Tag Archives: molecules

Scientists record video of atoms forming chemical bonds in real time

Using transmission electron microscopy (TEM) to both image and energize a bunch of atoms, scientists have for the very first time recorded footage of atoms forming and breaking bonds in real time.

“To our knowledge, this is the first time when bond evolution, breaking and formation was recorded on film at the atomic scale,” said Andrei Khlobystov, professor at the University of Nottingham and one of the lead authors of the new study.

https://www.youtube.com/watch?time_continue=1&v=byEqhd5Bpr4&feature=emb_title

TEM resembles traditional film photography, in the sense that it blasts a beam of electrons onto a very thin sample to produce images of such a high resolution that individual atoms can be discerned.

Chemical bonding takes place a microscopic scale of about half a million times smaller than the width of a human hair.

Imaging the ultra-fast processes that occur in such a tiny world was a huge challenge but the international team of researchers rose to the occasion.

The researchers, which included scientists from the University of Nottingham and the SALVE Project at the University of Ulm, introduced pairs of rhenium atoms into a nano-test tube made of single-walled carbon nanotubes. An individual rhenium atom is just 205 picometers across, or 205 trillionths of a meter, whereas a carbon nanotube’s diameter ranges from one nanometer to a few nanometers.

The rhenium atoms bonded right to the side of the carbon nanotubes, forming a quadruple bond between them — and this confinement proved critical for focusing and recording footage of the atomic bonding. Writing in the journal Science Advances, the authors explain that the curvature of the nanotubes influences the bonding modes available to the rhenium atoms to form rhenium molecules.

“It was surprisingly clear how the two atoms move in pairs, clearly indicating a bond between them,” said Kecheng Cao, an author of the study. “Importantly, as Re2 moves down the nanotube, the bond length changes, indicating that the bond becomes stronger or weaker depending on the environment around the atoms.”

Eventually, the researchers managed to record videos of the atoms forming pure metal-metal bonds in real-time. What’s more, the microscope’s electron beam not only recorded the experiment but also facilitated it by adding electron energy.

In the video, the atom pairs (black dots) travel along the narrow gap between the carbon nanotubes. When the length of the bond exceeded the size of the atoms, the bond broke. After traveling independently for a while, the two atoms reformed once more into a molecule because this more stable configuration lowers their energy.

The findings are exciting not just because they signify an unprecedented achievement, but also because they add to our knowledge of metallic bonds, which are still quite mysterious. Metallic bonds are notoriously difficult to study because other atoms and molecules are drawn to interact with them, distorting bond length and other factors that scientists would like to measure.

Buckyballs in space: how complex carbon molecules form in space

An artist’s conception showing spherical carbon molecules known as buckyballs coming out from a planetary nebula — material shed by a dying star. Researchers at the University of Arizona have now created these molecules under laboratory conditions thought to mimic those in their ‘natural’ habitat in space. NASA/JPL-Caltech

The mystery of how complex carbon molecules with a ‘soccer-ball’ type structure–nicknamed buckyballs–came to be found in interstellar space has puzzled scientists for some time.

But now, a team of researchers from the University of Arizona have proposed a potential formation mechanism for carbon-60 (C60)–a spherical molecule comprised of 60 carbon atoms in ring-like structures–in space.

The team discovered that silicon carbide dust left behind by dying stars then bombarded by high energy particles and extreme temperatures could shed silicates leaving behind pure carbon needed to create C60.

Their results are published in the journal Astrophysical Journal Letters.

The detection of buckyballs–named for their similarity to the dome-like architecture of Buckminister Fuller– and even larger C70 molecules a few years ago caused a rethink of the theory that such molecules could only be formed in the lab.

Additionally, and more importantly, the discovery overturned the idea that only light molecules–up to around 10 atoms–could be found scattered through interstellar space.

Another surprise emerged from the fact that the molecules detected were pure carbon.

In the lab, C60 is created by blasting together pure carbons sources such as graphite. This process should be almost impossible in the planetary nebulae that the interstellar C60 was found. This is because this environment– debris created in the violent death throes of stars–has about 10,000 hydrogen molecules for every carbon molecule.

“Any hydrogen should destroy fullerene synthesis,” says Jacob Bernal, an astrobiology and chemistry doctoral student and lead author of the paper. “If you have a box of balls, and for every 10,000 hydrogen balls you have one carbon, and you keep shaking them, how likely is it that you get 60 carbons to stick together?

“It’s very unlikely.”


Bernal and his team began investigating this conundrum with the aim of uncovering a potential C60 formation mechanism when they realised that the transmission electron microscope (TEM) located at the Kuiper Materials Imaging and Characterization Facility at the University of Arizona, was able to simulate the planetary nebula environment fairly well.

TEM’s 200,000-volt electron beam is able to probe matter down to 78 picometers in order to see individual atoms. The beam also operates in a vacuum with extremely low pressures. The incredibly low-pressure in TEM is very close to the pressure found in circumstellar environments. But this is more by luck than design.

“It’s not that we necessarily tailored the instrument to have these specific kinds of pressures,” explains study co-author Tom Zega, an associate professor in the Univerity of Arizona Lunar and Planetary Lab. “These instruments operate at those kinds of very low pressures not because we want them to be like stars, but because molecules of the atmosphere get in the way when you’re trying to do high-resolution imaging with electron microscopes.”

The team drafted the assistance of the U.S. Department of Energy’s Argonne National Lab, Chicago, which has a TEM capable of studying the radiation responses of materials. Placing silicon carbide–a common form of dust produced by stars– in the low-pressure environment of the TEM, the team in Chicago subjected it to temperatures up to 1,830 degrees Fahrenheit whilst bombarding it with high-energy xenon ions.

Tom Zega at the control panel of the 12-foot tall transmission electron microscope at the Kuiper Materials Imaging and Characterization Facility at the UArizona Lunar and Planetary Lab. The instrument revealed that buckyballs had formed in samples exposed to conditions thought to reflect those in planetary nebulae. Daniel Stolte/University Communications

Following this, the sample was returned to the University of Arizona so researchers could employ the higher resolution and better analytical capabilities of the TEM located there. The team’s hypothesis would be validated if they observed the silicon shedding and exposing pure carbon.

“Sure enough, the silicon came off, and you were left with layers of carbon in six-membered ring sets called graphite,” adds co-author Lucy Ziurys, Regents Professor of astronomy, chemistry and biochemistry. “And then when the grains had an uneven surface, five-membered and six-membered rings formed and made spherical structures matching the diameter of C60.

“So, we think we’re seeing C60.”

This work suggests that C60 is derived from the silicon carbide dust made by dying stars–hit by high temperatures, shockwaves and high energy particles. These violent conditions leech silicon from the surface and leaving carbon behind.

These big molecules are dispersed because dying stars eject their material into the interstellar medium – the spaces in between stars – thus accounting for their presence outside of planetary nebulae.

Buckyballs are very stable to radiation, allowing them to survive for billions of years if shielded from the harsh environment of space.

“The conditions in the universe where we would expect complex things to be destroyed are actually the conditions that create them,” says Bernal, also adding that the implications of the findings are endless.

“If this mechanism is forming C60, it’s probably forming all kinds of carbon nanostructures,” Ziurys concludes. “And if you read the chemical literature, these are all thought to be synthetic materials only made in the lab, and yet, interstellar space seems to be making them naturally.”

Original research: “Formation of Interstellar C60 from Silicon Carbide Circumstellar Grains,” The Astrophysical Journal Letters, 2019.

Enceladus interior.

Enceladus “the only body besides Earth to satisfy all of the basic requirements for life,” Cassini reveals

Data beamed back by the Cassini spacecraft reveals that Enceladus, Saturn’s sixth-largest moon, isn’t shy about blasting large organic molecules into space.

Enceladus interior.

Hydrothermal processes in the moon’s rocky core could synthesize organics from inorganic precursors. Alternatively, these processes could be transforming preexisting organics by heating, or they could even generate geochemical conditions in the subsurface ocean of Enceladus that would allow possible forms of alien life to synthesize biological molecules.
Image credits NASA/JPL-Caltech/Space Science Institute/LPG-CNRS/Nantes-Angers/ESA

Mass spectrometry readings beamed back by NASA’s Cassini craft show that Enceladus is bursting with organic molecules. The moon’s icy surface is pockmarked with deep cracks that spew complex, carbon-rich compounds into space. Scientists at the Southwest Research Institute (SwRI) say these compounds are likely the result of interactions between the moon’s rocky core and warm waters from its subsurface ocean.

Why so organic?

“We are, yet again, blown away by Enceladus,” said SwRI’s Dr. Christopher Glein, co-author of a paper describin the discovery.

“Now we’ve found organic molecules with masses above 200 atomic mass units. That’s over ten times heavier than methane. With complex organic molecules emanating from its liquid water ocean, this moon is the only body besides Earth known to simultaneously satisfy all of the basic requirements for life as we know it.”

The Cassini mission, a cooperative project of NASA, ESA (European Space Agency) and the Italian Space Agency, is widely-held to be one of the most ambitious space exploration missions we’ve ever embarked upon. Launched on October 15, 1997, Cassini spent some 13 years studying the gas giant and its moons. The craft also flew by Venus (April 1998 and July 1999), Earth (August 1999), the asteroid 2685 Masursky, and Jupiter (December 2000), before settling in on Saturn’s orbit on July 1st, 2001.

Enceladus. Image credits: NASA/JPL.

On September 15, 2017, NASA de-commissioned the aging craft with a bang: they deorbited Cassini, letting it fall towards Saturn’s core and burn up in its atmosphere.

However, the wealth of information this tiny craft beamed back from its travels is still giving astronomers a lot to work on. Before its fiery demise, Cassini sampled the plume material ejected from the subsurface of Enceladus. Using its Cosmic Dust Analyzer (CDA) and the SwRI-led Ion and Neutral Mass Spectrometer (INMS) instruments, the craft analyzed both the plume itself and Saturn’s E-ring — which is formed by ice grains from the plumes trapped in Saturn’s gravity well.

Chemicals Enceladus.

Synthesis path of different aromatic cations identified in Enceladus’ plume.
Image credits F. Postberg et al., 2018, Nature.

During one of Cassini’s particularly close flybys of Enceladus (Oct. 28, 2015), the INMS detected molecular hydrogen in the moon’s plume ejections. Previous flybys also revealed the presence of a global subsurface ocean and a rocky core. This was the first indication that the moon can boast active geochemical below the surface, most likely between water and rocks in hydrothermal vents.

The presence of hydrogen was also grounds for great enthusiasm at NASA — the element is a known source of chemical energy for microbes living in hydrothermal vents here on good ol’ Earth.

“Once you have identified a potential food source for microbes, the next question to ask is ‘what is the nature of the complex organics in the ocean?'” says SwRI’s Dr. Hunter Waite, INMS principal investigator and paper coauthor. “This paper represents the first step in that understanding — complexity in the organic chemistry beyond our expectations!”

The findings are significant enough to influence further exploration, Glen believes. Any spacecraft that flies towards Enceladus in the future should make a point of going through its plume to analyze these complex organic molecules with a high-resolution mass spectrometer to “help us determine how they were made.”

“We must be cautious, but it is exciting to ponder that this finding indicates that the biological synthesis of organic molecules on Enceladus is possible.”

The paper “Macromolecular organic compounds from the depths of Enceladus” has been published in the journal Nature.

What Can Quartz Crystals Really Do?

Image in public domain.

Crystals and quartz

Crystals have caught the eye of humans since the dawn of time. Some scientists have even speculated that the origins of life on Earth may trace its origins to crystals. It shouldn’t come as a surprise that these gleaming mineral formations appear frequently in pop culture often as having supernatural powers (even though they don’t). A few examples of this reoccurring theme are the Silmarils in the Lord of the Rings universe and the sunstones in James Gurney’s Dinotopia.

The atoms which make up a crystal lie in a lattice which repeats itself over and over. There are several methods for generating crystals artificially in a lab, with superheating being the most common process. Likewise, in nature, a hot liquid (eg: magma) cools down, and as this happens, the molecules are attracted to each other, bunching up and forming that repeating pattern which leads to crystal formation.

Quartz is one of the most abundant minerals found on the planet. This mineral is known to be transparent or have the hues of white, yellow, pink, green, blue, or even black. It is also the most common form of crystalline silica which has a rather high melting point and can be extremely dangerous if inhaled in its powdered form. This mineral compound is present in the majority of igneous rocks. Some quartzes are considered semiprecious stones. Aside from mere bedazzlement, they have been used in countless industries.

Industrial, not magical uses

If a pressure is applied to the surface of a quartz crystal, it can give off a small electrical charge. This effect is the result of the electrically charged atoms (the ions) dispersing and spreading away from the area to which the pressure is being applied. This can be done in a number of ways, including simply squeezing the crystal. It also dispenses an electric current if a precise cut is made at an angle to the axis.

Since it possesses this property, quartz has been a component of devices such as radios, TV’s, and radar systems. Some quartz crystals are capable of transmitting ultraviolet light better than glass (by the way, quartz sand is used in making glass). Because of this, low-quality quartz is often used for making specific lenses; optical quartz is made exclusively from quartz crystals. Quartz which is somewhat clouded or which is not as transparent as the stuff used for optics is frequently incorporated into lab instrumentation.

Scientists have employed quartz for many things, and they have considered its role in the Earth sciences a crucial one. Some have stated it directly brings about the reaction which forms mountains and causes earthquakes! It continues to be used in association with modern technology, and it likely will lead us to more discoveries in the future.

A model of a single-molecule car that can advance across a copper surface when electronically excited by an scanning tunneling microscope tip.

World’s tiniest race will pit nanocars against each other in Toulouse this April

This April, Toulouse, France will be host to the world’s first international molecule-car race. The vehicles will be made up of only a few atoms and rely on tiny electrical pulses to power them through the 36-hour race.

A model of a single-molecule car that can advance across a copper surface when electronically excited by an scanning tunneling microscope tip.

A model of a single-molecule car that can advance across a copper surface when electronically excited by a scanning tunneling microscope tip.
Image courtesy of Ben Feringa.

Races did wonders for the automotive industry. Vying for renown and that one second better lap time, engineers and drivers have pushed the limits of their cars farther and farther. Seeing the boon competition proved to be for the development of science and technology in pursuit of better performance, the French National Center for Scientific Research (Centre national de la recherche scientifique / CNRS) is taking racing to a whole new level — the molecular level.

From April 28th to the 29th, six international teams will compete in Toulouse, France, in a 36-hour long nanocar race. The vehicles will only be comprised of a few atoms and powered by light electrical impulses while they navigate a 100-nanometer racecourse made up of gold atoms.

The fast (relative to size) and sciency

The event is, first of all, an engineering and scientific challenge. The organizers hope to promote research into the creation, control, and observation of nanomachines through the competition. Such devices show great promise for future applications, where their small size and nimbleness would allow them to work individually or in groups for a huge range of industries — from building regular-sized machines or atom-by-atom recycling to medical applications, nanomachines could prove invaluable in the future. It’s such a hot topic in science that last year’s Nobel Prize for chemistry was awarded for discovering how to make more advanced parts for these machines.

But right now, nanomachines are kind of crude. Like really tiny Model T’s. To nudge researchers into improving this class of devices, the CNRS began the NanoCarsRace experiment back in 2013. It’s the brainchild of the center’s senior researcher Christian Joachim, who’s now director of the race, and Université Toulouse III – Paul Sabatier Professor of Chemistry Gwénaël Rapenne, both of whom have spent the last four years making sure everything is ready and equitable for the big event.

Some challenges they’ve faced were selecting the racecourse — which must accommodate all types of molecule-cars — and finding a way for participants to actually see their machines in action. Since witnessing a race so small unfurl could prove beyond the limitations of the human eye, the vehicles will compete under the four tips of a unique tunneling microscope housed at the CNRS’s Centre d’élaboration de matériaux et d’études structurales (CEMES) in Toulouse. It’s currently the only microscope in the world allowing four different experimenters to work on the same surface.

Scanning Tunneling Microscope explained.

Image credits CNRS Universite Paris-Sud / Physics Reimagined, via YouTube.

Scanning Tunneling Microscope in action.

Image credits CNRS Universite Paris-Sud / Physics Reimagined, via YouTube.

The teams have also been hard at work, facing several challenges. Beyond the difficulty of monitoring and putting together working devices only atoms in size, they also had to meet several design criteria such as limitations on molecular structures and form of propulsion. At the scale they’re working on, the distinction between physics and chemistry starts to blur. Atoms aren’t the things axles or rivets are made of — they’re the actual axles and rivets. So the researchers-turned-race-enthusiasts will likely be treading on novel ground for both of these fields of science, advancing our knowledge of the very-very-small.

Out of the initial nine teams which applied for the race before the deadline in May 2016, six were selected for the race. Four of them will go under the microscope on April 28th. The race is about scientific pursuit, but it’s also an undeniably cool event — so CNRS will be broadcasting it live on the YouTube Nanocar Race channel.

[panel style=”panel-info” title=”The rules of the race” footer=””]The race course will consist of a 20 nm stretch followed by one 45° turn, a 30 nm stretch followed by one 45° turn, and a final 20 nm dash — for a total of 100 nm.
Maximum duration of 36h.
The teams are allowed one change of their race cars in case of accidents.
Pushing another racecar a la Mario Kart is forbidden.
Each team is allotted one sector of the gold course.
A maximum of 6 hours are allowed before the race so each team can clean its portion of the course.
No tip changes will be allowed during the race.[/panel]

 

Meet the world’s most powerful X-Ray laser

homerThe first experiments with this laser (Linac Coherent Light Source) have been given the green light at the Department of Energy’s SLAC National Accelerator Laboratory. The illuminating of objects and processing speed will take place at an unprecedented scale, promising groundbreaking research in physics, chemistry, biology and numerous other fields.

“No one has ever had access to this kind of light before,” said LCLS Director Jo Stöhr. “The realization of the LCLS isn’t only a huge achievement for SLAC, but an achievement for the global science community. It will allow us to study the atomic world in ways never before possible.”

Early experiments are already showing some promise, providing insight on fundaments of atoms and molecules, underlying their properties. The short term goal is to create stop action frames for molecules in motion. By putting together many of these images to create a film, scientists will create for the first time a film with actual molecules in motion, being able to see chemical molecules bond and break, as well as actually see how atoms interact at a quantum level.

“It’s hard to overstate how successful these first experiments have been,” said AMO Instrument Scientist John Bozek. “We look forward to even better things to come.”