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El Mohammad S, Proux O, Aguilar A, Hazemann JL, Legens C, Chizallet C, Larmier K. Elucidation of Metal-Sugar Complexes: When Tungstate Combines with d-Mannose. Inorg Chem 2023; 62:7545-7556. [PMID: 37130307 DOI: 10.1021/acs.inorgchem.3c00911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The control of metal-sugar complexes speciation in solution is crucial in an energy transition context. Herein, the formation of tungstate-mannose complexes is unraveled in aqueous solution using a multitechnique experimental and theoretical approach. 13C nuclear magnetic resonance (NMR), as well as 13C-1H and 1H-1H correlation spectra, analyzed in the light of coordination-induced shift method and conformation analysis, were employed to characterize the structure of the sugar involved in the complexes. X-ray absorption near edge structure spectroscopy was performed to provide relevant information about the metal electronic and coordination environment. The calculation of 13C NMR chemical shifts for a series of tungstate-mannose complexes using density functional theory (DFT) is a key to identify the appropriate structure among several candidates. Furthermore, a parametric study based on several relevant parameters, namely, pH and tungstate concentration, was carried out to look over the change of the nature and concentrations of the complexes. Two series of complexes were detected, in which the metallic core is either in a ditungstate or a monotungstate form. With respect to previous proposals, we identify two new species. Dinuclear complexes involve both α- and β-furanose forms chelating the metallic center in a tetradentate fashion. A hydrate form chelating a ditungstate core is also revealed. One monotungstate complex appears at high pH, in which a tetrahedral tungstate center is bound to α-mannofuranose through a monodentate site at the second deprotonated hydroxyl group. This unequalled level of knowledge opens the door to structure-reactivity relationships.
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Affiliation(s)
- Sabah El Mohammad
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, Solaize 69360, France
| | - Olivier Proux
- OSUG, UAR 832 CNRS, Université Grenoble Alpes, Grenoble 38041, France
| | - Antonio Aguilar
- ICMG, UAR 2607 CNRS, Université Grenoble Alpes, Grenoble 38041, France
| | - Jean-Louis Hazemann
- Institut Néel, CNRS, Université Grenoble Alpes, 25 Avenue des Martyrs, Grenoble 38042, France
| | - Christèle Legens
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, Solaize 69360, France
| | - Céline Chizallet
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, Solaize 69360, France
| | - Kim Larmier
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, Solaize 69360, France
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Ukhanev SA, Fedorov SV, Krivdin LB. Stereochemical dependence of substituent γ-effects in the 19 F NMR shielding constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:869-876. [PMID: 35468229 DOI: 10.1002/mrc.5275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/07/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
The substituent α-, β-, and γ-effects of the elements of the second and third periods on 19 F NMR chemical shifts are evaluated including the establishment of stereochemical dependence of γ-effect, the latter particularly important in stereochemical studies of fluorine-containing compounds. Benchmark calculations performed for a series of 32 simple inorganic fluorine-containing molecules demonstrated a markedly good correlation between calculated and experimental fluorine chemical shifts characterized by a mean absolute error of 22.5 ppm in the range of about 900 ppm, which corresponds to a 2.5% error in the percentage terms.
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Affiliation(s)
- Stepan A Ukhanev
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Sergei V Fedorov
- 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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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: 2] [Impact Index Per Article: 1.0] [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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Semenov VA, Krivdin LB. Computational NMR of natural products: On the way to super large molecules exemplified with alasmontamine A. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:515-524. [PMID: 35137439 DOI: 10.1002/mrc.5256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts of a tetrakis monoterpene indole alkaloid alasmontamine A with a molecular formula of C84 H91 N8 O12 have been calculated at the PBE0/pcSseg-2//pcseg-2 level of theory on M06-2X/aug-cc-pVDZ geometry. In the course of the preliminary conformational search, six true minimum energy conformers were identified that can contribute to the actual conformation of this huge alkaloid. Calculated chemical shifts generally demonstrated a good agreement with available experimental data characterized with a corrected mean absolute error of 0.10 ppm for the range of about 7 ppm for protons and 1.1 ppm for the range of about 160 ppm for carbons.
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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
| | - 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, Krivdin LB. Combined Computational NMR and Molecular Docking Scrutiny of Potential Natural SARS-CoV-2 M pro Inhibitors. J Phys Chem B 2022; 126:2173-2187. [PMID: 35271277 PMCID: PMC8936056 DOI: 10.1021/acs.jpcb.1c10489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/25/2022] [Indexed: 11/30/2022]
Abstract
In continuation of the search for potential drugs that inhibit the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in this work, a combined approach based on the modeling of NMR chemical shifts and molecular docking is suggested to identify the possible suppressors of the main protease of this virus among a number of natural products of diverse nature. Primarily, with the aid of an artificial neural network, the problem of the reliable determination of the stereochemical structure of a number of studied compounds was solved. Complementary to the main goal of this study, theoretical modeling of NMR spectral parameters made it feasible to perform a number of signal reassignments together with introducing some missing NMR data. Finally, molecular docking formalism was applied to the analysis of several natural products that could be chosen as prospective candidates for the role of potential inhibitors of the main protease. The results of this study are believed to assist in further research aimed at the development of specific drugs based on the natural products against COVID-19.
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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
| | - 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, Krivdin LB. Computational NMR of natural products. RUSSIAN CHEMICAL REVIEWS 2022. [DOI: 10.1070/rcr5027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Pierens GK. A New Metric for Evaluating DFT Calculated Proton and Carbon Chemical Shifts of Natural Products and Organic Compounds. Chemphyschem 2021; 22:2207-2214. [PMID: 34546658 DOI: 10.1002/cphc.202100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/01/2021] [Indexed: 11/07/2022]
Abstract
The calculation of DFT (density functional theory) chemical shifts have become an important technique for the verification of a proposed structure. An easily calculated metric developed for proton and carbon chemical shifts of natural products and organic compounds, the calculated chemical shift index (CCSI), has been developed, which uses the deviation of each pair of calculated and experimental chemical shifts. The mean absolute deviation (MAD), which is commonly used as the goodness of fit metric for DFT calculated chemical shifts, can conceal large deviations in the calculated data. A classification strategy is also proposed for the CCSI to highlight when further assessment of the NMR data is required.
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Affiliation(s)
- Gregory K Pierens
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, 4072, Australia
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Kurutos A, Kamounah FS, Dobrikov GM, Pittelkow M, Sauer SPA, Hansen PE. Azo-hydrazone molecular switches: Synthesis and NMR conformational investigation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:1116-1125. [PMID: 33860564 DOI: 10.1002/mrc.5164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/05/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
A series of five intramolecularly hydrogen-bonded arylhydrazone (aryl = phenol, p-nitrophenol, anisole, quinoline) derived molecular switches have been synthesized and characterized by NMR and HRMS techniques. It was found that the compounds exist as different isomers in solution. An investigation of both conformational and/or configurational changes of the azo-hydrazone compounds was carried out by 1D 1 H- and 13 C- spectra, 2D NOESY, COSY, HSQC, and HMBC techniques. It was found that these stimuli-responsive molecular switches exist mainly in the E form by intramolecularly hydrogen bonded between NH and the pyridine nitrogen at equilibrium. Deprotonation of the neutral E form yields the E' deprotonated isomer. Prediction of 13 C-NMR chemical shifts was achieved by DFT quantum mechanical calculations. Anions have traditionally been difficult to calculate correctly, so calculations of the anion using different functionals, basis sets, and solvent effects are also included. Deuterium isotope effects on the 13 C-NMR chemical shifts were employed in the assignments and furthermore utilized as indicators of intramolecular hydrogen bonding. Studies in various organic solvents including CDCl3 , CD3 CN, and DMSO-d6 were also performed aiming to monitor dynamic changes over several days. The effect of the hydrogen bonded solvents leads to Z forms.
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Affiliation(s)
- Atanas Kurutos
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev str., bl. 9, Sofia, 1113, Bulgaria
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø, DK-2100, Denmark
| | - Georgi M Dobrikov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev str., bl. 9, Sofia, 1113, Bulgaria
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø, DK-2100, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø, DK-2100, Denmark
| | - Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Roskilde, DK-4000, Denmark
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Semenov VA, Krivdin LB. Computational 1 H and 13 C NMR of the trimeric monoterpenoid indole alkaloid strychnohexamine: Selected spectral updates. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:691-700. [PMID: 33386651 DOI: 10.1002/mrc.5129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Very large trimeric indole alkaloid strychnohexamine, with empirical formula C59 H60 N6 O (66 second-row atoms and 60 protons), has been subjected to the state-of-the-art computation of the 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts of its configurational isomers at each of the 14 asymmetric centers. Several spectral reassignments and corrections of 1 H and 13 C NMR spectra of this alkaloid were suggested based on the PBE0/pcSseg-2//pcseg-2 calculation of its NMR chemical shifts. Thus, all pairs of diastereotopic protons were assigned together with four aromatic carbon resonances of C-9 and C-11, C-9″, and C-11″. In addition, the unassigned chemical shifts of carbon C-23″ and proton at C-3' in, accordingly, 13 C and 1 H NMR spectra were predicted.
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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
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Elyashberg M, Argyropoulos D. Computer Assisted Structure Elucidation (CASE): Current and future perspectives. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:669-690. [PMID: 33197069 DOI: 10.1002/mrc.5115] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/31/2020] [Accepted: 11/08/2020] [Indexed: 06/11/2023]
Abstract
The first efforts for the development of methods for Computer-Assisted Structure Elucidation (CASE) were published more than 50 years ago. CASE expert systems based on one-dimensional (1D) and two-dimensional (2D) Nuclear Magnetic Resonance (NMR) data have matured considerably by now. The structures of a great number of complex natural products have been elucidated and/or revised using such programs. In this article, we discuss the most likely directions in which CASE will evolve. We act on the premise that a synergistic interaction exists between CASE, new NMR experiments, and methods of computational chemistry, which are continuously being improved. The new developments in NMR experiments (long-range correlation experiments, pure-shift methods, coupling constants measurement and prediction, residual dipolar couplings [RDCs]), and residual chemical shift anisotropies [RCSAs], evolution of density functional theory (DFT), and machine learning algorithms will have an influence on CASE systems and vice versa. This is true also for new techniques for chemical analysis (Atomic Force Microscopy [AFM], "crystalline sponge" X-ray analysis, and micro-Electron Diffraction [micro-ED]), which will be used in combination with expert systems. We foresee that CASE will be utilized widely and become a routine tool for NMR spectroscopists and analysts in academic and industrial laboratories. We believe that the "golden age" of CASE is still in the future.
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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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Semenov VA, Krivdin LB. Computational 1H and 13C NMR of strychnobaillonine: On the way to larger molecules calculated at lower computational costs. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:108-116. [PMID: 33428225 DOI: 10.1002/mrc.5088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/27/2020] [Accepted: 08/13/2020] [Indexed: 06/12/2023]
Abstract
The 1H and 13C NMR chemical shifts of strychnobaillonine, a very large dimeric indole alkaloid, consisting of as many as 46 nonhydrogen atoms, were calculated with using the established earlier the most effective computational protocol, PBE0/pcSseg-2//pcseg-2. A very good result was achieved at this level, characterized by the root mean square deviation of only 0.14 ppm for protons and 2.4 ppm for carbons, which enabled the verification of the configurations of its all 13 asymmetrical centers. Essential deviations of the calculated and experimental 1H NMR spectrum of strychnobaillonine were established in several cases, which enabled the performance of some additional NMR assignments and reassignments of the originally proposed structure.
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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
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Fedorov SV, Krivdin LB. Computational Protocols for the 19F NMR Chemical Shifts. Part 1: Methodological Aspects. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2020.109625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Rusakov YY, Rusakova IL. What Most Affects the Accuracy of 125Te NMR Chemical Shift Calculations. J Phys Chem A 2020; 124:6714-6725. [DOI: 10.1021/acs.jpca.0c05780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yu. Yu. Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - I. L. Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
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