In situ synchrotron-based near-edge x-ray absorption fine structure measurements and photoemission spectroscopy have been used to investigate the effect of molecular orientation on the interfacial dipole and the energy level alignment at the interfaces of organic heterojunctions comprising copper-hexadecafluoro-phthalocyanine (F16CuPc) on both standing-up and lying-down copper(II) phthalocyanine (CuPc) thin films. It is found that F16CuPc thin films adopt the same molecular orientation of the underlying CuPc thin films. An interfacial dipole of 0.45eV forms at the interface of lying-down F16CuPcCuPc on highly ordered pyrolytic graphite. In contrast, a much larger interfacial dipole of 1.35eV appears at the interface of standing-up F16CuPcCuPc on octane-1-thiol terminated Au(111).

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