Detection of mercury-TpT dinucleotide binding by raman spectra: A computational study

Ladislav Benda, Michal Straka, Vladimír Sychrovský, Petr Bouř, Yoshiyuki Tanaka

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

Abstract

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·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·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.

Original languageEnglish
Pages (from-to)8313-8320
Number of pages8
JournalJournal of Physical Chemistry A
Volume116
Issue number32
DOIs
Publication statusPublished - 2012 Aug 16

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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