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  1. Article ; Online: Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.

    Katsyuba, Sergey A / Burganov, Timur I

    Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

    2024  Volume 309, Page(s) 123832

    Abstract: As in the case of cytosine [Phys. Chem. Chem. Phys. 2023, 25, 24121-24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine- ... ...

    Abstract As in the case of cytosine [Phys. Chem. Chem. Phys. 2023, 25, 24121-24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d
    Language English
    Publishing date 2024-01-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 210413-1
    ISSN 1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
    ISSN (online) 1873-3557
    ISSN 0370-8322 ; 0584-8539 ; 1386-1425
    DOI 10.1016/j.saa.2023.123832
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Computational analysis of the vibrational spectra and structure of aqueous cytosine.

    Katsyuba, Sergey A / Burganov, Timur I

    Physical chemistry chemical physics : PCCP

    2023  Volume 25, Issue 35, Page(s) 24121–24128

    Abstract: The recently developed efficient protocol for the explicit quantum mechanical modeling of the structure and IR spectra of liquids and solutions [ ... ...

    Abstract The recently developed efficient protocol for the explicit quantum mechanical modeling of the structure and IR spectra of liquids and solutions [Katsyuba
    Language English
    Publishing date 2023-09-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp03059h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: 2,3-(Dibenzimidazol-2-yl)quinoxalines: Unexpected Dynamical Effect on Steady-State Electronic Absorption Spectra.

    Burganov, Timur I / Monari, Antonio / Katsyuba, Sergey A / Mamedov, Vakhid A / Zhukova, Nataliya A / Assfeld, Xavier

    The journal of physical chemistry. B

    2019  Volume 123, Issue 26, Page(s) 5514–5523

    Abstract: We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ ... ...

    Abstract We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ solutions cannot be assigned to electronic excitations of the equilibrium ground-state DBIQ structure. Extended consideration including the nonequilibrium structures within the framework of ab initio molecular dynamics (MD) revealed the importance of torsion molecular motions not covered by the static case. The strong impact of solute-solvent hydrogen bonding on stabilization of these nonequilibrium structures and on conformational composition of DBIQ was demonstrated. A presence of twisted nonplanar geometries along the whole MD trajectory was shown to drastically influence not only energies but also characters of electronic excitations, resulting in a change of local π-π* character in a solution of 1,2-dichloroethane to charge-transfer character in polar dimethylsulfoxide.
    Language English
    Publishing date 2019-06-26
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.9b00974
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  4. Article: 2,3-(Dibenzimidazol-2-yl)quinoxalines: Unexpected Dynamical Effect on Steady-State Electronic Absorption Spectra

    Burganov, Timur I / Monari, Antonio / Katsyuba, Sergey A / Mamedov, Vakhid A / Zhukova, Nataliya A / Assfeld, Xavier

    Journal of physical chemistry. 2019 June 13, v. 123, no. 26

    2019  

    Abstract: We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ ... ...

    Abstract We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ solutions cannot be assigned to electronic excitations of the equilibrium ground-state DBIQ structure. Extended consideration including the nonequilibrium structures within the framework of ab initio molecular dynamics (MD) revealed the importance of torsion molecular motions not covered by the static case. The strong impact of solute–solvent hydrogen bonding on stabilization of these nonequilibrium structures and on conformational composition of DBIQ was demonstrated. A presence of twisted nonplanar geometries along the whole MD trajectory was shown to drastically influence not only energies but also characters of electronic excitations, resulting in a change of local π–π* character in a solution of 1,2-dichloroethane to charge-transfer character in polar dimethylsulfoxide.
    Keywords dimethyl sulfoxide ; ethylene dichloride ; geometry ; hydrogen bonding ; molecular dynamics ; quinoxalines ; solvents ; spectral analysis
    Language English
    Dates of publication 2019-0613
    Size p. 5514-5523.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.9b00974
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Is there a simple way to reliable simulations of infrared spectra of organic compounds?

    Katsyuba, Sergey A / Zvereva, Elena E / Burganov, Timur I

    The journal of physical chemistry. A

    2013  Volume 117, Issue 30, Page(s) 6664–6670

    Abstract: To assess the ability of the quantum-chemical computations to reproduce the experimental relative intensities in the infrared (IR) spectra of both the gas- and condensed-phase systems, the hybrid DFT functional B3LYP has been applied to simulation of IR ... ...

    Abstract To assess the ability of the quantum-chemical computations to reproduce the experimental relative intensities in the infrared (IR) spectra of both the gas- and condensed-phase systems, the hybrid DFT functional B3LYP has been applied to simulation of IR spectra for species containing from three to twelve first- or second-row atoms, both in the gas phase and in CCl4 solutions. The results demonstrate that B3LYP, combined with the highly compact double-ζ basis set 6-31+G* and "scaled quantum mechanics" techniques, offers excellent quantitative performance in the calculations of relative IR intensities and frequencies (ν ≤ 2200 cm(-1)) for the bands of vibrations of medium-size isolated molecules, whereas it produces unsatisfactory results for the solutions of the same species. Neither larger basis sets nor implicit treatment of the media effects improve the agreement of the simulated spectra with the condensed-phase experiment. At the same time, some preliminary results suggest that explicit modeling of media effects could offer better quality of the IR spectral simulations for the condensed-phase systems.
    Language English
    Publishing date 2013-08-01
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/jp404574m
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Benzimidazolylquinoxalines: novel fluorophores with tuneable sensitivity to solvent effects.

    Burganov, Timur I / Zhukova, Nataliya A / Mamedov, Vakhid A / Bannwarth, Christoph / Grimme, Stefan / Katsyuba, Sergey A

    Physical chemistry chemical physics : PCCP

    2017  Volume 19, Issue 8, Page(s) 6095–6104

    Abstract: We report on the photophysical properties, conjugation, conformational behavior, intra- and intermolecular hydrogen bonds (HBs) of a series of novel fluorophores, consisting of 3-arylquinoxaline and benzimidazole moieties linked by a single CC bond. ... ...

    Abstract We report on the photophysical properties, conjugation, conformational behavior, intra- and intermolecular hydrogen bonds (HBs) of a series of novel fluorophores, consisting of 3-arylquinoxaline and benzimidazole moieties linked by a single CC bond. Computations employing density functional theory (DFT) reveal that conjugation between these moieties stabilizes syn-conformers with two HB centers located on the same side of the molecule. Anti-conformers form stronger intermolecular HBs with DMSO and DMF than syn-conformers, and this influences the energy gap between syn- and anti-forms, especially upon excitation of the molecules to the S
    Language English
    Publishing date 2017-02-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c6cp06658e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Supramolecular Organization of Solid Azobenzene Chromophore Disperse Orange 3, Its Chloroform Solutions, and PMMA-Based Films

    Burganov, Timur I / Anastasiya V. Sharipova / Marina Yu. Balakina / Olga D. Fominykh / Sergey A. Katsyuba / Tatiana A. Vakhonina

    Journal of physical chemistry. 2018 Jan. 25, v. 122, no. 3

    2018  

    Abstract: Quantum chemical modeling in combination with vibrational and electronic absorption spectroscopy has delivered detailed information about supramolecular organization of azochromophore 4-amino-4′-nitroazobenzene (DO3), its solutions, and blends with poly( ... ...

    Abstract Quantum chemical modeling in combination with vibrational and electronic absorption spectroscopy has delivered detailed information about supramolecular organization of azochromophore 4-amino-4′-nitroazobenzene (DO3), its solutions, and blends with poly(methyl methacrylate) (PMMA) polymer of various concentrations. It is shown that the neat chromophore contains both antistacked forms and hydrogen bonded associations of the “head-to-tail” type, while separate DO3 molecules dominate in diluted solutions of DO3 in chloroform. In PMMA/DO3 films with low concentrations of the chromophore, DO3 is mainly H-bonded to C═O moieties of PMMA matrix, while in the blends with high concentrations of DO3 molecules, the latter form hydrogen bonds both with PMMA and with each other. Infrared, Raman, and UV–vis spectroscopic markers of isolated DO3 molecules and various modes of their supramolecular associations are revealed.
    Keywords chloroform ; hydrogen bonding ; models ; moieties ; polymethylmethacrylate ; Raman spectroscopy
    Language English
    Dates of publication 2018-0125
    Size p. 1779-1785.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1932-7455
    DOI 10.1021/acs.jpcc.7b10543
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Characterization of Conjugation Effects in the Series of Quinoxaline-2-ones by Means of Vibrational Raman Spectroscopy.

    Burganov, Timur I / Katsyuba, Sergey A / Islamova, Liliya N / Fazleeva, Guzel M / Sharipova, Sirina M / Kalinin, Alexey A / Dobrynin, Alexey B / Monari, Antonio / Assfeld, Xavier

    The journal of physical chemistry. A

    2020  Volume 124, Issue 19, Page(s) 3865–3875

    Abstract: A broad series of quinoxalinone-based π-conjugated donor-acceptor fluoro- and NLO-phores is characterized by means of Raman spectroscopy and single-crystal X-ray analysis supported by quantum chemical computations. Intense Raman spectroscopic markers ... ...

    Abstract A broad series of quinoxalinone-based π-conjugated donor-acceptor fluoro- and NLO-phores is characterized by means of Raman spectroscopy and single-crystal X-ray analysis supported by quantum chemical computations. Intense Raman spectroscopic markers that allow the differentiation of even closely related structures are identified. The intensities of these bands are shown to be related to the conjugation of the different molecular moieties, and they can provide an estimation of its extent. The intensity redistribution between these markers serves as a source of auxiliary structural information capable of pointing to a distortion of the conjugation or to the influence of aggregation effects in the condensed state. A simple relation between the intensity of the marker and the position and oscillator strength of the lowest-energy electronic absorption band of quinoxalinones allows a linking of the Raman effect with the optical properties of these compounds, which can be used for the rational design of novel species with improved optical characteristics.
    Language English
    Publishing date 2020-04-29
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.0c01838
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Conjugation in and optical properties of 1-R-1,2-diphospholes and 1-R-phospholes.

    Katsyuba, Sergey A / Burganov, Timur I / Zvereva, Elena E / Zagidullin, Almaz A / Miluykov, Vasily A / Lönnecke, Peter / Hey-Hawkins, Evamarie / Sinyashin, Oleg G

    The journal of physical chemistry. A

    2014  Volume 118, Issue 51, Page(s) 12168–12177

    Abstract: The strength of conjugation between the diene moieties of 1-R-1,2-diphospholes and 1-R-phospholes and exocyclic phenyl groups of these P-heteroles has been quantitatively characterized by the use of Raman activities of the bands of the phenyl ... ...

    Abstract The strength of conjugation between the diene moieties of 1-R-1,2-diphospholes and 1-R-phospholes and exocyclic phenyl groups of these P-heteroles has been quantitatively characterized by the use of Raman activities of the bands of the phenyl substituents. It is shown that conjugation in both types of phospholes is very similar to the conjugation of phenyl groups with the diene system of cyclopentadiene. Introduction of substituents (-OMe, -C(═O)H, -NO2, -NMe2, and -CH═CH2) in the para-position of the phenyl groups of 1-R-1,2-diphospholes extends π-delocalization of exocyclic groups into the electronic system of the 1,2-diphosphole ring, producing bathochromic shifts of the absorption bands up to 63 nm. In contrast, hypsochromic shifts up to 40 nm can be achieved by introduction of SnMe3 or SiMe3 groups at the phosphorus(III) atom of the 1,2-diphosphole and concomitant increase of aromaticity of the P-heterole. Conjugation shifts the "centre of gravity" of the whole electronic absorption spectrum, whereas positions of separate absorption bands are not simply dependent on conjugation lengths.
    Language English
    Publishing date 2014-12-26
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/jp510712s
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Application of time-dependent density functional theory and optical spectroscopy toward the rational design of novel 3,4,5-triaryl-1-R-1,2-diphospholes.

    Zvereva, Elena E / Grimme, Stefan / Katsyuba, Sergey A / Burganov, Timur I / Zagidullin, Almaz A / Milyukov, Vasily A / Sinyashin, Oleg G

    The journal of physical chemistry. A

    2013  Volume 117, Issue 31, Page(s) 6827–6834

    Abstract: Twenty 3,4,5-triaryl-1-R-1,2-diphospholes were studied within the framework of density functional theory (DFT) and experimentally by UV/vis spectroscopy to check their suitability for opto-electronic applications. Time-dependent DFT (TD-DFT) calculations ...

    Abstract Twenty 3,4,5-triaryl-1-R-1,2-diphospholes were studied within the framework of density functional theory (DFT) and experimentally by UV/vis spectroscopy to check their suitability for opto-electronic applications. Time-dependent DFT (TD-DFT) calculations employing the PBE0 hybrid density functional combined with moderately sized def-TZVP basis set were shown to excellently reproduce the experimental absorption spectra of various 1,2-diphospholes. Frontier molecular orbital analysis reveals that HOMO and LUMO are mainly localized on the diphosphole ring and, to some extent, on the aryl moieties. The HOMO-LUMO energy gap can be easily tuned by variation of substituents introduced in para-positions of the aryl moieties and, to a lesser extent, by modification of the R group at phosphorus atom. As a result, both position and intensity of the absorption bands with highest wavelength are strongly influenced by the above structural changes. The UV-spectra simulations reveal that the introduction of donor groups like para-OMe, para-NMe2, and para-N(H)Ph, which are in n-π conjugation with the aryl moieties, should result in absorption of visible light by the corresponding 1,2-diphospholes, thus making them promising candidates for new functional materials.
    Language English
    Publishing date 2013-08-08
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/jp4043914
    Database MEDical Literature Analysis and Retrieval System OnLINE

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