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Laser-induced molecular alignment is well understood within the framework of the Born-Oppenheimer (BO) approximation Without the BO approximation, however, the concept of molecular structure is lost, making alignment hard to define precisely. In this work, we demonstrate the emergence of alignment from the first-ever non-BO quantum dynamics simulations, using the HD molecule exposed to ultrashort laser pulses as a few-body test case We extract the degree of alignment from the non-BO wave function by means of an operator expressed in terms of pseudo-proton coordinates that mimics the BO-based definition of alignment The only essential approximation, in addition to the semiclassical electric-dipole approximation for the matter-field interaction, is the choice of time-independent explicitly correlated Gaussian basis functions. We use a variational, electric-field-dependent basis-set construction procedure, which allows us to keep the basis-set dimension low whilst capturing the main effects of electric polarization on the nuclear and electronic degrees of freedom. The basis-set construction procedure is validated by comparing with virtually exact grid-based simulations for two one-dimensional model systems: laser-driven electron dynamics in a soft attractive Coulomb potential and nuclear rovibrational dynamics in a Morse potential.