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Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum
Author(s) -
Padula Daniele,
Jurinovich Sandro,
Di Bari Lorenzo,
Mennucci Benedetta
Publication year - 2016
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201602777
Subject(s) - polarizability , electronic structure , circular dichroism , ab initio , nucleic acid , chemistry , base (topology) , spectrum (functional analysis) , embedding , molecular physics , molecular dynamics , statistical physics , quantum , chemical physics , computational chemistry , physics , quantum mechanics , crystallography , molecule , computer science , mathematics , mathematical analysis , biochemistry , artificial intelligence
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.