Alkyl-substituted quaterthiophenes on Au(111) form dimers linked by their alkyl substituents and, instead of adopting the trans conformation found in bulk oligothiophene crystals, assume cis conformations. Surprisingly, the impact of the conformation is not decisive in determining the lowest unoccupied molecular orbital energy. Scanning tunneling microscopy and spectroscopy of the adsorption geometries and electronic structures of alkyl-substituted quaterthiophenes show that the orbital energies vary substantially because of local variations in the Au(111) surface reactivity. These results demonstrate that interfacial oligothiophene conformations and electronic structures may differ substantially from those expected based on the band structures of bulk oligothiophene crystals.