Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone

Frey, Jann; Ottiger, Philipp; Leutwyler, Samuel (2014). Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone. Journal of physical chemistry - B, 118(3), pp. 682-691. American Chemical Society 10.1021/jp409660b

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While keto-amino cytosine is the dominant species in aqueous solution, spectroscopic studies in molecular beams and in noble gas matrices show that other cytosine tautomers prevail in apolar environments. Each of these offers two or three H-bonding sites (Watson–Crick, wobble, sugar-edge). The mass- and isomer-specific S1 ← S0 vibronic spectra of cytosine·2-pyridone (Cyt·2PY) and 1-methylcytosine·2PY are measured using UV laser resonant two-photon ionization (R2PI), UV/UV depletion, and IR depletion spectroscopy. The UV spectra of the Watson–Crick and sugar-edge isomers of Cyt·2PY are separated using UV/UV spectral hole-burning. Five different isomers of Cyt·2PY are observed in a supersonic beam. We show that the Watson–Crick and sugar-edge dimers of keto-amino cytosine with 2PY are the most abundant in the beam, although keto-amino-cytosine is only the third most abundant tautomer in the gas phase. We identify the different isomers by combining three different diagnostic tools: (1) methylation of the cytosine N1–H group prevents formation of both the sugar-edge and wobble isomers and gives the Watson–Crick isomer exclusively. (2) The calculated ground state binding and dissociation energies, relative gas-phase abundances, excitation and the ionization energies are in agreement with the assignment of the dominant Cyt·2PY isomers to the Watson–Crick and sugar-edge complexes of keto-amino cytosine. (3) The comparison of calculated ground state vibrational frequencies to the experimental IR spectra in the carbonyl stretch and NH/OH/CH stretch ranges strengthen this identification.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Departement of Chemistry and Biochemistry
13 Central Units > Services of the Rector's Office > Forum für Universität und Gesellschaft
08 Faculty of Science > Other Institutions > Teaching Staff, Faculty of Science

UniBE Contributor:

Frey, Jann; Ottiger, Philipp and Leutwyler, Samuel


500 Science
500 Science > 540 Chemistry




American Chemical Society


[4] Swiss National Science Foundation




Beatrice Niederhauser

Date Deposited:

05 Apr 2014 00:22

Last Modified:

19 Mar 2015 11:30

Publisher DOI:






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