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

Carbon (C-13) and oxygen (O-18) 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 (?A(sic)) compared to pristine calcite. Regarding water-assisted isotopic exchange, the H+-O coordination distorts the transition state configuration and reduces ?A(sic). We proposed a water-mediated exchange mechanism showing the lowest ?A(sic) involving a reaction pathway with a hydroxylated four-coordinated carbon atom, confirming that internal water facilitates clumped isotope reordering.

Automated summary

Carbon (C-13) and oxygen (O-18) isotopes in carbonates can serve as a valuable paleothermometer for sedimentary carbonates and fossils, but their signal resets with increasing temperature after burial. This study investigates the atomistic mechanism of carbonate-clumped isotope reordering in calcite through first-principles simulations. The research reveals the preferred configuration and the role of impurities, trapped water, and Mg2+ substitution in lowering the free energy of activation (?A(sic)) compared to pristine calcite. Additionally, a water-mediated exchange mechanism involving a hydroxylated four-coordinated carbon atom is proposed, showing the lowest ?A(sic) and confirming the facilitation of clumped isotope reordering by internal water.