Density functional theory and ab initio molecular dynamics reveal atomistic mechanisms for carbonate clumped isotope reordering

Carbon (13C) and oxygen (18O) isotopes in carbonates form clumped isotope species inversely correlated with temperature, providing a valuable paleothermometer for sedimentary carbonates and fossils. However, this signal resets ("reorders") with increasing temperature after burial. Research on reordering kinetics has characterized reordering rates and hypothesized the effects of impurities and trapped water, but the atomistic mechanism remains obscure. This work studies carbonate-clumped isotope reordering in calcite via first-principles simulations. We developed an atomistic view of the isotope exchange reaction between carbonate pairs in calcite, discovering a preferred configuration and elucidating how Mg2+ substitution and Ca2+ vacancies lower the free energy of activation (ΔA‡) compared to pristine calcite. Regarding water-assisted isotopic exchange, the H+-O coordination distorts the transition state configuration and reduces ΔA‡. We proposed a water-mediated exchange mechanism showing the lowest ΔA‡ involving a reaction pathway with a hydroxylated four-coordinated carbon atom, confirming that internal water facilitates clumped isotope reordering.