T. E. Moskovskaya

Tautomerism in cytosine and uracil: an experimental and theoretical core level spectroscopic study

The O, N, and C 1s core level photoemission spectra of the nucleobases cytosine and uracil have been measured in the vapor phase, and the results have been interpreted via theoretical calculations. Our calculations accurately predict the relative binding energies of the core level features observed in the experimental photoemission results and provide a full assignment. In agreement with previous work, a single tautomer of uracil is populated at 405 K, giving rise to relatively simple spectra. At 450 K, three tautomers of cytosine, one of which may consist of two rotamers, are identified, and their populations are determined. This resolves inconsistencies between recent laser studies of this molecule in which the rare imino-oxo tautomer was not observed and older microwave spectra in which it was reported.

An Experimental and Theoretical Core-Level Study of Tautomerism in Guanine

The core level photoemission and near edge X-ray photoabsorption spectra of guanine in the gas phase have been measured and the results interpreted with the aid of high level ab initio calculations. Tautomers are clearly identified spectroscopically, and their relative free energies and Boltzmann populations at the temperature of the experiment (600 K) have been calculated and compared with the experimental results and with previous calculations. We obtain good agreement between experiment and the Boltzmann weighted theoretical photoemission spectra, which allows a quantitative determination of the ratio of oxo to hydroxy tautomer populations. For the photoabsorption spectra, good agreement is found for the C 1s and O 1s spectra but only fair agreement for the N 1s edge.

X-ray Spectroscopy of Heterocyclic Biochemicals: Xanthine, Hypoxanthine, and Caffeine

The electronic structures of the purine derivatives xanthine, hypoxanthine and caffeine have been investigated in the gas phase using C, N, and O 1s X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results have been interpreted by means of ab initio calculations using the third-order algebraic-diagrammatic construction (ADC(3)) method for the one-particle Greens function and the second-order ADC method (ADC(2)) for the polarization propagator. The carbon, nitrogen and oxygen K-edge NEXAFS spectra of xanthine and caffeine are very similar, since the molecules differ only by substitution of three hydrogen atoms by methyl groups. For hypoxanthine, the electronic structure and spectra differ considerably from xanthine as the purine ring is more highly conjugated, and there is one less oxo group. Effects due to oxo-hydroxy tautomerism were not observed. However, the two oxo tautomeric forms of hypoxanthine oxo-N(9)-H and oxo-N(7)-H are populated in the gas phase, and the C 1s spectra can be simulated only by taking account of these two tautomers, with appropriate Boltzmann population ratios which we have also calculated. For xanthine and caffeine, single tautomeric forms were observed.

Core-level electronic spectra in ADC(2) approximation for polarization propagator: Carbon monoxide and nitrogen molecules

An effective ab initio approach to core-level electronic spectral studies is discussed. The approach uses polarization propagator theory in a second-order algebraic diagram construction ADC(2) approximation for calculating the characteristics of electron transitions; it also uses the linear vibronic model LVM for investigating the vibrational structure of transitions. The core excitation specialization of ADC(2) is achieved by introducing the core valence separation (CVS) approximation. K-excitation spectra of CO and N2 molecules are calculated to examine the potential of the approach. The calculated spectra and the available experimental data are analyzed to characterize the method. A number of additional facts of methodological and practical value are found, and new transitions are predicted. It is concluded that ADC(2)/CVS/LVM is a promising approach to problem solving in core level spectroscopy, which requires qualitatively reliable theoretical estimations.

Comprehensive core-level study of the effects of isomerism, halogenation, and methylation on the tautomeric equilibrium of cytosine.

Core-level X-ray photoemission and near-edge X-ray absorption fine structure spectra of 5-methylcytosine, 5-fluorocytosine, and isocytosine are presented and discussed with the aid of high-level ab initio calculations. The effects of the methylation, halogenation, and isomerization on the relative stabilities of cytosine tautomers are clearly identified spectroscopically. The hydroxy-oxo tautomeric forms of these molecules have been identified, and their quantitative populations at the experimental temperature are calculated and compared with the experimental results and with previous calculations. The calculated values of Gibbs free energy and Boltzmann population ratios are in good agreement with the experimental results characterizing tautomer equilibrium.

Theoretical evidence for a bound doubly-excited 1B2(C 1s,n→π*2) state in H2CO below the C 1s ionization threshold

The group of three lowest singlet C 1s-excited states of formaldehyde H2CO is studied theoretically. The equilibrium geometries are determined at the restricted open-shell Hartree–Fock (ROHF) level and refined total energies are obtained using the multireference configuration interaction (MRCI) approach. In agreement with an earlier prediction [Chem. Phys. 122, 9 (1988)] the second lowest singlet state, 1B2, is characterized by a doubly excited, “two particle–two hole” (2p–2h), configuration C 1s,n→π*2. Our calculations predict that H2CO in the 1B2(2p–2h) state has a stable pyramidal equilibrium structure with a barrier to inversion of 0.28 eV, the valence angle being close to 107°. The calculated length of the CO bond is 1.390 A. The 1B2(2p–2h) state is shown to be also bound with respect to all possible dissociation and rearrangement processes. The lowest predicted dissociation energy for the 1B2 state (H2CO*→H2+CO* reaction) is 0.29 eV (6.69 kcal/mol). The rationalization of the great stability of the ...

Propagator quantum chemical study of S-cis-(Z)-2-(2-formylethenyl)pyrrole: electronic structure and aspects of intramolecular hydrogen bond manifestation in ionization spectra

For the purpose of investigation of the electronic structures of functionalized pyrroles with potential biological activity the electronic structures and ionization spectra of S-cis-(Z)-2-(2-formylethenyl)pyrrole (FP) were calculated by the propagator quantum chemical method. The calculations were performed using the third-order algebraic diagrammatic construction method (ADC(3)) for one-particle Green´s function (electronic propagator) and the 6–31G** basis set. Going from FP (possessing the intramolecular hydrogen bond H⋯O) to its conformation FPR (without H⋯O bonding), the O1s-ionization energy and the ionization energy of the σ-type lone electron pair orbital of the O atom decrease by ~0.2 eV, which is a consequence of stopping the electron density transfer from the O atom. A strong electron density transfer through the hydrogen bond from the O atom to the NH group occurs in the nitrogen core level ionization spectrum as evidenced by a lower N1s-ionization energy of FP (by ~0.7 eV ) compared to that of FPR. The valence shell ionization spectra of FP and FPR calculated using the ADC(3) method are characterized by a high density of the satellite states. The results obtained indicate that the electronic structures of the compounds of the considered class are characterized by pronounced effects of electron correlation.

An experimental and theoretical study of the valence shell photoelectron spectra of 2-chloropyridine and 3-chloropyridine

The valence shell photoelectron spectra of 2-chloropyridine and 3-chloropyridine have been studied both experimentally and theoretically. Synchrotron radiation has been employed to record angle resolved photoelectron spectra in the photon energy range 20-100 eV, and these have enabled anisotropy parameters and branching ratios to be derived. The experimental results have been compared with theoretical predictions obtained using the continuum multiple scattering Xα approach. This comparison shows that the anisotropy parameter associated with the nominally chlorine lone-pair orbital lying in the molecular plane is strongly affected by the atomic Cooper minimum. In contrast, the photoionization dynamics of the second lone-pair orbital, orientated perpendicular to the molecular plane, seem relatively unaffected by this atomic phenomenon. The outer valence ionization has been studied theoretically using the third-order algebraic-diagrammatic construction (ADC(3)) approximation scheme for the one-particle Greens function, the outer valence Greens function method, and the equation-of-motion (EOM) coupled cluster (CC) theory at the level of the EOM-IP-CCSD and EOM-EE-CC3 models. The convergence of the results to the complete basis set limit has been investigated. The ADC(3) method has been employed to compute the complete valence shell ionization spectra of 2-chloropyridine and 3-chloropyridine. The relaxation mechanism for ionization of the nitrogen σ-type lone-pair orbital (σN LP) has been found to be different to that for the corresponding chlorine lone-pair (σCl LP). For the σN LP orbital, π-π* excitations play the main role in the screening of the lone-pair hole. In contrast, excitations localized at the chlorine site involving the chlorine πCl LP lone-pair and the Cl 4p Rydberg orbital are the most important for the σCl LP orbital. The calculated photoelectron spectra have allowed assignments to be proposed for most of the structure observed in the experimental spectra. The theoretical work also highlights the formation of satellite states, due to the breakdown of the single particle model of ionization, in the inner valence region.

Quantum chemical study of the interaction of acetylene with lithium hydroxide and hydrosulfide

Conclusions1.Calculations using the MNDO method have been carried out for the intermediate and end products of the interaction between the acetylene and vinylidene molecules with molecules of LiOH and LiSH, and possible pathways for these reactions have been suggested.2.The optimal structures and the energies of formation of thermodynamically stable anions formed by the interaction of−SH and−OH with the molecules C2H2 and H2CC have been obtained, and it has been demonstrated that Li+ contributes to the nucleophilic attachment of the−OH and−SH anions to the triple bond to the same degree that the nucleophile contributes to the attachment of the electrophile Li+.

Theoretical study of the structure of molecules of alkali metal acetylenides and carbides

Conclusions1.According to data from nonempirical calculations, the reactivity of alkali metal acetylenide molecules toward electrophilic and nucleophilic reagents increases relative to the acetylene molecule.2.The vinylidene forms MHC=C rearrange to MC=CH in a barrier-free manner as a result of migration of the alkali metal atom. Acetylenides are structurally nonrigid molecules due to the quasifree motion of the alkali metal atom (but not of the H atom).3.The nonrigidity of the alkali metal carbide molecules is connected with the possibility of synchronous shift of the metal atoms.