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In this work, we explore the role of chemical reactions on the properties of buffer gas-cooled molecular beams. In particular, we focus on scenarios relevant to the formation of AlF and CaF via chemical reactions between the Ca and Al atoms ablated from a solid target in an atmosphere of a fluorine-containing gas, in this case, SF6 and NF3. Reactions are studied following an ab initio molecular dynamics approach, and the results are rationalized following a tree-shaped reaction model based on Bayesian inference. We find that NF3 reacts more efficiently with hot metal atoms to form monofluoride molecules than SF6. In addition, when using NF3, the reaction products have lower kinetic energy, requiring fewer collisions to thermalize with the cryogenic helium. Furthermore, we find that the reaction probability for AlF formation is much higher than for CaF across a broad range of temperatures.