Proteins are the building blocks of all living things, and they exist in virtually unlimited varieties, most of whose highly complex structures have not yet been determined. Those structures could be key to developing new drugs or to understanding basic biological processes. But figuring out the arrangement of atoms in these complicated, folded molecules usually requires getting them to form crystals large enough to be observed in detail — and for many proteins, that is either impossible or dauntingly difficult. Now a new technique being developed by researchers at MIT and elsewhere shows great promise for producing highly detailed images of individual proteins, no matter how complicated their structure, without the need for crystallization. The findings are described in the journal ("Atomic-Scale Nuclear Spin Imaging Using Quantum-Assisted Sensors in Diamond") by MIT graduate student Ashok Ajoy, postdoc Ulf Bissbort, associate professor of nuclear science and engineering Paola Cappellaro, and others at MIT, the Singapore University of Technology and Design, and Harvard University. 
Nitrogen vacancy (NV) centers in diamond could potentially determine the structure of single protein molecules at room temperature. Here the NV center is 2 to 3 nanometers below the surface, and the protein molecule is placed above it. (Image courtesy of the researchers) The technique makes use of microscopic defects within the crystal structure of diamond — defects that can be induced, in a controlled way, in the lab. These defects, called nitrogen-vacancy (NV) centers, occur when nitrogen atoms are introduced into the crystal structure, each replacing one carbon atom in a perfectly spaced diamond lattice. Such lattices may also include naturally occurring vacancies — imperfections where a carbon atom is missing from its normal place in the lattice. When a nitrogen atom and a vacancy come together, they form an NV center, which can be harnessed to detect the position and attributes — specifically, the spin states — of protons and electrons in atoms placed very close to them. That’s done by shining laser light at the diamond surface, which causes the NV centers to fluoresce. By detecting and analyzing the emitted light, it is possible to reconstruct details of the spin of nearby particles. The ability to use NV centers in diamond has developed in the last few years, Ajoy says, and many groups are now working to make use of them for applications in quantum computation and quantum communication. When the NV centers are very close to a diamond’s surface — within a few nanometers — they can also be used to sense the spin states of particles within a molecule placed on the surface. The individual atoms and their positions can then, in principle, be detected and mapped out, revealing the molecular structure. The idea is to “place a biological molecule on top of the diamond, and try to determine its structure,” Ajoy explains. With proteins, “the structure and function are closely related,” he says, so being able to map out that structure precisely could help in understanding both how some basic biological processes work, and how new drugs might be developed to interact with specific molecular targets. 
The spin of an NV center can be completely polarized optically. The transfer of this polarization from the NV center to nuclear spins in the protein molecule allows us to unravel couplings between spins in the molecule. Protein structure can be computed from information contained in these couplings. (Image courtesy of the researchers) “It could help in developing something that fits on or around [a target molecule], or blocks it,” Ajoy says. “The first step is to know the structure.” Efforts to decode the molecular structure of proteins have mostly used X-ray crystallography, transmission electron microscopy, or nuclear magnetic resonance. But all of these methods require large sample volumes — for example, X-ray diffraction requires aggregating the molecules as crystals — so none of them can be used to study individual molecules. This greatly limits the applicability of such techniques. “There are many molecules where this doesn’t work out, because you can’t grow the crystals, or they are very hard to grow,” Ajoy says. “For these molecules, our method might be useful because you don’t need the crystals, you just need a single molecule.” What’s more, while other techniques require specialized conditions such as very low temperatures or a vacuum, the new technique “perhaps can determine structure at room temperature, under ambient conditions,” he says. The work so far is theoretical; the next step, which the team has already begun, is to produce actual images based on this technique. “We started building this setup a year ago, and we have preliminary experiments,” Ajoy says. Actual images of molecules are probably still a few years away, he says. This technique is a “very important breakthrough in the development of new techniques for biomolecular structure determination,” says Fedor Jelezko, a professor of quantum optics at the University of Ulm, in Germany, who was not involved in this research. “This is excellent work which will provide very high impact on many fields of science. I am sure that several groups around the world will attempt to realize experiments” based on the ideas in this paper.
Nitrogen vacancy (NV) centers in diamond could potentially determine the structure of single protein molecules at room temperature. Here the NV center is 2 to 3 nanometers below the surface, and the protein molecule is placed above it. (Image courtesy of the researchers) The technique makes use of microscopic defects within the crystal structure of diamond — defects that can be induced, in a controlled way, in the lab. These defects, called nitrogen-vacancy (NV) centers, occur when nitrogen atoms are introduced into the crystal structure, each replacing one carbon atom in a perfectly spaced diamond lattice. Such lattices may also include naturally occurring vacancies — imperfections where a carbon atom is missing from its normal place in the lattice. When a nitrogen atom and a vacancy come together, they form an NV center, which can be harnessed to detect the position and attributes — specifically, the spin states — of protons and electrons in atoms placed very close to them. That’s done by shining laser light at the diamond surface, which causes the NV centers to fluoresce. By detecting and analyzing the emitted light, it is possible to reconstruct details of the spin of nearby particles. The ability to use NV centers in diamond has developed in the last few years, Ajoy says, and many groups are now working to make use of them for applications in quantum computation and quantum communication. When the NV centers are very close to a diamond’s surface — within a few nanometers — they can also be used to sense the spin states of particles within a molecule placed on the surface. The individual atoms and their positions can then, in principle, be detected and mapped out, revealing the molecular structure. The idea is to “place a biological molecule on top of the diamond, and try to determine its structure,” Ajoy explains. With proteins, “the structure and function are closely related,” he says, so being able to map out that structure precisely could help in understanding both how some basic biological processes work, and how new drugs might be developed to interact with specific molecular targets. The spin of an NV center can be completely polarized optically. The transfer of this polarization from the NV center to nuclear spins in the protein molecule allows us to unravel couplings between spins in the molecule. Protein structure can be computed from information contained in these couplings. (Image courtesy of the researchers) “It could help in developing something that fits on or around [a target molecule], or blocks it,” Ajoy says. “The first step is to know the structure.” Efforts to decode the molecular structure of proteins have mostly used X-ray crystallography, transmission electron microscopy, or nuclear magnetic resonance. But all of these methods require large sample volumes — for example, X-ray diffraction requires aggregating the molecules as crystals — so none of them can be used to study individual molecules. This greatly limits the applicability of such techniques. “There are many molecules where this doesn’t work out, because you can’t grow the crystals, or they are very hard to grow,” Ajoy says. “For these molecules, our method might be useful because you don’t need the crystals, you just need a single molecule.” What’s more, while other techniques require specialized conditions such as very low temperatures or a vacuum, the new technique “perhaps can determine structure at room temperature, under ambient conditions,” he says. The work so far is theoretical; the next step, which the team has already begun, is to produce actual images based on this technique. “We started building this setup a year ago, and we have preliminary experiments,” Ajoy says. Actual images of molecules are probably still a few years away, he says. This technique is a “very important breakthrough in the development of new techniques for biomolecular structure determination,” says Fedor Jelezko, a professor of quantum optics at the University of Ulm, in Germany, who was not involved in this research. “This is excellent work which will provide very high impact on many fields of science. I am sure that several groups around the world will attempt to realize experiments” based on the ideas in this paper.
Nanowires grown using catalyst rich in gold (top) and nickel (bottom). (Image: Berkeley Lab) Since the early 2000s, scientists have made steady progress in cultivating nanowires. Initially, early nanowire samples resembled “tangled noodles or wildfire-ravaged forests,” according to the researchers. More recently, scientists have found various conditions lead to the growth of more orderly nanowire arrays. For instance, certain substrates on which the nanowires grow create conditions so that the nanowire growth orientation is dictated by the substrate’s underlying crystal structure. Unfortunately, this and other approaches haven’t been foolproof and some nanowires still go rogue. Moreover, there is no simple way to grow different types of nanowires in the same environment and on the same substrate. This would be useful if you wanted to selectively grow nanowires with different electronic or optical properties in the same batch, for example. “At the Molecular Foundry we are aiming to develop new strategies and add new tools to the bag of tricks used for nanomaterials synthesis,” says Aloni. “For years we were searching for cleverer ways to grow nanostructures with different optical properties in identical growth conditions. Engineering the catalyst brings us closer to achieving this goal.” The researchers focused on nanowires made of gallium nitride. In its bulk (non-nanoscale) form, gallium nitride emits light in the blue or ultraviolet range. If indium atoms are added to it, the range can be extended to include red, essentially making it a broad-spectrum tunable light source in the visible range. The problem is that adding indium atoms puts the crystal structure of gallium nitride under stress, which leads to poorly performing devices. Gallium nitride nanowires, however, don’t experience the same sort of crystal strain, so scientists hope to use them as tunable, broad-spectrum light sources. To achieve their control, the team focused on the catalysis which guide the nanowire growth. Normally, researchers use catalysts made of a single metal. The Berkeley team decided to use metallic mixtures of gold and nickel, called alloys, as catalysts instead. In the study, the researchers found that the gallium-nitride nanowire growth orientation strongly depended on the relative concentration of nickel and gold within the catalyst. By altering the concentrations in the alloy, the researchers could precisely manipulate, even on the same substrate in the same batch, the orientation of the nanowires. “No one had used bi-metalic catalysts to control growth direction before,” says Tevye Kuykendall, scientist at Berkeley Lab’s Molecular Foundry. Kuykendall says the mechanism driving the new growth process is not fully understood, but it involves the different tendencies of gold and nickel to align with various crystallographic surfaces at point where nanowires start to grow. The researchers also showed that depending on the growth direction chosen, different optical properties were observed thanks to the crystal surfaces exposed at the surface of the nanowire. “One of the things that make nanostructures interesting, is that the surface plays a larger role in defining the material’s properties,” says Aloni. This leads to changes in optical properties not seen in larger-bulk materials, making them more useful. Aloni says the team will next focus more on the chemistry of the different nanowire surfaces to further tailor the nanowire’s optical properties. All aspects of the work were conducted at the Molecular Foundry, under the leadership of Aloni. Virginia Altoe imaged the nanowires using transmission electron microscopy in the imaging facility of the Molecular Foundry. Frank Ogletree, Molecular Foundry staff scientist, assisted in mapping the optical properties of the nanowires. And Kuykendall fabricated the wires in the Foundry’s inorganic facility. The methods and materials described in the paper are available free of charge to researchers from around the world through the Molecular Foundry’s user program.
Scanning tunnelling microscope image of a 47-nanometer square area of the surface of a topological insulator showing variations in the Dirac-mass gap - a measure of conductance - from high (yellow) to low (blue). Red trianges are chromium atoms, concentratd in the high gap areas. The inset plots the correlation between Dirac-mass gap and chromium atom density. Topological insulators are insulators in bulk, but an electric current flows smoothly on their surface. “They are very weird compounds with a conducting sheen one electron thick,” explained J.C. Seamus Davis, Cornell’s James Gilbert White Distinguished Professor in the Physical Sciences and a senior physicist at Brookhaven. “For five or more years people have been trying to develop all the exotic potential, but with very few results.” Theorists predicted that topological insulators might be used in new kinds of electronic devices, including quantum computers, and that they could display unusual physical phenomena, including simulations of magnetic monopoles or of axions – particles theorized to be associated with dark matter. To make these things happen, theory says, the conducting electrons would have to be exposed to a high magnetic field that would lock them into a particular quantum energy level – roughly, the amount of energy it would take to yank an electron out of the system – where they are “protected” from change. So materials scientists synthesized new versions of topological insulators “doped” with atoms of magnetic elements, such as chromium, making them “ferromagnetic.” Still, none of the expected phenomena appeared. “We have to find those magnetic atoms and look at their relationship with the electrons,” Davis said. “This is right up our alley.” Davis has designed and built several ultrasensitive scanning tunneling microscopes (STMs) that can move a probe across a surface in steps smaller than the diameter of an atom, and read the energy levels of electrons under the probe. Chung Koo Kim, a former member of Davis’ research group at Cornell and now a member of his group at Brookhaven, used a specially built STM to scan a sample of a topological insulator composed of bismuth, antimony and tellurium doped with chromium atoms. Magnetic fields of the chromium atoms interact with those of the electrons to give them what physicists call a Dirac-mass. Just as the inertial mass of a physical object resists moving the object, the Dirac-mass of an electron resists moving it through a conductor. Stopping at each point on the scan, the STM measured the energy levels of electrons under the probe, finding that the movement of electrons through the conducting surface – and therefore the Dirac-mass – was very different from place to place. The scan also showed the locations of the chromium atoms, which are distributed randomly around the surface, and the most disorderly regions were in the vicinity of those atoms. The very atoms that protect the energy levels of he electrons are also the source of the destruction of the promised effects, Davis noted. “The Dirac-mass chaos eventually destroys the exotic surface state,” he explained. “This new understanding will likely result in revisions of the basic research directions in this field.” One possible approach, he said, might be to somehow synthesize materials in which the magnetic atoms are arranged in orderly rows. Another would be to apply a very large, uniform external magnetic field.
The “Nanorama Laboratory“, an interactive online tool on the safe handling of nanomaterials, is now available in English. The tool, developed in close collaboration with the German Social Accident Insurance Institution for the raw materials and chemical industry (BG RCI), was devised by the Innovation Society, St. Gallen. It is part of the nano-platform “Safe Handling of Nanomaterials” of the German Social Accident Insurance (DGUV). The “Nanorama Laboratory” was developed by the Innovation Society, St. Gallen, in close collaboration with the German Social Accident Insurance Institution for the raw materials and chemical industry (BG RCI). It offers insights into the safe handling of nanomaterials and installations used to manufacture or process nanomaterials in laboratories. Complementary to hazard evaluation assessments, it enables users to assess the occupational exposure to nanomaterials and to identify necessary protective measures when handling said materials in laboratories. "Due to the attractive visual implementation and the interactive contents, the “Nanorama Laboratory“ offers a great introduction to protective measures in laboratories", says Dr. Thomas H. Brock, Head of the Expert Committee on Hazardous Substances of the BG RCI. The “Nanorama Laboratory” inspires curiosity in users and instigates them to reflect on the conditions in their respective workplaces. "By exploring the “Nanorama Labora-tory”, laboratory staff actively deals with occupational health and safety in laboratories and its practical implementation with regard to nanomaterials." Nanoramas – Multipurpose E-Learning Tools A “Nanorama” – a lexical blend of “Nano” and “Panorama”, – is a novel 360°-E-learning module in which the user enters a virtual space and moves around in it. By completing a “Nanorama”, users acquire knowledge in an entertaining manner. “Nanoramas” can be applied in many areas of education and communication. They were developed by the In-novation Society, St. Gallen. More information on the tool can be found here. The remaining modules, the “Nanorama Construction” and the “Nanorama Car Workshop” can be visited on http://bit.ly/1xoMB1A and http://bit.ly/1ziYewA, respectively. They offer insights into the use and applications of nanomaterials in the construction industry respectively in car workshops. The existing “Nanoramas” will be joined by another “Nanorama”-module soon.
Although encapsulation always implies a compromise between the protection offered by polystyrene and the pore accessibility of the encapsulated porous material, spray-drying has enabled the authors to fine-tune the HKUST-1/PS ratio to achieve optimal trade-off in their HKUST-1@PS composites: they are resistant to liquid or vapour water yet retain most of the excellent gas sorption capacity of HKUST-1. In these composites, the polymer protects the embedded MOF crystals against water molecules, without substantially decreasing their initial sorption capacity, and increases their water resistance in terms of porosity properties. As in Metal-Organic Framework (MOF) mix matrix membranes, the permeability of the organic polymer in the composite should be one of the key factors to understand and enhance the gas and vapour transport towards the embedded MOF crystals. Here, for example, further experimentation aimed to study the water uptake kinetics is currently underway. Nevertheless, this method should enable molecular fabrication of various functional composites, based on the ever-expanding pool of MOFs and organic polymers, for a wide array of industrial applications such as CO2 capture from flue gas streams, heat pumps, or adsorption chillers.