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Understanding the self-organization and structural transformations of molecular ensembles is important to explore the complexity of biological systems. Here, we illustrate the crucial role of cosolvents and solvation effects in thermodynamic and kinetic control over peptide association into ultrathin Janus nanosheets, elongated nanobelts, and amyloid-like fibrils. We gained further insight into the solvation-directed self-assembly (SDSA) by investigating residue-specific peptide solvation using molecular dynamics modeling. We proposed the preferential solvation of the aromatic and alkyl domains on the peptide backbone and protofibril surface, which results in volume exclusion effects and restricts the peptide association between hydrophobic walls. We explored the SDSA phenomenon in a library of cosolvents (protic and aprotic), where less polar cosolvents were found to exert a stronger influence on the energetic balance at play during peptide propagation. By tailoring cosolvent polarity, we were able to achieve precise control of the peptide nanostructures with 1D/2D shape selection. We also illustrated the complexity of the SDSA system with pathway-dependent peptide aggregation, where two self-assembly states ( i.e., thermodynamic equilibrium state and kinetically trapped state) from different sample preparation methods were obtained.

The structure of the it-/st-poly(methyl methacrylate) (PMMA) triple-helix stereocomplex is composed of a double helix of it-PMMA of 9 units per turn surrounded by a single helix of st-PMMA with an average of 20 units per turn., In this study, by using X-ray powder diffraction profiles as blueprints, we successfully mapped the most probable molecular-level structural arrangement of the PMMA super-helix stereocomplexes through molecular dynamic simulations. Molecular-level resolution of the PMMA triple-helix supramolecule was not previously achievable by experimental methods. After constructing molecular models of stereo-regular complexes composed of linear it- and st-PMMAs, our all-atom molecular dynamics simulations identified the stereocomplex structure that best reproduces experimental diffraction profiles and thermodynamic properties as a double helix of isotactic (it-)PMMA with a helical pitch of 1.8 nm and 9 units per turn surrounded by a single helix of syndiotactic (st-)PMMA with an average helical pitch of 0.9 nm and 20 units per turn. The it-/st- complexing stoichiometry in the PMMA triple-helix is therefore 9 : 20. This presents the first all-atom model of the it-/st-PMMA triple-helix stereocomplex that accurately fits experimental X-ray diffraction profiles. In addition, the simulation results revealed the outer st-PMMA helix of the PMMA stereocomplex has a fiber diameter of at least 1.85 nm and adopts a non-ideal helical geometry. Furthermore, through dynamic simulations, surprising new sights into the effect of the structural configuration of the PMMA stereocomplex (i.e., helical pitch and direction, and tilt angle) on the physical properties of their crystal structures were obtained. Those crystal properties include X-ray diffraction profile, packing density, chain–chain spacing, chain width and cohesive energy density.

New aromatic molecule–seed particle interactions are examined and exploited to control and guide seed-mediated gold nanorod (Au NR) growth. This new approach enables better understanding of how small molecules impact the synthesis of metallic nanostructures, catalysing their use in various biomedical applications, such as plasmonic biosensing. We perform experimental studies and theoretical molecular simulations using a library of aromatic molecules where we take advantage of the chemical versatility of the molecules with varied spatial arrangements of electron donating/withdrawing groups, charge, and Au-binding propensity. Au NR growth is regulated by two principal mechanisms, producing either a red or blue shift in the longitudinal localized surface plasmon resonance (LLSPR) peaks. Aromatic molecules with high redox potentials produced an increase in NR aspect ratio and red shift of LLSPR peaks. In contrast, molecules that strongly bind gold surfaces resulted in blue shifts, demonstrating a strong correlation between their binding energy and blue shifts produced. Through enzymatic conversion of selected molecules, 4-aminophenylphosphate to 4-aminophenol, we obtained opposing growth mechanisms at opposite extremes of target concentration, and established a chemical pathway for performing plasmonic ELISA. This unlocks new strategies for tailoring substrate design and enzymatic mechanisms for controlling plasmonic response to target detection in biosensing applications.

In this study, the stereocomplexation between a novel stereospecific cyclic vinyl polymer, that is, cyclic syndiotactic poly(methyl methacrylate) (st-PMMA), with the complementary linear isotactic (it-) PMMA was investigated. Surprising new insight into the effects of the topology (i.e., end groups), size, and tacticity of the assembling components on stereocomplex formation was obtained. Characterization of the stereocomplexes revealed that the self-assembly of cyclic st-PMMAs and linear it-PMMAs resulted in the formation of an unprecedented “polypseudorotaxane-type” supramolecular assembly. This stereocomplex exhibited remarkably different physical properties as compared to the conventional PMMA triple-helix stereocomplex as a result of the restricted topology imposed by the cyclic st-PMMA assembling component.