title: The Ethidium-UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State.
abstract: We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned into electrostatic, exchange, delocalization, and correlation components. Various pairwise interaction models built from chemically intuitive fragments reproduce within a few percent values obtained when treating the intercalation site as a whole. Gas phase results are very sensitive to the charge state of the two phosphate groups, with the electrostatic term nearly tripling when the counterions are removed. But this is largely compensated by solvation, an effect represented here within the polarizable continuum model. In a few cases, more diffuse and larger basis sets as well as QCISD(T) corrections were applied in an effort to estimate plausible ethidium-nucleobase electron correlation effects.
authors.affiliation: Institute of Physical and Theoretical Chemistry, Wrocław University of Technology , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland.|Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands.
authors.forename: Karol M
authors.initials: KM
authors.lastname: Langner
authors.affiliation: Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas , Fayetteville, Arkansas 72701, United States.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Janowski
authors.affiliation: Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Góra
authors.affiliation: Wrocław Center for Networking and Supercomputing , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland.
authors.forename: Paweł
authors.initials: P
authors.lastname: Dziekoński
authors.affiliation: Institute of Physical and Theoretical Chemistry, Wrocław University of Technology , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland.
authors.forename: W Andrzej
authors.initials: WA
authors.lastname: Sokalski
authors.affiliation: Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas , Fayetteville, Arkansas 72701, United States.
authors.forename: Peter
authors.initials: P
authors.lastname: Pulay