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Zubir MZM, Maulida NF, Abe Y, Nakamura Y, Abdelrasoul M, Taniguchi T, Monde K. Deuterium labelling to extract local stereochemical information by VCD spectroscopy in the C-D stretching region: a case study of sugars. Org Biomol Chem 2022; 20:1067-1072. [PMID: 35019932 DOI: 10.1039/d1ob02317a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stereochemical elucidation of molecules with multiple chiral centers is difficult. Even with VCD spectroscopy, excluding all but one diastereomeric structural candidate is challenging because the stereochemical inversion of one chiral center among many centers does not always result in noticeable differences in their VCD spectra. This work demonstrates that the introduction of a suitable VCD chromophore with absorption in the 2300-1900 cm-1 region can be used for extracting local stereochemical information and for the stereochemical assignment of the C-1 position of various sugars as a case study. Through studies on a series of epimeric pairs of monosaccharides and their derivatives, we found that the introduction of one -OCD3 group to each C-1 position produced almost mirror-image VCD patterns in the 2300-1900 cm-1 region depending on the C-1 stereochemistry irrespective of the other molecular moieties. This work also shows that comparison of the observed VCD signals and the calculated ones enables the stereochemical assignment of a chiral center in the vicinity of the chromophore. This study provides a proof of concept that the use of a VCD chromophore in the 2300-1900 cm-1 region enables the analysis of selected stereochemistry of suitable molecular systems. Further studies on this concept should lead to the development of a method useful for the structural elucidation of other types of complex molecules.
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Affiliation(s)
| | - Nurul Fajry Maulida
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Yoshihiro Abe
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Yuta Nakamura
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Mariam Abdelrasoul
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.,Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
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Scholten K, Engelage E, Merten C. Basis set dependence of S[double bond, length as m-dash]O stretching frequencies and its consequences for IR and VCD spectra predictions. Phys Chem Chem Phys 2020; 22:27979-27986. [PMID: 33290469 DOI: 10.1039/d0cp05420h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Benchmarking functionals and basis sets for the computational prediction of molecular properties is usually done on very small model systems. Larger organic molecules containing heavier second row atoms are not the typical model structures. We herein present the first survey of basis sets and functionals for the prediction of the IR and VCD spectra of chiral tosylates and sulfinates as we noted drastic deviations between computed harmonic frequencies obtained at B3LYP/6-311++G(2d,p) level of theory and those observed in experimental solution phase IR and VCD spectra. We show that the harmonic frequencies of the asymmetric and symmetric S[double bond, length as m-dash]O stretching modes of tosylates are predicted at significantly too low vibrational frequencies if the employed basis set does not provide higher order polarization functions. The results of our benchmarks show that at least the 6-311G(3df,2dp) basis (or equivalent Dunning and Ahlrichs variants) should be used.
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Affiliation(s)
- Kevin Scholten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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Taniguchi T, Nakano K, Baba R, Monde K. Analysis of Configuration and Conformation of Furanose Ring in Carbohydrate and Nucleoside by Vibrational Circular Dichroism. Org Lett 2017; 19:404-407. [PMID: 28045273 DOI: 10.1021/acs.orglett.6b03626] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A reliable and convenient method for determining the configuration and conformation of the furanose ring in carbohydrates and nucleosides by vibrational circular dichroism (VCD) spectroscopy is described. Diastereomeric pairs of several furanose monosaccharides and nucleosides were prepared, and their VCD spectra were analyzed. The results revealed that VCD spectroscopy elucidates the equibrated state of the furanose ring puckers, which is often difficult to study by other techniques.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Kie Nakano
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Ryosuke Baba
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
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Nugroho AE, Morita H. Circular dichroism calculation for natural products. J Nat Med 2013; 68:1-10. [PMID: 23564068 PMCID: PMC3853375 DOI: 10.1007/s11418-013-0768-x] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/21/2013] [Indexed: 11/03/2022]
Abstract
Determination of the absolute configuration (AC) is often a challenging aspect in the structure elucidation of natural products. When chiral compounds possess appropriate chromophore(s), electronic circular dichroism (ECD) may provide a powerful approach to the determination of their absolute configuration. Recently, ECD calculations by time-dependent density functional theory (TDDFT) have come to be used more commonly. In the present review, we give several examples of recent studies using TDDFT-calculated ECD spectra for the AC determination of natural products.
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Affiliation(s)
- Alfarius Eko Nugroho
- Faculty of Pharmaceutical Sciences, Hoshi University, Ebara 2-4-41 Shinagawa-ku, Tokyo, 142-8501, Japan
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Cano R, Ramón DJ, Yus M. Impregnated Ruthenium on Magnetite as a Recyclable Catalyst for the N-Alkylation of Amines, Sulfonamides, Sulfinamides, and Nitroarenes Using Alcohols as Electrophiles by a Hydrogen Autotransfer Process. J Org Chem 2011; 76:5547-57. [DOI: 10.1021/jo200559h] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Ding S, Kolbanovskiy A, Durandin A, Crean C, Shafirovich V, Broyde S, Geacintov NE. Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations. Chirality 2010; 21 Suppl 1:E231-41. [PMID: 19937959 DOI: 10.1002/chir.20804] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The usefulness of modern density functional theory (DFT) methods is considered for establishing the absolute configurations of DNA lesions by comparisons of computed and experimentally measured optical rotatory dispersion (ORD) and electronic circular dichroism (ECD) spectra. Two rigid, structurally different DNA lesions (two spiroiminodihydantoin stereoisomers and four equine estrogen 4-hydoxyequilenin-DNA stereoisomeric adducts) have been investigated. In all cases, the signs and shapes of the computed ORD spectra reproduced the experimentally measured ORD spectra, although the magnitudes of the computed and experimental ORD values do not coincide exactly. The computed ECD spectra also reproduced the shapes of the experimental ECD spectra rather well, but are blue-shifted by 10-20 nm. Since the assignments of the absolute configurations of the DNA lesions studied based on computed and experimental ORD and ECD spectra are fully consistent with one another, the computational DFT method shows significant promise for determining the absolute configurations of DNA lesions. Establishing the stereochemistry of DNA lesions is highly useful for understanding their biological impact, especially when sufficient amounts of material are not available for other methods of structural characterization.
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Affiliation(s)
- Shuang Ding
- Department of Biology, New York University, New York, USA
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Merten C, Amkreutz M, Hartwig A. VCD study of α-methylbenzyl amine derivatives: Detection of the unchanged chiral motif. Chirality 2010; 22:754-61. [DOI: 10.1002/chir.20830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Autschbach J, Nitsch-Velasquez L, Rudolph M. Time-dependent density functional response theory for electronic chiroptical properties of chiral molecules. Top Curr Chem (Cham) 2010; 298:1-98. [PMID: 21321799 DOI: 10.1007/128_2010_72] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Methodology to calculate electronic chiroptical properties from time-dependent density functional theory (TDDFT) is outlined. Applications of TDDFT to computations of electronic circular dichroism, optical rotation, and optical rotatory dispersion are reviewed. Emphasis is put on publications from 2005 to 2010, but much of the older literature is also cited and discussed. The determination of the absolute configuration of chiral molecules by combined measurements and computations is an important application of TDDFT chiroptical methods and discussed in some detail. Raman optical activity (ROA) spectra are obtained from normal-mode derivatives of the optical rotation tensor and other linear response tensors. A few selected (ROA) benchmarks are reviewed.
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Affiliation(s)
- Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, New York, NY, USA.
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Kwit M, Rozwadowska MD, Gawroński J, Grajewska A. Density Functional Theory Calculations of the Optical Rotation and Electronic Circular Dichroism: The Absolute Configuration of the Highly Flexible trans-Isocytoxazone Revised. J Org Chem 2009; 74:8051-63. [DOI: 10.1021/jo901175s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Marcin Kwit
- Department of Chemistry, Adam Mickiewicz University, 60-780 Poznań, Poland
| | | | - Jacek Gawroński
- Department of Chemistry, Adam Mickiewicz University, 60-780 Poznań, Poland
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Warnke I, Ay S, Bräse S, Furche F. Chiral Cooperativity and Solvent-Induced Tautomerism Effects in Electronic Circular Dichroism Spectra of [2.2]Paracyclophane Ketimines. J Phys Chem A 2009; 113:6987-93. [DOI: 10.1021/jp902563z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ingolf Warnke
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, and Institut für Organische Chemie, Universität Karlsruhe (TH), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Sefer Ay
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, and Institut für Organische Chemie, Universität Karlsruhe (TH), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, and Institut für Organische Chemie, Universität Karlsruhe (TH), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, and Institut für Organische Chemie, Universität Karlsruhe (TH), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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Stephens PJ, Harada N. ECD cotton effect approximated by the Gaussian curve and other methods. Chirality 2009; 22:229-33. [DOI: 10.1002/chir.20733] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Taniguchi T, Monde K, Nakanishi K, Berova N. Chiral sulfinates studied by optical rotation, ECD and VCD: the absolute configuration of a cruciferous phytoalexin brassicanal C. Org Biomol Chem 2008; 6:4399-405. [DOI: 10.1039/b813437e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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