Researchers have looked at the possibility of using single molecules as functional building blocks in electronics circuits since the 1970s. The field of molecular electronics, despite its experimental and theoretical challenges, has continued to grow incessantly from a simple scientific curiosity to an emerging field with hundreds of publications per year. Thanks to the development of scanning probe microscopy a variety of techniques currently used to characterise the electrical properties of single molecules has been developed, and molecular systems mimicking the behaviour of traditional electronic components, such as transistors or rectifiers, have been prepared. Despite the obvious fact that supramolecular interactions must play a role in the charge transfer process, only a small number of reports on the subject have been published. In this thesis a set of molecular wires with an oligothiophene central unit, sandwiched between two insulating chains, has been used to probe the effect of such interactions on molecular conductance using several scanning tunnelling microscopy techniques. It has been found that the side-chain length has little effect on molecular conductance, but the presence of water in the surrounding environment triggers an increase in conductance and a switch in the behaviour from activationless to thermally-activated. Furthermore, upon exposure to electron-withdrawing small molecules, these oligothiophene molecular wires form charge transfer complexes, with conductance enhanced by a factor up to 100. Measurements performed in UHV confirmed the observed behaviour, and theoretical calculations were performed to explain it in the coherent tunnelling regime. A gateway state arising from coupling of the molecular backbone to the sulfur contacts accounts for the observed shallow decay of conductance with length, while shifting of transport resonances upon interaction with water and the appearance of interference features upon charge transfer complexation explained the temperature dependence and the conductance enhancement, with experimental observation closely matched by DFT calculations.