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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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Amini SK. Assignment of the absolute configuration of fischerin by computed nmr chemical shifts. J STRUCT CHEM+ 2016. [DOI: 10.1134/s0022476615070148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Veinberg SL, Johnston KE, Jaroszewicz MJ, Kispal BM, Mireault CR, Kobayashi T, Pruski M, Schurko RW. Natural abundance 14N and 15N solid-state NMR of pharmaceuticals and their polymorphs. Phys Chem Chem Phys 2016; 18:17713-30. [DOI: 10.1039/c6cp02855a] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
14N and 15N solid-state NMR at natural abundance are used in tandem for the investigation of pharmaceuticals and their polymorphs.
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Affiliation(s)
| | | | | | - Brianna M. Kispal
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | | | | | - Marek Pruski
- U.S. DOE Ames Laboratory
- Iowa State University
- Ames
- USA
- Department of Chemistry
| | - Robert W. Schurko
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
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4
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Rorick A, Michael MA, Yang L, Zhang Y. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds. J Phys Chem B 2015; 119:11618-25. [PMID: 26274812 PMCID: PMC4583422 DOI: 10.1021/acs.jpcb.5b06536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.
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Affiliation(s)
- Amber Rorick
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
| | - Matthew A. Michael
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
| | - Liu Yang
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
| | - Yong Zhang
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
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5
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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6
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Amini SK. A systematic investigation of cooperativity between two types of hydrogen bonding in the nonlinear clusters of an aromatic molecule: Pyrazole. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.03.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Theoretically describing the 17O magnetic shielding constant of biomolecular systems: uracil and 5-fluorouracil in water environment. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1424-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Amini SK. Assignment of absolute configuration of holadyson by computed NMR chemical shifts. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2013. [DOI: 10.1007/s13738-013-0288-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Amini SK. Assignment of absolute configuration of 8α-hydroxy-13-hydroperoxylabd-14,17-dien-19,16;23,6α-diolide by computed NMR chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:328-333. [PMID: 23495125 DOI: 10.1002/mrc.3948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 02/12/2013] [Indexed: 06/01/2023]
Abstract
Unassigned configurations of 8α-hydroxy-13-hydroperoxylabd-14,17-dien-19,16;23,6α-diolide, extracted from Iranian salvia, in the C13 and C16 were assigned as S and R, respectively. Extensive ab initio calculations followed by chemical shift predictions were employed in this assignment. Predicted chemical shifts were correlated to experimental ones in order to find the correct configuration, shown here.
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Affiliation(s)
- Saeed K Amini
- Chemistry and Chemical Engineering Research Center of Iran, P.O. Box 14335-186, Tehran, Iran.
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10
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Shaghaghi H, Ebrahimi HP, Bahrami Panah N, Tafazzoli M. Layer selection effect on solid state 13C and 15N chemical shifts calculation using ONIOM approach. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 51-52:31-36. [PMID: 23414630 DOI: 10.1016/j.ssnmr.2013.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/15/2013] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
Solid state (13)C and (15)N chemical shifts of uracil and imidazole have been calculated using a 2-layer ONIOM approach at 32 levels of theory. The effect of electron correlation between two layers has been investigated by choosing two different kinds of layer selection. Factorial design has been applied as a multivariate technique to analyze the effect of wave function and layer selection on solid state (13)C and (15)N chemical shifts calculations. PBEPBE/6-311+G(d,p) was recommended as an optimally selected level of theory for high layer in both models. It is illustrated that considering the electron correlation of two layers of ONIOM models is important factor to calculate solid state (15)N chemical shifts. The agreement between the calculated and experimental values of solid state (13)C and (15)N chemical shifts using ONIOM (PBEPBE/6-311+G(d,p):AM1) for both uracil and imidazole confirmed the reliability of the selected wave functions and layer selection.
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Affiliation(s)
- Hoora Shaghaghi
- Department of Chemistry, Sharif University of Technology, Tehran, Iran
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11
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Esrafili MD, Behzadi H. A theoretical study on H-bonding interactions in maleic acid: calculated17O,1H NMR parameters and QTAIM analysis. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.669477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Yamada H, Mizusawa K, Igarashi R, Tochio H, Shirakawa M, Tabata Y, Kimura Y, Kondo T, Aoyama Y, Sando S. Substrate/Product-targeted NMR monitoring of pyrimidine catabolism and its inhibition by a clinical drug. ACS Chem Biol 2012; 7:535-42. [PMID: 22260358 DOI: 10.1021/cb2003972] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We report the application of one-dimensional triple-resonance NMR to metabolic analysis and thereon-based evaluation of drug activity. Doubly (13)C/(15)N-labeled uracil ([(15)N1,(13)C6]-uracil) was prepared. Its catabolic (degradative) conversion to [(13)C3,(15)N4]-β-alanine and inhibition thereof by gimeracil, a clinical co-drug used with the antitumor agent 5-fluorouracil, in mouse liver lysates were monitored specifically using one-dimensional triple-resonance ((1)H-{(13)C-(15)N}) NMR, but not double-resonance ((1)H-{(13)C}) NMR, in a ratiometric manner. The administration of labeled uracil to a mouse resulted in its non-selective distribution in various organs, with efficient catabolism to labeled β-alanine exclusively in the liver. The co-administration of gimeracil inhibited the catabolic conversion of uracil in the liver. In marked contrast to in vitro results, however, gimeracil had practically no effect on the level of uracil in the liver. The potentiality of triple-resonance NMR in the analysis of in vivo pharmaceutical activity of drugs targeting particular metabolic reactions is discussed.
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Affiliation(s)
- Hisatsugu Yamada
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | | | | | | - Yasuhiko Tabata
- Department of Biomaterials, Field
of Tissue Engineering, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku,
Kyoto 606-8507, Japan
| | - Yu Kimura
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | - Teruyuki Kondo
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yasuhiro Aoyama
- Department
of Molecular Chemistry
and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Shinsuke Sando
- INAMORI Frontier Research Center, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
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13
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Alkorta I, Elguero J. Influence of the basis set on the calculation of the absolute 13C shieldings of methyl derivatives (CH3X with X = CH3, CN, NH2, NO2, OH, F) with special emphasis in the cases of X = Cl, Br, SH, SeH, and PH2. Struct Chem 2010. [DOI: 10.1007/s11224-010-9608-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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