1
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Covington CL, Puente AR, Polavarapu PL. Pitfalls in the Optimization of Conformer Populations to Maximize the Similarity between Predicted and Experimental Chiroptical Spectra. J Phys Chem A 2024; 128:129-138. [PMID: 38154123 DOI: 10.1021/acs.jpca.3c06544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
The conformational populations of pantolactone, epichlorohydrin, and N-acetyl-tryptophan methyl ester were investigated by using similarity analysis between their calculated and experimental chiroptical spectra. By performing the analysis on pantolactone using two different chiroptical methods, namely, vibrational circular dichroism and Raman optical activity, it was found that the optimal sets of conformers do not match between the two methods, indicating that the conformational populations obtained by optimizing the similarity between calculated and experimental spectra are unlikely to be more accurate than energy-based Boltzmann populations. Also, it was found for pantolactone, epichlorohydrin, and N-acetyl-tryptophan methyl ester that the similarity between calculated and experimental spectra would often not vary significantly if each of the populated conformers was discarded, one at a time. This observation indicates that more than one set of conformers can provide acceptable similarity between the predicted and experimental spectra. Therefore, the correct set of conformers cannot be accurately determined by similarity analysis.
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Affiliation(s)
- Cody L Covington
- Department of Chemistry, Austin Peay State University, Clarksville, Tennessee 37044, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Prasad L Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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2
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Groß J, Kühlborn J, Pusch S, Weber C, Andernach L, Renzer G, Eckhardt P, Brauer J, Opatz T. Comparison of different density functional theory methods for the calculation of vibrational circular dichroism spectra. Chirality 2023; 35:753-765. [PMID: 37227055 DOI: 10.1002/chir.23580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023]
Abstract
The determination of the absolute configuration (AC) of an organic molecule is still a challenging task for which the combination of spectroscopic with quantum-mechanical methods has become a promising approach. In this study, we investigated the accuracy of DFT methods (480 overall combinations of 15 functionals, 16 basis sets, and 2 solvation models) to calculate the VCD spectra of six chiral organic molecules in order to benchmark their capability to facilitate the determination of the AC.
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Affiliation(s)
- Jonathan Groß
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jonas Kühlborn
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Pusch
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Carina Weber
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Lars Andernach
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Galit Renzer
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Paul Eckhardt
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jan Brauer
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
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3
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Puente AR, Polavarapu PL. Chiral explosives: A theoretical investigation of structure and chiroptical properties of triacetone triperoxide and hexamethylene triperoxide diamine. Chirality 2023; 35:211-226. [PMID: 36651721 DOI: 10.1002/chir.23532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
Triacetone triperoxide (TATP) and hexamethylene triperoxide diamine (HMTD) are cyclic peroxides that exhibit atropisomerism resulting from restricted rotation around three peroxide bonds. As a result, one pair of enantiomers with D3 symmetry and another pair of enantiomers with C2 symmetry can be identified. Previous studies, based on mass spectrometry data and computational results, have shown that conformations of TATP with D3 and C2 symmetry can be isolated. Assuming that enantiomer samples of TATP and HMTD can be obtained with sufficient enantiopurity, we investigated their chiroptical properties, namely, optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and Raman optical activity (VROA). ORD curves and VCD spectra are seen to be very similar for D3 - and C2 -symmetric atropisomers with the same overall helicity. Predicted VROA results, however, show significant differences between D3 - and C2 -symmetric atropisomers with the same overall helicity. The D3 -symmetric atropisomer is predicted to exhibit considerably larger magnitude vibrational optical activity signals than the C2 -symmetric atropisomer.
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Affiliation(s)
- Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
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4
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Puente AR, Nagabhushanam K, Ganjihal S, Majeed M, Polavarapu PL. Chiroptical spectroscopic studies for the absolute configuration determination of hexahydrocurcumin and octahydrocurcumin. Chirality 2022; 34:1515-1525. [DOI: 10.1002/chir.23511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Andrew R. Puente
- Department of Chemistry Vanderbilt University Nashville Tennessee USA
| | | | | | - Muhammed Majeed
- Sabinsa Corporation East Windsor New Jersey USA
- Sami‐Sabinsa Group Bangalore India
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5
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Morgante P, Ludowieg HD, Autschbach J. Comparative Study of Vibrational Raman Optical Activity with Different Time-Dependent Density Functional Approximations: The VROA36 Database. J Phys Chem A 2022; 126:2909-2927. [PMID: 35512708 DOI: 10.1021/acs.jpca.2c00951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new database, VROA36, is introduced to investigate the performance of computational approaches for vibrational Raman optical activity (VROA) calculations. The database is composed of 36 molecules with known experimental VROA spectra. It includes 93 conformers. Normal modes calculated with B3LYP-D3(BJ)/def2-TZVP are used to compute the VROA spectra with four functionals, B3LYP-D3(BJ), ωB97X-D, M11, and optimally tuned LC-PBE, as well as several basis sets. SimROA indices and frequency scaling factors are used to compare calculated spectra with each other and with experimental data. The four functionals perform equally well independently of the basis set and usually achieve good agreement with the experimental data. For molecules in near- or at-resonance conditions, the inclusion of a complex (damped) linear response approach is important to obtain physically meaningful VROA intensities. The use of any of the tested functional approximations with the def2-SVPD Gaussian-type basis set, or a basis of similar flexibility, can be recommended for efficient and reliable theoretical VROA studies.
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Affiliation(s)
- Pierpaolo Morgante
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Herbert D Ludowieg
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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6
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Szabó Z, Paczal A, Kovács T, Mándi A, Kotschy A, Kurtán T. Synthesis and Vibrational Circular Dichroism Analysis of N-Heterocyclic Carbene Precursors Containing Remote Chirality Centers. Int J Mol Sci 2022; 23:ijms23073471. [PMID: 35408831 PMCID: PMC8999040 DOI: 10.3390/ijms23073471] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 01/01/2023] Open
Abstract
VCD analysis of 16 diastereomeric pairs of NHC precursors containing two isolated chirality centers and different substitution patterns identified VCD transitions characteristic of the chirality center in the imidazolium ring or in the side chain, which, in contrast to ECD and OR, could be utilized to assign the two chirality centers separately by simple comparison, regardless of the type and position of achiral aromatic substituents. While the ECD and OR data showed great dependence on the position of an achiral substituent such as a methoxy group, characteristic experimental VCD transitions remained consistent and they could be used to determine the absolute configuration of all the regio- and stereoisomers and substituted analogues. VCD, ECD and OR approaches were evaluated, and several carbene precursors were found, for which only the VCD method could distinguish the four stereoisomers. With t-butyl, phenyl or 2-naphthyl substituents at the C-1′ chirality center, the ECD spectra of the C-1′ epimers were near-identical, and hence it was only the VCD approach that showed distinct differences suitable for the configurational assignment. The chiroptical characterization of our diastereomeric pairs of NHC precursors enables the future application of related derivatives having different substitution patterns in stereoselective transformations.
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Affiliation(s)
- Zita Szabó
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., 1031 Budapest, Hungary; (Z.S.); (A.P.)
| | - Attila Paczal
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., 1031 Budapest, Hungary; (Z.S.); (A.P.)
| | - Tibor Kovács
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (T.K.); (A.M.)
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (T.K.); (A.M.)
| | - Andras Kotschy
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., 1031 Budapest, Hungary; (Z.S.); (A.P.)
- Correspondence: (A.K.); (T.K.)
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (T.K.); (A.M.)
- Correspondence: (A.K.); (T.K.)
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7
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Puente AR, Bessaguet A, Pairault N, Pieters G, Crassous J, Polavarapu PL, Opalinski I, Papot S. Absolute configuration of a [1]rotaxane determined from vibrational and electronic circular dichroism spectra. Chirality 2021; 33:773-782. [PMID: 34590354 DOI: 10.1002/chir.23365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 11/07/2022]
Abstract
The experimental vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectra were measured for the enantiomers of [1]rotaxane 1. These experimental spectra have been analyzed using predicted VCD and ECD spectra for (S, Rmp ) or (S, Smp ) diastereomers using density functional theory. This comparison allowed for a definitive assignment of the absolute configuration of 1.
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Affiliation(s)
- Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Adrien Bessaguet
- Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), Groupe "Système Moléculaires Programmés", UMR CNRS 7285, Université de Poitiers, Poitiers Cedex 9, France
| | - Noël Pairault
- Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), Groupe "Système Moléculaires Programmés", UMR CNRS 7285, Université de Poitiers, Poitiers Cedex 9, France
| | - Grégory Pieters
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191 Gif-sur-Yvette, France, Gif-sur-Yvette, France
| | - Jeanne Crassous
- Institut des Sciences Chimiques de Rennes, UMR CNRS 6226, Campus de Beaulieu, Univ Rennes, Rennes Cedex, France
| | | | - Isabelle Opalinski
- Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), Groupe "Système Moléculaires Programmés", UMR CNRS 7285, Université de Poitiers, Poitiers Cedex 9, France
| | - Sébastien Papot
- Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), Groupe "Système Moléculaires Programmés", UMR CNRS 7285, Université de Poitiers, Poitiers Cedex 9, France
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8
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Johnson JL, Polavarapu PL. Chiral Molecular Structure Determination for a Desired Compound Just from Its Molecular Formula and Vibrational Optical Activity Spectra. J Phys Chem A 2021; 125:8000-8013. [PMID: 34478311 DOI: 10.1021/acs.jpca.1c06369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel proof-of-concept model for chiral molecular structure determination using just the molecular formula and vibrational optical activity (VOA) spectra is presented. To verify this concept, the molecular formula of a desired compound is used to generate all possible chiral structural isomers and their VOA spectra are predicted. The similarity analyses of predicted VOA spectra were then carried out in two different ways: (a) similarity between VOA spectrum of one structural isomer with those of the rest, referred to as cross-correlations; (b) similarity between VOA spectra of all chiral structural isomers with the experimental VOA spectra of the desired compound. Three different molecular formulae, C4H8O, C3H5ClO, and C6H10O, and their chiral structural isomers (6, 9, and 75 respectively), were investigated. In each case, the correct chiral molecular structure of the desired compound was identified without ambiguity. Cross-correlation analysis revealed the uniqueness of VOA spectra in deducing the chiral molecular structure solely from its molecular formula. Different chiral structural isomers associated with the molecular formula CH3NO2 were also found to have no significant cross-correlations between their VOA spectra, opening a pathway to detect and identify the elusive chiral N-hydroxyoxaziridine from its VOA spectra.
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Affiliation(s)
- Jordan L Johnson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Prasad L Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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9
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Johnson JL, Santoro E, Zatout R, Petrovic AG, Cimmino A, Superchi S, Evidente A, Berova ND, Polavarapu PL. Absolute configuration of seco-eudesmanolide inuloxin D from experimental and predicted chiroptical studies of its 4-O-acetyl derivative. Chirality 2021; 33:233-241. [PMID: 33598968 DOI: 10.1002/chir.23301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022]
Abstract
Sesquitepenoids inuloxins A-D, belonging to different subgroups, were isolated from Dittrichia viscosa and showed potential biocontrol of some parasitic plants as Pelipanche, Orobanche, and Cuscuta species. The absolute configurations of the first three inuloxins A-C were previously determined by using experimental and computational chiroptical spectroscopic methods. The absolute configuration of inuloxin D remains to be established. The bioactive inuloxin E, closely related to inuloxin D, was recently isolated from the same plant organic extract. The same relative configuration of inuloxin D was assigned to inuloxin E by comparison of their NMR spectroscopic data. The absolute configurations of inuloxin D and inuloxin E are suggested in this work by analysis of the experimental and predicted chiroptical properties of the 4-O-acetyl derivative of inuloxin D.
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Affiliation(s)
- Jordan L Johnson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Ernesto Santoro
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Roukia Zatout
- Department of chemical Sciences, University of Naples Federico II, Naples, Italy
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri, Constantine, Algeria
| | - Ana G Petrovic
- Department of Chemical and Biological Sciences, New York Institute of Technology, New York, New York, USA
| | - Alessio Cimmino
- Department of chemical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Antonio Evidente
- Department of chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Nina D Berova
- Department of Chemistry, Columbia University, New York, New York, USA
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10
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Polavarapu PL, Santoro E, Covington CL, Johnson JL, Puente AR, Schley ND, Kallingathodi Z, Prakasan PC, Haleema S, Thomas AA, Ibnusaud I. How important are the intermolecular hydrogen bonding interactions in methanol solvent for interpreting the chiroptical properties? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119094. [PMID: 33142265 DOI: 10.1016/j.saa.2020.119094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Two crispine A analogs and tetrahydrofuro[2,3-b]furan-3,3a(6aH)-diol, endowed with hydroxyl groups that can participate in intramolecular hydrogen bonding, have been synthesized and experimental vibrational circular dichroism (VCD) spectra and optical rotatory dispersion (ORD) data have been measured in CD3OD/CH3OH solvents. The absolute configurations (ACs) of these compounds have been determined using their synthetic schemes, supplemented wherever possible with X-ray diffraction data. The ACs are also analyzed with quantum chemical (QC) calculations of VCD and ORD utilizing implicit solvation as well as explicit solvation models, with the later employing classical molecular dynamics (MD) simulations. It is found that VCD calculations with implicit solvation model are adequate for determining the ACs, despite propensity of studied compounds for intermolecular hydrogen bonding between solute and solvent molecules. This observation is important because time-consuming MD simulations may not be necessary in the type of situations studied here. Additionally, it is found that the QC predicted VCD spectra provided enough diastereomer discrimination for determining the correct AC of studied compounds independently. The same observation did not apply to ORD.
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Affiliation(s)
| | - Ernesto Santoro
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Cody L Covington
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Austin Peay State University, Clarksville, TN 37044, USA
| | - Jordan L Johnson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Nathan D Schley
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
| | - Zabeera Kallingathodi
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Prasanth C Prakasan
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Simimole Haleema
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Annu Anna Thomas
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Ibrahim Ibnusaud
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India.
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11
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Al-Khdhairawi AAQ, Low YY, Manshoor N, Arya A, Jelecki M, Alshawsh MA, Kamran S, Suliman RS, Low A, Shivanagere Nagojappa NB, Weber JFF. Asperginols A and B, Diterpene Pyrones, from an Aspergillus sp. and the Structure Revision of Previously Reported Analogues. JOURNAL OF NATURAL PRODUCTS 2020; 83:3564-3570. [PMID: 33305943 DOI: 10.1021/acs.jnatprod.0c00618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Two new diterpene pyrones, asperginols A (1) and B (2), and four known analogues (3-6) were isolated from the endophytic fungus Aspergillus sp. HAB10R12. The structures and absolute configurations of these compounds were elucidated based on the analysis of their NMR, MS, and X-ray diffraction data. The revision of the absolute configurations at C-10, C-11, and C-14 of the known diterpene pyrones (3-6) and the determination of the configuration at the polyene side chain for compounds (4-6) were made using chemical methods and vibrational circular dichroism analysis. This group of diterpene pyrone compounds showed unique structural features including a 7/6/6 tricyclic diterpene moiety with an unusual trans-syn-trans stereochemical arrangement. Compound 6 showed moderate activity against the HT-29 colon cancer cell line.
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Affiliation(s)
- Amjad Ayad Qatran Al-Khdhairawi
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University Lakeside Campus, 47500 Subang Jaya, Selangor, Malaysia
| | - Yun-Yee Low
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nurhuda Manshoor
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA (UiTM) Selangor Branch, 42300 Bandar Puncak Alam, Selangor, Malaysia
| | - Aditya Arya
- Department of Pharmacology and Therapeutics, School of Medicine, Faculty of Health and Medical Sciences, Taylor's University, 47500 Subang Jaya, Malaysia
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Maciej Jelecki
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | | | - Sareh Kamran
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Rasha Saad Suliman
- College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences Ministry of National Guard Health Affairs, 3177 Riyadh, Saudi Arabia
| | - Anis Low
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA (UiTM) Selangor Branch, 42300 Bandar Puncak Alam, Selangor, Malaysia
| | | | - Jean-Frédéric F Weber
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA (UiTM) Selangor Branch, 42300 Bandar Puncak Alam, Selangor, Malaysia
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12
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Bisio A, Schito AM, Pedrelli F, Danton O, Reinhardt JK, Poli G, Tuccinardi T, Bürgi T, De Riccardis F, Giacomini M, Calzia D, Panfoli I, Schito GC, Hamburger M, De Tommasi N. Antibacterial and ATP Synthesis Modulating Compounds from Salvia tingitana. JOURNAL OF NATURAL PRODUCTS 2020; 83:1027-1042. [PMID: 32182064 PMCID: PMC7997632 DOI: 10.1021/acs.jnatprod.9b01024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Indexed: 05/05/2023]
Abstract
A surface extract of the aerial parts of Salvia tingitana afforded a nor-sesterterpenoid (1) and eight new sesterterpenoids (2-̵9), along with five known sesterterpenoids, five labdane and one abietane diterpenoid, one sesquiterpenoid, and four flavonoids. The structures of the new compounds were established by 1D and 2D NMR spectroscopy, HRESIMS, and VCD data and Mosher's esters analysis. The antimicrobial activity of compounds was evaluated against 30 human pathogens including 27 clinical strains and three isolates of marine origin for their possible implications on human health. The methyl ester of salvileucolide (10), salvileucolide-6,23-lactone (11), sclareol (15), and manool (17) were the most active against Gram-positive bacteria. The compounds were also tested for the inhibition of ATP production in purified mammalian rod outer segments. Terpenoids 10, 11, 15, and 17 inhibited ATP production, while only 17 inhibited also ATP hydrolysis. Molecular modeling studies confirmed the capacity of 17 to interact with mammalian ATP synthase. A significant reduction of ATP production in the presence of 17 was observed in Enterococcus faecalis and E. faecium isolates.
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Affiliation(s)
- Angela Bisio
- Department
of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy
| | - Anna M. Schito
- Department
of Integrated Surgical and Diagnostical Sciences, University of Genova, Largo Rosanna Benzi 8, 16145 Genova, Italy
| | - Francesca Pedrelli
- Department
of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy
| | - Ombeline Danton
- Department
of Pharmaceutical Sciences, University of
Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Jakob K. Reinhardt
- Department
of Pharmaceutical Sciences, University of
Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Giulio Poli
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Thomas Bürgi
- Department
of Chemical Physics, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Francesco De Riccardis
- Department
of Chemistry and Biology, University of
Salerno, Via Giovanni Paolo II 132, 84084 Salerno, Italy
| | - Mauro Giacomini
- Department
of Informatics Bioengineering Robotics and System Engineering, University of Genova, Via all’Opera Pia, 13, 16145 Genova, Italy
| | - Daniela Calzia
- Department
of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy
| | - Isabella Panfoli
- Department
of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy
| | - Gian Carlo Schito
- Department
of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy
| | - Matthias Hamburger
- Department
of Pharmaceutical Sciences, University of
Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Nunziatina De Tommasi
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Salerno, Italy
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13
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Polavarapu PL, Santoro E, Covington CL, Raghavan V. Enhancement of the chiroptical response of α-amino acids via N-substitution for molecular structure determination using vibrational circular dichroism. Chirality 2020; 32:564-578. [PMID: 32115784 DOI: 10.1002/chir.23205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/23/2020] [Accepted: 02/14/2020] [Indexed: 11/12/2022]
Abstract
The chiroptical response in the form of vibrational circular dichroism (VCD) in the midinfrared region is found to be enhanced when a hydrogen of amino group of l-tryptophan is substituted with acetyl, acryloyl, or maleyl group. The order of preference for VCD enhancement is found to be acryloyl > acetyl > maleyl group. The resulting experimental VCD spectra are also found to be satisfactorily reproduced by the quantum mechanical (QM) predicted spectra. The QM predicted spectra were simulated using the conformer populations, (a) predicted by Gibbs energies and (b) optimized to maximize the similarity between experimental and predicted VCD spectra. It is found that the conformer populations predicted by Gibbs energies do not yield the maximum possible similarity between experimental and the QM predicted spectra. This work identifies the N-substitution of α-amino acids and determining the conformer populations that best reproduce the experimental spectra as two new approaches for molecular structure determination.
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Affiliation(s)
| | - Ernesto Santoro
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Cody L Covington
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee.,Department of Chemistry, Austin Peay State University, Clarksville, Tennessee
| | - Vijay Raghavan
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
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14
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Králík F, Fagan P, Kuchař M, Setnička V. Structure of heroin in a solution revealed by chiroptical spectroscopy. Chirality 2020; 32:854-865. [DOI: 10.1002/chir.23196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/30/2022]
Affiliation(s)
- František Králík
- Department of Analytical ChemistryUniversity of Chemistry and Technology Prague Czech Republic
| | - Patrik Fagan
- Department of Analytical ChemistryUniversity of Chemistry and Technology Prague Czech Republic
| | - Martin Kuchař
- Forensic Laboratory of Biologically Active Substances and Department of Chemistry of Natural CompoundsUniversity of Chemistry and Technology Prague Czech Republic
| | - Vladimír Setnička
- Department of Analytical ChemistryUniversity of Chemistry and Technology Prague Czech Republic
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15
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Rojo-Portillo T, Reyes-López E, Hernández-Huerta E, Quiroz-García B, Joseph-Nathan P, Sánchez-Castellanos M, Cuétara-Guadarrama F, Cuevas G. Is the VCD spectrum a fingerprint of the conformational population? The conformation of perezone in the spotlight. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Paoloni L, Mazzeo G, Longhi G, Abbate S, Fusè M, Bloino J, Barone V. Toward Fully Unsupervised Anharmonic Computations Complementing Experiment for Robust and Reliable Assignment and Interpretation of IR and VCD Spectra from Mid-IR to NIR: The Case of 2,3-Butanediol and trans-1,2-Cyclohexanediol. J Phys Chem A 2020; 124:1011-1024. [PMID: 31922423 PMCID: PMC7993639 DOI: 10.1021/acs.jpca.9b11025] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
The infrared (IR)
and vibrational circular dichroism (VCD) spectra
of 2,3-butanediol and trans-1,2-cyclohexanediol from
900 to 7500 cm–1 (including mid-IR, fundamental
CH and OH stretchings, and near-infrared regions) have been investigated
by a combined experimental and computational strategy. The computational
approach is rooted in density functional theory (DFT) computations
of harmonic and leading anharmonic mechanical, electrical, and magnetic
contributions, followed by a generalized second-order perturbative
(GVPT2) evaluation of frequencies and intensities for all the above
regions without introducing any ad hoc scaling factor. After proper
characterization of large-amplitude motions, all resonances plaguing
frequencies and intensities are taken into proper account. Comparison
of experimental and simulated spectra allows unbiased assignment and
interpretation of the most interesting features. The reliability of
the GVPT2 approach for OH stretching fundamentals and overtones is
confirmed by the remarkable agreement with a local mode model purposely
tailored for the latter two regions. Together with the specific interest
of the studied molecules, our results confirm that an unbiased assignment
and interpretation of vibrational spectra for flexible medium-size
molecules can be achieved by means of a nearly unsupervised reliable,
robust, and user-friendly DFT/GVPT2 model.
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Affiliation(s)
- Lorenzo Paoloni
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Viale Europa 11 , 25123 Brescia , Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Viale Europa 11 , 25123 Brescia , Italy.,Consiglio Nazionale delle Ricerche-I.N.O. , c/o CSMT via Branze, 45 , 25123 Brescia , Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Viale Europa 11 , 25123 Brescia , Italy.,Consiglio Nazionale delle Ricerche-I.N.O. , c/o CSMT via Branze, 45 , 25123 Brescia , Italy
| | - Marco Fusè
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Julien Bloino
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Vincenzo Barone
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
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17
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Polavarapu PL, Santoro E. Vibrational optical activity for structural characterization of natural products. Nat Prod Rep 2020; 37:1661-1699. [DOI: 10.1039/d0np00025f] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.
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18
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Bogaerts J, Desmet F, Aerts R, Bultinck P, Herrebout W, Johannessen C. A combined Raman optical activity and vibrational circular dichroism study on artemisinin-type products. Phys Chem Chem Phys 2020; 22:18014-18024. [DOI: 10.1039/d0cp03257c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Artemisinin and two of its derivatives, dihydroartemisinin and artesunate, front line drugs against malaria, were studied using Raman optical activity (ROA), vibrational circular dichroism (VCD) experiments and density functional theory (DFT) calculations.
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Affiliation(s)
| | - Filip Desmet
- Department of Chemistry
- University of Antwerp
- B-2020 Antwerp
- Belgium
| | - Roy Aerts
- Department of Chemistry
- University of Antwerp
- B-2020 Antwerp
- Belgium
| | | | - Wouter Herrebout
- Department of Chemistry
- University of Antwerp
- B-2020 Antwerp
- Belgium
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19
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Analytical chemistry on many-center chiral compounds based on vibrational circular dichroism: Absolute configuration assignments and determination of contaminant levels. Anal Chim Acta 2019; 1090:100-105. [DOI: 10.1016/j.aca.2019.09.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 01/04/2023]
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20
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El-Kashef DH, Daletos G, Plenker M, Hartmann R, Mándi A, Kurtán T, Weber H, Lin W, Ancheeva E, Proksch P. Polyketides and a Dihydroquinolone Alkaloid from a Marine-Derived Strain of the Fungus Metarhizium marquandii. JOURNAL OF NATURAL PRODUCTS 2019; 82:2460-2469. [PMID: 31432669 DOI: 10.1021/acs.jnatprod.9b00125] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Three new natural products (1-3), including two butenolide derivatives (1 and 2) and one dihydroquinolone derivative (3), together with nine known natural products were isolated from a marine-derived strain of the fungus Metarhizium marquandii. The structures of the new compounds were unambiguously deduced by spectroscopic means including HRESIMS and 1D/2D NMR spectroscopy, ECD, VCD, OR measurements, and calculations. The absolute configuration of marqualide (1) was determined by a combination of modified Mosher's method with TDDFT-ECD calculations at different levels, which revealed the importance of intramolecular hydrogen bonding in determining the ECD features. The (3R,4R) absolute configuration of aflaquinolone I (3), determined by OR, ECD, and VCD calculations, was found to be opposite of the (3S,4S) absolute configuration of the related aflaquinolones A-G, suggesting that the fungus M. marquandii produces aflaquinolone I with a different configuration (chiral switching). The absolute configuration of the known natural product terrestric acid hydrate (4) was likewise determined for the first time in this study. TDDFT-ECD calculations allowed determination of the absolute configuration of its chirality center remote from the stereogenic unsaturated γ-lactone chromophore. ECD calculations aided by solvent models revealed the importance of intramolecular hydrogen bond networks in stabilizing conformers and determining relationships between ECD transitions and absolute configurations.
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Affiliation(s)
- Dina H El-Kashef
- Institut für Pharmazeutische Biologie und Biotechnologie , Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1 , 40225 Düsseldorf , Germany
- Department of Pharmacognosy, Faculty of Pharmacy , Minia University , 61519 Minia , Egypt
| | - Georgios Daletos
- Institut für Pharmazeutische Biologie und Biotechnologie , Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1 , 40225 Düsseldorf , Germany
| | - Malte Plenker
- Institute of Complex Systems: Strukturbiochemie , Forschungszentrum Jülich GmbH , ICS-6, 52425 Jülich , Germany
| | - Rudolf Hartmann
- Institute of Complex Systems: Strukturbiochemie , Forschungszentrum Jülich GmbH , ICS-6, 52425 Jülich , Germany
| | - Attila Mándi
- Department of Organic Chemistry , University of Debrecen , P.O.B. 400, 4002 Debrecen , Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry , University of Debrecen , P.O.B. 400, 4002 Debrecen , Hungary
| | - Horst Weber
- Institut für Pharmazeutische und Medizinische Chemie , Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1 , 40225 Düsseldorf , Germany
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Elena Ancheeva
- Institut für Pharmazeutische Biologie und Biotechnologie , Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1 , 40225 Düsseldorf , Germany
| | - Peter Proksch
- Institut für Pharmazeutische Biologie und Biotechnologie , Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1 , 40225 Düsseldorf , Germany
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21
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Tran-Cong NM, Mándi A, Kurtán T, Müller WEG, Kalscheuer R, Lin W, Liu Z, Proksch P. Induction of cryptic metabolites of the endophytic fungus Trichocladium sp. through OSMAC and co-cultivation. RSC Adv 2019; 9:27279-27288. [PMID: 35529238 PMCID: PMC9070598 DOI: 10.1039/c9ra05469c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/20/2019] [Indexed: 01/17/2023] Open
Abstract
The endophytic fungus Trichocladium sp. isolated from roots of Houttuynia cordata was cultured on solid rice medium, yielding a new amidepsine derivative (1) and a new reduced spiro azaphilone derivative (3) together with eight known compounds (4-11). Co-cultivation of Trichocladium sp. with Bacillus subtilis resulted in induction of a further new compound (2) and a 10-fold increase of 11 compared to the axenic fungal culture. Moreover, when the fungus was cultivated on peas instead of rice, a new sesquiterpene derivative (13) and two known compounds (12 and 14) were obtained. Addition of 2% tryptophan to rice medium led to the isolation of a new bismacrolactone (15). The structures of the new compounds were elucidated by HRESIMS, 1D and 2D NMR as well as by comparison with the literature. A combination of TDDFT-ECD, TDDFT-SOR, DFT-VCD and DFT-NMR calculations were applied to determine the absolute and relative configurations of 13 and 15. Compounds 7, 11 and 15 exhibited strong cytotoxicity against the L5178Y mouse lymphoma cell line with IC50 values of 0.3, 0.5 and 0.2 μM, respectively.
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Affiliation(s)
- Nam Michael Tran-Cong
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen P. O. Box 400 H-4002 Debrecen Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen P. O. Box 400 H-4002 Debrecen Hungary
| | - Werner E G Müller
- Institute of Physiological Chemistry, Universitätsmedizin der Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University Beijing 100191 China
| | - Zhen Liu
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Peter Proksch
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
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22
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Koenis MAJ, Xia Y, Domingos SR, Visscher L, Buma WJ, Nicu VP. Taming conformational heterogeneity in and with vibrational circular dichroism spectroscopy. Chem Sci 2019; 10:7680-7689. [PMID: 31803406 PMCID: PMC6844231 DOI: 10.1039/c9sc02866h] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/08/2019] [Indexed: 01/19/2023] Open
Abstract
Genetic fitting algorithm accounting for the uncertainty in computed energies allows a significantly more reliable assignment of stereochemistry and conformational heterogeneity of chiral compounds using vibrational circular dichroism.
The flexibility of a molecule has important consequences on its function and application. Vibrational Circular Dichroism (VCD) is intrinsically an excellent experimental technique to get a hold on this flexibility as it is highly sensitive to key conformational details and able to distinguish rapidly interconverting conformers. One of the major challenges in analyzing the spectra by comparison to theoretical predictions is the uncertainty in the computed energies of the multitude of conformations. This uncertainty also affects the reliability of the stereochemical assignment it is normally used for. We present here a novel approach that explicitly takes the energy uncertainties into account in a genetic algorithm based method that fits calculated to the experimental spectra. We show that this approach leads to significant improvements over previously used methodologies. Importantly, statistical validation studies provide quantitative measures for the reliability of relevant parameters used such as the energy uncertainty and the extent to which conformational heterogeneity can be determined. Similarly, quantitative measures can be obtained for the possibility that the flexibility that is introduced in the fit might lead to an incorrect assignment of the stereochemistry. These results break new ground for different techniques based on VCD to elucidate conformational flexibility.
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Affiliation(s)
- Mark A J Koenis
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands .
| | - Yiyin Xia
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands .
| | - Sérgio R Domingos
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling , Division Theoretical Chemistry , Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands . .,Radboud University , Institute for Molecules and Materials , FELIX Laboratory , Toernooiveld 7c , 6525 ED Nijmegen , The Netherlands
| | - Valentin P Nicu
- Department of Environmental Science, Physics, Physical Education and Sport , Lucian Blaga University of Sibiu , loan Ratiu Street Nr. 7-9 , 550012 Sibiu , Romania .
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23
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Reinhardt JK, Klemd AM, Danton O, De Mieri M, Smieško M, Huber R, Bürgi T, Gründemann C, Hamburger M. Sesquiterpene Lactones from Artemisia argyi: Absolute Configuration and Immunosuppressant Activity. JOURNAL OF NATURAL PRODUCTS 2019; 82:1424-1433. [PMID: 31181920 DOI: 10.1021/acs.jnatprod.8b00791] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A library of extracts from plants used in Chinese Traditional Medicine was screened for inhibition of T lymphocyte proliferation. An ethyl acetate extract from aerial parts of Artemisia argyi showed promising activity and was submitted to HPLC-based activity profiling to track the active compounds. From the most active time window, three guaianolides (1, 2, and 5) and two seco-tanapartholides (3 and 4) were identified and, in a less active time window, five new sesquiterpene lactones (8-11, 17), along with six known sesquiterpene lactones and two known flavonoids. The absolute configurations of compounds 1, 2, 5-10, 13-15, 17, and 18 were established by comparison of experimental with calculated electronic circular dichroism (ECD) spectra. For seco-tanapartholides B (3) and A (4), ECD yielded ambiguous results, and their absolute configurations were determined by comparing experimental and calculated vibrational circular dichroism (VCD) spectra. Compounds 1-5 showed significant, noncytotoxic inhibition of T lymphocyte proliferation, with IC50 values between 1.0 and 3.7 μM.
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Affiliation(s)
- Jakob K Reinhardt
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Amy M Klemd
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine , University of Freiburg , Breisacher Straße 115 B , 79106 Freiburg , Germany
| | - Ombeline Danton
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Maria De Mieri
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Martin Smieško
- Department of Molecular Modeling , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Roman Huber
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine , University of Freiburg , Breisacher Straße 115 B , 79106 Freiburg , Germany
| | - Thomas Bürgi
- Department of Physical Chemistry , University of Geneva , 30 Quai Ernest Ansermet , 1211 Geneva , Switzerland
| | - Carsten Gründemann
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine , University of Freiburg , Breisacher Straße 115 B , 79106 Freiburg , Germany
| | - Matthias Hamburger
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
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24
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Merten C, Golub TP, Kreienborg NM. Absolute Configurations of Synthetic Molecular Scaffolds from Vibrational CD Spectroscopy. J Org Chem 2019; 84:8797-8814. [PMID: 31046276 DOI: 10.1021/acs.joc.9b00466] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is one of the most powerful techniques for the determination of absolute configurations (AC), as it does not require any specific UV/vis chromophores, no chemical derivatization, and no growth of suitable crystals. In the past decade, it has become increasingly recognized by chemists from various fields of synthetic chemistry such as total synthesis and drug discovery as well as from developers of asymmetric catalysts. This perspective article gives an overview about the most important experimental aspects of a VCD-based AC determination and explains the theoretical analysis. The comparison of experimental and computational spectra that leads to the final conclusion about the AC of the target molecules is described. In addition, the review summarizes unique VCD studies carried out in the period 2008-2018 that focus on the determination of unknown ACs of new compounds, which were obtained in its enantiopure form either through direct asymmetric synthesis or chiral chromatography.
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Affiliation(s)
- Christian Merten
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Tino P Golub
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Nora M Kreienborg
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
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25
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Johnson J, Nair DS, Pillai SM, Johnson D, Kallingathodi Z, Ibnusaud I, Polavarapu PL. Dissymmetry Factor Spectral Analysis Can Provide Useful Diastereomer Discrimination: Chiral Molecular Structure of an Analogue of (-)-Crispine A. ACS OMEGA 2019; 4:6154-6164. [PMID: 31459760 PMCID: PMC6648312 DOI: 10.1021/acsomega.8b03678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/20/2019] [Indexed: 06/10/2023]
Abstract
(1R,10bR)-1'-((R)-1,2-Dihydroxyethyl)-1-hydroxy-8,9-dimethoxy1,5,6,10b-tetrahydropyrrolo [2,1-a]isoquinolin-3(2H)-one, an analogue of (-)-crispine A, with three stereogenic centers is synthesized and its absolute configuration (AC) established using the combined information derived from the synthetic scheme and single crystal X-ray diffraction data. The experimental chiroptical spectra (namely, optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD)) and the corresponding quantum chemical (QC) predicted spectra for all diastereomers are used to evaluate the AC. The AC of the synthesized compound could be correctly established using any one of the three chiroptical spectroscopic methods (ORD, ECD, or VCD) when the relative configuration is constrained to be that derived from X-ray data or when the ACs of two of the chiral centers are constrained to be those derived from the synthetic scheme. In the absence of this outside information, the QC predicted ORD, ECD, and VCD for incorrect diastereomers are also found to satisfactorily reproduce the corresponding experimental spectra. Nevertheless, incorrect diastereomers could be eliminated when combined electronic dissymmetry factor (EDF) and vibrational dissymmetry factor (VDF) spectral analyses are included, leaving the correct diastereomer as the sole choice. Thus, the combined EDF and VDF spectral analysis is seen to be a helpful diastereomer discrimination tool.
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Affiliation(s)
- Jordan
L. Johnson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Divya Sadasivan Nair
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Sarath Muraleedharan Pillai
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Didimos Johnson
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Zabeera Kallingathodi
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Ibrahim Ibnusaud
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Prasad L. Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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26
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Johnson J, Polavarapu PL. Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism. ACS OMEGA 2019; 4:4963-4976. [PMID: 31459680 PMCID: PMC6648482 DOI: 10.1021/acsomega.8b03628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/21/2019] [Indexed: 05/06/2023]
Abstract
The chiral molecular structures of four different substituted indans, namely, (S)-1-methylindan, (R)-1-methylindan-1-d, (R)-1-aminoindan, and (S)-1-indanol, were investigated using experimental vibrational absorption and vibrational circular dichroism spectra and corresponding spectra predicted using quantum chemical (QC) calculations. All of these molecules possess two ring puckering conformations, with ring puckering leading to the pseudoequatorial substituent being approximately four times more abundant over that leading to the pseudoaxial substituent. The amino group in 1-aminoindan has three conformations arising from the rotation of NH2 group, for each ring puckering conformation, resulting in a total of six conformations. Whereas 1-indanol in the nonhydrogen-bonding solvent CCl4 also has six conformations similar to those of 1-aminoindan, 1-indanol in the hydrogen-bonding solvent DMSO-d 6 adopts numerous conformations, of which 30 conformers are considered to have at least ∼1% or more population. In DMSO solution, ring puckering leading to pseudoequatorial substituent accounts for 77% population and 23% for pseudoaxial substituent. The QC spectra predicted for the geometry optimized conformers are found to be in excellent quantitative agreement with corresponding experimental spectra in all of the molecules considered. The procedures suggested in this work are hoped to provide successful pathways for future chiral molecular structural analyses.
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27
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Zajac G, Machalska E, Kaczor A, Kessler J, Bouř P, Baranska M. Structure of supramolecular astaxanthin aggregates revealed by molecular dynamics and electronic circular dichroism spectroscopy. Phys Chem Chem Phys 2019; 20:18038-18046. [PMID: 29932184 DOI: 10.1039/c8cp01742e] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biomolecular aggregation is omnipresent in nature and important for metabolic processes or in medical treatment; however, the phenomenon is rather difficult to predict or understand on the basis of computational models. Recently, we found that electronic circular dichroism (ECD) spectroscopy and closely related resonance Raman optical activity (RROA) are extremely sensitive to the aggregation mechanism and structure of the astaxanthin dye. In the present study, molecular dynamics (MD) and quantum chemical (QC) computations (ZIndo/S, TDDFT) are used to link the aggregate structure with ECD spectral shapes. Realistic absorption and ECD intensities were obtained and the simulations reproduced many trends observed experimentally, such as the prevalent sign pattern and dependence of the aggregate structure on the solvent type. The computationally cheaper ZIndo/S method provided results very similar to those obtained by TDDFT. In the future, the accuracy of the combined MD/QC methodology of spectra interpretation should be improved to provide more detailed information on astaxanthin aggregates and similar macromolecular systems.
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Affiliation(s)
- Grzegorz Zajac
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland.
| | - Ewa Machalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland.
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland. and Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague, 16610, Czech Republic.
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague, 16610, Czech Republic.
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland. and Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
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28
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Johnson JL, Raghavan V, Cimmino A, Moeini A, Petrovic AG, Santoro E, Superchi S, Berova N, Evidente A, Polavarapu PL. Absolute configurations of chiral molecules with multiple stereogenic centers without prior knowledge of the relative configurations: A case study of inuloxin C. Chirality 2018; 30:1206-1214. [DOI: 10.1002/chir.23013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/13/2018] [Accepted: 08/10/2018] [Indexed: 12/20/2022]
Affiliation(s)
| | - Vijay Raghavan
- Department of Chemistry Vanderbilt University Nashville TN USA
| | - Alessio Cimmino
- Department of Chemical Science University of Naples Federico II Naples Italy
| | - Arash Moeini
- Department of Chemical Science University of Naples Federico II Naples Italy
| | - Ana G. Petrovic
- Department of Chemistry Columbia University New York NY USA
- Department of Life Sciences New York Institute of Technology New York NY USA
| | - Ernesto Santoro
- Department of Science University of Basilicata Potenza Italy
| | | | - Nina Berova
- Department of Chemistry Columbia University New York NY USA
| | - Antonio Evidente
- Department of Chemical Science University of Naples Federico II Naples Italy
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29
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Absolute configuration assignment to anticancer Amaryllidaceae alkaloid jonquailine. Fitoterapia 2018; 129:78-84. [DOI: 10.1016/j.fitote.2018.06.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 01/18/2023]
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30
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Peixoto D, Ferreira EP, Lourenço AM, Johnson JL, Lobo AM, Polavarapu PL. (R)-Metacycloprodigiosin-HCl: Chiroptical properties and structure. Chirality 2018; 30:932-942. [PMID: 29746716 DOI: 10.1002/chir.22867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/29/2018] [Accepted: 04/04/2018] [Indexed: 01/15/2023]
Abstract
(R)-Metacycloprodigiosin can exist in three different tautomeric forms, each with hydrogens at C9' and C12 in syn or anti orientation. With the addition of HCl, this structural diversity reduces to syn-(R)-metacycloprodigiosin-HCl (1a) and anti-(R)-metacycloprodigiosin-HCl (1b), each with multiple conformers. Energetics and chiroptical properties, namely, electronic circular dichroism (ECD) and specific optical rotation (SOR), of (R)-metacycloprodigiosin-HCl have been investigated at B3LYP/6-311++G(2d,2p) level. The experimental ECD spectra of (R)-metacycloprodigiosin-HCl have also been measured. Calculations indicated that the lowest energy conformer of 1b is approximately 2.7 kcal/mol lower in energy than that of 1a, and the energy barrier for anti to syn conversion is approximately 13 kcal/mol. The population weighted calculated SORs of 1a and 1b are, respectively, positive and negative. The respective calculated ECD spectra of these pseudoenantiomers show an almost mirror image relationship between them. The experimental SOR and ECD compare well with those predicted for 1b. Thus, 1b is expected to be predominant, a situation confirmed also by nuclear Overhauser effect (NOE) data, with a similar conclusion reached for prodigiosin R1.
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Affiliation(s)
- Daniela Peixoto
- Department of Chemistry, REQUIMTE/LAQV & UCIBIO, NOVA University of Lisbon, Caparica, Portugal
| | - Elisabete P Ferreira
- Department of Chemistry, REQUIMTE/LAQV & UCIBIO, NOVA University of Lisbon, Caparica, Portugal
| | - Ana M Lourenço
- Department of Chemistry, REQUIMTE/LAQV & UCIBIO, NOVA University of Lisbon, Caparica, Portugal
| | - Jordan L Johnson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Ana M Lobo
- Department of Chemistry, REQUIMTE/LAQV & UCIBIO, NOVA University of Lisbon, Caparica, Portugal
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31
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Spálovská D, Králík F, Kohout M, Jurásek B, Habartová L, Kuchař M, Setnička V. Structure determination of butylone as a new psychoactive substance using chiroptical and vibrational spectroscopies. Chirality 2018; 30:548-559. [DOI: 10.1002/chir.22825] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Dita Spálovská
- Department of Analytical Chemistry; University of Chemistry and Technology; Prague 6 Czech Republic
| | - František Králík
- Department of Analytical Chemistry; University of Chemistry and Technology; Prague 6 Czech Republic
| | - Michal Kohout
- Department of Organic Chemistry; University of Chemistry and Technology; Prague 6 Czech Republic
| | - Bronislav Jurásek
- Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Prague 6 Czech Republic
- Department of Chemistry of Natural Compounds; University of Chemistry and Technology; Prague 6 Czech Republic
| | - Lucie Habartová
- Department of Analytical Chemistry; University of Chemistry and Technology; Prague 6 Czech Republic
| | - Martin Kuchař
- Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Prague 6 Czech Republic
- Department of Chemistry of Natural Compounds; University of Chemistry and Technology; Prague 6 Czech Republic
| | - Vladimír Setnička
- Department of Analytical Chemistry; University of Chemistry and Technology; Prague 6 Czech Republic
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32
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Králík F, Jirmásek P, Kuchař M, Setnička V. Chiroptical and vibrational spectroscopic study of genuine and counterfeit medicines containing tadalafil. Chirality 2018; 30:560-567. [PMID: 29419887 DOI: 10.1002/chir.22828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 11/09/2022]
Abstract
The production and distribution of counterfeit pharmaceuticals present a serious problem worldwide. This is true especially in case of phosphodiesterase type 5 inhibitors for treating erectile dysfunction, where consumers often prefer buying them anonymously from unverified sources. In this study, genuine and counterfeit Cialis® 20 mg tablets were analyzed by electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy. The characteristic spectral patterns were identified by comparison with the spectra of tadalafil standard as an active pharmaceutical ingredient, and its presence was confirmed in all samples. The amount of tadalafil, however, was markedly lower in the case of counterfeit tablet as the observed band intensities were considerably lower. No other significant differences between the genuine and counterfeit tablets were revealed. Ab initio density functional theory calculations provided a detailed description of the stable conformers of tadalafil in a solution and enabled thorough interpretation of the experimental spectra.
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Affiliation(s)
- František Králík
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Patrik Jirmásek
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Martin Kuchař
- Forensic Laboratory of Biologically Active Substances, University of Chemistry and Technology, Prague, Czech Republic.,Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague, Czech Republic
| | - Vladimír Setnička
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
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33
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Xia Y, Koenis MAJ, Collados JF, Ortiz P, Harutyunyan SR, Visscher L, Buma WJ, Nicu VP. Regional Susceptibility in VCD Spectra to Dynamic Molecular Motions: The Case of a Benzyl α-Hydroxysilane. Chemphyschem 2018; 19:561-565. [PMID: 29244237 DOI: 10.1002/cphc.201701335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 01/24/2023]
Abstract
Experimental and theoretical studies of the vibrational circular dichroism (VCD) spectrum of 3-methyl-1-(methyldiphenlsilyl)-1-phenylbutan-1-ol, whose absolute configuration is key to elucidating the Brook rearrangement of tertiary benzylic α-hydroxylsilanes, are presented. It is found that the entire OH-bending region in this spectrum-a region that provides important marker bands-cannot be reproduced at all by standard theoretical approaches even though other regions are well described. Using a novel approach to disentangle contributions to the rotational strength of these bands, internal coordinates are identified that critically influence the appearance of this part of the spectrum. We show that the agreement between experiment and theory is greatly improved when structural dynamics along these coordinates are explicitly taken into account. The general applicability of the approach underlines its usefulness for structurally flexible chiral systems, a situation that is more the rule rather than the exception.
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Affiliation(s)
- Yiyin Xia
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Mark A J Koenis
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Juan F Collados
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Pablo Ortiz
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Syuzanna R Harutyunyan
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling, Section Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Wybren J Buma
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Valentin P Nicu
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Lucian Blaga University of Sibiu, Faculty of Agricultural Sciences, Food Industry and Environmental Protection, 7-9 Ioan Ratiu Street, 550012, Sibiu, Romania
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34
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Covington CL, Raghavan V, Smuts JP, Armstrong DW, Polavarapu PL. Absolute configuration of an axially chiral sulfonate determined from its optical rotatory dispersion, electronic circular dichroism, and vibrational circular dichroism spectra. Chirality 2017; 29:670-676. [DOI: 10.1002/chir.22739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/06/2017] [Accepted: 07/09/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Cody L. Covington
- Department of Chemistry; Vanderbilt University; Nashville Tennessee USA
| | - Vijay Raghavan
- Department of Chemistry; Vanderbilt University; Nashville Tennessee USA
| | - Jonathan P. Smuts
- Department of Chemistry; University of Texas at Arlington; Arlington Texas USA
| | - Daniel W. Armstrong
- Department of Chemistry; University of Texas at Arlington; Arlington Texas USA
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35
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Polavarapu PL, Covington CL, Raghavan V. To Avoid Chasing Incorrect Chemical Structures of Chiral Compounds: Raman Optical Activity and Vibrational Circular Dichroism Spectroscopies. Chemphyschem 2017; 18:2459-2465. [DOI: 10.1002/cphc.201700764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Prasad L. Polavarapu
- Department of Chemistry Vanderbilt University 7330 Stevenson Center Nashville TN 37235 USA
| | - Cody L. Covington
- Department of Chemistry Vanderbilt University 7330 Stevenson Center Nashville TN 37235 USA
| | - Vijay Raghavan
- Department of Chemistry Vanderbilt University 7330 Stevenson Center Nashville TN 37235 USA
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