Computational Approach for Studying Optical Properties of DNA Systems in Solution

Morten Steen Nørby, Casper Steinmann, Jógvan Magnus Haugaard Olsen, Hui Li, Jacob Kongsted

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)5050-5057
Number of pages8
JournalJournal of Chemical Theory and Computation
Issue number10
StatePublished - Oct 11 2016

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry


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