Detection of Mercury - TpT Dinucleotide Binding by Raman Spectra: A Computional Study

0382049 - ÚOCHB 2013 RIV US eng J - Journal Article
Benda, Ladislav - Straka, Michal - Sychrovský, Vladimír - Bouř, Petr - Tanaka, Y.
Detection of Mercury - TpT Dinucleotide Binding by Raman Spectra: A Computional Study.
Journal of Physical Chemistry A. Roč. 116, č. 32 (2012), s. 8313-8320. ISSN 1089-5639. E-ISSN 1520-5215
R&D Projects: GA ČR GAP208/11/0105; GA ČR GAP205/10/0228; GA MŠMT(CZ) LH11033
Grant - others:GA ČR(CZ) GAP206/12/0539
Institutional research plan: CEZ:AV0Z40550506
Keywords : nucleic acids * mercury complexes * density functional theory * Raman spectroscopy * vibrational analysis
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 2.771, year: 2012

The Hg2+ ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT center dot Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT center dot Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg2+ binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.
Permanent Link: http://hdl.handle.net/11104/0007179