Success in designing and tailoring solid-state reactions depends on the knowledge of the mechanisms regulating the reactivity at the microscopic level. In spite of several attempts to rationalize the reactivity of crystals, the question of the existence of a critical distance for a reaction to occur remains unsolved. In this framework, the role of lattice phonons, which continuously tune the relative distance and orientation of the molecules, is still not fully understood. Here, we show that at the onset of the transformation of crystalline benzene to an amorphous hydrogenated carbon the intermolecular C-C distance is always the same (about 2.6 A) once collective motions are taken into account, and it is independent of the pressure and temperature conditions. This conclusion is supported by first-principles molecular-dynamics simulations. This is a clear demonstration of the role of lattice phonons in driving the reactivity in the crystalline phase by fine-tuning of the nearest-neighbour distances. The knowledge of the critical C-C distance can be crucial in planning solid-state reactions at moderate pressure.

The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

The chemical transformation of benzene under pressure is investigated, at room temperature and at 100 K, by means of infrared spectroscopy. Pressurization-decompression cycles in the 0–50 GPa pressure range have been performed to achieve the complete transformation of the monomer. The yellow-brownish recovered sample has been identified as an amorphous hydrogenated carbon (a-C:H). A correlation has been established between the pressure behavior of the frequencies of both Raman and infrared internal modes, and the corresponding vibrational energies in the S1 excited state (1B2u). From this comparison we conclude that pressure induces a mixing between the ground and the S1 electronic states. The increased ring flexibility enhances the interactions among nearest-neighbor molecules inducing the formation of a network of interconnected benzene units where the aromatic character is lost. The bond breaking mainly occurs during the decompression cycle favored by the density decrease. Radical species form in this stage and rapidly propagate to give the denser a-C:H final product.

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