The electrochemical behavior of hydrogen peroxide (H2O2) at carbon nanotubes (CNTs) and nitrogen-doped carbon nanotubes (N-CNTs) was investigated over a wide potential window. At CNTs, H2O2 will be oxidized or reduced at large overpotentials, with a large potential region between these two processes where electrochemical activity is negligible. At N-CNTs, the overpotential for both H2O2 oxidation and reduction is significantly reduced; however, the reduction current from H2O2, especially at low overpotentials, is attributed to increased oxygen reduction rather than the direct reduction of H2O2, due to a fast chemical disproportionation of H2O2 at the N-CNT surface. Additionally, N-CNTs do not display separation between observable oxidation and reduction currents from H2O2. Overall, the analytical sensitivity of N-CNTs to H2O2, either by oxidation or reduction, is considerably higher than CNTs, and obtained at significantly lower overpotentials. N-CNTs display an anodic sensitivity and limit of detection of 830 mA M(-1) cm(-2) and 0.5 μM at 0.05 V, and a cathodic sensitivity and limit of detection of 270 mA M(-1) cm(-2) and 10 μM at -0.25 V (V vs Hg/Hg2SO4). N-CNTs are also a superior platform for the creation of bioelectrodes from the spontaneous adsorption of enzyme, compared to CNTs. Glucose oxidase (GOx) was allowed to adsorb onto N-CNTs, producing a bioelectrode with a sensitivity and limit of detection to glucose of 80 mA M(-1) cm(-2) and 7 μM after only 30 s of adsorption time from a 81.3 μM GOx solution.

Functional RNAs can fold into intricate structures using a number of different secondary and tertiary structural motifs. Many factors contribute to the overall free energy of the target fold. This study aims at quantifying the entropic costs coming from the loss of conformational freedom when the sugar-phosphate backbone is subjected to constraints imposed by secondary and tertiary contacts. Motivated by insights from topology theory, we design a diagrammatic scheme to represent different types of RNA structures so that constraints associated with a folded structure may be segregated into mutually independent subsets, enabling the total conformational entropy loss to be easily calculated as a sum of independent terms. We used high-throughput Monte Carlo simulations to simulate large ensembles of single-stranded RNA sequences in solution to validate the assumptions behind our diagrammatic scheme, examining the entropic costs for hairpin initiation and formation of many multiway junctions. Our diagrammatic scheme aids in the factorization of secondary/tertiary constraints into distinct topological classes and facilitates the discovery of interrelationships among multiple constraints on RNA folds. This perspective, which to our knowledge is novel, leads to useful insights into the inner workings of some functional RNA sequences, demonstrating how they might operate by transforming their structures among different topological classes.

Polyaromatic dye molecules employed in photovoltaic and electronic applications are often processed in organic solvents. The aggregation of these dyes is key to their applications, but a fundamental molecular understanding of how the solvent environment controls the stacking of polyaromatics is unclear. This study reports initial results from Monte Carlo simulations of how various acene molecule dimers stack when they are dissolved in different solvents. Free energies computed using full dispersion interactions versus those with sterics only suggest that solvent entropy alone accounts for the majority of the stacking free energy in solvents with compact molecular geometries such as carbon tetrachloride. However, in contrast with carbon tetrachloride, we also observe significant variations in the stacking free energies of naphthalene, anthracene, and tetracene across other solvents such as toluene and cyclohexane. The weak attractive dispersion interactions between the acene solutes and planar and near-planar solvent molecules enable them to intercalate between the acene monomers, inducing extra stability beyond what solvent entropic driving force alone could predict. In all three solvents studied (carbon tetrachloride, cyclohexane, toluene) the solvent environment helps facilitate stacking of all three acenes studied (naphthalene, anthracene, tetracene), inducing a significant stabilization free energy between −4 and −8 kcal/mol. Extensive free energy umbrella sampling along the other orthogonal directions allows us to accurately calculate the dimerization equilibrium constants of all three acenes, which vary over several orders of magnitude in a way that depends intricately on the solvent they are in. Given the prevalence of solution-based processing techniques for organic electronic and photonic devices, these results provide useful insights into the critical role that solvent structure and characteristics play in the solution-based aggregation of organic dyes.

Trinucleotide repeat expansion disorders (TREDs) exhibit complex mechanisms of pathogenesis, some of which have been attributed to RNA transcripts of overexpanded CNG repeats, resulting in possibly a gain-of-function. In this paper, we aim to probe the structures of these expanded transcript by analyzing the structural diversity of their conformational ensembles. We used graphs to catalog the structures of an NG-(CNG)16-CN oligomer and grouped them into subensembles based on their characters and calculated the structural diversity and thermodynamic stability for these ensembles using a previously described graph factorization scheme. Our findings show that the generally assumed structure for CNG repeats-a series of canonical helices connected by two-way junctions and capped with a hairpin loop-may not be the most thermodynamically favorable, and the ensembles are characterized by largely open and less structured conformations. Furthermore, a length-dependence is observed for the behavior of the ensembles' diversity as higher-order diagrams are included, suggesting that further studies of CNG repeats are needed at the length scale of TREDs onset to properly understand their structural diversity and how this might relate to their functions. STATEMENT OF SIGNIFICANCETrinucleotide repeats are DNA satellites that are prone to mutations in the human genome. A family of diverse disorders are associated with an overexpansion of CNG repeats occurring in noncoding regions, and the RNA transcripts of the expanded regions have been implicated as the origin of toxicity. Our understanding of the structures of these expanded RNA transcripts is based on sequences that have limited lengths compared to the scale of the expanded transcripts found in patients. In this paper, we introduce a theoretical method aimed at analyzing the structure and conformational diversity of CNG repeats, which has the potential of overcoming the current length limitations in the studies of trinucleotide repeat sequences.