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Krivdin LB. Liquid-phase NMR of asphaltenes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:670-685. [PMID: 38807559 DOI: 10.1002/mrc.5454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024]
Abstract
The present review focuses on the most recent advances in liquid-phase NMR of asphaltenes, leaving apart an overwhelming amount of publications dealing with solid-state NMR investigations in this field. Owing to the complexity of the coal-derived products, and in particular, asphaltenes, their 1H and 13C NMR spectra consist of a number of overlapping signals belonging to different hydrocarbon types. Comprehensive studies of asphaltenes by means of NMR reveal the characteristic functional groups of their fractions together with the spectral regions in which they resonate. NMR studies of asphaltenes provide a straightforward guideline for their chemical composition and that of the related coal-derived products.
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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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2
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Krivdin LB. 17 O nuclear magnetic resonance: Recent advances and applications. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:507-529. [PMID: 37449419 DOI: 10.1002/mrc.5378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
The present review is focused on the most recent achievements in the application of liquid phase 17 O nuclear magnetic resonance (NMR) to inorganic, organic, and biochemical molecules focusing on their structure, conformations, and (bio)chemical behavior. The review is composed of four basic parts, namely, (1) simple molecules; (2) water and hydrogen bonding; (3) metal oxides, clusters, and complexes; and (4) biological molecules. Experimental 17 O NMR chemical shifts are thoroughly tabulated. They span a range of as much as almost 650 ppm (from -35.6 to +610.0 ppm) for inorganic and organic molecules, whereas this range is much wider for biological species being of about 1350 ppm (from -12 to +1332 ppm), and in the case of hemoproteins and heme-model compounds, isotropic chemical shifts of up to 2500 ppm were observed. The general prospects and caveats in the modern development of the liquid phase 17 O NMR in chemistry and biochemistry are critically discussed and briefly outlined in view of their future applications.
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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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3
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Bugaj-Zarębska M, Jaźwiński J. Properties of 3-fluoroprop-2-enoic acids, chemical shifts and indirect spin-spin coupling constants: A DFT study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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4
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Ukhanev SA, Fedorov SV, Krivdin LB. Computational 19 F NMR of trifluoromethyl derivatives of alkenes, pyrimidines, and indenes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:306-317. [PMID: 36740363 DOI: 10.1002/mrc.5335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
The 19 F NMR chemical shifts of 13 trifluoromethyl derivatives of alkenes, pyrimidines, and indenes were calculated at the DFT level using the BhandHLYP, BHandH, PBE, PBE0, O3LYP, B3LYP, KT2, and KT3 functionals in combination with the pcS-2 basis set. Best result was documented for the BHandHLYP functional: The mean absolute error (MAE) of 0.66 ppm for the scaled values was achieved for the range of about 20 ppm. Solvent, vibrational, and relativistic corrections were found to be rather small, especially when taken in combination, generally demonstrating a slight decrease in the difference between calculated and experimental fluorine chemical shifts. As a measure of the practical importance of these compounds, one should recall that the growing number of life science products that contain trifluoromethyl groups provides a continuing driving force for the development of an effective methodology that enables both regio- and stereoselective introduction of trifluoromethyl groups into both aliphatic and aromatic systems.
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Affiliation(s)
- Stepan A Ukhanev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Sergei V Fedorov
- 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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5
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Krivdin LB. Tritium NMR: A compilation of data and a practical guide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:195-247. [PMID: 36593685 DOI: 10.1002/mrc.5329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The present review is focused on experimental methods and structural applications of tritium NMR. It consists of five parts covering accordingly, introduction, brief overview, early (based on the papers appearing before 2000), more recent (based on the papers appeared in the interim of 2000 to 2015), and recent (based on the papers that appeared after 2015) reports. A special interest in this review is focused on practical aspects of tritium NMR spectroscopy, which is thoroughly illustrated by its numerous applications in chemistry and biochemistry.
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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. Recent advances in the liquid-phase 6,7 Li nuclear magnetic resonance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:138-161. [PMID: 36330776 DOI: 10.1002/mrc.5323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
The present review is focused on experimental methods and structural applications, including computational aspects, of classical lithium liquid-phase nuclear magnetic resonance (NMR). It consists of four parts covering accordingly a brief overview, early experimental reports (papers of up to about 2015) and more recent (papers appearing in the interim of about 2015 until 2022) results, together with very few but highly prospective computational results.
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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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7
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Ukhanev SA, Fedorov SV, Rusakov YY, Rusakova IL, Krivdin LB. Computational protocols for the 19F NMR parameters. Part 2: Fluorobenzenes. J Fluor Chem 2023. [DOI: 10.1016/j.jfluchem.2023.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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8
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de Andrade Souza L, Moreira DR, Ricardo NMPS, Maier ME, Filho PRCFR, Luna FMT, Petzhold CL. Esters from castor oil functionalized with aromatic amines as a potential lubricant. J AM OIL CHEM SOC 2023. [DOI: 10.1002/aocs.12648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Laura de Andrade Souza
- Chemistry Institute Federal University of Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
- Infrastructure Department Federal Institute of Rio Grande do Sul Farroupilha Rio Grande do Sul Brazil
| | - Denise Ramos Moreira
- Laboratory of Polymers and Materials Innovation, Department of Organic and Inorganic Chemistry, Sciences Center Federal University of Ceará Fortaleza CE Brazil
| | - Nágila Maria Pontes Silva Ricardo
- Laboratory of Polymers and Materials Innovation, Department of Organic and Inorganic Chemistry, Sciences Center Federal University of Ceará Fortaleza CE Brazil
| | | | | | - Francisco Murilo Tavares Luna
- Lubricants Research Center, Department of Chemical Engineering Technology Center, Pici Campus, Federal University of Ceará Fortaleza CE Brazil
| | - Cesar Liberato Petzhold
- Chemistry Institute Federal University of Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
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Lin F, Zhang M, Mao S, Zhang J, Wang K, Luo J, Chen X, Wang B, Wei Y. The Influence of Metal Lithium and Alkyl Chain in the Nucleating Agent Lauroyloxy-Substituted Aryl Aluminum Phosphate on the Crystallization and Optical Properties for iPP. Polymers (Basel) 2022; 14:polym14173637. [PMID: 36080711 PMCID: PMC9460898 DOI: 10.3390/polym14173637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, a kind of aryl phosphate salt nucleating agent (APAl-12C) was synthesized, which was replaced in the hydroxyl group on the aluminum hydroxy bis [2,2′-methylene-bis(4,6-di-tert-butylphenyl) phosphate] (APAl-OH) by lauroyloxy, which could improve the dispersion between the nucleating agent and the iPP matrix and reduce the migration potential of the nucleating agent in the iPP matrix by increasing the molecular weight. The structure of the nucleating agent APAl-12C was analyzed by fourier infrared spectroscopy (FT-IR ) and 1H NMR. The differential scanning calorimeter (DSC) results indicated that the addition of APAl-OH or APAl-12C alone was inferior to the commercial nucleating agent NA-21 (compounds of APAl-OH and Lithium laurate) in terms of the crystallization behavior, which may be due to the importance of metal Li in the crystallization property. Thus, the iPP/A12C-Li composites were prepared with APAl-12C, lithium laurate (lilaurate) and the iPP matrix. The crystallization behavior, morphology, optical and mechanical properties for the iPP/A12C-Li composites were systematically studied and compared with that of the iPP/NA-21 composite. Among the iPP/A12C-Li composites with the addition of 0.5 wt%, APAl-12C/Lilaurate had the fastest crystallization rate and reduced the haze value of the neat iPP from 36.03% to 9.89% without changing the clarity, which was better than that of the iPP/NA-21 composite. This was due to the weakening of the polarity of the APAl-12C after lauroyloxy substitution and better dispersion in the iPP matrix, resulting in a significant improvement in the optical properties.
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Affiliation(s)
- Fuhua Lin
- School of Materials Science and Engineering, Taiyuan University of Science and Technology, Taiyuan 030024, China
- Shanxi Provincial Institute of Chemical Industry (Co., Ltd.), Jinzhong 030600, China
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Mi Zhang
- Shanxi Provincial Institute of Chemical Industry (Co., Ltd.), Jinzhong 030600, China
| | - Shuangdan Mao
- School of Chemical Engineering and Technology, Taiyuan University of Science and Technology, Taiyuan 030024, China
| | - Jianjun Zhang
- Shanxi Provincial Institute of Chemical Industry (Co., Ltd.), Jinzhong 030600, China
| | - Kezhi Wang
- Shanxi Provincial Institute of Chemical Industry (Co., Ltd.), Jinzhong 030600, China
| | - Jun Luo
- Guangzhou Fibre Product Testing and Research Institute, Guangzhou 510220, China
| | - Xinde Chen
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Bo Wang
- School of Chemical Engineering and Technology, Taiyuan University of Science and Technology, Taiyuan 030024, China
- Correspondence: (B.W.); (Y.W.); Tel.: +86-351-6938220 (B.W.)
| | - Yinghui Wei
- School of Materials Science and Engineering, Taiyuan University of Science and Technology, Taiyuan 030024, China
- Correspondence: (B.W.); (Y.W.); Tel.: +86-351-6938220 (B.W.)
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Ukhanev SA, Fedorov SV, Rusakov YY, Rusakova IL, Krivdin LB. Fluorine spin-spin coupling constants of pentafluorobenzene revisited at the ab initio correlated levels. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:901-914. [PMID: 35470458 DOI: 10.1002/mrc.5276] [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: 02/09/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
All possible spin-spin coupling constants, 19 F-19 F, 19 F-13 C, and 19 F-1 H, of pentafluorobenzene were calculated at five different levels of theory, HF, DFT, SOPPA (CCSD), CCSD, and the SOPPA (CCSD)-based composite scheme with taking into account solvent, vibrational, relativistic, and correlation corrections. Most corrections were next to negligible for the long-range couplings but quite essential for the one-bond carbon-fluorine coupling constants. Hartree-Fock calculations were found to be entirely unreliable, while DFT results were comparable in accuracy with the data obtained using the wave function-based methods.
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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
| | - Yuriy Y Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Irina L Rusakova
- 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: 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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12
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Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantum chemical methods for the calculation of indirect NMR spin–spin coupling constants and chemical shifts are always in progress. They never stay the same due to permanently developing computational facilities, which open new perspectives and create new challenges every now and then. This review starts from the fundamentals of the nonrelativistic and relativistic theory of nuclear magnetic resonance parameters, and gradually moves towards the discussion of the most popular common and newly developed methodologies for quantum chemical modeling of NMR spectra.
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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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Krivdin LB. Computational NMR of charged systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:8-79. [PMID: 34355823 DOI: 10.1002/mrc.5201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
This review covers NMR computational aspects of charged systems-carbocations, heterocations, and heteroanions, which were extensively studied in a number of laboratories worldwide, first of all, at the Loker Hydrocarbon Research Institute in California directed for several decades by a distinguished scientist, the Nobel laureate George Andrew Olah. The first part of the review briefly outlines computational background of the modern theoretical 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 historical results, advances, and perspectives of the computational NMR of classical carbocations like methyl cation, CH3+ , and protonated methane, CH5+ , together with their numerous homologs and derivatives. The third and the forth parts of this survey are focused on the NMR computational aspects of accordingly, heterocations and heteroanions, the organic and inorganic ions with a charge localized mainly on heteroatoms like boron, oxygen, nitrogen, and heavier elements.
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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. 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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Steinmann C, Sauer SPA. The aug-cc-pVTZ-J basis set for the p-block fourth-row elements Ga, Ge, As, Se, and Br. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:1134-1145. [PMID: 33929770 DOI: 10.1002/mrc.5166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The aug-cc-pVTZ-J basis set family is extended to include the fourth-row p-block elements Ga, Ge, As, Se, and Br. We use the established approach outlined by Sauer and coworkers (J. Chem. Phys. 115, 1324 [2001], J. Chem. Phys. 133, 054308 [2010], J. Chem. Theory Comput. 7, 4070 [2011], and J. Chem. Theory Comput. 7, 4077 [2011]) where the completely uncontracted aug-cc-pVTZ basis set is saturated with tight s-, p-, d-, and f-functions to form the aug-cc-pVTZ-Juc basis set for the tested elements. The saturation is carried out on the simplest hydrides possible for the tested elements GaH, GeH4 , AsH3 , H2 Se, and HBr until an improvement is less than 0.01% for all s-, p-, and d-functions added. f-Functions are added to an improvement less than or equal to 1.0% due to the computational expense these functions add. The saturated aug-cc-pVTZ-Juc (26s16p12d5f) is then recontracted using the molecular orbital coefficients from self-consistent field calculations on the simple hydrides to improve computational efficiency. During contraction of the basis set, we observe that the linear hydrogen bromide molecule has a slower convergence than the other tested molecules which sets a limit on the accuracy obtained. All calculations with the contracted aug-cc-pVTZ-J [17s10p7d5f] gives results that are within 1.0% of the uncontracted results at considerable computational savings.
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Affiliation(s)
- Casper Steinmann
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Krivdin LB. Computational NMR of heavy nuclei involving 109Ag, 113Cd, 119Sn, 125Te, 195Pt, 199Hg, 205Tl, and 207Pb. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4976] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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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Novitskiy IM, Holt TA, Kutateladze AG. Structure revision of ent-kaurane diterpenoids, isoserrins A, B, and D, enabled by DU8+ computation of their NMR spectral data. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Novitskiy IM, Holt TA, Kutateladze AG. Structure revision of ent-kaurane diterpenoids, isoserrins A, B, and D, enabled by DU8+ computation of their NMR spectral data. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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Kostelnik TI, Scheiber H, Cappai R, Choudhary N, Lindheimer F, Guadalupe Jaraquemada-Peláez MD, Orvig C. Phosphonate Chelators for Medicinal Metal Ions. Inorg Chem 2021; 60:5343-5361. [PMID: 33719399 DOI: 10.1021/acs.inorgchem.1c00290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A family of phosphonate-bearing chelators was synthesized to study their potential in metal-based (radio)pharmaceuticals. Three ligands (H6phospa, H6dipedpa, H6eppy; structures illustrated in manuscript) were fully characterized, including X-ray crystallographic structures of H6phospa and H6dipedpa. NMR spectroscopy techniques were used to confirm the complexation of each ligand with selected trivalent metal ions. These methods were particularly useful in discerning structural information for Sc3+ and La3+ complexes. Solution studies were conducted to evaluate the complex stability of 15 metal complexes. As a general trend, H6phospa was noted to form the most stable complexes, and H6eppy associated with the least stable complexes. Moreover, In3+ complexes were determined to be the most stable, and complexes with La3+ were the least stable, across all metals. Density functional theory (DFT) was employed to calculate structures of H6phospa and H6dipedpa complexes with La3+ and Sc3+. A comparison of experimental 1H NMR spectra with calculated 1H NMR spectra using DFT-optimized structures was used as a method of structure validation. It was noted that theoretical NMR spectra were very sensitive to a number of variables, such as ligand configuration, protonation state, and the number/orientation of explicit water molecules. In general, the inclusion of an explicit second shell of water molecules qualitatively improved the agreement between theoretical and experimental NMR spectra versus a polarizable continuum solvent model alone. Formation constants were also calculated from DFT results using potential-energy optimized structures. Strong dependence of molecular free energies on explicit water molecule number, water molecule configuration, and protonation state was observed, highlighting the need for dynamic data in accurate first-principles calculations of metal-ligand stability constants.
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Affiliation(s)
- Thomas I Kostelnik
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, 2036 Main Mall, V6T 1Z1 Vancouver, British Columbia, Canada.,Life Sciences Division, TRIUMF, 4004 Wesbrook Mall, V6T 2A3 Vancouver, British Columbia, Canada
| | - Hayden Scheiber
- Department of Chemistry, University of British Columbia, V6T 1Z1 Vancouver, British Columbia, Canada
| | - Rosita Cappai
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, 2036 Main Mall, V6T 1Z1 Vancouver, British Columbia, Canada.,Dipartimento di Scienze della Vita e dell'Ambiente, University of Cagliari, 09042 Cagliari, Italy
| | - Neha Choudhary
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, 2036 Main Mall, V6T 1Z1 Vancouver, British Columbia, Canada.,Life Sciences Division, TRIUMF, 4004 Wesbrook Mall, V6T 2A3 Vancouver, British Columbia, Canada
| | - Felix Lindheimer
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, 2036 Main Mall, V6T 1Z1 Vancouver, British Columbia, Canada.,Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 276, 69120 Heidelberg, Germany
| | - María de Guadalupe Jaraquemada-Peláez
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, 2036 Main Mall, V6T 1Z1 Vancouver, British Columbia, Canada
| | - Chris Orvig
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, 2036 Main Mall, V6T 1Z1 Vancouver, British Columbia, Canada
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Torrent KBA, Alvarenga ES. Synthesis and Identification of Epoxy Derivatives of 5-Methylhexahydroisoindole-1,3-dione and Biological Evaluation. Molecules 2021; 26:1923. [PMID: 33808049 PMCID: PMC8037305 DOI: 10.3390/molecules26071923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/25/2023] Open
Abstract
Cyclic imides belong to a well-known class of organic compounds with various biological activities, promoting a great interest in compounds with this functional group. Due to the structural complexity of some molecules and their spectra, it is necessary to use several spectrometric methods associated with auxiliary tools, such as the theoretical calculation for the structural elucidation of complex structures. In this work, the synthesis of epoxy derivatives of 5-methylhexahydroisoindole-1,3-diones was carried out in five steps. Diels-Alder reaction of isoprene and maleic anhydride followed by reaction with m-anisidine afforded the amide (2). Esterification of amide (2) with methanol in the presence of sulfuric acid provided the ester (3) that cyclized in situ to give imides 4 and 4-ent. Epoxidation of 4 and 4-ent with meta-chloroperbenzoic acid (MCPBA) afforded 5a and 5b. The diastereomers were separated by silica gel flash column chromatography, and their structures were determined by analyses of the spectrometric methods. Their structures were confirmed by matching the calculated 1H and 13C NMR chemical shifts of (5a and 5b) with the experimental data of the diastereomers using MAE, CP3, and DP4 statistical analyses. Biological assays were carried out to evaluate the potential herbicide activity of the imides. Compounds 5a and 5b inhibited root growth of the weed Bidens pilosa by more than 70% at all the concentrations evaluated.
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Affiliation(s)
| | - Elson S. Alvarenga
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil;
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Krivdin LB. Recent advances in computational liquid-phase 77Se NMR. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4960] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review aims to highlight significant progress in the calculation of 77Se NMR chemical shifts and spin – spin coupling constants involving selenium substantiated with a vast amount of experimental data. The material is arranged in two basic sections: the first one dealing with the calculation of 77Se NMR chemical shifts and the second one dealing with the computation of spin – spin coupling constants involving 77Se nucleus, namely 77Se–1H, 77Se–13C and 77Se–77Se together with some more exotic types of couplings, 77Se – 15N, 77Se–19F, 77Se–29Si and 77Se–31P. A special attention is focused on the stereoelectronic effects involving selenium atom and their manifestation in the 77Se NMR spectra of organoselenium compounds studied with the aid of the modern calculation of 77Se NMR parametres in combination with experimental results.
The bibliography includes 114 references.
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Abstract
Halogens cause pronounced and systematic effects on the 13C NMR chemical shift (δ13C) of an adjacent carbon nucleus, usually leading to a decrease in the values across the halogen series. Although this normal halogen dependence (NHD) is known in organic and inorganic compounds containing the carbon atom in its neutral and cationic forms, information about carbanions is scarce. To understand how δ13C changes in molecules with different charges, the shielding mechanisms of CHX3, CX3+, and CX3- (X = Cl, Br, or I) systems are investigated via density functional theory calculations and further analyzed by decomposition into contributions of natural localized molecular orbitals. An inverse halogen dependence (IHD) is determined for the anion series as a result of the negative spin-orbit contribution instead of scalar paramagnetic effects. The presence of a carbon nonbonding orbital in anions allows magnetic couplings that generate a deshielding effect on the nucleus and contradicts the classical association between δ13C and atomic charge.
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Affiliation(s)
- Renan V Viesser
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
| | - Cláudio F Tormena
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
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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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Semenov VA, Samultsev DO, Krivdin LB. Four-component relativistic computational NMR study of ferrous, cobalt and nickel bisglycinates. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Krivdin LB. Computational liquid-phase and solid-state 29Si NMR. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4927] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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