Skip to main content

Role of Ca in Organic Matter Preservation

EMSL Project ID


Calcium can play a major role in the preservation of carbon in the subsurface due to its ability to participate in cation bridging. Ca2+ can link together two negatively charged moieties, such as two organic functional groups, or an organic functional group and a mineral surface, thereby enhancing organic matter (OM) aggregation and sorption to mineral surfaces. Ultimately, this protects OM from microbial degradation and conversion to CO2. Although cation bridging is an important process in soils and sediments, there is little experimental insight into the molecular-scale mechanism by which Ca bridges OM to mineral surfaces. We seek to identify which OM functional groups participate in Ca bridging, and whether/under what conditions Ca bridging occurs via a (strong) inner sphere or (weak) outer sphere mechanism.

To this end, we have obtained calcite-rich sediments from a semi-arid shallow aquifer and subjected them to density fractionation to separate organic and mineral matter. Calcite, which is abundant in these sediments, is separated into the heaviest density ("mineral") fraction. The light and middle density fractions, termed the "particulate organic matter" and "mineral-organic aggregate" fractions contain Ca, which we hypothesize is organic bound. To elucidate whether Ca is organic-bound, and the nature of Ca-organic binding, we plan to use Ca K-edge micro-X-ray fluorescence (XRF) mapping and micro-X-ray absorption near edge structure (XANES) performed at the Stanford Synchrotron Radiation Lightsource in combination with time dependent density functional (TDDFT) theory calculations performed at EMSL.

Features in Ca K-edge XANES spectroscopy arise from electronic transitions from core Ca 1s orbitals to antibonding molecular orbitals that can be predicted by TDDFT, thereby yielding information on the electronic structure and thus binding environment of Ca. Our approach will be to apply XANES and TDDFT to a series of reference compounds in which Ca is bound to different organic ligands to determine how the XANES features shift depending upon the symmetry of the complex and the ligand coordinating Ca. We will then compare our reference spectra to sample spectra and infer whether specific features observed in the sample spectra are associated with a particular Ca binding environment. We expect that our combined spectroscopic-theoretical analysis will yield conclusive evidence for the inner-sphere complexation of Ca by specific organic compounds. Our work provides foundational understanding of Ca-organic matter complexation, which is necessary to develop thermodynamic and kinetic models of Ca complexation in the subsurface.

Project Details

Project type
Large-Scale EMSL Research
Start Date
End Date


Principal Investigator

Sharon Bone
Stanford Linear Accelerator Center

Team Members

Xiao You
Stanford Linear Accelerator Center

John Bargar
Environmental Molecular Sciences Laboratory

Niranjan Govind
Pacific Northwest National Laboratory