End-Group Influence on Frontier Molecular Orbital Reorganization and Thermoelectric Properties of Molecular Junctions

The reorganization of frontier molecular orbitals (FMOs) upon formation of molecular junctions plays an important role in the resulting transport and thermoelectric properties. By considering a wide range of Au–molecule–Au junctions—created from phenyl molecules with different lengths and end-groups—we demonstrate that the extent of reorganization of FMOs is based on: (i) stabilization due to the physical presence of electrodes, and (ii) change in the electron–electron (e–e) interactions due to charge transfer. In molecular systems with charge (electron) transfer into the molecule, the opposing effects of stabilization and increased e–e interactions result in a small overall reorganization of FMOs. In contrast, for molecular systems with charge transfer out of the molecule, the complementary effects of stabilization and reduced e–e interactions result in a large overall reorganization of FMOs to lower energies. Further, we present a computationally efficient approach to quantitatively compute the extent of reorganization, which has potential for high-throughput analysis of molecular junctions.