Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes

The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.

Theoretical investigation on the interaction between RhIII octaethylporphyrin and a graphite basal surface: a comparison study of DFT, DFT-D, and AFM

Using density functional theory based calculations and atomic-force-microscopy observations, we investigated the interaction between [RhIII(OEP)(Cl)] (OEP = octaethylporphyrin) and a graphite basal surface, and the electronic structure of [RhIII(OEP)(Cl)]/graphite. The [RhIII(OEP)(Cl)] complex has an electronic structure effective for CO activation, possessing a closed singlet structure as its ground state; hence, both σ-donation from the CO molecule (anode-reaction reactant) to RhIII, and π-back-donation from RhIII to CO, occur, because the [RhIII(OEP)(Cl)] complex does not have a singlet occupied molecular orbital on the porphyrin ring, the π-π stacking interaction between porphyrin and graphite is not present and their interaction is dominated by dispersion forces. The [RhIII(OEP)(Cl)] complex easily diffused on the graphite basal surface, and an aggregated structure of [RhIII(OEP)(Cl)] was observed by atomic force microscopy. The difference of the electronic structures of [RhIII(OEP)(Cl)] before and after its adsorption is very small, the dispersion force being the dominant force for the adsorption. However, the lowest unoccupied molecular orbital of [RhIII(OEP)(Cl)]/graphite is a σ bonding orbital between RhIII and graphite that will cause fast electron transfer from [RhIII(OEP)(Cl)] to graphite during the CO electro-oxidation; this would be a reason why the carbon-supported [RhIII(OEP)(Cl)] has high catalytic activity for CO electro-oxidation.