natural bond orbitals.
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Affiliation(s)
- Wesley J Transue
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yizhe Dai
- Department of Chemistry, Queen's University, Kingston, Ontario K7L3N6, Canada
| | - Martin-Louis Y Riu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L3N6, Canada
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Muniyappan S, Lin Y, Lee YH, Kim JH. 17O NMR Spectroscopy: A Novel Probe for Characterizing Protein Structure and Folding. BIOLOGY 2021; 10:biology10060453. [PMID: 34064021 PMCID: PMC8223985 DOI: 10.3390/biology10060453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022]
Abstract
Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) 17O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3) oxygen atoms are frequently involved in essential hydrogen bonds for the structural and functional integrity of proteins or related biomolecules. Although 17O NMR spectroscopic investigations of biomolecules have been considerably hampered due to low natural abundance and the quadruple characteristics of the 17O nucleus, recent theoretical and technical developments have revolutionized this methodology to be optimally poised as a unique and widely applicable tool for determining protein structure and dynamics. In this review, we recapitulate recent developments in 17O NMR spectroscopy to characterize protein structure and folding. In addition, we discuss the highly promising advantages of this methodology over other techniques and explain why further technical and experimental advancements are highly desired.
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Affiliation(s)
- Srinivasan Muniyappan
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea;
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea;
- Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
- Research Headquarters, Korea Brain Research Institute, Daegu 41068, Korea
- Correspondence: (Y.-H.L.); (J.H.K.)
| | - Jin Hae Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
- Correspondence: (Y.-H.L.); (J.H.K.)
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7
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Klein BA, Tkachuk DG, Terskikh VV, Michaelis VK. Expanding the NMR toolkit for biological solids: oxygen-17 enriched Fmoc-amino acids. NEW J CHEM 2021. [DOI: 10.1039/d1nj02847b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the solid-state 17O NMR parameters for five previously uncharacterized N-α-fluoren-9-yl-methoxycarbonyl-O-t-butyl (Fmoc) protected amino acids.
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8
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Lin B, Hung I, Gan Z, Chien PH, Spencer HL, Smith SP, Wu G. 17 O NMR Studies of Yeast Ubiquitin in Aqueous Solution and in the Solid State. Chembiochem 2020; 22:826-829. [PMID: 33058374 DOI: 10.1002/cbic.202000659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Indexed: 12/18/2022]
Abstract
We report a general method for amino acid-type specific 17 O-labeling of recombinant proteins in Escherichia coli. In particular, we have prepared several [1-13 C,17 O]-labeled yeast ubiquitin (Ub) samples including Ub-[1-13 C,17 O]Gly, Ub-[1-13 C,17 O]Tyr, and Ub-[1-13 C,17 O]Phe using the auxotrophic E. coli strain DL39 GlyA λDE3 (aspC- tyrB- ilvE- glyA- λDE3). We have also produced Ub-[η-17 O]Tyr, in which the phenolic group of Tyr59 is 17 O-labeled. We show for the first time that 17 O NMR signals from protein terminal residues and side chains can be readily detected in aqueous solution. We also reported solid-state 17 O NMR spectra for Ub-[1-13 C,17 O]Tyr and Ub-[1-13 C,17 O]Phe obtained at an ultrahigh magnetic field, 35.2 T (1.5 GHz for 1 H). This work represents a significant advance in the field of 17 O NMR studies of proteins.
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Affiliation(s)
- Binyang Lin
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ivan Hung
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Zhehong Gan
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Po-Hsiu Chien
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Holly L Spencer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
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9
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Rinald A, Terskikh V, Schatte G, Wu G. A combined solid-state 17O NMR, crystallographic, and computational study of oxiranes. CAN J CHEM 2020. [DOI: 10.1139/cjc-2020-0114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the synthesis and solid-state 17O NMR characterization of three 17O-labeled oxiranes: (2S*,3S*)-2,3-bis(4-nitrophenyl)-[17O]oxirane, (2S*,3R*)-2,3-bis(4-nitrophenyl)-[17O]oxirane, and 2,2,3-triphenyl-[17O]oxirane. In addition, we have determined the crystal structure of (2S*,3R*)-2,3-bis(4-nitrophenyl)oxirane by X-ray crystallography. When the experimentally determined 17O NMR tensors for oxiranes (where the C–O–C bond angle is about 60°) are compared with those for dimethyl ether (where the C–O–C bond angle is 113°) and other R–O–R′ functional groups, we found that the highly constrained geometry of oxiranes results in distinct tensor orientations in the molecular frame of reference. The experimental results are complemented by quantum chemical computations. This study represents the first time that 17O chemical shift and quadrupole coupling tensors are simultaneously determined for oxirane compounds.
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Affiliation(s)
- Andrew Rinald
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Victor Terskikh
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, ON K1A 0R6, Canada
| | - Gabriele Schatte
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
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10
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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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11
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Wu G. 17O NMR studies of organic and biological molecules in aqueous solution and in the solid state. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:135-191. [PMID: 31779879 DOI: 10.1016/j.pnmrs.2019.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
This review describes the latest developments in the field of 17O NMR spectroscopy of organic and biological molecules both in aqueous solution and in the solid state. In the first part of the review, a general theoretical description of the nuclear quadrupole relaxation process in isotropic liquids is presented at a mathematical level suitable for non-specialists. In addition to the first-order quadrupole interaction, the theory also includes additional relaxation mechanisms such as the second-order quadrupole interaction and its cross correlation with shielding anisotropy. This complete theoretical treatment allows one to assess the transverse relaxation rate (thus the line width) of NMR signals from half-integer quadrupolar nuclei in solution over the entire range of motion. On the basis of this theoretical framework, we discuss general features of quadrupole-central-transition (QCT) NMR, which is a particularly powerful method of studying biomolecules in the slow motion regime. Then we review recent advances in 17O QCT NMR studies of biological macromolecules in aqueous solution. The second part of the review is concerned with solid-state 17O NMR studies of organic and biological molecules. As a sequel to the previous review on the same subject [G. Wu, Prog. Nucl. Magn. Reson. Spectrosc. 52 (2008) 118-169], the current review provides a complete coverage of the literature published since 2008 in this area.
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Affiliation(s)
- Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.
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12
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Gupta R, Stringer J, Struppe J, Rehder D, Polenova T. Direct detection and characterization of bioinorganic peroxo moieties in a vanadium complex by 17O solid-state NMR and density functional theory. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 91:15-20. [PMID: 29506770 PMCID: PMC6267778 DOI: 10.1016/j.ssnmr.2018.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Electronic and structural properties of short-lived metal-peroxido complexes, which are key intermediates in many enzymatic reactions, are not fully understood. While detected in various enzymes, their catalytic properties remain elusive because of their transient nature, making them difficult to study spectroscopically. We integrated 17O solid-state NMR and density functional theory (DFT) to directly detect and characterize the peroxido ligand in a bioinorganic V(V) complex mimicking intermediates non-heme vanadium haloperoxidases. 17O chemical shift and quadrupolar tensors, measured by solid-state NMR spectroscopy, probe the electronic structure of the peroxido ligand and its interaction with the metal. DFT analysis reveals the unusually large chemical shift anisotropy arising from the metal orbitals contributing towards the magnetic shielding of the ligand. The results illustrate the power of an integrated approach for studies of oxygen centers in enzyme reaction intermediates.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
| | - John Stringer
- PhoenixNMR, 4921 Eagle Lake Drive, Fort Collins, CO, USA
| | | | - Dieter Rehder
- Department of Chemistry, University of Hamburg, D-20146, Hamburg, Germany
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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13
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Foppa L, Yamamoto K, Liao WC, Comas-Vives A, Copéret C. Electronic Structure-Reactivity Relationship on Ruthenium Step-Edge Sites from Carbonyl 13C Chemical Shift Analysis. J Phys Chem Lett 2018; 9:3348-3353. [PMID: 29851348 DOI: 10.1021/acs.jpclett.8b01332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ru nanoparticles are highly active catalysts for the Fischer-Tropsch and the Haber-Bosch processes. They show various types of surface sites upon CO adsorption according to NMR spectroscopy. Compared to terminal and bridging η1 adsorption modes on terraces or edges, little is known about side-on η2 CO species coordinated to B5 or B6 step-edges, the proposed active sites for CO and N2 cleavage. By using solid-state NMR and DFT calculations, we analyze 13C chemical shift tensors (CSTs) of carbonyl ligands on the molecular cluster model for Ru nanoparticles, Ru6(η2-μ4-CO)2(CO)13(η6-C6Me6), and show that, contrary to η1 carbonyls, the CST principal components parallel to the C-O bond are extremely deshielded in the η2 species due to the population of the C-O π* antibonding orbital, which weakens the bond prior to dissociation. The carbonyl CST is thus an indicator of the reactivity of both Ru clusters and Ru nanoparticles step-edge sites toward C-O bond cleavage.
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Affiliation(s)
- Lucas Foppa
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
| | - Keishi Yamamoto
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
| | - Wei-Chih Liao
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
| | - Aleix Comas-Vives
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
| | - Christophe Copéret
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
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14
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Keeler EG, Michaelis VK, Colvin MT, Hung I, Gor'kov PL, Cross TA, Gan Z, Griffin RG. 17O MAS NMR Correlation Spectroscopy at High Magnetic Fields. J Am Chem Soc 2017; 139:17953-17963. [PMID: 29111706 DOI: 10.1021/jacs.7b08989] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structure of two protected amino acids, FMOC-l-leucine and FMOC-l-valine, and a dipeptide, N-acetyl-l-valyl-l-leucine (N-Ac-VL), were studied via one- and two-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy. Utilizing 17O magic-angle spinning (MAS) NMR at multiple magnetic fields (17.6-35.2 T/750-1500 MHz for 1H) the 17O quadrupolar and chemical shift parameters were determined for the two oxygen sites of each FMOC-protected amino acids and the three distinct oxygen environments of the dipeptide. The one- and two-dimensional, 17O, 15N-17O, 13C-17O, and 1H-17O double-resonance correlation experiments performed on the uniformly 13C,15N and 70% 17O-labeled dipeptide prove the attainability of 17O as a probe for structure studies of biological systems. 15N-17O and 13C-17O distances were measured via one-dimensional REAPDOR and ZF-TEDOR experimental buildup curves and determined to be within 15% of previously reported distances, thus demonstrating the use of 17O NMR to quantitate interatomic distances in a fully labeled dipeptide. Through-space hydrogen bonding of N-Ac-VL was investigated by a two-dimensional 1H-detected 17O R3-R-INEPT experiment, furthering the importance of 17O for studies of structure in biomolecular solids.
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Affiliation(s)
- Eric G Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Vladimir K Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Michael T Colvin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Timothy A Cross
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Zhehong Gan
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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15
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Kong X, Dai Y, Wu G. Solid-state 17O NMR study of 2-acylbenzoic acids and warfarin. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 84:59-64. [PMID: 28057400 DOI: 10.1016/j.ssnmr.2016.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/14/2016] [Accepted: 12/16/2016] [Indexed: 06/06/2023]
Abstract
We report synthesis and solid-state 17O NMR characterization of four site-specifically 17O-labeled 2-acylbenzoic acids (2-RC(O)C6H4COOH) where R=H and CH3): 2-[3-17O]formylbenzoic acid, 2-[1,2-17O2]formylbenzoic acid, 2-[3-17O]acetylbenzoic acid, and 2-[1,2,3-17O3]acetylbenzoic acid. In the solid state, both 2-formyl- and 2-acetyl-benzoic acids exist as the cyclic phthalide form each containing a five-membered lactone ring and a cyclic hemiacetal/hemiketal group. Static and magic-angle-spinning 17O NMR spectra were recorded at 14.1 and 21.1T for these compounds, from which the 17O chemical shift and nuclear quadrupolar coupling tensors were determined for each oxygen site. These results represent the first time that 17O NMR tensors are fully characterized for lactone, cyclic hemiacetal, and cyclic hemiketal functional groups. We also report solid-state 17O NMR data for the cyclic hemiketal group an anticoagulant drug, warfarin. Experimental 17O NMR tensors in these compounds were compared with computational results obtained with a periodic DFT code BAND.
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Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
| | - Yizhe Dai
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
| | - Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6.
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16
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Shigeta A, Ito S, Inoue K, Okitsu T, Wada A, Kandori H, Kawamura I. Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin. Biochemistry 2017; 56:543-550. [PMID: 28040890 DOI: 10.1021/acs.biochem.6b00999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique among other microbial rhodopsins. Here we present solid-state nuclear magnetic resonance (NMR) characterization of retinal and functionally important residues in the vicinity of retinal in the ground state. We assigned chemical shifts of retinal C14 and C20 atoms, and Tyr218Cζ, Lys255Cε, and the protonated Schiff base of KR2 in lipid environments at acidic and neutral pH. 15N NMR signals of the protonated Schiff base showed a twist around the N-Cε bond under neutral conditions, compared with other microbial rhodopsins. These data indicated that the location of the counterion Asp116 is one helical pitch toward the cytoplasmic side. In acidic environments, the 15N Schiff base signal was shifted to a lower field, indicating that protonation of Asp116 induces reorientation during interactions between the Schiff base and Asp116. In addition, the Tyr218 residue in the vicinity of retinal formed a weak hydrogen bond with Asp251, a temporary Na+-binding site during the photocycle. These features may indicate unique mechanisms of sodium ion pumps.
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Affiliation(s)
- Arisu Shigeta
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
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17
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Kong X, Brinkmann A, Terskikh V, Wasylishen RE, Bernard GM, Duan Z, Wu Q, Wu G. Proton Probability Distribution in the O···H···O Low-Barrier Hydrogen Bond: A Combined Solid-State NMR and Quantum Chemical Computational Study of Dibenzoylmethane and Curcumin. J Phys Chem B 2016; 120:11692-11704. [PMID: 27782387 DOI: 10.1021/acs.jpcb.6b08091] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a combined solid-state (1H, 2H, 13C, 17O) NMR and plane-wave density functional theory (DFT) computational study of the O···H···O low-barrier hydrogen bonds (LBHBs) in two 1,3-diketone compounds: dibenzoylmethane (1) and curcumin (2). In the solid state, both 1 and 2 exist in the cis-keto-enol tautomeric form, each exhibiting an intramolecular LBHB with a short O···O distance (2.435 Å in 1 and 2.455 Å in 2). Whereas numerous experimental (structural and spectroscopic) and computational studies have been reported for the enol isomers of 1,3-diketones, a unified picture about the proton location within an LBHB is still lacking. This work reports for the first time the solid-state 17O NMR data for the O···H···O LBHBs in 1,3-diketones. The central conclusion of this work is that detailed information about the probability density distribution of the proton (nuclear zero-point motion) across an LBHB can be obtained from a combination of solid-state NMR and plane-wave DFT computations (both NMR parameter calculations and ab initio molecular dynamics simulations). We propose that the precise proton probability distribution across an LBHB should provide a common basis on which different and sometimes seemingly contradicting experimental results obtained from complementary techniques, such as X-ray diffraction, neutron diffraction, and solid-state NMR, can be reconciled.
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Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
| | - Andreas Brinkmann
- Measurement Science and Standards, National Research Council Canada , 1200 Montreal Road, M-40, Ottawa, Ontario, Canada K1A 0R6
| | - Victor Terskikh
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6.,Department of Chemistry, University of Ottawa , 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | | | - Guy M Bernard
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Zhuang Duan
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Qichao Wu
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Gang Wu
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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18
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Shen J, Terskikh V, Wu G. Observation of the Second-Order Quadrupolar Interaction as a Dominating NMR Relaxation Mechanism in Liquids: The Ultraslow Regime of Motion. J Phys Chem Lett 2016; 7:3412-3418. [PMID: 27525537 DOI: 10.1021/acs.jpclett.6b01530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report variable-temperature (VT) (17)O NMR spectra of [5-(17)O]-d-glucose in an aqueous solution and in glycerol at 14.1 and 21.1 T. The VT (17)O NMR data cover a wide range of motion for which the molecular rotational correlation time (τc) of glucose changes more than 5 orders of magnitude. The observed line width of the (17)O NMR signal for [5-(17)O]-d-glucose displays a maximum at ω0τc ≈ 1 and a minimum at ω0τc ≈ 150, where ω0 is the angular Larmor frequency of (17)O. Under the ultraslow motion condition (i.e., ω0τc > 150), the line width of the observed (17)O NMR signal increases drastically with τc, suggesting that the second-order quadrupolar interaction becomes the predominant relaxation mechanism. While this relaxation mechanism has long been predicted by theory, the current study reports the first experimental observation of such a phenomenon. The implications of this new relaxation mechanism on the spectral resolution limit in liquid-state NMR spectroscopy for half-integer spins are discussed.
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Affiliation(s)
- Jiahui Shen
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
| | - Victor Terskikh
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
- Department of Chemistry, University of Ottawa , Ottawa, Ontario K1N 6N5 Canada
| | - Gang Wu
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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19
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Wu G. Solid-State ¹⁷O NMR studies of organic and biological molecules: Recent advances and future directions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 73:1-14. [PMID: 26651417 DOI: 10.1016/j.ssnmr.2015.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/20/2015] [Accepted: 11/24/2015] [Indexed: 05/04/2023]
Abstract
This Trends article highlights the recent advances published between 2012 and 2015 in solid-state (17)O NMR for organic and biological molecules. New developments in the following areas are described: (1) new oxygen-containing functional groups, (2) metal organic frameworks, (3) pharmaceuticals, (4) probing molecular motion in organic solids, (5) dynamic nuclear polarization, and (6) paramagnetic coordination compounds. For each of these areas, the author offers his personal views on important problems to be solved and possible future directions.
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Affiliation(s)
- Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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20
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Pinter B, Smith KT, Kamitani M, Zolnhofer EM, Tran BL, Fortier S, Pink M, Wu G, Manor BC, Meyer K, Baik MH, Mindiola DJ. Cyclo-P3 Complexes of Vanadium: Redox Properties and Origin of the 31P NMR Chemical Shift. J Am Chem Soc 2015; 137:15247-61. [DOI: 10.1021/jacs.5b10074] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Balazs Pinter
- Department
of Chemistry and the Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
- Eenheid
Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan
2, 1050 Brussels, Belgium
| | - Kyle T. Smith
- Department
of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia Pennsylvania 19104, United States
| | - Masahiro Kamitani
- Department
of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia Pennsylvania 19104, United States
| | - Eva M. Zolnhofer
- Department
of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich Alexander University Erlangen-Nürnberg (FAU), Egerlandstr. 1, 91058 Erlangen, Germany
| | - Ba L. Tran
- Department
of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia Pennsylvania 19104, United States
| | - Skye Fortier
- Department
of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia Pennsylvania 19104, United States
| | - Maren Pink
- Department
of Chemistry and the Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
| | - Gang Wu
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Brian C. Manor
- Department
of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia Pennsylvania 19104, United States
| | - Karsten Meyer
- Department
of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich Alexander University Erlangen-Nürnberg (FAU), Egerlandstr. 1, 91058 Erlangen, Germany
| | - Mu-Hyun Baik
- Department
of Chemistry and the Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
- Department
of Chemistry, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Korea
| | - Daniel J. Mindiola
- Department
of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia Pennsylvania 19104, United States
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21
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Kong X, Terskikh V, Toubaei A, Wu G. A solid-state 17O NMR study of platinum-carboxylate complexes: carboplatin and oxaliplatin. CAN J CHEM 2015. [DOI: 10.1139/cjc-2015-0019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report synthesis and solid-state NMR characterization of two 17O-labeled platinum anticancer drugs: cis-diammine(1,1-cyclobutane-[17O4]dicarboxylato)platinum(II) (carboplatin) and ([17O4]oxalato)[(1R, 2R)-(−)-1,2-cyclohexanediamine)]platinum(II) (oxaliplatin). Both 17O chemical shift (CS) and quadrupolar coupling (QC) tensors were measured for the carboxylate groups in these two compounds. With the aid of plane wave DFT computations, the 17O CS and QC tensor orientations were determined in the molecular frame of reference. Significant changes in the 17O CS and QC tensors were observed for the carboxylate oxygen atom upon its coordination to Pt(II). In particular, the 17O isotropic chemical shifts for the oxygen atoms directly bonded to Pt(II) are found to be smaller (more shielded) by 200 ppm than those for the non-Pt-coordinated oxygen atoms within the same carboxylate group. Examination of the 17O CS tensor components reveals that such a large 17O coordination shift is primarily due to the shielding increase along the direction that is within the O=C–O–Pt plane and perpendicular to the O–Pt bond. This result is interpreted as due to the σ donation from the oxygen nonbonding orbital (electron lone pair) to the Pt(II) empty dyz orbital, which results in large energy gaps between σ(Pt–O) and unoccupied molecular orbitals, thus reducing the paramagnetic shielding contribution along the direction perpendicular to the O–Pt bond. We found that the 17O QC tensor of the carboxylate oxygen is also sensitive to Pt(II) coordination, and that 17O CS and QC tensors provide complementary information about the O–Pt bonding.
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Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Victor Terskikh
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Abouzar Toubaei
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
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22
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Lu J, Kong X, Terskikh V, Wu G. Solid-State (17)O NMR of Oxygen-Nitrogen Singly Bonded Compounds: Hydroxylammonium Chloride and Sodium Trioxodinitrate (Angeli's Salt). J Phys Chem A 2015; 119:8133-8. [PMID: 26107984 DOI: 10.1021/acs.jpca.5b05466] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a solid-state NMR study of (17)O-labeled hydroxylammonium chloride ([H(17)O-NH3]Cl) and sodium trioxodinitrate monohydrate (Na2[(17)ONNO2]·H2O, Angeli's salt). The common feature in these two compounds is that they both contain oxygen atoms that are singly bonded to nitrogen. For this class of oxygen-containing functional groups, there is very limited solid-state (17)O NMR data in the literature. In this work, we experimentally measured the (17)O chemical shift and quadrupolar coupling tensors. With the aid of plane-wave DFT computation, the (17)O NMR tensor orientations were determined in the molecular frame of reference. We found that the characteristic feature of an O-N single bond is that the (17)O nucleus exhibits a large quadrupolar coupling constant (13-15 MHz) but a rather small chemical shift anisotropy (100-250 ppm), in sharp contrast with the nitroso (O═N) functional group for which both quantities are very large (e.g., 16 MHz and 3000 ppm, respectively).
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Affiliation(s)
- Jiasheng Lu
- †Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Xianqi Kong
- †Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Victor Terskikh
- †Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.,‡Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Gang Wu
- †Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
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23
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Michaelis VK, Keeler EG, Ong TC, Craigen KN, Penzel S, Wren JEC, Kroeker S, Griffin RG. Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR. J Phys Chem B 2015; 119:8024-36. [PMID: 25996165 PMCID: PMC4894719 DOI: 10.1021/acs.jpcb.5b04647] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.
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Affiliation(s)
- Vladimir K. Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Ta-Chung Ong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Kimberley N. Craigen
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Susanne Penzel
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - John E. C. Wren
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Scott Kroeker
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
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24
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Czernek J, Brus J. The covariance of the differences between experimental and theoretical chemical shifts as an aid for assigning two-dimensional heteronuclear correlation solid-state NMR spectra. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Miller AF. Solid-state NMR of flavins and flavoproteins. Methods Mol Biol 2014; 1146:307-40. [PMID: 24764096 DOI: 10.1007/978-1-4939-0452-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Why apply solid-state NMR (SSNMR) to flavins and flavoproteins? NMR provides information on an atom-specific basis about chemical functionality, structure, proximity to other groups, and dynamics of the system. Thus, it has become indispensable to the study of chemicals, materials, catalysts, and biomolecules. It is no surprise then that NMR has a great deal to offer in the study of flavins and flavoenzymes. In general, their catalytic or electron-transfer activity resides essentially in the flavin, a molecule eminently accessible by NMR. However, the specific reactivity displayed depends on a host of subtle interactions whereby the protein biases and reshapes the flavin's propensities to activate it for one reaction while suppressing other aspects of this cofactor's prodigious repertoire (Massey et al., J Biol Chem 244:3999-4006, 1969; Müller, Z Naturforsch 27B:1023-1026, 1972; Joosten and van Berkel, Curr Opin Struct Biol 11:195-202, 2007). Thus, we are fascinated to learn about how the flavin cofactor of one enzyme is, and is not, like the flavin cofactor of another. In what follows, we describe how the capabilities of SSNMR can help and are beginning to bear fruit in this exciting endeavor.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, 505 Rose St, Lexington, KY, 40506-0055, USA,
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26
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Michaelis VK, Corzilius B, Smith AA, Griffin RG. Dynamic nuclear polarization of 17O: direct polarization. J Phys Chem B 2013; 117:14894-906. [PMID: 24195759 PMCID: PMC3922122 DOI: 10.1021/jp408440z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dynamic nuclear polarization of (17)O was studied using four different polarizing agents: the biradical TOTAPOL and the monoradicals trityl and SA-BDPA, as well as a mixture of the latter two. Field profiles, DNP mechanisms, and enhancements were measured to better understand and optimize directly polarizing this low-gamma quadrupolar nucleus using both mono- and biradical polarizing agents. Enhancements were recorded at <88 K and were >100 using the trityl (OX063) radical and <10 with the other polarizing agents. The >10,000-fold savings in acquisition time enabled a series of biologically relevant small molecules to be studied with small sample sizes and the measurement of various quadrupolar parameters. The results are discussed with comparison to room temperature studies and GIPAW quantum chemical calculations. These experimental results illustrate the strength of high field DNP and the importance of radical selection for studying low-gamma nuclei.
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Affiliation(s)
- Vladimir K. Michaelis
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | | | | | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
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27
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Kong X, Shan M, Terskikh V, Hung I, Gan Z, Wu G. Solid-State 17O NMR of Pharmaceutical Compounds: Salicylic Acid and Aspirin. J Phys Chem B 2013; 117:9643-54. [DOI: 10.1021/jp405233f] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xianqi Kong
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
| | - Melissa Shan
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
| | - Victor Terskikh
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A
0R6, Canada
| | - Ivan Hung
- Center of Interdisciplinary
Magnetic
Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United
States
| | - Zhehong Gan
- Center of Interdisciplinary
Magnetic
Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United
States
| | - Gang Wu
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
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28
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Esrafili MD. A DFT investigation on hydrogen- and halogen-bonding interactions in dichloroacetic acid: application of NMR-GIAO and Bader theories. Struct Chem 2012. [DOI: 10.1007/s11224-012-0024-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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29
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DFT study of 17O, 1H and 13C NMR chemical shifts in two forms of native cellulose, I and I. Carbohydr Res 2012; 347:99-106. [DOI: 10.1016/j.carres.2011.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 10/19/2011] [Accepted: 10/26/2011] [Indexed: 11/19/2022]
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Esrafili MD. Intra- and inter-molecular interactions in salicylic acid — Theoretical calculations of 17O and 1H chemical shielding tensors and QTAIM analysis. CAN J CHEM 2011. [DOI: 10.1139/v11-105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A density functional theory (DFT) study was performed to examine intra- and inter-molecular hydrogen bond (HB) properties in crystalline salicylic acid (SA). BLYP, B3LYP, and M06 functionals with 6–311++G** basis set were employed to calculate NMR chemical shielding isotropy (σiso) and anisotropy (Δσ) at the sites of the 17O and 1H nuclei of SA. From this study, it appears that the intra- and inter-molecular O–H···O as well as C–H···O HBs around the SA molecule in the crystal lattice have a major influence on the chemical shielding tensors and more specifically on the carbonyl 17O isotropy value. The quantum theory of atoms in molecules (QTAIM) analysis was also employed to elucidate the interaction characteristics in SA H-bonded network. Based on QTAIM results, a partial covalent character is attributed to the intra- and inter-molecular O–H···O HBs in SA.
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Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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Wong A, Smith ME, Terskikh V, Wu G. Obtaining accurate chemical shifts for all magnetic nuclei (1H, 13C, 17O, and 27Al) in tris(2,4-pentanedionato-O,O′)aluminium(III) — A solid-state NMR case study. CAN J CHEM 2011. [DOI: 10.1139/v11-046] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report a complete set of high-resolution solid-state NMR spectra for all magnetic nuclei (1H, 13C, 17O, and 27Al) in the α-form of tris(2,4-pentanedionato-O,O′)aluminium(III), α-Al(acac)3. These high-resolution NMR spectra were obtained by using a host of solid-state NMR techniques: standard cross-polarization under the magic-angle spinning (CPMAS) method for 13C, 1-D homonuclear decoupling using the windowed DUMBO sequence for 1H, double-rotation (DOR) for 17O and 27Al, and multiple-quantum MAS for 27Al. Some experiments were performed at multiple magnetic fields. We show that the isotropic chemical shifts obtained for 1H, 13C, 17O, and 27Al nuclei in α-Al(acac)3 are highly resolved and accurate, regardless of the nature of the targeted nuclear spins (i.e., spin-1/2 or quadrupolar) and, as such, can be treated equally in comparison with computational chemical shifts obtained from a gauge-including projector-augmented wave (GIPAW) plane-wave pseudopotential DFT method.
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Affiliation(s)
- Alan Wong
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark E. Smith
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Victor Terskikh
- Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Gang Wu
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
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Charpentier T. The PAW/GIPAW approach for computing NMR parameters: a new dimension added to NMR study of solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2011; 40:1-20. [PMID: 21612895 DOI: 10.1016/j.ssnmr.2011.04.006] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/24/2011] [Accepted: 04/25/2011] [Indexed: 05/18/2023]
Abstract
In 2001, Mauri and Pickard introduced the gauge including projected augmented wave (GIPAW) method that enabled for the first time the calculation of all-electron NMR parameters in solids, i.e. accounting for periodic boundary conditions. The GIPAW method roots in the plane wave pseudopotential formalism of the density functional theory (DFT), and avoids the use of the cluster approximation. This method has undoubtedly revitalized the interest in quantum chemical calculations in the solid-state NMR community. It has quickly evolved and improved so that the calculation of the key components of NMR interactions, namely the shielding and electric field gradient tensors, has now become a routine for most of the common nuclei studied in NMR. Availability of reliable implementations in several software packages (CASTEP, Quantum Espresso, PARATEC) make its usage more and more increasingly popular, maybe indispensable in near future for all material NMR studies. The majority of nuclei of the periodic table have already been investigated by GIPAW, and because of its high accuracy it is quickly becoming an essential tool for interpreting and understanding experimental NMR spectra, providing reliable assignments of the observed resonances to crystallographic sites or enabling a priori prediction of NMR data. The continuous increase of computing power makes ever larger (and thus more realistic) systems amenable to first-principles analysis. In the near future perspectives, as the incorporation of dynamical effects and/or disorder are still at their early developments, these areas will certainly be the prime target.
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Affiliation(s)
- Thibault Charpentier
- CEA, IRAMIS, SIS2M, Laboratoire de Structure et Dynamique par Résonance Magnétique, UMR CEA-CNRS 3299, F-91191 Gif-sur-Yvette cedex, France.
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Esrafili MD, Alizadeh V. A theoretical investigation of hydrogen bonding effects on oxygen and hydrogen chemical shielding tensors of aspirin. Struct Chem 2011. [DOI: 10.1007/s11224-011-9810-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Zhu J, Wu G. Quadrupole central transition 17O NMR spectroscopy of biological macromolecules in aqueous solution. J Am Chem Soc 2010; 133:920-32. [PMID: 21175170 DOI: 10.1021/ja1079207] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate a general nuclear magnetic resonance (NMR) spectroscopic approach in obtaining high-resolution (17)O (spin-5/2) NMR spectra for biological macromolecules in aqueous solution. This approach, termed quadrupole central transition (QCT) NMR, is based on the multiexponential relaxation properties of half-integer quadrupolar nuclei in molecules undergoing slow isotropic tumbling motion. Under such a circumstance, Redfield's relaxation theory predicts that the central transition, m(I) = +1/2 ↔ -1/2, can exhibit relatively long transverse relaxation time constants, thus giving rise to relatively narrow spectral lines. Using three robust protein-ligand complexes of size ranging from 65 to 240 kDa, we have obtained (17)O QCT NMR spectra with unprecedented resolution, allowing the chemical environment around the targeted oxygen atoms to be directly probed for the first time. The new QCT approach increases the size limit of molecular systems previously attainable by solution (17)O NMR by nearly 3 orders of magnitude (1000-fold). We have also shown that, when both quadrupole and shielding anisotropy interactions are operative, (17)O QCT NMR spectra display an analogous transverse relaxation optimized spectroscopy type behavior in that the condition for optimal resolution depends on the applied magnetic field. We conclude that, with the currently available moderate and ultrahigh magnetic fields (14 T and higher), this (17)O QCT NMR approach is applicable to a wide variety of biological macromolecules. The new (17)O NMR parameters so obtained for biological molecules are complementary to those obtained from (1)H, (13)C, and (15)N NMR studies.
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Affiliation(s)
- Jianfeng Zhu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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