Tag Archives: Crystalography

The discovery of quasicrystals —crystalline structures that show order while lacking periodicity—forced a paradigm shift in crystallography. Scanning tunneling microscopy image (measuring 15 nm x 10 nm) showing individual surface atoms in a new two-dimensional quasicrystal. (c) Wolf Widdra

2-D quasicrystals discovered by accident: chem structure not that impossible it seems

The discovery of quasicrystals —crystalline structures that show order while lacking periodicity—forced a paradigm shift in crystallography. Scanning tunneling microscopy image (measuring 15 nm x 10 nm) showing individual surface atoms in a new two-dimensional quasicrystal. (c)  Wolf Widdra

The discovery of quasicrystals —crystalline structures that show order while lacking periodicity—forced a paradigm shift in crystallography. Scanning tunneling microscopy image (measuring 15 nm x 10 nm) showing individual surface atoms in a new two-dimensional quasicrystal. (c) Wolf Widdra

Scientists from Germany have developed by accident a peculiar new substance consisting of 12-sided, non-repeating atomic units. Typically this weird structure is called a quasicrystal, a chemical structure thought impossible a few decades ago. Pioneering work on this subject landed Professor Daniel Shechtman the Nobel Prize for Chemistry in 2011.

Klaus Meinel, Stefan Forster and Wolf Widdra, scientists  at Germany’s Martin Luther University, were making trials with an interface made out of two materials under various conditions to engineer properties not found in nature (meta-material). Totally by accident, the team ended up replicating the conditions necessary for the formation of a quasicrystal – crystals that break all the rules of being a crystal at all. Quasicrystals are structural forms that are ordered but not periodic. They form patterns that fill all the space though they lack translational symmetry.

Most crystals are composed of a three-dimensional arrangement of atoms that repeat in an orderly pattern. Depending on their chemical composition, they have different symmetries. For example, atoms arranged in repeating cubes have fourfold symmetry. Atoms arranged as equilateral triangles have threefold symmetries. But quasicrystals behave differently than other crystals. They have an orderly pattern that includes pentagons, fivefold shapes, but unlike other crystals, the pattern never repeats itself exactly.

A crystal that shouldn’t exist

Neither repetitive, nor disorganized in structural quasicrystals have bewildered and astonished scientists. Shechtman, the scientist who first worked with these peculiar structures and who was awarded the Nobel Prize for Chemistry in 2011, was ridiculed for his ideas and findings. Quasicrystals requires extremely precise conditions to form, including vacuum and an argon atmosphere. This has prompted many to claim these are improbable to find in nature. In 2007, however, Shechtman and geologist Luca Bindi from the University of Florence discovered strange quasicrystal-like formations inside a rock from Bindi’s collection. The rock in question was actually a meteorite, and following analysis indeed confirmed that the scientists were looking at quasicrystals. The researchers proved in 2012 that the crystals were formed in space by astrophysical phenomenonae, and not as a consequence of Earth collision or atmosphere entry. This demonstrated that quasicrystals could be found anywhere in the Universe.

Model building blocks of the  12-sided quasicrystal. (c) Wolf Widdra

Model building blocks of the 12-sided quasicrystal. (c) Wolf Widdra

In Germany, the Martin Luther Uni scientists were studying how a certain kind of mineral called perovskite behaved when layered atop metallic platinum. The perovskite film was heated to high temperature. Upon inspection they found a 12-fold symmetry pattern – something that was thought to be impossible. Forster tried to resolve the 12-fold pattern, which clearly now was possible sitting right in front of them, into two groups with six-fold symmetry. It wasn’t possible. The only viable explanation was that they   had created a thin, two-dimensional quasicrystalline layer.

“We were very surprised,” Widdra said. “It took quite a while until we were convinced that we had a new form of two-dimensional quasicrystal.”

The resulting quasicrystal is made out of  12-sided, dodecagonal arrangements with internal patterns of squares, triangles, and rhomboids. “They have a perfect order, but never repeat themselves,” Widdra said.

“This is another beautiful example of just how commonly quasicrystalline structures form,” said physicist Alan Goldman of Iowa State University and the U.S. Department of Energy’s Ames Laboratory, who was not involved in this study. “The number of examples continues to grow and continues to surprise us.”

The actual mechanics of quasicrystal formation are largely unknown so far. Why some materials can retain this structures and other can not is still a mystery.

“We really don’t understand why,” Goldman said. “Each new system provides us with some clues, and the more examples we find, the closer we come to answering that question.”

The 12-sided 2-D quasicrystal was described in a paper published in the journal Nature. [via Wired]

 

The Martian sand collected by the Curiosity rover turns out to be similar to volcanic soil on Hawaii, NASA scientists say. (c) AP

Mars bite tastes like Earth – soil similar to Hawaii

The Martian sand collected by the Curiosity rover turns out to be similar to volcanic soil on Hawaii, NASA scientists say. (c) AP

The Martian sand collected by the Curiosity rover turns out to be similar to volcanic soil on Hawaii, NASA scientists say. (c) AP

After Curiosity had a bite of Martian turf at the site of Rocknest a few days earlier, soil analysis results have finally come in. According to scientists at NASA, the Martian sand in the rover’s vicinity is very much akin to volcanic soils found on Earth such as those of  Hawaii. Though Mars is far from being a resort itself.

The findings follow a slew of premiering successes from Curiosity, as the high-tech lab on wheels recently performed for the first time analysis using the alpha particle X-ray spectrometer at the end of its arm, and shot the ChemCam laser on its mast at spots up to 23 feet away to analyze the rock it vaporizes. The next instrument in lined was  its chemistry and mineralogy module, known as CheMin, which bombards soil samples with X-rays to reveal their mineral composition and abundance.

Like I said, Curiosity successfully trialed other instruments on-board in the past few weeks, some of which also offered detailed elemental analysis. But knowing what atoms and molecules make up a sample is far from being enough, since the manner in which they are arranged counts just as much. Take carbon for instance, the most famous allotrope; it can occur as graphite, a very soft material typically used in pencils, or diamond, one of the hardest materials known to man. So you see while the chemical mark-up is the same, the way the carbon atoms are connected with one another makes all the difference in the world.

The instrument, called CheMin, for chemistry and mineralogy, is a marvel of miniaturization. No larger than a shoe box, it fits inside the rover and does the same analytic work as X-ray diffraction instruments the size of refrigerators. After  Curiosity uses a scoop at the end of its arm to collect soil, it carefully positions the tablet sized sample in the CheMin instrument. Before analysis can begin, however, the instruments shooks the sample 2000 times per second to filter out larger grains; the remaining crystals are then bombarded with X-rays in order to revelad their precise atomic structure. This was the first time X-rays from Earth have been deployed on an alien planet.

Roughly half the Martian soil, NASA scientists say, appears to be noncrystalline particles, meaning they’re like obsidian, a form of volcanic glass that the CheMin instrument’s x-rays cannot probe. This will be tasked to other instruments.

The Curiosity Rover main objective in its 2-year mission is that of reaching the Gale Crater’s Mt. Sharp, a 3-mile-high mountain in the middle of the crater whose lower layers may hold clues to whether Mars is capable of sustaining life or not.

Free-electron X-ray laser reveals protein architecture at unprecedented detail

Curious enough, one hundred years after renowned physicist Max von Lauefirst used X-ray diffraction to unravel the intricate atomic architecture of molecules, a team of international scientists have analyzed tiny protein crystals at an unprecedent scale of resolution, premiering in the process the world’s first hard X-ray free-electron laser. Called the Linac Coherent Light Source at Stanford, the X-ray laser was made possible after a 300 million dollars investment from behalf of the US Department of Energy.

Most of our current knowledge regarding the 3D spatial architecture of molecules has come as a result of X-ray crystallography, a field of science which has seen much progress in the past few decades, making possible equally amounts of achievements in molecular analysis.  Crystalography basically studies the spatial arrangements of atoms in solids. Modern crystallography relies on the amplification of the scattering signal of the molecules by their arrangement into relatively large crystals, often on the order of some tenths of a millimeter.

Large crystals, extremelly helpful for accurate analysis, are very difficult to obtain, however, especially in the case of bio-molecules due to instability and low abundance. This is where free-electron lasers come in, revealing structural information from crystals otherwise unobtainable through conventioanl methods, since radiation irremedially damages them before anything useful can be drawn.

The innovative X-ray free-electron lasers are new X-ray sources of extreme potency, capable of releasing high intensity ultrashort flashes of light. The intensity of such an X-ray pulse is more than a billion times higher than that provided by the most brilliant state-of-the-art X-ray sources, with a thousand-fold shorter pulse length, on the order of a few millionths of a billionth of a second, or femtoseconds. These properties provide scientists with novel tools to explore the nano-world, including the structure of biological materials.

This extremely high frequency of firing light flashes allows the X-ray free-electron laser to record information from the sample before damage irremediably occurs. The crystals samples are destroyed in the process, much like by conventional means, but it’s so fast it gets what it needs from the crystal before interferring damage gets a change to disrupt analysis.

The structure of the protein lysozyme, the first ever molecule to have its architecture revealed. Depicted is the schematic of the spatial arrangement of the 129 amino acids shown in the form of spirals (helices) and arrows (pleated sheets). © MPI for Medical Research

The structure of the protein lysozyme, the first ever molecule to have its architecture revealed. Depicted is the schematic of the spatial arrangement of the 129 amino acids shown in the form of spirals (helices) and arrows (pleated sheets). © MPI for Medical Research

To benchmark the method, the researchers investigated the structure of an exhaustively studied molecule, the small protein lysozyme, the first enzyme ever to have its structure revealed. Ten thousand snapshot exposures from crystals that measured only a thousandth of a millimeter, showed that the data compared well with those collected using conventional approaches and hundred-fold larger lysozyme crystals.

“This proof-of-principle experiment shows that the X-ray free-electron laser indeed lives up to its promise as an important new tool for structural biology on large macromolecular assemblies and membrane proteins. It really opens up a completely new terrain in structural biology”, Ilme Schlichting, leading the Max-Planck team, says.

The reserach was spearheaded by scientists at the Max Planck Institute for Medical Research in Heidelberg and the Max Planck Advanced Study Group in Hamburg. The findings were reported in a recent edition of the journal Science – you can read more about it in the magazine.

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