Divalent metal hydroxycarbonates with M2CO3(OH)(2), stoichiometry are widely used in industry and are abundant in nature as the malachite/rosasite group of minerals. Essential to their performance as catalytic precursors and in nanoelectronics, these materials and minerals exhibit a high degree of cation ordering in mixed metal systems due to differences in distortion of the octahedral metal sites. Density-functional theory (DFT) calculations on pokrovskite Mg2CO3(OH)(2) in the rosasite structure and Mg analogues of monoclinic and orthorhombic forms of malachite determine that the octahedral sites are innately distorted, and that d(9) Cu(II) Jahn-Teller distortion accommodates this distortion rather than causes it, leading to the significant preference of Cu for the type I octahedral sites. This distortion also leads to a high propensity for formation of cation vacancies charge balanced by proton substitution. Ab initio thermodynamics is used to determine that there are conditions under which proton substitution defects are slightly more stable than the stoichiometric structure, consistent with the widespread observation of such defects in pokrovskite in nature. Pokrovskite itself is most likely to form under CO2-rich/low water conditions, particularly those utilizing supercritical CO2 for carbon sequestration and is sufficiently thermodynamically stable to trap CO2 under geological conditions. Low temperature and high water concentration promotes the formation of proton substitution defects, which has implications for synthesis of any material where octahedral strain may be relieved by proton substitution defects.