Biomedical subjects

Matteo Cococcioni

Publications and source records attributed to Matteo Cococcioni.

4 recordsLinked to original sources

PubMed2006

Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach.

Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on generalized-gradient approximations often fail to describe energetics, multiplet structures, reaction barriers, and geometries around the active sites. We suggest here an alternative approach, derived from the Hubbard U correction to solid-state problems, that provides an excellent agreement with correlated-electron quantum chemistry calculations in test cases that range from the ground state of Fe2 and Fe2- to the addition elimination of molecular hydrogen on FeO+. The Hubbard U is determined with a novel self-consistent procedure based on a linear-response approach.

Journal Article↗

PubMed2006

Realistic quantitative descriptions of electron transfer reactions: diabatic free-energy surfaces from first-principles molecular dynamics.

A general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the transfer of an electron at any given ionic configuration (the Marcus energy gap) is accurately assessed within ground-state density-functional theory via a novel penalty functional for oxidation-reduction reactions that appropriately acts on the electronic degrees of freedom alone. The self-interaction error intrinsic to common exchange-correlation functionals is also corrected by the same penalty functional. The diabatic free-energy surfaces are then constructed from umbrella sampling on large ensembles of configurations. As a paradigmatic case study, the self-exchange reaction between ferrous and ferric ions in water is studied in detail.

Electron Transport↗

PubMed2006

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution.

The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

Journal Article↗

PubMed2005

Electronic-enthalpy functional for finite systems under pressure.

We introduce the notion of electronic enthalpy for first-principles structural and dynamical calculations of finite systems under pressure. An external pressure field is allowed to act directly on the electronic structure of the system studied via the ground-state minimization of the functional E+PV(q), where V(q) is the quantum volume enclosed by a charge isosurface. The Hellmann-Feynman theorem applies, and assures that the ionic equations of motion follow an isoenthalpic dynamics. No pressurizing medium is explicitly required, while coatings of environmental ions or ligands can be introduced if chemically relevant. We apply this novel approach to the study of group-IV nanoparticles during a shock wave, highlighting the significant differences in the plastic or elastic response of the diamond cage under load, and their potential use as novel nanostructured impact-absorbing materials.

Journal Article↗