Molecular dynamics simulations have been used to examine the response of monolayers composed of alkyne chains, which contain diacetylene moieties, to compression and shear. The simulations show that both compression and shear result in cross-linking, or polymerization, between chains. Irregular polymerization patterns appear among the carbon backbones. The vertical positioning of the diacetylene moieties within the alkyne chains (spacer length) and the sliding direction have an influence on the pattern of cross-linking and friction. In addition, chemical reactions between the chains of the monolayer and the amorphous carbon tip occur when diacetylene moieties are located at the ends of the chains closest to the tip. These adhesive interactions increase friction.