Translocation of flexible and tensioned ssDNA through designed hydrophobic nanopores with two constrictions.

Protein-inspired nanopores with hydrophobic constriction regions have previously been shown to offer some promise for DNA sequencing. Here we explore a series of pores with two hydrophobic constrictions. The impact of nanopore radius, the nature of residues that define the constriction region and the flexibility of the ssDNA is explored.

Interaction of Metamitron and Fenhexamid with Ca -Montmorillonite Clay Surfaces: A Density Functional Theory Molecular Dynamics Study.

Metamitron (Meta), an herbicide, and fenhexamid (Fen), a fungicide, are authorized by the European Union to be used in agriculture. This article reports theoretical calculations about Meta and Fen in interaction with a clay surface: a Ca-montmorillonite (Mont). Conformational searches have been performed thanks to Car-Parrinello molecular dynamics simulations from which geometries have been extracted.

Theoretical study of the atrazine pesticide interaction with pyrophyllite and Ca(2+) -montmorillonite clay surfaces.

Atrazine, a pesticide belonging to the s-triazine family, is one of the most employed pesticides. Due to its negative impact on the environment, it has been forbidden within the European Union since 2004 but remains abundant in soils. For these reasons, its behavior in soils and water at the atomic scale is of great interest.

Attenuated MP2 with a Long-Range Dispersion Correction for Treating Nonbonded Interactions.

Attenuated second order Møller-Plesset theory (MP2) captures intermolecular binding energies at equilibrium geometries with high fidelity with respect to reference methods, yet must fail to reproduce dispersion energies at stretched geometries due to the removal of fully long-range dispersion. For this problem to be ameliorated, long-range correction using the VV10 van der Waals density functional is added to attenuated MP2, capturing short-range correlation with attenuated MP2 and long-range dispersion with VV10. Attenuated MP2 with long-range VV10 dispersion in the aug-cc-pVTZ (aTZ) basis set, MP2-V(terfc, aTZ), is parametrized for noncovalent interactions using the S66 database and tested on a variety of noncovalent databases, describing potential energy surfaces and equilibrium binding energies equally well.