PubMed Health⌕ Search

Biomedical subjects

P Cabral do Couto

Publications and source records attributed to P Cabral do Couto.

3 recordsLinked to original sources

An all-atom force field for metallocenes.

A new all-atom force field, for the molecular modeling of metallocenes was constructed. Quantum chemical calculations were performed to obtain several force field terms not yet defined in the literature. The remainder were transferred from the OPLS-AA/AMBER framework. The parametrization work included the obtention of geometrical parameters, torsion energy profiles, and distributions of atomic charges that blend smoothly with the OPLS-AA specification for a variety of organic molecular fragments. Validation was carried out by comparing simulated and experimental data for five different ferrocene derivatives in the crystalline phase. The present model can be regarded as a step toward a general force field for metallocenes, built in a systematic way, easily integrated with OPLS-AA, and transferable between different metal-ligand combinations.

Journal Article↗

The Kohn-Sham density of states and band gap of water: from small clusters to liquid water.

Electronic properties of water clusters (H2O)(n), with n=2, 4, 8, 10, 15, 20, and 30 molecules were investigated by sequential Monte Carlo/density-functional theory (DFT) calculations. DFT calculations were carried out over uncorrelated configurations generated by Monte Carlo simulations of liquid water with a reparametrized exchange-correlation functional that reproduces the experimental information on the electronic properties (first ionization energy and highest occupied molecular orbital-lowest unoccupied molecular orbital gap) of the water dimer. The dependence of electronic properties on the cluster size (n) shows that the density of states (DOS) of small water clusters (n>10) exhibits the same basic features that are typical of larger aggregates, such as the mixing of the 3a1 and 1b1 valence bands. When long-ranged polarization effects are taken into account by the introduction of embedding charges, the DOS associated with 3a1 orbitals is significantly enhanced. In agreement with valence-band photoelectron spectra of liquid water, the 1b1, 3a1, and 1b2 electron binding energies in water aggregates are redshifted by approximately 1 eV relative to the isolated molecule. By extrapolating the results for larger clusters the threshold energy for photoelectron emission is 9.6+/-0.15 eV (free clusters) and 10.58+/-0.10 eV (embedded clusters). Our results for the electron affinity (V0=-0.17+/-0.05 eV) and adiabatic band gap (E(G,Ad)=6.83+/-0.05 eV) of liquid water are in excellent agreement with recent information from theoretical and experimental works.

Chemistry, Physical↗

Polarization effects and charge separation in AgCl-water clusters.

Structural, energetic, vibrational, and electronic properties of salt ion pairs (AgCl and NaCl) in water (W) clusters were investigated by density functional theory. In agreement with recent theoretical studies of NaCl-water clusters, structures where the salt ion pair is separated by solvent molecules or solvent separated ion pair (SSIP) were found in AgCl-W(6) and AgCl-W(8) aggregates. Our results indicate that for small AgCl-water clusters, contact ion pair (CIP) structures are energetically more stable than SSIP, whereas an opposite tendency was observed for NaCl-water clusters. In comparison with CIP, SSIP are characterized by extensive electronic density reorganization, reflecting enhanced polarization effects. A major difference between AgCl-water and NaCl-water CIP aggregates concerns charge transfer. In AgCl-water CIP clusters, charge is transferred from the solvent (water) to the ion pair. However, in NaCl-water CIP clusters charge is transferred from the ion pair to the water molecules. The electronic density reorganization in the aggregates was also discussed through the analysis of electronic density difference isosurfaces. Time dependent density functional theory calculations show that upon complexation of AgCl and NaCl with water molecules, excitation energies are significantly blueshifted relative to the isolated ion pairs ( approximately 2 eV for AgCl-W(8) SSIP). In keeping with results for NaI-water clusters [Peslherbe et al., J. Phys. Chem. A 104, 4533 (2000)], electronic oscillator strengths of transitions to excited states are weaker for SSIP than for CIP structures. However, our results also suggest that the difference between excitation energies and oscillator strengths of CIP and SSIP structures may decrease with increasing cluster size.

Journal Article↗