A Stable Neutral Hydrocarbon Radical: Synthesis, Crystal Structure, and Physical Properties of 2,5,8-Tri-tert-butyl-phenalenyl

Tautomeric equilibria in relation to pi-electron delocalization.

Using synchrotron radiation as excitation source in the 6–22 eV photon energy region, a photoionization mass spectrometry study of three nucleic acid bases, adenine, thymine and uracil, revealed VUV-induced degradation pathways of these important biological molecules. The fragmentation patterns, ionization energies and ion appearance energies (AE) are reported, many for the first time, and are compared with results of electron impact and other studies. AE values enabled heats of formation of parent and some fragment ions to be revised or determined for the first time. Thermochemical data, coupled with the observed AEs, were also useful in clarifying dissociative photoionization pathways. The main neutral loss species are HCN for adenine, HNCO and CO for thymine and uracil, but many subsequent and other fragmentation pathways, including some not suggested previously, are observed and discussed. The hyperconjugation properties of the methyl group make CO loss easier in thymine than in uracil. The astrophysically important fragment ion HCNH + is shown to be formed by several fragmentation pathways in all three nucleobases. The relative importance of competitive fragmentation processes was determined in some cases. Some astrophysical implications concerning the prospects for observation and survival of these nucleic acid bases in the interstellar medium and in meteorites are briefly discussed.

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Photoion mass spectrometry of adenine, thymine and uracil in the 6–22 eV photon energy range

Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.

Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations.

The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31 + + G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm -1 in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.

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Infrared spectra of protonated uracil, thymine and cytosine.

Electronic structure of uracil and uridine derivatives studied by photoelectron spectroscopy

Electronic structures of melatonin and related compounds studied by photoelectron spectroscopy

The photoelectron spectra of xanthone, thioxanthone, and acridone

Electronic structure of some pyridylacetylenes studied by He I photoelectron spectroscopy: A weak orbital interaction between the nonbonding electron pair on the nitrogen atom and the in-plane π orbital in the ethynyl group

Electronic structure of dicyanobarrelenes studied by integration of photoelectron spectroscopy, cyclic voltammetry, electronic spectroscopy, molecular orbital theory, and composite molecule theory

Tsunetoshi Kobayashi

Papers

Electronic structure of uracil and uridine derivatives studied by photoelectron spectroscopy

Electronic structures of melatonin and related compounds studied by photoelectron spectroscopy

The photoelectron spectra of xanthone, thioxanthone, and acridone

Electronic structure of some pyridylacetylenes studied by He I photoelectron spectroscopy: A weak orbital interaction between the nonbonding electron pair on the nitrogen atom and the in-plane π orbital in the ethynyl group

Electronic structure of dicyanobarrelenes studied by integration of photoelectron spectroscopy, cyclic voltammetry, electronic spectroscopy, molecular orbital theory, and composite molecule theory