title: Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.
abstract: Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds of nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of noncanonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on 14 stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for the results of high-level quantum chemistry (QC) on the total interaction energies, and the individual energy contributions and their nonisotropic behaviors. Good agreements are found at both uncorrelated HF and correlated DFT and CCSD(T) levels. Resorting in SIBFA to distributed QC multipoles and to an explicit representation of the lone pairs is essential to respectively account for the anisotropies of the Coulomb and of the exchange-repulsion QC contributions.
authors.affiliation: ‡Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier 137, 4, place Jussieu, Paris, F75252, France.|§Laboratoire de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France.
authors.forename: Nohad
authors.initials: N
authors.lastname: Gresh
authors.affiliation: ∥Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska, 135, 612 65 Brno, Czech Republic.|⊥CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Judit E
authors.initials: JE
authors.lastname: Sponer
authors.affiliation: #Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH 4056, Switzerland.
authors.forename: Mike
authors.initials: M
authors.lastname: Devereux
authors.affiliation: ∥Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska, 135, 612 65 Brno, Czech Republic.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Gkionis
authors.affiliation: ‡Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier 137, 4, place Jussieu, Paris, F75252, France.|§Laboratoire de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France.
authors.forename: Benoit
authors.initials: B
authors.lastname: de Courcy
authors.affiliation: ‡Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier 137, 4, place Jussieu, Paris, F75252, France.|§Laboratoire de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France.
authors.forename: Jean-Philip
authors.initials: JP
authors.lastname: Piquemal
authors.affiliation: ∥Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska, 135, 612 65 Brno, Czech Republic.|⊥CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Jiri
authors.initials: J
authors.lastname: Sponer
mesh_terms: D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D019281:Dimerization; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D011789:Quantum Theory; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D003596:Cytosine; D004247:DNA; D008274:Magnesium