The formation of stars and planetary systems is a complex phenomenon, which relies on the interplay of multiple physical processes. Nonetheless, it represents a crucial stage for our understanding of the Universe, and in particular of the conditions leading to the formation of key molecules (e.g. water) on comets and planets. {it Herschel} observations demonstrated that stars form out of gaseous filamentary structures in which the main constituent is molecular hydrogen (H$_2$). Depending on its nuclear spin H$_2$ can be found in two forms: `ortho with parallel spins and `para where the spins are anti-parallel. The relative ratio among these isomers, i.e.,the ortho-to-para ratio (OPR), plays a crucial role in a variety of processes related to the thermodynamics of star-forming gas and to the fundamental chemistry affecting the formation of water in molecular clouds and its subsequent deuteration, commonly used to determine the origin of water in Solar Systems bodies. Here, for the first time, we assess the evolution of the OPR starting from the warm neutral medium, by means of state-of-the-art three-dimensional magneto-hydrodynamic simulations of turbulent molecular clouds. Our results show that star-forming clouds exhibit a low OPR ($ll 0.1$) already at moderate densities ($sim$1000 cm$^{-3}$). We also constrain the cosmic rays ionisation rate, finding that $10^{-16},rm s^{-1}$ is the lower limit required to explain the observations of diffuse clouds. Our results represent a step forward in the understanding of the star and planet formation process providing a robust determination of the chemical initial conditions for both theoretical and observational studies.
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