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Chiari C, Batista PR, Viesser RV, Schenberg LA, Ducati LC, Linclau B, Tormena CF. Molecular dynamics and NMR reveal the coexistence of H-bond-assisted and through-space JFH coupling in fluorinated amino alcohols. Org Biomol Chem 2024; 22:2580-2595. [PMID: 38441115 DOI: 10.1039/d4ob00049h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The JFH coupling constants in fluorinated amino alcohols were investigated through experimental and theoretical approaches. The experimental JFH couplings were only reproduced theoretically when explicit solvation through molecular dynamics (MD) simulations was conducted in DMSO as the solvent. The combination of MD conformation sampling and DFT NMR spin-spin coupling calculations for these compounds reveals the simultaneous presence of through-space (TS) and hydrogen bond (H-bond) assisted JFH coupling between fluorine and hydrogen of the NH group. Furthermore, MD simulations indicate that the hydrogen in the amino group participates in both an intermolecular bifurcated H-bond with DMSO and in transmitting the observed JFH coupling. The contribution of TS to the JFH coupling is due to the spatial proximity of the fluorine and the NH group, aided by a combination of the non-bonding transmission pathway and the hydrogen bonding pathway. The experimental JFH coupling observed for the molecules studied should be represented as 4TS/1hJFH coupling.
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Affiliation(s)
- Cassia Chiari
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
| | - Patrick R Batista
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
| | - Renan V Viesser
- Department of Chemistry, University of Houston, Houston, TX 77024, USA
| | - Leonardo A Schenberg
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
| | - Lucas C Ducati
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
| | - Bruno Linclau
- Department of Organic and Macromolecular Chemistry, Ghent University, Ghent 9000, Belgium
| | - Cláudio F Tormena
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
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2
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Malkina OL, Hierso JC, Malkin VG. Distinguishing "Through-Space" from "Through-Bonds" Contribution in Indirect Nuclear Spin-Spin Coupling: General Approaches Applied to Complex JPP and JPSe Scalar Couplings. J Am Chem Soc 2022; 144:10768-10784. [PMID: 35687121 DOI: 10.1021/jacs.2c01637] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present herein two complementary theoretical approaches for analyzing the transmission pathways of indirect nuclear spin-spin couplings in high-resolution nuclear magnetic resonance. This phenomenon is notably conceptually poorly understood in complex experimental situations in which both nonbonded ["through-space" (TS)] and more "classical" bonding ("through-bond") spin-spin coupling pathways are potentially involved. The computational approaches we propose allow the visualization and discussion of individual transmission pathways and estimation of their relative weight from numerical contributions to the spin-spin coupling constant J-value. The first approach is based on the analysis of contributions limited to occupied molecular orbitals [focused on occupied molecular orbitals (FOMO)]. The second approach encompasses the consideration of both occupied and vacant orbitals [global molecular orbital contributions (GMOC)], and, besides the contributions from individual pathways, also considers their cross contributions. Both approaches are applicable to large systems with complex interactions of nuclear magnetic moments. Herein, we have first applied the FOMO and GMOC computational approaches to simple diphosphine models and then extended the analysis to JPP and JPSe experimentally measured in a constrained selenated (diphosphino)naphthalene compound. The new computational tools contributed evidence for the importance of the single lone pair not only from phosphorus but also from selenium in TS spin-spin transmission. It evidenced and modeled for the first time the existence of spin-spin transmission pathways mixing classical covalent bonding parts with a lone pair overlap of proximate heteroatoms (P and Se).
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Affiliation(s)
- Olga L Malkina
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 84 536, Slovakia
| | - Jean-Cyrille Hierso
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR CNRS 6302), Université Bourgogne-Franche-Comté (UBFC), 9 Avenue Alain Savary, Dijon, 21078, France.,Institut Universitaire de France (IUF), 103 Bd. Saint Michel, 75005 Paris Cedex 5, France
| | - Vladimir G Malkin
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 84 536, Slovakia
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Komorovsky S, Jakubowska K, Świder P, Repisky M, Jaszuński M. NMR Spin–Spin Coupling Constants Derived from Relativistic Four-Component DFT Theory—Analysis and Visualization. J Phys Chem A 2020; 124:5157-5169. [DOI: 10.1021/acs.jpca.0c02807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stanislav Komorovsky
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 36, Slovakia
| | | | - Paweł Świder
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warszawa 01-224, Poland
| | - Michal Repisky
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT − The Arctic University of Norway, Tromsø N-9037, Norway
| | - Michał Jaszuński
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warszawa 01-224, Poland
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4
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Shenderovich IG, Denisov GS. Solvent effects on acid-base complexes. What is more important: A macroscopic reaction field or solute-solvent interactions? J Chem Phys 2019; 150:204505. [PMID: 31153188 DOI: 10.1063/1.5096946] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Can the geometry of an acid-base complex in solution be reproduced in calculations using an implicit accounting for the solvent effect in the form of a macroscopic reaction field? The answer is, "Yes, it can." Is this field equal to the real electric field experienced by the complex in solution? The answer is, "No, it is not." How can the geometry be correct under wrong conditions? This question is answered using density functional theory modeling of geometric and NMR parameters of pyridine⋯HF⋯(HCF3)n adducts in the absence and presence of an external electric field. This adduct under field approach shows that the N⋯H distance is a function of the H-F distance whatever method is used to change the geometry of the latter. An explicit account for solute-solvent interactions is required to get a realistic value of the solvent reaction field. Besides that, this approach reveals how certain NMR parameters depend on the solvent reaction field, the solute-solvent interactions, and the geometry of the N⋯H-F hydrogen bond. For some of them, the obtained dependences are far from self-evident.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
| | - Gleb S Denisov
- Department of Physics, St.Petersburg State University, Saint Petersburg, Russia
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5
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Lino JBDR, Ramalho TC. Exploring Through-Space Spin-Spin Couplings for Quantum Information Processing: Facing the Challenge of Coherence Time and Control Quantum States. J Phys Chem A 2019; 123:1372-1379. [PMID: 30673241 DOI: 10.1021/acs.jpca.8b09425] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear magnetic resonance (NMR) is a powerful tool for studying quantum information processing (QIP). Recently quantum technologies have been proposed to overcome the challenges in large-scale NMR QIP. Furthermore, computational chemistry can promote its improvement. Nuclear spins-1/2 are natural qubits and have been used in most NMR quantum computation experiments. However, molecules that enable many qubits NMR QIP implementations should meet some requirements regarding their spectroscopic properties. Exceptionally large through-space (TS) P-P spin-spin coupling constants (SSCC or J) observed in 1,8-diphosphanaphthalenes (PPN) and in naphtho[1,8- cd]-1,2-dithiole phenylphosphines (NTP) were proposed and investigated to provide more accurate control within large-scale NMR QIP. Spectroscopic properties of PPN and NTP derivatives were explored by theoretical strategies using locally dense basis sets (LDBS). 31P chemical shifts (δ) calculated at the B3LYP/aug-cc-pVTZ-J level and TS P-P SSCCs at the PBE1PBE/pcJ-2 (LDBS-1) level are very close to the experimental data for the PPN molecule. Differently, for the NTP dimer, PBE1PBE/pcJ-2 (LDBS-2) predicts more accurate 31P δ, whereas PBE1PBE/Def2-TZVP (LDBS-1) forecasts more accurate TS P-P SSCCs. From our results, PPNo-F, PPNo-ethyl, and PPNo-NH2 were the best candidates for NMR QIP, in which the large TS SSCCS could face the need of long-time quantum gates implementations. Therefore, it could overcome natural limitations concerning the development of large-scale NMR.
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Affiliation(s)
| | - Teodorico Castro Ramalho
- Chemistry Department , Federal University of Lavras , 37200-000 Lavras , MG Brazil.,Center for Basic and Applied Research, Faculty of Informatics and Management , University Hradec Kralove , 50003 Hradec Kralove , Czech Republic
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Dračínský M, Buchta M, Buděšínský M, Vacek-Chocholoušová J, Stará IG, Starý I, Malkina OL. Dihydrogen contacts observed by through-space indirect NMR coupling. Chem Sci 2018; 9:7437-7446. [PMID: 30319744 PMCID: PMC6180313 DOI: 10.1039/c8sc02859a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/11/2018] [Indexed: 11/21/2022] Open
Abstract
"Through-space" indirect spin-spin couplings between hydrogen atoms formally separated by up to 18 covalent bonds have been detected by NMR experiments in model helical molecules. It is demonstrated that this coupling can provide crucial structural information on the molecular conformation in solution. The coupling pathways have been visualised and analysed by computational methods. The conformational dependence of the coupling is explained in terms of orbital interactions.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Michal Buchta
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Jana Vacek-Chocholoušová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Irena G Stará
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Olga L Malkina
- Institute of Inorganic Chemistry , Slovak Academy of Sciences , Dúbravská cesta 9 , SK-84536 Bratislava , Slovakia .
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7
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Shenderovich IG. Simplified calculation approaches designed to reproduce the geometry of hydrogen bonds in molecular complexes in aprotic solvents. J Chem Phys 2018; 148:124313. [PMID: 29604820 DOI: 10.1063/1.5011163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The impact of the environment onto the geometry of hydrogen bonds can be critically important for the properties of the questioned molecular system. The paper reports on the design of calculation approaches capable to simulate the effect of aprotic polar solvents on the geometric and NMR parameters of intermolecular hydrogen bonds. A hydrogen fluoride and pyridine complex has been used as the main model system because the experimental estimates of these parameters are available for it. Specifically, F-H, F⋯N, and H-N distances, the values of 15N NMR shift, and spin-spin coupling constants 1J(19F1H), 1hJ(1H15N), and 2hJ(19F15N) have been analyzed. Calculation approaches based on the gas-phase and the Polarizable Continuum Model (PCM) approximations and their combinations with geometric constraints and additional noncovalent interactions have been probed. The main result of this work is that the effect of an aprotic polar solvent on the geometry of a proton-donor⋯H⋯proton-acceptor complex cannot be reproduced under the PCM approximation if no correction for solvent-solute interactions is made. These interactions can be implicitly accounted for using a simple computational protocol.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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Tormena CF. Conformational analysis of small molecules: NMR and quantum mechanics calculations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:73-88. [PMID: 27573182 DOI: 10.1016/j.pnmrs.2016.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/14/2016] [Accepted: 04/14/2016] [Indexed: 06/06/2023]
Abstract
This review deals with conformational analysis in small organic molecules, and describes the stereoelectronic interactions responsible for conformational stability. Conformational analysis is usually performed using NMR spectroscopy through measurement of coupling constants at room or low temperature in different solvents to determine the populations of conformers in solution. Quantum mechanical calculations are used to address the interactions responsible for conformer stability. The conformational analysis of a large number of small molecules is described, using coupling constant measurements in different solvents and at low temperature, as well as recent applications of through-space and through-hydrogen bond coupling constants JFH as tools for the conformational analysis of fluorinated molecules. Besides NMR parameters, stereoelectronic interactions such as conjugative, hyperconjugative, steric and intramolecular hydrogen bond interactions involved in conformational preferences are discussed.
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Affiliation(s)
- Cláudio F Tormena
- Institute of Chemistry, University of Campinas, PO Box 6154, 13083-970 Campinas, Sao Paulo, Brazil.
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9
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Arras J, Eichele K, Maryasin B, Schubert H, Ochsenfeld C, Wesemann L. Intermolecular 119Sn,31P Through-Space Spin–Spin Coupling in a Solid Bivalent Tin Phosphido Complex. Inorg Chem 2016; 55:4669-75. [DOI: 10.1021/acs.inorgchem.6b00573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janet Arras
- Institut
für Anorganische Chemie, Universität Tübingen, Auf
der Morgenstelle 18, 72076 Tübingen, Germany
- Theoretische
Chemie, University of Munich (LMU Munich), Butenandtstraße 7, 81377 Munich, Germany
| | - Klaus Eichele
- Institut
für Anorganische Chemie, Universität Tübingen, Auf
der Morgenstelle 18, 72076 Tübingen, Germany
| | - Boris Maryasin
- Theoretische
Chemie, University of Munich (LMU Munich), Butenandtstraße 7, 81377 Munich, Germany
| | - Hartmut Schubert
- Institut
für Anorganische Chemie, Universität Tübingen, Auf
der Morgenstelle 18, 72076 Tübingen, Germany
| | - Christian Ochsenfeld
- Theoretische
Chemie, University of Munich (LMU Munich), Butenandtstraße 7, 81377 Munich, Germany
| | - Lars Wesemann
- Institut
für Anorganische Chemie, Universität Tübingen, Auf
der Morgenstelle 18, 72076 Tübingen, Germany
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10
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Wiegand T, Eckert H, Ren J, Brunklaus G, Fröhlich R, Daniliuc CG, Lübbe G, Bussmann K, Kehr G, Erker G, Grimme S. Indirect “No-Bond” 31P···31P Spin–Spin Couplings in P,P-[3]Ferrocenophanes: Insights from Solid-State NMR Spectroscopy and DFT Calculations. J Phys Chem A 2014; 118:2316-31. [DOI: 10.1021/jp500172b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Thomas Wiegand
- Institut
für Physikalische Chemie and Graduate School of Chemistry, WWU Münster, Corrensstrasse 30, D 48149 Münster, Germany
| | - Hellmut Eckert
- Institut
für Physikalische Chemie and Graduate School of Chemistry, WWU Münster, Corrensstrasse 30, D 48149 Münster, Germany
| | - Jinjun Ren
- Institut
für Physikalische Chemie and Graduate School of Chemistry, WWU Münster, Corrensstrasse 30, D 48149 Münster, Germany
| | - Gunther Brunklaus
- Institut
für Physikalische Chemie and Graduate School of Chemistry, WWU Münster, Corrensstrasse 30, D 48149 Münster, Germany
| | - Roland Fröhlich
- Organisch-Chemisches
Institut, WWU Münster, Corrensstrasse 40, D 48149 Münster, Germany
| | | | - Gerrit Lübbe
- Organisch-Chemisches
Institut, WWU Münster, Corrensstrasse 40, D 48149 Münster, Germany
| | - Kathrin Bussmann
- Organisch-Chemisches
Institut, WWU Münster, Corrensstrasse 40, D 48149 Münster, Germany
| | - Gerald Kehr
- Organisch-Chemisches
Institut, WWU Münster, Corrensstrasse 40, D 48149 Münster, Germany
| | - Gerhard Erker
- Organisch-Chemisches
Institut, WWU Münster, Corrensstrasse 40, D 48149 Münster, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische
und Theoretische Chemie, Universität Bonn, Beringstrasse 4, D 53155 Bonn, Germany
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11
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Křístková A, Asher JR, Malkin VG, Malkina OL. Indirect Nuclear 15N–15N Scalar Coupling through a Hydrogen Bond: Dependence on Structural Parameters Studied by Quantum Chemistry Tools. J Phys Chem A 2013; 117:9235-44. [DOI: 10.1021/jp404650b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anežka Křístková
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská
cesta 9, SK-84536 Bratislava, Slovakia
| | - James R. Asher
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská
cesta 9, SK-84536 Bratislava, Slovakia
| | - Vladimir G. Malkin
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská
cesta 9, SK-84536 Bratislava, Slovakia
- Faculty
of Materials Science and Technology, Slovak University of Technology in Bratislava, Paulínska 16, SK-91724 Trnava, Slovakia
| | - Olga L. Malkina
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská
cesta 9, SK-84536 Bratislava, Slovakia
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Bühl M, Knight FR, Křístková A, Malkin Ondík I, Malkina OL, Randall RAM, Slawin AMZ, Woollins JD. Weak Te,Te interactions through the looking glass of NMR spin-spin coupling. Angew Chem Int Ed Engl 2013; 52:2495-8. [PMID: 23345140 PMCID: PMC3625736 DOI: 10.1002/anie.201205998] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/14/2012] [Indexed: 11/18/2022]
Affiliation(s)
- Michael Bühl
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK.
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13
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Bühl M, Knight FR, Křístková A, Malkin Ondík I, Malkina OL, Randall RAM, Slawin AMZ, Woollins JD. Weak Te,Te Interactions through the Looking Glass of NMR Spin-Spin Coupling. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201205998] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Contreras RH, Tormena CF, Ducati LC. Transmission Mechanisms of the Fermi-Contact Term of Spin–Spin Couplings. SCIENCE AND TECHNOLOGY OF ATOMIC, MOLECULAR, CONDENSED MATTER & BIOLOGICAL SYSTEMS 2013. [DOI: 10.1016/b978-0-444-59411-2.00008-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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García de la Vega J, San Fabián J. Analysis of Contributions to Spin–Spin Coupling Constants by the Natural J-Coupling Method. SCIENCE AND TECHNOLOGY OF ATOMIC, MOLECULAR, CONDENSED MATTER & BIOLOGICAL SYSTEMS 2013. [DOI: 10.1016/b978-0-444-59411-2.00006-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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