Unexpected Decarbonylation of Acylethynylpyrroles under the Action of Cyanomethyl Carbanion: A Robust Access to Ethynylpyrroles.

It has been found that the addition of CH2CN- anion to the carbonyl group of acylethynylpyrroles, generated from acetonitrile and t-BuOK, results in the formation of acetylenic alcohols, which undergo unexpectedly easy (room temperature) decomposition to ethynylpyrroles and cyanomethylphenylketones (retro-Favorsky reaction). This finding allows a robust synthesis of ethynylpyrroles in up to 95% yields to be developed. Since acylethynylpyrroles became available, the strategy thus found makes ethynylpyrroles more accessible than earlier. The quantum-chemical calculations (B2PLYP/6-311G**//B3LYP/6-311G**+C-PCM/acetonitrile) confirm the thermodynamic preference of the decomposition of the intermediate acetylenic alcohols to free ethynylpyrroles rather than their potassium derivatives.

Two-Sided Impact of Water on the Relaxation of Inner-Valence Vacancies of Biologically Relevant Molecules.

After ionization of an inner-valence electron of molecules, the resulting cation-radicals store substantial internal energy which, if sufficient, can trigger ejection of an additional electron in an Auger decay usually followed by molecule fragmentation. In the environment, intermolecular Coulombic decay (ICD) and electron-transfer mediated decay (ETMD) are also operative, resulting in one or two electrons being ejected from a neighbor, thus preventing the fragmentation of the initially ionized molecule. These relaxation processes are investigated theoretically for prototypical heterocycle-water complexes of imidazole, pyrrole, and pyridine. It is found that the hydrogen-bonding site of the water molecule critically influences the nature and energetics of the electronic states involved, opening or closing certain relaxation processes of the inner-valence ionized system. Our results indicate that the relaxation mechanisms of biologically relevant systems with inner-valence vacancies on their carbon atoms can strongly depend on the presence of the electron-density donating or accepting neighbor, either water or another biomolecule.

XPS and quantum chemical analysis of 4Me-BODIPY derivatives.

The results of a X-ray photoelectron spectroscopy (XPS) and steady-state absorption spectroscopy study of the electronic structure, and cationic and excited states of a series of 1,3,5,7-tetramethyl-substituted BODIPYs (4Me,2R-BODIPYs) are presented. The experimental data were interpreted using high-level ab initio quantum chemical computations, including the algebraic diagrammatic construction method for the polarization propagator of the second order (ADC(2)), the outer-valence Green's function (OVGF) method, the density functional (DFT) approach, and the time-dependent DFT (TD-DFT) approach. Substitution effects on the XPS and absorption spectra were determined for 2,6-positions of 4Me,2R-BODIPY pyrrole nuclei (R = H, Br, Bu, benzyl). A very satisfactory performance of the DFT Koopmans theorem analogue was demonstrated with respect to the energy intervals between the electronic levels of 4Me,2R-BODIPY above 13 eV (BHHLYP functional) and the values of the HOMO-LUMO energy gap (ωB97X functional).

Positional and Conformational Isomerism in Hydroxybenzoic Acid: A Core-Level Study and Comparison with Phenol and Benzoic Acid.

Three positional isomers of hydroxybenzoic acid, as well as phenol and benzoic acid, were studied using core-level photoemission and X-ray absorption spectroscopies, supported by quantum chemical calculations. While 2-hydroxybenzoic (salicylic) acid exists as a single conformer with an internal hydrogen bond, 3- and 4-hydroxybenzoic acids are mixtures of multiple conformers. The effects due to isomerism are clearly seen in the C 1s and O 1s photoelectron spectra, whereas the conformational effects on the binding energies are less pronounced. The O 1s photoelectron spectrum of salicylic acid is significantly different from that of the other two isomers, providing a signature of the hydrogen bond. In contrast, the oxygen K edge X-ray absorption spectra of the three hydroxybenzoic acids show only minor differences. The salicylic acid absorption spectrum at the carbon K edge shows a more resolved vibrational structure than the spectra of the other molecules, which can be explained in part by the existence of a single conformer. Our theoretical study of vibrational excitations in the lowest C 1s absorption bands of salicylic and 4-hydroxybenzoic acids indicates that the observed structure can be assigned to 0-0 lines of various electronic transitions since most of the totally symmetric vibrational modes with sufficiently large frequencies to be resolved are predicted to be inactive. Significant sensitivity of the C 1s excitations in 3-hydroxybenzoic acid to rotational conformerism was predicted but not observed due to spectral crowding.

CAP/EA-ADC method for metastable anions: Computational aspects and application to π* resonances of norbornadiene and 1,4-cyclohexadiene.

The second- and third-order algebraic-diagrammatic construction schemes for the electron propagator for studies of electron attachment processes [EA-ADC(2) and EA-ADC(3)] have been extended to include the complex absorbing potential (CAP) method for the treatment of electronic resonances. Theoretical and conceptual aspects of the new CAP/EA-ADC methodology are studied in detail at the example of the well-known 2Πg resonance of the nitrogen anion N2 -. The methodology is further applied to π* shape resonances, for which ethylene is considered as a prototype. Furthermore, the first many-body treatment of the π+ * and π- * resonances of norbornadiene and 1,4-cyclohexadiene is provided, which have served as model systems for the concept of through-space and through-bond interactions for a long time.

Intermediate state representation approach to physical properties of molecular electron-attached states: Theory, implementation, and benchmarking.

Computational schemes for comprehensive studies of molecular electron-attached states and the calculation of electron affinities (EAs) are formulated and implemented employing the intermediate state representation (ISR) formalism and the algebraic-diagrammatic construction approximation for the electron propagator (EA-ADC). These EA-ADC(n)/ISR(m) schemes allow for a consistent treatment of not only electron affinities and pole strengths up to third-order of perturbation theory (n = 3) but also one-electron properties of electron-attached states up to second order (m = 2). The EA-ADC/ISR equations were implemented in the Q-Chem program for Sz-adapted intermediate states, allowing also open-shell systems to be studied using unrestricted Hartree-Fock references. For benchmarking of the EA-(U)ADC/ISR schemes, EAs and dipole moments of various electron-attached states of small closed- and open-shell molecules were computed and compared to full configuration interaction data. As an illustrative example, EA-ADC(3)/ISR(2) has been applied to the thymine-thymine (6-4) DNA photolesion.

Intermediate state representation approach to physical properties of molecular electron-detached states. II. Benchmarking.

The third-order algebraic-diagrammatic construction method for studies of electron detachment processes within the electron propagator framework [IP-ADC(3)] was extended to treat the properties of molecular states with a detached electron using the intermediate state representation (ISR) formalism. The second-order ISR(2) equations for the one-particle (transition) density matrix have been derived and implemented as an extension of the IP-(U)ADC(3) method available in the Q-CHEM program. As a first systematic test of the present IP-(U)ADC(3)/ISR(2) method, the dipole moments of various electronic states of closed- and open-shell molecules have been computed and compared to full configuration interaction (FCI) results. The present study employing FCI benchmarks also provides the first rigorous estimates for the accuracy of electron detachment energies obtained using the IP-ADC(3) method.

Intermediate state representation approach to physical properties of molecular electron-detached states. I. Theory and implementation.

The third-order non-Dyson algebraic-diagrammatic construction approach to the electron propagator [IP-ADC(3)] is extended using the intermediate state representation (ISR) formalism, allowing the wave functions and properties of molecular states with detached electron to be studied. The second-order ISR equations [ISR(2)] for the one-particle (transition) density matrix have been derived and implemented in the Q-CHEM program. The approach is completely general and enables evaluation of arbitrary one-particle operators and interpretation of electron detachment processes in terms of density-based quantities. The IP-ADC(3)/ISR(2) equations were implemented for Sz-adapted intermediate states, allowing open-shell molecules to be studied using unrestricted Hartree-Fock references. As a first test for computations of ground state properties, dipole moments of various closed- and open-shell molecules have been computed by means of electron detachment from the corresponding anions. The results are in good agreement with experimental data. The potential of IP-ADC(3)/ISR(2) for the interpretation of photoelectron spectra is demonstrated for the galvinoxyl free radical.

Acetylene-Triggered Reductive Incorporation of Phosphine Chalcogenides into a Quinoline Scaffold: Toward SNHAr Reaction.

Quinolines react with acylacetylenes and secondary phosphine chalcogenides at 20-75 °C to afford N-acylvinyl-2(1)-chalcogenophosphoryldihydroquinolines in good and excellent yields. Unlike the pyridine-derived similar intermediates, which eliminate E-alkenes to give aromatic chalcogenophosphorylpyridines, thereby completing SNHAr reaction, with quinolines, the reaction stops at the formation of the above phosphorylated N-acylvinyl-dihydroquinolines, thus representing a pendant SNHAr process. This reaction opens a one-pot atom-economic single-step access to pharmaceutically targeted phosphorylated functionalized dihydroquinolines and isoquinolines.

Spectroscopic and quantum chemical study of difluoroboron ß-diketonate luminophores: Isomeric acetylnaphtholate chelates.

The electronic structure and optical properties of the isomeric difluoroboron ß-diketonates, 2,2-difluoro-4-methylnaphtho-[2,1-e]-1,3,2-dioxaborin (I) and 2,2-difluoro-4-methylnaphtho-[1,2-e]-1,3,2-dioxaborin (II), were studied by means of X-ray photoelectron, absorption and luminescence spectroscopies. The experimental results were interpreted using high-level ab initio quantum chemical computations, including the algebraic-diagrammatic construction method for the polarization propagator of the second and third orders (ADC(2) and ADC(3)), the outer-valence Green's function (OVGF) method, and the time-dependent density functional (TDDFT) approach. The X-ray photoelectron measurements were assigned in the entire energy range using the results of the Kohn-Sham orbital calculations which employed the B3LYP functional. Pronounced hypsochromic shift of crystal-state fluorescence was observed in I upon the lowering of temperature, which can be explained by the deterioration of the conditions for excimers formation. According to our results, remarkable feature of II, absent in I, is its phosphorescence at room temperature. Basing on our calculations, a decay mechanism for the S1 state was proposed, explaining the observed differences in the phosphorescence of I and II.

Four-Component Polarization Propagator Calculations of Electron Excitations: Spectroscopic Implications of Spin-Orbit Coupling Effects.

A complete implementation of the polarization propagator based on the Dirac-Coulomb Hamiltonian is presented and applied to excitation spectra of various systems. Hereby the effect of spin-orbit coupling on excitation energies and transition moments is investigated in detail. The individual perturbational contributions to the transition moments could now be separately analyzed for the first time and show the relevance of one- and two-particle terms. In some systems different contributions to the transition moments partially cancel each other and do not allow for simple predictions. For the outer valence spectrum of the H2Os(CO)4 complex a detailed final state analysis is performed explaining the sensitivity of the excitation spectrum to spin-orbit effects. Finally, technical issues of handling double group symmetry in the relativistic framework and methodological aspects of our parallel implementation are discussed.

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 Green's 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.

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.

Tautomerism in cytosine and uracil: a theoretical and experimental X-ray absorption and resonant auger study.

The core level photoabsorption spectra of the nucleobases cytosine and uracil in the gas phase have been measured and the results interpreted with theoretical calculations using an ab initio Green's function approach. A single tautomer of uracil is populated, in agreement with previous work, while three tautomers of cytosine are clearly identified, whose identity and relative populations at the temperature of the experiment were reported previously. The second-order ADC approach to polarization propagator was employed in calculations of X-ray photoabsorption energies and intensities. The theoretical spectra have been constructed as Boltzmann-factor-weighted sums of individual tautomer spectra. These theoretical spectra are in good agreement with the experimental photoabsorption results at the oxygen, nitrogen, and carbon edges. In addition we report resonant Auger spectra of the valence band of cytosine, which support previous assignments of the character of the valence band states.

Theoretical and experimental study of valence-shell ionization spectra of guanine.

The full valence-shell ionization spectra of the four most stable guanine tautomers were studied theoretically. The third-order algebraic-diagrammatic construction (ADC(3)) method for the one-particle Green's function was used to calculate the energies and relative intensities of the vertical ionization transitions. For low-lying transitions, the influence of planar and nonplanar guanine configurations on the ionization energies, as well as the convergence of the results with respect to basis set was studied at the level of the outer-valence Green's function (OVGF) approximation scheme. The results of the calculations were used to interpret recent synchrotron radiation valence-shell photoionization spectra of guanine in the gas phase under thermal equilibrium conditions. The photoelectron spectrum was modeled by summing individual tautomer spectra weighted by Boltzmann population ratios (BPR) of tautomers from our previous high-level ab initio thermochemical calculations. The theoretical spectra are in good agreement with the experimental results, providing assignments of most observed structures and offering insight into tautomerism of guanine in the gas phase. The first six molecular orbitals give rise to single-hole states with a binding energy of about 7-12 eV. At higher binding energy the spectral features are mainly due to satellite states.

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.

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.