Context <p>A systematic computational investigation was conducted to evaluate the efficacy of sulfur- and nitrogen-based linking agents in facilitating charge transport between a gold electrode and 2,5-bis(thiophen-2-ylethynyl)thiophene, a prototypical molecular wire. The study further examines the influence of an external electric field on electrode–molecule–electrode junctions, providing insights into charge redistribution and molecular stability under operational conditions. The results reveal notable variations in molecular orbital evolution, energy level alignment, and charge transfer pathways as function of linker type and applied electric field. Enhanced electronic coupling is observed for sulfur linkers compared to nitrogen linkers, leading to improved charge transport characteristics. These findings provide fundamental insights into linker-dependent transport behavior and offer practical guidelines for the design and optimization of molecular electronic devices.</p> Methods <p>All calculations were performed using density functional theory (DFT) as implemented in the Gaussian 09 software package. Geometry optimizations were carried out using the B3LYP exchange–correlation functional. The 6-31G(d,p) basis set was employed for C, H, N, and S atoms, while the LANL2DZ basis set with effective core potential was used for Au atoms to account for relativistic effects. The electrode–molecule junction was modeled by attaching gold clusters to the molecule via sulfur and nitrogen linkers. External electric fields were applied along the molecular axis to simulate bias conditions. Molecular orbital analysis, energy level alignment, and charge distribution were evaluated using natural population analysis (NPA) and Mulliken charge schemes. Visualization and post-processing of electronic properties were performed using GaussView.</p>