X-ray Absorption Spectroscopy

XAS is a core-level spectroscopy technique, using a photo-excited electron from a core level (e.g. 1s or 2p) to probe unoccupied valence levels as well as the neighboring atomic structure. The ionization of core levels requires photons in the energy in the X-ray range, and spectroscopy requires an intensive continuous energy-spectrum, hence XAS is carried out at synchrotron radiation sources that provide both.

The measurement is conducted by scanning the incident photon energy using a monochromator. Once a sufficient energy is reached to ionize the atom at its core level, the absorption steeply increases at what is known as an absorption edge. Every element in the periodic table has a unique absorption edge, making the technique conveniently element-specific. The portion of the spectrum around the edge, known as the X-ray absorption near-edge structure (XANES) is a rich probe for the electronic structure of the unoccupied states as the low-energy photoelectron occupies these states. Chemical information about the oxidation state and local geometry is obtained from the XANES. As the incident energy is increased, more energy is transferred to the photoelectron, exciting it to the continuum of states and enabling it to back-scatter from neighboring atoms within ca. 10 Å. The back-scattering of the photo-electron causes a quantum-mechanical overlap between its initial and final state, causing an oscillatory modulation of absorption, or the extended X-ray absorption fine-structure (EXAFS). The Fourier-transform of the EXAFS is a radial distribution function, from which bond distances, number and speciation of neighboring atoms can be extracted.

XAS is the core technique of our group, since it is powerful in observing the chemical state and atomic structure in catalysts, especially under reaction conditions.

Solvent Tuning of Properties of Iron-Sulfur Clusters in Proteins

November 29, 2007

Proteins containing iron-sulfur clusters are ubiquitous in nature and catalyze one-electron transfer processes. These proteins have evolved into two classes that have large differences in their electrochemical potentials: high potential iron-sulfur proteins (HiPIPs) and bacterial ferredoxins (Fds). The role of the surrounding protein environment in tuning these redox potentials has been a persistent puzzle in the understanding of biological electron transfer. Although high potential iron-sulfur proteins and ferredoxins have the same iron-sulfur structural motif, there are large differences in their electrochemical potentials.

The Structure of a Reaction Intermediate in Enzymatic Halogenation

March 31, 2008

Halogenated natural products play important roles as antibiotics, antifungals, and antitumor agents. The process of halogenation involves the replacement of a hydrogen with a halide (such as chloride or bromide), and is a challenging task for a synthetic chemist. However, the iron-containing enzymes in the haloperoxidase and halogenase families readily catalyze these reactions. It is thought that when this reaction occurs, the iron in the enzyme is at a high-valent Fe(IV) state, and that this species is responsible for removing a hydrogen atom (called an abstraction) from the substrate, creating a substrate radical, and that a halogen radical is subsequently transferred to the substrate to complete the halogenation reaction.

In situ Observation of Sulfur in Living Mammalian Cells: Uptake of Taurine into MDCK Cells

May 30, 2008

Sulfur is essential for life, playing important roles in metabolism and protein structure and function. Although information on sulfur biochemistry is highly desirable, it is an element that is difficult to study as it is not easily accessible with most biophysical techniques. However, sulfur x-ray absorption spectroscopy (XAS) is one such method and has become increasingly used for the study of sulfur in biological systems. Recently, a group of researchers from Stanford University, the University of Saskatchewan, SSRL, and ExxonMobil used SSRL's Beam Line 6-2 for an in situ sulfur XAS study of living mammalian cell cultures.

Insights into the Role of the Tyr-Cys Cross-link in Galactose Oxidase from Sulfur K-edge Spectroscopy

May 29, 2012

The continuous advancement of X-ray spectroscopic techniques allows us to probe the structure of biological machineries for smaller samples in more dilute concentrations and thus to ask tough scientific questions about problems that have not been possible in the past. Careful biochemical preparation and systematic analytical characterization resulted in galactose oxidase samples that could be interrogated by X-rays. This metalloenzyme contains a copper at its active site that is coordinated to a cross-linked tyrosine and cysteine ligand, which both are essential to convert alcohols and sugars to their oxidized aldehyde forms by oxygen molecule. The remarkable feature of this reaction that it is selective and does not results in formation of carboxylates (a form of vinegar).

Beamline 4-3 and the Rescue of Ancient Warships

May 29, 2012

Nearly 400 years ago, the Swedish warship Vasa sank to its watery grave. In 287 BCE, a Roman warship with its bronze naval ram sank after battle to the bottom of the sea. And in 1545, the flagship of Henry VIII’s navy, the Mary Rose, sank outside of Portsmouth while maneuvering to engage the French fleet. Using SSRL Beam Line 4-3, a team of SSRL and University of Palermo researchers measured x-ray spectra of the sulfur inside wooden sections of the Roman ram, revealing the kinds of sulfur hidden within.

Potential Implications for Cataract Formation - Redox Changes at the Sulfur Atom of Methionine

May 29, 2009

In a similar way to your old pick-up truck rusting in the driveway, your body experiences a continuous battle against the elements. A constant barrage of oxidative stress attacks your cells and their constituent parts, including proteins. Like rust-proof paint on your vehicle, you have defense mechanisms that seek to prevent damage before it starts. But also like your trusty truck, once a weakness in the armor presents itself, it can spread rapidly — and often unnoticed — until you suddenly discover significant damage. Numerous diseases, as well as aging itself, are linked to uncontrolled oxidative processes that lead to irreversible damage and ultimately death. Understanding these oxidative processes may lead toward stopping and possibly even reversing damage.

Microbial Life on the Seafloor: Where's the Energy?

February 22, 2010

New rock formed by deep undersea volcanoes does not stay bare long. Microbes quickly move onto these basalts to form communities in the form of biofilms. As these biofilms grow and develop, they change the geology of their environment, forming mineral deposits. Since many of these communities are deep in the cold ocean waters, where sunlight does not reach, they must use alternative sources of energy. What these might be is unknown, but a common theory posits that the microbes may be obtaining energy using materials from the rock itself.

The New Face of Protein-bound Copper: The Type Zero Copper Site

February 22, 2010

Copper is an essential ingredient for animal and plant life. Some proteins specifically bind copper for both structural and catalytic purposes. Up until now, mononuclear copper(II) ion binding sites fit into two categories, type 1 and type 2, defined by both their functional roles, structures, and the physical properties of the interactions.

Research Sheds Light on Workings of Anti-cancer Drug

May 24, 2010

Cells need copper to function, but too much copper can be toxic, leading to liver damage and neurological problems, as happens in disorders such as Wilson disease. The inorganic small molecule tetrathiomolybdate (TM), assumed to be a copper chelator, is commonly used to treat Wilson disease. TM may also be an effective treatment of some cancers by starving the cancer cells of the copper they need to grow. Despite its common use, its molecular mechanism was unknown.

Importance of Iron Speciation to Aerosol Solubility: Potential Effects of Aerosol Source on Ocean Photosynthesis

June 30, 2009

The world's animals depend on plants, plants depend on photosynthesis, and photosynthesis depends on iron. Despite a relative abundance of this element, iron in a form useable by plants can be rare. Living organisms require soluble iron, which generally comes from environments in flux since iron settles into stable minerals unavailable to life. Since around 30-40% of oceans are iron-limited, understanding the sources of soluble iron is critical to understanding oceanic ecosystems, which are responsible for taking significant amounts of carbon out of the air.

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