Mario Bossa

AB INITIO STUDY OF INTRAMOLECULAR PROTON TRANSFER REACTIONS IN CYTOSINE

Abstract The activation energies of intramolecular proton transfer reactions of cytosine in the gas phase were computed through ab initio calculations. MP2/6-31G ** and MP2/D95 ** energy calculations were performed over geometries obtained at the HF/3-21G, HF/6-31G(N8 * ) and HF/D95(N8 * ) level (d-type polarisation functions were added on the N8 atom). Corrections for the zero-point vibrational energy were included. It is suggested that not only thermodynamic but also kinetic factors may be responsible for the distribution of the tautomeric species in the gas phase. Results are discussed with reference to spectroscopic data in the literature.

Critical test of PM3-calculated proton transfer activation energies: a comparison with ab initio and AM1 calculations

Abstract Intra- and intermolecular proton transfer activation energies are calculated by means of the semiempirical PM3 method and compared with ab initio results obtained at MP2/6–31G ∗ or MP2/6–31G ∗∗ level. It is shown that corrections for zero-point vibrational energy (ZPVE) and thermal contributions do not affect the correlation between semiempirical and ab initio results. The linear relationship obtained suggests that PM3, in spite of some weaknesses, can be employed with a certain confidence to predict proton transfer activation barriers of large molecules or to obtain semi-quantitative trends for large numbers of interrelated systems. It is also shown that PM3 and AM1 results are of comparable quality for intramolecular proton transfers, whereas PM3 is to be preferred for intermolecular reactions, in particular when water molecules are involved.

ON the conjugation in macrocycles: the electronic structure and spectrum of hemiporphyrazine

Abstract The differences in conjugation existing in macrocycles like porphyrin, phthalocyanine and hemiporphyrazine are explained in terms of elementary resonance theory and of π-interaction energy. The electronic spectrum of hemiporphyrazine is interpreted via the CNDO/CI method and the results are compared with those obtained for the other two macrocycles.

A theoretical study on proton transfer in the mutarotation of sugars

The epimerisation process of the model sugar 2-tetrahydropyranol was studied by means of ab initio calculations. The results suggest that the rate limiting step of sugar ring opening involves a high-energy intramolecular proton transfer reaction or a low-energy process in which the proton transfer is mediated by a catalyst molecule, formic acid in the case investigated. The catalysed process is an asynchronous concerted double proton transfer reaction, where both protons are transferred within the same elementary step but one of them is transferred much earlier than the other one along the reaction coordinate. The motion of both protons in the transition state of the catalysed process is strongly coupled with the breaking of the C–O bond of the sugar ring. Geometry optimisation at the B3LYP/6-31G* level, with additional p polarisation functions located on the hydrogen atoms involved in proton transfer, appears to be suitable for further MP2/6-31G** single point energy calculations, as it provides hydrogen bond and activation energies in good agreement with those obtained from geometry optimisation at the full MP2 level of theory.

A computational study on N2 adsorption in Cu-ZSM-5

The present computational study investigates the adsorption of N(2) by Cu-ZSM-5, with particular regard to the interaction with pairs of Cu(+) ions, employing simple cluster models in the calculations. It shows that several interaction patterns between N(2) and couples of Cu(+) sites are possible within the Cu-ZSM-5 structure. In particular, when pairs of Cu(+) ions are located at opposite sides of ten-membered rings, in the region where linear and sinusoidal channels intersect each other, a quasi-linear Cu-N-N-Cu adsorption occurs. Although lattice restraints cause small deviations from linearity, such interaction turned out to be more favourable than other adsorption patterns within the Cu-ZSM-5 structure. The linearity of the Cu-N-N-Cu fragment and the relatively low concentration of the related sites cause a low extinction coefficient for the N-N IR stretching mode, which is usually detected with very low intensity or not detected at all. The results of the present calculations may explain the experimental evidence for a nearly IR-silent fraction of nitrogen strongly adsorbed in the Cu-ZSM-5 catalyst which, as shown in a previous work, is linearly related to the number of active sites for NO decomposition.

The epimerisation of 2-tetrahydropyranol catalysed by the tautomeric couples 2-pyridone/2-hydroxypyridine and formamide/formamidic acid as a model for the sugar's mutarotation: a theoretical study

In the present computational study a complete reaction mechanism for the sugars mutarotation promoted by tautomeric catalysts in vacuum is outlined. The rate determining step of the process consists in the breaking of the C–O bond of the sugar ring which occurs by a concerted double proton transfer between the substrate and the catalyst. After ring opening, the –CHO group of the substrate rotates around the C2–C3 bond without dissociation of the substrate–catalyst adduct. The activation energy of this step is generally less than 8–9 kcal mol−1. Alternative reaction paths which require the dissociation of the substrate–catalyst complex are less favourable for both probability and energetic reasons. When the mutarotation is catalysed by the 2-pyridone/2-hydroxypyridine (PD/HP) tautomeric couple, the process may be promoted by either PD or HP derived from the dissociation of the (PD)2, (HP)2 or PD–HP dimers. According to B3LYP and MP4 (SDQ) calculations the HP-promoted reaction path should be faster than the PD-promoted one. When the process is catalysed by the formamide/formamidic acid (F/FA) tautomeric couple, the reaction path promoted by FA, which is derived from the dissociation of the F–FA dimer, should be the most favourable, according to B3LYP, MP2 and MP4(SDQ) calculations. Solvent effects in benzene, calculated by the PCM method, did not affect to a relevant extent the mechanism outlined in vacuum. The present study suggests, differing from the hypothesis formulated in many experimental studies, that the sugars mutarotation process is more efficiently catalysed by the less stable tautomer or catalyst dimer rather than by the more stable one of both the PD/HP and F/FA couples.

On the electronic states of the extended porphyrin family

Abstract The ground and lower excited electronic singlet and triplet states of eight macrocycles resulting from porphyrin by replacing pyrroles with pyridines or indoles and the meso methines by nitrogens (the extended porphyrin family) have been treated by Skalas version of the CNDO/S method in view of providing systematic reference computational data. The results are especially useful for comparisons capable of throwing light on the structure-property relations that make some of those macrocycles especially active for energy and electron transfer. A brief discussion is given. The uniqueness of porphyrin stands out clearly, but some of its features may be strictly related to the biochemical environment of heme groups, so that other macrocycles of the family might be better suited for technological applications simulating the in vivo behavior of porphyrin derivatives. Hints concerning the effect of coordination to metal atoms are given, pending the completion of a parallel study on some metal complexes of the family. A few novel experimental results from our laboratories are mentioned in the discussion.

On the electronic states of macrocycles of the extended porphyrin family and their coordination compounds

Abstract The electronic absorption spectra of Ni, Zn and Mg hemiporphyrazine derivatives are presented and discussed together with theoretical results obtained by INDO/S computations. The absorption spectra of all the metal derivatives show marked red shifts of the lowest energy absorption bands with respect to those of the metal free hemiporphyrazine. The possible explanation that in metal derivatives low lying excited states with a fully conjugated π electron system are present is supported by theoretical computations.

Molecular orbital analysis of some ligand-bridged iron binuclear complexes by UV photoelectron spectroscopy and DV-Xα calculations

Abstract The electronic structure of [FeCpCO] 2 (μ-CO) 2 , [FeCpCO] 2 (μ-CO)(μ-CH 2 ) (hereafter Cp = η 5 -C 5 H 5 ) and their methyl-substituted Cp derivatives have been accurately investigated by carrying out DV-Xα calculations and comparing the results with gas-phase UV photoelectron (PE) spectra. Some minor changes in the PE data on passing from the (μ-CO) 2 to the (μ-CO)(μ-CH 2 ) complexes have been interpreted in the light of the different properties of the frontier orbitals of the bridges. The reported theoretical and experimental data support the hypothesis of the lack of a direct FeFe bond, in agreement with previous ab-initio theoretical results.

UV photoelectron spectra and pseudopotential ab initio calculations of (CH3)3PbCCCH3

Abstract Gas-phase UV photoelectron spectroscopy (UPS) and pseudopotential ab initio calculations were used to analyse the electronic structure of (CH3)3PbCCCH3, with particular interest in the possible σ-π interaction between the π(CC) system and the σ(PbC) bonds. The results obtained, compared with the UPS data already known for the tin analogue, and with the pseudopotential calculations performed during the present work for both compounds, showed that the bonding is similar in the two molecules. In particular the σ-π interaction is quite weak and the HOMO has mainly π(CC) character. The present interpretation is supported by the analysis of the NMR results.