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Nazarski RB. Ambient temperature 1H/ 13C NMR spectra of sodium 3-(trimethylsilyl)propane-1-sulfonate (DSS) in D 2O referenced to external TMS: A discussion of these and closely related results. Corrections for the bulk magnetic susceptibility effect for aqueous NMR samples. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:535-543. [PMID: 38404187 DOI: 10.1002/mrc.5440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
This study aimed to obtain the title spectra and verify the temperature dependence of δDSS of the HOD signal from D2O of the NMR sample. However, the analysis of the collected δX data, extended by the results of other closely related measurements reported in the literature, provided important guidelines for performing routine 1H/13C NMR spectra in aqueous solvents externally referenced to neat liquid TMS contained in a coaxial capillary. Therefore, it is recommended that the previously proposed correction of δX data thus determined, which is mainly due to the difference in volume magnetic susceptibility χv between the sample and the external standard used, usually called the bulk magnetic susceptibility (BMS) correction, has been increased by +0.05 ppm (7%). The new value of this correction, +0.73 ppm, based on NMR experiments carried out at a standard temperature of 25°C, was confirmed in a classical approach using critically reviewed χm, χM, and ρ data for TMS, D2O, and H2O. The BMS correction for H2O solutions is +0.75 ppm. Important issues concerning magnetic susceptibility measurements for D2O and H2O, coaxial bulb-ended inserts, and the geometry of two-tube NMR cells (shape factor αav) are also critically discussed here, partly from a historical perspective.
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Affiliation(s)
- Ryszard B Nazarski
- University of Lodz, Faculty of Chemistry, Department of Physical Chemistry, Theoretical and Structural Chemistry Group, Łódź, Poland
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Nazarski RB. Summary of DFT calculations coupled with current statistical and/or artificial neural network (ANN) methods to assist experimental NMR data in identifying diastereomeric structures. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Köcher SS, Düwel S, Hundshammer C, Glaser SJ, Schilling F, Granwehr J, Scheurer C. Ab Initio Simulation of pH-Sensitive Biomarkers in Magnetic Resonance Imaging. J Phys Chem A 2018; 122:7983-7990. [PMID: 30222345 DOI: 10.1021/acs.jpca.8b04665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An ab initio simulation scheme is introduced as a theoretical prescreening approach to facilitate and enhance the research for pH-sensitive biomarkers. The proton 1H and carbon 13C nuclear magnetic resonance (NMR) chemical shifts of the recently published marker for extracellular pH, [1,5-13C2]zymonic acid (ZA), and the as yet unpublished ( Z)-4-methyl-2-oxopent-3-enedioic acid (OMPD) were calculated with ab initio methods as a function of the pH. The influence of the aqueous solvent was taken into account either by an implicit solvent model or by explicit water molecules, where the latter improved the accuracy of the calculated chemical shifts considerably. The theoretically predicted chemical shifts allowed for a reliable NMR peak assignment. The p Ka value of the first deprotonation of ZA and OMPD was simulated successfully whereas the parametrization of the implicit solvent model does not allow for an accurate description of the second p Ka. The theoretical models reproduce the pH-induced chemical shift changes and the first p Ka with sufficient accuracy to establish the ab initio prescreening approach as a valuable support to guide the experimental search for pH-sensitive biomarkers.
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Affiliation(s)
- Simone S Köcher
- Chair for Theoretical Chemistry and Catalysis Research Center , Technische Universität München , Lichtenbergstr. 4 , D-85747 Garching , Germany.,Institute of Energy and Climate Research (IEK-9) , Forschungszentrum Jülich , D-52425 Jülich , Germany.,Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Worringerweg 1-2 , D-52074 Aachen , Germany
| | - Stephan Düwel
- Department of Nuclear Medicine, Klinikum rechts der Isar , Technische Universität München , Ismaninger Str. 22 , D-81675 München , Germany.,Department of Chemistry , Technische Universität München , Lichtenbergstr. 4 , D-85747 Garching , Germany.,Munich School of BioEngineering , Technische Universität München , Boltzmannstr. 11 , D-85748 Garching , Germany
| | - Christian Hundshammer
- Department of Nuclear Medicine, Klinikum rechts der Isar , Technische Universität München , Ismaninger Str. 22 , D-81675 München , Germany.,Department of Chemistry , Technische Universität München , Lichtenbergstr. 4 , D-85747 Garching , Germany
| | - Steffen J Glaser
- Department of Chemistry , Technische Universität München , Lichtenbergstr. 4 , D-85747 Garching , Germany
| | - Franz Schilling
- Department of Nuclear Medicine, Klinikum rechts der Isar , Technische Universität München , Ismaninger Str. 22 , D-81675 München , Germany
| | - Josef Granwehr
- Institute of Energy and Climate Research (IEK-9) , Forschungszentrum Jülich , D-52425 Jülich , Germany.,Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Worringerweg 1-2 , D-52074 Aachen , Germany
| | - Christoph Scheurer
- Chair for Theoretical Chemistry and Catalysis Research Center , Technische Universität München , Lichtenbergstr. 4 , D-85747 Garching , Germany
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Nazarski RB, Justyna K, Leśniak S, Chrostowska A. A Benefit of Using the IDSCRF- over UFF-Radii Cavities and Why Joint Correlations of NMR Chemical Shifts Can Be Advantageous: Condensed Pyridines as an IEF-PCM/GIAO/DFT Case Study. J Phys Chem A 2016; 120:9519-9528. [PMID: 27933911 DOI: 10.1021/acs.jpca.6b10457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, an advantage of the use of IDSCRF- over UFF-radii-based solute cavities in GIAO/DFT calculations is presented for the 13C and especially 15N NMR chemical shifts made for several bicyclic aromatic nitrogen heterocycles in CDCl3 solution treated within the classical IEF-PCM solvation scheme. Successful application of the IDSCRF-radii in the non 1:1 joint multinuclear 1H/13C and particularly 1H/13C/15N correlations of the measured δH,C(,N) values to those obtained theoretically is also documented for a series of test systems (-268 ≤ δN ≤ -72 ppm). The experimentally yet unknown δN's were found in this way for the title compounds via a trinuclear eq 1 determined for an optimally chosen value of the multiplication factor of initial raw δH data (mH = 10). Such a simultaneous analysis of the δH,C(,N) data is proposed as a novel method to study the solution structure of the other similar conformationally homogeneous (bio)organic compounds. The issue of small spurious imaginary vibrational frequencies computed for a few molecular systems using the Gaussian 09 default UFF-radii is briefly considered as well.
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Affiliation(s)
- Ryszard B Nazarski
- Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź , Pomorska 163, 90-236 Łódź, Poland
| | - Katarzyna Justyna
- Department of Organic and Applied Chemistry, Faculty of Chemistry, University of Łódź , Tamka 12, 91-403 Łódź, Poland.,Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Université de Pau et des Pays de l'Adour , 2 av. Président Pierre Angot, 64053 Pau Cedex 9, France
| | - Stanisław Leśniak
- Department of Organic and Applied Chemistry, Faculty of Chemistry, University of Łódź , Tamka 12, 91-403 Łódź, Poland
| | - Anna Chrostowska
- Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Université de Pau et des Pays de l'Adour , 2 av. Président Pierre Angot, 64053 Pau Cedex 9, France
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Nazarski RB, Wałejko P, Witkowski S. Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound. Org Biomol Chem 2016; 14:3142-58. [DOI: 10.1039/c5ob01865j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl3and relatedδH,C/nJHHIEF-PCM(UFF,CHCl3)/DFT calculational results.
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Affiliation(s)
- Ryszard B. Nazarski
- University of Łódź
- Faculty of Chemistry
- Department of Theoretical and Structural Chemistry
- 90-236 Łódź
- Poland
| | - Piotr Wałejko
- University of Białystok
- Institute of Chemistry
- 15-245 Białystok
- Poland
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Mancini DT, Souza EF, Caetano MS, Ramalho TC. 99Tc NMR as a promising technique for structural investigation of biomolecules: theoretical studies on the solvent and thermal effects of phenylbenzothiazole complex. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:129-137. [PMID: 24446055 DOI: 10.1002/mrc.4043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 12/15/2013] [Accepted: 12/18/2013] [Indexed: 06/03/2023]
Abstract
The phenylbenzothiazole compounds show antitumor properties and are highly selective. In this paper, the (99)Tc chemical shifts based on the ((99m)Tc)(CO)3 (NNO) complex conjugated to the antitumor agent 2-(4'-aminophenyl)benzothiazole are reported. Thermal and solvent effects were studied computationally by quantum-chemical methods, using the density functional theory (DFT) (DFT level BPW91/aug-cc-pVTZ for the Tc and BPW91/IGLO-II for the other atoms) to compute the NMR parameters for the complex. We have calculated the (99)Tc NMR chemical shifts of the complex in gas phase and solution using different solvation models (polarizable continuum model and explicit solvation). To evaluate the thermal effect, molecular dynamics simulations were carried, using the atom-centered density matrix propagation method at the DFT level (BP86/LanL2dz). The results highlight that the (99)Tc NMR spectroscopy can be a promising technique for structural investigation of biomolecules, at the molecular level, in different environments.
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Affiliation(s)
- Daiana T Mancini
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
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Skorupska EA, Nazarski RB, Ciechańska M, Jóźwiak A, Kłys A. Dynamic 1H NMR spectroscopic study of hindered internal rotation in selected N,N-dialkyl isonicotinamides: an experimental and DFT analysis. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.07.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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