Closing the Gap between Experiment and Simulation─A Holistic Study on the Complexation of Small Interfering RNAs with Polyethylenimine.

Rational design is pivotal in the modern development of nucleic acid nanocarrier systems. With the rising prominence of polymeric materials as alternatives to lipid-based carriers, understanding their structure-function relationships becomes paramount. Here, we introduce a newly developed coarse-grained model of polyethylenimine (PEI) based on the Martini 3 force field. This model facilitates molecular dynamics simulations of true-sized PEI molecules, exemplified by molecules with molecular weights of 1.3, 5, 10, and 25 kDa, with degrees of branching between 50.0 and 61.5%. We employed this model to investigate the thermodynamics of small interfering RNA (siRNA) complexation with PEI. Our simulations underscore the pivotal role of electrostatic interactions in the complexation process. Thermodynamic analyses revealed a stronger binding affinity with increased protonation, notably in acidic (endosomal) pH, compared to neutral conditions. Furthermore, the molecular weight of PEI was found to be a critical determinant of binding dynamics: smaller PEI molecules closely enveloped the siRNA, whereas larger ones extended outward, facilitating the formation of complexes with multiple RNA molecules. Experimental validations, encompassing isothermal titration calorimetry and single-molecule fluorescence spectroscopy, aligned well with our computational predictions. Our findings not only validate the fidelity of our PEI model but also accentuate the importance of in silico data in the rational design of polymeric drug carriers. The synergy between computational predictions and experimental validations, as showcased here, signals a refined and precise approach to drug carrier design.

Introducing a new 7-ring fused diindenone-dithieno[3,2-b:2',3'-d]thiophene unit as a promising component for organic semiconductor materials.

A novel π-conjugated molecule, EtH-T-DI-DTT is reported, which is fused, rigid, and planar, featuring the electron-rich dithieno[3,2-b:2',3'-d]thiophene (DTT) unit in the core of the structure. Adjacent to the electron-donating DTT core, there are indenone units with electron-withdrawing keto groups. To enable solubility in common organic solvents, the fused system is flanked by ethylhexylthiophene groups. The material is a dark, amorphous solid with an onset of absorption at 638 nm in CH2Cl2 solution, which corresponds to an optical gap of 1.94 eV. In films, the absorption onset wavelength is at 701 nm, which corresponds to 1.77 eV. An ionisation energy of 5.5 eV and an electron affinity of 3.3 eV were estimated by cyclic voltammetry measurements. We have applied this new molecule in organic field effect transistors. The material exhibited a p-type mobility up to 1.33 × 10-4 cm2 V-1 s-1.