Computational Approach for Studying Optical Properties of DNA Systems in Solution
journal contributionposted on 01.09.2016 by Morten Steen Nørby, Casper Steinmann, Jógvan Magnus Haugaard Olsen, Hui Li, Jacob Kongsted
Any type of content formally published in an academic journal, usually following a peer-review process.
In this paper we present a study of the methodological aspects regarding calculations of optical properties for DNA systems in solution. Our computational approach will be built upon a fully polarizable QM/MM/Continuum model within a damped linear response theory framework. In this approach the environment is given a highly advanced description in terms of the electrostatic potential through the polarizable embedding model. Furthermore, bulk solvent effects are included in an efficient manner through a conductor-like screening model. With the aim of reducing the computational cost we develop a set of averaged partial charges and distributed isotropic dipole–dipole polarizabilities for DNA suitable for describing the classical region in ground-state and excited-state calculations. Calculations of the UV-spectrum of the 2-aminopurine optical probe embedded in a DNA double helical structure are presented. We show that inclusion of polarizabilities in the embedding potential stemming from the DNA double helix is of crucial importance, while the water cluster surrounding the DNA system is well represented using a continuum approach.