title: Computational Approach for Studying Optical Properties of DNA Systems in Solution.
abstract: 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.
authors: Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark.
authors: Morten Steen
authors: MS
authors: Nørby
authors: Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom.
authors: Casper
authors: C
authors: Steinmann
authors: Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark.
authors: Jógvan Magnus Haugaard
authors: JM
authors: Olsen
authors: Department of Chemistry and Nebraska Center for Materials and Nanoscience, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States.
authors: Hui
authors: H
authors: Li
authors: Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark.
authors: Jacob
authors: J
authors: Kongsted
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet
chemical_list: D012997:Solvents; D004247:DNA