Abstract—This paper describes different molecular junctions with different alligator clips connected to gold electrodes at nanometre-scale. Our objective was to determine the charge transport characteristics of these junctions and determine the optimum alligator clip pair. We scrutinised anthracenedithiol (ADT), anthracenediamine (ADA) and anthracenethiolamine (ATA) and computed their conductance parameters through our simulations via Semi Emperical Extended Huckel Theory Approach. We aimed at finding that whether symmetrical (same alligator clips at each side) or asymmetrical (different alligator clips at each side) is the optimised approach to connect the anthracene molecule with gold electrodes and found that different alligator clips i.e. thiol and amine exhibited more conduction than that of same clip pair i.e. ADT and ADA. We further examined the effect of changing alligator clips positions from para to meta and found varied quantum interference effects. Peak to valley current ratios (PVR) for ADT was found to be maximum as 7.05 whereas meta ATA exhibited lowest peak to valley current ratio of 1.44.