Born-Oppenheimer dynamics is shown to provide an accurate approximation of time-independent Schr\"odinger observables for a molecular system with an electron spectral gap, in the limit of large ratio of nuclei and electron masses, without assuming that the nuclei are localized to vanishing domains. The derivation, based on a Hamiltonian system interpretation of the Schr\"odinger equation and stability of the corresponding Hamilton-Jacobi equation, bypasses the usual separation of nuclei and electron wave functions, includes caustic states and gives a different perspective on the Born-Oppenheimer approximation, Schr\"odinger Hamiltonian systems and numerical simulation in molecular dynamics modeling at constant energy microcanonical ensembles.