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Gold-dithiol molecular junctions have been studied both experimentally and theoretically. However, the nature of the gold-thiolate bond as it relates to the solvent has been seldom investigated. It is known that solvents can impact the electronic structure of single molecule junctions, but the correlation between the solvent and dithiol-linked single-molecule junction conductance is not well understood. We study molecular junctions formed with thiol terminated phenylenes from both 1-chloronaphthalene and 1-bromonaphthalene solutions. We find that the most probable conductance and the distribution of conductances are both affected by the solvent. First-principles calculations show that junction conductance depends on the binding configurations (adatom, atop, bridge) of the thiolate on the Au surface as has been shown previously. More importantly, we find that brominated solvents can restrict the binding of thiols to specific Au sites. This mechanism offers new insight into the effects of the solvent environment on covalent bonding in molecular junctions.