In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector. A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained.

A quantum mechanical investigation on the effects of the solvent and the structure on nonlinear optical activity of a class of merocyanine compounds has been conducted. The interplay of the two effects on the first hyperpolarizability, computed at density functional theory and second-order Møller-Plesset level, has been analyzed in combination with ground state properties and geometries and excited state energies and dipoles. A critical analysis of the simplified two-level model has also been presented.

A relevant number of experiments on short peptides has been performed in recent years. One of the major problems rises from the simultaneous presence of slightly different conformers at equilibrium in solution. In the present paper, the conformational characteristics of the Gly-l-Ala-Methyl amide dipeptide in D2O and DMSO solutions are investigated by nonlinear IR spectroscopy. The pump-probe scheme with ultrashort mid-infrared pulses, in the Amide I region, is used to determine the mutual orientation of the two C═O bonds and the dynamics due to solute-solvent interactions. The coupling between Amide I modes is evaluated from both linear and 2D spectra. The interconversion between the different conformations occurs on time scales longer than the vibrational lifetime, and the spectral diffusion observed in 2D spectra is attributed to the solvent dynamics. Quantum mechanical calculations and molecular dynamics simulations are performed to identify the most stable geometries. By comparing the experimental and the theoretical data, we establish the prevalence of β-like polar conformers in both water and DMSO solvents.

Multi-phase ceramics based on ZrB 2 , TiB 2 and doped with CrB 2 and SiC were prepared by powder metallurgy and hot pressing to explore the possibility of obtaining multi-scale microstructures by super-saturation of complex (Zr,Ti,Cr)B 2 solid solutions. Core-shell structures formed in TiB 2 grains, whereas ZrB 2 appeared to form a homogeneous solid solution with the other metals. Precipitation of nano-inclusions within both micron-sized borides was assessed by transmission electron microscopy and thermodynamics elucidated the preferential formation of boride inclusions due to the specific sintering atmosphere. In addition, atomic size factors explicated the precipitation of CrB 2 nano-particles into ZrB 2 -rich grains and of ZrB 2 nano-particles into TiB 2 -rich grains. The hardness of the constituent phases measured by nanoindentation ranged from 36 to 43 GPa.