Understanding (and possibly solving) chemical problems, especially of industrial relevance, is our main activity. To this end we use the armory of tools known as computational chemistry. The areas of interest span from understanding structure and function relationship in organometallic compounds, to unraveling the mechanistic of catalysts at work, to soft condensed matter simulations. Finally, we are not shy to tackle systems of biological interest. In all cases we try to interact as much as possible with experimentalists. Often we are unsatisfied with the available tools and/or models and we develop new ones. Particular interest is devoted to development of methods for modelling systems across time and length scales.

• Structure function relationship in organometallic compounds

• Mechanism of catalyst at work

• Host guest interactions in nanoporous materials

• Systems of biological interest

Quantum Mechanical Studies.

We have been happy that bioinformatics groups asked for our QM expertise. Of course, they provided all the biological background and expertise. This way, we contributed to characterize rhodamine, a fluorescent probe used to follow dynamics of proteins. Recently, we started to work on H-bonded nucleic base complexes, and we contributed to the first characterization of the full set of the nine tertiary interactions in tRNA, see Figure. Particular attention has been focused on the effect of chemical modifications and of metal binding.

Schematic representation of the tRNA standard structure. Nucleotides involved in tertiary interactions are enclosed in colored squares.

Classical and Steered Molecular Dynamics Studies.

Interaction of Synthetic Polymers and Biomembranes. The understanding of interactions of polyethylene glycol (PEG) or polyethylenoxide (PEO) with biological interfaces has important technological application in industry and in medicine. In collaboration with Danilo Roccatano (International University Bremen, Germany) and Sandeep Pal (International Centre for Life Newcastle, UK) we studied structural and dynamical properties of the PEO at dimyristoylphospatidylcholine (DMPC) bilayer/water interface by Molecular Dynamics (MD) and Steered Molecular Dynamics (SMD)

DMPC density profile (dotted line) and the running averaged force from pulling experiments (bold line) versus Z distance of the PEO centre of mass. The insets on right show snapshots of the trajectory along one of the pulling experiments. PEO chain is in yellow.

References
1) Sandeep Pal, Giuseppe Milano, Danilo Roccatano, "Synthetic Polymers and Biomembranes. How Do They Interact?: Atomistic Molecular Dynamics Simulation Study of PEO in Contact with a DMPC Lipid Bilayer", J. Phys. Chem. B In press

• Development of computational tools