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Fusè M, Mazzeo G, Longhi G, Abbate S, Yang Q, Bloino J. Scaling-up VPT2: A feasible route to include anharmonic correction on large molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 311:123969. [PMID: 38330757 DOI: 10.1016/j.saa.2024.123969] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Vibrational analysis plays a crucial role in the investigation of molecular systems. Though methodologies like second-order vibrational perturbation theory (VPT2) have paved the way to more accurate simulations, the computational cost remains a difficult barrier to overcome when the molecular size increases. Building upon recent advances in the identification of resonances, we propose an approach making anharmonic simulations possible for large-size systems, typically unreachable by standard means. This relies on the fact that, often, only portions of the whole spectra are of actual interest. Therefore, the anharmonic corrections can be included selectively on subsets of normal modes directly related to the regions of interest. Starting from the VPT2 equations, we evaluate rigorously and systematically the impact of the truncated anharmonic treatment onto simulations. The limit and feasibility of the reduced-dimensionality approach are detailed, starting on a smaller model system. The methodology is then challenged on the IR absorption and vibrational circular dichroism spectra of an organometallic complex in three different spectral ranges.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, 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; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, 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; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123, Brescia, Italy
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, 56125, Pisa, Italy.
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2
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Fusè M, Mazzeo G, Abbate S, Ruzziconi R, Bloino J, Longhi G. Mid-IR and CH stretching vibrational circular dichroism spectroscopy to distinguish various sources of chirality: The case of quinophaneoxazoline based ruthenium(II) complexes. Chirality 2024; 36:e23649. [PMID: 38409881 DOI: 10.1002/chir.23649] [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: 12/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Abstract
Five diastereomers of ruthenium(II) complexes based on quinolinophaneoxazoline ligands were investigated by vibrational circular dichroism (VCD) in the mid-IR and CH stretching regions. Diastereomers differ in three sources of chirality: the planar chirality of the quinolinophane moiety, the central chirality of an asymmetric carbon atom of the oxazoline ring, and the chirality of the ruthenium atom. VCD, allied to DFT calculations, has been found to be effective in disentangling the various forms of chirality. In particular, a VCD band is identified in the CH stretching region directly connected to the chirality of the metal. The analysis of the calculated VCD spectra is carried out by partitioning the complexes into fragments. The anharmonic analysis is also performed with a recently proposed reduced-dimensionality approach: such treatment is particularly important when examining spectroscopic regions highly perturbed by resonances, like the CH stretching region.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
| | - Renzo Ruzziconi
- Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
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3
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Muñoz MA, Burgueño-Tapia E, Joseph-Nathan P. Individual scale factor approach for the vibrational circular dichroism similarity-guided spectral and conformational analysis of perezone and dihydroperezone. Chirality 2023; 35:67-79. [PMID: 36398355 DOI: 10.1002/chir.23517] [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: 07/07/2022] [Revised: 10/18/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
Evaluation of DFT calculated vibrational parameters for the IR and VCD spectra similarity of perezone (1) and dihydroperezone (2) was undertaken. Conformational sets were obtained using different search engines, and the parameters needed for spectra prediction were obtained using several combinations of commonly employed functionals and basis sets, and then weighted spectra were generated and compared with observed traces to provide infrared similarity (SIR ) and enantiomeric similarity index (ESI) values. These values evidenced a poor performance of the evaluated levels of theory that were overcome when using the individual scaling factors approach, providing 16% to 139% increases of the ESI values. The best performing level of theory was the B3LYP/DGDZVP2 with ESI values of 0.722 and 0.792 for 1 and 2. Moreover, a correlation analysis showed that the irregular DFT performance arises from rotational strength deviations, which suggests to discard conformational abundance accuracy as the main source of differences. Furthermore, a similarity guided conformational analysis showed that conformations with high ESI values prefer particular orientations of the CC bonds directly attached to the stereogenic carbon atom, with more distant dihedral angles having less influence. Additionally, folded and extended conformers appear to be equally capable to yield high individual ESI values, although abundances of folded conformers just account for 16% of the total population. Nevertheless, abundance optimization showed that a high ESI similarity value of 0.834, is possible when the population of these conformers is increased to 26%, suggesting that a larger abundance of these conformers might be present in solution.
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Affiliation(s)
- Marcelo A Muñoz
- Instituto de Ciencias Químicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Eleuterio Burgueño-Tapia
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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4
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Taniguchi T, Ida N, Kitahara T, Agbo DO, Monde K. Stereostructural analysis of flexible oxidized fatty acids by VCD spectroscopy. Chem Commun (Camb) 2022; 58:6116-6119. [PMID: 35506441 DOI: 10.1039/d2cc01337a] [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
Oxidation of polyunsaturated fatty acids produces various oxidized lipids whose absolute configuration (AC) and conformations are difficult to analyze due to their flexibility. Through studies on hydroxy fatty acids, lipid hydroperoxides, and lipid epoxides, this work demonstrates the effectiveness of VCD spectroscopy to elucidate their AC and conformational preferences.
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Affiliation(s)
- 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.
| | - Naka Ida
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Takuya Kitahara
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Davidson Obinna Agbo
- 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, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
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5
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Mazzeo G, Cimmino A, Longhi G, Masi M, Evidente A, Abbate S. The Assignment of the Absolute Configuration of Non-Cyclic Sesquiterpenes by Vibrational and Electronic Circular Dichroism: The Example of Chiliadenus lopadusanus Metabolites. Biomolecules 2021; 11:biom11121902. [PMID: 34944545 PMCID: PMC8699476 DOI: 10.3390/biom11121902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
9-Hydroxynerolidol, 9-oxonerolidol, and chiliadenol B are three farnesane-type sesquiterpenoids isolated from Chiliadenus lopadusanus that have shown an interesting activity against human pathogens as Gram+ and Gram- bacteria resistant to antibiotics. However, the absolute configuration (AC) of these interesting sesquiterpenes has not been assigned so far. Vibrational and electronic circular dichroism spectra have been recorded and correlations are pointed out for the three compounds. Density functional theory (DFT) calculations are used in conjunction with Mosher's method of investigation to assign AC. Statistical analysis is considered to quantitatively define the choice of AC from VCD spectra.
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Affiliation(s)
- Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy; (G.M.); (G.L.)
| | - Alessio Cimmino
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy; (A.C.); (M.M.); (A.E.)
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy; (G.M.); (G.L.)
| | - Marco Masi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy; (A.C.); (M.M.); (A.E.)
| | - Antonio Evidente
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy; (A.C.); (M.M.); (A.E.)
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy; (G.M.); (G.L.)
- Correspondence: ; Tel.: +39-030-3717415
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6
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Demarque DP, Kemper M, Merten C. VCD spectroscopy reveals that a water molecule determines the conformation of azithromycin in solution. Chem Commun (Camb) 2021; 57:4031-4034. [PMID: 33885696 DOI: 10.1039/d1cc00932j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the IR and VCD spectra of azithromycin, a macrolide antibiotic with a total of 18 stereogenic centers. The computational analysis of the spectra reveals that a single water molecule has to be considered in the conformational search. Its key role is the stabilization of an extended hydrogen bonding network and an otherwise unstable conformation that determines the VCD spectral signatures.
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Affiliation(s)
- Daniel P Demarque
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Michael Kemper
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Christian Merten
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
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7
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del Río RE, Joseph-Nathan P. Vibrational Circular Dichroism Absolute Configuration of Natural Products From 2015 to 2019. Nat Prod Commun 2021. [DOI: 10.1177/1934578x21996166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although demonstrated in 1975, vibrational circular dichroism (VCD) finally started to popularize during this century as a reliable tool to determine the absolute configuration (AC) of organic molecules. This research field continues to be a very dynamic one, in particular for the study of natural products which are a unlimited source of chiral molecules. It therefore turns of interest to summarize the accomplishments published in recent years and to comment on some eventual difficulties that emerged in rare cases to complete the AC determination task. Therefore the aim of this review is to update VCD results for the AC assignment of natural products published from 2015 to 2019, a period in which VCD was reported in some 126 publications involving almost 300 molecules. They are organized according the type of studied metabolite allowing an easily search. The molecules correspond to 28 monoterpenes concerning 17 papers, to 42 sesquiterpenes in 14 papers, to 51 diterpenes in 19 publications, to 5 other terpenoids in three papers, to 48 aromatic molecules in 15 reports, to 20 polyketides in 10 publications, to 27 miscellaneous formulas also in 10 papers, and to 76 nitrogen containing compounds, which include alkaloids and their synthetic analogs, in 38 articles. The landscape of reviewed molecules is quite wide as it goes from simple monoterpenes, like borneol or camphor, to very relevant biological molecules like the alkaloid cocaine or tadalafil samples to distinguish genuine and counterfeit Cialis®. In addition, 5 natural products and a simple derivative published outside the reviewed period, were used to illustrate some aspects of density functional theory calculations.
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Affiliation(s)
- Rosa E. del Río
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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8
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Smyrniotopoulos V, Firsova D, Fearnhead H, Grauso L, Mangoni A, Tasdemir D. Density Functional Theory (DFT)-Aided Structure Elucidation of Linear Diterpenes from the Irish Brown Seaweed Bifurcaria bifurcata. Mar Drugs 2021; 19:42. [PMID: 33477773 PMCID: PMC7832306 DOI: 10.3390/md19010042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
Brown alga Bifurcaria bifurcata is an extraordinarily rich source of linear (acylic) diterpenes with enormous structural diversity. As part of our interest into secondary metabolites of the Irish seaweeds, here we report four new acyclic diterpenes (1-4) and seven known terpenoids (5-11) from the CHCl3 extract of B. bifurcata. The planar structures of the new metabolites were elucidated by means of 1D and 2D NMR, HRMS, and FT-IR spectroscopy. Since linear diterpenes are highly flexible compounds, the assignment of their stereochemistry by conventional methods, e.g., NOESY NMR, is difficult. Therefore, we employed extensive quantum-mechanical prediction of NMR chemical shifts and optical rotation analyses to identify the relative and absolute configurations of the new compounds 1-4. Several compounds moderately inhibited the human breast cancer cell line (MDA-MB-231) with IC50 values ranging from 10.0 to 33.5 μg/mL. This study not only demonstrates the vast capacity of the Irish B. bifurcata to produce highly oxygenated linear diterpenoids, but also highlights the potential of new methodologies for assignment of their stereogenic centers.
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Affiliation(s)
- Vangelis Smyrniotopoulos
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland; (V.S.); (D.F.)
| | - Daria Firsova
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland; (V.S.); (D.F.)
| | - Howard Fearnhead
- Pharmacology and Therapeutics, School of Medicine, National University of Ireland Galway, University Road, H91 W2TY Galway, Ireland;
| | - Laura Grauso
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici (NA), Italy;
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy;
| | - Deniz Tasdemir
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland; (V.S.); (D.F.)
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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9
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Smyrniotopoulos V, Merten C, Firsova D, Fearnhead H, Tasdemir D. Oxygenated Acyclic Diterpenes with Anticancer Activity from the Irish Brown Seaweed Bifurcaria bifurcata. Mar Drugs 2020; 18:E581. [PMID: 33238388 PMCID: PMC7700283 DOI: 10.3390/md18110581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 01/04/2023] Open
Abstract
Brown alga Bifurcaria bifurcata is a prolific source of bioactive acyclic (linear) diterpenes with high structural diversity. In the continuation of our investigations on Irish brown algae, we undertook an in-depth chemical study on the n-hexanes and chloroform subextracts of B. bifurcata that led to isolation of six new (1-6) and two known (7-8) acyclic diterpenes. Chemical structures of the compounds were elucidated by a combination of 1D and 2D NMR, HRMS, FT-IR, [α]D and vibrational circular dichroism (VCD) spectroscopy. Compounds 1-8, as well as three additional linear diterpenes (9-11), which we isolated from the same seaweed before, were tested against the human breast cancer cell line (MDA-MB-231). Several compounds moderately inhibited the growth of the MDA-MB-231 cell line with IC50 values ranging from 11.6 to 32.0 μg/mL. The present study carried out on the lipophilic extracts of the Irish B. bifurcata shows the enormous capacity of this seaweed to produce a large palette of acyclic diterpenes with diverse oxygenation and substitution patterns and promising bioactivities.
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Affiliation(s)
- Vangelis Smyrniotopoulos
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland; (V.S.); (D.F.)
| | - Christian Merten
- Organische Chemie 2, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany;
| | - Daria Firsova
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland; (V.S.); (D.F.)
| | - Howard Fearnhead
- Pharmacology and Therapeutics, School of Medicine, National University of Ireland Galway, University Road, H91 W2TY Galway, Ireland;
| | - Deniz Tasdemir
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland; (V.S.); (D.F.)
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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10
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Demarque DP, Heinrich S, Schulz F, Merten C. Sensitivity of VCD spectroscopy for small structural and stereochemical changes of macrolide antibiotics. Chem Commun (Camb) 2020; 56:10926-10929. [PMID: 32807999 DOI: 10.1039/d0cc03838e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report the application of VCD spectroscopy for the characterization of clarithromycin and erythromycin. We show that the VCD spectra of these large macrolides are distinctly different and that spectra calculations reproduce the experimentally observed VCD signatures. In addition, computed VCD spectra of different epimers indicate that they should also be distinguishable from the correct structure of clarithromycin.
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Affiliation(s)
- Daniel P Demarque
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Sascha Heinrich
- Ruhr-Universität Bochum, Organische Chemie 1, Natural Products Chemistry, 44801 Bochum, Germany
| | - Frank Schulz
- Ruhr-Universität Bochum, Organische Chemie 1, Natural Products Chemistry, 44801 Bochum, Germany
| | - Christian Merten
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
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11
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Merten C. Recent Advances in the Application of Vibrational Circular Dichroism Spectroscopy for the Characterization of Asymmetric Catalysts. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000876] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christian Merten
- Fakultät für Chemie und Biochemie Organische Chemie II Ruhr Universität Bochum Universitätsstraße 150 44801 Bochum Germany
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12
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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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13
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Böselt L, Sidler D, Kittelmann T, Stohner J, Zindel D, Wagner T, Riniker S. Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. J Chem Inf Model 2019; 59:1826-1838. [DOI: 10.1021/acs.jcim.8b00789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lennard Böselt
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Dominik Sidler
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Tobias Kittelmann
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Jürgen Stohner
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Daniel Zindel
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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14
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Le Barbu-Debus K, Scherrer A, Bouchet A, Sebastiani D, Vuilleumier R, Zehnacker A. Effect of puckering motion and hydrogen bond formation on the vibrational circular dichroism spectrum of a flexible molecule: the case of (S)-1-indanol. Phys Chem Chem Phys 2018; 20:14635-14646. [DOI: 10.1039/c8cp01695j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Vibrational circular dichroism spectra of (S)-1-indanol in DMSO and CCl4 are described by cluster-in-the-bulk static calculations and first principles molecular dynamics.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- F-91405 Orsay
| | - Arne Scherrer
- PASTEUR
- Département de chimie
- École normale supérieure
- PSL University
- Sorbonne Université
| | - Aude Bouchet
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- F-91405 Orsay
| | - Daniel Sebastiani
- Martin-Luther-Universität Halle-Wittenberg
- Institut für Chemie
- 06120 Halle
- Germany
| | - Rodolphe Vuilleumier
- PASTEUR
- Département de chimie
- École normale supérieure
- PSL University
- Sorbonne Université
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- F-91405 Orsay
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15
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Molinski TF, Broaddus CD, Morinaka BI. Liposomal Circular Dichroism (L-CD) of Arenoyl Derivatives of Sphingolipids. Amplification of Cotton Effects in Ordered Lipid Bilayers. Mar Drugs 2017; 15:E352. [PMID: 29261105 PMCID: PMC5742824 DOI: 10.3390/md15120352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 11/17/2022] Open
Abstract
Liposomal circular dichroism (L-CD) of acyclic amino alcohols exhibit amplification of Cotton effects when measured in highly uniform, unilamellar liposomes. The effect is likely due to intermolecular associations-H-aggregates-that self-assemble spontaneously within the lipid bilayer, and persists over long time scales. L-CD spectra of N,O,O'-tri-(6'methoxy-2'-naphthoyl)-d-erythro-sphingosine, or the corresponding dihydro-derivative (sphinganine), shows ~10-fold amplification of magnitudes of Cotton effects over conventional CD spectra recorded in isotropic solution.
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Affiliation(s)
- Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive MC0358, La Jolla, CA 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive MC0358, La Jolla, CA 92093, USA.
| | - Caroline D Broaddus
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive MC0358, La Jolla, CA 92093, USA.
| | - Brandon I Morinaka
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive MC0358, La Jolla, CA 92093, USA.
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16
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Kong J, Joyce LA, Liu J, Jarrell TM, Culberson JC, Sherer EC. Absolute configuration assignment of (+)-fluralaner using vibrational circular dichroism. Chirality 2017; 29:854-864. [PMID: 28981965 DOI: 10.1002/chir.22770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 01/01/2023]
Abstract
The absolute configurations of the separated enantiomers of fluralaner, a racemic animal health product used to prevent fleas and ticks, have been assigned using vibrational circular dichroism (VCD). The crystallographic structure of the active enantiomer (+)-fluralaner has previously been shown to have the (S) configuration using small molecule crystallography. We sought a faster analytical method to determine the absolute configuration of the separated enantiomers. When comparing the measured IR (infrared) and VCD spectra, it is apparent that the amide carbonyl groups appear in the IR but are nearly absent in the VCD. Computational work to calculate the VCD and IR using in vacuo models, implicit solvation, and explicitly solvated complexes has implicated conformational averaging of the carbonyl VCD intensities.
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Affiliation(s)
- John Kong
- Animal Health, Intervet, Inc., Rahway, New Jersey
| | - Leo A Joyce
- Process Research & Development, MRL, Rahway, New Jersey
| | - Jinchu Liu
- Process Research & Development, MRL, Rahway, New Jersey
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17
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Górecki M, Groszek G, Frelek J. Chirality sensing of bioactive compounds with amino alcohol unit via circular dichroism. Chirality 2017; 29:589-598. [PMID: 28771833 DOI: 10.1002/chir.22736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022]
Abstract
The aim of the present work was to test various chiroptical techniques, including in particular the in situ dirhodium methodology, to assign the absolute configuration of 1,2- and 1,3-amino alcohols. As models, we selected mainly compounds that have both an additional strongly absorbing and interfering chromophoric system and application in medicinal chemistry. Determination of the absolute configuration (AC) of the tested molecules such as cinchona alkaloids, Tamiflu, and others was carried out using a combination of electronic and vibrational circular dichroism (ECD, VCD) spectroscopy. It has been demonstrated that both 1,2- and 1,3-aminol moieties are subject to the same sector rule correlating stereostructure of formed Rh2 -complex with chiroptical properties, and that the changes in the position of the stereogenic center do not affect its proper use.
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Affiliation(s)
- Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Grażyna Groszek
- Faculty of Chemistry, Rzeszów University of Technology, Rzeszów, Poland
| | - Jadwiga Frelek
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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18
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Pollok CH, Zhang Q, Tiefenbacher K, Merten C. Chirality Induction from a Chiral Guest to the Hydrogen-Bonding Network of Its Hexameric Resorcinarene Host Capsule. Chemphyschem 2017; 18:1987-1991. [PMID: 28577348 DOI: 10.1002/cphc.201700610] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Indexed: 12/19/2022]
Abstract
The hexameric capsule of resorcin[4]arene 1 is capable of encapsulating tertiary amines, which has recently been used in the application of [(1)6 (H2 O)8 ] as (co-)catalyst in various asymmetric reactions. However, not much is known about the highly asymmetric but conformationally very dynamic structure of the capsule after uptake of chiral molecules. Therefore, in this contribution, we utilize electronic circular dichroism and vibrational circular dichroism spectroscopy to investigate how several chiral guest molecules affect the structural preferences of the capsule [(1)6 (H2 O)8 ]. In particular, we show that one small chiral amine encapsulated in [(1)6 (H2 O)8 ] is sufficient to control and dictate the stereochemical preferences of the entire capsule. Furthermore, neither strong π-π interactions nor a significant steric bulk are required for this induction. The observation of such a chiral imprint of the guest's stereochemistry onto its host molecule is expected to have implications also for other supramolecular capsules.
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Affiliation(s)
- Corina H Pollok
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie 2, Universitätsstraße 150, 44801, Bochum, Germany
| | - Qi Zhang
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie 2, Universitätsstraße 150, 44801, Bochum, Germany
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19
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Smyrniotopoulos V, Merten C, Kaiser M, Tasdemir D. Bifurcatriol, a New Antiprotozoal Acyclic Diterpene from the Brown Alga Bifurcaria bifurcata. Mar Drugs 2017; 15:E245. [PMID: 28767061 PMCID: PMC5577600 DOI: 10.3390/md15080245] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 11/18/2022] Open
Abstract
Linear diterpenes that are commonly found in brown algae are of high chemotaxonomic and ecological importance. This study reports bifurcatriol (1), a new linear diterpene featuring two stereogenic centers isolated from the Irish brown alga Bifurcariabifurcata. The gross structure of this new natural product was elucidated based on its spectroscopic data (IR, 1D and 2D-NMR, HRMS). Its absolute configuration was identified by experimental and computational vibrational circular dichroism (VCD) spectroscopy, combined with the calculation of 13C-NMR chemical shielding constants. Bifurcatriol (1) was tested for in vitro antiprotozoal activity towards a small panel of parasites (Plasmodium falciparum, Trypanosoma brucei rhodesiense, T. cruzi, and Leishmania donovani) and cytotoxicity against mammalian primary cells. The highest activity was exerted against the malaria parasite P. falciparum (IC50 value 0.65 μg/mL) with low cytotoxicity (IC50 value 56.6 μg/mL). To our knowledge, this is the first successful application of VCD and DP4 probability analysis of the calculated 13C-NMR chemical shifts for the simultaneous assignment of the absolute configuration of multiple stereogenic centers in a long-chain acyclic natural product.
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Affiliation(s)
| | - Christian Merten
- Lehrstuhl für Organische Chemie 2, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.
- University of Basel, 4003 Basel, Switzerland.
| | - Deniz Tasdemir
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, Research Division Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany.
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20
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Merten C, Dirkmann M, Schulz F. Stereochemical assignment of fusiccocadiene from NMR shielding constants and vibrational circular dichroism spectroscopy. Chirality 2017; 29:409-414. [DOI: 10.1002/chir.22708] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Christian Merten
- Organic Chemistry 2, Physical Organic Chemistry; Ruhr-University Bochum; Bochum Germany
| | - Michael Dirkmann
- Organic Chemistry 1, Natural Products Chemistry; Ruhr-University Bochum; Bochum Germany
| | - Frank Schulz
- Organic Chemistry 1, Natural Products Chemistry; Ruhr-University Bochum; Bochum Germany
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21
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Abstract
Covering: 2015. Previous review: Nat. Prod. Rep., 2016, 33, 382-431This review covers the literature published in 2015 for marine natural products (MNPs), with 1220 citations (792 for the period January to December 2015) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1340 in 429 papers for 2015), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Murray H G Munro
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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22
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Taniguchi T, Monde K. Practical Use of Circular Dichroism and Vibrational Circular Dichroism for Structural Analysis. J SYN ORG CHEM JPN 2017. [DOI: 10.5059/yukigoseikyokaishi.75.522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Kenji Monde
- Faculty of Advanced Life Science, Hokkaido University
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23
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Bünnemann K, Merten C. Solvation of a chiral carboxylic acid: effects of hydrogen bonding on the IR and VCD spectra of α-methoxyphenylacetic acid. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp02049j] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Taking the title compound as a representative example of a chiral carboxylic acid, we investigate how its VCD spectral pattern is affected by hydrogen bonding of different solvents.
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24
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Merten C. Vibrational optical activity as probe for intermolecular interactions. Phys Chem Chem Phys 2017; 19:18803-18812. [DOI: 10.1039/c7cp02544k] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A detailed VCD spectroscopic analysis of well-selected chiral model systems can give valuable and unprecedented insights into intermolecular interactions such as solvation or reactant–substrate binding in catalysis.
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25
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Passareli F, Batista ANL, Cavalheiro AJ, Herrebout WA, Batista Junior JM. Vibrational spectroscopy as a direct stereochemical probe for polyhydroxylated molecules. Phys Chem Chem Phys 2016; 18:30903-30906. [DOI: 10.1039/c6cp07171f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relative and absolute configurations of polyhydroxylated molecules via acetonide derivatives: the power of IR and VCD.
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Affiliation(s)
- F. Passareli
- Institute of Chemistry
- São Paulo State University – UNESP
- Araraquara
- Brazil
| | - A. N. L. Batista
- Institute of Chemistry
- São Paulo State University – UNESP
- Araraquara
- Brazil
| | - A. J. Cavalheiro
- Institute of Chemistry
- São Paulo State University – UNESP
- Araraquara
- Brazil
| | - W. A. Herrebout
- Department of Chemistry
- University of Antwerp
- Antwerp B2020
- Belgium
| | - J. M. Batista Junior
- Department of Chemistry
- Federal University of São Carlos – UFSCAr
- São Carlos
- Brazil
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26
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Wang S, Taniguchi T, Monde K, Kawahata M, Yamaguchi K, Otani Y, Ohwada T. Hydrogen bonding to carbonyl oxygen of nitrogen-pyramidalized amide – detection of pyramidalization direction preference by vibrational circular dichroism spectroscopy. Chem Commun (Camb) 2016; 52:4018-21. [DOI: 10.1039/c6cc00284f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-bonding to carbonyl of nitrogen-pyramidalized bicyclic β-proline amides can switch the preferred nitrogen-pyramidalization direction, as detected by VCD spectroscopy.
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Affiliation(s)
- Siyuan Wang
- Graduate School of Pharmaceutical Sciences
- University of Tokyo
- Tokyo 113-0033
- Japan
- Research Foundation Itsuu Laboratory
| | - Tohru Taniguchi
- Frontier Research Center for Post-Genome Science and Technology
- Faculty of Advanced Life Science
- Hokkaido University
- Sapporo 001-0021
- Japan
| | - Kenji Monde
- Frontier Research Center for Post-Genome Science and Technology
- Faculty of Advanced Life Science
- Hokkaido University
- Sapporo 001-0021
- Japan
| | - Masatoshi Kawahata
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Kagawa 769-2193
- Japan
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Kagawa 769-2193
- Japan
| | - Yuko Otani
- Graduate School of Pharmaceutical Sciences
- University of Tokyo
- Tokyo 113-0033
- Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences
- University of Tokyo
- Tokyo 113-0033
- Japan
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27
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Zinna F, Pescitelli G. Towards the Limits of Vibrational Circular Dichroism Spectroscopy: VCD Spectra of Some Alkyl Vinylethers. Chirality 2015; 28:143-6. [DOI: 10.1002/chir.22555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 10/23/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Francesco Zinna
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Pisa Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Pisa Italy
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