DOI:10.1088/0953-4075/49/7/075602

We study theoretically the molecular dynamics of nitrogen molecules (N_2) exposed to x rays at a wavelength of 1.1 nm (1100 eV photon energy) from the Linac Coherent Light Source (LCLS) free electron laser. Molecular rate equations are derived to describe the intertwined photoionization, decay, and dissociation processes occurring for N2 in intense and ultrafast x rays from LCLS. This model complements our earlier phenomenological approaches, the single-atom, symmetric-sharing, and fragmentation-matrix models of J. Chem. Phys. \mathbf{136}, 214310 (2012). Our rate-equations are used to obtain the effective pulse energy at the sample and the time scale for the dissociation of the metastable dication N_2^{2+}. This leads to a very good agreement between the theoretically and experimentally obtained ion yields and, consequently, the average charge states. The effective pulse energy is found to decrease with shortening pulse duration. This variation in the effective pulse energy together with a change in the molecular fragmentation pattern and the effect of frustrated absorption---an effect that reduces absorption of x rays due to (double) core hole formation---are the causes for the drop of the average charge state with shortening LCLS pulse duration discovered previously. Show Partial Abstract