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Olszewska K, Mizera A, Ławniczak P, Kamińska A, Santillan R, Morales-Chamorro M, Ochoa ME, Farfán N, Łapiński A, Górecki M, Jastrzebska I, Runka T. Molecular Dynamics of Steroidal Rotors Probed by Theoretical, Spectroscopic and Dielectric Methods. Chemistry 2024; 30:e202303933. [PMID: 38311598 DOI: 10.1002/chem.202303933] [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: 11/27/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/06/2024]
Abstract
Our study focuses on molecular rotors with fast-moving rotators and their potential applications in the development of new amphidynamic crystals. Steroidal molecular rotors with a dipolar fluorine-substituted phenyl group as the rotator were synthesized and characterized. Three different rotors were investigated with varying numbers of fluorine atoms. A comprehensive analysis was performed using vibrational spectroscopy (Raman, FT-IR), electronic circular dichroism (ECD), and dielectric response to understand the behavior of the investigated model rotors. The results were supported by theoretical calculations using Density Functional Theory (DFT) methods. The angle-dependent polarized Raman spectra confirmed the crystallinity of the samples. Nearly frequency and temperature-independent permittivity suggest low-frequency librational motion of stators. An in-depth analysis of ECD spectra revealed high conformational flexibility in solution, resulting in low ECD effects, while in the solid-state with restricted rotation, significant ECD effects were observed. These findings shed light on the conformational behavior and potential applications of the studied steroidal molecular rotors.
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Affiliation(s)
- Karolina Olszewska
- Faculty of Materials Engineering and Technical Physics, Institute of Materials Research and Quantum Engineering, Poznan University of Technology Piotrowo, 3, 60-965, Poznań, Poland
| | - Adam Mizera
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179, Poznań, Poland
| | - Paweł Ławniczak
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179, Poznań, Poland
| | - Anna Kamińska
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Rosa Santillan
- Departamento de Química Centro de Investigación y de Estudios Avanzados del IPN, México D.F. Apdo. Postal 14-740, 07000, México
| | - Maricela Morales-Chamorro
- Departamento de Química Centro de Investigación y de Estudios Avanzados del IPN, México D.F. Apdo. Postal 14-740, 07000, México
| | - Ma Eugenia Ochoa
- Departamento de Química Centro de Investigación y de Estudios Avanzados del IPN, México D.F. Apdo. Postal 14-740, 07000, México
| | - Norberto Farfán
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Andrzej Łapiński
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179, Poznań, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Izabella Jastrzebska
- Institute of Chemistry, University of Białystok, Ciołkowskiego 1 K, 15-254, Białystok, Poland
| | - Tomasz Runka
- Faculty of Materials Engineering and Technical Physics, Institute of Materials Research and Quantum Engineering, Poznan University of Technology Piotrowo, 3, 60-965, Poznań, Poland
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2
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Vermeyen T, Cunha A, Bultinck P, Herrebout W. Impact of conformation and intramolecular interactions on vibrational circular dichroism spectra identified with machine learning. Commun Chem 2023; 6:148. [PMID: 37438485 DOI: 10.1038/s42004-023-00944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Vibrational Circular Dichroism (VCD) spectra often differ strongly from one conformer to another, even within the same absolute configuration of a molecule. Simulated molecular VCD spectra typically require expensive quantum chemical calculations for all conformers to generate a Boltzmann averaged total spectrum. This paper reports whether machine learning (ML) can partly replace these quantum chemical calculations by capturing the intricate connection between a conformer geometry and its VCD spectrum. Three hypotheses concerning the added value of ML are tested. First, it is shown that for a single stereoisomer, ML can predict the VCD spectrum of a conformer from solely the conformer geometry. Second, it is found that the ML approach results in important time savings. Third, the ML model produced is unfortunately hardly transferable from one stereoisomer to another.
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Affiliation(s)
- Tom Vermeyen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium.
- Department of Chemistry, Ghent University, Krijgslaan 281, Gent, 9000, Belgium.
| | - Ana Cunha
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
| | - Patrick Bultinck
- Department of Chemistry, Ghent University, Krijgslaan 281, Gent, 9000, Belgium.
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
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3
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Vakili M, Romano E, Darugar V, Brandán SA. Behaviours of antiviral Oseltamivir in different media: DFT and SQMFF calculations. J Mol Model 2021; 27:357. [PMID: 34812947 PMCID: PMC8608578 DOI: 10.1007/s00894-021-04962-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/20/2021] [Indexed: 01/18/2023]
Abstract
The synthetic cyclohexenecarboxylate ester antiviral Oseltamivir (O) have been theoretically studied by B3LYP/6–311 + + G** calculations to estimate its reactivity and behaviour in gas and aqueous media. The most stable structure obtained in above media is consistent with that reported experimental for Oseltamivir phosphate. The solvation energy value of (O) in aqueous media is between the predicted for antiviral Idoxuridine and Ribavirin. Besides, (O) containing a NH2 group and NH group reveals lower solvation energy compared with other antiviral agents with an NH2 group, such as Ribavirin, Cidofovir, and Brincidofovir. Atomic charges on N and O atoms in acceptors and donor groups reveal different behaviours in both media, while the natural bond orbital (NBO) studies show a raised stability of (O) in aqueous solution. This latter resulted is in concordance with the lower reactivity evidenced in water. Frontier orbital studies have revealed that (O) in gas phase has a very similar gap value to antiviral Cidofovir used against the ebola disease, while Chloroquine in the two media are more reactive than (O). This study will allow to identify (O) by using vibrational spectroscopy because the 144 vibration modes expected have been assigned using the harmonic force fields calculated from the scaled mechanical force field methodology (SQMFF). Scaled force constants for (O) in the mentioned media are also reported for first time. Due to hydration of the C = O and NH2 groups by solvent molecules, the calculations in solution produce variations not only in the IR wavenumbers bands, but also in their intensities.
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Affiliation(s)
- Mohammad Vakili
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Elida Romano
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química Y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucuman, Tucumán, Argentina
| | - Vahidreza Darugar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Silvia Antonia Brandán
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química Y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucuman, Tucumán, Argentina.
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4
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Michalak M, Bisek B, Nowacki M, Górecki M. Base-Catalyzed, Solvent-Free Synthesis of Rigid V-Shaped Epoxydibenzo[ b, f][1,5]diazocines. J Org Chem 2021; 86:8955-8969. [PMID: 34161097 PMCID: PMC8279491 DOI: 10.1021/acs.joc.1c00884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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A novel method for
the synthesis of epoxydibenzo[b,f][1,5]diazocines exhibiting a V-shaped molecular
architecture is reported. The unique approach is based on unprecedented
base-catalyzed, solvent-free autocondensation and cross-condensation
of fluorinated o-aminophenones. The structure of
the newly synthesized diazocines was confirmed independently by X-ray
analysis and chiroptical methods. The rigidity of the diazocine scaffold
allowed for the separation of the racemate into single enantiomers
that proved to be thermally stable up to 140 °C. Furthermore,
the inertness of the diazocine scaffold was demonstrated by performing
a series of typical transformations, including transition metal-catalyzed
reactions, proceeding without affecting the bis-hemiaminal subunit.
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Affiliation(s)
- Michał Michalak
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Bartosz Bisek
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michał Nowacki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Szyszka Ł, Górecki M, Cmoch P, Jarosz S. Fluorescent Molecular Cages with Sucrose and Cyclotriveratrylene Units for the Selective Recognition of Choline and Acetylcholine. J Org Chem 2021; 86:5129-5141. [PMID: 33710904 PMCID: PMC8041319 DOI: 10.1021/acs.joc.1c00019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The synthesis of
four fluorescent diastereoisomeric molecular cages
containing cyclotriveratrylene and sucrose moieties connected via the naphthalene linkers is reported. These diastereoisomers
were found to be selective and efficient receptors for acetylcholine
and choline. Compound P-5a has a better
affinity for choline over acetylcholine, while cage M-5a exhibits a higher association constant for acetylcholine
over choline. The highest selectivity value was observed for compound M-5a (KACh/KCh = 3.1). Cages P-5a, P-5b, M-5a, and M-5b were fully characterized
by the advanced NMR techniques, and ECD spectroscopy was supported
by DFT calculations. The binding constants Ka of these receptors were determined by fluorescence titration
experiments in acetonitrile.
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Affiliation(s)
- Łukasz Szyszka
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
| | - Piotr Cmoch
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
| | - Sławomir Jarosz
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
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6
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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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7
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Pendrill R, Mutter ST, Mensch C, Barron LD, Blanch EW, Popelier PLA, Widmalm G, Johannessen C. Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity. Chemphyschem 2019; 20:695-705. [PMID: 30688397 DOI: 10.1002/cphc.201801172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/25/2019] [Indexed: 01/31/2023]
Abstract
Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.
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Affiliation(s)
- Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
| | - Shaun T Mutter
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Natural Sciences, Middlesex University, NW4 4BT, London, UK
| | - Carl Mensch
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Ghent Quantum Chemistry Group Department of Chemistry, University of Ghent, Krijgslaan 281, 9000, Ghent, Belgium
| | - Laurence D Barron
- School of Chemistry, University of Glasgow Joseph Black Building, Glasgow, G12 8QQ, UK
| | - Ewan W Blanch
- School of Science, RMIT University GPO Box 2476, Melbourne, VIC 3001, Australia
| | - Paul L A Popelier
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171, 2020, Antwerp, Belgium
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8
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Isolation and Structure Elucidation of Cembranoids from a Dongsha Atoll Soft Coral Sarcophyton stellatum. Mar Drugs 2018; 16:md16060210. [PMID: 29903990 PMCID: PMC6025080 DOI: 10.3390/md16060210] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/27/2022] Open
Abstract
Six new polyoxygenated cembrane-based diterpenoids, stellatumolides A–C (1–3), stellatumonins A and B (4 and 5), and stellatumonone (6), were isolated together with ten known related compounds (7–16) from the ethyl acetate (EtOAc) extract of soft coral Sarcophyton stellatum. The structures of the new compounds were established by extensive spectroscopic analyses, including 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and data comparison with related structures. Compounds 8 and 14 were isolated from a natural source for the first time. The isolated metabolites were shown to be not cytotoxic against a limited panel of cancer cells. Compound 9 showed anti-inflammatory activity by reducing the expression of proinflammatory cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) proteins in lipopolysaccharide (LPS)-stimulated mouse leukaemic monocyte macrophage (RAW 264.7) cells.
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9
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Azzena U, Carraro M, Pisano L. Addressing Stereochemistry of Heterocyclic Compounds by DFT NMR Calculations. Chem Heterocycl Compd (N Y) 2018. [DOI: 10.1007/s10593-018-2279-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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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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11
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Mazzeo G, Longhi G, Corless VB, Zajdlik A, Yudin AK, Abbate S. Vibrational Circular Dichroism Unveils Chiroptical, Electrical, and Magnetic Properties of Borylated Isocyanides and Aldehydes. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- 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
| | - Victoria B. Corless
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. M5S 3H6 Toronto ON Canada
| | - Adam Zajdlik
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. M5S 3H6 Toronto ON Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. M5S 3H6 Toronto ON Canada
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Viale Europa 11 25123 Brescia Italy
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12
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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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13
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14
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The role of chirality in a set of key intermediates of pharmaceutical interest, 3-aryl-substituted-γ-butyrolactones, evidenced by chiral HPLC separation and by chiroptical spectroscopies. J Pharm Biomed Anal 2017; 144:41-51. [PMID: 28118957 DOI: 10.1016/j.jpba.2017.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/14/2016] [Accepted: 01/04/2017] [Indexed: 11/20/2022]
Abstract
The enantiomers of four chiral 3-aryl-substituted-γ-butyrolactones, key intermediates for the preparation of compounds of pharmaceutical interest, were successfully isolated by enantioselective chromatography, employing the Chiralpak AD-H chiral stationary phase. For all compounds the same elution order was observed, as monitored by a full set of chiroptical methods that we employed, namely ORD (optical rotatory dispersion), ECD (electronic circular dichroism, or CD in the UV range), and VCD (vibrational circular dichroism, or CD in the IR range). By density functional theory (DFT) calculations we were able to determine that the first eluted enantiomer has (S) absolute configuration in all four cases. We were able to justify the elution order by molecular docking calculations for all four enantiomeric pairs and suitable modeling of the stationary and mobile phases of the employed columns. The optimal performance of the chiroptical spectroscopies and of the DFT calculations allows us to formulate a lactone chirality rule out of the CO stretching region of the VCD spectra.
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15
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Hajzer V, Fišera R, Latika A, Durmis J, Kollár J, Frecer V, Tučeková Z, Miertuš S, Kostolanský F, Varečková E, Šebesta R. Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation. Org Biomol Chem 2017; 15:1828-1841. [DOI: 10.1039/c6ob02673g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Three diastereoisomers of oseltamivir were synthesized, their properties predicted by quantum-chemical calculations and their antiviral activities evaluated.
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Affiliation(s)
| | | | | | | | - Jakub Kollár
- Comenius University in Bratislava
- Faculty of Pharmacy
- Department of Pharmaceutical Analysis and Nuclear Pharmacy
- SK-83232 Bratislava
- Slovakia
| | - Vladimír Frecer
- Comenius University in Bratislava
- Faculty of Pharmacy
- Department of Physical Chemistry of Drugs
- SK-83232 Bratislava
- Slovakia
| | - Zuzana Tučeková
- University of SS. Cyril and Methodius
- Faculty of Natural Sciences
- Department of Biotechnologies
- SK-91701 Trnava
- Slovakia
| | - Stanislav Miertuš
- ICARST n.o
- SK-84104 Bratislava
- Slovakia
- University of SS. Cyril and Methodius
- Faculty of Natural Sciences
| | - František Kostolanský
- Biomedical Research Center
- Institute of Virology
- Slovak Academy of Sciences
- Department of Orthomyxovirus Research
- SK-84505 Bratislava
| | - Eva Varečková
- Biomedical Research Center
- Institute of Virology
- Slovak Academy of Sciences
- Department of Orthomyxovirus Research
- SK-84505 Bratislava
| | - Radovan Šebesta
- Comenius University in Bratislava
- Faculty of Natural Sciences
- Department of Organic Chemistry
- SK-84215 Bratislava
- Slovakia
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16
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Jiménez-Romero C, Rode JE, Rodríguez AD. Reassignment of the absolute configuration of plakinidone from the sponge consortium Plakortis halichondrioides-Xestospongia deweerdtae using a combination of synthesis and a chiroptical approach. TETRAHEDRON, ASYMMETRY 2016; 27:410-419. [PMID: 28190935 PMCID: PMC5295471 DOI: 10.1016/j.tetasy.2016.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recent work by Wu et al. in connection with the first synthesis of the marine natural product plakinidone revealed that the most salient feature of its purported structure, a six-membered perlactone moiety, was in fact a five-membered lactone, i.e. a 3-methyl-4-hydroxy-2(5H)-furanone or tetronic acid ring. With the planar structure of plakinidone confidently revised, we undertook a new investigation to unambiguously establish its absolute configuration. Upon preparing two stable derivatives 1 and 5 from a sample of naturally occurring plakinidone extracted from the sponge association Plakortis halichondriodes-Xetospongia deweerdtae, the absolute configuration was assigned by synthesis and vibrational and electronic circular dichroism (VCD and ECD) measurements in combination with density functional theory calculations at the B3LYP/aug-cc-pVDZ/PCM(CH3CN) level of theory. Our combined efforts and the agreement between the experimental and calculated VCD/ECD spectra of 1 revealed that the absolute configuration of plakinidone was in fact (11S,17R) and not the formerly reported (11S,17S) diastereomer assigned by Wu et al.. Therefore, we propose that natural plakinidone is accurately represented by structure 12.
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Affiliation(s)
- Carlos Jiménez-Romero
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, Puerto Rico 00926
| | - Joanna E. Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Abimael D. Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, Puerto Rico 00926
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Rossi D, Nasti R, Marra A, Meneghini S, Mazzeo G, Longhi G, Memo M, Cosimelli B, Greco G, Novellino E, Da Settimo F, Martini C, Taliani S, Abbate S, Collina S. Enantiomeric 4-Acylamino-6-alkyloxy-2 Alkylthiopyrimidines As Potential A3Adenosine Receptor Antagonists: HPLC Chiral Resolution and Absolute Configuration Assignment by a Full Set of Chiroptical Spectroscopy. Chirality 2016; 28:434-40. [DOI: 10.1002/chir.22599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/19/2016] [Accepted: 03/01/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Daniela Rossi
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
| | - Rita Nasti
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
| | - Annamaria Marra
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
| | - Silvia Meneghini
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Maurizio Memo
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Barbara Cosimelli
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Napoli Italy
| | - Giovanni Greco
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Napoli Italy
| | - Ettore Novellino
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Napoli Italy
| | | | | | | | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Simona Collina
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
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18
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Zielinski F, Mutter ST, Johannessen C, Blanch EW, Popelier PLA. The Raman optical activity of β-D-xylose: where experiment and computation meet. Phys Chem Chem Phys 2015; 17:21799-809. [PMID: 26122177 DOI: 10.1039/c5cp02969d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure-spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved.
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Affiliation(s)
- François Zielinski
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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19
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Górecki M. Transmission vs. Diffuse Transmission in Circular Dichroism: What to Choose for Probing Solid-State Samples? Chirality 2015; 27:441-8. [DOI: 10.1002/chir.22468] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/17/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Marcin Górecki
- Institute of Organic Chemistry; Polish Academy of Sciences; Warsaw Poland
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