title: Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum.
abstract: 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.
authors.affiliation: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Padula
authors.affiliation: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
authors.forename: Sandro
authors.initials: S
authors.lastname: Jurinovich
authors.affiliation: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Di Bari
authors.affiliation: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
authors.forename: Benedetta
authors.identifier: http://orcid.org/0000-0002-4394-0129
authors.initials: B
authors.lastname: Mennucci
mesh_terms: D002942:Circular Dichroism; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D009696:Nucleic Acids
keywords: circular dichroism; computational chemistry; electronic structure; molecular dynamics; nucleic acids