Electronic structure, spectra, and mechanism of photodimerization of pyrimidine bases

Abstract

AbstractsVarious e!ectronic indices calculated by the CNDO/S-CI method for uracil, 5-fluorouracil, thymine, and cytosine and the Woodward-Hoffmann rule applied to the photodimerization of these molecules lead us to the following conclusions: (i) decrease of the C5-C6 bond order consequent to excitation is generally correlated with the photodimerization reaction for all the biological pyrimidines; (ii) excited pyrimidine molecules may be nonplanar and the excitation would be delocalized over both the molecules which photodimerize; (iii) electrostatic interactions may play a significant role in the initial stages of the photodimerization reaction; (iv) singlet precursors to the stable triplet photodimers may exist; and (v) electron density does not, in general, increase in the C5-C6 bond in the excited state as compared to the ground state, contradicting the proposals of some earlier workers. Hybrid population densities and v-bond orders have been calculated for the first time for the molecules. Fluorine in 5-fluorouracil perturbs the hybrid populations as compared to those of uracil mainly in its vicinity.Des indices tlectroniques divers calculks par la mbthode CNDO/S-CI pour l'uracile, la 5 -fluorouracile, la thymine et la cytosine et la regle de Woodward-Hoffmann appliquee a la photodimerisation de ces molecules menent aux conclusions suivantes: (i) la reduction de I'ordre de la liaison C -C 6 suivant I'excitation est gineralement correlee a la reaction de photodimerisation pour toutes les pyrimidines biologiques. (ii) les molecules de pyrimidine excitees peuvent &tre nonplanes et I'excitation peut alors &tre delocaliste sur les deux molecules photodimerisees; (iii) les interactions electrostatiques peuvent jouer un r81e significatif dans les &tapes initiales de la reaction de photodimerisation; (iv) des prtcurseurs singulets aux photodimeres triplets peuvent exister; (v) la densite electronique en gtneral n'augmente pas dans la liaison C5-C6 dans I'etat excitt en comparaison avec I'etat fondamental, ce qui est contradictoire aux suggestions de certains chercheurs. Des densites de population hybrides et des ordres des liaisons u ont CtC calcules pour la premiere fois pour ces molecules. Le fluor dans la 5-fluorouracile perturbe les populations hybrides en comparaison avec celles de I'uracile du voisinage.Verschiedene mit der cNDo/s-cI-Methode berechnete Elektronenindizes fur Uracil, 5-fluorouracil, Thymin und Cytosin zusammen mit der auf die Photodimerisierung dieser Molekule angewandten Woodward-Hoffmann'schen Regel fiihren zu den folgenden Folgerungen: (i) die Abnahme der C5-C6-Bindungsordnung nach einer Anregung ist im allgemeinen mit der Photodimerisierungsreaktion fur alle biologischen Pyrimidinen korreliert; (ii) angeregte Pyrimidinmolekule konnen nicht-eben sein und die Anregung ware iiber beide photodimerisierte Molekule delokalisiert; (iii) elektrostatische Wechselwirkungen konnen eine bedeutsame Rolle in den Anfangsstufen der Photodimerisierungsreaktion spielen; (iv) Singulettvorlaufer zu den stabilen ...

Electronic spectra of nucleic acid bases: Variable electronegativity calculations and an analysis of existing results

“…Electronic excitation energies, oscillator strengths, and directions of polarization for several transitions (4) of uracil, 5-fluorouracil, thymine, cytosine, adenine, and guanine as obtained in the PPP calculations by Berthod et al [2] and Bailey [6] and the CNDO/S-CI calculations performed by one of the present authors with others [16][17][18]201 have been compared with the present VE-PPP results as well as the experimental ones [8] in Table I. Several singlet T * t T , two triplet T * t 7r (obtained witH and without CI), and two T * t n excitation energies, the last quantities being obtained by the CNDO/S-CI method, have been included in Table I for each molecule.…”

“…The results of the CNDO/S-CI studies on uracil, 5-fluorouracil, and guanine carried out by us and on thymine, cytosine, and adenine carried out earlier by one of the present authors with others [16][17][18]201 have also been compared with the VE-PPP and experimental results [S]. When the excitation energies calculated by the various methods differ appreciably from one another and/or from the experimental values, we tried to use the calculated directions of polarization of the transitions for their identification.…”

Quantum theoretical study of mechanism of the reaction between guanine radical cation and carbonate radical anion: Formation of 8‐oxoguanine

“…The study of mechanisms of DNA damage by chemical species or radiation, repair of damaged DNA, structural modifications of DNA components or their complexation with metals or other species, and scavenging the reactive species from biological media by antioxidants are important from the point of view of fundamental understanding about disorders of biological systems and diseases [11][12][13]. Theoretical studies have proved to be highly useful to explain molecular mechanisms of various types of events observed experimentally [14,15]. Among the DNA bases, guanine has the lowest ionization potential due to which it is the primary target of many reactive chemical agents [16,17].…”

Reactions of the OOH radical with guanine: Mechanisms of formation of 8-oxoguanine and other products

“…Occurrence of 8-oxoGua due to oxidation of DNA by peroxyl radicals has been observed experimentally [7,9,19]. Base level DNA damage caused by different environmental agents and prevention of the damage are subjects of great importance in chemistry, biology and medicine [20][21][22][23][24][25][26][27][28]. Further, study of mechanisms of formation of 8-oxoGua and other mutagenic products due to reactions involving ROS and RNOS is of immense current research interest [29][30][31][32][33][34][35][36].…”