Biomedical subjects

Leonardo Bernasconi

Publications and source records attributed to Leonardo Bernasconi.

5 recordsLinked to original sources

PubMed2006

Long-range solvent effects on the orbital interaction mechanism of water acidity enhancement in metal ion solutions: a comparative study of the electronic structure of aqueous Mg and Zn dications.

We study the dissociation of water coordinated to a divalent metal ion center, M2+ = Mg2+, Zn2+ using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. First, the proton affinity of a coordinated OH- group is computed from gas-phase Mg2+(H2O)5(OH-), which yields a relative higher gas-phase acidity for a Zn2+-coordinated as compared to a Mg2+-coordinated water molecule, DeltapKa(gp) = 5.3. We explain this difference on the basis of a gain in stabilization energy of the Zn2+(H2O)5(OH-) system arising from direct orbital interaction between the coordinated OH- and the empty 4s state of the cation. Next, we compute the acidity of coordinated water molecules in solution using free-energy thermodynamic integration with constrained AIMD. This approach yields pKa Mg2+ = 11.2 and pKa Zn2+ = 8.4, which compare favorably to experimental data. Finally, we examine the factors responsible for the apparent decrease in the relative Zn2+-coordinated water acidity in going from the gas-phase (DeltapKa(gp) = 5.3) to the solvated (DeltapKa = 2.8) regime. We propose two simultaneously occurring solvation-induced processes affecting the relative stability of Zn2+(H2O)5(OH-), namely: (a) reduction of the Zn 4s character in solution states near the bottom of the conduction band; (b) hybridization between OH- orbitals and valence-band states of the solvent. Both effects contribute to hindering the OH- --> Zn2+ charge transfer, either by making it energetically unfavorable or by delocalizing the ligand charge density over several water molecules.

Acids↗

PubMed2005

Time-dependent density functional theory description of on-site electron repulsion and ligand field effects in the optical spectrum of hexaaquoruthenium(II) in solution.

Time-dependent density functional theory (TDDFT) and density functional-based molecular dynamics were used to simulate the finite temperature t(2g)5 e(g) <-- t(2g)6 absorption band of the Ru2+ hexahydrate coordination complex in aqueous solution. The (1)T1 <-- (1)A1 and (1)T2 <-- (1)A1 molecular term splitting of this transition, which is not accounted for by the Kohn-Sham excitation spectrum, is shown to be satisfactorily reproduced by TDDFT at the BLYP/ALDA level of theory. Comparison to the spectrum of the Ru2+ (H2O)6 complex in vacuo computed by similar density functional classical molecular dynamics methods leads to the observation that bulk solvation has a negligible effect on the position and the shape of the absorption profile.

Journal Article↗

PubMed2004

Density functional calculation of the electronic absorption spectrum of Cu+ and Ag+ aqua ions.

The UV absorption of aqueous Cu+ and Ag+ has been studied using Time Dependent Density Functional Theory (TDDFT) response techniques. The TDDFT electronic spectrum was computed from finite temperature dynamical trajectories in solution generated using the Density Functional Theory (DFT) based Ab Initio Molecular Dynamics (AIMD) method. The absorption of the two ions is shown to arise from similar excitation mechanisms, namely transitions from d orbitals localized on the metal center to a rather delocalized state originating from hybridization of the metal s orbital to the conduction band edge of the solvent. The ions differ in the way the spectral profile builds up as a consequence of solvent thermal motion. The Cu+ absorption is widely modulated, both in transition energies and intensities by fluctuations in the coordination environment which is characterized by the formation of strong coordination bonds to two water molecules in an approximately linear geometry. Though, on average, absorption intensities are typical of symmetry forbidden transitions of metal ions in the solid state, occasionally very short (<100 fs) bursts in intensity are observed, associated with anomalous Cu-H interactions. Absorption by the Ag+ complex is in comparison relatively stable in time, and can be interpreted in terms of the energy splitting of the metal 4d manifold in an average crystal field corresponding to a fourfold coordination in a distorted tetrahedral arrangement. Whereas the spectral profile of the Ag+ aqua ion is in good agreement with experiment, the overall position of the band is underestimated by 2 eV in the BLYP approximation to DFT. The discrepancy with experiment is reduced to 1.3 eV when a hybrid functional (PBE0) is used. The remaining inaccuracy of TDDFT in this situation is related to the delocalized character of the target state in d-->s transitions.

Journal Article↗

PubMed2004

Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction.

Electronic states and solvation of Cu and Ag aqua ions are investigated by comparing the Cu(2+) + e(-)--> Cu(+) and Ag(2+) + e(-)--> Ag(+) redox reactions using density functional-based computational methods. The coordination number of aqueous Cu(2+) is found to fluctuate between 5 and 6 and reduces to 2 for Cu(+), which forms a tightly bound linear dihydrate. Reduction of Ag(2+) changes the coordination number from 5 to 4. The energetics of the oxidation reactions is analyzed by comparing vertical ionization potentials, relaxation energies, and vertical electron affinities. The model is validated by a computation of the free energy of the full redox reaction Ag(2+) + Cu(+) --> Ag(+) + Cu(2+). Investigation of the one-electron states shows that the redox active frontier orbitals are confined to the energy gap between occupied and empty states of the pure solvent and localized on the metal ion hydration complex. The effect of solvent fluctuations on the electronic states is highlighted in a computation of the UV absorption spectrum of Cu(+) and Ag(+).

Journal Article↗

PubMed2003

Multipoles and interaction potentials in ionic materials from planewave-DFT calculations.

Oxide potentials which transfer well between different materials have to account explicitly for many-body contributions to the interaction potentials between the ions. These include dipole and quadrupole polarization effects and the compression and deformation of an oxide ion by its immediate coordination environment. Such complex potentials necessarily involve many parameters. We examine how the results of ab initio electronic structure calculations, based upon planewave DFT methods, on general configurations of ions derived from simulations at finite temperature, may be used to parameterize an "aspherical ion method" (AIM) potential (A. J. Rowley, P. Jemmer, M. Wilson and P. A. Madden, J Chem. Phys., 1998, 108, 10209). Dipoles and quadrupoles on the individual ions are obtained via a transformation of the Kohn Sham orbitals to localized orbitals on each ion, which enables a distorted charge density for each ion to be obtained. The dipoles and quadrupoles appearing in polarization parts of the AIM potential are fit to those obtained from the ab initio ionic charge densities obtained in this way. The remaining parts of the potential, describing short-range repulsive interactions between ions with compressed and deformed charge densities, are fit to the ab initio forces and the stress tensor. By using a sufficiently large and varied set of configurations on which to carry out this optimization, an excellent transferable potential is obtained.

Journal Article↗