Crystal of the Week: Ammonium Nitrate!

An interesting NSF-funded study this week examined trends in various cities and their residents’ quests for perfect lawns. That naturally led those of us involved in celebrating 2014 International Year of Crystallography to think of fertilizer, which naturally led to ammonium nitrate, a perfect crystal of the week….

Have you ever had your shoes, luggage, or hands swabbed by TSA when passing through an airport security checkpoint? The TSA officers are looking for trace residues of compounds used to manufacture explosives. One compound that their explosive trace detection (ETD) systems search for is ammonium nitrate (NH4NO3), a common fertilizing agent. All crops require nitrogen to grow, but even though 78 percent of our atmosphere is gaseous nitrogen (N2), the natural incorporation of nitrogen into the soil in sufficient quantities to supply the rapid growth of dense crop fields is poor. For this reason, farmers use fertilizing agents to supply additional nitrogen and promote crop growth.

Originally, farmers used urea to fertilize their fields. However, even though urea has a higher density of nitrogen than ammonium nitrate, it also tends to break down more quickly once exposed to the open environment of a field. For this reason, many farmers turned to ammonium nitrate as their fertilizer of choice. Ammonium nitrate is a white, crystalline solid at standard pressure and temperature. It’s also relatively stable under normal conditions. But if you expose ammonium nitrate to high temperatures, open flames, or significant mechanical shock (i.e., the detonation of an explosive), then ammonium nitrate decomposes very rapidly and very energetically—that is, the ammonium nitrate explodes.

Remember a catastrophic fertilizer plant explosion in West, Texas in 2013? Unfortunately, that plant had a large stockpile of ammonium nitrate, which was exposed to open flames as a fire spread through the facility. Likewise, the Oklahoma City federal building attack in 1995 was also fueled by detonating barrels of ammonium nitrate, among other compounds.

So, if you use ammonium-based fertilizers in your garden, be careful with their storage! Or better yet, take a cue from organic growers who use plant rotations to infuse nitrogen into their gardens in a more natural manner. One can also till plant waste back into garden beds or mix manure into the soil to supply nitrogen slowly as the organic matter decays.


Crystal of the Week: Luciferase!

A great story in the news this week had to do with bioluminescence:  Scientists have shown for the first time that deep-sea fish that use bioluminescence for communication are diversifying into different species faster than other glowing fish that use light for camouflage. The new research indicates that bioluminescence – a phenomenon in which animals generate visible light through a chemical reaction – could promote communication and mating in the open ocean, an environment with few barriers to reproduction.

Based on such an interesting story, and in particular – during this International Year of Crystallography – we thought it would be neat to look at how the proteins that cause bioluminescence in fish, fireflies, click beetles and other living organisms are studied by scientists and for what applications. Each bioluminescent species produces its own slight variation of the luciferase molecule, based on slight changes in the peptide sequence in the protein. Each protein is made of several hundred peptide units, which means each protein is composed of thousands of atoms. To understand the differences in luciferase molecules between species, scientists must be able to probe the atomic level. For protein crystallography experiments, scientists use high-intensity X-ray beams produced in facilities called synchrotrons.  In comparison to the visible light that our eyes can see, X-rays are also a type of light, except that X-ray photons are very high energy and have short wavelengths. The wavelength of an X-ray is about the size of the distance between two atoms in a molecule, which is key when trying to determine the structure of a luciferase protein. But first, a protein crystallographer studying luciferase has to remove the molecules from solution (the cytoplasm of the bioluminescent cells). By doing so, scientists grow tiny crystals of luciferase proteins, where the molecules are tightly packed into crystalline structures that would not form under natural conditions.

Within a cell, luciferase molecules mix with luciferin molecules in an enzyme-substrate complex to create the amazing blues and greens we see emitted by so many of nature’s wonderful creatures. In fact, the chemical reactions that occur for bioluminescence based on the luciferase-luciferin system represent some of the most efficient reactions in nature. The efficiency of a chemical reaction or process can be measured in terms of energy: more efficient reactions and processes return a greater fraction of the energy initially put into the system to drive it forward. For example, in comparison to a bioluminescent reaction, which tends to be 80-90% efficient (a return of 80-90% of the energy put into the reaction), using an incandescent bulb as a light source is poorly efficient. In the case of the incandescent bulb, only 10% of the energy is used to create light. The other 90% is essentially “lost” as heat, which also explains why incandescent bulbs are so hot to the touch!

Clearly, luciferase proteins have a lot to offer scientists, some of whom are already evaluating these molecules for use as possible eco-friendly light sources in the future.  Luciferase also has already been used to help investigators at crime scenes uncover traces of blood, as well as by blood banks to determine the viability of red blood cells. (Photo credit: Thinkstock)


Learning to like acid oceans: Purple sea urchins (Strongylocentrotus purpuratus) along the California and Oregon coasts may have the potential to genetically adapt to the acidic seawater associated with coastal upwelling, according to a team of NSF-funded researchers. Their study findings suggest that natural genetic variation and subsequent evolutionary change may lessen some of the adverse effects of ocean acidification. Learn more …


Sensorbots monitor the deep ocean: Deep-sea fish may meet some odd-looking creatures as researchers deploy Sensorbots to monitor environmental conditions in the ocean. The orb-shaped robots acquire details about pH, dissolved oxygen, and temperature and relay this data through brilliant blue pulses of light. High-speed cameras capture the information for future analysis. Learn more … 


Crystal of the Week: Iron!

An interesting piece on One Species at a Time featured NSF-funded Microbiologist David Emerson who studies microbes that feed on iron. Working at the Bigelow Laboratory for Ocean Sciences in Maine, Emerson studies Leptothrix lucretia and its potential for filtering water and other uses. However, the piece got us to thinking about iron and its many crystal forms, making it perfect for our Crystal of the Week in celebration of International Year of Crystallography

Modern materials engineers carefully manipulate iron for a variety of applications, ranging from ship hulls to steel foundations in skyscrapers to magnets to cookware. But the history of iron engineering actually dates back thousands of years to the earliest civilizations, and before engineers used iron, some of the earliest life forms on the planet developed metabolic systems that relied on iron for energy.

Like other transition metals, iron can exist in its metallic, neutral-charge state, or iron can undergo reduction and oxidation (“redox”) reactions, where electrons are gained or lost, to attain new charge states. Changes in the electronic structure of iron dictate how it bonds with other elements, such as oxygen. For example, iron (II), where the iron atom has lost two electrons, readily forms black FeO. If oxidized further, iron (III) can combine with oxygen to create Fe2O3, otherwise known as hematite, which is not only the color of iron rust but also chemically related. Another familiar iron oxide is magnetite (Fe3O4), which is used in magnets (pictured above). The chemical structure of this mineral is complex, based on a combination of iron (II) and iron (III), which disrupts electronic pairing within the structure, giving rise to its magnetic properties.

These minerals have a lot more in common than just their chemistry. These iron oxides, and many other iron hydrides and oxyhydroxides, are regularly used as basic pigments in everything from plastic to paint. In fact, you’re probably already familiar with some iron oxide-based pigments, such as “iron black” and “burnt sienna.” And if you’ve ever wondered how mascara can make eyelashes appear longer – think magnetite!

The family of iron oxides, however, represents only a small fraction of the family of iron-based compounds. Most iron used by engineers is in the form of steel, where different elements are added in varying amounts to alter the mechanical properties of the steel, as well as its susceptibility to oxidation. And let us not forget that iron is the fourth most abundant element in Earth’s crust, with everything beneath being molten iron and nickel (another alloy of iron!).


Researchers develop searchable pollen database: A multidisciplinary team of researchers at the University of Massachusetts Boston has developed the Human Impact Pollen Database, an online image resource of pollen from plants typically associated with human activities. Researchers worldwide can use this tool to study changes in modern as well as historical ecosystems. In addition, the resource includes data for studies of human-plant interactions during the last 1000 years.

The pollen reference images enable scientists to identify unknown plants, reconstruct past environments, assess the movement of plants, and, ultimately, examine human influences on the environment. The database can also assist researchers studying the nature and trajectory of climate change. Learn more… 

Image Credit: Fiske Center, University of Massachusetts Boston


As drifting microorganisms, individual phytoplankton species should be able to show up anywhere in the ocean, but they don’t. To learn why, NSF-funded researchers studied water temperatures (among several other factors) to see if they somehow limit phytoplankton distribution.

Through a combination of ocean sampling, experimentation and eco-evolutionary modeling, the team found evidence that the species evolved over time in response to local average ocean temperatures; essentially each species became best-suited to a local temperature. This adaptation prevents other species from moving in but also prevents the native species from invading areas beyond its local area.

Caption: Phytoplankton in a dark sea.

Credit: NOAA


A spectacular image of the Bubble Nebula (NGC 7635) demonstrates the potential of the One Degree Imager, located at the WIYN 3.5-meter telescope at Kitt Peak National Observatory. The imager is sensitive to visible light and features a 1000 megapixel camera. When capturing an image of a celestial object with the ODI, astronomers must translate what the telescope sees into something human eyes can see. To generate an image, the astronomers use a series of filters and assign different colors to each one. These colors roughly correspond to what the human eye would see. Learn more …

Caption:The Bubble Nebula.

Credit: T.A. Rector, University of Alaska, WIYN ODI team and NOAO/AURA/NSF


Crystal of the Week: Zircon!

A new NSF-funded study suggests that the magma sitting 4-5 kilometers beneath the surface of Oregon’s Mount Hood has been stored in near-solid conditions for thousands of years, but that the time it takes to liquefy and potentially erupt is surprisingly short—perhaps as little as a couple of months.

Well, if that weren’t interesting enough, zircon crystals form in magma, making it a great candidate for Crystal of the Week in celebration of 2014 International Year of Crystallography. No, Zircon is not a cartoon’s evil villain or even something passed off as a fake diamond (aka cubic zirconia). Zircon is FAR more interesting.

Zircon is EVERYWHERE in the Earth’s crust and is a bit of a historian, when it comes to crystallography, able to reveal its age fairly easily because of the way it forms and grows. As zircon crystals form in magma, they collect uranium. However, lead is also present, which comes from the decay of uranium after the crystal forms. The ratio of uranium to lead tells researchers how much time has passed since formation, allowing them to estimate not just the age of the crystal but things around that crystal. Because crystals grow in layers, as well, some compare zircon to the rings in tree trunks that reveal a tree’s age.  It’s not unusual for researchers to measure compositional changes in those rings to see how they correspond with geologic events, such as volcano eruptions.

Unlike cubic zirconia which sounds so similar to zircon, it doesn’t usually grow into very large crystals—most are very, very small like grains of sand.  Its greatest commercial use is as an opacifier in decorative ceramics, reportedly, but because of its naturally occurring radioactive properties, it must undergo metamictization to remove that radioactivity. 


Revealing early cosmic radiation: Researchers use the 10-meter South Pole Telescope to make the most precise measurement yet of the primordial radiation known as the Cosmic Microwave Background (CMB). The researchers have extracted important information on the dynamics of the early universe by measuring the small-scale structure in the CMB.

Learn more: South Pole Telescope Reveals Early Cosmic Radiation

Caption: The South Pole Telescope, which is funded by NSF, measures structure in the cosmic microwave background. Credit: Daniel Luong-Van, NSF


Crystal of the Week: Diamonds!

Come on.  How could we resist?  It’s Valentine’s Day after all…And if you can believe Yahoo’s search engine statistics, people love their diamonds on this love-entwined occasion. Reportedly, diamond earrings as a search term have spiked 370%, and have thus far been “the most popular jewelry search in the days leading up to Valentine’s.”  The search term, “engagement rings” also went up 177% this week, according to Yahoo.

That said, here at the National Science Foundation, our interest in diamonds is not relegated to one day a year and has more to do with science and logic than with any emotion. Indeed, diamonds are a symbol of love, but they are also precious for their amazing physical and chemical properties. Afterall, there are more things to do with diamonds than just put one on your finger. Here are just a few examples of how scientists and engineers use diamonds:

1.  Enormous synthetic diamonds are now grown quickly and cheaply in labs thanks to a technique known as chemical vapor deposition.

2.  Because they form within the bowels of our planet – in the Earth’s molten middle layer aka mantle – and are millions of years old, diamonds can tell us a lot about our geological history.

3. You may not want to give your beloved a flawed diamond, but in the case of materials for quantum computing, it’s the diamond’s defect that may make computation possible.

4.  Wastewater is often polluted with organic matter, not just heavy metals. Diamond electrodes are now used to treat wastewater by oxidizing organic pollutants — a cheaper, more environmentally friendly filtering method.

5.  Diamonds are extremely stable, so nanodiamonds — teeny tiny diamonds — are used to learn how nanoparticles interact with cells.

6.  The Large Hadron Collider uses diamonds to prevent stray particles from damaging sensitive electronics, but it turns out diamond sensors can also offer incredibly precise measurements of the timing of passing particles.

7.  Synthetic, industrial diamonds may provide just the right chemistry to transform atmospheric nitrogen into liquid and ultimately generate the valuable agricultural fertilizer ammonia.

8.  Apply the highest pressure possible with the strongest material known, and you can learn a lot about crystals. Laser-heated diamond anvil cells mimic pressure within Earth’s center and convert modest graphite into fabulous diamonds.

9. This same laser-induced process can also be used to reproduce the expected conditions and pressures within the cores of supergiant planets to learn more about what could or could not exist there.

10. Synthetic diamonds are as hard as real diamonds but are much cheaper. So inexpensive diamond drill bits are now used to cut through rocks.

11. Researchers now believe that black diamonds (aka carbonados) have extraterrestrial origins in the form of an ancient supernova. These diamonds drifted through space for more than a billion years before falling to Earth as a meteorite that shattered and dispersed into Brazil and the Central African Republic.

12. Diamond-coated precision tools have less friction, are more durable and are less likely to crack delicate materials as they’re made, such as ceramics used in the dental and medical industries.

13. Yes, even titanium yields to diamond’s properties. Diamond tools are used to drill precise holes in titanium parts for the aerospace industry.

14. Lastly, historian, author and President’s National Medal of Science winner Jared Diamond is a favorite among researchers for his ability to communicate the historical impact of scientific advances. Want to learn how discoveries change the world? Diamond’s your guy.

Happy Valentine’s Day and Happy International Year of Crystallography!


A Tropical Antarctic


Persistent pollen: Scientists participating in the International Ocean Drilling Program found pollen from tropical plant species, including tree ferns and palms, in deep sea cores drilled off the east Antarctic shelf. The sediments in the cores—laid down 48 to 55 million years ago in the early Eocene epoch—show that the tropical forest persisted for millions of years. The researchers also found that average temperatures remained a balmy 10 degrees Celsius (50 degrees Fahrenheit) during the Antarctic winter. The findings were reported in NatureLearn more…

Caption: Tree ferns and palms in New Zealand.
Credit: Sandra Paschier, Moinclair State University