The heat capacities of two different molecule-containing melanophlogites of approximate composition 46SiO2 · 1.80CH4 · 3.54N2 · 1.02CO2 from Mt. Hamilton, California, and 46SiO2 · 3.59CH4 · 3.10N2 · 1.31CO2 from Racalmuto, Sicily, along with a heat-treated (molecule-free) sample of composition SiO2, were studied between 5 and 300 K using heat-pulse microcalorimetry. The molecule-free sample was obtained by heating natural Racalmuto crystals at 1173 K for 24 h. The standard third-law entropy of the molecule-free sample is S° = 2216.3 ± 6.6 J/(mol · K) for 46SiO2 and the natural Mt. Hamilton and Racalmuto samples give S° = 2805.7 ± 8.4 J/(mol · K) and S° = 2956.8 ± 8.9 J/(mol · K), respectively. The entropy and Gibbs free energy for molecule-free melanophlogite relative to quartz at 298 K are Δ Strans = 6.7 J/(mol · K) and ΔGtrans = 7.5 kJ/mol, respectively and, thus, it does not have a thermodynamic field of stability in the SiO2 system. The difference in CP values between molecule-containing and molecule-free melanophlogite is characterized by an increase in CP from 0 to ~70 K, and it then reaches a roughly constant value at 70 K < T < 250 K. The ΔSrxn at 298 K for 46SiO2(melan.) + xCH4(gas) + yCO2(gas) + zN2(gas) = 46SiO2 · (xCH4)12 · (yCO2, zN2)14 is estimated to be about −642 and −802 J/(mol · K) for the Mt. Hamilton and Racalmuto samples, respectively. The thermodynamic data, as well as published results on the occurrence of natural molecule-containing samples suggest that melanophlogite crystallizes metastabily. The occurrence of melanophlogite and the lack of other porosils in nature are probably due to the essential role of molecular structure-directing agents. For melanophlogite they can be CO2, N2, and CH4, whereas the crystallization of other porosils requires more chemically and structurally complex molecules that are not naturally abundant.