Insights into the influence of molecular structure and thermodynamic phase on the chemical mechanisms of hydroxyl radical-initiated heterogeneous oxidation are obtained by identifying reaction products of submicrometer particles composed of either n-octacosane (C28H58, a linear alkane) or squalane (C30H62, a highly branched alkane) and OH. A common pattern is observed in the positional isomers of octacosanone and octacosanol, with functionalization enhanced toward the end of the molecule. This suggests that relatively large linear alkanes are structured in submicrometer particles such that their ends are oriented toward the surface. For squalane, positional isomers of first-generation ketones and alcohols also form in distinct patterns. Ketones are favored on carbons adjacent to tertiary carbons, while hydroxyl groups are primarily found on tertiary carbons but also tend to form toward the end of the molecule. Some first-generation products, viz., hydroxycarbonyls and diols, contain two oxygen atoms. These results suggest that alkoxy radicals are important intermediates and undergo both intramolecular and intermolecular (chain propagation) hydrogen abstraction reactions. Oxidation products with carbon number less than the parent alkane's are observed to a much greater extent for squalane than for n-octacosane oxidation and can be explained by the preferential cleavage of bonds involving tertiary carbons.