  Recently, rectifying direction inversion has been observed in
dipyrimidinyl-diphenyl (PMPH) diblock molecular wire [J. Am. Chem. Soc. (2005)
127, 10456], and a protonation mechanism was suggested to explain this
interesting phenomena. In this paper, we study the protonation effect on
transport properties of PMPH molecule by first principles calculations. No
significant rectification is found for the pristine diblock molecular wire.
Protonation leads to conductance enhancement and rectification. However, for
all considered junctions with rectifying effect, the preferential current
directions are samely from dipyrimidinyl side to diphenyl side. Effect of
molecule-electrode anchoring geometry is studied, and it is not responsible for
the discrepancy between experiment and theory.
