Pair interaction potentials with explicit polarization for molecular dynamics simulations of La(3+) in bulk water.

Pair interaction potentials (IPs) were defined to describe the La(3+)-OH(2) interaction for simulating the La(3+) hydration in aqueous solution. La(3+)-OH(2) IPs are taken from the literature or parametrized essentially to reproduce ab initio calculations at the second-order Moller-Plesset level of theory on La(H(2)O)(8) (3+). The IPs are compared and used with molecular dynamics (MD) including explicit polarization, periodic boundary conditions of La(H(2)O)(216) (3+) boxes, and TIP3P water model modified to include explicit polarization.

Structures and fragmentations of cobalt(II)-cysteine complexes in the gas phase.

The electronebulization of a cobalt(II)/cysteine(Cys) mixture in water/methanol (50/50) produced mainly cobalt-cationized species. Three main groups of the Co-cationized species can be distinguished in the ESI-MS spectrum: (1) the cobalt complexes including the cysteine amino acid only (they can be singly charged, for example, [Co(Cys)n- H]+ with n = 1-3 or doubly charged such as [Co + (Cys)2]2+); (2) the cobalt complexes with methanol: [Co(CH3OH)n- H]+ with n = 1-3, [Co(CH3OH)4]2+; and (3) the complexes with the two different types of ligands: [Co(Cys)(CH3OH) - H]+. Only the singly charged complexes were observed.

A coupled Car-Parrinello molecular dynamics and EXAFS data analysis investigation of aqueous Co(2+).

We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range.

Co2+ binding cysteine and selenocysteine: a DFT study.

In this paper we report structural and energetic data for cysteine and selenocysteine in the gas phase and the effect of Co(2+) complexation on their properties. Different conformers are analyzed at the DFT/B3LYP level of both bound and unbound species. Geometries, vibrational frequencies, and natural population analysis are reported and used to understand the activity of these species.

Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides.

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules.