M. D'Alessandro

Theoretical characterization of electronic states in interacting chemical systems

In this article we characterize, by means of the perturbed matrix method, the response of the electronic states of a chemical system to the perturbing environment. In the theory section we describe in detail the basic derivations and implications of the method, extending its theoretical framework to treat possible excitonic effects, and we show how to characterize the perturbed electronic states. Finally, by using a set of chemical systems interacting with complex atomic-molecular environments, we describe the nature and general features of the electronic state mixing and transitions as caused by atomic and molecular interactions.

Structural, Thermodynamic, and Kinetic Properties of Gramicidin Analogue GS6 Studied by Molecular Dynamics Simulations and Statistical Mechanics

Gramicidin S (GS) analogues belong to an important class of cyclic peptides, characterized by an antiparallel double‐stranded β‐sheet structure with Type II′ β‐turns. Such compounds can be used as model systems to understand the folding/unfolding process of β‐hairpins and more in general of β‐structures. In the present study, we specifically investigate the folding/unfolding behavior of the hexameric Gramicidin S analogue GS6 by using all‐atoms molecular dynamics (MD) simulations at different temperatures, coupled to a statistical mechanical model based on the Quasi Gaussian Entropy theory. Such an approach permits to describe the structural, thermodynamic, and kinetic properties of the peptide and to quantitatively characterize its folding/unfolding transitions.