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Krivdin LB. Liquid-Phase NMR of Humic and Fulvic Acids. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2025; 63:128-150. [PMID: 39548772 DOI: 10.1002/mrc.5493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 10/11/2024] [Accepted: 10/14/2024] [Indexed: 11/18/2024]
Abstract
Present review focuses on the most recent advances in the NMR of the coal-derived humic and fulvic acids, covering exclusively the results of the liquid-phase NMR and leaving apart an overwhelming amount of publications dealing with the solid-state NMR investigations in this field (the latter are comprehensively reviewed elsewhere). Owing to the complexity of humic and fulvic acids together with other coal-derived products, their 1H and 13C NMR spectra consist of a number of overlapping signals belonging to different hydrocarbon types. Comprehensive studies of humic and fulvic acids by means of NMR revealed characteristic functional groups of their composition together with spectral regions in which they resonate. Quantitative 1H and 13C NMR spectra characterize aromatic and saturated carbons spread over many structural moieties, which provides a solid guideline into molecular structure of humic and fulvic acids together with parent coal-derived products. Nowadays, quantitative 13C NMR measurements yield information about a variety of structural parameters such as functional group distribution, aromaticity, degree of condensation of aromatic rings, and medium chain lengths together with many other more specific parameters. The structural NMR studies of the coal-derived products are developing on a background of a marked progress in experimental and computational NMR. Discussed in the present review are the most recent advances in the liquid-state NMR studies of the coal-derived humic and fulvic acids together with their processing 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. Recent advances in liquid-phase NMR of the coal-derived products. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:775-802. [PMID: 39081064 DOI: 10.1002/mrc.5476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 10/03/2024]
Abstract
Present review focuses on the most recent advances in a liquid-phase nuclear magnetic resonance (NMR) of the coal-derived products-coal tar pitches, asphaltenes, and humic and fulvic acids, covering exclusively the results in the liquid-phase NMR studies leaving apart an overwhelming amount of publications dealing with the solid-state NMR investigations in this field (which are comprehensively reviewed elsewhere). Owing to the complexity of the coal-derived products, their 1H and 13C NMR spectra consist of a number of overlapping signals belonging to different hydrocarbon types. Comprehensive studies of coal tar pitches, asphaltenes, and humic and fulvic acids by means of NMR over the past several decades revealed characteristic functional groups of those fractions together with spectral regions in which they resonate. Quantitative 1H and 13C NMR spectra characterize aromatic and saturated carbons spread over many structural moieties, which provides a solid guideline into molecular structure of the coal-derived products. Nowadays, quantitative 13C NMR measurements yield information about a variety of structural parameters such as functional group distribution, aromaticity, degree of condensation of aromatic rings, and medium chain lengths together with many other more specific parameters. The structural NMR studies of coal and coal-derived products are developing on a backdrop of a marked progress in computational NMR. At present, we are witnessing an unprecedentedly fast development of theoretical and computational methods in the field of NMR spectroscopy. Discussed in the present review are the most recent advances in the NMR studies of the processing products of peat, lignite or brown coal, anthracite or hard coal, and graphite in solution, like coal tar pitches, asphaltenes, and humic and fulvic acids.
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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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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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Rusakov YY, Rusakova IL. New pecJ- n ( n = 1, 2) Basis Sets for Selenium Atom Purposed for the Calculations of NMR Spin-Spin Coupling Constants Involving Selenium. Int J Mol Sci 2023; 24:ijms24097841. [PMID: 37175548 PMCID: PMC10178039 DOI: 10.3390/ijms24097841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
We present new compact pecJ-n (n = 1, 2) basis sets for the selenium atom developed for the quantum-chemical calculations of NMR spin-spin coupling constants (SSCCs) involving selenium nuclei. These basis sets were obtained at the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes (SOPPA(CCSD)) level with the property-energy consistent (PEC) method, which was introduced in our previous papers. The existing SSCC-oriented selenium basis sets are rather large in size, while the PEC method gives more compact basis sets that are capable of providing accuracy comparable to that reached using the property-oriented basis sets of larger sizes generated with a standard even-tempered technique. This is due to the fact that the PEC method is very different in its essence from the even-tempered approaches. It generates new exponents through the total optimization of angular spaces of trial basis sets with respect to the property under consideration and the total molecular energy. New basis sets were tested on the coupled cluster singles and doubles (CCSD) calculations of SSCCs involving selenium in the representative series of molecules, taking into account relativistic, solvent, and vibrational corrections. The comparison with the experiment showed that the accuracy of the results obtained with the pecJ-2 basis set is almost the same as that provided by a significantly larger basis set, aug-cc-pVTZ-J, while that achieved with a very compact pecJ-1 basis set is only slightly inferior to the accuracy provided by the former.
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Affiliation(s)
- Yuriy Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
| | - Irina L Rusakova
- 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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Aucar IA, Colombo Jofré MT, Aucar GA. A relativistic relationship between parity-violating nuclear spin-rotation tensors and parity-violating NMR shielding tensors. J Chem Phys 2023; 158:094306. [PMID: 36889958 DOI: 10.1063/5.0141176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
The nuclear-spin-dependent parity-violation contributions to the nuclear magnetic resonance shielding and nuclear spin-rotation tensors (σPV and MPV, respectively) are known to be formally related to one another in the non-relativistic regime. In this work, the polarization propagator formalism and the linear response within the elimination of small components model are used to show a new and more general relationship between them, which is valid within the relativistic framework. The full set of the zeroth- and first-order relativistic contributions to σPV and MPV are also given here for the first time, and these results are compared with previous findings. According to four-component relativistic calculations, the electronic spin-orbit effects are the most significant ones for the isotropic values of σPV and MPV in the H2X2 series of molecules (with X = O, S, Se, Te, and Po). When only scalar relativistic effects are taken into account, the non-relativistic relationship between σPV and MPV does hold. However, when the spin-orbit effects are taken into consideration, this old non-relativistic relationship breaks down, and therefore, the new one must be considered.
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Affiliation(s)
- I Agustín Aucar
- Instituto de Modelado e Innovación Tecnológica, CONICET, and Departamento de Física, Facultad de Ciencias Exactas y Naturales, UNNE, Avenida Libertad 5460, W3404AAS Corrientes, Argentina
| | - Mariano T Colombo Jofré
- Instituto de Modelado e Innovación Tecnológica, CONICET, and Departamento de Física, Facultad de Ciencias Exactas y Naturales, UNNE, Avenida Libertad 5460, W3404AAS Corrientes, Argentina
| | - Gustavo A Aucar
- Instituto de Modelado e Innovación Tecnológica, CONICET, and Departamento de Física, Facultad de Ciencias Exactas y Naturales, UNNE, Avenida Libertad 5460, W3404AAS Corrientes, Argentina
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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: 3] [Impact Index Per Article: 1.5] [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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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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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: 0.7] [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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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: 18] [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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11
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Colombo Jofre M, Kozioł K, Aucar IA, Gaul KJ, Berger R, Aucar GA. Relativistic and QED corrections to one-bond indirect nuclear spin-spin couplings in X$_2^{2+}$ and X$_3^{2+}$ ions (X = Zn, Cd, Hg). J Chem Phys 2022; 157:064103. [DOI: 10.1063/5.0095586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The indirect spin-spin coupling tensor, $\bm J$, between mercury nuclei in systems containing this element can be of the order of few kHz and one of the largest measured. We analysed the physics behind the electronic mechanisms that contribute to the one- and two-bond couplings $^n \bm{J}_{\mathrm{Hg}-\mathrm{Hg}}$ ($n=1, 2$). For doing so, we performed calculations for $J$-couplings in the ionized $X_2^{2+}$ and $X_3^{2+}$ linear molecules ($X$ = Zn, Cd, Hg) within polarization propagator theory, using the random phase approximation and the pure zeroth--order approximation with Dirac--Hartree--Fock and Dirac--Kohn--Sham orbitals, both at four-component and ZORA levels. We show that the ``paramagnetic-like' mechanism contribute with more than 99.98\% to the total isotropic value of the coupling tensor. By analyzing the molecular and atomic orbitals involved in the total value of the response function, we find that the $s$-type valence atomic orbitals have a predominant role in the description of the coupling. This fact allows us to develop an effective model from which QED effects on $J$-couplings in the aforementioned ions can be estimated. Those effects were found to be within the interval $(0.7;~1.7)$\% of the total relativistic effect on isotropic one-bond $^1\bm{J}$ coupling, though ranging those corrections between the interval $(-0.4;~-0.2)$\% in Zn-containing ions, to $(-1.2;~-0.8)$\% in Hg-containing ions, of the total isotropic coupling constant in the studied systems. The estimated QED corrections show a visible dependence on the nuclear charge $Z$ of each atom $X$ in the form of a power-law proportional to $Z_X^5$.
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Affiliation(s)
| | - Karol Kozioł
- National Centre for Nuclear Research (NCBJ), Poland
| | | | | | - Robert Berger
- Fachbereich Chemie, Philipps-Universitat Marburg Fachbereich Chemie, Germany
| | - Gustavo Adolfo Aucar
- Physics - Natural and Exact Faculty of the Northeastern University of Argentina, UNNE, Argentina
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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: 3.3] [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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Samultsev DO, Semenov VA, Krivdin LB. Four-component relativistic calculations of NMR shielding constants of the transition metal complexes. Part 1: Pentaammines of cobalt, rhodium, and iridium. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:463-468. [PMID: 34978105 DOI: 10.1002/mrc.5245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
The nonrelativistic and four-component fully relativistic calculations of 1 H, 15 N, 59 Co, 103 Rh, and 193 Ir shielding constants of pentaammineaquacomplexes of cobalt(III), rhodium(III), and iridium(III) were carried out at the density functional theory (DFT) level of theory. The noticeable deshielding relativistic corrections were observed for nitrogen shielding constants (chemical shifts), whereas those corrections were found to be negligible for protons. For the transition metals cobalt, rhodium, and iridium, relativistic corrections to their nuclear magnetic resonance (NMR) shielding constants were found to be rather small for cobalt and rhodium (some 5-10%), whereas they are essentially larger for iridium (up to 70%).
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Affiliation(s)
- Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - 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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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: 2.0] [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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15
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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: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Semenov VA, Krivdin LB. Simple and Versatile Scheme for the Stereochemical Identification of Natural Products and Diverse Organic Compounds with Multiple Asymmetric Centers. J Phys Chem A 2021; 125:10359-10372. [PMID: 34817185 DOI: 10.1021/acs.jpca.1c08687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple and versatile scheme of stereochemical identification of the stereochemically rich natural products and organic compounds with multiple asymmetric centers is proposed based on a detailed parsing of calculated 1H and 13C NMR chemical shifts in combination with their DP4+ analysis, as exemplified for three natural products: sungucine, physalin D, and anabsinthin. Performed benchmark calculations of the considered diastereomers provided very good agreement with their known experimental stereochemical structures.
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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, Russian Federation
| | - Leonid B Krivdin
- 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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Fernandes DDS, Lago ADF, Thomasi SS, Freitas MP. Conformational analysis of halobenzaldehydes: A theoretical and spectroscopic study. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Giovanetti MD, Bitencourt LFF, Cormanich R, Sauer SPA. On the Unexpected Accuracy of the M06L Functional in the Calculation of 1JFC Spin-Spin Coupling Constants. J Chem Theory Comput 2021; 17:7712-7723. [PMID: 34751577 DOI: 10.1021/acs.jctc.1c00287] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One-bond spin-spin coupling constants (SSCCs) between F and C are computed with density functional theory (DFT). Surprisingly, M06L stands out for its striking accuracy, outperforming any other investigated functional, including PBE0, otherwise considered one of the most reliable for couplings involving F. Although the computation of nuclear magnetic resonance (NMR) parameters involving F is known to be a challenging task, even with a rather small basis set as pcJ-1, M06L provides results with a MAD = 11.7 Hz, whereas the average deviation gets as much as 5 times larger for PBE0 (MAD = 60.0 Hz). In the context of SSCCs on the order of 300 Hz, this is particularly remarkable. We find that the accuracy of M06L/pcJ-1 in predicting 1JFC constants does not stem from a well-suited exchange or correlation part of the functional. Instead, it is believed to arise from a fortuitous cancellation of errors, as revealed by investigating the convergence of the basis set. Our findings also indicate that 1JFC constants are highly dependent on the amount of exact exchange included in the expression of the functional, with large fractions being critically important to achieving satisfactory results. Studying the effects of the geometry on 1JFC, we find that optimizing the geometry at the level of theory used to calculate SSCCs generally improves the quality of the results, although the combination of a M06-2X/aug-cc-pVTZ geometry with M06L/pcJ-1 1JFC constants best reproduces the experimental data for organofluorine compounds (with the exception of fluoroalkenes).
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Affiliation(s)
- Marinella de Giovanetti
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | | - Rodrigo Cormanich
- Chemistry Institute, State University of Campinas, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Mirzaeva I. Large relativistic effects in 119Sn NMR parameters: A case study of complex anions [Cp*M(SnCl3)nCl3−n]−, where M = Rh, Ir; n = 1, 2, 3. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Aucar IA, Borschevsky A. Relativistic study of parity-violating nuclear spin-rotation tensors. J Chem Phys 2021; 155:134307. [PMID: 34624973 DOI: 10.1063/5.0065487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a four-component relativistic approach to describe the effects of the nuclear spin-dependent parity-violating (PV) weak nuclear forces on nuclear spin-rotation (NSR) tensors. The formalism is derived within the four-component polarization propagator theory based on the Dirac-Coulomb Hamiltonian. Such calculations are important for planning and interpretation of possible future experiments aimed at stringent tests of the standard model through the observation of PV effects in NSR spectroscopy. An exploratory application of this theory to the chiral molecules H2X2 (X = 17O, 33S, 77Se, 125Te, and 209Po) illustrates the dramatic effect of relativity on these contributions. In particular, spin-free and spin-orbit effects are even of opposite signs for some dihedral angles, and the latter fully dominate for the heavier nuclei. Relativistic four-component calculations of isotropic nuclear spin-rotation constants, including parity-violating electroweak interactions, give frequency differences of up to 4.2 mHz between the H2Po2 enantiomers; on the nonrelativistic level of theory, this energy difference is 0.1 mHz only.
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Affiliation(s)
- Ignacio Agustín Aucar
- Instituto de Modelado e Innovación Tecnológica (UNNE-CONICET), Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad, 5460 Corrientes, Argentina
| | - Anastasia Borschevsky
- Faculty of Science and Engineering, Van Swinderen Institute for Particle Physics and Gravity, University of Groningen, 9747 AG Groningen, The Netherlands
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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: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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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: 1.8] [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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24
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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: 2.5] [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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26
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Rusakova IL, Rusakov YY. Quantum chemical calculations of 77 Se and 125 Te nuclear magnetic resonance spectral parameters and their structural applications. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:359-407. [PMID: 33095923 DOI: 10.1002/mrc.5111] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
An accurate quantum chemical (QC) modeling of 77 Se and 125 Te nuclear magnetic resonance (NMR) spectra is deeply involved in the NMR structural assignment for selenium and tellurium compounds that are of utmost importance both in organic and inorganic chemistry nowadays due to their huge application potential in many fields, like biology, medicine, and metallurgy. The main interest of this review is focused on the progress in QC computations of 77 Se and 125 Te NMR chemical shifts and indirect spin-spin coupling constants involving these nuclei. Different computational methodologies that have been used to simulate the NMR spectra of selenium and tellurium compounds since the middle of the 1990s are discussed with a strong emphasis on their accuracy. A special accent is placed on the calculations resorting to the relativistic methodologies, because taking into account the relativistic effects appreciably influences the precision of NMR calculations of selenium and, especially, tellurium compounds. Stereochemical applications of quantum chemical calculations of 77 Se and 125 Te NMR parameters are discussed so as to exemplify the importance of integrated approach of experimental and computational NMR techniques.
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Affiliation(s)
- Irina L Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Yuriy Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
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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: 1.8] [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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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: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Rusakov YY, Rusakova IL, Semenov VA, Krivdin LB. A New Basis Set for the Calculation of 13C NMR Chemical Shifts within a Non-empirical Correlated Framework. J Phys Chem A 2020; 124:7322-7330. [DOI: 10.1021/acs.jpca.0c06038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuriy Yu. Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Irina L. Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Valentin A. Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Leonid B. Krivdin
- 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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Elguero J, Alkorta I, Del Bene JE. Calculated coupling constants 1 J(X-Y) and 1 K(X-Y), and fundamental relationships among the reduced coupling constants for molecules H m X-YH n , with X, Y ═ 1 H, 7 Li, 9 Be, 11 B, 13 C, 15 N, 17 O, 19 F, 31 P, 33 S, and 35 Cl. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:727-732. [PMID: 32247293 DOI: 10.1002/mrc.5026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) calculations have been performed to determine coupling constants 1 J(X-Y) for 65 molecules Hm X-YHn , with X,Y ═ 1 H, 7 Li, 9 Be, 11 B, 13 C, 15 N, 17 O, 19 F, 31 P, 33 S, and 35 Cl. The computed 1 J(X-Y) values are in good agreement with available experimental data. The reduced coupling constants 1 K(X-Y) have been derived from 1 J(X-Y) by removing the dependence on the magnetogyric ratios of X and Y. Patterns are found for the reduced coupling constants on a 1 K(X-Y) surface that are related to the positions of X and Y in the periodic table.
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Affiliation(s)
- José Elguero
- Instituto de Química Médica (CSIC), Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Madrid, Spain
| | - Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio, USA
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32
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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: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Krivdin LB. Recent advances in computational 31 P NMR: Part 1. Chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:478-499. [PMID: 31703153 DOI: 10.1002/mrc.4965] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
This is the first part of two closely related reviews dealing with the computation of phosphorus-31 nuclear magnetic resonance chemical shifts in a wide series of organophosphorus compounds including complexes, clusters, and bioorganic phosphorus compounds. In particular, the analysis of the accuracy factors, such as substitution effects, solvent effects, vibrational corrections, and relativistic effects, is presented. This review is dedicated to the Full Member of the Russian Academy of Sciences Professor Boris A. Trofimov in view of his invaluable contribution to the field of synthesis, nuclear magnetic resonance, and computation studies of organophosphorus compounds.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- Angarsk State Technical University, Irkutsk Region, Russia
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Krivdin LB. Recent advances in computational 31 P NMR: Part 2. Spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:500-511. [PMID: 31808570 DOI: 10.1002/mrc.4973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
This is the second part of two closely related reviews dealing with the computation of 31 P nuclear magnetic resonance (NMR) parameters in a wide range of phosphorous containing compounds. The first part of this review concentrated primarily on the computation of 31 P NMR chemical shifts, whereas the second part concerns the calculation of spin-spin coupling constants involving phosphorus nucleus, focusing primarily on their stereochemical dependencies and stereodynamic behavior in particular classes of organophosphorus compounds. This review is dedicated to the Full Member of the Russian Academy of Sciences Professor Boris A. Trofimov in view of his invaluable contribution to the field of synthesis, NMR, and computation studies of organophosphorus compounds.
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Affiliation(s)
- Leonid B Krivdin
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Irkutsk, Russia
- Department of Chemistry, Angarsk State Technical University, Angarsk, Russia
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35
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Semenov VA, Samultsev DO, Krivdin LB. The 1 H and 13 C NMR chemical shifts of Strychnos alkaloids revisited at the DFT level. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:532-539. [PMID: 31663170 DOI: 10.1002/mrc.4948] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
The density functional theory calculation of 1 H and 13 C NMR chemical shifts in a series of ten 10 classically known Strychnos alkaloids with a strychnine skeleton was performed at the PBE0/pcSseg-2//pcseg-2 level. It was found that calculated 1 H and 13 C NMR chemical shifts provided a markedly good correlation with experiment characterized by a mean absolute error of 0.08 ppm in the range of 7 ppm for protons and 1.67 ppm in the range of 150 ppm for carbons, so that a mean absolute percentage error was as small as ~1% in both cases.
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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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36
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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: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Semenov VA, Krivdin LB. DFT computational schemes for 1 H and 13 C NMR chemical shifts of natural products, exemplified by strychnine. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:56-64. [PMID: 31291478 DOI: 10.1002/mrc.4922] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/24/2019] [Accepted: 07/05/2019] [Indexed: 06/09/2023]
Abstract
A number of computational schemes based on different Density Functional Theory (DFT) functionals in combination with a number of basis sets were tested in the calculation of 1 H and 13 C NMR chemical shifts of strychnine, as a typical representative of the vitally important natural products, and used as a challenging benchmark and a rigorous test for such calculations. It was found that the most accurate computational scheme, as compared with experiment, was PBE0/pcSseg-4//pcseg-3 characterized by a mean absolute error of 0.07 ppm for the range of about 7 ppm for 1 H NMR chemical shifts and that of only 1.13 ppm for 13 C NMR chemical shifts spread over the range of about 150 ppm. For more practical purposes, including investigation of larger molecules from this series, a much more economical computational scheme, PBE0/pcSseg-2//pcseg-2, characterized by almost the same accuracy and much less computational demand, was recommended.
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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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Krivdin LB. Computational 1 H NMR: Part 3. Biochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:15-30. [PMID: 31286566 DOI: 10.1002/mrc.4895] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
This is the third and the last part of three closely interrelated reviews dealing with computation of 1 H nuclear magnetic resonance chemical shifts and 1 H-1 H spin-spin coupling constants. Present review deals with the computation of these parameters in biologically active natural products, carbohydrates, and other molecules of biological origin focusing on stereochemical applications of computational 1 H nuclear magnetic resonance to these objects.
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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
- Department of Chemistry, Angarsk State Technical University, Angarsk, Russia
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Rusakova IL, Rusakov YY. On the heavy atom on light atom relativistic effect in the NMR shielding constants of phosphine tellurides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:1071-1083. [PMID: 31077441 DOI: 10.1002/mrc.4889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 04/27/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
The relativistic HALA effect has been shown to depend on the spatial deformation of the lone electron pairs of a heavy atom, as demonstrated for alkyl and alkene phosphine tellurides. It was found that HALA effect on phosphorous nuclear magnetic resonance shielding constant is strongly dependent on the spatial arrangements of light substituents on phosphorus, resulting in the deformation of the lone electron pairs of tellurium.
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Affiliation(s)
- Irina L Rusakova
- A.E. Favorsky Irkutsk Institute of Chemistry, SB RAS, Irkutsk, Russia
| | - Yuriy Yu Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, SB RAS, Irkutsk, Russia
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40
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Krivdin LB. Computational 1 H NMR: Part 1. Theoretical background. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:897-914. [PMID: 30963636 DOI: 10.1002/mrc.4873] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
This is the first one of the three closely interrelated reviews to be published in Magnetic Resonance in Chemistry dealing with accordingly theoretical background, chemical applications, and biochemical studies of and by means of computational 1 H NMR. Presented in the first part of the review is a general outline of the modern theoretical methods and accuracy factors of computational 1 H NMR involving locally dense basis set schemes, solvent effects, vibrational corrections, and relativistic effects performed at the density functional theory and/or nonempirical levels. This review is dedicated to Prof. Stephan Sauer in view of his invaluable contribution to the field of computational nuclear magnetic resonance.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- Angarsk State Technical University, Angarsk, Russia
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41
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Silla JM, Andrade LAF, Freitas MP. Influence of stereoelectronic effects on the 1 J C─F spin-spin coupling constant in fluorinated heterocyclic compounds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:373-379. [PMID: 30776853 DOI: 10.1002/mrc.4854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/05/2019] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
The Perlin effect and its analog for fluorinated compounds (the fluorine Perlin-like effect) manifest on one-bond C─H (C─F for the fluorine Perlin-like effect) spin-spin coupling constants (SSCCs) in six-membered rings. These effects can be useful to probe the stereochemistry (axial or equatorial) of the C─H and C─F bonds, respectively. The origin of these effects has been debatable in the literature as being due to hyperconjugative interactions, dipolar effects, and induced current density. Accordingly, a variety of model compounds has been used to probe such effects since the cyclohexanone carbonyl group and the endocyclic heteroatom lone pairs play different roles on the above-mentioned effects. Thus, the 1 JC─F SSCC in fluorinated lactams and lactones were theoretically studied to gain further insight on the nature of the fluorine Perlin-like effect. In addition, because the intramolecular α-effect has recently gained attention for its importance in the reactivity and stereoelectronic interactions in peroxide compounds, some fluorinated 1,2-dioxanes and 1,2-dithianes were studied to evaluate the role of the α-effect on the behavior of 1 JC─F SSCCs. Differently from fluorinated ketones and ethers, the fluorine Perlin-like effect in the amides and esters cannot be explained by hyperconjugative or dipolar interactions alone, because the resonance in these groups affect the 1 JC─F values. The O─O and S─S-containing systems exhibit a strong fluorine Perlin-like effect, but unlike the α-effect, this behavior cannot be explained neither by hyperconjugation nor by dipolar interactions alone; the spatial proximity of the C─F and O─O/S─S bonds is proposed to affect the magnitude of the 1 JC─F SSCC.
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Affiliation(s)
- Josué M Silla
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Laize A F Andrade
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
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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. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:346-358. [PMID: 30769377 DOI: 10.1002/mrc.4851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [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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43
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Rusakov YY, Rusakova IL, Fedorov SV, Gray GA, Krivdin LB. Stereochemical Dependences of 31P–13C Spin–Spin Coupling Constants of Heterocyclic Phosphines. J Phys Chem A 2019; 123:6298-6303. [DOI: 10.1021/acs.jpca.9b05385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yuriy Y. Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Irina L. Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Sergei V. Fedorov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - George A. Gray
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 95051, United States
| | - Leonid B. Krivdin
- 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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Krivdin LB. Computational protocols for calculating 13C NMR chemical shifts. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:103-156. [PMID: 31481156 DOI: 10.1016/j.pnmrs.2019.05.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 06/10/2023]
Abstract
The most recent results dealing with the computation of 13C NMR chemical shifts in chemistry (small molecules, saturated, unsaturated and aromatic compounds, heterocycles, functional derivatives, coordination complexes, carbocations, and natural products) are reviewed, paying special attention to theoretical background and accuracy, the latter involving solvent effects, vibrational corrections, and relativistic effects.
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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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Kozioł K, Aucar IA, Aucar GA. Relativistic and QED effects on NMR magnetic shielding constant of neutral and ionized atoms and diatomic molecules. J Chem Phys 2019; 150:184301. [PMID: 31091909 DOI: 10.1063/1.5095476] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We show here results of four-component calculations of nuclear magnetic resonance σ for atoms with 10 ≤ Z ≤ 86 and their ions, within the polarization propagator formalism at its random phase level of approach, and the first estimation of quantum electrodynamic (QED) effects and Breit interactions of those atomic systems by using two theoretical effective models. We also show QED corrections to σ(X) in simple diatomic HX and X2 (X = Br, I, At) molecules. We found that the Z dependence of QED corrections in bound-state many-electron systems is proportional to Z5, which is higher than its dependence in H-like systems. The analysis of relativistic ee (or paramagneticlike) and pp (or diamagneticlike) terms of σ exposes two different patterns: the pp contribution arises from virtual electron-positron pair creation/annihilation and the ee contribution is mainly given by 1s → ns and 2s → ns excitations. The QED effects on shieldings have a negative sign, and their magnitude is larger than 1% of the relativistic effects for high-Z atoms such as Hg and Rn, and up to 0.6% of its total four-component value for neutral Rn. Furthermore, percentual contributions of QED effects to the total shielding are larger for ionized than for neutral atoms. In a molecule, the contribution of QED effects to σ(X) is determined by its highest-Z atoms, being up to -0.6% of its total σ value for astatine compounds. It is found that QED effects grow faster than relativistic effects with Z.
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Affiliation(s)
- Karol Kozioł
- Institute for Modelling and Innovative Technology, IMIT, Corrientes, Argentina
| | - I Agustín Aucar
- Institute for Modelling and Innovative Technology, IMIT, Corrientes, Argentina
| | - Gustavo A Aucar
- Institute for Modelling and Innovative Technology, IMIT, Corrientes, Argentina
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Semenov VA, Rusakov YY, Samultsev DO, Krivdin LB. Geometries and NMR properties of cisplatin and transplatin revisited at the four-component relativistic level. MENDELEEV COMMUNICATIONS 2019. [DOI: 10.1016/j.mencom.2019.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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de Rezende FM, Freitas MP, Ramalho TC. The Perlin effect in 2-halocyclohexanones and 2-halocyclohexanethiones. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Afonin AV, Pavlov DV, Vashchenko AV. Case study of 2-vinyloxypyridine: Quantitative assessment of the intramolecular C H⋯N hydrogen bond energy and its contribution to the one-bond 13C1H coupling constant. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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49
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Krivdin LB. Theoretical calculations of carbon-hydrogen spin-spin coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 108:17-73. [PMID: 30538048 DOI: 10.1016/j.pnmrs.2018.10.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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de Rezende FMP, Freitas MP, Ramalho TC. Probing long-range spin-spin coupling constants in 2-halo-substituted cyclohexanones and cyclohexanethiones: The role of solvent and stereoelectronic effects. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:810-816. [PMID: 29667226 DOI: 10.1002/mrc.4739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Earlier studies with 2-bromocyclohexanone demonstrated a measurable long-range coupling constant (4 JH2,H6 ) for the equatorial conformer, although 4 JH2,H4 and 4 JH4,H6 were not observed; as a consequence, it is inferred that the carbonyl group plays an important role particularly due to hyperconjugative interactions σC2H2 →π*C═O and σC6H6 →π*C═O. In the present study, NBO analysis and coupling constant calculations were performed to cyclohexanone and cyclohexanethione alpha substituted with F, Cl, and Br, aiming to evaluate the halogen effect and acceptor character of the π* orbital on the long-range coupling pathway. The σC2H2 →π*C1═Y and σC6H6 →π*C1═Y (Y═O and S) hyperconjugative interactions for the equatorial conformer indeed contribute for the 4 JH2,H6 transmission mechanism. Surprisingly, the 4 JH2,H6 value is higher for the carbonyl compounds, although the interactions σC2H2 →π*C═Y and σC6H6 →π*C═Y are more efficient for the thiocarbonyl compounds. Accordingly, the Fermi contact (FC) contribution for the thiocarbonyl compounds decays deeper than in ketones, thus reducing more the 4 JH2,H6 values. Moreover, both πC═S →σ*C─X and πC═S →σ*C─H interactions seem to be stronger in thiocarbonyl than in carbonylic compounds. The implicit solvent effect (DMSO and water) on the coupling constant values was negligible when compared with the gas phase. On the other hand, an explicit solvent effect was found and 4 JH2,H6 for the thiocarbonyl compounds appeared to be more sensitive than for the cyclohexanones.
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Affiliation(s)
- Fátima M P de Rezende
- Department of Chemistry, Federal University of Lavras, Lavras, 37200-000, MG, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Federal University of Lavras, Lavras, 37200-000, MG, Brazil
| | - Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, 37200-000, MG, Brazil
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Rokitanskeho 62, Hradec Kralove, 50003, Czech Republic
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