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Biomedical subjects

Nico van der Vegt

Publications and source records attributed to Nico van der Vegt.

4 recordsLinked to original sources

Osmotic coefficients of atomistic NaCl (aq) force fields.

Solvated ions are becoming increasingly important for (bio)molecular simulations. But there are not much suitable data to validate the intermediate-range solution structure that ion-water force fields produce. We compare six selected combinations of four biomolecular Na-Cl force fields and four popular water models by means of effective ion-ion potentials. First we derive an effective potential at high dilution from simulations of two ions in explicit water. At higher ionic concentration multibody effects will become important. We propose to capture those by employing a concentration dependent dielectric permittivity. With the so obtained effective potentials we then perform implicit solvent simulations. We demonstrate that our effective potentials accurately reproduce ion-ion coordination numbers and the local structure. They allow us furthermore to calculate osmotic coefficients that can be directly compared with experimental data. We show that the osmotic coefficient is a sensitive and accurate measure for the effective ion-ion interactions and the intermediate-range structure of the solution. It is therefore a suitable and useful quantity for validating and parametrizing atomistic ion-water force fields.

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Modeling multibody effects in ionic solutions with a concentration dependent dielectric permittivity.

We report a new strategy to parametrize effective ion-ion potentials for implicit solvent simulations of charged systems. The effective potential includes a pair term and a Coulomb term that by means of a concentration dependent dielectric permittivity takes into account multibody effects. We demonstrate that this approach allows us to accurately reproduce the solution osmotic properties and the ion coordination up to concentrations of 2.8 M aqueous NaCl.

Journal Article↗

Modeling of molecular packing and conformation in oligofluorenes.

We describe the application of molecular modeling to study problems related to the packing and conformation of oligofluorene molecules in the solid state. First of all, we describe an improved force field for oligofluorenes. The model is based on the MM3 force field for the intramolecular degrees of freedom, but it relies on ab initio calculations for the torsion potential between two monomers and the electrostatic interactions. We also report ab initio calculations of the interaction potentials between fluorene and fluorenone units. The force field has been tested on the crystal structures of a fluorene monomer, a dimer, and a pentamer containing a fluorenone at the center. It has then been employed to study conformational defects of the chains, both in vacuo and in the bulk. We find that certain modes of inversion from right-handed to left-handed helices are also possible within the constraining environment of the crystals. The effect of the presence of two different types of side chains has been also addressed. Finally, the possibility of having two fluorene units parallel and close to each other has been investigated as a model of a ground-state precursor of an excimer. Our simulations show that this configuration is sterically and energetically unfavorable so that formation of an excimer following optical excitation appears to be unlikely.

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Dual-scale modeling of benzene adsorption onto Ni(111) and Au(111) surfaces in explicit water.

We present a multiscale modeling approach for studying interactions of organic molecules with metal surfaces in explicit water. The approach is based on combining adsorption energies of isolated molecules on transition metal surfaces calculated by ab initio density functional methods and classical molecular dynamics simulations using atomistically detailed force fields. The interaction of benzene with Ni(111) and Au(111) surfaces was studied. It is shown that a strong affinity of water for the hydrophilic surfaces makes benzene adsorption on Au thermodynamically unfavorable, while on Ni there is no preference. The work presented here serves as a first step in modeling the interactions of larger organic molecules with metal surfaces.

Adsorption↗