X-ray Absorption Spectroscopy

Visualizing the Mechanism of an Ancient Pathway in the Carbon Cycle

July 14, 2023

In the Wood-Ljungdahl pathway (WLP), nature has devised one of the most elegant methods for the chemical transformation of carbon.1 The WLP is ancient, present in the last universal common ancestor to life on earth and is the only carbon fixation pathway known to produce more energy than is consumed in terms of net ATP. The WLP functions to scrub our atmosphere of the key greenhouse gas CO2, utilizing the carbon for energy and for the creation of cellular building material.

Experimental Station 15-2

Beamline 15-2 is an undulator experimental station dedicated to advanced hard x-ray spectroscopy. The end station is equipped with sub-corehole lifetime resolution x-ray emission spectrometers (a 7-crystal Johann spectrometer and a 8 crystal von Hamos instrument) as well as a high-throughput and high energy resolution (0.3eV) 40-crystal low-q x-ray Raman spectrometer.

Functional CeOx Nanoglues for Robust Atomically Dispersed Catalysts

October 31, 2022

Many practical catalysts, illustrated by those used for fossil fuel conversion and vehicle exhaust clean-up, consist of expensive noble metals dispersed on high-area porous solid supports. When the metals are atomically dispersed and isolated from each other, they offer new properties and the highest efficiency of metal use—with each metal atom accessible to reacting molecules. But applications of supported noble metal catalysts are usually limited by the loss of accessibility of reactants to the metals that results from metal aggregation (sintering) during operation.

Multiphase, Multiscale Chemomechanics at Extreme Low Temperatures: Battery Electrodes for Operation in a Wide Temperature Range

September 30, 2021

Lithium ion batteries (LIBs), which are widely used in consumer electronics ranging from mobile phones to electric cars, have enabled our electronics to become smaller and last longer on a charge. However, their functionality is limited by environmental conditions.

Deciphering the Mechanism of Enzymatic Methane Synthesis

June 30, 2021

The biosynthesis of methane is significant because this molecule is both a good source of energy and a greenhouse gas. Despite its importance, the processes by which methane is made is not well understood. Methane is synthesized by methanogens, archaea found in anaerobic conditions like bogs and the guts of mammals. Only these microbes are able to perform the tricky reaction of turning hydrogen gas and carbon dioxide into methane and water.

Long-term Evolution of Noncrystalline Uranium in Lake Sediments

June 30, 2021

Uranium contamination in our environment is a serious threat to public health. Successfully managing the problem to mitigate health impacts requires an understanding of how environments affect the different forms of uranium, the chemical reactions at work, and the molecular species that are created over time.

Copper and Zinc Forms in Bottom Ash from Solid Waste Incineration

March 31, 2021

When trash is burned for energy, a residue called bottom ash (BA) is left behind. Each year the European Union alone creates millions of tons of BA, which can be used for construction after treatment. It is concerning that BA may contain metals like copper and zinc that leach into the environment, potentially harming wild life and, people. The amount of these metals in the ash does not indicate whether the material is a potential hazard since these metals are more or less able to mobilize into the surrounding environment depending on factors like pH and the solubility of their chemical form. To better understand which chemical forms of copper and zinc exist in bottom ash and if there is much variation between different ashes, a team of scientists from Sweden analyzed six samples from different waste-to-energy plants.

Modern Methods Applied to a Past Poisoning at Minamata Japan

August 31, 2020

In the 1950’s and 60’s a poisoning occurred in Minamata Japan.  In addition to the people, the local cat population was affected with what was called “Dancing Cat Disease” and shortly thereafter neurological signs and symptoms became more prominent in people.  The sickness became known as Minamata Disease.  Eventually it was shown to be a form of organic mercury poisoning.  During the episode, pregnant women who were minimally or not obviously affected delivered infants who had neurological disorders such as seizures, microcephaly, and cerebral palsy.

The local company that caused the pollution employed a physician who played a role in determining the cause.  He found that cats fed chemical effluent from the factory quickly developed signs similar to those seen in people with Minamata Disease. He preserved samples of brain tissue from one of the cats, and remarkably, these samples still exist. An international team of researchers used sophisticated modern techniques to analyze these samples and determine the chemical form of mercury within the tissue.

Reversible Cation and Anion Redox in Lithium-rich Sulfide Battery Cathodes

May 31, 2020

While steady improvement of lithium-ion batteries has allowed electronic technologies to perform better, researchers are nearing a theoretical limit to lithium-ion battery capacity. One way to overcome this limit is to change the chemistry of materials to allow more electrons to exchange between anode and cathode per unit of material. Currently, LiCoO2 lithium-ion batteries transfer one electron per unit of cathode, but other lithium-based materials may allow for higher capacity. A team of researchers has investigated the Li-rich layered sulfide Li2FeS2 and a novel analog LiNaFeS2 as potential higher capacity alternatives since they can store 1.5 or more electrons per unit.

Quantification of Heterogeneous Degradation in Li-ion Batteries

June 30, 2019

The development of better rechargeable batteries for consumer electronics and electric vehicles is difficult due to the complex interplay of many chemical, spatial, and temporal factors. Taken together, these factors are called the chemomechanical interplay, which includes chemical degradation, chemical heterogeneity, and mechanical stress that cause the battery to lose functionality over many charging and discharging cycles. A team of researchers has developed a combined methods approach that allows quantification of the processes of chemomechanical interplay over diverse length and time scales.

Large-Scale Production of 119mTe and 119Sb for Radiopharmaceutical Applications

May 31, 2019

Radioisotope therapies improve on traditional chemotherapies by being finely targeted to only the diseased cells and leaving surrounding healthy cells unharmed. A promising radioisotope for therapeutic uses is 119Sb, which releases low energy Auger electrons that can kill cancer cells. A problem with widespread use of drugs using 119Sb is its short half-life of around 38 hours. A team of scientists from Los Alamos National Laboratory have developed a novel strategy for utilizing 119Sb.

Shared-Ligand Intermediates of Metal Exchange Visualized by Rapid Freeze Quench and Selenium EXAFS of Se-Labeled Metallochaperones. A Paradigm for Studying Copper-Mediated Host-Pathogen Interactions

January 30, 2019

To defend against infections, our phagocyte cells form a vesicle called a phagosome around pathogens, which then merges with a lysosome to form a phagolysosome. To terminate the threat, the phagolysosome gives the invading cell toxic doses of copper. However, some bacteria have evolved mechanisms for pumping the copper back out of the cell, avoiding toxicity. Understanding the enzymes involved in these complicated processes is important to our understanding of disease.

Copper Mobilization and Immobilization along an Organic Matter and Redox Gradient – Insights from a Mofette Site

January 31, 2019

While a small amount of copper is essential for living organisms, too much copper contaminating our soils can be toxic and pose a serious problem. Copper has an affinity for organic matter in soils, where it mainly exists in the two redox states Cu(I) and Cu(II). In soils that fluctuate in redox conditions, the mobility of copper through the environment can be hard to predict. Mofette sites, produced by CO2 degassing usually found in seismically active areas, are good natural laboratories due to their wide range of soil redox conditions and of soil organic matter composition within a small area. Near the sites of CO2 degassing, the soil is anoxic and organic matter does not decompose well. The soils transition to oxic conditions just a few meters away. A team of researchers studied the behavior of copper in the natural gradient of a mofette site in the Czech Republic.

Gold Nanoparticle Biodissolution by a Freshwater Macrophyte and Its Associated Microbiome

September 30, 2018

Nanotechnology, which focuses on materials that measure between 1 and 100 nanometers in at least one dimension, is being applied to diverse areas of research including medicine, electronics, and biology. Yet it is unclear how these engineered nanomaterials might interact with and affect environments and ecosystems.

Direct Observation of the Kinetics of Gas–Solid Reactions Using in-Situ Kinetic and Spectroscopic Techniques

August 31, 2018

Hydrogen sulfide (H2S) is a poisonous and corrosive gas created in industrial and natural systems. Copper oxide (CuO), a crystalline solid, can be used to clean H2S from emissions by forming various copper sulfide species, a reaction that is thermodynamically favorable but often does not go to completion in industrial applications.

Activation of MnO2 Catalysts by Mn3+ Ions

July 31, 2018

The more widespread use of solar electricity is not currently limited by the technology for generating energy from sunlight but by the storage of that energy, so that it can be used when needed.  Converting water to O2 and H2 via the oxygen evolution reaction (OER) is a fossil fuel free way to store energy for later use; catalysts that improve the efficiency of OER are being sought. Manganese oxide (MnO2) films are good catalysts of OER, with additional benefits of being acid-stable and earth abundant.

Redox-transformation Kinetics of Aqueous Thio-arsenic Species Determining Arsenic Sequestration by Organic Thiol Groups of Peat

June 30, 2018

Arsenic is a well-known toxin that can contaminate our drinking supplies. Understanding how arsenic finds its way into drinking water requires research into its interaction with environmental conditions that affect redox reactions, including interactions with iron, sulfur, and carbon.

Operando Spectroscopic Microscopy of LiCoO2 Cathodes Outside Standard Operating Potentials

September 30, 2017

Given our increasing dependence of rechargeable battery containing electronic devices, including electric cars, it is important to engineer these systems to mitigate potential for catastrophic battery failure. One possible source of lithium ion battery failure is over-discharge (over-lithiation) of the cathode, which can permanently damage the battery. Electronic battery management systems are programmed to prevent and identify such failures, but sometimes do not catch problems of over-lithiation when they occur. To better understand the characteristics of battery failure from over-discharging, a team of scientists studied the chemical and morphological changes that occur from over-lithiation of a lithium battery cathode.

An Oxygen-insensitive Hydrogen Evolution Catalyst Coated by a Molybdenum-based Layer for Overall Water Splitting

July 31, 2017

Molecular hydrogen (H2) is a promising carrier of energy for a future that uses more sustainable sources of fuel. H2 created from splitting H2O using renewable energy methods could result in no carbon footprint energy use. While methods of water splitting are being developed, reverse reactions are a problem.

Direct and Efficient Utilization of Solid-phase Iron by Diatoms

July 31, 2017

Diatoms, single-celled marine algae that create beautiful, symmetric cell walls composed of silica, are critical to ocean ecosystems. Responsible for up to 20% of photosynthesis in oceans, these phytoplankton are also an important part of Earth’s carbon cycles. The potential of diatoms and other phytoplankton to sequester atmospheric CO2 has led to geoengineering ideas like “iron fertilization” of oceans.

Biogenic Non-crystalline Uranium Identified as the Major Component of Uranium Roll-fronts

June 30, 2017

The radioactive element uranium is well-known for its role in nuclear energy. People mine naturally occurring uranium from deep sandstone deposits called roll fronts. Scientists have long thought that abiotic chemical reactions that occur over millions of years resulted in formation of crystalline uranium. An international team of scientists has challenged this basic theory, finding evidence for a different genesis for uranium in roll front deposits. 

Thermodynamic Preservation of Carbon in Anoxic Environments

May 31, 2017

While scientists recognize that oxygen-free soil stores large amounts of carbon, knowledge about the processes that protect and preserve carbon-rich molecules in these environments is lacking. In oxygen-rich soil, microbes break down organic molecules through aerobic respiration, allowing carbon to escape the ground as carbon dioxide gas.

Measuring Real-time Biological and Abiotic Manganese Oxide Reduction

May 31, 2016

The element manganese can have complex interactions with the environment, depending on the prevailing conditions. Manganese(IV) is a strong oxidant but can also bind to environmental toxins and heavy metals, rendering them less harmful. Both geochemical and microbial processes affect the reactions of manganese(IV) in the environment. A team of researchers were interested in following the complicated reactions and mineral products produced during the reduction of manganese(IV) under different environmental conditions.

Atomically Precise Electrocatalyst for Oxygen Evolution Reaction

March 31, 2016

The electrocatalytic conversion of carbon dioxide and water into useful chemicals and fuels is a promising way of mitigating greenhouse gas emissions and of providing sources for renewable energy. Part of these processes is the oxidation of water into molecular oxygen, a reaction that requires a catalyst. Previously, heterogeneous catalysts have been used, but adoption of homogeneous catalysts allows more understanding and fine-tuning of the atomic-level processes.

Geochemical Triggers of Arsenic Mobilization during Managed Aquifer Recharge

February 29, 2016

The practice of storing reclaimed or storm water by refilling an aquifer is called managed aquifer recharge (MAR). Advantages of MAR to regions vulnerable to drought or which have depleted aquifers include water storage for future use, reduced water loss of stored water from evaporation, and stabilization of the aquifers. However, refilling aquifers can change the chemistry, allowing naturally occurring toxins in aquifer sediments to dissolve into the water. Arsenic, a potential poison, is of particular concern, since use of MAR has led to arsenic-contaminated water.

Role of an Oxygen Vacancy Nanostructure on the Switchable Photovoltaic Effect in BiFeO3

February 29, 2016

The list of mechanical and electronic uses for oxide materials is continuously growing, piquing researchers’ interest in how the microscopic properties of these materials affect their functionalities. Oxygen vacancies, which affect electron hopping, have long been identified as a defect in oxide compounds, but researchers now view them as a way to create new, potentially useful, behaviors.

Identification of Highly Active Fe Sites in (Ni,Fe)OOH for Electrocatalytic Water Splitting

April 30, 2015

The sun provides more energy than what could ever possibly be consumed. However, switching to solar energy to end our dependence on fossil energy resources is made difficult not merely by how much is consumed, but rather by the pattern of how energy is used: significant amounts are consumed by road and air transportation and must be provided “on board” in the form of fuels. This problem could be solved with new devices that convert sunlight into renewable fuels, for example, by driving a light-induced current between two electrodes that split water by electrolysis into hydrogen and oxygen. Currently, the limiting step for the viability of this process is the oxygen evolution reaction (OER) that takes place at the anode. 

Unconventional Switching Behavior in La0.7Sr0.3MnO3/La0.7Sr0.3CoO3 Exchange-spring Bilayer

March 30, 2015

Advanced permanent magnets with low cost and high energy density are important for next-generation technologies, and one promising type of advanced magnet is the exchange spring magnet. This type of nanocomposite comprises two phases of magnetic materials: “hard” magnets, which can remain uniformly magnetized under large fluctuations in magnetic fields, and are often made of rare earth elements, and “soft” magnets, which have a high energy density but their magnetic states can easily be disturbed by small magnetic fields.

Experimental Station 10-2b

Beam line 10-2 is a wiggler end-station that splits time between the back hutch (BL10-2b), which is instrumented for x-ray absorption spectroscopy, and the front hutch (BL10-2a), which has a dedicated 2-circle diffractometer that is used for materials scattering. The beamline supports the use of multiple area detectors, as well as point detectors with a crystal analyzer for higher angular resolution. 

New Method Tracks Metal-ion Movement in Periplasmic Proteins

October 31, 2014

Copper is an essential element for many organisms, however, it becomes toxic to cells at high concentrations. Therefore, organisms have developed ways to tightly regulate cellular copper levels. An example of such a regulatory mechanism is the CusCBFA efflux pump in the bacterium Escherichia coli – a multi-protein system that removes toxic copper (Cu+) and silver (Ag+) ions from the space between the bacterium’s inner and outer cell membranes known as the periplasm. Researchers have recently obtained new insights into the mechanism of this system. This information may prove beneficial for the future development of antimicrobial drugs that shut down bacterial efflux pumps.

Experimental Station 13-3

Beam line 13-3 utilizes a spherical grating monochromator (SGM) on an elliptical polarized undulator (EPU) operating in the photon energy range from 230 eV to 1700 eV with full polarization control (linear vertical/horizontal and circular left/right) covering the C, O, F K-edges, 3d transition metal L-edges, and 4f rare-earth element M-edges.

Experimental Station 10-1

Beam line 10-1 is a wiggler side-station beam line for soft x-ray core-level spectroscopy. The endstation is equipped with a hemispherical photoelectron analyzer (SES-100), and detectors for Total Fluorescence Yield (TFY; Diode), Total Electron Yield (TEY; Channeltron) and Partial Electron Yield (PEY). It has a generic chamber that is compatible with both ex-situ and in-situ characterization of a large number of samples simultaneously. XAS can be recorded in AEY, TEY, FY yields.

Experimental Station 8-2

Beam line 8-2 can be used to probe a wide range of core levels using photoemission and x-ray absorption spectroscopies. At BL 8-2, currently only one end-stations is available for the general user program. The first end-station is a high throughput setup for soft x-ray spectroscopy measurement – upgrades in progress include a fixed position multipurpose chamber with a load lock system for high throughput sample loading, capable of probing a wide range of materials with absorption and photoemission techniques. 

Experimental Station 14-3a

Beam line 14-3a, located on the upstream table of the hutch of the BL14-3 bending magnet side station, is dedicated to bulk x-ray absorption spectroscopy of biological, materials, and geological samples in the tender x-ray photon energy range 2.1-5.0 keV. BL14-3 is the only beam line at SSRL capable of obtaining spectroscopy data at the phosphorous K edge. In this configuration the beam is unfocused over a size of 1 mm x 6 mm to allow for high energy-resolution measurements on homogenous samples.

Mass-selected Nanoparticles of PtxY as Model Catalysts for Oxygen Electroreduction

July 31, 2014

A team of researchers from the Technical University of Denmark and  the SUNCAT Institute at the SLAC National Accelerator Laboratory and Stanford University has demonstrated the superior performance of nanoparticles of platinum-yttrium (PtxY) as catalysts for oxygen electroreduction.

Correlation of Lithium-Ion Battery Performance with Structural and Chemical Transformations

April 30, 2014

Rechargeable lithium-ion batteries are widely used in applications ranging from consumer electronics to electric vehicles. An important feature of a high-quality battery is a long lifetime, i.e. a large number of possible charge-discharge cycles. However, every cycle introduces changes in the battery’s electrode material, limiting its cyclability. A research collaboration has recently examined the occurring structural and chemical changes in the electrode material during cycling and linked them to the performance of lithium-ion batteries.


Hydrogen Adsorption Induces Interlayer Carbon Bond Formation in Supported Few-Layer Graphene

February 28, 2014

Graphite and diamond are two distinct forms of the same element, carbon. Nevertheless, their properties could not be any more different. For instance, diamond is extremely hard and can be used in cutting tools. Graphite, on the other hand, is soft and used in pencils. Graphite can be converted into diamond in a process that usually requires very high pressure. However, scientists have recently suggested an alternative route to obtain diamond-like structures from graphite – at least on the nanoscale.

Revealing the Nature of Emergent Ferromagnetism at an Oxide Heterointerface

September 30, 2013

Perovskites are mineral oxides with unique properties of great interest to scientists. Many of these materials show remarkable transitions in their behavior. The perovskites lanthanum aluminium oxide (LAO) and strontium titanium oxide (STO), for instance, are insulators. However, when sandwiched together to an LAO/STO heterostructure, the material can conduct electricity at its interface. Researchers can tune conductivity and other emergent properties by doping the perovskites and hope to exploit heterostructures in future industrial applications such as new electronic devices.

Nanoparticulate FeS as an Effective Redox Buffer to Prevent Uraninite (UO2) Oxidation

August 31, 2013

Uranium (U) is one of the most prevalent radionuclide contaminants in soils and groundwater across the world as a result of nuclear fuel production, weapons manufacturing, and research activities. The environmental risks posed by U are determined largely by the degree of its mobility, which strongly depends on redox conditions.  Under oxic conditions, U(VI) is soluble and forms stable complexes with carbonate and calcium in groundwater.

Biotic-Abiotic Pathways: A New Paradigm for Uranium Reduction in Sediments

March 31, 2013

As part of a larger, DOE-funded investigation into bioremediation of uranium in contaminated aquifers, a group of SSRL scientists made a surprising discovery about how uranium ions behave in the environment. In addition to overturning current scientific models, this research will lead to more efficient, less costly methods for uranium cleanup and mining.

The Chemistry of Bromine in Terrestrial and Marine Environments

November 30, 2012

Recent work at SSRL has helped reveal a previously unrecognized wealth of bromine chemistry in the environment, where bromine in seawater has long been thought to exist as inorganic bromide, while bromides in soil were considered so unreactive that they've routinely been used as a hydrological tracer.

The reality bromine chemistry in the environment is much more complex. X-ray absorption spectroscopic (XAS) studies conducted by Leri, et al. at SSRL Beam Lines 2-3 and 4-3, as well as at the ALS and NSLS, reveal a complicated association between bromine and organic carbon in both sea water and soil.

A New Slant on a Cellular Balancing Act — the Copper-sensing Repressor of Mycobacterium tuberculosis

January 31, 2007

Scientists have discovered a gene for a protein that regulates the cellular response to copper in the bacterium that causes tuberculosis. These findings, reported in the January issue of Nature Chemical Biology, explain how a wide variety of bacteria control copper concentrations within their cells, and this understanding could lead to new treatments for tuberculosis.

Delocalized Molecular Orbitals of the [6Fe6S] Cluster of the FeFe-Hydrogenase

February 28, 2007

The FeFe-hydrogenases are of great interest because they can catalyze both the forward and reversed dihydrogen uptake/evolution reactions. Under optimal conditions a single molecule of FeFe-hydrogenase can produce approximately 9000 molecules of hydrogen per second. This translates into a theoretical capacity for refueling the hydrogen tank of the Space Shuttle within 30 minutes. Thus, hydrogenases are considered as desirable biological targets for hydrogen-based energy production and utilization technologies.

Structural Insights into FeMo Cofactor Biosynthesis

February 27, 2006

SSRL and Stanford scientists, in collaboration with a team from UC Irvine, have gotten the first look into how the metal active center of an enzyme that is largely responsible for fertilizing plants is assembled. This enzyme, which is called nitrogenase, certain bacteria employ to turn nitrogen from the air into a form that plants can use for healthy growth. In contrast to the enzymatic reaction, manufacturing nitrogen fertilizer chemically requires extreme pressures and temperatures and thus huge amounts of energy.

Holey Germanium - New Routes to Ordered Nanoporous Semiconductors

July 25, 2006

Porous nanoscale materials often have useful properties because of their proportionally large surface areas. Now, UCLA scientists have devised a way to make porous germanium, a semiconductor used in fiber optics and electrical components. This discovery means that nanoporous materials could soon be used to develop new kinds of solar cells or highly sensitive electronic sensors.

An Octahedral Coordination Complex of Iron(VI)

July 25, 2006

Chemists have synthesized and characterized a new, highly reactive form of iron that promises to deepen our understanding of this important element. Iron is found in abundance in the natural world, and in its ionized form plays a crucial role in virtually all living processes.

A Fern Fatale - X-ray Absorption Spectroscopy Imaging of an Arsenic-Loving Fern

September 25, 2006

The toxicity of arsenic is widely known, but perhaps less widely appreciated is that it's the level of toxicity critically depends on the chemical form. The fern Pteris vittata, is one of a small group of plants that actively accumulates to a startling degree - an arsenic hyperaccumuatlor. P. vittata absorbs arsenic from soil, typically present as the relatively benign arsenate, and changes its chemical form to arsenite, which is one of the more toxic kinds of arsenic. The plant thrives on this toxic regimen, and it most likely does this to defends itself from hungry herbivores. The ability of P. vittata to take up arsenic has generated much excitement because of potential applications for environmental cleanup of drinking water and of contaminated sites.

Structural Sequestration of Uranium in Bacteriogenic Manganese Oxides

October 30, 2006

Uranium contamination is a major concern at Department of Energy sites and decommissioned mining and ore processing facilities around the U.S. Migration of uranium has contaminated ground water in several locations, and the threat remains for further contamination unless costly measures are taken to isolate the contaminates and stop their spread.

Where Water is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster

November 30, 2006

Billions of years ago, primitive bacteria developed a way to harness sunlight to split water molecules into protons, electrons and oxygen-the cornerstone of photosynthesis. Now, a team of scientists has taken a major step toward understanding this process by deriving the precise structure of the catalytic metal-cluster center containing four manganese atoms and one calcium atom (Mn4Ca) that drives this water-splitting reaction. This catalytic center resides in a large protein complex, called photosystem II, found in plants, green algae, and cyanobacteria. The international team was led by scientists from LBNL, and includes scientists from Germany's Technical and Free Universities in Berlin, the Max Planck Institute in Mülheim, and from SSRL.

Compositions of Stardust Impact Tracks and Terminal Particles in Aerogel by Hard X-ray Microprobe at SSRL

December 19, 2006

An international collaboration that included researchers at SSRL has used x-ray scanning microprobe fluorescence techniques at BL6-2 to characterize the elemental chemistry of samples from comet 81P/Wild-2 brought back aboard the Stardust spacecraft last January. Twenty-three aerogel samples containing cometary particles were analyzed by the 175-member Preliminary Examination Team, and five of those samples were studied at SSRL. This collaboration provided the first look at the Stardust samples after the return, and results are presented in several publications in the December 15 issue of Science.

Reexamination of Lead(II) Coordination Preferences in Sulfur-Rich Sites:Implications for a Critical Mechanism of Lead Poisoning

December 21, 2005

Research performed at SSRL has provided insight into why lead is so damaging to the healthy development of young children. Scientists from the University of Michigan and Northwestern University used x-ray absorption spectroscopy at SSRL to understand how lead can interfere with proteins that help transform DNA blueprints into working proteins that run the body.

Damage by X-rays: A Case Study for Metallo-Protein Crystallography

September 30, 2005

X-rays intended to elucidate the structure of biomolecules may actually damage and alter key parts of the molecules. A research team led by a group from Lawrence Berkeley National Laboratory (in collaboration with researchers from Max-Planck-Institut Mülheim, ESRF, SSRL, and TU Berlin and Freie Universität, Berlin) discovered this while investigating the Mn4Ca complex, a site crucial for splitting water into oxygen during photosynthesis.

Characterization of a Genuine S=1/2 Fe(V) Complex

June 30, 2005

Iron metals oxidize to rust, losing electrons and gaining positive charge. Iron metals typically exist in an oxidation state of +2 or +3 (2 or 3 electrons less than a neutral iron atom). However, chemists have long thought that iron compounds with even higher oxidation states play important roles in enabling chemical reactions in metal-containing proteins.

The First Cadmium Enzyme - Carbonic Anhydrase 2 from the Marine Diatom Thalassiosira weissflogii

May 31, 2005

Cadmium is known to be extremely toxic to mammals, and is generally viewed alongside mercury as an environmental problem and toxic element that is not used by nature in any way. A Brief Communication in the May 5 issue of the journal Nature shows that we need to revise our opinion of cadmium. The paper reports the purification and characterization of a previously unknown metalloenzyme from the marine diatom Thalassiosira weissflogii that specifically uses cadmium to achieve its biological function. This is the first cadmium enzyme that has been discovered.

Catalyst Design: X-rays Cross-examine the Fuel Cell Volcano Plot

June 22, 2012

Changing the electronic structure of a metal in order to “tune” its affinity to catalytic reaction intermediates is a key element in catalyst design. Tailor-made catalysts with a carefully adjusted ratio of two or more different alloy components are particularly needed in fuel cells, which could efficiently power electric vehicles – without the range limitations of current batteries.

The Structure of the First Coordination Shell in Liquid Water

April 30, 2004

In ice, each water molecule is surrounding by 4 other molecules in a tetrahedral arrangement (left). The new result on liquid water shows that the molecules are connected only with 2 others. This implies that most molecules are arranged in strongly hydrogen bonded rings (middle) or chains (right) embedded in a disordered clusternetwork connected mainly by weak hydrogen bonds. The oxygen atoms are red and the hydrogen atoms grey in the water (H2O) molecules.

Remediation of Uranium-contaminated Ground Water at Fry Canyon, Utah

November 28, 2003

A new technology that acts like a giant underground filter is successfully beginning to clean up the uranium contaminating an aquifer in a remote Utah canyon. Uranium contamination in groundwater is a serious problem because the toxic metal can travel long distances in underground aquifers, which are vital sources of fresh water for people, animals and agriculture. Recent research at SSRL showed that the filters-called PRBs (permeable reactive barrier) do intercept uranium, but in an unexpected way that has important implications for monitoring, costs, and future technology selection.

X-ray Absorption Spectroscopy Catches the Chemical Form of Mercury in Fish

August 29, 2003

The presence of "methyl mercury" in fish is well-known, but until now the detailed chemical identity of the mercury has remained a mystery. In an x-ray absorption spectroscopy study published in the August 29 issue of Science (Science 301, 2003: 1203;Science now: Murky Picture on Fish Mercury), SSRL scientists report that the chemical form of mercury involves a sulfur atom (most likely in a so-called aliphatic form). The study presents significant new knowledge - because the toxic properties of mercury (or any element) are critically dependent upon its chemical form - and represents an important milestone in developing an understanding of how harmful mercury in fish might actually be. The study was carried out by SSRL staff scientists Ingrid Pickering and Graham George and postdoctoral fellow Hugh Harris using SSRL's structural molecular biology beam line 9-3. The very high flux, excellent beam stability and state-of-the-art detector technology allowed the team to measure samples of fish containing micromolar levels of mercury, much lower than had previously been possible.

Fate and Stability of Cr Following Reduction by Microbially Generated Fe(II)

May 30, 2003

Industrial activities have led to widespread chromium (Cr) contamination in the environment. Although Cr is an essential element for humans, the hexavalent form is toxic, mutagenic and carcinogenic. Consequently, the presence of Cr in the environment poses a serious threat to human and animal welfare. However, the toxicity of Cr is a function of oxidation state. For example, hexavalent Cr has a high solubility in soils and groundwater and, as a consequence, tends to be mobile in the environment.

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.

How were Lekythoi used in Ancient Greek Funeral Practices?

July 26, 2010

Anthropologists learn about ancient cultures through the objects left behind. Ritualistic artifacts give glimpses into the religious and belief systems of nonextant societies. Application of new techniques of chemical and structural analysis to the study of ancient objects can give more insight into how they were made and used.

A Bacterium that can Grow by Using Arsenic Instead of Phosphorus

December 14, 2010

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorous.  Although these six elements make up biomolecules such as nucleic acids, proteins, and lipids, it is theoretically possible that some other elements in the periodic table could serve similar functions.  In a paper published in Science, Wolfe-Simon et. al., describe a bacterium of the Halomonadaceae family, strain GFAJ-1 which appears to substitute arsenic for phosphorous to sustain its growth.

Synchrotron X-ray Analysis Demonstrate Phosphate-Bound Gadolinium in Skin in Nephrogenic Systemic Fibrosis

December 13, 2010

Nephrogenic systemic fibrosis, or NSF, is a relatively new disease in which the skin becomes hardened, joint movement becomes difficult and, in extreme cases, an excessive and sometimes fatal fibrosis tissue forms around organs. So far, NSF has only been observed in patients with kidney dysfunction who have undergone an MRI that required the injection of gadolinium-based contrast agents (GBCAs). Researchers speculate that the patient's kidneys cannot break down the gadolinium, causing NSF, but until now there has been no direct evidence for such a link.

Electrochemical Surface Science: Hard X-rays Probe Fuel Cell Model Catalyst in situ

December 14, 2010

Researchers at SSRL have developed a new, more powerful way to probe the behavior of a key component in hydrogen fuel cells. The group, led by Daniel Friebel of SSRL and Anders Nilsson of SSRL and SIMES, coated a single crystal of rhodium with one layer of platinum atoms, creating a platinum catalyst that was in essence "all surface." The unique sample design allowed them to observe how the catalyst surface interacted with the type of acid–water environment typical of fuel cells.

Electronic Structure of O2-Bound Metal Sites in Biomimetic Model Complexes

March 28, 2011

Dioxygen (O2), critical for many of our cellular processes, is carried and activated by a variety of enzymes. These enzymes contain metals that contact the oxygen in different ways to form reactive intermediates. Oxygen’s reactivity is affected by the arrangement of the enzymes’ amino acid residues. Often, the enzyme active site will have a unique structure to stabilize oxygen binding.

Estimating Cr(VI) in Coal-Derived Fly-Ash

June 27, 2011

The element chromium is found in the environment in two common forms: Cr(VI), which is easily absorbed by the human body, and Cr(III), which is not. The first of these in the form of chromates can have severe adverse effects on the human body, including cancerous tumor formation and gene damage.  Normally Cr(VI) forms are not present in the approximately one billion tons of coal used annually for electricity generation in the U.S., however, a fraction of the Cr(III) in coal can become oxidized during coal combustion ending up as a Cr(VI) component in fly-ash, the major waste product from coal combustion. 

Structure and Reactivity of a Mononuclear Non-Haem Iron(III)–Peroxo Complex

November 28, 2011

The life-sustaining element oxygen can’t do its job alone. Specialized enzymes, containing metallic elements including iron, cause O2to split into two separate oxygen atoms.  In this form, oxygen can react with other biological molecules. The precise mechanism of oxygen activation by iron complexes has long eluded researchers, in part because the reaction—which proceeds through multiple intermediate stages—happens in mere fractions of a second.

Manganese-II Oxidation: A Biotic and Abiotic Process

December 12, 2011

Manganese, one of the most abundant metals in soils and rocks, is important to the health of the environment: As it cycles between manganese-II and nanocrystalline manganese-III/IV oxides, it plays an important role in controlling the cycle and transport of soil nutrients and contaminants.  Yet because the process is kinetically hindered, manganese will not oxidize rapidly in air; manganese needs a catalyst, often bacteria, to spur the process into action.

Towards the Chemically Specific Structure of Amorphous Materials: Anomalous X-ray Scattering from a Molybdenum-Germanium Alloy

November 29, 2002

Attempting to determine and describe the atomic arrangements in an amorphous material is a daunting prospect. A considerable advance has been made in the anomalous X-ray scattering approach to determining these arrangements in materials containing two atomic species.

Plants with the Midas Touch: Formation of Gold Nanoparticles by Alfalfa Plants

July 31, 2002

In the well-known Greek legend the touch of King Midas would convert anything to metallic gold. Recently, a team working at SSRL lead by Professor Jorge Gardea-Torresdey from the University of Texas at El Paso have shown that ordinary alfalfa plants can accumulate very small particles (nanoparticles) of metallic gold (1). The best-known materials that contain nanoparticles of metallic gold are gold colloids. These lack the familiar metallic luster, but show bright colors which range from red, violet or blue, depending upon the size of the nanoparticles (2,3). 

Bacterial Sulfur Storage Globules

January 31, 2002

Sulfur is essential for all life, but it plays a particularly central role in the metabolism of many anaerobic microorganisms. Prominent among these are the sulfide-oxidizing bacteria that oxidize sulfide (S2-) to sulfate (SO42-). Many of these organisms can store elemental sulfur (S0) in "globules" for use when food is in short supply (Fig. 1). The chemical nature of the sulfur in these globules has been an enigma since they were first described as far back as 1887 (1); all known forms (or allotropes) of elemental sulfur are solid at room temperature, but globule sulfur has been described as "liquid", and it apparently has a low density – 1.3 compared to 2.1 for the common yellow allotrope α-sulfur.

Intercation of Toxic Metals with Complex BioFilm/Mineral/Solution Interfaces

November 30, 2001

Sorption reactions on particle surfaces can dramatically affect the speciation, cycling and bioavailability of essential micronutrients (i.e. PO43-, Cu, Zn etc.) and toxic metals and metalloids (i.e. Pb, Hg, Se, As) in soils and aquatic environments. Considerable attention has been focused on understanding metal sorption reactions at a molecular/mechanistic level and the effects of metal concentration, pH, ionic strength, and complexing ligands on the ways in which metal ions bind to the surfaces of common mineral phases such as Fe-, Mn- and Al-(hydr)oxides and clays. However, a significant fraction of mineral surfaces in natural environments are extensively colonized by microbial organisms, which can also be potent sorbents for metals due to the large number of reactive functional groups that decorate the cell walls and outer membranes of bacterial surfaces. 

Experimental Station 11-2

Beam line 11-2 is a high-flux XAS station dedicated to molecular biogeochemical and interface sciences. It is optimized for challenging XAS measurements on dilute or radioactive samples and interfaces. To support these experiments, BL11-2 is equipped with collimating and focusing optics, a "double double" Si(220) LN2-cooled monochromator, and a 100-pixel monolithic solid state Ge detector array.

Experimental Station 9-3

Beam line 9-3 is a wiggler side-station dedicated to biological x-ray absorption spectroscopy and EXAFS measurements of dilute solutions and single crystals. BL9-3 is equipped with a 100-element Ge monolithic solid-state detector in addition to ionization chambers and PIPS/Lytle detectors. A dedicated LHe cryostat allows for routine low temperature measurements on solutions. A Huber-Kappa goniometer, a LHe cryostream, a focusing polycapillary and a MAR CCD detector are available (in addition to specialized software) for single crystal measurements.

Experimental Station 7-3

Beam line 7-3 is a wiggler side-station dedicated for x-ray absorption spectroscopy and EXAFS measurements on dilute biological systems. BL7-3 is equipped with a 30-element Ge solid-state detector in addition to ionization chambers and Lytle/PIPS detectors. A dedicated LHe cryostat allows for routine low temperature measurements. The unfocused beam on BL7-3 is ideal for samples especially susceptible to radiation damage, such as high-valent intermediates and other oxidized species.

Experimental Station 4-3

Beam line 4-3 is a wiggler side-station dedicated for x-ray absorption spectroscopy and EXAFS measurements on biological, environmental, catalysis, and materials systems. This station enables tender x-ray measurement (S K-edge and up, i.e. 2.4-5 keV) in addition to hard x-rays ( up to 11 keV).  It is setup with a He flight path from the beam line optics to the sample. The beam is collimated and unfocused to allow for high energy-resolution measurements on homogenous samples.

Experimental Station 4-1

Beam line 4-1 is a high-flux station optimized for x-ray absorption spectroscopy and EXAFS experiments requiring x-rays with energies between ~ 6 and 38 keV.  This energy range includes most of the transition metals (all rows), lanthanides and actinides, P-block elements, alkaline and alkaline earths.

Experimental Station 2-2

Beam line 2-2 is a bending magnet side-station beam line for x-ray absorption spectroscopy, Quick-EXAFS, and EXAFS measurements of samples with absorption edges in the energy range 4.5 - 37 keV. BL2-2 is equipped with a water-cooled double crystal monochromator, with multiple crystal sets available [Si(111), Si(220)]. Available detectors include ionization chambers, Lytle, 13-element Ge array, and Vortex detectors. Specialized facilities for in-situ catalysis research include gas handling systems and mass flow control.  The beam line sees limited use for white beam experiments.

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