Density functional theory, in conjunction with a cluster expansion model, has been used to study the structure and stability of the positionally disordered iron-nickel sulfide mineral pentlandite (Pn), (Fe,Ni)9S8, with results indicating heterogeneous nearest neighbor metal contacts are more energetically favorable than homogeneous contacts. The virtual crystal approximation was also explored as a means to address positional disorder, but while reliable results could be obtained for the bulk model, the same was not true for the surface, as local distortions which affected the surface model energies could not be reproduced. We also address the binding of ethyl xanthate (CH3CH2OCS2 -), water, and hydroxide to the  Pn surface to understand the mode of action of industrial xanthate flotation agents better. In order to model anionic ligands bound to a periodic boundary condition surface we propose applying a correction derived from the surface work function to remove the additional charge introduced by the ligand. The results obtained from the ligand binding studies indicate that while ethyl xanthate could readily displace up to a full monolayer of water per unit cell it is likely that Fe-enriched surfaces will bind xanthate in competition with the hydroxide anion, while a Ni-enriched surface will preferentially bind hydroxide anions over xanthate.