Density functional theory prediction of p K a for carboxylated single-wall carbon nanotubes and graphene

Calculating the Aqueous pKa of Phenols: Predictions for Antioxidants and Cannabinoids

We aim to develop a theoretical methodology for the accurate aqueous pK_a prediction of structurally complex phenolic antioxidants and cannabinoids. In this study, five functionals (M06-2X, B3LYP, BHandHLYP, PBE0, and TPSS) and two solvent models (SMD and PCM) were combined with the 6-311++G(d,p) basis set to predict pK_a values for twenty structurally simple phenols. None of the direct calculations produced good results. However, the correlations between the calculated Gibbs energy difference of each acid and its conjugate base, ΔGaq(BA)°=ΔGaqA-°-ΔGaq(HA)°, and the experimental aqueous pK_a values had superior predictive accuracy, which was also tested relative to an independent set of ten molecules of which six were structurally complex phenols. New correlations were built with twenty-seven phenols (including the phenols with experimental pK_a values from the test set), which were used to make predictions. The best correlation equations used the PCM method and produced mean absolute errors of 0.26-0.27 pK_a units and R² values of 0.957-0.960. The average range of predictions for the potential antioxidants (cannabinoids) was 0.15 (0.25) pK_a units, which indicates good agreement between our methodologies. The new correlation equations could be used to make pK_a predictions for other phenols in water and potentially in other solvents where they might be more soluble.

Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields

Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems.

Differences in Neonicotinoid and Metabolite Sorption to Activated Carbon Are Driven by Alterations to the Insecticidal Pharmacophore

Widespread application of neonicotinoids has led to their proliferation in waters. Despite low neonicotinoid hydrophobicity, our prior studies implicated granular activated carbon (GAC) in neonicotinoid removal. Based on known receptor binding characteristics, we hypothesized that the insecticidal pharmacophore influences neonicotinoid sorption. Our objectives were to illuminate drivers of neonicotinoid sorption for parent neonicotinoids (imidacloprid, clothianidin, thiamethoxam, and thiacloprid) and pharmacophore-altered metabolites (desnitro-imidacloprid and imidacloprid urea) to GAC, powdered activated carbon, and carbon nanotubes (CNTs). Neonicotinoid sorption to GAC was extensive and largely irreversible, with significantly greater sorption of imidacloprid than desnitro-imidacloprid. Imidacloprid and imidacloprid urea (electronegative pharmacophores) sorbed most extensively to nonfunctionalized CNTs, whereas desnitro-imidacloprid (positive pharmacophore) sorbed most to COOH-CNTs, indicating the importance of charge interactions and/or hydrogen bonding between the pharmacophore and carbon surface. Water chemistry parameters (temperature, alkalinity, ionic strength, and humic acid) inhibited overall neonicotinoid sorption, suggesting that pharmacophore-driven sorption in real waters may be diminished. Analysis of a full-scale drinking water treatment plant GAC filter influent, effluent, and spent GAC attributes neonicotinoid/metabolite removal to GAC under real-world conditions for the first time. Our results demonstrate that the neonicotinoid pharmacophore not only confers insecticide selectivity but also impacts sorption behavior, leading to less effective removal of metabolites by GAC filters in water treatment.