Much of Baldridge's research involves finding better ways to use quantum mechanical methodologies to study complex molecules. For example, she used quantum mechanical approaches to study reaction paths and rates, inclusion of solvent effects, and evaluation of DFT functionals with dispersion correction for studying large polynuclear aromatic molecules.

Baldridge has contributed to quantum mechanical computer programs such as GAMESS (US), QMView, and GEMSTONE. GAMESS stands for General Atomic and Molecular Electronic System, and is an advanced chemistry program for calculations including generalized valence bond, the Hartree-Fock method, and density functional theory.