Sources of X-rays such as active galactic nuclei and X-ray binaries are often variable by orders of magnitude in luminosity over timescales of years. During and after these flares the surrounding gas is out of chemical and thermal equilibrium. We introduce a new implementation of X-ray radiative transfer coupled to a time-dependent chemical network for use in 3D magnetohydrodynamical simulations. A static fractal molecular cloud is irradiated with X-rays of different intensity, and the chemical and thermal evolution of the cloud are studied. For a simulated $10^5$ M$_odot$ fractal cloud an X-ray flux $<0.01$ erg cm$^{-2}$ s$^{-1}$ allows the cloud to remain molecular, whereas most of the CO and H$_2$ are destroyed for a flux of $>1$ erg cm$^{-2}$ s$^{-1}$. The effects of an X-ray flare, which suddenly increases the X-ray flux by $10^5 times$ are then studied. A cloud exposed to a bright flare has 99% of its CO destroyed in 10-20 years, whereas it takes $>10^3$ years for 99% of the H$_2$ to be destroyed. CO is primarily destroyed by locally generated far-UV emission from collisions between non-thermal electrons and H$_2$; He$^+$ only becomes an important destruction agent when the CO abundance is already very small. After the flare is over, CO re-forms and approaches its equilibrium abundance after $10^3-10^5$ years. This implies that molecular clouds close to Sgr A$^*$ in the Galactic Centre may still be out of chemical equilibrium, and we predict the existence of clouds near flaring X-ray sources in which CO has been mostly destroyed but H is fully molecular.
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