Stanford Synchrotron Radiation Lightsource

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 (Pt_xY) as catalysts for oxygen electroreduction.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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. 

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.

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). 

Sorption reactions on particle surfaces can dramatically affect the speciation, cycling and bioavailability of essential micronutrients (i.e. PO₄^3-, 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.