Effect of bridge type on electronic structure and rectification in molecular junctions

This study links the chemistry of isolated molecules with the physics of two-probe systems by exploring the role of molecular bridges in rectification through density functional theory (DFT) and nonequilibrium Green's function (DFT-NEGF) methods. Two classes of molecules are studied: Group A (A-bridge-D), which is based on a pyrimidinyl-phenyl dithiol scaffold where the pyrimidinyl ring acts as an electron acceptor (A) and the phenyl ring as a donor (D), with thiol anchoring groups; and Group B (2A-bridge-2D), which uses dipyrimidinyl-diphenyl dithiol scaffolds designed to examine the impact of extended conjugation. For both groups, three types of bridges are investigated: σ-bridge, π-bridge, and direct linkage. The computational workflow includes (i) DFT calculations to evaluate how external electric fields influence the structural and electronic properties of isolated molecules, and (ii) DFT-NEGF simulations of two-probe systems, where molecules are placed between gold electrodes. Electron transport properties-such as current-voltage (I-V) characteristics, density of states (DOS), and transmission spectra-are analyzed systematically. The results indicate that σ-bridge molecules exhibit the strongest rectification, with the 2A-σ-2D molecule reaching the highest rectification ratio of 6.7 at 2 V. These findings demonstrate a clear link between the chemistry of isolated molecules and the physics of molecular junctions, further supported by a linear regression correlation.