Hammes-Schiffer has also pioneered work in what she calls the Nuclear-electronic orbital method (NEO) which allows for a more accurate estimate of nuclear properties such as density, geometry, frequencies, electronic coupling, and nuclear motions. As described in her paper, "Incorporation of Nuclear Quantum effects in electronic structure," Radial basis function kernel, a gaussian algorithm used to support vector machines,  is applied to determine electronic and molecular orbitals. The NEO approach is specifically applicable in determining the exact mechanisms of hydrogen transfer reactions while accounting for other variables such as quantum tunneling and zero point energy. Hammes-Schiffer claims that the NEO approach is significantly advantageous over other methods that incorporate nuclear quantum effects because of the method's ability to calculate vibrational states, its avoidance of Born–Oppenheimer approximation and its apparent and inherent incorporation of quantum effects.
In her study, published in September 2016, Hammes-Schiffer contributed towards discovering the effects of the active site of the magnesium ion in the Scissile Phosphate cofactor complex. She discovered that rather than the magnesium ion lying in the center of the complex, the ion lies in a separate site, termed the Hoogsteen Face, where it lowers the pKa of the complex in order to facilitate a deprotonation reaction necessary for a self-cleavage reaction.