Electronic aspects of the photodimerization of pyrimidine bases and their derivatives

Results of calculations for the lower excited triplet and singlet states of pyrimidine bases and a number of their derivatives, calculated by the self-consistent field (SCF) method for open shells and by the configuration interaction (CI) method for self-consistent orbitals, are presented. It is shown that excitation to the T₁ and S₁ states primarily affects the C₅—C₆ bond while triplet excitation is almost completely localized on this bond. This leads to exceptionally pronounced weakening of the C₅—C₆ bond in the T₁ state. All other conditions being equal, the conditions in the T₁ state are more favorable for the dimerization of the bases than in the S₁ state. A correlation between the degree of localization of the triplet excitation at the C₅—C₆ bond and the ease of photodimerization has been established. The experimental facts associated with the formation of thymine free radicals in DNA are explained.The authors thank G. G. Dyadyusha and O. V. Shramko for discussing our results. The program for calculation of the bond orders by the CI method was kindly given to us by G. M. Kagan and G. I. Kagan.     

Electronic aspects of photodimerization of the pyrimidine bases and of their derivatives

We present the results of a computation for the lowest excited triplet and singlet states of the pyrimidine bases and of some of their derivatives by the SCF open shell theory and CI method on SCF virtual orbitals. It is shown that excitation to the lowest singlet S ₁ and triplet T ₁ states mostly affects the bond C₅-C₆ and that triplet excitation is almost completely localized on this bond. The latter effect leads to exceptionally strong weakening of the bond C₅-C₆ in the triplet state T ₁. It is concluded that under otherwise equal circumstances the triplet state T ₁ presents more favourable conditions for dimerization reaction than the lowest excited singlet state S ₁ does. Correlation between the degree of the triplet excitation localization on the bond C₅-C₆ and the easiness of the photodimerization is established. An explanation of the experimental facts concerned with the formation of the thymine free radicals in DNA is also suggested.

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Zusammenfassung Wir prÄsentieren Resultate von der Berechnung der niedrigsten angeregten Triplett- und Singulett-ZustÄnde der Pyrimidin Basen und einiger ihrer Derivate mittels der SCF-Theorie der offenen Schalen sowie der CI-Methode angewandt auf virtuelle SCF-Orbitale. Es wird gezeigt, da\ die Anregung der niedrigsten Singulett S ₁- und Triplett T ₁-ZustÄnde meistens die C₅ und C₆-Bindung berührt und da\ die Triplett-Anregung fast vollstÄndig auf diese Bindung lokalisiert ist. Der letztere Effekt führt zu einer au\erordentlich starken SchwÄchung der C₅-C₆-Bindung im Triplett-Zustand T ₁. Es wird daraus geschlossen, da\ unter sonst gleichen UmstÄnden der Triplett-Zustand T ₁ günstigere Bedingungen für eine Dimerisationsreaktion liefert als der niedrigste angeregte Singulett-Zustand S ₁. Ein Zusammenhang zwischen dem Grad der Lokalisierung der Triplett-Anregung auf die C₅-C₆-Bindung und der Photodimerisierbarkeit wird hergestellt. Eine ErklÄrung der experimentellen Tatsachen, welche die Anordnung der freien Thymin Radikale in der DNA betreffen, wird ebenfalls angegeben.

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Résumé Nous présentons les résultats d'un calcul pour les états excités singulet et triplet les plus bas des bases pyrimidiques et de certains de leurs dérivés, effectués par les méthodes SCF à couche ouverte et interaction de configurations. L'excitation dans ces plus bas états excités affecte essentiellement la liaison C₅-C₆, l'excitation triplet étant pratiquement totalement localisée sur cette liaison. Ceci conduit à un affaiblissement important de la liaison C₅-C₆ dans l'état triplet. On en conclut qu'à circonstances égales l'état triplet présente des conditions plus favorables pour une réaction de dimérisation que le plus bas état excité singulet. Une corrélation est établie entre le degré de localisation 5–6 de l'excitation triplet et la facilité de photodimérisation. On suggère aussi une explication des faits expérimentaux liés à la formation de radicaux libres thymine dans le DNA.

     

Theoretical study of the photodimerization of pyrimidine bases

The experimental results are correctly interpreted as from the delocalized model of the transition state and the theory of perturbations. The surfaces of the energy of interaction between both molecules in function of different coordinates of reaction make it possible to discuss the concerted nature of photodimerization and permit the two conjugated systems to be added between carbon atoms 5 and 6 of both molecules.

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Zusammenfassung Die experimentellen Resultate werden mit Hilfe eines delokalisierten Modells des Übergangszustandes und der Störungstheorie richtig interpretiert. Die Energiehyperfläche der Wechselwirkung zwischen den beiden Molekülen als Funktion verschiedener Reaktionskoordinaten erlaubt die Diskussion des konzertierten Ablaufs der Photodimerisation und der Addition der beiden konjugierten Systeme, die zwischen den Kohlenstoffatomen 5 und 6 der beiden Moleküle stattfindet.

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Résumé Les résultats expérimentaux sont correctement interprétés à partir du modèle delocalisé de l'état de transition et de la théorie des perturbations. Les surfaces de l'énergie d'interaction entre les deux molécules en fonction aux différentes coordonnées de réaction permettent de discuter le caractère concerté de la photodimerisation et que l'addition des deux systèmes conjugués se réalise entre les carbones 5 et 6 des deux molécules.

     

Electronic structure and spectroscopy of nucleic acid bases: ionization energies, ionization-induced structural changes, and photoelectron spectra

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C), and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized the five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using the equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the ωB97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series, G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25, and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67, and 7.75-7.87 eV for A, T, C, and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 ± 0.05, 8.95 ± 0.05, 8.60 ± 0.05, and 7.75 ± 0.05 eV). Vibrational progressions for the S(0)-D(0) vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra and differentiated PIE curves.     

Relationship between retention and molecular structure of pyrimidine bases

Summary The influence of the type and position of CH₃, NH₂ and OH groups in the pyrimidine ring, the eluent composition and the surface chemistry of the stationary phase on the retention of pyrimidine bases in reversed-phase liquid chromatography was investigated. On the basis of the hypothesis about the additivity of the adsorption energy the contribution of various structural groups on retention has been established.     

Electronic spectra and structure of nitroanilines

Vapour spectra and solution spectra in a variety of solvents were recorded for some D,D′A_rA and A,A′A_rD molecules, where DD′NH₂ and AA′NO₂. Ground state dipole moments of D,D′A_rA molecules were determined in dioxane solution.The molecules in molecules (MIM) molecular orbital method was used to calculate the properties associates with the electronic states. It was found that to the first band in the spectra both charge-transfer and locally excited configurations contribute. The dipole moment in the excited state associated with the first intense electronic transition was evaluated from the solvent shift of the band. A general comparison of theoretical results with experiment reveals a good agreement.     

Transient absorption spectra and photochromic mechanism of schiff bases

The transient absorption spectra of salicylideneaniline (SA) and salicylidenebenzylamine (SBA) have been investigated by means of the nanosecond laser flash photolysis. It has been found that the intermediates from the two compounds have different properties. According to the properties of the intermediates for compound SA, the primary photoproduct is a zwitterion produced by the excited singlet state, rather than a trans- keto isomer. The intermediate of compound SBA also was found to be a zwitterion, but produced not only by the excited singlet state but also by the excited triplet state. The photochromic mechanisms of the two compounds are proposed and discussed respectively.     

Electronic structure,spectra, and thermodynamical functions of molybdenum pentachloride

The SCF-X -SW method in non-relativistic and quasi-relativistic versions has been used to calculate the electronic structure, ionization potentials, energies and oscillator strengths of the optical transitions in MoCl₅. The electronic absorption spectrum of the gaseous MoCl₅ has been measured. The interpretation of the photoelectron and optical spectra of MoCl₅ is given. Spinpolarization effects and relativistic corrections are discussed. The thermodynamical functions of MoCl₅ (gas) are calculated.     

Electronic structure and spectra of organic molecules

Calculations of the singlet-singlet ( * type) transitions of a series of 2,6-disubstituted purines are presented. The Pariser-Parr-Pople method is used throughout and the agreement with experiment is good. The effects of the 2-X and 6-X substituents on the purine spectrum are discussed.For Part VIII (SCF MO CI Calculations for Hypoxanthine and Guanine Isomers) see Kwiatkowski, J. S.: Acta physica polon. 36 (1969), in press.     

Electronic structure and spectra of organic molecules

The Pariser-Parr-Pople method is used to predict the singlet-singlet ( ^* type). Electronic transition energies for the anions of hydroxy derivatives of benzene, pyridine and pyrimidine. The core integral for the -O^– substituent was treated as an empirical parameter and its value was chosen to fit results for the phenoxide ion and then applied for the compounds with the -O^– substituents. The results of the calculations for molecules with the -O^– groups are compared with those of the corresponding molecules containing the -OH and -NH₂ substituents as well as with the experimental data. No serious deviations between theoretical and experimental data other than those which could be ascribed to steric hindrances occuring in the molecules were found.

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Zusammenfassung Die Pariser-Parr-Pople-Methode wird benutzt, um die Singlett-Singlett-Übergangsenergien (- ^*-Typ) von Benzol-, Pyridin- und Pyrimidinderivaten zu berechnen, die OH-Gruppen enthalten. Das Rumpfintegral des -O^–-Substituenten wurde wie ein empirischer Parameter behandelt. Sein Wert wurde so gewählt, daß er die Meßergebnisse für das Phenolat-Anion richtig wiedergibt. Die Resultate der Berechnungen für Moleküle mit der -O^–-Gruppe werden mit denjenigen für die entsprechenden Moleküle mit OH- und NH₂-Substituenten als auch mit den experimentellen Daten verglichen. Es werden keine ernsten Abweihungen zwischen theoretischen und experimentellen Daten gefunden, außer solchen, die einer sterischen Hinderung zugeschrieben werden können.

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Résumé La méthode de Pariser, Parr et Pople est utilisée pour prédire les transitions électroniques ( ^*) pour les formes anioniques des derivés hydroxy du benzène, pyridine et pyrimidine. La valeur d'integrale de coeur associée du substituant -O^– a été choisie de façon à reproduire les positions des bandes d'absorption de forme anionique du phenol et après elle a été appliquée pour les composés envisagés. Les resultats des calculs pour l'anions sont mis en comparaison avec les resultats obtenus pour les correspondantes derivés aminés et hydroxy et avec les donnés experimentales. Peu de déviations ont été obtenus, en dehors de ceux que l'on peut attribuer à des encombres steriques.

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Based in part on a M. Sci. thesis by M. Berndt, N. Copernikus University, Toru, 1969 (unpublished, in Polish).     

Electronic structure and absorption spectra of indolizines

The electronic structure and spectra of indolizine and a large number of its aza-derivatives have been calculated by the SCFMO-CI method, taking into account all the singlet monoexcited configurations. The results are in good agreement with the experiment. The assignment of the observed bands is also discussed.

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Zusammenfassung Mit dem SCFMO-CI-Verfahren werden Elektronenstruktur und Spektren des Indolizins und mehrerer seiner Derivate berechnet, wobei alle einzeln angeregten Singulett-Konfigurationen berücksichtigt werden. Die Ergebnisse stehen in ausgezeichneter Übereinstimmung mit dem Experiment. Die Zuordnung der beobachteten Banden wird diskutiert.

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Résumé La structure et les spectres électroniques de l'indolizine et de plusieurs ses aza-dérivés ont été calculés par la méthode SCFMO-CI, en considérant toutes les configurations singulets monoexcitées. Les résultats sont en bon accord avec l'expérience. L'attribution des bandes observées est aussi discutée.

     

Electronic structure and spectra of organic molecules

The Pariser-Parr-Pople method has been used to calculate the -electronic structures and spectra of 6-fluoro, 6-hydroxy, 6-methoxy, 6-amino, 6-methylamino, 6-dimethylaminopurine and their parent molecule purine. The purine and adenine (6-aminopurine) absorption spectra (singlet-singlet ^* type transitions) in particular are discussed in greater detail. The correlation among the absorption bands of the molecules in question and their ground state properties are also discussed. The theoretical results for singlet-singlet transition energies agree fairly well with the experimental data.

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Zusammenfassung Mit der Methode von Pariser, Parr und Pople werden Struktur und Spektren der -Elektronensysteme von Purin sowie 6-F-, 6-OH-, 6-OCH₃-, 6-NH₂-, 6-NHCH₃- und 6-N(CH₃)₂-Purin berechnet, wobei besonderes Gewicht auf spektrale Übergänge von Purin und Adenin gelegt wurde. Ferner wurde die Korrelation der Purin-Spektren mit den Eigenschaften des Grundzustandes untersucht. Die theoretischen Ergebnisse für Singulettübergänge stimmen ziemlich gut mit den experimentellen Daten überein.

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Résumé A l'aide de la méthode Pariser-Parr-Pople nous avons calculé les structures et les spectres électroniques d'une série de purines (purine, 6-F, 6-OH, 6-OCH₃, 6-NH₂, 6-NHCH₃ et 6-N(CH₃)₂-purine). L'accent a été mis en particulier sur les bandes d'absorption pour la purine et l'adénine. La corrélation entre les spectres d'absorption électronique et l'état fondamental de purines est étudiée. Les résultats théoriques concernant les énergies des transitions singulet-singulet sont en très bon accord avec les données expérimentales.

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Submitted in honour of the seventieth birthday of Professor Aleksander Jabloski.     

Electronic spectra and structure of some phenoxazone-type dyes

Quantum-mechanical calculations of the electronic structure and spectra of a number of phenoxazone dyes are given. The distribution analysis of pi-electron density in the ground and excited states makes clear the origin of the colour of these compounds and gives the possibility of direct assessment of organic reagents in terms of colour contrast and sensitivity of analytical reactions. This is illustrated for a series of dihydroxy derivatives of phenoxazone dyes.