A recent experiment, in which a molecular transistor based on the coordination chemistry of cobalt(II) and organic self-assembled monolayers is formed by means of self-aligned lithography,(2) is analyzed with a computational approach. The calculations reveal that a complex involving two cobalt(II) ions bridged by acetate ions can effectively span the nanogap. This bridged complex is shown to be both more flexible and more conductive than the alternative structure involving a single cobalt(II) ion. The single cobalt(II) ion complex is the more stable structure in a nonconfined environment (i.e., in solution) but is found to be less effective at connecting the leads of the fabricated gap and is less likely to result in a conductive device.