Amedeo Capobianco

Generating Function Approach to the Calculation of Spectral Band Shapes of Free-Base Chlorin Including Duschinsky and Herzberg–Teller Effects

A generating function approach to the calculation of spectral band shapes including Duschinsky and Herzberg-Teller effects is proposed and applied to the computation of the free-base chlorin Q absorption bands, using molecular geometries and normal vibrations obtained by density functional theory computations. The results clearly show that non-Condon effects can significantly affect the relative intensities of the weakest Q(y) and, to a lesser extent, Q(x) bands. The proposed approach is extremely powerful and can be used in the cases where the molecular size makes the direct calculation of Franck-Condon integrals by recurrence formulas prohibitive.

Franck–Condon factors in curvilinear coordinates: the photoelectron spectrum of ammonia

An approach to the calculation of Franck–Condon factors in curvilinear coordinates is outlined. The approach is based on curvilinear normal coordinates, which allows for an easy extension of Duschinsky’s transformation to the case of curvilinear coordinates, and on the power series expansion of the kinetic energy operator. Its usefulness in the case of molecules undergoing large displacements of their equilibrium nuclear configurations upon excitation is then demonstrated by an application to the vibrational structure of the photoelectron spectrum of ammonia, using an anharmonic potential only for the symmetric stretching and bending coordinates of the radical cation.

A series of compounds forming polar crystals and showing single-crystal-to-single-crystal transitions between polar phases

Condensation of 4-hydroxybenzohydrazide with a variety of non-chiral aliphatic ketones, methylethylketone, acetone, cyclohexanone and cyclobutanone, affords imine compounds crystallizing in polar space groups (Pna21 or Cc). For all the compounds synthesized, the crystal structure was determined by single crystal X-ray analysis and second harmonic generation experiments were performed on powder samples. The imine obtained using acetone shows solid state polymorphism with unusual behaviour; three different crystal phases have been identified (phases I, II and III), all having the same polar space group Pna21, and the transitions from I to II and from III to II are topotactic, i.e. single-crystal-to-single-crystal. During the irreversible transition from phase I to II, the polar axis undergoes a strong compression (about 15%) and single crystals of the parent phase are violently shattered into single crystal fragments of the new phase, while in the reversible transition from phase III to II, the polar axis expands (about 14%) and the integrity of single crystals is preserved.

Photoelectron spectrum of ammonia, a test case for the calculation of Franck-Condon factors in molecules undergoing large geometrical displacements upon photoionization.

The vibrational structure of the photoelectron spectrum of ammonia, the simplest molecule undergoing a large displacement of its equilibrium geometry upon photoionization, is analyzed by evaluating the Franck-Condon integrals at the anharmonic level of approximation. It is shown that if the rectilinear Cartesian representation of normal modes is adopted Duschinskys transformation yields a too large displacement of the bond distance coordinate, with the appearance of several progressions which are not observed in the experimental spectrum. This apparent failure is completely corrected by the inclusion of anharmonic couplings between the principal active mode, the out of plane bending of the planar cation, and the totally symmetric stretching mode, leading to a satisfying reproduction of the observed spectrum and to a more convincing assignment of the weaker progression observed in the high-resolution spectrum.

Stacking interactions between adenines in oxidized oligonucleotides.

The effects of stacking interactions on the oxidation potentials of single strand oligonucleotides containing up to four consecutive adenines, alternated with thymines and cytosines in different sequences and ratios, have been determined by means of differential pulse voltammetry. Voltammetric measurements point toward the establishment in solution of structured oligonucleotide conformations, in which the nucleobases are well stacked altogether. Molecular dynamics simulations confirm that finding, indicating that single strands assume geometrical parameters characteristic of the B-DNA form. The analysis of the voltammetric signals in terms of a simple effective tight binding quantum model leads one to infer a robust set of parameters for treating hole transfer in one-electron-oxidized DNA containing adenines and thymines.

Proton transfer in oxidized adenosine self-aggregates

The UV-vis and the IR spectra of derivativized adenosine in dichloromethane have been recorded during potentiostatic oxidation at an optically transparent thin layer electrode. Oxidized adenosine shows a broad Zundel like absorption extending from 2800 up to 3600 cm(-1), indicating that a proton transfer process is occurring. Theoretical computations predict that proton transfer is indeed favored in oxidized 1:1 self-association complexes and allow to assign all the observed transient spectroscopic signals.

The oxidization potential of AA steps in single strand DNA oligomers

Adiabatic ionization energies of short (3-mers) single strand oligonucleotides containing cytosine and adenine have been computed and compared with the oxidation potentials determined by differential pulse voltammetry. Different functionals and different ways of compensating backbone electric charges have been employed. In line with the experimental results, a lowering of the oxidation potential is predicted for oligomers containing two consecutive adenines. The computed oxidation potential shifts are slightly lower than the experimental one and in most of the cases the spin density distribution of the oligonucleotide radical cations is localized over a single adenine. Both results depend on electrostatic interactions between adenine and cytosine, which stabilize the radical cation containing a single adenine and make the two adenines inequivalent in sequences possessing two consecutive adenines.

Competitive H-bonding synthons in organic hydrazides

A theoretical, statistical and crystallographic analysis of the H-bonding patterns in organic monohydrazides is presented. The theoretical analysis has shown that the conformation of the hydrazido group with the two amino H atoms staggered with respect to the amide bond is energetically more favoured. Assuming this conformation, four intermolecular H-bonding patterns can be reasonably foreseen, two forming chains, C(4) and C22(8), and two forming rings, R22(10) or R22(6). The frequency of occurrence of the four patterns in the set of crystal structures of hydrazides retrieved from CSD was evaluated. In particular, it was found that the four motifs are present in 79% of the total number of crystal structures of hydrazides found in CSD. Finally, the crystal structures of four new benzohydrazides having additional H-bonding donor or acceptor groups in the para position are presented and discussed with reference to the H-bonding patterns.

One-pot highly diastereoselective annulation to N-unprotected tetrasubstituted 2-pyrrolines

A one-pot DABCO-catalysed Michael addition of glycine imine-derived esters to trans-2-aroyl-3-arylacrylonitriles followed by a deprotection/cyclization/tautomerization sequence afforded tetrasubstituted N-unprotected trans-2-pyrrolines in up to 96% yield.

Polar crystals in imines of 4-hydroxybenzohydrazide: a comparison between racemic and enantiomorphic crystals

Through the reaction of 4-hydroxybenzohydrazide with rac-3-methylcycplopentanone and R-(+)-3-methylcyclopentanone, racemic and enantiomorphic imines were obtained and characterized in the solid state. The racemic imine crystallizes either in the orthorhombic polar space group Pna21, and the crystal structure is polar and completely analogous to the structure of similar non-chiral imines we have recently studied, or in the monoclinic centrosymmetric space group P21/n. The enantiomorphic imine crystallizes in the monoclinic polar space group P21, but the crystal structure is actually non-polar and shows significant pseudo-centrosymmetry being quasi-isomorphous with the centrosymmetric structure of the racemic imine. The density of the enantiomorphic pseudocentric crystals is significantly higher than the polar orthorhombic racemic crystals and almost equal to the centrosymmetric racemic crystals.