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Structure of 2,4-Diaminopyrimidine–Theobromine Alternate Base Pairs

Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
Faculty of Natural Sciences, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
Department of Chemistry and Biochemistry, University of California Santa Barbara, California 93106-9510, United States
J. Phys. Chem. A, 2011, 115 (41), pp 11423–11427
DOI: 10.1021/jp205831n
Publication Date (Web): September 2, 2011
Copyright © 2011 American Chemical Society
This article is part of the Pavel Hobza Festschrift special issue.
Physical Organic Chemistry

Abstract

Abstract Image

We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine–cytosine. We have found the four lowest energy structures, which include the Watson–Crick base pairing motif. This Watson–Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

(Table S1) Structures found at the (B3LYP/6-311+G(d,p) level of theory. (Table S2) Frequencies (scaled by a factor of 0.957) and intensities for the two zitterionic isomers, shown in supplemental Table S1. This material is available free of charge via the Internet at http://pubs.acs.org.

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History

  • Published In Issue October 20, 2011
  • Article ASAPSeptember 02, 2011
  • Received: June 21, 2011
    Revised: August 17, 2011

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