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Maste S, Sharma B, Pongratz T, Grabe B, Hiller W, Erlach MB, Kremer W, Kalbitzer HR, Marx D, Kast SM. The accuracy limit of chemical shift predictions for species in aqueous solution. Phys Chem Chem Phys 2024; 26:6386-6395. [PMID: 38315169 DOI: 10.1039/d3cp05471c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Interpreting NMR experiments benefits from first-principles predictions of chemical shifts. Reaching the accuracy limit of theory is relevant for unambiguous structural analysis and dissecting theoretical approximations. Since accurate chemical shift measurements are based on using internal reference compounds such as trimethylsilylpropanesulfonate (DSS), a detailed comparison of experimental with theoretical data requires simultaneous consideration of both target and reference species ensembles in the same solvent environment. Here we show that ab initio molecular dynamics simulations to generate liquid-state ensembles of target and reference compounds, including explicitly their short-range solvation environments and combined with quantum-mechanical solvation models, allows for predicting highly accurate 1H (∼0.1-0.5 ppm) and aliphatic 13C (∼1.5 ppm) chemical shifts for aqueous solutions of the model compounds trimethylamine N-oxide (TMAO) and N-methylacetamide (NMA), referenced to DSS without any system-specific adjustments. This encompasses the two peptide bond conformations of NMA identified by NMR. The results are used to derive a general-purpose guideline set for predictive NMR chemical shift calculations of NMA in the liquid state and to identify artifacts of force field models. Accurate predictions are only obtained if a sufficient number of explicit water molecules is included in the quantum-mechanical calculations, disproving a purely electrostatic model of the solvent effect on chemical shifts.
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Affiliation(s)
- Stefan Maste
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Bikramjit Sharma
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Tim Pongratz
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Bastian Grabe
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Wolf Hiller
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Markus Beck Erlach
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Werner Kremer
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Hans Robert Kalbitzer
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Stefan M Kast
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
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Pem B, Toma M, Vrček V, Vinković Vrček I. Combined NMR and Computational Study of Cysteine Oxidation during Nucleation of Metallic Clusters in Biological Systems. Inorg Chem 2021; 60:4144-4161. [PMID: 33657797 DOI: 10.1021/acs.inorgchem.1c00321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The widespread biomedical applications of silver and gold nanoparticles (AgNPs and AuNPs, respectively) prompt the need for mechanistic evaluation of their interaction with biomolecules. In biological media, metallic NPs are known to transform by various pathways, especially in the presence of thiols. The interplay between metallic NPs and thiols may lead to unpredictable consequences for the health status of an organism. This study explored the potential events occurring during biotransformation, dissolution, and reformation of NPs in the thiol-rich biological media. The study employed a model system evaluating the interaction of cysteine with small-sized AgNPs and AuNPs. The interplay of cysteine on transformation and reformation pathways of these NPs was experimentally investigated by nuclear magnetic resonance (NMR) spectroscopy and supported by light scattering techniques and transmission electron microscopy (TEM). As the main outcome, Ag- or Au-catalyzed oxidation of cysteine to cystine was found to occur through generation of reactive oxygen species (ROS). Computational simulations confirmed this mechanism and the role of ROS in the oxidative dimerization of biothiol during NPs reformation. The obtained results represent valuable mechanistic data about the complex events during the transport of metallic NPs in thiol-rich biological systems that should be considered for the future biomedical applications of metal-based nanomaterials.
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Affiliation(s)
- Barbara Pem
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Mateja Toma
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Valerije Vrček
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Ivana Vinković Vrček
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000 Zagreb, Croatia
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Casabianca LB. Calculating nuclear magnetic resonance chemical shifts in solvated systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:611-624. [PMID: 31916612 DOI: 10.1002/mrc.4994] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
The nuclear magnetic resonance (NMR) chemical shift is extremely sensitive to molecular geometry, hydrogen bonding, solvent, temperature, pH, and concentration. Calculated magnetic shielding constants, converted to chemical shifts, can be valuable aids in NMR peak assignment and can also give detailed information about molecular geometry and intermolecular effects. Calculating chemical shifts in solution is complicated by the need to include solvent effects and conformational averaging. Here, we review the current state of NMR chemical shift calculations in solution, beginning with an introduction to the theory of calculating magnetic shielding in general, then covering methods for inclusion of solvent effects and conformational averaging, and finally discussing examples of applications using calculated chemical shifts to gain detailed structural information.
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Affiliation(s)
- Leah B Casabianca
- Department of Chemistry, Clemson University, Clemson, South Carolina
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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: 14] [Impact Index Per Article: 3.5] [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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Imamura K, Yamazaki T, Yokogawa D, Higashi M, Sato H. Nuclear magnetic shielding of molecule in solution based on reference interaction site model self-consistent field with spatial electron density distribution. J Chem Phys 2020; 152:194102. [DOI: 10.1063/5.0008903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Takeshi Yamazaki
- 1QB Information Technologies (1QBit), 200-1285 West Pender Street, Vancouver, British Columbia V6E 4B1, Canada
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Masahiro Higashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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Semenov VA, Samultsev DO, Krivdin LB. Calculation of 15N NMR Chemical Shifts in a Diversity of Nitrogen-Containing Compounds Using Composite Method Approximation at the DFT, MP2, and CCSD Levels. J Phys Chem A 2019; 123:8417-8426. [PMID: 31465226 DOI: 10.1021/acs.jpca.9b06780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computations of 15N NMR chemical shifts in 93 diverse nitrogen-containing compounds representing almost all known classes are performed at the density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2), and coupled cluster singles and doubles (CCSD) levels using the composite method approximation (CMA) in comparison with experimental results. It is shown that the CMA-DFT and CMA-CCSD methods provided the best performance characterized by a normalized mean absolute error of 1.1-1.3% as compared to 2.3% for the CMA-MP2 results. Taking into account solvent effects within the conductor-like polarizable continuum model decreased the normalized mean absolute error by 0.4% for the CMA-DFT and by 0.2% for the CMA-CCSD calculations.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry , Siberian Branch of the Russian Academy of Sciences , Favorsky St. 1 , 664033 Irkutsk , Russia
| | - Dmitry O Samultsev
- 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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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: 0.6] [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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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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