Competing single-chain folding and multi-chain aggregation pathways control solution-phase aggregate morphology of organic semiconducting polymers.

Understanding the solution-phase behaviour of organic semiconducting polymers is important for systematically improving the performance of devices based on solution-processed thin films of these molecules. Conventional polymer theory predicts that polymer conformations become more compact as solvent quality decreases, but recent experiments have shown the high-performance organic-semiconducting polymer P(NDI2OD-T2) to form extended rod-like aggregates much larger than a single chain in poor solvents, with the formation of these extended aggregates correlated with enhanced electron mobility in films deposited from these solutions. We explain the unexpected formation of extended aggregates using a novel coarse-grained simulation model of P(NDI2OD-T2) that we have developed to study the effect of solvent quality on its solution-phase behaviour. In poor solvents, we find that aggregation through only a few monomers gives effectively inseparable chains, leading to the formation of extended structures of partially overlapping chains via non-equilibrium assembly. This behaviour requires that multi-chain aggregation occurs faster than chain folding, which we show is the case for the chain lengths and concentrations shown experimentally to form rod-like aggregates. This kinetically controlled process introduces a dependence of aggregate structure on concentration, chain length, and chain flexibility, which we show is able to reconcile experimental findings and is generalisable to the solution-phase assembly of other semiflexible polymers.

A simple predictor of interface orientation of fluids of disk-like anisotropic particles and its implications for organic semiconductors.

From classical molecular dynamics simulations, we identify a simple and general predictor of molecular orientation at solid and vapour interfaces of isotropic fluids of disk-like anisotropic particles based on their shape and interaction anisotropy. For a wide variety of inter-particle interactions, temperatures, and substrate types within the range of typical organic semiconductors and their processing conditions, we find remarkable universal scaling of the orientation at the interface with the free energy calculated from pair interactions between close-packed nearest neighbours and an empirically derived universal relationship between the entropy and the shape anisotropy and bulk volume fraction of the fluid particles. The face-on orientation of fluid particles at the solid interface is generally predicted to be the equilibrium structure, although the alignment can be controlled by tuning the particle shape and substrate type, while changing the strength of fluid-fluid interactions is likely to play a less effective role. At the vapour interface, only the side-on structure is predicted, and conditions for which the face-on structure may be preferred, such as low temperature, low interaction anisotropy, or low shape anisotropy, are likely to result in little orientation preference (due to the low anisotropy) or be associated with a phase transition to an anisotropic bulk phase for systems with interactions in the range of typical organic semiconductors. Based on these results, we propose a set of guidelines for the rational design and processing of organic semiconductors to achieve a target orientation at a solid or vapour interface.

The interplay of interfaces, supramolecular assembly, and electronics in organic semiconductors.

Organic semiconductors, which include a diverse range of carbon-based small molecules and polymers with interesting optoelectronic properties, offer many advantages over conventional inorganic semiconductors such as silicon and are growing in importance in electronic applications. Although these materials are now the basis of a lucrative industry in electronic displays, many promising applications such as photovoltaics remain largely untapped. One major impediment to more rapid development and widespread adoption of organic semiconductor technologies is that device performance is not easily predicted from the chemical structure of the constituent molecules. Fundamentally, this is because organic semiconductor molecules, unlike inorganic materials, interact by weak non-covalent forces, resulting in significant structural disorder that can strongly impact electronic properties. Nevertheless, directional forces between generally anisotropic organic-semiconductor molecules, combined with translational symmetry breaking at interfaces, can be exploited to control supramolecular order and consequent electronic properties in these materials. This review surveys recent advances in understanding of supramolecular assembly at organic-semiconductor interfaces and its impact on device properties in a number of applications, including transistors, light-emitting diodes, and photovoltaics. Recent progress and challenges in computer simulations of supramolecular assembly and orientational anisotropy at these interfaces is also addressed.

Ion Mobility-Mass Spectrometry Reveals Details of Formation and Structure for GAA·TCC DNA and RNA Triplexes.

DNA and RNA triplexes are thought to play key roles in a range of cellular processes such as gene regulation and epigenetic remodeling and have been implicated in human disease such as Friedreich's ataxia. In this work, ion mobility-mass spectrometry (IM-MS) is used with supporting UV-visible spectroscopy to investigate DNA triplex assembly, considering stability and specificity, for GAA·TTC oligonucleotide sequences of relevance to Friedreich's ataxia. We demonstrate that, contrary to other examples, parallel triplex structures are favored for these sequences and that stability is enhanced by increasing oligonucleotide length and decreasing pH. We also provide evidence for the self-association of these triplexes, consistent with a proposed model of higher order DNA structures formed in Friedreich's ataxia. By comparing triplex assembly using DNA- and RNA-based triplex-forming oligonucleotides, we demonstrate more favorable formation of RNA triplexes, suggesting a role for their formation in vivo. Finally, we interrogate the binding properties of netropsin, a known polyamide triplex destabilizer, with RNA-DNA hybrid triplexes, where preference for duplex binding is evident. We show that IM-MS is able to report on relevant solution-phase populations of triplex DNA structures, thereby further highlighting the utility of this technology in structural biology. Our data therefore provides new insights into the possible DNA and RNA assemblies that may form as a result of GAA triplet repeats. Graphical Abstract ᅟ.

DNA triplex structure, thermodynamics, and destabilisation: insight from molecular simulations.

Molecular dynamics simulations are used to elucidate the structure and thermodynamics of DNA triplexes associated with the neurodegenerative disease Friedreich's ataxia (FRDA), as well as complexes of these triplexes with the small molecule netropsin, which is known to destabilise triplexes. The ability of molecular simulations in explicit solvent to accurately capture triplex thermodynamics is verified for the first time, with the free energy to dissociate a 15-base antiparallel purine triplex-forming oligomer (TFO) from the duplex found to be slightly higher than reported experimentally. The presence of netropsin in the minor groove destabilises the triplex as expected, reducing the dissociation free energy by approximately 50%. Netropsin binding is associated with localised narrowing of the minor groove near netropsin, an effect that has previously been under contention. This leads to localised widening of the major groove, weakening hydrogen bonds between the TFO and duplex. Consequently, destabilisation is found to be highly localised, occurring only when netropsin is bound directly opposite the TFO. The simulations also suggest that near saturation of the minor groove with ligand is required for complete triplex dissociation. A structural analysis of the DNA triplexes that can form with the FRDA-related duplex sequence indicates that the triplex with a parallel homopyrimidine TFO is likely to be more stable than the antiparallel homopurine-TFO triplex, which may have implications for disease onset and treatment.