This work demonstrates the impact of intramolecular hydrogen bonding (H-bonding) on the calculated p of octahedral tris-(pyridinethiolato)nickel(II), [Ni(PyS)3]-, proton reduction catalysts. Density Functional Theory (DFT) calculations on a [Ni(PyS)3]- catalyst, and eleven derivatives, demonstrate geometric isomer formation in the protonation step of the catalytic cycle. Through Quantum Theory of Atoms in Molecules (QTAIM), we show that the p of each isomer is driven by intramolecular H-bonding of the proton on the pyridyl nitrogen to a sulfur on a neighboring ligand. This work demonstrates that ligand modification the placement of electron-donating (ED) or electron-withdrawing (EW) groups may have unexpected effects on the catalyst's p due to intramolecular H-bonding and isomer formation. These factors need to be considered in computational work. This work suggests the possibility that modification of substituent placement on the ligands to manipulate H-bonding in homogeneous metal catalysts could be explored as a tool to simultaneously target both desired p and ° values in small molecule catalysts.