Following synthesis and chemical characterization, a scanning tunneling microscope-break junction (STM-BJ) technique was used to directly characterize the charge transport properties of these molecules. STM-BJ methods provide an ideal approach for understanding charge transport at the molecular level, thereby enabling quantitative structure-property relationships for organic materials. Our results show that molecular junctions with long alkyl side chains exhibit a bimodal conductance distribution with an unexpectedly high conductance state upon increasing concentration. Systematic control experiments using asymmetric, planarized, and sterically encumbered molecules indicate that the high conductance state results from surface adsorption and molecular planarization facilitated by long alkyl side chains. Our results further show that the choice of chemical anchors and side chains directly affects molecular adsorption, and density functional theory (DFT) simulations are in reasonable agreement with experiments. Taken together, these results highlight the use of automated chemical synthesis to understand molecular charge transport for the development of new organic electronic materials.