Translocation of flexible and tensioned ssDNA through in silico 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. Our results show that aromatic residues slow down DNA translocation, and in the case of short DNA strands, they cause deviations from a linear DNA conformation. When DNA is under tension, translocation is once again slower when aromatic residues are present in the constriction. However, the lack of flexibility in the DNA backbone provides a narrower window of opportunity for the DNA bases to be retained inside the pore via interaction with the aromatic residues, compared to more flexible strands. Consequently, there is more variability in translocation rates for strands under tension. DNA entry into the pores is correlated to pore width, but no such correlation between width and translocation rate is observed.

Interaction of Metamitron and Fenhexamid with Ca2+ -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. Interaction and adsorption energies have been calculated for isomers of Meta or Fen in interaction with Mont to understand the relative stability of various kinds of complexation. Substantial adsorption energies are comparable for Meta and Fen: around -40 kcal/mol. For Fen-Mont, the CO monodentate family is surprisingly the lowest in energy. Moreover, the 10 lowest-energy isomers involve complexation on Fen carbonyl oxygens. The Meta-Mont lowest-energy family, N-N, does not involve π delocalization breaking within Meta. At the same time, the stronger the interaction energy is, the larger the structural modifications within Mont are, particularly concerning the interacting cation distance to the surface. The non-negligible charge transfer and the magnitude of the adsorption energy speak in favor of the chemisorption of the pesticide on the surface. © 2019 Wiley Periodicals, Inc.

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. In this article, we have investigated, using DFT, the adsorption of atrazine onto two different clay surfaces: a pyrophyllite clay and an Mg-substituted clay named montmorillonite, with Ca2+ compensating cations on its surface. The calculations show that the atrazine molecule is physisorbed on the pyrophyllite surface, evidencing the necessity to use dispersion-corrected computational methods. The adsorption energies of atrazine on montmorillonite are two to three times larger than on pyrophyllite, depending on the adsorption pattern. The computed adsorption energy is of about -30 kcal mol-1 for the two most stable montmorillonite-atrazine studied isomers. For these complexes, the large adsorption energy is related to the strong interaction between the chlorine atom of the atrazine molecule and one of the Ca2+ compensating cations of the clay surface. The structural modifications induced by the adsorption are localized: for the surface, close to substitutions and particularly below the Ca2+ cations; in the molecule, around the chlorine atom when Ca2+ interacts strongly with this basic site in a monodentate mode. This study shows the important role of the alkaline earth cations on the adsorption of atrazine on clays, suggesting that the atrazine pesticide retention will be significant in Ca2+ -montmorillonite clays. © 2016 Wiley Periodicals, Inc.

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. Further, a spin-component scaled (SCS) version, SCS-MP2-V(2terfc, aTZ), is produced using the W4-11 database as a supplemental thermochemistry training set, and the resulting method reproduces the quality of MP2-V(terfc, aTZ) for noncovalent interactions and exceeds the performance of SCS-MP2/aTZ for thermochemistry.