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Powell J, Valenti D, Bobnar H, Drain E, Elliott B, Frank S, McCullough T, Moore S, Kettring A, Iuliucci R, Harper JK. Evaluating the accuracy of theoretical one-bond 13 C─ 13 C scalar couplings and their ability to predict structure in a natural product. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:979-989. [PMID: 28557141 DOI: 10.1002/mrc.4616] [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: 03/17/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
This study explores the feasibility of using a combination of experimental and theoretical 1-bond 13 C─13 C scalar couplings (1 JCC ) to establish structure in organic compounds, including unknowns. Historically, n JCC and n JCH studies have emphasized 2 and 3-bond couplings, yet 1 JCC couplings exhibit significantly larger variations. Moreover, recent improvements in experimental measurement and data processing methods have made 1 JCC data more available. Herein, an approach is evaluated in which a collection of theoretical structures is created from a partial nuclear magnetic resonance structural characterization. Computed 1 JCC values are compared to experimental data to identify candidates giving the best agreement. This process requires knowledge of the error in theoretical methods, thus the B3LYP, B3PW91, and PBE0 functionals are evaluated by comparing to 27 experimental values from INADEQUATE. Respective errors of ±1.2, ±3.8, and ±2.3 Hz are observed. An initial test of this methodology involves the natural product 5-methylmellein. In this case, only a single candidate matches experimental data with high statistical confidence. This analysis establishes the intramolecular hydrogen-bonding arrangement, ring heteroatom identity, and conformation at one position. This approach is then extended to hydroheptelidic acid, a natural product not fully characterized in prior studies. The experimental/theoretical approach proposed herein identifies a single best-fit structure from among 26 candidates and establishes, for the first time, 1 configuration and 3 conformations to complete the characterization. These results suggest that accurate and complete structural characterizations of many moderately sized organic structures (<800 Da) may be possible using only 1 JCC data.
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Affiliation(s)
- Jacob Powell
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Domenic Valenti
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Harley Bobnar
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Erika Drain
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Blaine Elliott
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sydney Frank
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Tyler McCullough
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sean Moore
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Andrew Kettring
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Robbie Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - James K Harper
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
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Williamson RT, Buevich AV, Martin GE. Experimental and Theoretical Investigation of 1JCC and nJCC Coupling Constants in Strychnine. Org Lett 2012; 14:5098-101. [DOI: 10.1021/ol302366s] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Thomas Williamson
- Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Rahway, New Jersey 07065, United States, Merck, Kenilworth, New Jersey 07033, United States, and Merck, Summit, New Jersey 07901, United States
| | - Alexei V. Buevich
- Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Rahway, New Jersey 07065, United States, Merck, Kenilworth, New Jersey 07033, United States, and Merck, Summit, New Jersey 07901, United States
| | - Gary E. Martin
- Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Rahway, New Jersey 07065, United States, Merck, Kenilworth, New Jersey 07033, United States, and Merck, Summit, New Jersey 07901, United States
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Nazarski RB, Pasternak B, Leśniak S. Three-component conformational equilibria of some flexible pyrrolidin-2-(thi)ones in solution by NMR data (δC, δH, and nJHH) and their DFT predictions: a confrontation of different approaches. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.095] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Smith SG, Paton RS, Burton JW, Goodman JM. Stereostructure Assignment of Flexible Five-Membered Rings by GIAO 13C NMR Calculations: Prediction of the Stereochemistry of Elatenyne. J Org Chem 2008; 73:4053-62. [DOI: 10.1021/jo8003138] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Steven G. Smith
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S. Paton
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Jonathan W. Burton
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Jonathan M. Goodman
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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Tamp S, Danilas K, Kreen M, Vares L, Kiirend E, Vija S, Pehk T, Parve O, Metsala A. A total conformational analysis of diastereomeric esters and calculation of their conformational shielding models. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Bifulco G, Dambruoso P, Gomez-Paloma L, Riccio R. Determination of relative configuration in organic compounds by NMR spectroscopy and computational methods. Chem Rev 2007; 107:3744-79. [PMID: 17649982 DOI: 10.1021/cr030733c] [Citation(s) in RCA: 458] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Giuseppe Bifulco
- Dipartimento di Scienze Farmaceutiche, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy.
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Quantum chemical prediction of the 13C NMR shifts in alkyl and chlorocorannulenes: correction of chlorine effects. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0291-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tähtinen P, Bagno A, Klika KD, Pihlaja K. Modeling NMR parameters by DFT methods as an aid to the conformational analysis of cis-fused 7a(8a)-methyl octa(hexa)hydrocyclopenta[d][1,3]oxazines and [3,1]benzoxazines. J Am Chem Soc 2003; 125:4609-18. [PMID: 12683833 DOI: 10.1021/ja021237t] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The energies of the preferred conformations of four 7a-methyl octa(or hexa)hydrocyclopenta[d][1,3]oxazines, five 8a-methyl octa(or hexa)hydro[3,1]benzoxazines, and 8a-methyl hexahydro[1,3]benzoxazinone, all cis-fused, were investigated by DFT methods. Following geometry optimization at the B3LYP/6-31G(d,p) level, both the proton chemical shifts and the vicinal coupling constants between H-4a and the H-4 and H-5 protons were calculated at the B3LYP/cc-pVTZ level and compared to the previously experimentally measured values. The agreement between the calculated and the experimental chemical shifts was found to be good. Similarly, the agreement between the calculated and the experimental vicinal coupling constants was also found to be good, thus providing a methodology for determining the conformational equilibria of such systems that is comparable in many respects to experimental approaches such as variable-temperature NMR or to the use of model coupling constant values, when available, from analogous compounds.
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Affiliation(s)
- Petri Tähtinen
- Structural Chemistry Group, Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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Solvent Effects on Nuclear Magnetic Resonance 2J(C,Hf) and 1J(C,Hf) Spin–Spin Coupling Constants in Acetaldehyde. Int J Mol Sci 2003. [DOI: 10.3390/i4030093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Cloran F, Carmichael I, Serianni AS. 2-Deoxy-beta-D-erythro-pentofuranose: hydroxymethyl group conformation and substituent effects on molecular structure, ring geometry, and NMR spin-spin coupling constants from quantum chemical calculations. J Am Chem Soc 2001; 123:4781-91. [PMID: 11457288 DOI: 10.1021/ja002525x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The effect of hydroxymethyl conformation (gg, gt, and tg rotamers about the C4-C5 bond) on the conformational energies and structural parameters (bond lengths, bond angles, bond torsions) of the 10 envelope forms of the biologically relevant aldopentofuranose, 2-deoxy-beta-D-erythro-pentofuranose (2-deoxy-D-ribofuranose) 2, has been investigated by ab initio molecular orbital calculations at the HF/6-31G level of theory. C4-C5 bond rotation induces significant changes in the conformational energy profile of 2 (2gt and 2tg exhibit one global energy minimum, whereas 2gg exhibits two nearly equivalent energy minima), and structural changes, especially those in bond lengths, are consistent with predictions based on previously reported vicinal, 1,3- and 1,4-oxygen lone pair effects. HF/6-31G-optimized envelope geometries of 2gg were re-optimized using density functional theory (DFT, B3LYP/6-31G), and the resulting structures were used in DFT calculations of NMR spin-spin coupling constants involving 13C (i.e., J(CH) and J(CC) over one, two, and three bonds) in 2gg according to methods described previously. The computed J-couplings were compared to those reported previously in 2gt to assess the effect of C4-C5 bond rotation on scalar couplings within the furanose ring and hydroxymethyl side chain. The results confirm prior predictions of correlations between 2J(CH), 3J(CH), 2J(CC) and 3J(CC), and ring conformation, and verify the usefulness of a concerted application of these couplings (both their magnitudes and signs) in assigning preferred ring and C4-C5 bond conformations in aldopentofuranosyl rings. The new calculated J-couplings in 2gg have particular relevance to related J-couplings in DNA (and RNA indirectly), where the gg rotamer, rather than the gt rotamer, is observed in most native structures. The effects of two additional structural perturbations on 2 were also studied, namely, deoxygenation at C5 (yielding 2,5-dideoxy-beta-D-erythro-pentofuranose 4) and methyl glycosidation at O1 (yielding methyl 2-deoxy-beta-D-erythro-pentofuranoside 5) at the HF/6-31G level. The conformational energy profile of 4 resembles that found for 2gt, not 2gg, indicating that 4 is an inappropriate structural mimic of the furanose ring in DNA. Glycosidation failed to induce differential stabilization of ring conformations containing an axial C1-O1 bond (anomeric effect), contrary to experimental data. The latter discrepancy indicates that either the magnitude of this differential stabilization depends on ring configuration or that solvent effects, which are neglected in these calculations, play a role in promoting this stabilization.
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Affiliation(s)
- F Cloran
- Department of Chemistry and Biochemistry, and the Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
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BAADEN M, GRANGER P, STRICH A. Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X. Mol Phys 2000. [DOI: 10.1080/00268970009483297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Czernek J, Lang J, Sklenář V. Ab Initio Calculations of Spin−Spin Coupling Constants in Anhydrodeoxythymidines. J Phys Chem A 2000. [DOI: 10.1021/jp9937050] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiří Czernek
- Laboratory of Biomolecular Structure and Dynamics, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic, Institute of Chemical Technology, Laboratory of NMR Spectroscopy, CZ-166 28 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague 2, Czech Republic
| | - Jan Lang
- Laboratory of Biomolecular Structure and Dynamics, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic, Institute of Chemical Technology, Laboratory of NMR Spectroscopy, CZ-166 28 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague 2, Czech Republic
| | - Vladimír Sklenář
- Laboratory of Biomolecular Structure and Dynamics, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic, Institute of Chemical Technology, Laboratory of NMR Spectroscopy, CZ-166 28 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague 2, Czech Republic
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Cloran F, Carmichael I, Serianni AS. Density Functional Calculations on Disaccharide Mimics: Studies of Molecular Geometries and Trans-O-glycosidic 3JCOCH and 3JCOCC Spin-Couplings. J Am Chem Soc 1999. [DOI: 10.1021/ja984384t] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francis Cloran
- Contribution from the Department of Chemistry and Biochemistry, and the Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
| | - Ian Carmichael
- Contribution from the Department of Chemistry and Biochemistry, and the Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
| | - Anthony S. Serianni
- Contribution from the Department of Chemistry and Biochemistry, and the Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
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16
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Cloran F, Carmichael I, Serianni AS. 13C−H and 13C−13C Spin Coupling Behavior in Aldofuranosyl Rings from Density Functional Theory. J Phys Chem A 1999. [DOI: 10.1021/jp9905676] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francis Cloran
- Department of Chemistry and Biochemistry and Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
| | - Ian Carmichael
- Department of Chemistry and Biochemistry and Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
| | - Anthony S. Serianni
- Department of Chemistry and Biochemistry and Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
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Hricovíni M, Malkina OL, Bízik F, Nagy LT, Malkin VG. Calculation of NMR Chemical Shifts and Spin−Spin Coupling Constants in the Monosaccharide Methyl-β-d-xylopyranoside Using a Density Functional Theory Approach. J Phys Chem A 1997. [DOI: 10.1021/jp972071z] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Hricovíni
- Institute of Chemistry, Computing Center, Institute of Virology, and Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
| | - O. L. Malkina
- Institute of Chemistry, Computing Center, Institute of Virology, and Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
| | - F. Bízik
- Institute of Chemistry, Computing Center, Institute of Virology, and Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
| | - L. Turi Nagy
- Institute of Chemistry, Computing Center, Institute of Virology, and Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
| | - V. G. Malkin
- Institute of Chemistry, Computing Center, Institute of Virology, and Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
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Hoffmann RW, Schopfer U, Stahl M. Z- and U-shaped open chain molecular backbones by conformation design. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00825-3] [Citation(s) in RCA: 3] [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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