Andrea Pieretti

Hydrogen bonding in barbituric and 2-thiobarbituric acids: a theoretical and FT-IR study

Abstract The effects of intermolecular hydrogen bonding on the molecular properties of barbituric acid (BA) and thiobarbituric acid are discussed on the basis of density functional theory calculations. B3LYP methods were applied to monomers and cyclic dimers. Trimer and hexamer of BA were studied as examples where several CO and NH groups are involved in hydrogen bonding. The theoretical IR spectra of monomers and all oligomers here considered are compared with the FT-IR spectra measured in Ar and nitrogen matrices at different concentrations.

Matrix and ab initio infrared spectra of thiourea and thiourea-d4

Abstract The FTIR spectrum of thiourea and thiourea-d 4 isolated in argon and nitrogen matrices are presented for the first time and discussed in terms of normal modes predicted by ab initio calculations. Vibrational frequencies, IR intensities and isotopic shifts obtained from the density functional B3-LYP/6-31+G(2d,p) calculations show the most satisfactory agreement with experiments. In contrast with previous results, the present theoretical study indicates non-planarity of the molecule. The lowest energy structure has C 2 symmetry and the less stable isomers has C s symmetry. Experimental data clearly indicate the presence of a single isomer in the vapor. The decomposition of thiourea for vaporization temperature over 410 K is also discussed.

Dimerisation of urea in water solution: a quantum mechanical investigation

The effect of water solvation on the structure and stability of cyclic dimers of urea has been investigated with the aid of density functional theory at the B3LYP/6-311++G** level. Several hydration models have been discussed. Specific solvent effects have been simulated through single and multiple water-urea interactions involving all the hydration sites of urea. The bulk solvent effects have been estimated through polarised continuum models. Under all the hydration patterns cyclic dimers continue to be stable structures although the solvent weakens the urea-urea interaction. Single and multiple specific urea-water interactions are competitive with urea dimerisation. The anticooperative nature of the two intermolecular interactions is largely due to the changes on sigma- and pi-electron density of urea caused by hydrogen bonding with water. The stability of the dimer is however, lost within a few ps when the hydrated dimer is described by a quantum mechanical molecular dynamics approach (ADMP). The cyclic dimer evolves towards structures where urea molecules are linked not more directly but through water molecules which have a bridge function.

On the hydrogen bonding in uracil: its effect on the vibrational spectrum

The effects of intermolecular hydrogen bonding on the vibrational frequencies of uracil are discussed on the basis of ab initio calculations. DFT methods are applied to calculated vibrational frequencies of various uracil dimers, namely six cyclic structures and four T-shaped arrangements, as well as eight uracil–water complexes. Frequency shifts experienced by some normal modes in the dimerisation are clearly correlated with acidity or basicity of the interaction sites. Interaction energies and frequency changes indicate that cooperativity plays a fundamental role in a self-association process. Moreover the cooperative effects increase their contribution with the strength of hydrogen bonding. The theoretical IR spectra of all the hydrogen bonded uracils considered here are compared with the FT-IR spectra of uracil and thymine measured in an N2 matrix at different concentrations.

SO2Cl2, SOCl2: energy dispersive X-ray diffraction, ab initio and molecular dynamics calculation

Abstract This work reports a new protocol for achieving microscopic structural information from theoretical (quantum-chemical (QC) and molecular dynamic (MD) calculations) and experimental methods (X-ray diffraction). The Lennard–Jones (L–J) parameters of the force field (FF) fit satisfactorily the X-ray diffraction results of the liquid samples. The study has been carried out on SOCl2 and SO2Cl2 molecular liquids.

Hydration of diazoles in water solution: pyrazole. A theoretical and X-ray diffraction study

The local structure of the hydration of pyrazole has been analysed through static and dynamical microsolvation models described by quantum mechanical methods. Then, a reliable classical force field of pyrazole has been obtained on the basis of the quantum mechanical results and the dynamical properties of aqueous pyrazole solutions have been studied by molecular dynamics simulations. Finally, the structure of pyrazole-water solutions at different concentrations has been investigated by energy dispersive X-ray diffraction and experimental results have been compared to calculations. This comparison provides both a tool for interpretation of experiments and a way to validate the computational protocol.

Complexes of dihydroxybenzenes with carbon monoxide by DFT calculations and FT-IR matrix spectroscopy

Abstract Weakly bound complexes of dihydroxybenzenes and nitrophenols with carbon monoxide were the objects of theoretical studies based on the Becke–Lee–Parr density functional. Stability and vibrational spectra of all stable bimolecular complexes were determined and the theoretical results were integrated by matrix isolation FT-IR spectroscopy measurements.

From DFT Cluster Calculations to Molecular Dynamics Simulation of N2 Formation on a Silica Model Surface

B3LYP-DFT electronic structure cluster calculations have been performed to evaluate the adsorption properties of N and N2 interacting with Si x O y clusters in a given adsorption site. To check the convergence of the calculated binding energy, clusters of different size were used in the calculations. As expected, the N atom is chemisorbed, E b ≅ 2.75eV, while N2 is weakly physisorbed. The ab initio results were used to build three PES of the LEPS-type having different activation barrier. The obtained PES have been used in the semiclassical scattering equations and the dynamics of the N2 formation after atom recombination on a model silica surface was studied in great detail.

Combined FTIR Matrix Isolation and Density Functional Studies of Indole-3-Pyruvic Acid Molecule. Spectroscopic Evidence of Gas-Phase Tautomerism

The vibrational spectrum of matrix-isolated indole-3-pyruvic acid has been studied aiming to obtain information about the structures of the stable vapour-phase forms of the molecule. Together with results from theoretical density functional calculations, the spectroscopic data enable to undertake an attribution for most of the observed bands. The FTIR spectrum of crystalline indole-3-pyruvic acid has been compared with that of matrix isolation study.