New Technique Uses Electrons to Map Nanoparticle Atomic Structures

Accessibility of electron microscopes could make technique standard practice

“The next generation of high-performance materials that scientists are studying for applications like batteries, fuel cells, drug delivery, and photovoltaics are highly complex. We are trying to engineer them at the nanoscale to give them particular properties to improve their performance. A huge experimental challenge is to characterize experimentally these heterogenous, nanostructured, complex materials — including determining where the atoms are located, their dynamics, and how they interact with outside stimuli such as photons of light. If people want lighter laptops with more computing power and longer battery life to take with them in their emission-free cars that go 400 miles without a fill-up/recharge — and which pull away from the stoplight like a Ferrari — then we scientists are going to have to solve these problems! Our research is a tiny (but important) step in that direction.”

— Simon Billinge

UPTON, NY — With dimensions measuring billionths of a meter, nanoparticles are way too small to see with the naked eye. Yet it is becoming possible for today’s scientists not only to see them, but also to look inside at how the atoms are arranged in three dimensions using a technique called nanocrystallography. Trouble is, the powerful machines that make this possible, such as x-ray synchrotrons, are only available at a handful of facilities around the world. The U.S. Department of Energy’s Brookhaven National Laboratory is one of them — home to the National Synchrotron Light Source (NSLS) and future NSLS-II, where scientists are using very bright, intense x-ray beams to explore the small-scale structure of new materials for energy applications, medicine, and more.

But a Brookhaven/Columbia Engineering School team of scientists, in collaboration with researchers at DOE’s Argonne National Laboratory (ANL) and Northwestern University, has also been working to develop nanocrystallography techniques that can be used in more ordinary science settings. They have shown how a powerful method called atomic pair distribution function (PDF) analysis — which normally requires synchrotron x-rays or neutrons to discern the atomic arrangements in nanoparticles — can be carried out using a transmission electron microscope (TEM) — an instrument found in many chemistry and materials science laboratories.

The researchers describe the TEM-based data-collection technique and computer-modeling analyses used to extract quantitative nanostructural information in a paper just published in the May 2012 issue of the journal Zeitschrift fur Kristallographie.

“The ability to collect PDF data using an electron microscope places this powerful nanocrystallographic analysis method into the hands of scientists who need it most — the people synthesizing novel nanoparticles and nanostructures,” said Simon Billinge, a researcher at both Brookhaven and Columbia University’s School of Engineering and Applied Science and a long-term user of the NSLS, who led the research.

 “State-of-the-art experiments will still be carried out at x-ray synchrotrons and high-tech neutron-scattering facilities,” said Billinge, a professor of Materials Science and Applied Physics and Applied Mathematics at Columbia Engineering. “But this new development removes significant barriers to more widespread use of the method, potentially making PDF part of the standard toolkit in materials synthesis labs. It’s rather like moving nanocrystallography from being available only with a prescription to being available over the counter,” he said.

In both the synchrotron and TEM-based methods, the essential technique is the same: bombard a sample with a beam — x-rays, in the case of a synchrotron, or electrons at a TEM — and measure how the rays/particles interact with and bounce off the atoms in the sample. The result is a diffraction pattern that can be translated into measurements of the distribution of distances between pairs of particles within a given volume — the atomic pair distribution function (PDF). Scientists then use computational programs to convert the PDFs into 3-D models of atomic structure.

Electron diffraction had been used to study the structure of molecules in the gas phase and amorphous thin films, but initially, scientists didn’t think that electrons would be appropriate for obtaining reliable PDFs from critical nanocrystalline materials because, unlike x-ray photons, electrons scatter strongly, distorting the diffraction pattern. This new work demonstrates that, under the right circumstances and with the correct data processing, quantitatively reliable PDFs of small nanoparticles — precisely the ones that are difficult to characterize using standard methods — can be obtained with the TEM.

Another advantage is that the technique allows analysis of atomic-level structural arrangements using the same tool already used to obtain low- and high-resolution images and chemical information for nanostructures — that is, the same TEM can be used to provide complementary kinds of information.

“The fact that the real-space images and the diffraction data suitable for structural analysis can be obtained at the same time from the same region of a material results in more complete information for the characterization of the sample,” said Milinda Abeykoon, a postdoctoral researcher at Brookhaven and the first author of the paper.

In the current study, scientists working with co-author Mercouri Kanatzidis at Northwestern University and ANL synthesized nanocrystalline thin films and gold and sodium chloride (NaCl) nanoparticles and used a TEM at Northwestern to acquire PDFs of these samples. The Brookhaven/Columbia group studied similar samples using synchrotron x-rays at NSLS, and analyzed all the data before comparing the resulting PDFs and atomic structures.

The PDFs from the x-ray and electron data were highly similar.

“In some cases the strong electron scattering did introduce some distortions in the PDF, as originally feared,” Billinge said. “However, surprisingly these problems only affected certain less important structural parameters — and even resulted in an enhancement of the signal in a way that may be used in the future to yield a higher resolution measurement. That was an unexpected gift!”

The research team is continuing to look for ways to remove barriers to data processing to make the method more straightforward — and move it from proof-of-principle concept into widespread standard use.

This research was funded by DOE’s Office of Science and by the National Science Foundation. The National Synchrotron Light Source at Brookhaven is also supported by the DOE Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Columbia Engineering

Columbia University's Fu Foundation School of Engineering and Applied Science, founded in 1864, offers programs in nine departments to both undergraduate and graduate students. With facilities specifically designed and equipped to meet the laboratory and research needs of faculty and students, Columbia Engineering is home to NSF-NIH funded centers in genomic science, molecular nanostructures, materials science, and energy, as well as one of the world’s leading programs in financial engineering. These interdisciplinary centers are leading the way in their respective fields while individual groups of engineers and scientists collaborate to solve some of modern society’s more difficult challenges. http://www.engineering.columbia.edu/

A Surprising New Kind of Proton Transfer

Berkeley Lab scientists and their colleagues have discovered an unsuspected way that protons can move among molecules – revealing new opportunities for research in biology, environmental science, and green chemistry

When a proton – the bare nucleus of a hydrogen atom – transfers from one molecule to another, or moves within a molecule, the result is a hydrogen bond, in which the proton and another atom like nitrogen or oxygen share electrons. Conventional wisdom has it that proton transfers can only happen using hydrogen bonds as conduits, “proton wires” of hydrogen-bonded networks that can connect and reconnect to alter molecular properties.

Hydrogen bonds are found everywhere in chemistry and biology and are critical in DNA and RNA, where they bond the base pairs that encode genes and map protein structures. Recently a team of researchers using the Advanced Light Source (ALS) at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) discovered to their surprise that in special cases protons can find ways to transfer even when hydrogen bonds are blocked. The team’s results appear in Nature Chemistry.

Stacking the odd molecules

A group led by Musahid Ahmed, a senior scientists in Berkeley Lab’s Chemical Sciences Division (CSD), has long collaborated with a theoretical research group at the University of Southern California (USC) headed by Anna Krylov. In recent work to understand how bases are bonded in staircase-like molecules like DNA and RNA, Krylov’s group made computer models of paired, ring-shaped uracil molecules, and investigated what might happen to these doubled forms (dimers) when they were subjected to ionization – the removal of one or more electrons with resulting net positive charge.

Uracil is one of the four nucleobases of RNA, whose structure is similar to DNA except that, while both use the bases adenine, cytosine, and guanine, in DNA the fourth base is thymine and in RNA it’s uracil. The USC group used a uracil dimer labeled 1,3-dimethyluracil – “a strange creature that doesn’t necessarily exist in nature,” says CSD’s Amir Golan, who led the Berkeley Lab team at the ALS. The purpose of this strange creature, Golan says, is to block hydrogen bonding of the two identical monomers of the uracil dimer by attaching a methyl group to each, “because methyl groups are poison to hydrogen bonds.”

The uracils could still bond in the vertical direction by means of pi bonds, which are perpendicular to the usual plane of bonding among the flat rings of uracil and other nucleobases. “Pi stacking” is important in the configuration of DNA and RNA, in protein folding, and in other chemical structures as well, and pi stacking was what interested the USC researchers. They brought their theoretical calculations to Berkeley Lab for experimental testing at the ALS’s Chemical Dynamics beamline 9.0.2.

To examine how the molecules were bonded, Golan and his colleagues first created a gaseous molecular beam of real methylated uracil monomers and dimers, then ionized them with a beam of energetic ultraviolet light from the ALS synchrotron. The resulting species were weighed in a mass spectrometer to see how the uracil had responded to the extra boost of energy.

 “Uracils could be joined by hydrogen bonds or by pi bonds, but these uracils had been methylated to block hydrogen bonds. So what we expected to see when we ionized them was that if they were bonded, they would have to be stacked on top of each other,” Golan says. Instead of holding together by pi bonds, however, when ionized some uracil dimers had fallen apart into monomers that carried an extra proton.

Where the protons come from

“What we did not expect to see was proton transfer,” Golan says. “Surprising as this was, we needed to find where the protons were coming from. The methyl groups consist of a single carbon atom and three hydrogen atoms, but methylated uracil has other hydrogens too. Still, the methyl groups were the natural suspects.”

To test this hypothesis, the researchers invited colleagues from Berkeley Lab’s Molecular Foundry to join the collaboration. They created methyl groups in which the hydrogen atoms – which like most hydrogen had single protons as their nuclei – were replaced by deuterium atoms, “heavy hydrogen” atoms with nuclei consisting of a proton and a neutron of virtually the same mass.

The molecular beam experiment was repeated at the ALS, and once again some of the methylated uracil dimers fell apart into monomers upon ionization. This time, however, the tell-tale monomers were not simply protonated, they were deuterated.

Says Golan, “By looking at the mass of the fragments we could see that instead of uracil plus one” – the mass of a single proton – “they were uracil plus two” – a proton and neutron, or deuteron. “This proved that indeed the transferred protons came from the methyl groups.”

The experiment showed that proton transfer in this case followed a very different route from the usual process of hydrogen bonding. Here the transfer involved not just an attraction between molecular arrangements that were slightly positively charged and others that were slightly negatively charged, as in a hydrogen bond. Instead it required significant rearrangements of the two uracil dimer fragments, to allow protons of hydrogen atoms in the methyl group on one monomer to move closer to an oxygen atom in the other. Theoretical calculations of the new pathway were led by USC’s Krylov and Ksenia Bravaya.

The moral of the story, says Golan, is that methyl groups do not always kill proton transfer. “Granted, this was a model system – what we did was ionize the uracil systems in the gas phase instead of in solution, as would be the case in a living organism,” he says. “Nevertheless, we showed that proton transfer is possible without hydrogen-bonding networks. Which means there could be unsuspected pathways for proton transfer in RNA and DNA and other biological processes – especially those that involve pi-stacking – as well as in environmental chemistry and in purely chemical processes like catalysis.”

The next step: a range of new experiments to directly map proton transfer rates and gain structural insight into the transfer mechanism, with the goal of visualizing these unexpected new pathways for proton transfer.

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“Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of H-bonds,” by Amir Golan, Ksenia B. Bravaya, Romas Kudirka, Oleg Kostko, Stephen R. Leone, Anna I. Krylov, and Musahid Ahmed, is published by Nature Chemistry and appears in advance online publication at http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.1298.html. Golan, Kostko, Leone, and Ahmed are with Berkeley Lab’s Chemical Sciences Division, and Golan and Leone are also with the Departments of Chemistry and Physics at the University of California at Berkeley. Bravaya and Krylov are with the University of Southern California. Kudirka is with Berkeley Lab’s Materials Sciences Division. This work was supported principally by the U.S. Department of Energy’s Office of Science, and by the Department of Defense and the National Science Foundation.

For more about the Chemical Dynamics Beamline at the ALS, visit www.chemicaldynamics.lbl.gov.

For more about Anna Krylov’s research, visit iopenshell.usc.edu/krylovgroup/.

The Advanced Light Source is a third-generation synchrotron light source producing light in the x-ray region of the spectrum that is a billion times brighter than the sun. A DOE national user facility, the ALS attracts scientists from around the world and supports its users in doing outstanding science in a safe environment. For more information visit www-als.lbl.gov/.

The Molecular Foundry is one of five DOE Nanoscale Science Research Centers (NSRCs), national user facilities for interdisciplinary research at the nanoscale, supported by the DOE Office of Science. Together the NSRCs comprise a suite of complementary facilities that provide researchers with state-of-the-art capabilities to fabricate, process, characterize, and model nanoscale materials, and constitute the largest infrastructure investment of the National Nanotechnology Initiative. For more information about the DOE NSRCs, please visit science.energy.gov.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit the Office of Science website at science.energy.gov/.

Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.

Atom-level View of Nanoscale Interface

An atom-level view of the nanoscale--mere billionths of a meter--interface between amorphous carbon and diamond. At such a small scale, the surfaces are rough, although researchers have been treating them as smooth. A team of engineers from the University of Wisconsin-Madison, used computer simulations to demonstrate that friction at the atomic level behaves similarly to friction generated between large objects. They found that friction is proportional to the number of atoms that interact between two nanoscale surfaces. The researchers' simulations showed that, at the nanoscale, materials in contact behave more like large, rough objects rubbing against each other, rather than as two perfectly smooth surfaces, as was previously imagined. The research was supported in part by a grant from the National Science Foundation.

Further information is available in the UW news story Models present a new view of nanoscale friction. (Date of Image: 2009)

Credit: Courtesy University of Wisconsin