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Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Krivdin LB. Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives. Molecules 2021; 26:molecules26092450. [PMID: 33922318 PMCID: PMC8122784 DOI: 10.3390/molecules26092450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
This review is written amid a marked progress in the calculation of NMR parameters of carbohydrates substantiated by a vast amount of experimental data coming from several laboratories worldwide. By no means are we trying to cover in the present compilation a huge amount of all available data. The main idea of the present review was only to outline general trends and perspectives in this dynamically developing area on the background of a marked progress in theoretical and computational NMR. Presented material is arranged in three basic sections: (1)-a brief theoretical introduction; (2)-applications and perspectives in computational NMR of monosaccharides; and (3)-calculation of NMR chemical shifts and spin-spin coupling constants of di- and polysaccharides.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
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Krivdin LB. Theoretical calculations of carbon-hydrogen spin-spin coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 108:17-73. [PMID: 30538048 DOI: 10.1016/j.pnmrs.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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Krivdin LB. Carbon-carbon spin-spin coupling constants: Practical applications of theoretical calculations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 105:54-99. [PMID: 29548367 DOI: 10.1016/j.pnmrs.2018.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
Practical applications of theoretical calculations of carbon-carbon spin-spin coupling constants in particular classes of organic and bioorganic molecules are reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives as well as on carbohydrates and natural compounds.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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Adamson J, Nazarski RB, Jarvet J, Pehk T, Aav R. Shortfall of B3LYP in Reproducing NMR J
CH
Couplings in Some Isomeric Epoxy Structures with Strong Stereoelectronic Effects: A Benchmark Study on DFT Functionals. Chemphyschem 2018; 19:631-642. [DOI: 10.1002/cphc.201701125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/17/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jasper Adamson
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
| | - Ryszard B. Nazarski
- Theoretical and Structural Chemistry Group; Department of Physical Chemistry; Faculty of Chemistry; University of Lodz; Pomorska 163/165 90-236 Łódź Poland
| | - Jüri Jarvet
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
- Current address: Department of Biochemistry and Biophysics; Arrhenius Laboratories; Stockholm University; Svante Arrhenius väg 16 10691 Stockholm Sweden
| | - Tõnis Pehk
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
| | - Riina Aav
- Department of Chemistry and Biotechnology; Tallinn University of Technology; Akadeemia tee 15 12618 Tallinn Estonia
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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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San Fabián J, García de la Vega JM, Suardíaz R, Fernández-Oliva M, Pérez C, Crespo-Otero R, Contreras RH. Computational NMR coupling constants: shifting and scaling factors for evaluating 1JCH. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:775-787. [PMID: 24123317 DOI: 10.1002/mrc.4014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 06/02/2023]
Abstract
Optimized shifting and/or scaling factors for calculating one-bond carbon-hydrogen spin-spin coupling constants have been determined for 35 combinations of representative functionals (PBE, B3LYP, B3P86, B97-2 and M06-L) and basis sets (TZVP, HIII-su3, EPR-III, aug-cc-pVTZ-J, ccJ-pVDZ, ccJ-pVTZ, ccJ-pVQZ, pcJ-2 and pcJ-3) using 68 organic molecular systems with 88 (1)JCH couplings including different types of hybridized carbon atoms. Density functional theory assessment for the determination of (1)JCH coupling constants is examined, comparing the computed and experimental values. The use of shifting constants for obtaining the calculated coupling improves substantially the results, and most models become qualitatively similar. Thus, for the whole set of couplings and for all approaches excluding those using the M06 functional, the root-mean-square deviations lie between 4.7 and 16.4 Hz and are reduced to 4-6.5 Hz when shifting constants are considered. Alternatively, when a specific rovibrational contribution of 5 Hz is subtracted from the experimental values, good results are obtained with PBE, B3P86 and B97-2 functionals in combination with HIII-su3, aug-cc-pVTZ-J and pcJ-2 basis sets.
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Affiliation(s)
- J San Fabián
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Anizelli PR, Favaro DC, Contreras RH, Tormena CF. Effect of Electronic Interactions on NMR 1JCF and 2JCF Couplings in cis- and trans-4-t-Butyl-2-fluorocyclohexanones and Their Alcohol Derivatives. J Phys Chem A 2011; 115:5684-92. [DOI: 10.1021/jp202592c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Pedro R. Anizelli
- Chemistry Institute, University of Campinas, Post Office Box 6154, 13084-971 Campinas, SP, Brazil
| | - Denize C. Favaro
- Chemistry Institute, University of Campinas, Post Office Box 6154, 13084-971 Campinas, SP, Brazil
| | - Rubén H. Contreras
- Department of Physics, FCEyN, University of Buenos Aires and IFIBA-CONICET, Buenos Aires, Argentina
| | - Cláudio F. Tormena
- Chemistry Institute, University of Campinas, Post Office Box 6154, 13084-971 Campinas, SP, Brazil
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Contreras RH, Provasi PF, dos Santos FP, Tormena CF. Stereochemical dependence of NMR geminal spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:113-120. [PMID: 18991325 DOI: 10.1002/mrc.2359] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work it was sought to explore the versatility of geminal spin-spin coupling constants, (2)J(XY) SSCCs, as probes for stereochemical studies. A set of compounds, where their experimental (2)J(XY) SSCCs through the X-C-Y molecular fragment are predicted to be sensitive to hyperconjugative interactions involving either bonding or antibonding orbitals containing the C carbon atom ('coupling pathway'), were analyzed. SSCC calculations were performed for some selected examples using the second order polarization propagator approximation (SOPPA) method or within the DFT-B3LYP framework. Hyperconjugative interactions were calculated within the Natural Bond Orbital (NBO) approach. Results are condensed in two qualitative rules: Rule I(M)-hyperconjugative interactions transferring charge into the coupling pathway yield a positive increase to the Fermi contact (FC), contribution to (2)K(XY) reduced spin-spin coupling constants (RSSCC), and Rule II(M)-hyperconjugative interactions transferring charge from the coupling pathway yield a negative increase to the FC contribution to (2)K(XY) RSSCC.
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Affiliation(s)
- Rubén H Contreras
- Department of Physics, FCEyN, University of Buenos Aires and CONICET, Buenos Aires, Argentina
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