Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine

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dc.contributor.authorChatterjee, Kuntal
dc.contributor.authorDopfer, Otto
dc.date.accessioned2020-08-17T08:38:57Z
dc.date.available2020-08-17T08:38:57Z
dc.date.issued2020-07-07
dc.description.abstractPyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1–2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.en
dc.description.sponsorshipTU Berlin, Open-Access-Mittel - 2020en
dc.identifier.eissn1463-9084
dc.identifier.issn1463-9076
dc.identifier.urihttps://depositonce.tu-berlin.de/handle/11303/11570
dc.identifier.urihttp://dx.doi.org/10.14279/depositonce-10457
dc.language.isoenen
dc.rights.urihttps://creativecommons.org/licenses/by-nc/3.0/en
dc.subject.ddc540 Chemie und zugeordnete Wissenschaftende
dc.subject.otherabiotic synthetic routeen
dc.subject.otherprimary fragment ionsen
dc.subject.otherspectroscopyen
dc.titleSpectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidineen
dc.typeArticleen
dc.type.versionpublishedVersionen
dcterms.bibliographicCitation.doi10.1039/D0CP02919Jen
dcterms.bibliographicCitation.issue30en
dcterms.bibliographicCitation.journaltitlePhysical Chemistry Chemical Physicsen
dcterms.bibliographicCitation.originalpublishernameRoyal Society of Chemistry (RSC)en
dcterms.bibliographicCitation.originalpublisherplaceCambridgeen
dcterms.bibliographicCitation.pageend17290en
dcterms.bibliographicCitation.pagestart17275en
dcterms.bibliographicCitation.volume22en
tub.accessrights.dnbfreeen
tub.affiliationFak. 2 Mathematik und Naturwissenschaften::Inst. Optik und Atomare Physik::FG Lasermolekülspektroskopie und Umweltphysikde
tub.affiliation.facultyFak. 2 Mathematik und Naturwissenschaftende
tub.affiliation.groupFG Lasermolekülspektroskopie und Umweltphysikde
tub.affiliation.instituteInst. Optik und Atomare Physikde
tub.publisher.universityorinstitutionTechnische Universität Berlinen
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