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Title: Ab Initio Molecular Dynamics Simulation of Divalent Metal Cation Incorporation in Calcite: Implications for Interpreting X-ray Absorption Spectroscopy Data

Abstract

Calcite (CaCO3) is a ubiquitous mineral with the ability to accommodate a wide range of impurities. Determination of the coordination environment and incorporation modes of impurities in calcite has historically relied primarily on the interpretation of extended X-ray absorption fine structure (EXAFS) spectroscopy. However, lack of standards combined with the large number of degrees of freedom involved in shell-by-shell fits have made the interpretation of EXAFS spectra challenging. As such, in this work, ab initio molecular dynamics (AIMD) simulations were performed to investigate the incorporation of seven divalent metal cation impurities, namely, Ba2+, Pb2+, Sr2+, Cd2+, Mn2+, Co2+, and Zn2+, in calcite. These cations span a wide range of sizes: 30.7 to –22.8% change in ionic radius with respect to Ca2+. The atomic trajectories were then used to compute EXAFS spectra for direct comparison with published experimental spectra. The simulations confirmed that all seven metal cations incorporate in calcite via substitution in the calcium site. The AIMD–EXAFS approach allowed for overcoming limitations of the shell-by-shell fitting approach, such as the difficulties in resolving weak backscatterers beyond the first coordination shell. As a result, the AIMD–EXAFS approach was able to provide a detailed and comprehensive characterization of the structural relaxation aroundmore » divalent metal cation impurities in calcite.« less

Authors:
ORCiD logo [1]; ORCiD logo [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division; USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1574896
Report Number(s):
PNNL-SA-146667
Journal ID: ISSN 2472-3452
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
ACS Earth and Space Chemistry
Additional Journal Information:
Journal Volume: 3; Journal Issue: 11; Journal ID: ISSN 2472-3452
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; calcium carbonate; ab initio molecular dynamics; extended x-ray absorption fine structure spectroscopy; isovalent substitution; impurity incorporation; structural relaxation; ST4

Citation Formats

Kerisit, Sebastien N., and Prange, Micah P. Ab Initio Molecular Dynamics Simulation of Divalent Metal Cation Incorporation in Calcite: Implications for Interpreting X-ray Absorption Spectroscopy Data. United States: N. p., 2019. Web. doi:10.1021/acsearthspacechem.9b00247.
Kerisit, Sebastien N., & Prange, Micah P. Ab Initio Molecular Dynamics Simulation of Divalent Metal Cation Incorporation in Calcite: Implications for Interpreting X-ray Absorption Spectroscopy Data. United States. https://doi.org/10.1021/acsearthspacechem.9b00247
Kerisit, Sebastien N., and Prange, Micah P. Mon . "Ab Initio Molecular Dynamics Simulation of Divalent Metal Cation Incorporation in Calcite: Implications for Interpreting X-ray Absorption Spectroscopy Data". United States. https://doi.org/10.1021/acsearthspacechem.9b00247. https://www.osti.gov/servlets/purl/1574896.
@article{osti_1574896,
title = {Ab Initio Molecular Dynamics Simulation of Divalent Metal Cation Incorporation in Calcite: Implications for Interpreting X-ray Absorption Spectroscopy Data},
author = {Kerisit, Sebastien N. and Prange, Micah P.},
abstractNote = {Calcite (CaCO3) is a ubiquitous mineral with the ability to accommodate a wide range of impurities. Determination of the coordination environment and incorporation modes of impurities in calcite has historically relied primarily on the interpretation of extended X-ray absorption fine structure (EXAFS) spectroscopy. However, lack of standards combined with the large number of degrees of freedom involved in shell-by-shell fits have made the interpretation of EXAFS spectra challenging. As such, in this work, ab initio molecular dynamics (AIMD) simulations were performed to investigate the incorporation of seven divalent metal cation impurities, namely, Ba2+, Pb2+, Sr2+, Cd2+, Mn2+, Co2+, and Zn2+, in calcite. These cations span a wide range of sizes: 30.7 to –22.8% change in ionic radius with respect to Ca2+. The atomic trajectories were then used to compute EXAFS spectra for direct comparison with published experimental spectra. The simulations confirmed that all seven metal cations incorporate in calcite via substitution in the calcium site. The AIMD–EXAFS approach allowed for overcoming limitations of the shell-by-shell fitting approach, such as the difficulties in resolving weak backscatterers beyond the first coordination shell. As a result, the AIMD–EXAFS approach was able to provide a detailed and comprehensive characterization of the structural relaxation around divalent metal cation impurities in calcite.},
doi = {10.1021/acsearthspacechem.9b00247},
journal = {ACS Earth and Space Chemistry},
number = 11,
volume = 3,
place = {United States},
year = {2019},
month = {10}
}

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Cited by: 9 works
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Figures / Tables:

Table 1 Table 1: Root mean square deviations of experimental and calculated lattice parameters of carbonates with either the aragonite or the calcite structure per XC functional.

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