We investigated the effect of anchoring group position on the formation and electric conductance of single molecule junctions for benzenedithiol and benzenediamine by the scanning tunneling microscope break junction technique. The conductances of the single 1,4-benzenedithiol, 1,3-benzenedithiol, 1,4-benzenediamine, and 1,3-benzenediamine molecules were 0.005 (±0.001) G0 (G0 = 2e2/h), 0.004 (±0.001) G0, 0.01 (±0.003) G0, and 0.005 (±0.002) G0, respectively. No 1,2-disubstituted benzene molecules formed junctions. While the 1,4-position provided larger conductance than the 1,3-position for both anchoring groups, the effect of the anchoring position on conductance was clearer for benzenediamine than benzenedithiol. The resulting anchoring position and its stability are discussed in consideration of the formation of the single molecular junction. The relationship between conductance and anchoring group (position) was analyzed based on ab initio transport calculations. The deformation and change of the energy alignment of the “conductive” molecular orbital give clearer insight to the anchoring position effect than to quantum interference.
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