4.6 Article

Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum

Journal

CHEMISTRY-A EUROPEAN JOURNAL
Volume 22, Issue 47, Pages 17009-17017

Publisher

WILEY-V C H VERLAG GMBH
DOI: 10.1002/chem.201602777

Keywords

circular dichroism; computational chemistry; electronic structure; molecular dynamics; nucleic acids

Funding

  1. European Research Council (ERC) [277755]
  2. European Research Council (ERC) [277755] Funding Source: European Research Council (ERC)

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We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.

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