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Krivdin LB. Recent advances in computational 31 P NMR: Part 1. Chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:478-499. [PMID: 31703153 DOI: 10.1002/mrc.4965] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
This is the first part of two closely related reviews dealing with the computation of phosphorus-31 nuclear magnetic resonance chemical shifts in a wide series of organophosphorus compounds including complexes, clusters, and bioorganic phosphorus compounds. In particular, the analysis of the accuracy factors, such as substitution effects, solvent effects, vibrational corrections, and relativistic effects, is presented. This review is dedicated to the Full Member of the Russian Academy of Sciences Professor Boris A. Trofimov in view of his invaluable contribution to the field of synthesis, nuclear magnetic resonance, and computation studies of organophosphorus 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, Irkutsk, Russia
- Angarsk State Technical University, Irkutsk Region, Russia
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2
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Mamedov VA, Zhukova NA, Kadyrova MS, Fazleeva RR, Bazanova OB, Beschastnova TN, Gubaidullin AT, Rizvanov IK, Yanilkin VV, Latypov SK, Sinyashin OG. Environmentally friendly and efficient method for the synthesis of the new
α
,
α
′‐diimine ligands with benzimidazole moiety. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vakhid A. Mamedov
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Nataliya A. Zhukova
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Milyausha S. Kadyrova
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Rezeda R. Fazleeva
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Olga B. Bazanova
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Tat'yana N. Beschastnova
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Aidar T. Gubaidullin
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Il'dar Kh. Rizvanov
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Vitaliy V. Yanilkin
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Shamil K. Latypov
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
| | - Oleg G. Sinyashin
- A.E. Arbuzov Institute of Organic and Physical ChemistryFRC Kazan Scientific Center, Russian Academy of Sciences Kazan Russian Federation
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3
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Theoretical conformational studies of podands containing (2S,4R)-4-hydroxyproline moieties. Chem Heterocycl Compd (N Y) 2019. [DOI: 10.1007/s10593-019-02531-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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4
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Polyancev FM, Metlushka KE, Sadkova DN, Khisametdinova ZR, Kataeva ON, Alfonsov VA, Latypov SK, Sinyashin OG. The isomeric structure of pentacoordinate chiral spirophosphoranes in solution by the combined use of NMR experiments and GIAO DFT calculations of NMR parameters. Dalton Trans 2017; 46:8146-8156. [PMID: 28607987 DOI: 10.1039/c7dt01605k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The interplay of NMR experiments and DFT calculations of NMR parameters is a reliable method for determining the relative configurations of pentacoordinate chiral spirophosphoranes bearing two six- or five-membered rings at the phosphorus atom in solution. The major product of the Betti based derivatives corresponds to the isomers with both substituents at chiral carbons being opposite to the P-H proton. The next populated product corresponds to the isomer with different chiralities at carbons. The least populated isomer is one with both substituents being at the same side of the heterocycle as the P-H bond.
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Affiliation(s)
- Fedor M Polyancev
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str. 8, Kazan, 420088, Russian Federation.
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5
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Wiitala KW, Hoye TR, Cramer CJ. Hybrid Density Functional Methods Empirically Optimized for the Computation of (13)C and (1)H Chemical Shifts in Chloroform Solution. J Chem Theory Comput 2015; 2:1085-92. [PMID: 26633067 DOI: 10.1021/ct6001016] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two hybrid generalized-gradient approximation density functionals, WC04 and WP04, are optimized for the prediction of (13)C and (1)H chemical shifts, respectively, using a training set of 43 molecules in chloroform solution. Tests on molecules not included in the training set, namely six stereoisomeric methylcyclohexanols and a β-lactam antibiotic, indicate the models to be robust and moreover to provide results more accurate than those from equivalent B3LYP, PBE1, or mPW1PW91 calculations, particularly for the prediction of downfield resonances in nuclear magnetic resonance spectra. However, linear regression of the B3LYP, PBE1, and mPW1PW91 predicted values on the experimental data improves the accuracy of those models so that they are comparable to WC04 and WP04.
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Affiliation(s)
- Keith W Wiitala
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Thomas R Hoye
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
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Latypov SK, Polyancev FM, Yakhvarov DG, Sinyashin OG. Quantum chemical calculations of31P NMR chemical shifts: scopes and limitations. Phys Chem Chem Phys 2015; 17:6976-87. [DOI: 10.1039/c5cp00240k] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High level of theory is not necessarily needed to obtain rather accurate predictions of31P chemical shifts by GIAO method. For example, the PBE1PBE/6-311G(2d,2p)//PBE1PBE/6-31+G(d) combination allowed to obtain good results for variety of middle-size organophosphorus compounds (M= 200–700 Da).
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Affiliation(s)
- Shamil K. Latypov
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
| | - Fedor M. Polyancev
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
| | - Dmitry G. Yakhvarov
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
| | - Oleg G. Sinyashin
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
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Tong J, Chen Y, Liu S, Xu X, Cheng F. Estimation and prediction of 13C NMR chemical shifts of carbon atoms in both alcohols and thiols. J STRUCT CHEM+ 2013. [DOI: 10.1134/s002247661206008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Zhang J, Peng Q, Zhang S, Li Y, Li S, Gao H, Zhou Z. Synthesis, mass spectral characterization, NMR analyses, and DFT calculations of 1-desoxymaquindox and 4-desoxymaquindox. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.11.057] [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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Mamedov VA, Zhukova NA, Beschastnova TN, Gubaidullin AT, Balandina AA, Latypov SK. A reaction for the synthesis of benzimidazoles and 1H-imidazo[4,5-b]pyridines via a novel rearrangement of quinoxalinones and their aza-analogues when exposed to 1,2-arylenediamines. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.10.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Borkowski EJ, Suvire FD, Enriz RD. Advances in correlation between experimental and DFT/GIAO computed 13C NMR chemical shifts: A theoretical study on pentacyclic terpenoids (fernenes). ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Chimichi S, Boccalini M, Matteucci A, Kharlamov SV, Latypov SK, Sinyashin OG. GIAO DFT 13C/15N chemical shifts in regioisomeric structure determination of fused pyrazoles. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:607-613. [PMID: 20589725 DOI: 10.1002/mrc.2633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The combined use of two-dimensional NMR correlation experiments and gauge including atomic orbital density functional theory in (13)C NMR chemical shift (CS) calculations allowed reliable and simple structural determination of regioisomeric heterocyclic systems that originate from the reactions of acylquinolinones with substituted hydrazines. Moreover, the results of differential analysis between the calculated (15)N NMR CSs for hypothetical structures and the experimental data of the title azaheterocyclic systems were even more advantageous with respect to (13)C because there was no need for correlational analysis: structures of the regioisomeric compounds could be determined just by direct comparison.
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Elyashberg M, Blinov K, Williams A. A systematic approach for the generation and verification of structural hypotheses. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:371-389. [PMID: 19197914 DOI: 10.1002/mrc.2397] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
During the process of molecular structure elucidation the selection of the most probable structural hypothesis may be based on chemical shift prediction. The prediction is carried out using either empirical or quantum-mechanical (QM) methods. When QM methods are used, NMR prediction commonly utilizes the GIAO option of the DFT approximation. In this approach the structural hypotheses are expected to be investigated by scientist. In this article we hope to show that the most rational manner by which to create structural hypotheses is actually by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data and specifically using 2D NMR data. When an expert system is used the best structure(s) can be distinguished using chemical shift prediction, which is best performed either by an incremental or neural net algorithm. The time-consuming QM calculations can then be applied, if necessary, to one or more of the 'best' structures to confirm the suggested solution.
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Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development, Moscow Department, 6 Akademik Bakulev Street, Moscow 117513, Russian Federation
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14
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Khairitdinova ED, Tsyrlina EM, Spirikhin LV, Balandina AA, Latypov SK, Yunusov MS. Norditerpenoid alkaloids from Aconitum septentrionale K. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2008. [DOI: 10.1134/s107042800804012x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Balandina AA, Latypov SK, Khairitdinova ED, Tsyrlina EM, Spirikhin LV, Yunusov MS. Accurate assignments in PMR and 13C NMR spectra of anhydrolycoctonine using 2D spectroscopy. Chem Nat Compd 2008. [DOI: 10.1007/s10600-008-9056-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Wiitala KW, Cramer CJ, Hoye TR. Comparison of various density functional methods for distinguishing stereoisomers based on computed (1)H or (13)C NMR chemical shifts using diastereomeric penam beta-lactams as a test set. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:819-29. [PMID: 17729215 DOI: 10.1002/mrc.2045] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Full (1)H and (13)C NMR chemical shift assignments were made for two sets of penam beta-lactams: namely, the diastereomeric (2S, 5S, 6S)-, (2S, 5R, 6R)-, (2S, 5S, 6R)-, and (2S, 5R, 6S)-methyl 6-(1,3-dioxoisoindolin-2-yl)-3,3-dimethyl-7-oxo-4-thia-1-aza-bicyclo[3.2.0]heptane-2-carboxylates (1-4) and (2S, 5R, 6R)-, (2S, 5S, 6R)-, and (2S, 5R, 6S)-6-(1,3-dioxoisoindolin-2-yl)-3,3-dimethyl-7-oxo-4-thia-1-aza-bicyclo[3.2.0]heptane-2-carboxylic acids (6-8). Each penam was then modeled as a family of conformers obtained from Monte Carlo searches using the AMBER* force field followed by IEFPCM/B3LYP/6-31G(d) geometry optimization of each conformer using chloroform solvation. (1)H and (13)C chemical shifts for each conformer were computed at the WP04, WC04, B3LYP, and PBE1 density functional levels as Boltzmann averages of IEFPCM/B3LYP/6-311 + G(2d,p) energies over each family. Comparisons between experimental and theoretical chemical shift data were made using the total absolute error (|Deltadelta| (T)) criterion. For the (1)H shift data, all methods were sufficiently accurate to identify the proper stereoisomers. Computed (13)C shifts were not always successful in identifying the correct stereoisomer, regardless of which DFT method was used. The relative ability of each theoretical approach to discriminate among stereoisomers on the basis of proton shifts was also evaluated.
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Affiliation(s)
- Keith W Wiitala
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
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Semenov VE, Galiullina LF, Lodochnikova OA, Kataeva ON, Gubaidullin AT, Chernova AV, Efremov YY, Latypov SK, Reznik VS. Triuracils – 1,3-Bis[ω-(N-methyluracil-1-yl)alkyl]thymines and Their 5,5′-Cyclic Counterparts. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700162] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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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: 452] [Impact Index Per Article: 26.6] [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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Tong J, Liu S, Zhou P, Zhang S, Li SZ. Quantitative structure spectroscopy relationships of carbon-13 nuclear magnetic resonance chemical shifts of steroids. J Mol Graph Model 2007; 26:86-92. [PMID: 17204441 DOI: 10.1016/j.jmgm.2006.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2006] [Revised: 09/27/2006] [Accepted: 09/27/2006] [Indexed: 11/20/2022]
Abstract
Quantitative structure spectroscopy relationships (QSSRs) are systematically studied for carbon-13 nuclear magnetic resonance ((13)C NMR) spectroscopic simulation of steroid compounds. Both the atomic electronegativity interaction vector (AEIV) and the atomic hybridization state index (AHSI) are used for the expression of local chemical microenvironment and atomic hybridization state of 4434 resonance carbon atoms in 203 steroid molecules. A multiple linear regression (MLR) model is built after screening some insignificant parameters with the stepwise multiple regression (SMR) technique. Correlation coefficients of the developed model are R(cum)(2)=0.9341 and Q(LOO)(2)=0.9336 for classical estimation of molecular modeling and the cross-validation with leave-one-out (LOO) procedures, respectively, primarily indicating that the MLR model has good modeling stability and prediction ability. Furthermore, the superior performance of the MLR model is tested by the leave-33%-out (L33%O) cross-validation method, where the mean correlation coefficients of three test sets are Q(2)=0.9310 and Q(ext)(2)=0.9196 for both internal and external sets. In conclusion, AEIV and AHSI descriptors can be used for estimating and predicting (13)C NMR chemical shifts of steroids.
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Affiliation(s)
- Jianbo Tong
- College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
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Figadère B, Hui X, Schmidt F, Akram Fakhfakh M, Franck X. Novel Highly Regioselective Syntheses of Unsymmetrical 2,3-Disubstituted Quinoxalines. HETEROCYCLES 2007. [DOI: 10.3987/com-06-s(k)19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Balandina AA, Mamedov VA, Khafizova EA, Latypov SK. Combined application of 2D NMR correlation methods and ab initio chemical shift calculations to the structure determination of new heterocyclic compounds. Russ Chem Bull 2006. [DOI: 10.1007/s11172-006-0580-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Balandina A, Saifina D, Mamedov V, Latypov S. Application of theoretically computed chemical shifts to structure determination of novel heterocyclic compounds. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Balandina A, Kalinin A, Mamedov V, Figadère B, Latypov S. Structure-NMR chemical shift relationships for novel functionalized derivatives of quinoxalines. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2005; 43:816-28. [PMID: 16041772 DOI: 10.1002/mrc.1612] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
(1)H, (13)C and (15)N NMR chemical shifts for a variety of novel quinoxalines were determined by different 2D methods and were calculated using the GIAO DFT approach. Comparison with experimental data shows good correlations in the case of (1)H, (13)C and (15)N chemical shifts. Different combinations of basis sets were tested. In non-polar solvents quinoxalines exist as dimers owing to strong hydrogen bonding. Calculations for dimers improve the correlation between experiment and theory. Additive empirical methods for estimating chemical shifts have drawbacks and have to be used with a great care for this type of compound.
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Affiliation(s)
- Alsu Balandina
- Institute of Organic and Physical Chemistry, Arbuzov str. 8, Kazan 420008, Russia
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