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Rode JE, Wasilczenko J, Górecki M. Differentiation of solvatomorphs of active pharmaceutical ingredients (API) by solid-state vibrational circular dichroism (VCD). Spectrochim Acta A Mol Biomol Spectrosc 2024; 310:123851. [PMID: 38295593 DOI: 10.1016/j.saa.2024.123851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Here, we present the new application of solid-state Vibrational Circular Dichroism (VCD) spectroscopy to differentiate several dutasteride (DS) solvatomorphs - the model active pharmaceutical ingredient (API). Several crystalline DS hydrochloride hydrates solvated with methanol, ethanol, acetonitrile, acetone, and acetic acid were prepared. In contrast to almost identical IR spectra, the VCD ones were very sensitive to changes in the sample composition. We marked significant differences in the shape of VCD spectra of studied DS solvatomorphs, DS hydrates, and DS polymorphic forms. Our findings, supported by DFT calculations, show that VCD spectroscopy has the pronounced ability to distinguish their crystal arrangements. We believe that this contribution will extend the use of VCD in the pharmaceutical industry for developing and designing new chiral drug products for the identification, description, and in-depth probing of several pharmaceutical solvatomorphs in the future.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, Dorodna 16 St., 03-195 Warsaw, Poland
| | - Justyna Wasilczenko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland.
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2
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Rode JE, Łyczko K, Kaczorek D, Kawęcki R, Dobrowolski JC. VCD spectra of chiral naphthalene-1-carboxamides in the solid-state. Spectrochim Acta A Mol Biomol Spectrosc 2024; 310:123939. [PMID: 38301569 DOI: 10.1016/j.saa.2024.123939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
The VCD spectra of chiral 2,3-dihydro-1H-benzo[de]isoquinolin-1-one (8-substituted naphthalene-1-carboxamide, BIQ) were studied in KBr pellets. The X-ray diffractometry revealed that the Me, Ph, and pClPh BIQs crystalize in the monoclinic P21, while nBu, pMePh, and oMeOPh BIQs in the orthorhombic P212121 space group. Only the Me-BIQ crystal exhibits the presence of cyclic amide dimers, while the others contain chains of the amid group hydrogen bonds. For all BIQs, except pMePh, the most intense IR band in the 1750-1550 cm-1 region is located at ca. 1680 cm-1 and is accompanied by two weak ones at ca. 1618 and 1590 cm-1. For the pMePh derivative, four almost equally intense IR bands at 1662, 1639, 1614, and 1588 cm-1 are observed. This region of the IR spectra of BIQs, but pMePh, is well reproduced by calculations based on BIQ monomers. On the other hand, the complex IR pattern of pMePh is computationally reproduced when larger crystal fragments, like octamers, are considered. Registration of the VCD spectra enabled recognizing the complexity of IR contours at ca. 1680 cm-1 by the corresponding VCD motives. For (i) Me, Ph and pClPh (R)-enantiomers, two (+)(-) bands were distinguished and for (ii) nBu and pMePh ones, one VCD band with right-side asymmetry was found. For (iii) oMeOPh the VCD pattern cannot be unambiguously assigned. Thus, the VCD spectra in the ν(C=O) range diverse the studied compounds. Among the set of molecules, pMePh has exceptional crystal geometry. Therefore, its most intense ν(C=O) band position and shape can be connected with the geometry of the hydrogen bonds, interactions, and crystal packing. Interpretation of the VCD spectra is based on linear and packed BIQ octamers. This cluster model can reproduce the main features of the solid-state VCD of BIQs.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland.
| | - Krzysztof Łyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
| | - Dorota Kaczorek
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Robert Kawęcki
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
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3
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Kamińska K, Iwan D, Trojnar J, Daszkiewicz M, Rode JE, Wojaczyński J, Wojaczyńska E. Rearrangement of thiazolidine derivatives - a synthesis of a chiral fused oxathiane-γ-lactam bicyclic system. Org Biomol Chem 2023; 21:9182-9191. [PMID: 37955209 DOI: 10.1039/d3ob01454a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Reaction of L-cysteine with carbonyl compounds leads to thiazolidine derivatives which undergo a stereoselective conversion to two types of chiral bicyclic products bearing two or three stereogenic centers, including the first fused oxathiane-γ-lactam system.
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Affiliation(s)
- Karolina Kamińska
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Dominika Iwan
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Jakub Trojnar
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Marek Daszkiewicz
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna St. 2, 50-422 Wrocław, Poland
| | - Joanna E Rode
- Institute of Nuclear Chemistry and Technology, Dorodna St. 16, 03-195 Warszawa, Poland
| | - Jacek Wojaczyński
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie St. 14, 50-383 Wrocław, Poland
| | - Elżbieta Wojaczyńska
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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4
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Karoń K, Rode JE, Kaczorek D, Kawęcki R, Pluczyk-Małek S, Łapkowski M, Ostrowski S, Lyczko K, Dobrowolski JC. UV-vis and ECD spectroelectrochemistry of atropisomeric naphthalenediimide derivative. Spectrochim Acta A Mol Biomol Spectrosc 2023; 288:122089. [PMID: 36436264 DOI: 10.1016/j.saa.2022.122089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/21/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The UV-vis and ECD spectroelectrochemistry (SEC) of a chiral binaphthalenylamine derivative of the N-butyl naphthalenediimide (NDIB-NH2) enantiomers were applied to measure UV-vis and ECD spectra of NDIB-NH2 radicals and dianion formed in the reduction and oxidation processes observed in cyclic voltammetry (CV). The CV curves and EPR spectroelectrochemistry enabled us to establish conditions at which a radical-anion [NDIB-NH2]̇.-, a dianion [NDIB-NH2]2-, and a radical-cation [NDIB-NH2]̇.+ are formed. The DFT restricted open-shell CAM-B3LYP-D3/def2TZVP/PCM calculations demonstrated that in the radical-anion [NDIB-NH2]̇.-, spin is spread over the NDI system while in the radical-cation [NDIB-NH2]̇+ it is spread over the aminonaphthalene moiety. The UV-vis spectra of radical-anion and dianion show the most significant changes in the 400-800 nm range. In that range, the ECD spectra varied with the change of electrode potential more than the UV-vis did and enabled the identification of a new ECD band of [NDIB-NH2]̇.- at ca. 400 nm hidden in the background in the UV spectra at -1000 mV. A broad structured ECD pattern with a maximum at ca. 530 nm was observed for [NDIB-NH2]̇.- (-1000 mV), while a single smooth ECD band of [NDIB-NH2]2- was located at 520 nm (-1750 mV). For the first time, an isosbestic point (455 nm) was found in ECD spectroelectrochemical measurements for the radical-cation [NDIB-NH2]̇.+ in equilibrium with the NDIB-NH2 neutral form. The TD-DFT CAM-B3LYP-D3/6-31G** calculations combined with the hybrid (explicit combined with implicit) solvation model fairly well reproduced the UV-vis and ECD SEC of neutral and redox forms of NDIB-NH2 but the ECD spectrum of [NDIB-NH2]̇.+ above 390 nm.
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Affiliation(s)
- Krzysztof Karoń
- Faculty of Chemistry, Silesian University of Technology, 9 Strzody Street, 44-100 Gliwice, Poland; Centre for Organic and Nanohybrid Electronics, Silesian University of Technology, 22b Konarskiego Street, 44-100 Gliwice, Poland.
| | - Joanna E Rode
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland.
| | - Dorota Kaczorek
- Faculty of Science, Siedlce University, 3 Maja Street No 54, 08-110 Siedlce, Poland
| | - Robert Kawęcki
- Faculty of Science, Siedlce University, 3 Maja Street No 54, 08-110 Siedlce, Poland
| | - Sandra Pluczyk-Małek
- Faculty of Chemistry, Silesian University of Technology, 9 Strzody Street, 44-100 Gliwice, Poland; Centre for Organic and Nanohybrid Electronics, Silesian University of Technology, 22b Konarskiego Street, 44-100 Gliwice, Poland
| | - Mieczysław Łapkowski
- Faculty of Chemistry, Silesian University of Technology, 9 Strzody Street, 44-100 Gliwice, Poland; Centre for Organic and Nanohybrid Electronics, Silesian University of Technology, 22b Konarskiego Street, 44-100 Gliwice, Poland; Centre of Polymer and Carbon Materials, Polish Academy of Science, 34 Curie Sklodowska Street, 41-800 Zabrze, Poland
| | - Sławomir Ostrowski
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Jan Cz Dobrowolski
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland.
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Machalska E, Zając G, Rode JE. Chirality transfer observed in Raman optical activity spectra. Spectrochim Acta A Mol Biomol Spectrosc 2022; 281:121604. [PMID: 35835058 DOI: 10.1016/j.saa.2022.121604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Chirality transfer (also called induced chirality) is a phenomenon present in chiroptical spectra that manifests itself as a new band or bands of an achiral molecule interacting with a chiral one. In the Raman optical activity (ROA) spectroscopy, the bands of achiral solvents have been recently observed, but the latest papers have shown that they corresponded to the new ECD-Raman (eCP-Raman) effect. Here, we show an unambiguous example of chirality transfer observed in the ROA spectra. The spectra registered for the (1:1) mixtures of achiral benzonitrile with the enantiomers of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol, and 1-phenylethylamine exhibited the v(CN) vibration band at about 2230 cm-1. The ROA measurements were repeated several times to ensure the reliability of the phenomenon. Calculations revealed the CN···HO or CN···HNH hydrogen bond formation accompanied by the π···π or CH···π interactions. The interaction strength was shown to be an important factor for the pronouncement of the ROA chirality transfer effect.
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Affiliation(s)
- Ewa Machalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-38 Krakow, Poland; Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland.
| | - Grzegorz Zając
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland.
| | - Joanna E Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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6
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Machalska E, Zając G, Baranska M, Bouř P, Kaczorek D, Kawęcki R, Rode JE, Lyczko K, Dobrowolski JC. New chiral ECD-Raman spectroscopy of atropisomeric naphthalenediimides. Chem Commun (Camb) 2022; 58:4524-4527. [PMID: 35302568 DOI: 10.1039/d1cc06974h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, we found that a recently discovered ECD-Raman effect dominated over the natural Raman optical activity in a series of atropisomeric naphthalenediimides, and we investigated the kind of information about the molecular structure that could be obtained from the spectra. The ECD-Raman effect is polarised Raman scattering modulated by electronic circular dichroism. We showed that the spectra significantly depended on the substitution of the solute and/or the change of the solvent. Moreover, the spectra could be well-predicted by the theory, thus providing an interesting tool to monitor the chirality of the binaphthyl compounds.
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Affiliation(s)
- Ewa Machalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Cracow, Poland.
| | - Grzegorz Zając
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Cracow, Poland. .,Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic.
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Cracow, Poland.
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic.
| | - Dorota Kaczorek
- Faculty of Science, Siedlce University, 3 Maja Street No. 54, 08-110 Siedlce, Poland.
| | - Robert Kawęcki
- Faculty of Science, Siedlce University, 3 Maja Street No. 54, 08-110 Siedlce, Poland.
| | - Joanna E Rode
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna-Street, 03-195 Warsaw, Poland.
| | - Krzysztof Lyczko
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna-Street, 03-195 Warsaw, Poland.
| | - Jan Cz Dobrowolski
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna-Street, 03-195 Warsaw, Poland.
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7
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Rode JE, Lyczko K, Kosińska K, Matalińska J, Dyniewicz J, Misicka A, Dobrowolski JC, Lipiński PFJ. The solid state VCD of a novel N-acylhydrazone trifluoroacetate. Spectrochim Acta A Mol Biomol Spectrosc 2022; 269:120761. [PMID: 34954483 DOI: 10.1016/j.saa.2021.120761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/23/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
A novel N-acylhydrazone with pharmaceutical importance was subject of structural and IR/VCD investigations in the solid state. In the crystal structure, dimers of anion-cation pairs are stabilized by H-bonding and ionic interactions. Some less common interaction types, like C=N···C-NH3+ (σ-hole) interactions, hydrazone-aromatic interactions and dispersive contacts of the CF3 groups are also present in the crystal. Satisfactory reproduction of the solid state IR and VCD spectra required that quantum-chemical calculations be done on a tetramer (four cation-anion pairs) cut out from the crystal structure, exhibiting key intermolecular interactions. Ten DFT functionals were assessed as to the agreement between the calculated and experimental spectra. Various approaches to scaling of the calculated frequencies were applied. The best results were yielded with individual (optimized) frequency scaling factors (FSFs) and band half-widths at half maximum-(HWHM) for four separate spectral subregions. The best matching between the experimental and theoretical spectra (according to SimIR, SimVCD and SimVDF indices) was found for the B3PW91 functional, however, a few other functionals follow closely in the ranking. Based on the quantum chemical calculations, spectral assignments have been made.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, PL 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, PL 03-195 Warsaw, Poland
| | - Katarzyna Kosińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Jolanta Dyniewicz
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Jan Cz Dobrowolski
- Department for Medicines Biotechnology and Bioinformatics, National Medicines Institute, 30/34 Chełmska Street, PL 00-725 Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland.
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8
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Machalska E, Zajac G, Baranska M, Kaczorek D, Kawęcki R, Lipiński PFJ, Rode JE, Dobrowolski JC. On Raman optical activity sign-switching between the ground and excited states leading to an unusual resonance ROA induced chirality. Chem Sci 2020; 12:911-916. [PMID: 34163857 PMCID: PMC8179112 DOI: 10.1039/d0sc05345g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Raman optical activity (ROA) spectra recorded for a chiral naphthalene diimide derivative (nBu-NDI–BINAM) dissolved in a series of solvents exhibit strong solute to solvent induced chirality with: (1) dominating bands of solvents, (2) nBu-NDI–BINAM resonance ROA (RROA) bands which are barely visible, (3) monosignate RROA Solvent spectra with an unexpected sign concordant with that of the ECD band of the resonant electronic state, (4) bisignate RROA bands for a few solvents, and (5) superposition of non-resonant and resonant ROA bands of the chiral solvents. The unusual ROA enhancement was explained in terms of resonance energy transfer with resonant Raman emission. The surprising RROA sign-switching was found to be due to specific conformational equilibria where one solute conformer dominates in the ground and the other in the first excited singlet state, and, the signs of the related ECD bands of these two conformers are opposite. Unusual solute to solvent induced chirality in ROA comes from specific conformer equilibria in the ground and the excited states.![]()
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Affiliation(s)
- Ewa Machalska
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 30-387 Cracow Poland .,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University Bobrzynskiego 14 30-348 Cracow Poland
| | - Grzegorz Zajac
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University Bobrzynskiego 14 30-348 Cracow Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 30-387 Cracow Poland .,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University Bobrzynskiego 14 30-348 Cracow Poland
| | - Dorota Kaczorek
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences Pawińskiego 5 02-106 Warsaw Poland
| | - Joanna E Rode
- Institute of Nuclear Chemistry and Technology 16 Dorodna-Street 03-195 Warsaw Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology 16 Dorodna-Street 03-195 Warsaw Poland
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9
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Kowalczyk A, Lipiński PFJ, Karoń K, Rode JE, Lyczko K, Dobrowolski JC, Donten M, Kaczorek D, Poszytek J, Kawęcki R, Łapkowski M, Malkowska A, Grudzinski IP, Nowicka AM. Enantioselective sensing of (S)-Thalidomide in blood plasma with a chiral naphthalene diimide derivative. Biosens Bioelectron 2020; 167:112446. [PMID: 32818748 DOI: 10.1016/j.bios.2020.112446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 10/23/2022]
Abstract
Fast, simple in use and highly effective voltammetric enantiosensor dedicated for determination of thalidomide (TD) enantiomers (especially towards the toxic (S)-enantiomer) in blood plasma is still desirable. Here we have proven that newly synthesized chiral naphthalene diimide (NDI) derivatives are excellent electroactive materials for TD enantiosensors. The recognition process relies on the specific interaction between the chiral NDI receptor and the thalidomide enantiomer of the opposite configuration. This unique specific interaction between (S)-thalidomide and (R)-NDI derivative counterparts, evident in the DPV voltammograms, was confirmed by molecular modeling. The demonstrated voltammetric enantiosensors are characterized by the low detection limit at the level of μg·L-1, wide analytical range from 5·10-4 - 10 mg·L-1, high selectivity and long lifetime. The results of the recovery rates showed a very good degree of accuracy towards the determination of (S)-thalidomide in the blood samples, so it can be successfully used in the analysis of clinical samples.
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Affiliation(s)
- Agata Kowalczyk
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., PL-02-093, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawińskiego 5 Str., PL-02-106, Warsaw, Poland
| | - Krzysztof Karoń
- Faculty of Chemistry, Silesian University of Technology, Strzody 9 Str., PL-44-100, Gliwice, Poland
| | - Joanna E Rode
- Institute of Nuclear Chemistry and Technology, Dorodna 16 Str., PL-03-195, Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, Dorodna 16 Str., PL-03-195, Warsaw, Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, Dorodna 16 Str., PL-03-195, Warsaw, Poland.
| | - Mikołaj Donten
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., PL-02-093, Warsaw, Poland; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101 Str., PL-02-089, Warsaw, Poland
| | - Dorota Kaczorek
- Siedlce University, Faculty of Science, 3 Maja 54 Str., PL-08-110, Siedlce, Poland
| | - Joanna Poszytek
- Siedlce University, Faculty of Science, 3 Maja 54 Str., PL-08-110, Siedlce, Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science, 3 Maja 54 Str., PL-08-110, Siedlce, Poland.
| | - Mieczysław Łapkowski
- Faculty of Chemistry, Silesian University of Technology, Strzody 9 Str., PL-44-100, Gliwice, Poland; Centre of Polymer and Carbon Materials, Polish Academy of Science, Curie Sklodowska 34 Str., PL-41-800, Zabrze, Poland
| | - Anna Malkowska
- Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., PL-02-097, Warsaw, Poland
| | - Ireneusz P Grudzinski
- Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., PL-02-097, Warsaw, Poland.
| | - Anna M Nowicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., PL-02-093, Warsaw, Poland.
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10
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Lyczko K, Rode JE, Dobrowolski JC. Chiral Lanthanide Complexes with l- and d-Alanine: An X-ray and Vibrational Circular Dichroism Study. Molecules 2020; 25:E2729. [PMID: 32545530 PMCID: PMC7357152 DOI: 10.3390/molecules25122729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/17/2023] Open
Abstract
A whole series of [Ln(H2O)4(Ala)2]26+ dimeric cationic lanthanide complexes with both L- and D-alanine enantiomers was synthesized. The single-crystal X-ray diffraction at 100 and 292 K shows the formation of two types of dimers (I and II) in crystals. Between the dimer centers, the alanine molecules behave as bridging (μ2-O,O'-) and chelating bridging (μ2-O,O,O'-) ligands. The first type of bridge is present in dimers I, while both bridge forms can be observed in dimers II. The IR and vibrational circular dichroism (VCD) spectra of all L- and D-alanine complexes were registered in the 1750-1250 cm-1 range as KBr pellets. Despite all the studied complexes are exhibiting similar crystal structures, the spectra reveal correlations or trends with the Ln-O1 distances which exemplify the lanthanide contraction effect in the IR spectra. This is especially true for the positions and intensities of some IR bands. Unexpectedly, the ν(C=O) VCD bands are quite intense and their composed shapes reveal the inequivalence of the C=O vibrators in the unit cell which vary with the lanthanide. Unlike in the IR spectra, the ν(C=O) VCD band positions are only weakly correlated with the change of Ln and the VCD intensities at most show some trends. Nevertheless, this is the first observation of the lanthanide contraction effect in the VCD spectra. Generally, for the heavier lanthanides (Ln: Dy-Lu), the VCD band maxima are very close to each other and the mirror reflection of the band of two enantiomers is usually better than that of the lighter Lns. DFT calculations show that the higher the multiplicity the higher the stability of the system. Actually, the molecular geometry in crystals (at 100 K) is well predicted based on the highest-spin structures. Also, the simulated IR and VCD spectra strongly depend on the Ln electron configuration but the best overall agreement was reached for the Lu complex, which is the only system with a fully filled f-shell.
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Affiliation(s)
- Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (J.E.R.); (J.C.D.)
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11
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Czajkowska-Szczykowska D, Jastrzebska I, Rode JE, Morzycki JW. Revision of the Structure of N, O-Diacetylsolasodine. Unusual Epimerization at the Spiro Carbon Atom during Acetylation of Solasodine. J Nat Prod 2019; 82:59-65. [PMID: 30614239 DOI: 10.1021/acs.jnatprod.8b00573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The steroidal alkaloid solasodine (1) undergoes inversion of configuration at the C-22 spiro atom when treated with acetic anhydride-pyridine at ambient temperature. The basic solvolysis of the N, O-diacetyl derivative (2) reverses the reaction, yielding the starting solasodine (1). The mechanisms of both processes (acetylation and deacetylation) were studied in terms of possible reaction pathways.
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Affiliation(s)
| | - Izabella Jastrzebska
- Institute of Chemistry , University of Białystok , ul. Ciołkowskiego 1K , 15-245 Białystok , Poland
| | - Joanna E Rode
- Institute of Organic Chemistry , Polish Academy of Sciences , ul. Kasprzaka 44/52 , 01-224 Warsaw , Poland
| | - Jacek W Morzycki
- Institute of Chemistry , University of Białystok , ul. Ciołkowskiego 1K , 15-245 Białystok , Poland
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12
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Rode JE, Górecki M, Witkowski S, Frelek J. Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking. Phys Chem Chem Phys 2018; 20:22525-22536. [PMID: 30140796 DOI: 10.1039/c8cp02491j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.
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Affiliation(s)
- Joanna E Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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13
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Rode JE, Lyczko K, Jawiczuk M, Kawęcki R, Stańczyk W, Jaglińska A, Dobrowolski JC. The Vibrational Circular Dichroism Pattern of the ν(C=O) Bands in Isoindolinones. Chemphyschem 2018; 19:2411-2422. [DOI: 10.1002/cphc.201800244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Joanna E. Rode
- Institute of Nuclear Chemistry and Technology 16 Dorodna Street 03-195 Warsaw Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology 16 Dorodna Street 03-195 Warsaw Poland
| | - Magdalena Jawiczuk
- Institute of Organic ChemistryPolish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
- Current address: Centre of New TechnologiesUniversity of Warsaw Banacha 2C 02-097 Warszawa Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Wojciech Stańczyk
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Agnieszka Jaglińska
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Jan Cz. Dobrowolski
- Institute of Nuclear Chemistry and Technology 16 Dorodna Street 03-195 Warsaw Poland
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14
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Rode JE, Frelek J. Circular dichroism spectroscopy and DFT calculations in determining absolute configuration and E/Z
isomers of conjugated oximes. Chirality 2017; 29:653-662. [DOI: 10.1002/chir.22750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/29/2017] [Accepted: 08/01/2017] [Indexed: 02/03/2023]
Affiliation(s)
- Joanna E. Rode
- Institute of Organic Chemistry; Polish Academy of Sciences; Warsaw Poland
| | - Jadwiga Frelek
- Institute of Organic Chemistry; Polish Academy of Sciences; Warsaw Poland
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15
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Jiménez-Romero C, Rode JE, Pérez YM, Franzblau SG, Rodríguez AD. Exploring the Sponge Consortium Plakortis symbiotica-Xestospongia deweerdtae as a Potential Source of Antimicrobial Compounds and Probing the Pharmacophore for Antituberculosis Activity of Smenothiazole A by Diverted Total Synthesis. J Nat Prod 2017; 80:2295-2303. [PMID: 28742349 DOI: 10.1021/acs.jnatprod.7b00300] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fractionation of the bioactive CHCl3-MeOH (1:1) extracts obtained from two collections of the sponge consortium Plakortis symbiotica-Xestospongia deweerdtae from Puerto Rico provided two new plakinidone analogues, designated as plakinidone B (2) and plakinidone C (3), as well as the known plakinidone (1), plakortolide F (4), and smenothiazole A (5). The structures of 1-5 were characterized on the basis of 1D and 2D NMR spectroscopic, IR, UV, and HRMS analysis. The absolute configurations of plakinidones 2 and 3 were established through chemical correlation methods, VCD/ECD experiments, and spectroscopic data comparisons. When assayed in vitro against Mycobacterium tuberculosis H37Rv, none of the plakinidones 1-3 displayed significant activity, whereas smenothiazole A (5) was the most active compound, exhibiting an MIC value of 4.1 μg/mL. Synthesis and subsequent biological screening of 8, a dechlorinated version of smenothiazole A, revealed that the chlorine atom in 5 is indispensable for anti-TB activity.
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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, United States
| | - Joanna E Rode
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Yeiry M Pérez
- Molecular Sciences Research Center, University of Puerto Rico , 1390 Ponce de León Avenue, San Juan, Puerto Rico 00926, United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Abimael D Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico , 1390 Ponce de León Avenue, San Juan, Puerto Rico 00926, United States
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16
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Rode JE, Dobrowolski JC, Lyczko K, Wasiewicz A, Kaczorek D, Kawęcki R, Zając G, Baranska M. Chiral Thiophene Sulfonamide—A Challenge for VOA Calculations. J Phys Chem A 2017; 121:6713-6726. [DOI: 10.1021/acs.jpca.6b11015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Joanna E. Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Aleksandra Wasiewicz
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Dorota Kaczorek
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Grzegorz Zając
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
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17
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Kovács A, Rode JE. Modelling the matrix shift on the vibrational frequency of ThO by DFT-D3 calculations. J Chem Phys 2017; 146:124301. [PMID: 28388137 DOI: 10.1063/1.4978064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Benchmark calculations with a goal to find dispersion-corrected DFT-D3 methods suitable for a reliable estimation of matrix shifts on the vibrational frequency were carried out on the ThO molecule in three rare gas (Rg = Ne, Ar, and Kr) matrices. The matrices were modelled by the explicit approach, in which a single and a double shell of Rg atoms around ThO was considered. The selection of exchange-correlation functionals was based on test calculations on triatomic ThO⋯Rg models. The B3LYP, PBE0, CAM-B3LYP, and LC-ωPBE functionals were found to be the best suited for the estimation of matrix shifts. The single shell of Rg's around ThO accounted for a major part of the shifts; the addition of a second Rg shell resulted only in a minor improvement. Continuum solvation models considerably overestimated the effect of Rg matrices both when the whole matrix was treated by the model and when the first shell was treated explicitly and the rest with a continuum solvation model.
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Affiliation(s)
- Attila Kovács
- European Commission, Joint Research Centre, P.O. Box 2340, 76125 Karlsruhe, Germany
| | - Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna-Street, 03-195 Warsaw, Poland
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Jastrzębska I, Morawiak M, Rode JE, Seroka B, Siergiejczyk L, Morzycki JW. Oxidation of Olefins with Benzeneseleninic Anhydride in the Presence of TMSOTf. J Org Chem 2015; 80:6052-61. [PMID: 26011517 DOI: 10.1021/acs.joc.5b00410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new oxidizing system for olefins, consisting of benzeneseleninic anhydride and trimethylsilyl triflate, was studied. The highly reactive benzeneseleninyl cation is presumably formed under these conditions. It has been shown that different products are formed with this species depending on the specific structure of olefin. The 1,1-disubstituted olefins afforded mostly α,β-unsaturated carbonyl compounds. The sterically encumbered tri- or tetrasubstituted olefins yielded 1,2- or 1,4-dihydroxylated products, presumably via four-membered cyclic intermediates.
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Affiliation(s)
- Izabella Jastrzębska
- †Institute of Chemistry, University of Białystok, ul. Ciołkowskiego 1K, 15-245 Białystok, Poland
| | - Maja Morawiak
- ‡Institute of Organic Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44, 01-224 Warsaw, Poland
| | - Joanna E Rode
- ‡Institute of Organic Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44, 01-224 Warsaw, Poland.,§Institute of Nuclear Chemistry and Technology, ul. Dorodna 16, 03-195 Warsaw, Poland
| | - Barbara Seroka
- †Institute of Chemistry, University of Białystok, ul. Ciołkowskiego 1K, 15-245 Białystok, Poland
| | - Leszek Siergiejczyk
- †Institute of Chemistry, University of Białystok, ul. Ciołkowskiego 1K, 15-245 Białystok, Poland
| | - Jacek W Morzycki
- †Institute of Chemistry, University of Białystok, ul. Ciołkowskiego 1K, 15-245 Białystok, Poland
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20
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Jawiczuk M, Rode JE, Suszczyńska A, Szugajew A, Frelek J. The utility of dimolybdenum tetrakis(μ-isovalerate) and tetrakis(μ-pivalate) in the stereochemical studies of various transparent compounds. RSC Adv 2014. [DOI: 10.1039/c4ra07408d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Affiliation(s)
- Joanna E. Rode
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
| | - Joanna Sadlej
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
- Faculty
of Chemistry, Warsaw University, 1 Pasteura Street, 02-093 Warsaw, Poland
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22
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Rode JE, Jamróz MH, Dobrowolski JC, Sadlej J. On Vibrational Circular Dichroism Chirality Transfer in Electron Donor–Acceptor Complexes: A Prediction for the Quinine···BF3 System. J Phys Chem A 2012; 116:7916-26. [DOI: 10.1021/jp304955v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Joanna E. Rode
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw,
Poland
| | - Michał H. Jamróz
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw,
Poland
| | - Jan Cz. Dobrowolski
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw,
Poland
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw,
Poland
| | - Joanna Sadlej
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw,
Poland
- Faculty of Chemistry, Warsaw University, 1 Pasteura Street, 02-093 Warsaw,
Poland
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23
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Affiliation(s)
- Michał H. Jamróz
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Joanna E. Rode
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Sławomir Ostrowski
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Piotr F. J. Lipiński
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
- National Medicines Institute,
30/34 Chełmska Street, 00-725 Warsaw, Poland
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24
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Ostrowski S, Jamróz MH, Rode JE, Dobrowolski JC. On stability, chirality measures, and theoretical VCD spectra of the chiral C58X2 fullerenes (X = N, B). J Phys Chem A 2012; 116:631-43. [PMID: 22077444 DOI: 10.1021/jp208687c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stability of all 23 C(58)N(2) and C(58)B(2) heterofullerenes in the singlet and triplet states was determined at the B3LYP/6-31G** level. In equilibrium mixture the achiral (1,4) C(58)N(2) isomer would be populated in ca. 95.8%, the chiral (1,16) one in ca. 3.3%, and the achiral (1,4) C(58)B(2) in 100%, whereas all triplet state isomers are less stable. Fourteen out of 23 C(58)X(2) are chiral. Four different chirality measures were calculated by our own CHIMEA program: pure geometrical, labeled, mass, and charge. Intercorrelations between the measures for all chiral compounds indicate that the pure geometrical chirality measure is unstable and should not be used in QSAR predictions of the other molecular properties, while the labeled and mass-weighted ones are promising QSAR descriptors. For each chiral C(58)N(2) molecule, some very strong VCD bands, of intensity comparable with that in the IR spectra, can serve in identification and characterization of the isomers.
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Affiliation(s)
- Sławomir Ostrowski
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
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25
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Rode JE, Dobrowolski JCZ. On chirality transfer in electron donor-acceptor complexes. A prediction for the sulfinimine···BF3 system. Chirality 2011; 24:5-16. [DOI: 10.1002/chir.21977] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 10/19/2011] [Indexed: 12/14/2022]
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27
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Rode JE, Dobrowolski JC, Sadlej J. Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers. J Mol Model 2010; 17:961-70. [PMID: 20623308 PMCID: PMC3094660 DOI: 10.1007/s00894-010-0783-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 06/11/2010] [Indexed: 11/04/2022]
Abstract
The conformational landscape of phenylisoserine (PhIS) was studied. Trial structures were generated by allowing for all combinations of single-bond rotamers. Based on the B3LYP/aug-cc-pVDZ calculations 54 conformers were found to be stable in the gas phase. The six most stable conformers were further optimized at the B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVDZ levels for which characteristic intramolecular hydrogen bond types were classified. To estimate the influence of water on PhIS conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 51 neutral and six zwitterionic conformers to be stable in water solution. According to DFT calculations, the conformer equilibrium in the gas phase is dominated by one conformer, whereas the MP2 calculations suggest three PhIS structures to be significantly populated. Comparison of DFT and MP2 energies of all 57 structures stable in water indicates that, in practice, one zwitterionic and one neutral conformer determine the equilibrium in water. Based on the AIM calculations, we found that for the neutral conformers in vacuum and in water, d(H...B) is linearly correlated with Laplacian at the H-bond critical point. Phenylisoserine (PhIS) is an active side chain of cytotoxic Paclitaxel medicine. The conformational landscape of phenylisoserine was studied. One zwitterionic and one neutralconformer determine the equilibrium in water whereas in the gas phase the MP2 calculations suggest three PhIS structures to be significantly populated. ![]()
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Affiliation(s)
- Joanna E Rode
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
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28
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Sadlej J, Dobrowolski JC, Rode JE. VCD spectroscopy as a novel probe for chirality transfer in molecular interactions. Chem Soc Rev 2010; 39:1478-88. [DOI: 10.1039/b915178h] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Dobrowolski JC, Jamróz MH, Kołos R, Rode JE, Cyrański MK, Sadlej J. IR low-temperature matrix, X-ray and ab initio study on l-isoserine conformations. Phys Chem Chem Phys 2010; 12:10818-30. [DOI: 10.1039/c0cp00016g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dobrowolski JC, Jamróz MH, Kołos R, Rode JE, Sadlej J. IR Low-Temperature Matrix and ab Initio Study on β-Alanine Conformers. Chemphyschem 2008; 9:2042-51. [DOI: 10.1002/cphc.200800383] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Rode JE, Dobrowolski JC. Variation of BCP ellipticities in the course of the pericyclic and pseudopericyclic [2+2] cycloaddition reactions of cumulenes. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.10.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Sadlej J, Dobrowolski JC, Rode JE, Jamróz MH. Density Functional Theory Study on Vibrational Circular Dichroism as a Tool for Analysis of Intermolecular Systems: (1:1) Cysteine−Water Complex Conformations. J Phys Chem A 2007; 111:10703-11. [PMID: 17914767 DOI: 10.1021/jp074067l] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper presents a discussion of the interaction energies for selected conformers of chiral l-cysteine and their (1:1) complexes with water at the B3LYP/aug-cc-pVDZ level. From among more than forty calculated 1:1 complexes three groups of complexes were singled out and examined by the B3LYP/aug-cc-pVDZ calculated vibrational circular dichroism (VCD) spectra. On the basis of analysis of the nu(OmicronEta) and nu(NuEta) and beta(OH2) and beta(NH2) ranges, the VCD spectra were found to be sensitive to conformational changes and water arrangement in cysteine complexes, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen-bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Moreover, for some water arrangements the VCD spectra can be sensitive to water-wagging conformers and, in temperatures low enough, the intensive nu(OmicronEtaWfree) and beta(H2O) VCD bands may be sufficiently separated to be splitted into pair of oppositely directed bands.
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Affiliation(s)
- Joanna Sadlej
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
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Dobrowolski JC, Rode JE, Kołos R, Jamróz MH, Bajdor K, Mazurek AP. Ar-matrix IR spectra of 5-halouracils interpreted by means of DFT calculations. J Phys Chem A 2007; 109:2167-82. [PMID: 16838988 DOI: 10.1021/jp045213f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The infrared low-temperature Ar-matrix spectra of 5-halouracils and unsubstituted uracil were measured and interpreted in terms of the spectra calculated at the DFT/B3PW91/6-311G level followed by a potential energy distribution (PED) analysis. For the PED analysis, the sets of halouracil mode definitions were constructed so that dissimilarities in the interpretations of the different spectra were minimized. Anharmonic frequency calculations enabled more light to be shed on the Fermi resonance (FR) phenomena occurring in the nu(C=O) stretching vibrations region. For each halouracil vibrational spectrum, several FRs manifest themselves in the nu(C=O) stretching vibrations region. We show that the most frequent components participating in these resonances are the nu(C(4)=O(10)) frequency, a beta(N-H) mode frequency, and a beta(C=O) mode frequency. The experimental nu(N-H) frequencies are reproduced by the calculated anharmonic frequencies better than by the scaled harmonic ones, and the nu(C=O) frequencies respond in the opposite manner. The experimental frequencies located below 1500 cm(-1) are reproduced equally well by the two kinds of calculations.
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Affiliation(s)
- Jan Cz Dobrowolski
- Industrial Chemistry Research Institute, Rydygiera 8, 01-793 Warsaw, Poland.
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Dobrowolski JC, Jamróz MH, Kołos R, Rode JE, Sadlej J. Theoretical Prediction and the First IR Matrix Observation of SeveralL-Cysteine Molecule Conformers. Chemphyschem 2007; 8:1085-94. [PMID: 17429824 DOI: 10.1002/cphc.200600784] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
For the first time the argon-matrix low-temperature IR spectra of cysteine are recorded. They reveal a quite complicated spectral pattern, which can also be reproduced in the N2 matrix. Assignment of the observed spectra is undertaken on the basis of comparison of the experimental and calculated B3LYP/aug-cc-pVDZ anharmonic IR spectra. The presence of at least three, and possibly even six or more, cysteine conformers with and without intramolecular hydrogen bonding is confirmed. On the basis of the calculated vibrational circular dichroism spectra, we predict this technique to be more distinctive for conformers than IR absorption is.
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Affiliation(s)
- Jan Cz Dobrowolski
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland.
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Abstract
The reaction paths of [2 + 2] cycloadditions of allene (H2C=C=CH2) to isocyanic acid (HN=C=O) and ketene (H2C=C=O) to vinylimine (H2C=C=NH), leading to all the possible 14 four-membered ring molecules, were investigated by the MP2/aug-cc-pVDZ method. In the two considered reactions, the 2-azetidinone (beta-lactam) ring compounds were predicted to be the most stable thermodynamically in the absence of an environment. Although 4-methylene-2-azetidinone is the most stable product of the ketene-vinylimine cycloaddition, its activation barrier is higher than that for 4-methylene-2-iminooxetane by ca. 6 kcal/mol. Therefore, the latter product can be obtained owing to kinetic control. The activation barriers in the allene-isocyanic acid reactions are quite high, 50-70 kcal/mol, whereas in the course of the ketene-vinylimine cycloaddition they are equal to ca. 30-55 kcal/mol. All the reactions studied were found to be concerted and mostly asynchronous. Simulation of the solvent environment (toluene, tetrahydrofuran, acetonitrile, and water) by using Tomasi's polarized continuum model with the integral equation formalism (IEF-PCM) method showed the allene-isocyanic reactions remained concerted, yet the activation barriers were somewhat higher than those in the gas phase, whereas the ketene-vinylimine reactions became stepwise. The larger the solvent dielectric constant, the lower the activation barriers found. The lowest-energy pathways in the gas phase and in solvent were confirmed by intrinsic reaction coordinate (IRC) calculations. The atoms in molecules (AIM) analysis of the electron density distribution in the transition-state (TS) structures allowed us to distinguish pericyclic from pseudopericyclic from nonplanar-pseudopericyclic types of reactions.
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Affiliation(s)
- Joanna E Rode
- Industrial Chemistry Research Institute, 01-793 Warsaw, 8 Rydygiera Street, Poland
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Abstract
This paper presents a discussion of the interaction energies, conformations, vibrational absorption (VA, harmonic and anharmonic) and vibrational circular dichroism (VCD) spectra for conformers of monomeric chiral d(-)-lactic acid and their complexes with water at the DFT(B3LYP)/aug-cc-pVDZ and DFT(B3LYP)/aug-cc-pVTZ levels. A detailed analysis has been performed principally for the two most stable complexes with water, differing by lactic acid conformation. The VCD spectra were found to be sensitive to conformational changes of both free and complexed molecules, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Using the theoretical prediction, we demonstrate that the VCD technique can be used as a powerful tool for structural investigation of intermolecular interactions of chiral molecules and can yield information complementary to data obtained through other molecular spectroscopy methods.
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Affiliation(s)
- Joanna Sadlej
- Department of Chemistry, Warsaw University, 1 Pasteura Street, 02-093 Warsaw, Poland
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Rode JE, Klos J, Rajchel L, Szczesniak MM, Chalasinski G, Buchachenko AA. Interactions in open-shell clusters: ab initio study of pre-reactive complex O(3P) + HCl. J Phys Chem A 2005; 109:11484-94. [PMID: 16354039 DOI: 10.1021/jp053419q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Van der Waals interactions between the ground-state triplet O(3P) atom and the closed-shell HCl molecule are investigated in the pre-reactive region. Three adiabatic (two of A'' symmetry and one of A' symmetry) and four non-relativistic diabatic potential energy surfaces are obtained by combining a restricted open-shell coupled cluster approach with the multireference configuration interaction method. The lower A'' adiabatic potential surface has a single minimum (D(e) = 589 cm(-1)) for a linear O...HCl configuration. The upper A'' potential has a weak (D(e) = 65 cm(-1)) minimum for a linear HCl...O configuration. The A' adiabatic potential has a weak (124 cm(-1)) T-shaped minimum. Adiabatic potentials intersect once in the O...HCl linear configuration and twice in the linear HCl...O geometry. The role of electrostatic interactions in shaping these potentials is discussed. The effects of spin-orbit coupling on this interaction are also investigated assuming a constant value of the SO parameter.
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Affiliation(s)
- Joanna E Rode
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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Abstract
The reaction paths of [2+2] cycloaddition of the X=C=Y cumulenes were modeled at the MP2/aug-cc-pVDZ level. Cycloadditions of allene and CO2, CS2, or OCS lead in part to the same four-membered products as dimerizations of either ketene or thioketene or addition of ketene and thioketene, respectively. All the reactions studied are concerted and mostly asynchronous. The majority of the allene cycloadditions studied are endoergic and proceed with much higher activation barriers than do the alternative (thio)ketene additions. In comparison with the energy of the substrates, the four-membered cycles incorporating S-atoms are stabilized more than the analogous structures with O-atoms built into the rings. There are also some products that are thermodynamically disfavored, yet seem to be obtainable thanks to a relatively low barrier of the reaction. The AIM analysis of the electron density distribution in the transition state structures allowed distinguishing pericyclic from pseudopericyclic and nonplanar-pseudopericyclic types of reaction.
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Affiliation(s)
- Joanna E Rode
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
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Rode JE, Dobrowolski JC, Borowiak MA, Mazurek AP. A theoretical study on the stability and spectra of cycloaddition products: Methylene-β-lactam isomers. Phys Chem Chem Phys 2002. [DOI: 10.1039/b200625c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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