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

Saul Perez-Beltran; Wasif Zaheer; Zeyang Sun; William F Defliese; Sarbajit Banerjee; Ethan L Grossman

doi:10.1126/sciadv.adf1701

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

Sci Adv. 2023 Jun 28;9(26):eadf1701. doi: 10.1126/sciadv.adf1701. Epub 2023 Jun 28.

Authors

Saul Perez-Beltran^{1

2}, Wasif Zaheer^{1

2}, Zeyang Sun³, William F Defliese⁴, Sarbajit Banerjee^{1

2}, Ethan L Grossman³

Affiliations

¹ Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
² Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843, USA.
³ Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA.
⁴ School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia.

Abstract

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.