Small Molecules Organic Co‐Assemblies as Functional Nanomaterials

Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies

Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.

Metal Ion Responsive Luminescent Bio-Templated Co-Assemblies: Label-Free Detection of Multi-Metal Ions in Aqueous Media

Recently, anionic bio-templates have emerged as promising platforms for designing dynamic and stimuli-responsive chromophoric assemblies capable of light harvesting in aqueous media thereby mimicking natural photosynthesis. Here, we present multi-metal ion-responsive luminescent co-assemblies between cationic pyrene-imidazolium amphiphile and anionic bio-templates (ATP, heparin, and DNA) in aqueous media. The anionic bio-templates enhance Förster resonance energy transfer (FRET) in the co-assemblies, with pyrene serving as an excellent donor for generating tunable multi-luminescent materials with embedded acceptor dyes. However, a significant loss in energy transfer towards acceptor dyes was observed in the presence of various metal ions, attributed to excimeric emission quenching facilitated by electron transfer between the pyrene chromophore and metal ions. Interestingly, detailed studies revealed that only ATP-based co-assemblies exhibited quenching phenomena in the presence of metal ions, contrasting with heparin and ctDNA co-assemblies. Additionally, label-free detection of multi-metal ions in aqueous environments, such as Fe2+, Fe3+, and Cu2+ ions, was successfully achieved with lower detection limits of 0.01 μM (3 ppb), 0.12 μM (30 ppb), and 0.58 μM (150 ppb) respectively. These co-assemblies hold significant promise for practical applications in environmental and biomedical sensing, enabling sensitive monitoring of metal ion concentrations.

Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly

The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.

Proton Conducting Membranes with Molecular Self Assemblies and Ionic Channels for Efficient Proton Conduction

Supramolecular assemblies are vital for biological systems. This phenomenon in artificial materials is directly related to their numerous properties and their performance. Here, a simple approach to supramolecular assemblies is employed to fabricate highly efficient proton conducting molecular wires for fuel cell applications. Small molecule-based molecular assembly leading to a discotic columnar architecture is achieved, simultaneously with proton conduction that can take place efficiently in the absence of water, which otherwise is very difficult to obtain in interconnected ionic channels. High boiling point proton facilitators are incorporated into these columns possessing central ionic channels, thereby increasing the conduction multifold. Larger and asymmetrical proton facilitators disintegrated the self-assembly, resulting in low proton conduction efficiency. The highest conductivity was found to be approaching 10^-2 S/cm for the molecular wires in an anhydrous state, which is ascribed to the continuous network of hydrogen bonds in which protons can hop between with a lower energy barrier. The molecular wires with ionic channels presented here have potential as an alternative to proton conductors operating under anhydrous conditions at both low and high temperatures.

Targeted Chemical Modifications Identify Key Features of Carbohydrate Assemblies and Generate Tailored Carbohydrate Materials

The molecular level description of carbohydrate assemblies is hampered by their structural complexity and the lack of suitable analytical methods. Here, we employed systematic chemical modifications to identify key non-covalent interactions that triggered the supramolecular assembly of a disaccharide model. While some modifications disrupted the supramolecular organization, others were tolerated, delivering important information on the aggregation process. The screening identified new geometries, including nanotubes, and twisted ribbons that were characterized with electron tomography and electron diffraction (ED) methods. This work demonstrates that the combination of synthetic chemistry and ED methods is a powerful tool to draw correlations between the molecular structure and the nanoscale architecture of carbohydrate assemblies.