title: Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters.
abstract: We report mid-infrared spectra and potential energy surfaces of four anionic, 2'-deoxynucleotide-5'-monophosphates (dNMPs) and the ionic DNA pairs [dGMP-dCMP-H](1-), [dAMP-dTMP-H](1-) with a total charge of the complex equal to -1. We recorded IR action spectra by resonant IR multiple-photon dissociation (IRMPD) using the FELIX free electron laser. The potential energy surface study employed an on-the-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1 method, followed by an optimization of the most stable structures using density functional theory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy in combination with high-level computational methods, we aim at a better understanding of the hydrogen bonding competition between the phosphate moieties and the nucleobases. We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds in these isolated nucleotide pairs are predominantly formed between the phosphate groups. This intermolecular interaction appears to exceed the stabilization energy resulting from base pairing and directs the overall cluster structure and alignment.
authors.affiliation: †Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States.
authors.forename: Marshall R
authors.initials: MR
authors.lastname: Ligare
authors.affiliation: ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.
authors.forename: Anouk M
authors.initials: AM
authors.lastname: Rijs
authors.affiliation: ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.
authors.forename: Giel
authors.initials: G
authors.lastname: Berden
authors.affiliation: §Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Kabeláč
authors.affiliation: ∥Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic.
authors.forename: Dana
authors.initials: D
authors.lastname: Nachtigallova
authors.affiliation: ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.|∥Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic.|⊥van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands.
authors.forename: Jos
authors.initials: J
authors.lastname: Oomens
authors.affiliation: †Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States.
authors.forename: Mattanjah S
authors.initials: MS
authors.lastname: de Vries
mesh_terms: D000838:Anions / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009711:Nucleotides / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry*; D013055:Spectrophotometry, Infrared / Q000295:instrumentation / Q000379:methods
chemical_list: D000838:Anions; D009711:Nucleotides; D010710:Phosphates; D004247:DNA