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Rusakov YY, Semenov VA, Rusakova IL. On the Efficiency of the Density Functional Theory (DFT)-Based Computational Protocol for 1H and 13C Nuclear Magnetic Resonance (NMR) Chemical Shifts of Natural Products: Studying the Accuracy of the pecS- n ( n = 1, 2) Basis Sets. Int J Mol Sci 2023; 24:14623. [PMID: 37834068 PMCID: PMC10572908 DOI: 10.3390/ijms241914623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The basis set issue has always been one of the most important factors of accuracy in the quantum chemical calculations of NMR chemical shifts. In a previous paper, we developed new pecS-n (n = 1, 2) basis sets purposed for the calculations of the NMR chemical shifts of the nuclei of the most popular NMR-active isotopes of 1-2 row elements and successfully approbated these on the DFT calculations of chemical shifts in a limited series of small molecules. In this paper, we demonstrate the performance of the pecS-n (n = 1, 2) basis sets on the calculations of as much as 713 1H and 767 13C chemical shifts of 23 biologically active natural products with complicated stereochemical structures, carried out using the GIAO-DFT(PBE0) approach. We also proposed new alternative contraction schemes for our basis sets characterized by less contraction depth of the p-shell. New contraction coefficients have been optimized with the property-energy consistent (PEC) method. The accuracies of the pecS-n (n = 1, 2) basis sets of both the original and newly contracted forms were assessed on massive benchmark calculations of proton and carbon chemical shifts of a vast variety of natural products. It was found that less contracted pecS-n (n = 1, 2) basis sets provide no noticeable improvement in accuracy. These calculations represent the most austere test of our basis sets as applied to routine calculations of the NMR chemical shifts of real-life compounds.
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Affiliation(s)
| | | | - Irina L. Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia; (Y.Y.R.); (V.A.S.)
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Larina LI, Albanov AI, Zelinskiy SN, Annenkov VV, Rusakova IL. Acrylamide derivatives: A dynamic nuclear magnetic resonance study. Magn Reson Chem 2023; 61:277-283. [PMID: 36606331 DOI: 10.1002/mrc.5331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Substituted acrylamides have found an extensive application in organic and medical chemistry; therefore, it is very important to get insight into their features such as electronic structure, spectral properties, and stereochemical transformations. A correct interpretation of the chemical behavior and biological activity of these heteroatomic systems is impossible without knowledge of the structure of stereodynamic forms and factors determining their relative stability. The structure and peculiarities of stereodynamic behavior of substituted acrylamides and their model compounds were studied by dynamic and multinuclear 1 H, 13 C, and 15 N nuclear magnetic resonance (NMR) spectroscopy in CDCl3 and DMSO-d6 solution. It has been established that acrylamides in solution are realized as Z- and E-isomers, with the E-rotamer being somewhat predominant. The obtained experimental values of the free activation energy of rotamers vary within 15-17 kcal/mol, depending on the stereochemical structure of the molecule. 15 N NMR spectroscopy is the most reliable and fastest method for determining the structural and stereochemical features of nitrogen-containing compounds.
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Affiliation(s)
- Lyudmila I Larina
- A.E. Favorsky Irkutsk Institute of Chemistry, Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Alexander I Albanov
- A.E. Favorsky Irkutsk Institute of Chemistry, Russian Academy of Sciences, Irkutsk, Russian Federation
| | | | - Vadim V Annenkov
- Limnological Institute, Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Irina L Rusakova
- A.E. Favorsky Irkutsk Institute of Chemistry, Russian Academy of Sciences, Irkutsk, Russian Federation
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Meneghetti F, Ferraboschi P, Grisenti P, Reza Elahi S, Mori M, Ciceri S. Crystallographic and NMR Investigation of Ergometrine and Methylergometrine, Two Alkaloids from Claviceps purpurea. Molecules 2020; 25:molecules25020331. [PMID: 31947568 PMCID: PMC7024318 DOI: 10.3390/molecules25020331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 11/16/2022]
Abstract
Ergometrine and methylergometrine are two alkaloids that are used as maleate salts for the prevention and control of postpartum hemorrhage. Although the two molecules have been known for a long time, few and discordant crystallographic and NMR spectroscopic data are available in the literature. With the aim of providing more conclusive data, we performed a careful NMR study for the complete assignment of the 1H, 13C, and 15N NMR signals of ergometrine, methylergometrine, and their maleate salts. This information allowed for a better definition of their conformational equilibria. In addition, the stereochemistry and the intermolecular interactions in the solid state of the two maleate salts were deeply investigated by means of single-crystal X-ray diffraction, showing the capability of these derivatives to act as both hydrogen-bond donors and acceptors, and evidencing a correlation between the number of intermolecular interactions and their different solubility.
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Affiliation(s)
- Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli, 25, 20133 Milano, Italy; (F.M.); (M.M.)
| | - Patrizia Ferraboschi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy; (P.F.); (S.R.E.)
| | - Paride Grisenti
- Chemical-Pharmaceutical Consulting and IP Management, Viale Giovanni da Cermenate 58, 20141 Milano, Italy;
| | - Shahrzad Reza Elahi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy; (P.F.); (S.R.E.)
| | - Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli, 25, 20133 Milano, Italy; (F.M.); (M.M.)
| | - Samuele Ciceri
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy; (P.F.); (S.R.E.)
- Correspondence: ; Tel.: +39-02-50316052
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Joubert V, Silvestre V, Lelièvre M, Ladroue V, Besacier F, Akoka S, Remaud GS. Position-specific 15 N isotope analysis in organic molecules: A high-precision 15 N NMR method to determine the intramolecular 15 N isotope composition and fractionation at natural abundance. Magn Reson Chem 2019; 57:1136-1142. [PMID: 31222922 DOI: 10.1002/mrc.4903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
The position-specific 15 N isotope content in organic molecules, at natural abundance, is for the first time determined by using a quantitative methodology based on 15 N Nuclear Magnetic Resonance (NMR) spectrometry. 15 N NMR spectra are obtained by using an adiabatic "Full-Spectrum" INEPT sequence in order to make possible 15 N NMR experiments with a high signal-to-noise ratio (>500), to reach a precision with a standard deviation below 1‰ (0.1%). This level of precision is required for observing small changes in 15 N content associated to 15 N isotope effects. As an illustration, the measurement of an isotopic enrichment factor ε for each 15 N isotopomer is presented for 1-methylimidazole induced during a separation process on a silica column. The precision expressed as the long-term repeatability of the methodology is good enough to evaluate small changes in the 15 N isotope contents for a given isotopomer. As observed for 13 C, inverse and normal 15 N isotope effects occur concomitantly, giving access to new information on the origin of the 15 N isotope effects, not detectable by other techniques such as isotope ratio measured by Mass Spectrometry for which bulk (average) values are obtained.
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Affiliation(s)
- Valentin Joubert
- EBSI Team, CEISAM, University of Nantes-CNRS UMR 6230, Nantes, France
| | | | - Maxime Lelièvre
- EBSI Team, CEISAM, University of Nantes-CNRS UMR 6230, Nantes, France
| | - Virginie Ladroue
- Laboratoire de Lyon, Institut National de Police Scientifique, Ecully, France
| | - Fabrice Besacier
- Laboratoire de Lyon, Institut National de Police Scientifique, Ecully, France
| | - Serge Akoka
- EBSI Team, CEISAM, University of Nantes-CNRS UMR 6230, Nantes, France
| | - Gérald S Remaud
- EBSI Team, CEISAM, University of Nantes-CNRS UMR 6230, Nantes, France
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Semenov VA, Samultsev DO, Krivdin LB. DFT computational schemes for 15 N NMR chemical shifts of the condensed nitrogen-containing heterocycles. Magn Reson Chem 2019; 57:346-358. [PMID: 30769377 DOI: 10.1002/mrc.4851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/08/2019] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
A systematic density functional theory (DFT) study of the accuracy factors (functionals, basis sets, and solvent effects) for the computation of 15 N NMR chemical shifts has been performed in the series of condensed nitrogen-containing heterocycles. The behavior of the most representative functionals was examined based on the benchmark calculations of 15 N NMR chemical shifts in the reference set of compounds. It was found that the best agreement with experiment was achieved with OLYP functional in combination with aug-pcS-3(N)//pc-2 locally dense basis set scheme providing mean absolute error of 5.2 ppm in the range of about 300 ppm. Taking into account solvent effects was performed within a general Tomasi's polarizable continuum model scheme. It was also found that computationally demanding supermolecular solvation model computations essentially improved some "difficult" cases, as was illustrated with phenanthroline dissolved in methanol. Based on the performed calculations, some 200 unknown 15 N NMR chemical shifts were predicted with a high level of confidence for about 50 real-life condensed nitrogen-containing heterocycles, which could serve as a practical guide in structural elucidation of this class of compounds.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Semenov VA, Samultsev DO, Krivdin LB. GIAO-DFT calculation of 15 N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects. Magn Reson Chem 2018; 56:727-739. [PMID: 29427330 DOI: 10.1002/mrc.4721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
15 N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated 15 N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
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Semenov VA, Samultsev DO, Krivdin LB. Substitution effects in the 15 N NMR chemical shifts of heterocyclic azines evaluated at the GIAO-DFT level. Magn Reson Chem 2018; 56:767-774. [PMID: 29504638 DOI: 10.1002/mrc.4731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
A systematic study of the accuracy factors for the computation of 15 N NMR chemical shifts in comparison with available experiment in the series of 72 diverse heterocyclic azines substituted with a classical series of substituents (CH3 , F, Cl, Br, NH2 , OCH3 , SCH3 , COCH3 , CONH2 , COOH, and CN) providing marked electronic σ- and π-electronic effects and strongly affecting 15 N NMR chemical shifts is performed. The best computational scheme for heterocyclic azines at the DFT level was found to be KT3/pcS-3//pc-2 (IEF-PCM). A vast amount of unknown 15 N NMR chemical shifts was predicted using the best computational protocol for substituted heterocyclic azines, especially for trizine, tetrazine, and pentazine where experimental 15 N NMR chemical shifts are almost totally unknown throughout the series. It was found that substitution effects in the classical series of substituents providing typical σ- and π-electronic effects followed the expected trends, as derived from the correlations of experimental and calculated 15 N NMR chemical shifts with Swain-Lupton's F and R constants.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - 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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Samultsev DO, Rusakov YY, Krivdin LB. On the long-range relativistic effects in the 15 N NMR chemical shifts of halogenated azines. Magn Reson Chem 2017; 55:990-995. [PMID: 28557069 DOI: 10.1002/mrc.4618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 06/07/2023]
Abstract
Long-range β- and γ-relativistic effects of halogens in 15 N NMR chemical shifts of 20 halogenated azines (pyridines, pyrimidines, pyrazines, and 1,3,5-triazines) are shown to be unessential for fluoro-, chloro-, and bromo-derivatives (1-2 ppm in average). However, for iodocontaining compounds, β- and γ-relativistic effects are important contributors to the accuracy of the 15 N calculation. Taking into account long-range relativistic effects slightly improves the agreement of calculation with experiment. Thus, mean average errors (MAE) of 15 N NMR chemical shifts of the title compounds calculated at the non-relativistic and full 4-component relativistic levels in gas phase are accordingly 7.8 and 5.5 ppm for the range of about 150 ppm. Taking into account solvent effects within the polarizable continuum model scheme marginally improves agreement of computational results with experiment decreasing MAEs from 7.8 to 7.4 ppm and from 5.5 to 5.3 ppm at the non-relativistic and relativistic levels, respectively. The best result (MAE: 5.3 ppm) is achieved at the 4-component relativistic level using Keal and Tozer's KT3 functional used in combination with Dyall's relativistic basis set dyall.av3z with taking into account solvent effects within the polarizable continuum solvation model. The long-range relativistic effects play a major role (of up to dozen of parts per million) in 15 N NMR chemical shifts of halogenated nitrogen-containing heterocycles, which is especially crucial for iodine derivatives. This effect should apparently be taken into account for practical purposes.
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Affiliation(s)
- Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Yury Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
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Samultsev DO, Semenov VA, Krivdin LB. On the accuracy factors and computational cost of the GIAO-DFT calculation of 15 N NMR chemical shifts of amides. Magn Reson Chem 2017; 55:1015-1021. [PMID: 28600816 DOI: 10.1002/mrc.4625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/04/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
The main factors affecting the accuracy and computational cost of Gauge-independent Atomic Orbital-density functional theory (GIAO-DFT) calculation of 15 N NMR chemical shifts in the benchmark series of 16 amides are considered. Among those are the choice of the DFT functional and basis set, solvent effects, internal reference conversion factor and applicability of the locally dense basis set (LDBS) scheme. Solvent effects are treated within the polarizable continuum model (PCM) scheme as well as at supermolecular level with solvent molecules considered in explicit way. The best result is found for Keal and Tozer's KT3 functional used in combination with Jensen's pcS-3 basis set with taking into account solvent effects within the polarizable continuum model. The proposed LDBS scheme implies pcS-3 on nitrogen and pc-2 elsewhere in the molecule. The resulting mean average error for the calculated 15 N NMR chemical shifts is about 6 ppm. The application of the LDBS approach tested in a series of 16 amides results in a dramatic decrease in computational cost (more than an order of magnitude in time scale) with insignificant loss of accuracy.
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Affiliation(s)
- Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 664033, Irkutsk, Russia
| | - Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 664033, Irkutsk, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 664033, Irkutsk, Russia
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Afonin AV, Vashchenko AV, Albanov AI, Nosyreva VV, Mal'kina AG, Trofimov BA. Study of spontaneous E/Z isomerization of bis[(Z)-cyanomethylidene]-diazapentacyclodienedicarboxylates by 1 H, 13 C, and 15 N NMR spectroscopy, X-ray, and quantum chemical calculation data. Magn Reson Chem 2017; 55:563-569. [PMID: 27859547 DOI: 10.1002/mrc.4551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/19/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
X-ray data show that the diethyl 6,13-bis[(Z)-cyanomethylidene]-5,5,14,14-tetramethyl-4,15-dioxa-7,12-diazapentacyclo[9.5.2.02,10 .03,7 .012,16 ]octadeca-8,17-diene-10,17-dicarboxylate is formed as the ZZ isomer and diastereomer with the (1R*,2R*,3R*,10S*,11R*,12R*,16R*) configuration. The 1 H, 13 C, and 15 N NMR data exhibit that on standing in chloroform-d solution, there is a spontaneous isomerization of this compound resulting in a thermodynamically stable mixture of the ZZ, ZE, EE, and EZ isomers with the same backbone. Using the 2D [1 H-1 H] COSY, [1 H-13 C] HSQC, and [1 H-13 C, 1 H-15 N] HMBC NMR techniques and quantum chemical calculations makes it possible a complete assignment of signals in the 1 H, 13 C, and 15 N NMR spectra of each of the isomers. Such isomerization does not occur for similar compounds with the more bulky substituents at the 1,3-oxazolidine rings. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Andrei V Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Alexander V Vashchenko
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Alexander I Albanov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Valentina V Nosyreva
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Anastasiya G Mal'kina
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Boris A Trofimov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Silva Elipe MV, Yoo C, Xia F, Simiens J, Crossley K, Huckins JR, Guo HX, Tedrow J, Wong-Moon K. Isolation and structure elucidation of unexpected in-process impurities during tetrazole ring formation of an investigational drug substance. Magn Reson Chem 2017; 55:253-262. [PMID: 26841697 DOI: 10.1002/mrc.4413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/16/2015] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
During the formation of a tetrazole ring on an investigational drug, two in-process impurities were detected and analyzed by LC-MS, which suggested that both impurities were drug-related with the same mass-to-charge ratio. To understand and control their formation, both impurities were isolated from the mother liquor of the reaction using a multi-step isolation procedure to obtain a sufficient amount for high-resolution mass spectrometry (HRMS) and NMR structural analysis. HRMS suggested a protonated mass of 577.32 Da for both impurities; however, MS fragmentation patterns provided limited information on their structures. NMR analysis indicated the presence on an additional NH functional group in both isolates with similar spatial and bond correlations to one of the dimethylcarbamoyl moieties and the corresponding aromatic ring. A phenyldimethylcarbamoylamino moiety was supported by the NMR and HRMS data and could be explained based on the 'Schmidt-like' reaction mechanism, which was an unexpected reaction pathway. Because the reaction conditions were fixed because of safety concerns, the crystallization protocol was redesigned to reduce the levels of these impurities significantly. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Chul Yoo
- Currently at St. Jude Medical, Sylmar, CA, USA
| | - Fang Xia
- Currently at ASK-Gene Pharma, Inc., Camarillo, CA, USA
| | - Jason Simiens
- Currently at Kythera Biopharmaceuticals, Westlake Village, CA, USA
| | - Kevin Crossley
- Department of Attribute Sciences, Amgen Inc., Thousand Oaks, CA, USA
| | - John R Huckins
- Department of Attribute Sciences, Amgen Inc., Thousand Oaks, CA, USA
| | - Hong-Xun Guo
- Currently at Gilead Sciences, Foster City, CA, USA
| | - Jason Tedrow
- Department of Attribute Sciences, Amgen Inc., Thousand Oaks, CA, USA
| | - Kirby Wong-Moon
- Currently at Kythera Biopharmaceuticals, Westlake Village, CA, USA
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Semenov VA, Samultsev DO, Rulev AY, Krivdin LB. Theoretical and experimental (15)N NMR study of enamine-imine tautomerism of 4-trifluoromethyl[b]benzo-1,4-diazepine system. Magn Reson Chem 2015; 53:1031-1034. [PMID: 26290420 DOI: 10.1002/mrc.4296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 06/04/2023]
Abstract
The tautomeric structure of 4-trifluoromethyl[b]benzo-1,4-diazepine system in solution has been evaluated by means of the calculation of (15)N NMR chemical shifts of individual tautomers in comparison with the averaged experimental shifts to show that the enamine-imine equilibrium is entirely shifted toward the imine form. The adequacy of the theoretical level used for the computation of (15)N NMR chemical shifts in this case has been verified based on the benchmark calculations in the series of the push-pull and captodative enamines together with related azomethynes, which demonstrated a good to excellent agreement with experiment.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Alexander Yu Rulev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - 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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Semenov VA, Samultsev DO, Krivdin LB. Theoretical and experimental study of 15N NMR protonation shifts. Magn Reson Chem 2015; 53:433-441. [PMID: 25891386 DOI: 10.1002/mrc.4231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/22/2015] [Accepted: 02/05/2015] [Indexed: 06/04/2023]
Abstract
A combined theoretical and experimental study revealed that the nature of the upfield (shielding) protonation effect in 15N NMR originates in the change of the contribution of the sp(2)-hybridized nitrogen lone pair on protonation resulting in a marked shielding of nitrogen of about 100 ppm. On the contrary, for amine-type nitrogen, protonation of the nitrogen lone pair results in the deshielding protonation effect of about 25 ppm, so that the total deshielding protonation effect of about 10 ppm is due to the interplay of the contributions of adjacent natural bond orbitals. A versatile computational scheme for the calculation of 15N NMR chemical shifts of protonated nitrogen species and their neutral precursors is proposed at the density functional theory level taking into account solvent effects within the supermolecule solvation model.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, Irkutsk Oblast, 664033, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, Irkutsk Oblast, 664033, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, Irkutsk Oblast, 664033, Russia
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Cheatham S, Kline M, Kupče E. Exploiting natural abundance 13C-15N coupling as a method for identification of nitrogen heterocycles: practical use of the HCNMBC sequence. Magn Reson Chem 2015; 53:363-368. [PMID: 25594305 DOI: 10.1002/mrc.4205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 06/04/2023]
Abstract
In this paper, we detail the results of (1)H-(15)N correlation data obtained via (13)C-(15)N coupling at natural abundance on a number of classes of azoles including pyrazoles, imidazoles and triazoles. The experiment produces data that is highly complementary to direct (1)H-(15)N HMBC type correlations in that it can provide (15)N chemical shift data for nitrogen that may not show up in the HMBC. This is particularly advantageous in the triazoles where (15)N chemical shift can be diagnostic of regiochemistry. Because of the consistency in JCN values among the azoles, the experiment produces distinctive correlation patterns that can be used for identification of regiochemistry. The experiment can also be used to directly measure (13)C-(15)N coupling constants.
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15
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Semenov VA, Samultsev DO, Krivdin LB. Solvent effects in the GIAO-DFT calculations of the 15N NMR chemical shifts of azoles and azines. Magn Reson Chem 2014; 52:686-693. [PMID: 25102971 DOI: 10.1002/mrc.4119] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/30/2014] [Accepted: 07/08/2014] [Indexed: 06/03/2023]
Abstract
The calculation of (15)N NMR chemical shifts of 27 azoles and azines in 10 different solvents each has been carried out at the gauge including atomic orbitals density functional theory level in gas phase and applying the integral equation formalism polarizable continuum model (IEF-PCM) and supermolecule solvation models to account for solvent effects. In the calculation of (15)N NMR, chemical shifts of the nitrogen-containing heterocycles dissolved in nonpolar and polar aprotic solvents, taking into account solvent effect is sufficient within the IEF-PCM scheme, whereas for polar protic solvents with large dielectric constants, the use of supermolecule solvation model is recommended. A good agreement between calculated 460 values of (15)N NMR chemical shifts and experiment is found with the IEF-PCM scheme characterized by MAE of 7.1 ppm in the range of more than 300 ppm (about 2%). The best result is achieved with the supermolecule solvation model performing slightly better (MAE 6.5 ppm).
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Affiliation(s)
- Valentin A Semenov
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Favorsky St. 1, 664033, Irkutsk, Russia
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16
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Pierens GK, Venkatachalam TK, Reutens D. A comparative study between para-aminophenyl and ortho-aminophenyl benzothiazoles using NMR and DFT calculations. Magn Reson Chem 2014; 52:453-459. [PMID: 24890025 DOI: 10.1002/mrc.4088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/11/2014] [Accepted: 05/15/2014] [Indexed: 06/03/2023]
Abstract
Ortho-substituted and para-substituted aminophenyl benzothiazoles were synthesised and characterised using NMR spectroscopy. A comparison of the proton chemical shift values reveals significant differences in the observed chemical shift values for the NH protons indicating the presence of a hydrogen bond in all ortho-substituted compounds as compared to the para compounds. The presence of intramolecular hydrogen bond in the ortho amino substituted aminophenyl benzothiazole forces the molecule to be planar which may be an additional advantage in developing these compounds as Alzheimer's imaging agent because the binding to amyloid fibrils prefers planar compounds. The splitting pattern of the methylene proton next to the amino group also showed significant coupling to the amino proton consistent with the notion of the existence of slow exchange and hydrogen bond in the ortho-substituted compounds. This is further verified by density functional theory calculations which yielded a near planar low energy conformer for all the o-aminophenyl benzothiazoles and displayed a hydrogen bond from the amine proton to the nitrogen of the thiazole ring. A detailed analysis of the (1)H, (13)C and (15)N NMR chemical shifts and density functional theory calculated structures of the compounds are described.
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Affiliation(s)
- G K Pierens
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
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17
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Samultsev DO, Semenov VA, Krivdin LB. On the accuracy of the GIAO-DFT calculation of 15N NMR chemical shifts of the nitrogen-containing heterocycles--a gateway to better agreement with experiment at lower computational cost. Magn Reson Chem 2014; 52:222-230. [PMID: 24573615 DOI: 10.1002/mrc.4055] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 01/21/2014] [Accepted: 01/31/2014] [Indexed: 06/03/2023]
Abstract
The main factors affecting the accuracy and computational cost of the gauge-independent atomic orbital density functional theory (GIAO-DFT) calculation of (15)N NMR chemical shifts in the representative series of key nitrogen-containing heterocycles--azoles and azines--have been systematically analyzed. In the calculation of (15)N NMR chemical shifts, the best result has been achieved with the KT3 functional used in combination with Jensen's pcS-3 basis set (GIAO-DFT-KT3/pcS-3) resulting in the value of mean absolute error as small as 5 ppm for a range exceeding 270 ppm in a benchmark series of 23 compounds with an overall number of 41 different (15)N NMR chemical shifts. Another essential finding is that basically, the application of the locally dense basis set approach is justified in the calculation of (15)N NMR chemical shifts within the 3-4 ppm error that results in a dramatic decrease in computational cost. Based on the present data, we recommend GIAO-DFT-KT3/pcS-3//pc-2 as one of the most effective locally dense basis set schemes for the calculation of (15)N NMR chemical shifts.
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Affiliation(s)
- Dmitry O Samultsev
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Favorsky St. 1, 664033, Irkutsk, Russia
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Egawa Y, Miki R, Seki T. Colorimetric Sugar Sensing Using Boronic Acid-Substituted Azobenzenes. Materials (Basel) 2014; 7:1201-1220. [PMID: 28788510 PMCID: PMC5453098 DOI: 10.3390/ma7021201] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 01/13/2014] [Accepted: 01/28/2014] [Indexed: 01/18/2023]
Abstract
In association with increasing diabetes prevalence, it is desirable to develop new glucose sensing systems with low cost, ease of use, high stability and good portability. Boronic acid is one of the potential candidates for a future alternative to enzyme-based glucose sensors. Boronic acid derivatives have been widely used for the sugar recognition motif, because boronic acids bind adjacent diols to form cyclic boronate esters. In order to develop colorimetric sugar sensors, boronic acid-conjugated azobenzenes have been synthesized. There are several types of boronic acid azobenzenes, and their characteristics tend to rely on the substitute position of the boronic acid moiety. For example, o-substitution of boronic acid to the azo group gives the advantage of a significant color change upon sugar addition. Nitrogen-15 Nuclear Magnetic Resonance (NMR) studies clearly show a signaling mechanism based on the formation and cleavage of the B-N dative bond between boronic acid and azo moieties in the dye. Some boronic acid-substituted azobenzenes were attached to a polymer or utilized for supramolecular chemistry to produce glucose-selective binding, in which two boronic acid moieties cooperatively bind one glucose molecule. In addition, boronic acid-substituted azobenzenes have been applied not only for glucose monitoring, but also for the sensing of glycated hemoglobin and dopamine.
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Affiliation(s)
- Yuya Egawa
- Faculty of Pharmaceutical Sciences, Josai University, Keyakidai, Sakado, Saitama 350-0295, Japan.
| | - Ryotaro Miki
- Faculty of Pharmaceutical Sciences, Josai University, Keyakidai, Sakado, Saitama 350-0295, Japan.
| | - Toshinobu Seki
- Faculty of Pharmaceutical Sciences, Josai University, Keyakidai, Sakado, Saitama 350-0295, Japan.
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Girreser U, Bluhm U, Clement B, Heber D. 1H, 13C and 15N NMR spectral analysis of substituted 1,2,3,4-tetrahydro-pyrido[1,2-a]pyrimidines. Magn Reson Chem 2013; 51:714-721. [PMID: 23996213 DOI: 10.1002/mrc.4005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/05/2013] [Accepted: 08/09/2013] [Indexed: 06/02/2023]
Abstract
The NMR spectroscopic data of a series of thirty-four 3-acylpyrido[1,2-a]pyrimidinium salts are analyzed, which were prepared as either perchlorates or chlorides. Methyl group substituted 3-aroyltetrahydropyrido[1,2-a]pyrimidines with the methyl substituent in positions 6, 8 and 9 as well as both in positions 6 and 8 were investigated bearing various aroyl substituents. Unequivocal assignment of all resonances was achieved via two-dimensional (1)H,(1)H-COSY measurements, (1)H,(13)C and (1)H,(15)N HSQC as well as HMBC experiments, and important diagnostic CH and NH couplings in the heteroaromatic ring system are evaluated. The influence of the methyl substituents was analyzed on the proton, carbon and nitrogen shifts. A significant effect of the counter ion on some chemical shifts of the nuclei under discussion of the pyridopyrimidines is found, allowing the indirect detection of the anion, which is confirmed by direct measurement of the (35)Cl nucleus of the perchlorates.
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Affiliation(s)
- Ulrich Girreser
- Pharmaceutical Institute, Department of Pharmaceutical Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118, Kiel, Germany
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Chapyshev SV, Ushakov EN, Chernyak AV. 15N NMR spectra and reactivity of 2,4,6-triazidopyridines, 2,4,6-triazidopyrimidine and 2,4,6-triazido-s-triazine. Magn Reson Chem 2013; 51:562-568. [PMID: 23877844 DOI: 10.1002/mrc.3987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/11/2013] [Accepted: 06/25/2013] [Indexed: 06/02/2023]
Abstract
2,4,6-Triazido-s-triazine, 2,4,6-triazidopyrimidine and six different 2,4,6-triazidopyridines were studied by (15)N NMR spectroscopy. The assignment of signals in the spectra was performed using the gauge-independent atomic orbital (GIAO)-Tao-Perdew-Staroverov-Scuseria exchange-correlation functional (TPSS)h/6-311+G(d,p) calculations on the M06-2X/6-311+G(d,p) optimized molecular geometries. The Truhlar and coworkers' continuum solvation model called SMD was applied to treat solvent effects. With this approach, the root mean square error in estimations of the (15)N chemical shifts for the azido groups was just 1.9 ppm. It was shown that the different reactivity of the α- and γ-azido groups in pyridines correlates well with the chemical shifts of the Nα signals of these groups. Of two nonequivalent azido groups of azines, the azido group with the most shielded Nα signal is the most electron-deficient and reactive toward electron-rich reagents. By contrast, the azido group of azines with the most deshielded Nα signal is the most reactive toward electron-poor reagents.
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Affiliation(s)
- Sergei V Chapyshev
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, 142432, Chernogolovka, Moscow Region, Russian Federation.
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