BER Structural Biology and Imaging Resources
Synchrotron, Neutron, and Cryo-EM
U.S. Department of Energy | Office of Science | Office of Biological and Environmental Research

X-Ray Absorption and Emission Spectroscopy

High-resolution structure, redox states, and bonding descriptions of metals in complex environments


Synchrotron-Based X-Ray Spectroscopy Techniques Enable Exploration of Metal Interactions in Biological and Biogeochemical Systems. Top and Bottom Left: Understanding the structure of the copper-dependent integral membrane metalloenzyme in methanotrophic bacteria that converts methane to methanol. Top right: Extended X-ray absorption fine structure (EXAFS) reveals the structure of the active site of a nitrogenase enzyme that converts dinitrogen (N2) to bioavailable ammonia (NH3), which is a fundamental step in the biogeochemical nitrogen cycle. Bottom right: Geogenic CO2 exhalations are excellent natural laboratories for studying the behavior of copper in soil. The natural gradients found in redox conditions and in soil organic matter enable interacting processes to be disentangled. [All images copyrighted. See credit information at bottom of page.]


Synchrotron-based X-ray spectroscopy techniques provide a powerful and synergistic toolkit to explore metal interactions within biological and biogeochemical systems and with the environment. These interactions can be observed on molecular scales to genomics-controlled mesoscales and include local environmental phenomena such as elemental uptake, catalytic behavior, storage, and bioavailability. The synchrotron-based X-ray spectroscopy suite encompasses standard and high-resolution X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES), extended X-ray absorption fine structure (EXAFS), and resonant inelastic X-ray scattering (RIXS).

Synchrotron-based X-ray spectroscopy techniques can probe how metalloproteins enable catalytic reactions like CO2 reduction and methane formation and how trace elements are involved in metabolism. They can also shed light on molecular transformations occurring in biogeochemical systems and processes by answering questions such as how the redox state and bonding description of a particular element evolve under various conditions and over time.

Instruments can be tuned to a specific element, providing complementary geometric and electronic structure information about the element and its nearest neighbors. The ability to probe one or more element independently under a variety of sample conditions allows detailed characterization of the chemistry in complex multifaceted systems. U.S. Department of Energy X-ray spectroscopy facilities can probe phosphorus through higher-atomic-number elements and enable structural dynamics studies on time scales into the sub-millisecond regime.

Key Features of X-ray Spectroscopy Techniques

  • Determination of the atomic-resolution geometric structure of metal sites in molecules (EXAFS)
  • Determination of oxidation states, metal-ligand interactions, bond strength, and structure-function correlation in molecules (XAS, XES, and RIXS)
  • Determination of metal geometry, redox, and bonding in a single X-ray spectroscopy experiment
  • X-ray energy range of 2 to 35 keV for studying phosphorus and higher-atomic-number elements
  • Capacity for diverse sample types, including ultra-dilute metalloenzyme solutions, environmental or biogeochemical solutions, crystalline and amorphous solids, metal-colloid complexes, clays and multiphase mixtures, and in situ reaction environments with time-resolved capabilities

BER Researchers Use X-ray Spectroscopy to Study:

  • Trace metal utilization in individual microbes and communities of organisms to understand their success or failure in ecosystems
  • Systems-scale consequences of metal and organic matter environments in biological, biomimetic, and bioinspired systems
  • Structure and function of metalloproteins and their intermediates in bioenergy, biogeochemical, and environmental enzymatic cycles
  • The role of metalloproteins in the global carbon cycle
  • Soil systems, both natural and environmentally compromised
  • Microbe-fungi interactions and the evolution of microbial communities
  • Biological remediation of toxic and radioactive waste

See more examples in Science Highlights

Sample Considerations

  • Versatile sample environments range from low cryogenic through room (and elevated) temperatures and are in either helium (for elements from phosphorus to scandium), anoxic nitrogen, or air.
  • Sample containment and preparation range from simple (“as-is”) to complex and are tailored to the experiment and X-ray energy range needs.
  • Liquid samples can be studied frozen, static, or flowing.
  • X-ray penetration of a sample depends on X-ray energy and sample density, thus the optimal approach to sample preparation varies between experiments.
  • X-ray spectroscopy can also be employed at less than 2 keV energies for low-atomic-number elements. These experiments require an in-vacuum environment, are surface sensitive, and are rarely used for biological/biogeochemical studies.
  • Users should discuss sample approaches with experts at the different beamline facilities.

X-ray Spectroscopy Beamlines at DOE User Facilities

Each beamline has unique characteristics. To determine the user facility and beamline best suited to your science questions, see additional information and beamline contacts at the links below.

Image Credits

Row 1, Image 1: Reprinted with permission from Elsevier from Sirajuddin, S., et al. 2014. “Effects of Zinc on Particulate Methane Monooxygenase Activity and Structure,” Journal of Biological Chemistry 289, 21782–794. DOI: 10.1074/jbc.M114.581363. Copyright 2014.

Row 1, Image 2: Reprinted with permission from Elsevier from Flores, R. M. 2014. “Chapter 3 – Origin of Coal as Gas Source and Reservoir Rocks,” In Coal and Coalbed Gas, 97-165. Ed. R.M. Fores, Elsevier. ISBN: 9780123969729, DOI: 10.1016/B978-0-12-396972-9.00003-3.

Row 1, Image 3: Reprinted with permission from Van Stappen, C., et al. 2019. “Spectroscopic Description of the E1 State of Mo Nitrogenase Based on Mo and Fe X-ray Absorption and Mössbauer Studies,” Inorganic Chemistry 58, 12365. DOI: 10.1021/acs.inorgchem.9b01951. Further permissions related to the material excerpted should be directed to the American Chemical Society.

Row 2, Image 1 and 2: Reprinted with permission from Elsevier from Ro, S. Y., et al. 2018. “From Micelles to Bicelles: Effect of the Membrane on Particulate Methane Monooxygenase Activity,” Journal of Biological Chemistry 293, 10457. DOI: 10.1074/jbc.RA118.003348.

Row 2, Image 3: Reprinted with permission from Mehlhorn, J., et al. 2018. “Copper Mobilization and Immobilization along an Organic Matter and Redox Gradient—Insights from a Mofette Site,” Environ. Sci. Technol52, 13698. DOI: 10.1021/acs.est.8b02668. Copyright 2018 American Chemical Society.