Design and Evaluation of Nanoscale Materials with Programmed Responsivity towards Epigenetic Enzymes

Self-assembled materials capable of modulating their assembly properties in response to specific enzymes play a pivotal role in advancing 'intelligent' encapsulation platforms for biotechnological applications. Here, we introduce a previously unreported class of synthetic nanomaterials that programmatically interact with histone deacetylase (HDAC) as the triggering stimulus for disassembly. These nanomaterials consist of co-polypeptides comprising poly (acetyl L-lysine) and poly(ethylene glycol) blocks. Under neutral pH conditions, they self-assemble into particles. However, their stability is compromised upon exposure to HDACs, depending on enzyme concentration and exposure time. Our investigation, utilizing HDAC8 as the model enzyme, revealed that the primary mechanism behind disassembly involves a decrease in amphiphilicity within the block copolymer due to the deacetylation of lysine residues within the particles' hydrophobic domains. To elucidate the response mechanism, we encapsulated a fluorescent dye within these nanoparticles. Upon incubation with HDAC, the nanoparticle structure collapsed, leading to controlled release of the dye over time. Notably, this release was not triggered by denatured HDAC8, other proteolytic enzymes like trypsin, or the co-presence of HDAC8 and its inhibitor. We further demonstrated the biocompatibility and cellular effects of these materials and conducted a comprehensive computational study to unveil the possible interaction mechanism between enzymes and particles. By drawing parallels to the mechanism of naturally occurring histone proteins, this research represents a pioneering step toward developing functional materials capable of harnessing the activity of epigenetic enzymes such as HDACs.

Quantitative Structure-Permittivity Relationship Study of a Series of Polymers

Dielectric constant is an important property which is widely utilized in many scientific fields and characterizes the degree of polarization of substances under the external electric field. In this work, a structure-property relationship of the dielectric constants (ε) for a diverse set of polymers was investigated. A transparent mechanistic model was developed with the application of a machine learning approach that combines genetic algorithm and multiple linear regression analysis, to obtain a mechanistically explainable and transparent model. Based on the evaluation conducted using various validation criteria, four- and eight-variable models were proposed. The best model showed a high predictive performance for training and test sets, with R2 values of 0.905 and 0.812, respectively. Obtained statistical performance results and selected descriptors in the best models were analyzed and discussed. With the validation procedures applied, the models were proven to have a good predictive ability and robustness for further applications in polymer permittivity prediction.

Hot Carrier Dynamics at Ligated Silicon(111) Surfaces: A Computational Study

We provide a case-study for thermal grafting of benzenediazonium bromide onto a hydrogenated Si(111) surface using ab initio molecular dynamics (AIMD) calculations. A sequence of reaction steps is identified in the AIMD trajectory, including the loss of N₂ from the diazonium salt, proton transfer from the surface to the bromide ion that eliminates HBr, and deposition of the phenyl group onto the surface. We next assess the influence of the phenyl groups on photophysics of hydrogen-terminated Si(111) slabs. The nonadiabatic couplings necessary for a description of the excited-state dynamics are calculated by combining ab initio electronic structures and reduced density matrix formalism with Redfield theory. The phenyl-terminated slab shows reduced nonradiative relaxation and recombination rates of hot charge carriers in comparison with the hydrogen-terminated slab. Altogether, our results provide atomistic insights revealing that (i) the diazonium salt thermally decomposes at the surface allowing the formation of covalently bonded phenyl group, and (ii) the coverage of phenyl groups on the surface slows down charge carrier cooling driven by electron-phonon interactions, which increases photoluminescence efficiency at the near-infrared spectral region.