Cobaltcarbonyl-tert-butylacetylene (CCTBA) is a conventional precursor for the selective atomic layer deposition of Co onto silicon surfaces. However, a limited understanding of the deposition mechanism of such cobalt precursors curbs rational improvements on their design for increased efficiency and tuneable selectivity. The impact of using a less reactive internal alkyne instead of a terminal alkyne was investigated using experimental and computational methods. Using electrospray-ionization mass spectrometry, the formation of CCTBA analogs and their gas phase decomposition pathways were studied. Decomposition experiments show very similar decomposition pathways between the two complexes. The internal alkyne dissociates from the Co complex at slightly lower energies than the terminal alkyne, suggesting that an internal alkynyl ligand may be more suited to low temperature ALD. In addition, transition state calculations using the nudged elastic band method confirm an increased reaction barrier between the internal alkyne and the Si-H surface bonds on Si(111). These results suggests that using a less reactive internal alkyne will result in fewer embedded carbon impurities during deposition onto Si wafers. DFT calculations using the PBE functional and periodic boundary conditions also predict increased surface binding with the metal centers of the internal alkynyl complex.