Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors.

The protein-only infectious agents known as prions exist within cellular matrices as populations of assembled polypeptide phases ranging from particles to amyloid fibres. These phases appear to undergo Darwinian-like selection and propagation, yet remarkably little is known about their accessible chemical and biological functions. Here we construct simple peptides that assemble into well-defined amyloid phases and define paracrystalline surfaces able to catalyse specific enantioselective chemical reactions. Structural adjustments of individual amino acid residues predictably control both the assembled crystalline order and their accessible catalytic repertoire. Notably, the density and proximity of the extended arrays of enantioselective catalytic sites achieve template-directed polymerization of new polymers. These diverse amyloid templates can now be extended as dynamic self-propagating templates for the construction of even more complex functional materials.

Conjugated semiconducting polymers have been the subject of intense study for over two decades with promising advances toward a printable electronics manufacturing ecosystem. These materials will deliver functional electronic devices that are lightweight, flexible, large-area, and cost-effective, with applications ranging from biomedical sensors to solar cells. Synthesis of novel molecules has led to significant improvements in charge carrier mobility, a defining electrical performance metric for many applications. However, the solution processing and thin film deposition of conjugated polymers must also be properly controlled to obtain reproducible device performance. This has led to an abundance of research on the process-structure-property relationships governing the microstructural evolution of the model semicrystalline poly(3-hexylthiophene) (P3HT) as applied to organic field effect transistor (OFET) fabrication. What followed was the production of an expansive body of work on the crystallization, self-assembly, and charge transport behavior of this semiflexible polymer whose strong π-π stacking interactions allow for highly creative methods of structural control, including the modulation of solvent and solution properties, flow-induced crystallization and alignment techniques, structural templating, and solid-state thermal and mechanical processing. This Account relates recent progress in the microstructural control of P3HT thin films through the nucleation, growth, and alignment of P3HT nanofibers. Solution-based nanofiber formation allows one to develop structural order prior to thin film deposition, mitigating the need for intricate deposition processes and enabling the use of batch and continuous chemical processing steps. Fiber growth is framed as a traditional crystallization problem, with the balance between nucleation and growth rates determining the fiber size and ultimately the distribution of grain boundaries in the solid state. Control of nucleation can be accomplished through a sonication-based seeding procedure, while growth can be modulated through supersaturation control via the tuning of solvent quality, the use of UV irradiation or through aging. These principles carry over to the flow-induced growth of P3HT nanofibers in a continuous microfluidic processing system, leading to thin films with significantly enhanced mobility. Further gains can be made by promoting long-range polymer chain alignment, achieved by depositing nanofibers through shear-based coating methods that promote high fiber packing density and alignment. All of these developments in processing were carried out on a standard OFET platform, enabling us to generalize quantitative structure-property relationships from structural data sources such as UV-vis, AFM, and GIWAXS. It is shown that a linear correlation exists between mobility and the in-plane orientational order of nanofibers, as extracted from AFM images using advanced computer vision software developed by our group. Herein, we discuss data-driven approaches to the d...

Very few studies have reported oriented crystallization of conjugated polymers directly in solution. Here, solution crystallization of conjugated polymers in a microfluidic system is found to produce tightly π-stacked fibers with commensurate improved charge transport characteristics. For poly(3-hexylthiophene) (P3HT) films, processing under flow caused exciton bandwidth to decrease from 140 to 25 meV, π-π stacking distance to decrease from 3.93 to 3.72 Å and hole mobility to increase from an average of 0.013 to 0.16 cm(2) V(-1) s(-1), vs films spin-coated from pristine, untreated solutions. Variation of the flow rate affected thin-film structure and properties, with an intermediate flow rate of 0.25 m s(-1) yielding the optimal π-π stacking distance and mobility. The flow process included sequential cooling followed by low-dose ultraviolet irradiation that promoted growth of conjugated polymer fibers. Image analysis coupled with mechanistic interpretation supports the supposition that "tie chains" provide for charge transport pathways between nanoaggregated structures. The "microfluidic flow enhanced semiconducting polymer crystal engineering" was also successfully applied to a representative electron transport polymer and a nonhalogenated solvent. The process can be applied as a general strategy and is expected to facilitate the fabrication of high-performance electrically active polymer devices.

Biopolymers exist within living cells as far-fromequilibrium metastable polymers. Living systems must constantly invest energy for biopolymer synthesis. In the earliest stages of life on Earth, the complex molecular machinery that contemporary life employs for the synthesis and maintenance of polymers did not exist. Thus, a major question regarding the origin of life is how the first far-from-equilibrium polymers emerged from a prebiotic "pool" of monomers. Here, we describe a proof-of-principle system, in which L-malic acid monomers form far-from-equilibrium, metastable oligoesters via repeated, cyclic changes in hydration and temperature. Such cycles would have been associated with day−night and/or seasonal cycles on the early Earth. In our model system, sample heating, which promotes water evaporation and ester bond formation, drives polymerization. Even though periodic sample rehydration and heating in the hydrated state promotes ester bond hydrolysis, successive iterations of wet−dry cycles result in polymer yields and molecular weight distributions in excess of that observed after a single drying cycle. We term this phenomenon a "polymerization ratchet". We have quantitatively characterized the "ratchet" of our particular system. Ester bond formation rates and oligoester hydrolysis rates were determined for temperatures ranging from 60 to 95°C. Based on these rates, a mathematical model was developed using polycondensation kinetics, from which conditions were predicted for oligoester growth. This model was verified experimentally by the demonstration that L-malic acid monomers subjected to multiple wet−dry cycles form oligoesters, which reach a steady-state concentration and mean length after several cycles. The concentration of oligoesters that persist between subsequent steady-state cycles depends on the temperature and durations of the dry and wet phases of the cycle. These results provide insights regarding the potential for very simple systems to exhibit features that would have been necessary for initiation of polymer evolution, before the emergence of genomes or enzymes.

Long-range ordering emerges in poly­(3-hexylthiophene) (P3HT) solutions during time-dependent aggregation. Here, aggregation of P3HT in chloroform solution was induced by ultrasonication, aging, and combinations thereof. UV–vis spectroscopy and polarized optical microscopy demonstrated that long-range ordering in the solution and subsequently the solid state depends on assembled P3HT fiber length, as determined by film atomic force microscopy. Ultrasonication induced the formation of fibers that were relatively short compared to those obtained through aging. As a result, ultrasonication afforded isotropic solutions and films, whereas aging afforded anisotropic solutions and films. The impact of fiber length and anisotropy on macroscopic charge transport performance was evaluated using an organic field-effect transistor (OFET) architecture. Both aged and sonicated solutions exhibited charge carrier mobilities that were an order of magnitude higher than that obtained for pristine samples. Aging of sonicated solutions enabled semiconducting thin films with significantly higher mobilities (1.5 × 10–1 cm2 V–1 s–1) than those of either solution processing technique. Furthermore, the results indicate that grain boundary morphology has a significant impact on macroscopic charge carrier mobility. Grazing incidence wide-angle X-ray scattering demonstrated that the combined sonication/aging method affords a solidified film where the semiconductor exhibits a highly edge-on orientation. The results suggest that the nucleation and growth of aggregates can be controlled via solution processing methods and thus may allow the manipulation of active layer orientation, crystal packing density, and crystallite size. The investigation provides insight into the conjugated polymer solution process parameters that impact polymer ordering and aggregation in solution and resultant thin films for high-performance organic electronic devices.

RiboVision is a visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex containing ribosomal RNA and ribosomal proteins and is a key component of life responsible for the synthesis of proteins in all living organisms. RiboVision is intended for rapid retrieval, analysis, filtering, and display of a variety of ribosomal data. Preloaded information includes 1D, 2D, and 3D structures augmented by base-pairing, base-stacking, and other molecular interactions. RiboVision is preloaded with rRNA secondary structures, rRNA domains and helical structures, phylogeny, crystallographic thermal factors, etc. RiboVision contains structures of ribosomal proteins and a database of their molecular interactions with rRNA. RiboVision contains preloaded structures and data for two bacterial ribosomes (Thermus thermophilus and Escherichia coli), one archaeal ribosome (Haloarcula marismortui), and three eukaryotic ribosomes (Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens). RiboVision revealed several major discrepancies between the 2D and 3D structures of the rRNAs of the small and large subunits (SSU and LSU). Revised structures mapped with a variety of data are available in RiboVision as well as in a public gallery (). RiboVision is designed to allow users to distill complex data quickly and to easily generate publication-quality images of data mapped onto secondary structures. Users can readily import and analyze their own data in the context of other work. This package allows users to import and map data from CSV files directly onto 1D, 2D, and 3D levels of structure. RiboVision has features in rough analogy with web-based map services capable of seamlessly switching the type of data displayed and the resolution or magnification of the display. RiboVision is available at .

We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).