skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: The Difficult Chore of Measuring Coordination by EXAFS

Abstract

Neither the theory nor the interpretation of Extended X-Ray-Absorption Fine-Structure (EXAFS) spectroscopy requires assumptions of crystalline symmetry or periodicity. As a result, EXAFS is a tool applied to a wide range of scientific disciplines and to a wide variety of experimental systems. A simple enumeration of the atoms in the coordination environment of the absorber is often the primary goal of an EXAFS experiment. There are, however, a number of pitfalls in the way of an accurate determination of coordination number (CN). These include statistical limitations of the EXAFS fitting problem, empirical effects due to sample preparation, and the assumptions made about the physical structure surrounding the absorber in the course of data analysis. In this paper we examine several of these pitfalls and their effects upon the determination of CN. Where possible, we offer suggestions for avoiding or mitigating the pitfalls. We hope this paper will help guide the general EXAFS practitioner through the difficult chore of accurately determining CN.

Authors:
;  [1]
  1. Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States)
Publication Date:
OSTI Identifier:
21054578
Resource Type:
Journal Article
Resource Relation:
Journal Name: AIP Conference Proceedings; Journal Volume: 882; Journal Issue: 1; Conference: XAFS13: 13. international conference on X-ray absorption fine structure, Stanford, CA (United States), 9-14 Jul 2006; Other Information: DOI: 10.1063/1.2644458; (c) 2007 American Institute of Physics; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ABSORPTION SPECTROSCOPY; ATOMS; COORDINATION NUMBER; CRYSTALS; DATA ANALYSIS; FINE STRUCTURE; PERIODICITY; SAMPLE PREPARATION; SYMMETRY; X RADIATION; X-RAY SPECTROSCOPY

Citation Formats

Ravel, B., and Kelly, S. D. The Difficult Chore of Measuring Coordination by EXAFS. United States: N. p., 2007. Web. doi:10.1063/1.2644458.
Ravel, B., & Kelly, S. D. The Difficult Chore of Measuring Coordination by EXAFS. United States. doi:10.1063/1.2644458.
Ravel, B., and Kelly, S. D. Fri . "The Difficult Chore of Measuring Coordination by EXAFS". United States. doi:10.1063/1.2644458.
@article{osti_21054578,
title = {The Difficult Chore of Measuring Coordination by EXAFS},
author = {Ravel, B. and Kelly, S. D.},
abstractNote = {Neither the theory nor the interpretation of Extended X-Ray-Absorption Fine-Structure (EXAFS) spectroscopy requires assumptions of crystalline symmetry or periodicity. As a result, EXAFS is a tool applied to a wide range of scientific disciplines and to a wide variety of experimental systems. A simple enumeration of the atoms in the coordination environment of the absorber is often the primary goal of an EXAFS experiment. There are, however, a number of pitfalls in the way of an accurate determination of coordination number (CN). These include statistical limitations of the EXAFS fitting problem, empirical effects due to sample preparation, and the assumptions made about the physical structure surrounding the absorber in the course of data analysis. In this paper we examine several of these pitfalls and their effects upon the determination of CN. Where possible, we offer suggestions for avoiding or mitigating the pitfalls. We hope this paper will help guide the general EXAFS practitioner through the difficult chore of accurately determining CN.},
doi = {10.1063/1.2644458},
journal = {AIP Conference Proceedings},
number = 1,
volume = 882,
place = {United States},
year = {Fri Feb 02 00:00:00 EST 2007},
month = {Fri Feb 02 00:00:00 EST 2007}
}
  • Neither the theory nor the interpretation of Extended X-Ray-Absorption Fine-Structure (EXAFS) spectroscopy requires assumptions of crystalline symmetry or periodicity. As a result, EXAFS is a tool applied to a wide range of scientific disciplines and to a wide variety of experimental systems. A simple enumeration of the atoms in the coordination environment of the absorber is often the primary goal of an EXAFS experiment. There are, however, a number of pitfalls in the way of an accurate determination of coordination number (CN). These include statistical limitations of the EXAFS fitting problem, empirical effects due to sample preparation, and the assumptionsmore » made about the physical structure surrounding the absorber in the course of data analysis. In this paper we examine several of these pitfalls and their effects upon the determination of CN. Where possible, we offer suggestions for avoiding or mitigating the pitfalls. We hope this paper will help guide the general EXAFS practitioner through the difficult chore of accurately determining CN.« less
  • The chemical speciation of inorganic mercury (Hg) is to a great extent controlling biologically mediated processes, such as mercury methylation, in soils, sediments, and surface waters. Of utmost importance are complexation reactions with functional groups of natural organic matter (NOM), indirectly determining concentrations of bioavailable, inorganic Hg species. Two previous extended X-ray absorption fine structure (EXAFS) spectroscopic studies have revealed that reduced organic sulfur (S) and oxygen/nitrogen (O/N) groups are involved in the complexation of Hg(II) to humic substances extracted from organic soils. In this work, covering intact organic soils and extending to much lower concentrations of Hg than before,more » we show that Hg is complexed by two reduced organic S groups (likely thiols) at a distance of 2.33 Angstroms in a linear configuration. Furthermore, a third reduced S (likely an organic sulfide) was indicated to contribute with a weaker second shell attraction at a distance of 2.92-3.08 Angstroms. When all high-affinity S sites, corresponding to 20-30% of total reduced organic S, were saturated, a structure involving one carbonyl-O or amino-N at 2.07 Angstroms and one carboxyl-O at 2.84 Angstroms in the first shell, and two second shell C atoms at an average distance of 3.14 Angstroms, gave the best fit to data. Similar results were obtained for humic acid extracted from an organic wetland soil. We conclude that models that are in current use to describe the biogeochemistry of mercury and to calculate thermodynamic processes need to include a two-coordinated complexation of Hg(II) to reduced organic sulfur groups in NOM in soils and waters.« less
  • The formation and the structure of the ternary complexes of trivalent Am, Cm, and Eu with mixtures of EDTA+NTA (ethylenediamine tetraacetate and nitrilotriacetate) have been studied by time-resolved laser fluorescence spectroscopy, {sup 13}C NMR, extended X-ray absorption fine structure, and two-phase metal ion equilibrium distribution at 6.60 m (NaClO{sub 4}) and a hydrogen ion concentration value (pcH) between 3.60 and 11.50. In the ternary complexes, EDTA binds via four carboxylates and two nitrogens, while the binding of the NTA varies with the hydrogen ion concentration, pcH, and the concentration ratios of the metal ion and the ligand. When the concentrationmore » ratios of the metal to ligand is low (1:1:1-1:1:2), two ternary complexes, M(EDTA)(NTAH){sup 3-} and M(EDTA)(NTA){sup 4-}, are formed at pcH ca. 9.00 in which NTA binds via three carboxylates, via two carboxylates and one nitrogen, or via two carboxylates and a H{sub 2}O. At higher ratios (1:1:20 and 1:10:10) and pcH's of ca. 9.00 and 11.50, one ternary complex, M(EDTA)(NTA){sup 4-}, is formed in which NTA binds via three carboxylates and not via nitrogen. The two-phase equilibrium distribution studies at tracer concentrations of Am, Cm, and Eu have also confirmed the formation of the ternary complex M(EDTA)(NTA){sup 4-} at temperatures between 0 and 60 {sup o}C. The stability constants (log{beta}{sub 111}) for these metal ions increase with increasing temperature. The endothermic enthalpy and positive entropy indicated a significant effect of cation dehydration in the formation of the ternary complexes at high ionic strength.« less