Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory.
The incomplete cancellation of the electron self-interaction can be a serious shortcoming of density-functional theory especially when treating odd-electron systems. In this work, several popular and potentially viable correction schemes are applied in order to characterize the electronic structure of stacked molecular pairs, consisting of a neutral molecule and adjacent radical cation, as a function of separation distance. The unphysical sharing of the positive charge between adjacent molecules separated by 6-7 A is corrected for by applying a new empirical scheme proposed by VandeVondele and Sprik [Phys. Chem. Chem. Phys. 2005, 7, 1363] with a unique choice of parameters. This method is subsequently applied to characterize the electronic structure of two neighboring guanines excised from a canonical Arnott B-DNA structure and will be used in future investigations of certain model DNA fibers.
Mantz
Yves A
YA
Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland. ymantz@phys.chem.ethz.ch
Gervasio
Francesco Luigi
FL
Laino
Teodoro
T
Parrinello
Michele
M
D020029:Base Pairing; D001554:Benzene / Q000737:chemistry*; D002412:Cations / Q000737:chemistry*; D002627:Chemistry, Physical / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D012984:Software
D002412:Cations; D006147:Guanine; D004247:DNA; D001554:Benzene