Conformational analysis of Gly-Ala-NHMe in D(2)O and DMSO solutions: a two-dimensional infrared spectroscopy study.

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.

Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field.

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.

Structure versus solvent effects on nonlinear optical properties of push-pull systems: a quantum-mechanical study based on a polarizable continuum model.

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.