The conductance of molecular junctions containing one of five-atom cyclic unit cyclopentadiene, furan, and thiophene sandwiched between two gold electrodes is theoretically investigated. It shows that when the molecules are adsorbed on pyramidal protruding or single atom protruding electrode surfaces, the conductance of these junctions show a negative relationship with their aromaticity, which is consistent with the experimental finding [34]. The analysis of the transmission coefficients and the molecular projected self-consistent Hamiltonian attributes this to the aromaticity dependent alignment of frontier molecular orbitals with the Fermi energy of electrodes. (C) 2015 Elsevier B.V. All rights reserved.