Hydroperoxyalkylperoxy (OOQOOH) radicals are important intermediates in combustion chemistry. The conventional isomerization of OOQOOH radicals to form ketohydroperoxides has been long believed to be the most important chain branching reaction under the low-temperature combustion conditions. In this work, the kinetics of competing pathways (alternative isomerization, concerted elimination, and H-exchange pathways) to the conventional isomerization of different β-, γ- and Δ-OOQOOH butane isomers are investigated. Six- and seven-membered ring conventional isomerizations are found to be the dominant pathways, whereas alternative isomerizations are more important than conventional isomerization, when the latter proceeded via a more strained transition state ring. The oxygen atoms in OOQOOH radicals introduce intramolecular hydrogen bonding (HB) that significantly affects the energies of reacting species and transition states, ultimately influencing chemical kinetics. Conceptually, HB has a dual effect on the stability of chemical species, the first being the stabilizing effect of the actual intramolecular HB force, and the second being the destabilizing effect of ring strain imposed by the HB conformer. The overall effect can be quantified by determining the difference between the minimum energy conformers of a chemical species or transition state that have HB and that do not have HB (non-hydrogen bonding (NHB)). The stabilization effect of HB on the species and transition sates is assessed, and its effect on the calculated rate constants is also considered. Our results show that, for most species and transition states, HB stabilizes their energies by as much as 2.5 kcal/mol. However, NHB conformers are found to be more stable by up to 2.7 kcal/mol for a few of the considered species. To study the effect of HB on rate constants, reactions are categorized into two groups ( groups one and two) based on the structural similarity of the minimum energy conformers of the reactant and transition state, for a particular reaction. For cases where the reactant and transition state conformers are similar (i.e., both HB or NHB structures), group one, the effect of HB on reaction kinetics is major only if the magnitudes of the stabilization energy of the reactant and transition state are quite different. Meanwhile, for group two, where the reactant and transition state prefer different conformers (one HB and the other NHB), HB affects the kinetics when the stabilization energy of the reactant or transition state is significant or the entropy effect is important. This information is useful in determining corrections accounting for HB effects when assigning rate parameters for chemical reactions using estimation and/or analogy, where analogies usually result in inaccuracies when modeling atmospheric and combustion processes.