We study hexagonal assemblies of M6 X6 (M=Mo and W and X=S, Se and Te) nanowires from first-principles calculations to understand their structural stability, electronic properties and the effects of Li intercalation. It is shown that due to van der Waals interactions between the nanowires, the intercalation is achieved without a significant change in their atomic structure. With an increase in Li concentration, we predict a new phase for Li3 Mo6 S6 compound, in which the hexagonal assembly transforms to a monoclinic structure by a change in the orientation of nanowires. The Lix Mo6 S6 assemblies are electrically conductive and can be potentially used as cathode materials in Li-ion batteries for nanoscale applications. The voltage of such a battery, calculated to be 1.7 V, can be manipulated such as by iodine doping without a significant change in the atomic structure. {\textcopyright} 2008 American Institute of Physics.