  Modeling the chemistry of molecular clouds is critical to accurately
simulating their evolution. To reduce computational cost, 3D simulations
generally restrict their chemistry to species with strong heating and cooling
effects. Time-dependent information about the evolution of other species is
therefore often neglected. We address this gap by post-processing tracer
particles in the SILCC-Zoom molecular cloud simulations. Using a chemical
network of 39 species and 301 reactions (including freeze-out of CO and
H$_{2}$O), and a novel algorithm to reconstruct a density grid from sparse
tracer particle data, we produce time-dependent density distributions for
various species. We focus upon the evolution of HCO$^{+}$, which is a critical
formation reactant of CO but is not typically modeled on-the-fly. We find that
$\sim90$% of the HCO$^{+}$ content of the cold molecular gas forms in situ
around $n_\textrm{{HCO$^+$}}\simeq10^3$-$10^4$ cm$^{-3}$, over a time-scale of
approximately 1 Myr. The remaining $\sim10$% forms at high extinction sites,
with minimal turbulent mixing out into the less dense gas. We further show that
the dominant HCO$^{+}$ formation pathway is dependent on the visual extinction,
with the reaction H$_{3}^{+}$ + CO contributing 90% of the total HCO$^{+}$
production above $A_\textrm{V,3D}=3$. We produce the very first maps of the
HCO$^{+}$ column density, $N$(HCO$^{+}$), and show that it reaches values as
high as $10^{15}$ cm$^{-2}$. We find that 50% of the HCO$^+$ mass is located
within $A_\textrm{V}\sim10$-30, in a density range of $10^{3.5}$-$10^{4.5}$
cm$^{-3}$. Our maps of $N$(HCO$^{+}$) are shown to be in good agreement with
recent observations of the W49A star-forming region.
