Self-assembled monolayers generated by alkanethiols on gold substrates are prototypical systems in today's nanotechnology, but their structure still constitutes an unresolved puzzle. An important step forward is made here by focusing on the long-debated case of decanethiols and using unprecedented large-scale simulations that accurately account for the interplay between the chemistry at the interface and the interchain interactions. It is established that thiolates are thermodynamically favored relative to sulfur-paired chains and that the energy difference decreases linearly with chain length. The nature of the chemical bonding at the interface is understood for both adsorbates. It is also shown that experimental data always reveal the presence of thiolates but that disulfides may coexist in some cases. These results open a new perspective for the molecular-scale characterization of complex self-assembled monolayers on metal supports and for simulations-aided nanotechnology.