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Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment
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SYSNO ASEP 0541262 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment Author(s) Kaminský, Jakub (UOCHB-X) RID, ORCID
Andrushchenko, Valery (UOCHB-X) RID, ORCID
Bouř, Petr (UOCHB-X) RID, ORCIDSource Title RSC Advances. - : Royal Society of Chemistry
Roč. 11, č. 14 (2021), s. 8411-8419Number of pages 9 s. Language eng - English Country GB - United Kingdom Keywords nucleosides ; magnetic circular dichroism ; density functional theory ; spectra modelling OECD category Physical chemistry R&D Projects GA20-10144S GA ČR - Czech Science Foundation (CSF) LTAUSA18085 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) EF16_019/0000729 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Research Infrastructure e-INFRA CZ - 90140 - CESNET, zájmové sdružení právnických osob Method of publishing Open access Institutional support UOCHB-X - RVO:61388963 UT WOS 000622073000065 EID SCOPUS 85101635046 DOI 10.1039/d1ra00076d Annotation Chiroptical spectroscopic methods are excellent tools to study structure and interactions of biomolecules. However, their sensitivity to different structural aspects varies. To understand the dependence of absorption, electronic and magnetic circular dichroism (ECD, MCD) intensities on the structure, dynamics and environment, we measured and simulated spectra of nucleosides and other nucleic acid model components. The conformation space was explored by molecular dynamics (MD), the electronic spectra were generated using time dependent density functional theory (TDDFT). The sum over state (SOS) method was employed for MCD. The results show that accounting for the dynamics is crucial for reproduction of the experiment. While unpolarized absorption spectroscopy is relatively indifferent, ECD reflects the conformation and geometry dispersion more. MCD spectra provide variable response dependent on the wavelength and structural change. In general, MCD samples the structure more locally than ECD. Simple computational tests suggest that the optical spectroscopies coupled with the computational tools provide useful information about nucleic acid components, including base pairing and stacking. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Year of Publishing 2022 Electronic address https://doi.org/10.1039/D1RA00076D
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