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Rusakova IL, Rusakov YY. On the Utmost Importance of the Basis Set Choice for the Calculations of the Relativistic Corrections to NMR Shielding Constants. Int J Mol Sci 2023; 24:ijms24076231. [PMID: 37047204 PMCID: PMC10094374 DOI: 10.3390/ijms24076231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The investigation of the sensitivity of the relativistic corrections to the NMR shielding constants (σ) to the configuration of angular spaces of the basis sets used on the atoms of interest was carried out within the four-component density functional theory (DFT). Both types of relativistic effects were considered, namely the so-called heavy atom on light atom and heavy atom on heavy atom effects, though the main attention was paid to the former. As a main result, it was found that the dependence of the relativistic corrections to σ of light nuclei (exemplified here by 1H and 13C) located in close vicinity to a heavy atom (exemplified here by In, Sn, Sb, Te, and I) on the basis set used on the light spectator atom was very much in common with that of the Fermi-contact contribution to the corresponding nonrelativistic spin-spin coupling constant (J). In general, it has been shown that the nonrelativistic J-oriented and σ-oriented basis sets, artificially saturated in the tight s-region, provided much better accuracy than the standard nonrelativistic σ-oriented basis sets when calculating the relativistic corrections to the NMR shielding constants of light nuclei at the relativistic four-component level of the DFT theory.
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New pecJ-n (n = 1, 2) Basis Sets for High-Quality Calculations of Indirect Nuclear Spin–Spin Coupling Constants Involving 31P and 29Si: The Advanced PEC Method. Molecules 2022; 27:molecules27196145. [PMID: 36234706 PMCID: PMC9573013 DOI: 10.3390/molecules27196145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/21/2022] Open
Abstract
In this paper, we presented new J-oriented basis sets, pecJ-n (n = 1, 2), for phosphorus and silicon, purposed for the high-quality correlated calculations of the NMR spin–spin coupling constants involving these nuclei. The pecJ-n basis sets were generated using the modified version of the property-energy consistent (PEC) method, which was introduced in our earlier paper. The modifications applied to the original PEC procedure increased the overall accuracy and robustness of the generated basis sets in relation to the diversity of electronic systems. Our new basis sets were successfully tested on a great number of spin–spin coupling constants, involving phosphorus or/and silicon, calculated within the SOPPA(CCSD) method. In general, it was found that our new pecJ-1 and pecJ-2 basis sets are very efficient, providing the overall accuracy that can be characterized by MAEs of about 3.80 and 1.98 Hz, respectively, against the benchmark data obtained with a large dyall.aae4z+ basis set of quadruple-ζ quality.
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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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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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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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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: 7.8] [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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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: 11.6] [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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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: 27] [Impact Index Per Article: 4.5] [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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Krivdin LB. Carbon-carbon spin-spin coupling constants: Practical applications of theoretical calculations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 105:54-99. [PMID: 29548367 DOI: 10.1016/j.pnmrs.2018.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
Practical applications of theoretical calculations of carbon-carbon spin-spin coupling constants in particular classes of organic and bioorganic molecules are reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives as well as on carbohydrates and natural 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, Favorsky St. 1, 664033 Irkutsk, Russia.
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Fedorov SV, Rusakov YY, Krivdin LB. Relativistic Environmental Effects in 29Si NMR Chemical Shifts of Halosilanes: Light Nucleus, Heavy Environment. J Phys Chem A 2015; 119:5778-89. [DOI: 10.1021/acs.jpca.5b02337] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergey V. Fedorov
- A.E. Favorsky Irkutsk Institute
of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
| | - Yury Yu. Rusakov
- 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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Rusakova IL, Rusakov YY, Krivdin LB. Nonempirical calculations of the one-bond (29)Si-(13)C spin-spin coupling constants taking into account relativistic and solvent corrections. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:413-421. [PMID: 24796525 DOI: 10.1002/mrc.4080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 06/03/2023]
Abstract
The computational study of the one-bond (29)Si-(13)C spin-spin coupling constants has been performed at the second-order polarization propagator approximation (SOPPA) level in the series of 60 diverse silanes with a special focus on the main factors affecting the accuracy of the calculation including the level of theory, the quality of the basis set, and the contribution of solvent and relativistic effects. Among three SOPPA-based methods, SOPPA(MP2), SOPPA(CC2), and SOPPA(CCSD), the best result was achieved with SOPPA(CCSD) when used in combination with Sauer's basis set aug-cc-pVTZ-J characterized by the mean absolute error of calculated coupling constants against the experiment of ca 2 Hz in the range of ca 200 Hz. The SOPPA(CCSD)/aug-cc-pVTZ-J method is recommended as the most accurate and effective computational scheme for the calculation of (1)J(Si,C). The slightly less accurate but essentially more economical SOPPA(MP2)/aug-cc-pVTZ-J and/or SOPPA(CC2)/aug-cc-pVTZ-J methods are recommended for larger molecular systems. It was shown that solvent and relativistic corrections do not play a major role in the computation of the total values of (1)J(Si,C); however, taking them into account noticeably improves agreement with the experiment. The rovibrational corrections are estimated to be of about 1 Hz or 1-1.5% of the total value of (1)J(Si,C).
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Affiliation(s)
- Irina L Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St 1, 664033, Irkutsk, Russia
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Rusakov YY, Krivdin LB, Østerstrøm FF, Sauer SPA, Potapov VA, Amosova SV. First example of a high-level correlated calculation of the indirect spin-spin coupling constants involving tellurium: tellurophene and divinyl telluride. Phys Chem Chem Phys 2014; 15:13101-13107. [PMID: 23824065 DOI: 10.1039/c3cp51462e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper documents the very first example of a high-level correlated calculation of spin-spin coupling constants involving tellurium taking into account relativistic effects, vibrational corrections and solvent effects for medium sized organotellurium molecules. The (125)Te-(1)H spin-spin coupling constants of tellurophene and divinyl telluride were calculated at the SOPPA and DFT levels, in good agreement with experimental data. A new full-electron basis set, av3z-J, for tellurium derived from the "relativistic" Dyall's basis set, dyall.av3z, and specifically optimized for the correlated calculations of spin-spin coupling constants involving tellurium was developed. The SOPPA method shows a much better performance compared to DFT, if relativistic effects calculated within the ZORA scheme are taken into account. Vibrational and solvent corrections are next to negligible, while conformational averaging is of prime importance in the calculation of (125)Te-(1)H spin-spin couplings. Based on the performed calculations at the SOPPA(CCSD) level, a marked stereospecificity of geminal and vicinal (125)Te-(1)H spin-spin coupling constants originating in the orientational lone pair effect of tellurium has been established, which opens a new guideline in organotellurium stereochemistry.
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Affiliation(s)
- Yury Yu Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Russian Academy of Sciences, Siberian Branch, 1 Favorsky St., 664033 Irkutsk, Russia.
| | - Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Russian Academy of Sciences, Siberian Branch, 1 Favorsky St., 664033 Irkutsk, Russia.
| | - Freja F Østerstrøm
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Vladimir A Potapov
- A.E. Favorsky Irkutsk Institute of Chemistry, Russian Academy of Sciences, Siberian Branch, 1 Favorsky St., 664033 Irkutsk, Russia.
| | - Svetlana V Amosova
- A.E. Favorsky Irkutsk Institute of Chemistry, Russian Academy of Sciences, Siberian Branch, 1 Favorsky St., 664033 Irkutsk, Russia.
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Rusakov YY, Krivdin LB. One-bond 29Si-1H spin-spin coupling constants in the series of halosilanes: benchmark SOPPA and DFT calculations, relativistic effects, and vibrational corrections. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:557-561. [PMID: 23836682 DOI: 10.1002/mrc.3986] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/02/2013] [Accepted: 06/10/2013] [Indexed: 06/02/2023]
Abstract
A number of most representative second order polarization propagator approach (SOPPA) based wavefunction methods, SOPPA, SOPPA(CC2) and SOPPA(CCSD), and density functional theory (DFT) based methods, B3LYP, PBE0, KT2, and KT3, have been benchmarked in the calculation of the one-bond (29)Si-(1)H spin-spin coupling constants in the series of halosilanes SiH(n)X(4-n) (X = F, Cl, Br, I), both at the non-relativistic and full four-parameter Dirac's relativistic levels taking into account vibrational corrections. At the non-relativistic level, the wavefunction methods showed much better results as compared with those of DFT. At the DFT level, out of four tested functionals, the Perdew, Burke, and Ernzerhof's PBE0 showed best performance. Taking into account, relativistic effects and vibrational corrections noticeably improves wavefunction methods results, but generally worsens DFT results.
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Affiliation(s)
- Yury Yu Rusakov
- 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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Rusakov YY, Krivdin LB. Modern quantum chemical methods for calculating spin–spin coupling constants: theoretical basis and structural applications in chemistry. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n02abeh004350] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rusakov YY, Krivdin LB, Nosova VM, Kisin AV, Lakhtin VG. Structural trends of 29Si-1H spin-spin coupling constants across double bond. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:665-671. [PMID: 22936622 DOI: 10.1002/mrc.3860] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/04/2012] [Accepted: 07/18/2012] [Indexed: 06/01/2023]
Abstract
The calculations of geminal and vicinal (29)Si-(1)H spin-spin coupling constants across double bond in 15 alkenylmethylsilanes and alkenylchlorosilanes were carried out at the second-order polarization propagator approach level in a good agreement with experiment. Two structural trends, namely, (i) the geometry of the coupling pathway and (ii) the effect of the electrowithdrawing substituent, have been interpreted in terms of the natural J-coupling analysis within the framework of the natural bond orbital approach. Thus, the marked difference between cisoidal and transoidal (29)Si-(1)H spin-spin coupling constants across double bond was accounted for the delocalization contributions including bonding and antibonding Si-C and C-H orbitals, whereas the chlorine effect was explained in terms of the steric contributions including bonding Si-Cl orbitals.
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Affiliation(s)
- Yury Yu Rusakov
- A E Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Rusakov YY, Krivdin LB, Penzik MV, Potapov VA, Amosova SV. Open-chain unsaturated selanyl sulfides: stereochemical structure and stereochemical behavior of their 77Se-1H spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:653-658. [PMID: 22936611 DOI: 10.1002/mrc.3858] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 06/01/2023]
Abstract
Stereochemical structure of nine Z-2-(vinylsulfanyl)ethenylselanyl organyl sulfides has been investigated by means of experimental measurements and second-order polarization propagator approach calculations of their (1)H-(1)H, (13)C-(1)H, and (77)Se-(1)H spin-spin coupling constants together with a theoretical conformational analysis performed at the MP2/6-311G** level. All nine compounds were shown to adopt the preferable skewed s-cis conformation of their terminal vinylsulfanyl group, whereas the favorable rotational conformations with respect to the internal rotations around the C-S and C-Se bonds of the internal ethenyl group are both skewed s-trans. Stereochemical trends of (77)Se-(1)H spin-spin coupling constants originating in the geometry of their coupling pathways and the selenium lone pair effect were rationalized in terms of the natural J-coupling analysis within the framework of the natural bond orbital approach.
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Affiliation(s)
- Yury Yu Rusakov
- AE Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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