During the last few decades, considerable advances in quantum information theory have shown deep existing connections between quantum correlation effects (like entanglement and quantum discord) and thermodynamics. Here the concept of conditional entropy plays a considerable role. In contrast to the classical case, quantum conditional entropy can take negative values. This counter-intuitive feature, already well understood in the context of information theory, was recently shown theoretically to also have a physical meaning in quantum thermodynamics [del Rio et al. Nature 2011, 474, 61]. Extending this existing work, here we provide evidence of the significance of negative conditional entropy in a concrete experimental context: Incoherent Neutron Scattering (INS) from protons of H2 in nano-scale environments; e.g., in INS from H2 in C-nanotubes, the data of the H2 translational motion along the nanotube axis seems to show that the neutron apparently scatters from a fictitious particle with mass of 0.64 atomic mass units (a.m.u.)—instead of the value of 2 a.m.u. as conventionally expected. An independent second experiment confirms this finding. However, taking into account the possible negativity of conditional entropy, we explain that this effect has a natural interpretation in terms of quantum thermodynamics. Moreover, it is intrinsically related to the number of qubits capturing the interaction of the two quantum systems H2 and C-nanotube. The considered effect may have technological applications (e.g., in H-storage materials and fuel cells).