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Pankin D, Povolotckaia A, Borisov E, Belyakov M, Borzenko S, Gulyaev A, Moskovskiy M. Theoretical modelling of structure, vibrational and UV-vis absorbance spectra of rubrofusarin molecule. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 293:122469. [PMID: 36801731 DOI: 10.1016/j.saa.2023.122469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
The structure of the rubrofusarin molecule (CAS: 3567-00-8, IUPAC name 5,6-dihydroxy-8-methoxy-2-methyl-4H-benzo[g]chromen-4-one, molecular formula C15H12O5) and its possible rotational conformers and tautomer were investigated within DFT approach. It was noted that for a stable molecules the group symmetry is close to Cs. The smallest potential barrier for rotational conformers is associated with the methoxy group rotation. The rotation of hydroxyl groups leads to a stable states that are substantially higher in energy than the ground state. Modeling and interpretation of vibrational spectra for the case of the ground state molecule in the gas phase and methanol solution was carried out, the influence of the solvent is discussed. The modelling of electronic singlet transition within the TD-DFT approach and the interpretation of obtained UV-vis absorbance spectra were carried out. A relatively small shift in the two most active absorption bands wavelength takes place for methoxy group rotation conformer. At the same time the redshift of the HOMO-LUMO transition takes place for this conformer. Much larger long wavelength shift of the absorption bands was noted for the tautomer.
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Affiliation(s)
- D Pankin
- Center for Optical and Laser Materials Research, St. Petersburg State University, Ulianovskaya 5, 198504 St. Petersburg, Russia
| | - A Povolotckaia
- Center for Optical and Laser Materials Research, St. Petersburg State University, Ulianovskaya 5, 198504 St. Petersburg, Russia
| | - E Borisov
- Center for Optical and Laser Materials Research, St. Petersburg State University, Ulianovskaya 5, 198504 St. Petersburg, Russia
| | - M Belyakov
- Federal Scientific Agro-Engineering Center VIM, 1st Institutskiy proezd 5, 109428 Moscow, Russia
| | - S Borzenko
- Federal Scientific Agro-Engineering Center VIM, 1st Institutskiy proezd 5, 109428 Moscow, Russia
| | - A Gulyaev
- Federal Scientific Agro-Engineering Center VIM, 1st Institutskiy proezd 5, 109428 Moscow, Russia
| | - M Moskovskiy
- Federal Scientific Agro-Engineering Center VIM, 1st Institutskiy proezd 5, 109428 Moscow, Russia
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Pocheć M, Kułacz K, Panek JJ, Jezierska A. How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features-Multifactor Studies. Int J Mol Sci 2021; 22:ijms221910357. [PMID: 34638700 PMCID: PMC8508802 DOI: 10.3390/ijms221910357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Substitution is well-known to modulate the physico-chemical properties of molecules. In this study, a combined, multifactor approach was employed to determine a plethora of substitution patterns using –Br and –O-H in 1,4-naphthoquinone and its derivatives. On the basis of classical Density Functional Theory (DFT), 25 models divided into three groups were developed. The first group contains 1,4-naphthoquinone and its derivatives substituted only by –Br. The second group consists of compounds substituted by –Br and one –O-H group. As a result of the substitution, an intramolecular hydrogen bond was formed. The third group also contains –Br as a substituent, but two –O-H groups were introduced and two intramolecular hydrogen bonds were established. The simulations were performed at the ωB97XD/6-311++G(2d,2p) level of theory. The presence of substituents influenced the electronic structure of the parent compound and its derivatives by inductive effects, but it also affected the geometry of the 2 and 3 groups, due to the intramolecular hydrogen bonding and the formation of a quasi-ring/rings. The static DFT models were applied to investigate the aromaticity changes in the fused rings based on the Harmonic Oscillator Model of Aromaticity (HOMA). The OH stretching was detected for the compounds from groups 2 and 3 and further used to find correlations with energetic parameters. The evolution of the electronic structure was analyzed using Hirshfeld atomic charges and the Substituent Active Region (cSAR) parameter. The proton reaction path was investigated to provide information on the modulation of hydrogen bridge properties by diverse substitution positions on the donor and acceptor sides. Subsequently, Car–Parrinello Molecular Dynamics (CPMD) was carried out in the double-bridged systems (group 3) to assess the cooperative effects in double –O-H-substituted systems. It was determined that the –O-H influence on the core of the molecule is more significant than that of –Br, but the latter has a major impact on the bridge dynamics. The competitive or synergic effect of two –Br substituents was found to depend on the coupling between the intramolecular hydrogen bridges. Thus, the novel mechanism of a secondary (cooperative) substituent effect was established in the double-bridged systems via DFT and CPMD results comparison, consisting of a mediation of the bromine substitutions’ influence by the cooperative proton transfer events in the hydrogen bridges.
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Affiliation(s)
| | | | | | - Aneta Jezierska
- Correspondence: ; Tel.: +48-71-3757-224; Fax: +48-71-3282-348
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Jezierska A, Błaziak K, Klahm S, Lüchow A, Panek JJ. Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches. Int J Mol Sci 2021; 22:ijms22158033. [PMID: 34360798 PMCID: PMC8348774 DOI: 10.3390/ijms22158033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/27/2022] Open
Abstract
Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.
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Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
- Correspondence: (A.J.); (K.B.)
| | - Kacper Błaziak
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 01-224 Warsaw, Poland
- Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 01-224 Warsaw, Poland
- Correspondence: (A.J.); (K.B.)
| | - Sebastian Klahm
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (S.K.); (A.L.)
| | - Arne Lüchow
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (S.K.); (A.L.)
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
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Xuan X, Wang X, Wang N. Theoretical study of molecular structure and vibrational spectra of 1,4-dihydroxyanthraquinone. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 79:1091-1098. [PMID: 21561800 DOI: 10.1016/j.saa.2011.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/14/2011] [Accepted: 04/13/2011] [Indexed: 05/30/2023]
Abstract
Molecular structure and vibrational spectra of 1,4-dihydroxyanthraquinone (1,4-DAQ) are studied theoretically and experimentally. FT-infrared and Raman spectra of 1,4-DAQ are recorded in solid phase in regions of 4000-400 and 3500-100 cm(-1), respectively. The geometry of 1,4-DAQ is optimized by B3LYP and B3PW91 methods, and the most stable structure with C2v point group is found. The harmonic vibration frequencies, infrared intensities, and the Raman scattering activities of the compound are calculated, analyzed, and compared with experimental data. Our calculated frequencies agree well with the experimental results.
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Affiliation(s)
- Xiaopeng Xuan
- Key Laboratory of Green Chemistry of China, School of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007, China.
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Jacquemin D, Peltier C, Ciofini I. Visible spectrum of naphthazarin investigated through Time-Dependent Density Functional Theory. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.04.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tomura M, Yamaguchi H, Ono K, Saito K. 6,11-Dihydroxy-naphthacene-5,12-dione. Acta Crystallogr Sect E Struct Rep Online 2007; 64:o172-3. [PMID: 21200737 PMCID: PMC2924183 DOI: 10.1107/s1600536807063726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 11/27/2007] [Indexed: 11/11/2022]
Abstract
The mol-ecule of the title compound, C(18)H(10)O(4), is centrosymmetric and planar. A long phenolic O-H bond is observed [1.19 (9) Å], which is involved in an intra-molecular hydrogen bond between the phenolic and quinonoid O atoms. The mol-ecules pack in a herringbone pattern and are linked to each other via inter-molecular C-H⋯O hydrogen bonds (2.73-2.77 Å).
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Affiliation(s)
- Masaaki Tomura
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Hiroyuki Yamaguchi
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan
| | - Katsuhiko Ono
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan
| | - Katsuhiro Saito
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan
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Savko M, Kaščáková S, Gbur P, Miškovský P, Uličný J. Performance of Time Dependent Density Functional Theory on excitations of medium sized molecules – Test on ionic forms of anthraquinone dihydroxy derivatives. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.08.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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