Recent experimental work has shown that addition of acetone molecules to hydrogen-terminated Si(001) surfaces leads to the formation of one-dimensional molecular structures through a chain reaction mechanism. These structures are observed experimentally to be parallel to dimer rows on the Si(001)(2×1)–H surface. Using periodic density functional theory calculations, we have studied the initial steps of the radical chain mechanism of these reactions, and we have determined whether (or not) perpendicular growth could be possible. Our results show that, while the calculated difference of 0.03 eV between parallel and perpendicular attachment may not be enough to exclude growth between rows on Si(001)(2×1)–H at room temperature, the growth between dimers rows is kinetically less favorable because of the additional energy barrier associated with the hydrogen diffusion to the adjacent dangling bond on the same Si dimer (intradimer hopping motion), a necessary step to avoid steric repulsion between close proximity adsorbed acetone molecules.