Molecules with several flexible coordinates have potential energy surfaces with a large number of minima and many transition states separating them. A general experimental protocol is described that is capable of studying conformational isomerization in such circumstances, measuring the product quantum yields following conformation-specific infrared excitation, and measuring energy thresholds for isomerization of specific X -> Y reactant-product isomer pairs following excitation via stimulated emission pumping (SEP). These methods have been applied to a series of molecules of varying size and conformational complexity, including 3-indolepropionic acid (IPA), meta-ethynylstyrene, N-acetyltryptophan methyl amide (NATMA), N-acetyltryptophan arnide (NATA), and rnelatonin. Studies of isornerization in solute-solvent complexes are also described, including a measurement of the barrier to isomerization in the IPA-H2O complex, and a unique isornerization reaction in which a single water molecule is shuttled between H-bonding sites oil the trans-formanilide (TFA) molecule.