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Ahmed R, Siskos MG, Siddiqui H, Gerothanassis IP. Density functional theory calculations of δ( 13 C) and δ( 1 H) chemical shifts and 3 J( 13 COO 1 H) coupling constants as structural and analytical tools in hydroperoxides: Prospects and limitations of 1 H 13 C heteronuclear multiple bond correlation experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:970-984. [PMID: 35830967 DOI: 10.1002/mrc.5298] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/18/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
Density functional theory (DFT) calculations of δ(13 C) and δ(1 H) chemical shifts and 3 J(13 COO1 H) coupling constants of three model hydroperoxides of the naturally occurring cis-11-OOH and trans-9-OOH isomers of oleate and 9-cis, 11-trans-16-OOH endo hydroperoxide of methyl linolenate are reported. The computational δ(OOH) for various functionals and basis sets were found to be nearly identical for the cis/trans geometric isomers. The chemical shifts of the methine CHOOH protons and carbons, on the contrary, are highly diagnostic for the identification of cis/trans geometric isomerism. The chemical shifts of the olefinic protons and carbons strongly depend on the orientation of the hydroperoxide unit relative to the double bond and, thus, of importance in conformational analysis. The results are in very good agreement with the available experimental data. For the various diastereomeric pairs of the model endo-hydroperoxide, the strongly deshielded OOH resonances, due to the presence of an intramolecular hydrogen bond between the hydroperoxide proton and an oxygen of the endo-peroxide ring, along with the δ(CHOOH), are highly diagnostic for identification and structure elucidation of complex erythro- and threo- diastereomeric pairs of endo-hydroperoxides; the computational results are in very good agreement with the available experimental data. The 3 J(13 COO1 H) coupling constants were found to be < 2 Hz for the cis-trans geometric models and < 0.5 Hz for the endo-hydroperoxide and, thus, unimportant in stereochemical analysis. Sharp resonances of the hydroperoxide protons, with Δν1/2 < 3 Hz, are required for the successful implementation of the 1 H13 C heteronuclear multiple bond correlation (HMBC) technique.
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Affiliation(s)
- Raheel Ahmed
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Michael G Siskos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - Hina Siddiqui
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ioannis P Gerothanassis
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
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2
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Kontogianni VG, Gerothanassis IP. Analytical and Structural Tools of Lipid Hydroperoxides: Present State and Future Perspectives. Molecules 2022; 27:2139. [PMID: 35408537 PMCID: PMC9000705 DOI: 10.3390/molecules27072139] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/17/2022] Open
Abstract
Mono- and polyunsaturated lipids are particularly susceptible to peroxidation, which results in the formation of lipid hydroperoxides (LOOHs) as primary nonradical-reaction products. LOOHs may undergo degradation to various products that have been implicated in vital biological reactions, and thus in the pathogenesis of various diseases. The structure elucidation and qualitative and quantitative analysis of lipid hydroperoxides are therefore of great importance. The objectives of the present review are to provide a critical analysis of various methods that have been widely applied, and more specifically on volumetric methods, applications of UV-visible, infrared, Raman/surface-enhanced Raman, fluorescence and chemiluminescence spectroscopies, chromatographic methods, hyphenated MS techniques, NMR and chromatographic methods, NMR spectroscopy in mixture analysis, structural investigations based on quantum chemical calculations of NMR parameters, applications in living cells, and metabolomics. Emphasis will be given to analytical and structural methods that can contribute significantly to the molecular basis of the chemical process involved in the formation of lipid hydroperoxides without the need for the isolation of the individual components. Furthermore, future developments in the field will be discussed.
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Affiliation(s)
- Vassiliki G. Kontogianni
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
| | - Ioannis P. Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
- International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi 75270, Pakistan
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Szell PMJ, Nilsson Lill SO, Blade H, Brown SP, Hughes LP. A toolbox for improving the workflow of NMR crystallography. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 116:101761. [PMID: 34736104 DOI: 10.1016/j.ssnmr.2021.101761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
NMR crystallography is a powerful tool with applications in structural characterization and crystal structure verification, to name two. However, applying this tool presents several challenges, especially for industrial users, in terms of consistency, workflow, time consumption, and the requirement for a high level of understanding of experimental solid-state NMR and GIPAW-DFT calculations. Here, we have developed a series of fully parameterized scripts for use in Materials Studio and TopSpin, based on the .magres file format, with a focus on organic molecules (e.g. pharmaceuticals), improving efficiency, robustness, and workflow. We separate these tools into three major categories: performing the DFT calculations, extracting & visualizing the results, and crystallographic modelling. These scripts will rapidly submit fully parameterized CASTEP jobs, extract data from the calculations, assist in visualizing the results, and expedite the process of structural modelling. Accompanied with these tools is a description on their functionality, documentation on how to get started and use the scripts, and links to video tutorials for guiding new users. Through the use of these tools, we hope to facilitate NMR crystallography and to harmonize the process across users.
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Affiliation(s)
| | - Sten O Nilsson Lill
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Helen Blade
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
| | - Leslie P Hughes
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK.
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Fatima S, Varras PC, Atia-Tul-Wahab, Choudhary MI, Siskos MG, Gerothanassis IP. On the molecular basis of H 2O/DMSO eutectic mixtures by using phenol compounds as molecular sensors: a combined NMR and DFT study. Phys Chem Chem Phys 2021; 23:15645-15658. [PMID: 34268541 DOI: 10.1039/d0cp05861k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NMR and DFT studies of phenol compounds as molecular sensors were carried out to investigate H2O/DMSO eutectic mixtures at a molecular level. The experimental 1H NMR chemical shifts of the OH groups, δexp(OH), of phenol, paracoumaric acid, and vanillic acid show maximum deshielding and, thus, hydrogen bond interactions in the range of mole fractions 0.20 < χ(DMSO) < 0.33. In the mole fractions χ(DMSO) < 0.2, a progressive decrease in δexp(OH) was observed which demonstrates a decrease in hydrogen bond interactions at infinite dilution in H2O, despite the increase in the number of available hydrogen bond acceptor and donor sites. DFT calculated δcalc(OH) of minimum energy solvation clusters were shown to be in reasonable agreement with the pattern in experimental δexp(OH) data. The chemical shift deshielding and, thus, increased hydrogen bond interactions in the natural product + DMSO + nH2O (n = 2, 3) solvation clusters, relative to complexes in DMSO or H2O solutions, cannot be attributed to a single structural parameter of the cooperative interactions between H2O and DMSO molecules with the phenol OH groups of the natural products. The minimum energy conformers of phenol compounds + 2H2O + DMSO complexes are in excellent agreement with a recent low temperature neutron diffraction experiment of 3D2O + DMSO and demonstrate a general structural motif of solvation complexes. The combined use of 1H NMR and DFT studies with emphasis on δ(OH) of phenol compounds, as molecular sensors, can provide an effective method for the study of solute-solvent interactions at the atomic level.
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Affiliation(s)
- Sana Fatima
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 7527, Pakistan
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DFT Calculations of 1H NMR Chemical Shifts of Geometric Isomers of Conjugated Linolenic Acids, Hexadecatrienyl Pheromones, and Model Triene-Containing Compounds: Structures in Solution and Revision of NMR Assignments. Molecules 2021; 26:molecules26113477. [PMID: 34200468 PMCID: PMC8201138 DOI: 10.3390/molecules26113477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
A DFT study of the 1H NMR chemical shifts, δ(1H), of geometric isomers of 18:3 conjugated linolenic acids (CLnAs), hexadecatrienyl pheromones, and model triene-containing compounds is presented, using standard functionals (B3LYP and PBE0) as well as corrections for dispersion interactions (B3LYP-D3, APFD, M06–2X and ωB97XD). The results are compared with literature experimental δ(1H) data in solution. The closely spaced “inside” olefinic protons are significantly more deshielded due to short-range through-space H…H steric interactions and appear close to or even beyond δ-values of aromatic systems. Several regularities of the computational δ(1H) of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest-energy DFT-optimized single conformer for all functionals used and are in very good agreement with experimental δ(1H) in solution. Examples are provided of literature studies in which experimental resonance assignments deviate significantly from DFT predictions and, thus, should be revised. We conclude that DFT calculations of 1H chemical shifts of trienyl compounds are powerful tools (i) for the accurate prediction of δ(1H) even with less demanding functionals and basis sets; (ii) for the unequivocal identification of geometric isomerism of conjugated trienyl systems that occur in nature; (iii) for tackling complex problems of experimental resonance assignments due to extensive signal overlap; and (iv) for structure elucidation in solution.
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Ahmed R, Varras PC, Siskos MG, Siddiqui H, Choudhary MI, Gerothanassis IP. NMR and Computational Studies as Analytical and High-Resolution Structural Tool for Complex Hydroperoxides and Diastereomeric Endo-Hydroperoxides of Fatty Acids in Solution-Exemplified by Methyl Linolenate. Molecules 2020; 25:E4902. [PMID: 33113947 PMCID: PMC7660186 DOI: 10.3390/molecules25214902] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/17/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022] Open
Abstract
A combination of selective 1D Total Correlation Spectroscopy (TOCSY) and 1H-13C Heteronuclear Multiple Bond Correlation (HMBC) NMR techniques has been employed for the identification of methyl linolenate primary oxidation products without the need for laborious isolation of the individual compounds. Complex hydroperoxides and diastereomeric endo-hydroperoxides were identified and quantified. Strongly deshielded C-O-O-H 1H-NMR resonances of diastereomeric endo-hydroperoxides in the region of 8.8 to 9.6 ppm were shown to be due to intramolecular hydrogen bonding interactions of the hydroperoxide proton with an oxygen atom of the five-member endo-peroxide ring. These strongly deshielded resonances were utilized as a new method to derive, for the first time, three-dimensional structures with an assignment of pairs of diastereomers in solution with the combined use of 1H-NMR chemical shifts, Density Functional Theory (DFT), and Our N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) calculations.
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Affiliation(s)
- Raheel Ahmed
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (R.A.); (M.I.C.)
| | - Panayiotis C. Varras
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (P.C.V.); (M.G.S.)
| | - Michael G. Siskos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (P.C.V.); (M.G.S.)
| | - Hina Siddiqui
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (R.A.); (M.I.C.)
| | - M. Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (R.A.); (M.I.C.)
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 214412, Saudi Arabia
| | - Ioannis P. Gerothanassis
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (R.A.); (M.I.C.)
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (P.C.V.); (M.G.S.)
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DFT Calculations of 1H- and 13C-NMR Chemical Shifts of Geometric Isomers of Conjugated Linoleic Acid (18:2 ω-7) and Model Compounds in Solution. Molecules 2020; 25:molecules25163660. [PMID: 32796664 PMCID: PMC7463970 DOI: 10.3390/molecules25163660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
A density functional theory (DFT) study of the 1H- and 13C-NMR chemical shifts of the geometric isomers of 18:2 ω-7 conjugated linoleic acid (CLA) and nine model compounds is presented, using five functionals and two basis sets. The results are compared with available experimental data from solution high resolution nuclear magnetic resonance (NMR). The experimental 1H chemical shifts exhibit highly diagnostic resonances due to the olefinic protons of the conjugated double bonds. The "inside" olefinic protons of the conjugated double bonds are deshielded than those of the "outside" protons. Furthermore, in the cis/trans isomers, the signals of the cis bonds are more deshielded than those of the trans bonds. These regularities of the experimental 1H chemical shifts of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest energy DFT optimized single conformer, for all functionals and basis sets used. The other low energy conformers have negligible effects on the computational 1H-NMR chemical shifts. We conclude that proton NMR chemical shifts are more discriminating than carbon, and DFT calculations can provide a valuable tool for (i) the accurate prediction of 1H-NMR chemical shifts even with less demanding functionals and basis sets; (ii) the unequivocal identification of geometric isomerism of CLAs that occur in nature, and (iii) to derive high resolution structures in solution.
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Siskos MG, Varras PC, Gerothanassis IP. DFT calculations of O–H⋯O 1H NMR chemical shifts in investigating enol-enol tautomeric equilibria: Probing the impacts of intramolecular hydrogen bonding vs stereoelectronic interactions. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.130979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhou S, Wang L. Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects. Phys Chem Chem Phys 2020; 22:4884-4895. [DOI: 10.1039/c9cp06840f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electronic and nuclear quantum effects determine the symmetry and highly downfield 1H NMR chemical shifts of short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
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Mari SH, Varras PC, Atia-tul-Wahab, Choudhary IM, Siskos MG, Gerothanassis IP. Solvent-Dependent Structures of Natural Products Based on the Combined Use of DFT Calculations and 1H-NMR Chemical Shifts. Molecules 2019; 24:E2290. [PMID: 31226776 PMCID: PMC6631582 DOI: 10.3390/molecules24122290] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 01/09/2023] Open
Abstract
Detailed solvent and temperature effects on the experimental 1H-NMR chemical shifts of the natural products chrysophanol (1), emodin (2), and physcion (3) are reported for the investigation of hydrogen bonding, solvation and conformation effects in solution. Very small chemical shift of │Δδ│ < 0.3 ppm and temperature coefficients │Δδ/ΔΤ│ ≤ 2.1 ppb/K were observed in DMSO-d6, acetone-d6 and CDCl3 for the C(1)-OH and C(8)-OH groups which demonstrate that they are involved in a strong intramolecular hydrogen bond. On the contrary, large chemical shift differences of 5.23 ppm at 298 K and Δδ/ΔΤ values in the range of -5.3 to -19.1 ppb/K between DMSO-d6 and CDCl3 were observed for the C(3)-OH group which demonstrate that the solvation state of the hydroxyl proton is a key factor in determining the value of the chemical shift. DFT calculated 1H-NMR chemical shifts, using various functionals and basis sets, the conductor-like polarizable continuum model, and discrete solute-solvent hydrogen bond interactions, were found to be in very good agreement with the experimental 1H-NMR chemical shifts even with computationally less demanding level of theory. The 1H-NMR chemical shifts of the OH groups which participate in intramolecular hydrogen bond are dependent on the conformational state of substituents and, thus, can be used as molecular sensors in conformational analysis. When the X-ray structures of chrysophanol (1), emodin (2), and physcion (3) were used as input geometries, the DFT-calculated 1H-NMR chemical shifts were shown to strongly deviate from the experimental chemical shifts and no functional dependence could be obtained. Comparison of the most important intramolecular data of the DFT calculated and the X-ray structures demonstrate significant differences for distances involving hydrogen atoms, most notably the intramolecular hydrogen bond O-H and C-H bond lengths which deviate by 0.152 tο 0.132 Å and 0.133 to 0.100 Å, respectively, in the two structural methods. Further differences were observed in the conformation of -OH, -CH3, and -OCH3 substituents.
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Affiliation(s)
- Saima H. Mari
- H.E.J. Research Institute of chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 7527, Pakistan; Saimahassanmari123@gmail (S.H.M.); (I.M.C.)
| | - Panayiotis C. Varras
- Section of Organic Chemistry & Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (P.C.V.); (M.G.S.)
| | - Atia-tul-Wahab
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 7527, Pakistan
| | - Iqbal M. Choudhary
- H.E.J. Research Institute of chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 7527, Pakistan; Saimahassanmari123@gmail (S.H.M.); (I.M.C.)
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 7527, Pakistan
| | - Michael G. Siskos
- Section of Organic Chemistry & Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (P.C.V.); (M.G.S.)
| | - Ioannis P. Gerothanassis
- H.E.J. Research Institute of chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 7527, Pakistan; Saimahassanmari123@gmail (S.H.M.); (I.M.C.)
- Section of Organic Chemistry & Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (P.C.V.); (M.G.S.)
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 7527, Pakistan
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Knorr R, Nadolny A, Hauer H, Böhrer P. Short Syntheses of some ‘Decalin‐1,8‐diones’ and their Derivatives: Breaking the Pretended Symmetry. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201800231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rudolf Knorr
- Department ChemieLudwig-Maximilians-Universität München Butenandtstrasse 5–13 (Haus F) DE-81377 München Germany
| | - Annette Nadolny
- Department ChemieLudwig-Maximilians-Universität München Butenandtstrasse 5–13 (Haus F) DE-81377 München Germany
| | - Hermann Hauer
- Department ChemieLudwig-Maximilians-Universität München Butenandtstrasse 5–13 (Haus F) DE-81377 München Germany
| | - Petra Böhrer
- Department ChemieLudwig-Maximilians-Universität München Butenandtstrasse 5–13 (Haus F) DE-81377 München Germany
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DFT-calculated structures based on 1H NMR chemical shifts in solution vs. structures solved by single-crystal X-ray and crystalline-sponge methods: Assessing specific sources of discrepancies. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Tarazona G, Benedit G, Fernández R, Pérez M, Rodríguez J, Jiménez C, Cuevas C. Can Stereoclusters Separated by Two Methylene Groups Be Related by DFT Studies? The Case of the Cytotoxic Meroditerpenes Halioxepines. JOURNAL OF NATURAL PRODUCTS 2018; 81:343-348. [PMID: 29393646 DOI: 10.1021/acs.jnatprod.7b00807] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
QM/NMR-DFT (quantum mechanics combined with nuclear magnetic resonance parameters calculated by density functional theory approximations) studies allowed us to link two stereoclusters separated by two methylene groups present in the new meroditerpenes halioxepine B (2) and halioxepine C (3) and the known halioxepine (1), isolated from two Indonesian sponges of the genus Haliclona (Reniera). DP4 and DP4+ probabilities were used to discriminate the two diastereotopic arrangements of the two stereoclusters, whose unconnected relative configurations were determined by ROESY and J-based configurational analysis. To confirm the DFT studies, the full relative configuration of 1 was deduced using a mixture of benzene-d6 and pyridine-d5 as the NMR solvent. ROESY measurements connected the two stereoclusters and demonstrated that DFT calculations accurately predict the configuration when two methylenes separate the two stereoclusters. The different arrangements of the distant stereoclusters C-1/C-2/C-7 and C-10/C-15 for compounds 2 and 3 were deduced by DFT calculations and explained the opposite optical rotations observed for the two compounds. Halioxepines B (2) and C (3) display moderate cytotoxicity against different human cancer cell lines.
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Affiliation(s)
- Guillermo Tarazona
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Gonzalo Benedit
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Rogelio Fernández
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Marta Pérez
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Jaime Rodríguez
- Departamento de Química, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña , 15071, A Coruña, Spain
| | - Carlos Jiménez
- Departamento de Química, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña , 15071, A Coruña, Spain
| | - Carmen Cuevas
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
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Li D, Han Y, Li H, Zhang P, Kang Q, Li Z, Shen D. The influence of isolated and penta-hydrated Zn 2+ on some of the intramolecular proton-transfer processes of thymine: a quantum chemical study. RSC Adv 2018; 8:11021-11026. [PMID: 35541537 PMCID: PMC9078977 DOI: 10.1039/c7ra13750h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/27/2018] [Indexed: 02/02/2023] Open
Abstract
The influence of isolated and penta-hydrated Zn2+ on some of the intramolecular proton-transfer processes of thymine is investigated by DFT modeling.
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Affiliation(s)
- Dejie Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Ying Han
- National Engineering Research Center for Colloidal Materials
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- P. R. China
| | - Huijuan Li
- College of Chemical and Environmental Engineering
- Shandong University of Science and Technology
- Qingdao
- P. R. China
| | - Ping Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Qi Kang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Zhihua Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Dazhong Shen
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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Alexandri E, Ahmed R, Siddiqui H, Choudhary MI, Tsiafoulis CG, Gerothanassis IP. High Resolution NMR Spectroscopy as a Structural and Analytical Tool for Unsaturated Lipids in Solution. Molecules 2017; 22:E1663. [PMID: 28981459 PMCID: PMC6151582 DOI: 10.3390/molecules22101663] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 09/28/2017] [Accepted: 10/01/2017] [Indexed: 12/13/2022] Open
Abstract
Mono- and polyunsaturated lipids are widely distributed in Nature, and are structurally and functionally a diverse class of molecules with a variety of physicochemical, biological, medicinal and nutritional properties. High resolution NMR spectroscopic techniques including 1H-, 13C- and 31P-NMR have been successfully employed as a structural and analytical tool for unsaturated lipids. The objective of this review article is to provide: (i) an overview of the critical 1H-, 13C- and 31P-NMR parameters for structural and analytical investigations; (ii) an overview of various 1D and 2D NMR techniques that have been used for resonance assignments; (iii) selected analytical and structural studies with emphasis in the identification of major and minor unsaturated fatty acids in complex lipid extracts without the need for the isolation of the individual components; (iv) selected investigations of oxidation products of lipids; (v) applications in the emerging field of lipidomics; (vi) studies of protein-lipid interactions at a molecular level; (vii) practical considerations and (viii) an overview of future developments in the field.
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Affiliation(s)
- Eleni Alexandri
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece.
| | - Raheel Ahmed
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Hina Siddiqui
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Muhammad I Choudhary
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 214412, Saudi Arabia.
| | | | - Ioannis P Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece.
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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