PubMed Health⌕ Search

Biomedical subjects

Evert Jan Meijer

Publications and source records attributed to Evert Jan Meijer.

7 recordsLinked to original sources
PubMed2006

First principles and experimental 1H NMR signatures of solvated ions: The case of HCl(aq).

A combined experimental and ab initio study is presented of the 1H NMR chemical shift distribution of aqueous hydrogen chloride solution as a function of acid concentration, based on Car-Parrinello molecular dynamics simulations and fully periodic NMR chemical-shift calculations. The agreement of computed and experimental spectra is very good. From first-principles calculations, we can show that the individual contributions of Eigen and Zundel ions, regular water molecules, and the chlorine solvation shell to the NMR line are very distinct and almost independent of the acid concentration. From the computed instantaneous NMR distributions, it is further possible to characterize the average variation in hydrogen-bond strength of the different complexes.

Journal Article↗
PubMed2006

Density functional theory study of tetrathiafulvalene and thianthrene in acetonitrile: structure, dynamics, and redox properties.

The redox potentials of the organic compounds tetrathiafulvalene (TTF) and thianthrene (TH) in an explicit aprotic polar solvent, acetonitrile, have been computed using ab initio molecular dynamics simulation based on a Gaussian basis set methodology. The density functional description of the pure solvent yields a diffuse and mobile liquid, with structural and dynamical properties that are in good agreement with earlier classical models and experiment. Molecular dynamics simulation of both solute species in their neutral and radical cation states combined with free energy difference calculations result in estimates for the redox potentials of the reactions TH*+ + TTF --> TH + TTF*+ and TH2+ + TTF*+ --> TH*+ + TTF2+. The obtained values are 0.95 +/- 0.06 and 1.09 +/- 0.06 V, respectively, in excellent agreement with experimental data of 0.93 and 1.08 V. Our computational approach is based on Marcus theory, assuming quadratic free energy surfaces. We show that this approximation can still be accurate in systems, such as TH, that undergo a significant change in geometry upon oxidation. Furthermore, despite the different localization of the spin density in the radical cations, results based on self-interaction-corrected functionals and on standard generalized gradient approximations are identical to within 10 meV.

Journal Article↗
PubMed2005

Phosphorus: first principle simulation of a liquid-liquid phase transition.

We report a Car-Parrinello molecular dynamics study of the liquid-liquid phase transition in phosphorus. We employed a gradient corrected density functional (B-LYP) to describe the electronic structure and performed simulations at constant pressure. Upon increasing pressure we observed, along the 1500 K isotherm, a structural transition converting the molecular P4 liquid into an atomic liquid with a network structure. Our calculations suggest this transition to be first order with a discontinuous density increase accompanied by an insulator into metal transition. The transition pressure is significantly higher than obtained by employing the less accurate local density functional (LDA) [Morishita, Phys. Rev. Lett. 87, 105701 (2001)], which matches the experimental value for the pressure. We argue why the LDA result should be considered fortuitous. The change of the calculated structure factor upon the transition shows the same trend as experimentally observed. Analysis of the structural changes during the phase transition revealed that a chain of linked and opened up ("butterfly") P4 molecules may serve as a seed triggering the transition from the molecular to the network phase.

Journal Article↗
PubMed2005

Modeling the phase diagram of carbon.

We determined the phase diagram involving diamond, graphite, and liquid carbon using a recently developed semiempirical potential. Using accurate free-energy calculations, we computed the solid-solid and solid-liquid phase boundaries for pressures and temperatures up to 400 GPa and 12 000 K, respectively. The graphite-diamond transition line that we computed is in good agreement with experimental data, confirming the accuracy of the employed empirical potential. On the basis of the computed slope of the graphite melting line, we rule out the hotly debated liquid-liquid phase transition of carbon. Our simulations allow us to give accurate estimates of the location of the diamond melting curve and of the graphite-diamond-liquid triple point.

Journal Article↗
PubMed2004

Density-functional theory-based molecular simulation study of liquid methanol.

We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials.

Journal Article↗
PubMed2003

Colloid-polymer mixtures in the protein limit.

We computed the phase-separation behavior and effective interactions of colloid-polymer mixtures in the "protein limit," where the polymer radius of gyration is much larger than the colloid radius. For ideal polymers, the critical colloidal packing fraction tends to zero, whereas for interacting polymers in a good solvent the behavior is governed by a universal binodal, implying a constant critical colloid packing fraction. In both systems the depletion interaction is not well described by effective pair potentials but requires the incorporation of many-body contributions.

Colloids↗