Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: the vertical transition approximation.

In this paper we describe in detail a general and efficient methodology, based on the perturbed matrix method and molecular dynamics simulations, to model UV-Vis absorption and emission spectra including vibrational and conformational effects. The basic approximation used is to consider all the chromophore atomic coordinates as semiclassical degrees of freedom, hence allowing the calculation of the complete spectral signal by using the electronic vertical transitions as obtained at each possible chromophore configuration, thus including the contributions of vibrations and conformational transitions into the spectrum. As shown for the model system utilized in this paper, solvated 1-phenyl-naphthalene, such an approximation can be rather accurate to reproduce the absorption and emission spectral line shape and properties when, as it often occurs, the vertical vibronic transition largely overlaps the other non-negligible vibronic transitions.

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.

Ordered and chaotic dynamics of collective variables in a butane molecule.

We have simulated the dynamics of a butane molecule and computed the time evolution of two sets of collective variables: (a) internal variables (stretchings, bendings, and dihedral angle) and (b) variables derived from a principal component analysis (PCA). We have characterized each collective variable by a coherence time, the time needed to develop its chaotic behavior. The coherence times diminish significantly when the temperature is raised into and above the range where conformational transitions of the dihedral angle set in. Below this transition region the coherence times of some variables reach hundreds of picoseconds (principal components) or even nanoseconds (internal variables); moreover, there are large differences among variables, as their coherence time can be much larger or much smaller than the Lyapunov time of the whole molecule. This result reflects the prediction of Nekhoroshev's theorem. Crossing the transition region, the coherence times of both sets of variables drop to few picoseconds, and the differences among variables diminish. Still, the coordinates and velocities characterized by the largest fluctuations in the PCA appear to be also the most coherent ones, below and above the transition region.

On the effect of a point mutation on the reactivity of CuZn superoxide dismutase: a theoretical study.

In this paper, we investigate the effects of a point mutation on the enzymatic activity of copper-zinc superoxide dismutase, which we recently studied in detail by means of a theoretical-computational procedure. Comparison of the reactivity of the initial catalytic steps in this mutant (G93A mutation far from the active site) with our previous data, reveals the beautiful mechanical-dynamical architecture of the enzyme, altered by such an apparently irrelevant mutation. Finally, our results suggest a possible atomic-molecular-based explanation for the mutant-pathology correlation, in line with the most recent experimental data.

Coherent dynamics in a butane molecule.

We have simulated by molecular dynamics a single molecule of butane in a thermal bath at different temperatures. We have found that the collective degrees of freedom of the essential dynamics are endowed with quite different degrees of coherence, and that those subject to the largest fluctuations are also the most coherent, that is, the least chaotic. We suggest that this pattern may be characteristic also of larger molecules. A detailed assessment of the degree of coherence has been obtained by computing in the tangent space the whole set of generalized coherence angles.

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 beta-sheet structure with Type II' beta-turns. Such compounds can be used as model systems to understand the folding/unfolding process of beta-hairpins and more in general of beta-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.

Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study.

By using the quasi Gaussian entropy theory in combination with molecular dynamics simulations and the perturbed matrix method, we investigate the ground and excited state thermodynamics of aqueous carbon monoxide. Results show that the model used is rather accurate and provides a great detail in the description of the excitation thermodynamics.

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: solvated carbon monoxide, a test case.

In this paper we extend the perturbed matrix method by explicitly including the nuclear degrees of freedom, in order to treat quantum vibrational states in a perturbed molecule. In a previous paper we showed how to include, in a simple way, nuclear degrees of freedom for the calculation of molecular polarizability. In the present work we extend and generalize this approach to model vibroelectronic transitions, requiring a more sophisticated treatment.