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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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2
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Vı́cha J, Novotný J, Komorovsky S, Straka M, Kaupp M, Marek R. Relativistic Heavy-Neighbor-Atom Effects on NMR Shifts: Concepts and Trends Across the Periodic Table. Chem Rev 2020; 120:7065-7103. [DOI: 10.1021/acs.chemrev.9b00785] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jan Vı́cha
- Centre of Polymer Systems, Tomas Bata University in Zlı́n, tř. Tomáše Bati 5678, CZ-76001 Zlı́n, Czechia
| | - Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Stanislav Komorovsky
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84536 Bratislava, Slovakia
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague, Czechia
| | - Martin Kaupp
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
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3
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Krivdin LB. Computational 1 H NMR: Part 2. Chemical applications. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:5-14. [PMID: 31125992 DOI: 10.1002/mrc.4896] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/12/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
This is the second one of three closely interrelated reviews dealing with computation of 1 H NMR chemical shifts and 1 H-1 H spin-spin coupling constants prepared for Magnetic Resonance in Chemistry. Presented in this review are some basic notes and illustrative examples of how modern computational 1 H NMR could be used for structural elucidation and stereoelectronic studies of the medium-sized organic molecules involving saturated, unsaturated, aromatic, and heteroaromatic compounds together with their functional derivatives and coordination complexes to get deeper insight into their stereochemical structure and stereodynamic behavior.
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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
- Chair of Chemistry, Angarsk State Technical University, Tchaikovsky St. 60, 665835, Angarsk, Russia
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Frańska M, Konował E. Nucleoside-AuCl 4 - interactions as studied by electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1164-1168. [PMID: 30964959 DOI: 10.1002/rcm.8452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/24/2019] [Accepted: 03/31/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Emilia Konował
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
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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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Novotný J, Vícha J, Bora PL, Repisky M, Straka M, Komorovsky S, Marek R. Linking the Character of the Metal–Ligand Bond to the Ligand NMR Shielding in Transition-Metal Complexes: NMR Contributions from Spin–Orbit Coupling. J Chem Theory Comput 2017; 13:3586-3601. [DOI: 10.1021/acs.jctc.7b00444] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Novotný
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia
| | - Jan Vícha
- Centre
of
Polymer Systems, University Institute, Tomas Bata University in Zlín, Třída T. Bati, 5678, CZ-76001 Zlín, Czechia
| | - Pankaj L. Bora
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia
| | - Michal Repisky
- Center
for Theoretical and Computational Chemistry, Department of Chemistry, UiT − The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Michal Straka
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia
- Institute of Organic
Chemistry and Biochemistry of the ASCR, Flemingovo nám. 2, CZ-16610 Praha, Czechia
| | - Stanislav Komorovsky
- Institute
of Inorganic Chemistry, Slovak Academy of Science, Dúbravská
cesta 9, SK-84536 Bratislava, Slovakia
| | - Radek Marek
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia
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Štarha P, Vančo J, Trávníček Z. Platinum complexes containing adenine-based ligands: An overview of selected structural features. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Synthesis, characterization, X-ray structural determination and theoretical study of the complexes [RuCp(8MTT-κS)LL′] (8MTT=8-methylthio-theophyllinate; L,L′=PTA, mPTA; L=mPTA, L′=PPh3; PTA=1,3,5-triaza-7-phosphaadamantane, mPTA=N-methyl-1,3,5-triaza-7-phosphaadamantane). Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.05.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Roukala J, Orr ST, Hanna JV, Vaara J, Ivanov AV, Antzutkin ON, Lantto P. Experimental and First-Principles NMR Analysis of Pt(II) Complexes With O,O′-Dialkyldithiophosphate Ligands. J Phys Chem A 2016; 120:8326-8338. [PMID: 27687143 DOI: 10.1021/acs.jpca.6b09586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juho Roukala
- NMR
Research Unit, University of Oulu, P.O. Box 3000, FI-90400 Oulu, Finland
| | - Simon T. Orr
- Department
of Physics, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - John V. Hanna
- Department
of Physics, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Juha Vaara
- NMR
Research Unit, University of Oulu, P.O. Box 3000, FI-90400 Oulu, Finland
| | - Alexander V. Ivanov
- Institute
of Geology and Nature Management, Far Eastern Branch of the Russian Academy of Sciences, Ryolochny Lane 1, Blagoveshchensk 675000, Amur Region, Russia
| | - Oleg N. Antzutkin
- Department
of Physics, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
- Chemistry
of Interfaces, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Perttu Lantto
- NMR
Research Unit, University of Oulu, P.O. Box 3000, FI-90400 Oulu, Finland
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Vícha J, Marek R, Straka M. High-Frequency 13C and 29Si NMR Chemical Shifts in Diamagnetic Low-Valence Compounds of TlI and PbII: Decisive Role of Relativistic Effects. Inorg Chem 2016; 55:1770-81. [DOI: 10.1021/acs.inorgchem.5b02689] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Vícha
- Center of Polymer Systems, University Institute, Tomas Bata University in Zlín, Třída T. Bati, 5678, CZ-76001, Zlín, Czech Republic
| | - Radek Marek
- CEITEC - Central European Institute of
Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague, Czech Republic
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Vícha J, Novotný J, Straka M, Repisky M, Ruud K, Komorovsky S, Marek R. Structure, solvent, and relativistic effects on the NMR chemical shifts in square-planar transition-metal complexes: assessment of DFT approaches. Phys Chem Chem Phys 2015; 17:24944-55. [DOI: 10.1039/c5cp04214c] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The role of various factors (geometry, solvent, relativistic treatment, functional) influencing the relativistic NMR chemical shift calculations for square-planar transition-metal complexes.
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Affiliation(s)
- Jan Vícha
- CEITEC – Central European Institute of Technology
- Masaryk University
- CZ-62500 Brno
- Czech Republic
- Centre of Polymer Systems
| | - Jan Novotný
- CEITEC – Central European Institute of Technology
- Masaryk University
- CZ-62500 Brno
- Czech Republic
| | - Michal Straka
- CEITEC – Central European Institute of Technology
- Masaryk University
- CZ-62500 Brno
- Czech Republic
- Institute of Organic Chemistry and Biochemistry
| | - Michal Repisky
- Centre for Theoretical and Computational Chemistry
- Department of Chemistry
- UiT – The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry
- Department of Chemistry
- UiT – The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Stanislav Komorovsky
- Centre for Theoretical and Computational Chemistry
- Department of Chemistry
- UiT – The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Radek Marek
- CEITEC – Central European Institute of Technology
- Masaryk University
- CZ-62500 Brno
- Czech Republic
- Department of Chemistry
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Hajji L, Saraiba-Bello C, Serrano-Ruiz M, Romerosa A. Binuclear ruthenium complexes containing mPTA and alkyl-bis(8-thiotheophylline) derivatives (mPTA = N-methyl-1,3,5-triaza-7-phosphaadamantane). J COORD CHEM 2014. [DOI: 10.1080/00958972.2014.947970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Lazhar Hajji
- Facultad de Ciencias Experimentales, Área de Química Inorgánica-CIESOL, Universidad de Almería, Almería, Spain
| | - Cristobal Saraiba-Bello
- Facultad de Ciencias Experimentales, Área de Química Inorgánica-CIESOL, Universidad de Almería, Almería, Spain
| | - Manuel Serrano-Ruiz
- Facultad de Ciencias Experimentales, Área de Química Inorgánica-CIESOL, Universidad de Almería, Almería, Spain
| | - Antonio Romerosa
- Facultad de Ciencias Experimentales, Área de Química Inorgánica-CIESOL, Universidad de Almería, Almería, Spain
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Vícha J, Straka M, Munzarová ML, Marek R. Mechanism of Spin–Orbit Effects on the Ligand NMR Chemical Shift in Transition-Metal Complexes: Linking NMR to EPR. J Chem Theory Comput 2014; 10:1489-99. [DOI: 10.1021/ct400726y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jan Vícha
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Michal Straka
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the ASCR, Flemingovo nám. 2, CZ-16610 Praha, Czech Republic
| | - Markéta L. Munzarová
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, CZ-62500 Brno, Czech Republic
| | - Radek Marek
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, CZ-62500 Brno, Czech Republic
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Investigation of Ag(I) complexes involving 6-(benzylamino)purine derivatives. MONATSHEFTE FUR CHEMIE 2013. [DOI: 10.1007/s00706-013-1078-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Domínguez-Martín A, García-Raso A, Cabot C, Choquesillo-Lazarte D, Pérez-Toro I, Matilla-Hernández A, Castiñeiras A, Niclós-Gutiérrez J. Structural insights on the molecular recognition patterns between N(6)-substituted adenines and N-(aryl-methyl)iminodiacetate copper(II) chelates. J Inorg Biochem 2013; 127:141-9. [PMID: 23490423 DOI: 10.1016/j.jinorgbio.2013.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/07/2013] [Accepted: 02/08/2013] [Indexed: 10/27/2022]
Abstract
For a better understanding of the metal binding pattern of N(6)-substituted adenines, six novel ternary Cu(II) complexes have been structurally characterized by single crystal X-ray diffraction: [Cu(NBzIDA)(HCy5ade)(H2O)]·H2O (1), [Cu(NBzIDA)(HCy6ade)(H2O)]·H2O (2), [Cu(FurIDA)(HCy6ade)(H2O)]·H2O (3), [Cu(MEBIDA)(HBAP)(H2O)]·H2O (4), [Cu(FurIDA)(HBAP)]n (5) and {[Cu(NBzIDA)(HdimAP)]·H2O}n (6). In these compounds NBzIDA, FurIDA and MEBIDA are N-substituted iminodiacetates with a non-coordinating aryl-methyl pendant arm (benzyl in NBzIDA, p-tolyl in MEBIDA and furfuryl in FurIDA) whereas HBAP, HCy5ade, HCy6ade and HdimAP are N(6)-substituted adenine derivatives with a N-benzyl, N-cyclopentyl, N-cyclohexyl or two N-methyl groups, respectively. Regardless of the molecular (1-4) or polymeric (5-6) nature of the studied compounds, the Cu(II) centre exhibits a type 4+1 coordination where the tridentate IDA-like chelators adopt a mer-conformation. In 1-5 the N(6)-R-adenines use their most stable tautomer H(N9)adenine-like, and molecular recognition consists of the cooperation of the CuN3(purine) bond and the intra-molecular interligand N9H···O(coordinated carboxy) interaction. In contrast, N(6),N(6)-dimethyl-adenine shows the rare tautomer H(N3)dimAP in 6, so that the molecular recognition with the Cu(NBzIDA) chelate consist of the CuN9 bond and the N3H···O intra-molecular interligand interaction. Contrastingly to the cytokinin activity found in the free ligands HBAP (natural cytokinin), HCy5ade and HCy6ade, the corresponding Cu(II) ternary complexes did not show any activity.
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Affiliation(s)
- Alicia Domínguez-Martín
- Department of Inorganic Chemistry, Faculty of Pharmacy, Campus Cartuja, University of Granada, E-18071 Granada, Spain.
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Vícha J, Patzschke M, Marek R. A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes. Phys Chem Chem Phys 2013; 15:7740-54. [DOI: 10.1039/c3cp44440f] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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