Tag: crystals

Picking up good vibrations – of proteins – at CHESS

Picking up good vibrations – of proteins – at CHESS

A new method for analyzing protein crystals – developed by Cornell researchers and given a funky two-part name – could open up applications for new drug discovery and other areas of biotechnology and biochemistry.

The development, outlined in a paper published March 3 in Nature Communications, provides researchers with the tools to interpret the once-discarded data from X-ray crystallography experiments – an essential method used to study the structures of proteins. This work, which builds on a study released in 2020, could lead to a better understanding of a protein’s movement, structure and overall function.

Protein crystallography produces bright spots, known as Bragg peaks, from the crystals, providing high-resolution information about the shape and structure of a protein. This process also captures blurry images – patterns and clouds related to the movement and vibrations of the proteins – hidden in the background of the Bragg peaks.

These background images are typically discarded, with priority given to the bright Bragg peak imagery that is more easily analyzed.

“We know that this pattern is related to the motion of the atoms of the protein, but we haven’t been able to use that information,” said lead author Steve Meisburger, Ph.D. ’14, a former postdoctoral researcher in the lab of Nozomi Ando, M.S. ’04, Ph.D. ’09, associate professor of chemistry and chemical biology in the College of Arts and Sciences. “The information is there, but we didn’t know how to use it.  Now we do.”

Meisburger worked closely with Ando to develop the robust workflow to decode the weak background signals from crystallography experiments called diffuse scattering. This allows researchers to analyze the total scattering from crystals, which depends on both the protein’s structure and the subtle blur of its movements.

Their two-part method – which the team dubbed GOODVIBES and DISCOBALL – simultaneously provides a high-resolution structure of the protein and information on its correlated atomic movements.

GOODVIBES analyzes the X-ray data by separating the movements – subtle vibrations – of the protein from other proteins that might be moving around it. DISCOBALL independently validates these movements for certain proteins directly from the data, allowing researchers to trust the results from GOODVIBES and understand what the protein might be doing.

Read more on CHESS website

Image: Meisburger, Case, & Ando (2020) Nat Commun 11, 1271

Determination of interatomic coupling between two-dimensional crystals

Determination of interatomic coupling between two-dimensional crystals

Following the isolation of graphene, many other atomically thin two-dimensional crystals have been produced and can even be stacked on top of each other in a desired order to form so called van der Waals heterostructures.

Subtle changes in the stacking, especially the angle between the crystallographic axes of two adjacent layers, can have big impact on the properties of the whole heterostructure. We use angle-resolved photoemission spectroscopy measurements carried out at the Spectromicroscopy beamline at Elettra to obtain interatomic coupling for carbon atoms by studying a three-layer stack of graphene. The coupling between atoms in two two-dimensional crystals, knowledge of which is necessary to describe the properties of the stack, can be determined by studying a structure made of three layers with two similar interfaces but one with crystallographic axes aligned and one twisted. This is because each of the interfaces provides complementary information and together they enable self-consistent determination of the coupling.

Read more on the Elettra website

Image: Angle resolved photoemission spectrum revealing the electronic bands of a microscopic three layer device having aligned and twisted graphene-graphene interfaces. Measurable band gaps are used to self-consistently determine fundamental parameters of interatomic coupling.

FIRST EXPERIMENTS ARE CARRIED OUT ON SIRIUS

FIRST EXPERIMENTS ARE CARRIED OUT ON SIRIUS

The new Brazilian synchrotron light source, Sirius, from the Brazilian Synchrotron Light Laboratory (LNLS) at the Brazilian Center for Research in Energy and Materials (CNPEM), carried out the first experiments on one of its beamlines this week. The first research station to start operating, still in the commissioning stage, can reveal details of the structure of biological molecules, such as viral proteins. These first experiments are part of an effort by CNPEM to provide a cutting-edge tool to the Brazilian scientific community working in SARS-CoV-2 research.

In these initial analyses, CNPEM researchers observed crystals of a coronavirus protein, essential for the development of COVID-19. The first results reveal details of the structure of this protein, important for understanding the biology of the virus and supporting research that seeks new drugs against the disease.

>Read more on the LNLS website

Crystals, lasers, glasses, and bent molecules: adventures in nonlinear optics

Crystals, lasers, glasses, and bent molecules: adventures in nonlinear optics

Light is an indispensable scientific tool. For example, laser-based optical sensors can detect oxygen in the environment, proteins in biomedical samples, and process markers in industrial settings, among other applications. However, not all wavelengths of light can be generated by a single laser, which limits what chemicals can be detected with optical sensing. That’s where nonlinear optical crystals can help. By shining multiple lasers with different wavelengths through such crystals, researchers can tune laser beams via frequency conversion and cover more of the optical spectra. This has been a successful approach for wavelengths from ultraviolet to near-infrared(IR), but the mid-IR region has lacked practical nonlinear optical crystals. However, crystals may not be the only game in town. A multi-institution international research team is exploring a possible solution to the crystal problem: cutting-edge glasses containing mercuric iodide. The idea is that these glasses could behave like nonlinear optical crystals, offering an enticing approach to the generation of novel amorphous optical materials. But first, the researchers needed to figure out what these glasses look like at the atomic scale. For that, they went to the U.S. Department of Energy’s (DOE’s) Advanced Photon Source (APS) to collect high-energy x-ray diffraction data. By combining the diffraction data with other structural data and computer modeling, the team uncovered the secrets behind how a glass can act like a crystal.

Nonlinear optical crystals are widely used in photonics applications, but can be challenging to synthesize. To sidestep the need for crystals, scientists have been pursuing glassy materials that can tune lasers. One challenge is that glassy materials with isotropic internal structures aren’t able to perform the frequency conversion necessary to tune lasers. However, glasses with chiral asymmetric properties have nonlinear optical potential. This research team is investigating hybrid molecular/network glasses with non-centrosymmetric mercuric iodide (HgI2).

>Read more on the Advanced Photon Source (APS) website

Image: Schematic representation of second harmonic generation as light passes through bent HgI2 molecules adopting a non-random orientation within mesoscopic domains of sulfide glass.

Preparation and characterization of mesoscale single crystals

Preparation and characterization of mesoscale single crystals

What did the Scientists Discover?
Single crystals are materials with periodic structure that extends across macroscopic distances as a coherent lattice free of grain boundaries. By isolating and studying their properties, bulk single crystals have revolutionized our fundamental understanding of materials from semiconductors to biomacromolecules, fueling innovations from microelectronic devices to pharmaceutical compounds. In contrast, our understanding of many mesostructured materials is still in its infancy in part due to the lack of available single crystals. Block copolymer self-assembly of mesostructured systems presented here is a promising method to prepare periodic 10–100 nm structures with coherent orientation over macroscopic lengths enabling their study.

Why is this important?
The method presented here can prepare macroscopic bulk single crystals with other block copolymer systems, suggesting that the method is broadly applicable to block copolymer materials assembled by solvent evaporation. It is expected that such bulk single crystals will enable fundamental understanding and control of emergent mesostructure-based properties in block-copolymer-directed metal, semiconductor, and superconductor materials.

>Read more on the CHESS website

Image: (extract, full image see here) Representative SAXS patterns with log scale colors from locations as indicated in (c), exhibiting polycrystalline (e), multi-(three) crystalline (f), and single crystal (g) behavior. Diagonal bars across bottom are shadows from photodiode wire.

Tuneable self-organisation of liquid crystals in nanopores

Tuneable self-organisation of liquid crystals in nanopores

Innovative path to novel materials with adaptive electrical and optical properties

A team of researchers has used X-rays from DESY’s research light source PETRA III to explore the amazingly diverse self-organisation of liquid crystals in nanometre-sized pores. The study, led by Patrick Huber from the Hamburg University of Technology (TUHH), shows how liquid crystals arrange themselves in pores of different sizes, exhibiting different electrical and optical properties. These could be of interest for applications such as sensors and novel optical metamaterials, as the group around first author Kathrin Sentker from TUHH reports in the journal Nanoscale. The research, which Huber presented at the annual DESY Users’ Meeting running until this Friday, will be continued within the framework of the planned Centre for Multiscale Materials Systems (CIMMS), in which TUHH, University of Hamburg, Helmholtz-Zentrum Geesthacht and DESY are involved and for which the Hamburg Science Authority has just approved approximately four million euros funding.

The researchers had studied a special liquid crystal material called HAT6 (2,3,6,7,10,11-hexakis(hexyloxy)triphenylene; C54H84O6), whose single molecules are disc-shaped. Below about 70 degrees Celsius, they arrange themselves into a liquid crystal; by heating to about 100 degrees, the order can be broken. The scientists filled this material into pores in an aluminium oxide substrate and cooled it down. The cylindrical pores were 17 to 160 nanometres (millionths of a millimeter) in diameter, 0.1 millimetres long and situated on a regular, hexagonal lattice.

Read more on the PETRA III website

Image: Simulation of the different orders of the liquid crystal, matching the measurements. Simulation: Marco D. Mazza, Max Planck Institute for dynamics and self-organisation and und Loughborough University

Optical ​“tweezers” combine with X-rays to enable analysis of crystals in liquids

Optical ​“tweezers” combine with X-rays to enable analysis of crystals in liquids

Understanding how chemical reactions happen on tiny crystals in liquid solutions is central to a variety of fields, including materials synthesis and heterogeneous catalysis, but obtaining such an understanding requires that scientists observe reactions as they occur.

By using coherent X-ray diffraction techniques, scientists can measure the exterior shape of and strain in nanocrystalline materials with a high degree of precision. However, carrying out such measurements requires precise control of the position and angles of the tiny crystal with respect to the incoming X-ray beam. Traditionally, this has meant adhering or gluing the crystal to a surface, which in turn strains the crystal, thus altering its structure and potentially affecting reactivity.

>Read more on the Advanced Photon Source at Argonne Laboratory website

Image: Scientists have found a way to use “optical tweezers” by employing lasers, a mirror and a light modulator to anchor a crystal in solution. The “tweezers” have made it possible to conduct X-ray diffraction measurements of a crystal suspended in solution.
Credit: Robert Horn/Argonne National Laboratory.

The best topological conductor yet: spiraling crystal is the key to exotic discovery

The best topological conductor yet: spiraling crystal is the key to exotic discovery

X-ray research at Berkeley Lab reveals samples are a new state of matter

The realization of so-called topological materials – which exhibit exotic, defect-resistant properties and are expected to have applications in electronics, optics, quantum computing, and other fields – has opened up a new realm in materials discovery.
Several of the hotly studied topological materials to date are known as topological insulators. Their surfaces are expected to conduct electricity with very little resistance, somewhat akin to superconductors but without the need for incredibly chilly temperatures, while their interiors – the so-called “bulk” of the material – do not conduct current.
Now, a team of researchers working at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has discovered the strongest topological conductor yet, in the form of thin crystal samples that have a spiral-staircase structure. The team’s study of crystals, dubbed topological chiral crystals, is reported in the March 20 edition of the journal Nature.

>Read more on the ALS at Berkeley Lab website

Image: This illustration shows a repeated 2D patterning of a property related to electrical conductivity, known as the surface Fermi arc, in rhodium-silicon crystal samples.
Credit: Hasan Lab/Princeton University

Students use AI for sample positioning at BioMAX

Students use AI for sample positioning at BioMAX

The samples at BioMAX beamline are very sensitive biomolecule crystals. It could, for example, be one of the many proteins you have in your body. They only last for a short time in the intense X-ray light before being damaged and needs to be placed exactly right before the researchers switch on the beam. In their masters’ project, Isak Lindhé, and Jonathan Schurmann have used methods of artificial intelligence to train the computer how to do it.

Hundreds of thousands of proteins
You have hundreds of thousands of different proteins in your body. They do everything from transporting oxygen in your blood to letting your cells take up nutrients after you’ve eaten or make your heart beat. And when things go wrong, you get prescribed medication. The pharmaceutical molecules connect to the proteins in your body to change how they work. To develop new pharmaceuticals with few side effects, the researchers, therefore, need to understand what different proteins look like in detail.

A tedious task
To get high-quality data from a sample it needs to be correctly positioned in the X-ray beam. The conventional model for finding the right position is to scan the sample in the beam to optimize the position. At MAX IV, the X-ray light is very intense, which is good because smaller crystals can be used. But at the same time, very often the sample can’t be scanned in the beam since it would be damaged long before the right position is found. The researchers, therefore, have to perform the rather tedious task of positioning it manually.

>Read more on the MAX IV Laboratory website

Nanoparticles form supercrystals under pressure

Nanoparticles form supercrystals under pressure

Investigations at Diamond may lead to easier ways to synthesise nanoparticle supercrystals

Self-assembly and crystallisation of nanoparticles (NPs) is generally a complex process, based on the evaporation or precipitation of NP-building blocks. Obtaining high-quality supercrystals is slow, dependent on forming and maintaining homogenous crystallisation conditions. Recent studies have used applied pressure as a homogeneous method to induce various structural transformations and phase transitions in pre-ordered nanoparticle assemblies. Now, in work recently published in the Journal of Physical Chemistry Letters, a team of German researchers studying solutions of gold nanoparticles coated with poly(ethylene glycol)- (PEG-) based ligands has discovered that supercrystals can be induced to form rapidly within the whole suspension.

>Read more on the Diamond Light Source website

Figure: 2D SAXS patterns of PEG-coated gold nanoparticles (AuNP) with 2 M CsCl added at different pressures. Left: 1 bar; Middle: 4000 bar; Right: After pressure release at 1 bar. The scheme on top illustrates the structural assembly of the coated AuNPs at different pressures: At 1 bar, the particle ensemble is in an amorphous, liquid state. Upon reaching the crystallization pressure, face-centred cubic crystallites are formed by the AuNPs. After pressure release, the AuNPs return to the liquid state. 

Movie directors with extra roles

Movie directors with extra roles

Data storage devices based on novel materials are expected to make it possible to record information in a smaller space, at higher speed, and with greater energy efficiency than ever before.

Movies shot with the X-ray laser show what happens inside potential new storage media, as well as how the processes by which the material switches between two states can be optimised.
Henrik Lemke comes to work on his bicycle. Private cars are not allowed to drive to the SwissFEL building in the Würenlingen forest, and delivery vans and lorries need a permit. As a beamline scientist, the physicist is responsible for the experiment station named for Switzerland’s Bernina Pass. At the end of 2017, he led the first experiment at the Swiss free-electron X-ray laser, acting in effect as a movie director while SwissFEL was used, like a high-speed camera, to record how a material was selectively converted from a semiconducting to a conducting state – and back again. To this end the PSI team, together with a research group from the University of Rennes in France, studied a powder of nanocrystals made of titanium pentoxide. The sample was illuminated with infrared laser pulses that made the substance change its properties. Then X-ray pulses revealed how the crystal structure was deformed and enlarged – a cascade of dynamic processes that evidently depend on the size of the crystals.

Image: The directors: Henrik Lemke and Gerhard Ingold
Credit: Scanderbeg Sauer Photography
The enigma of Rembrandt’s vivid white

The enigma of Rembrandt’s vivid white

Some of Rembrandt’s masterpieces are at the ESRF for some days, albeit only in minuscule form. The goal: to unveil the secrets of the artist’s white pigment.

Seven medical students surround a dead body while they attentively look at how the doctor is dissecting the deceased. The scene is set in a dark and gloomy environment, where even the faces of the characters show a grey tinge. Strangely, the only light in the scene is that coming from their white collars and the white sheet that partially covers the body. The vivid white creates a perplexing light-reflecting effect. Welcome to painting The anatomy lesson of Dr. Nicolaes Tulp, a piece of art displaying the baffling technique of the impasto, of which Rembrandt, its author, was a master.

Impasto is thick paint laid on the canvas in an amount that makes it stand from the surface. The relief of impasto increases the perceptibility of the paint by increasing its light-reflecting textural properties. Scientists know that Rembrandt achieved the impasto effect by using materials traditionally available on the 17th century Dutch colour market, namely the lead white pigment (mix of hydrocerussite Pb3(CO3)2.(OH)2 and cerussite PbCO3), chalk (calcite CaCO3) and organic mediums (mainly linseed oil). The precise recipe he used is, however, still unknown.

>Read more on the European Synchrotron website

Image: The anatomy lesson of Dr. Nicolaes Tulp, by Rembrandt.

 

Respiratory virus study points to likely vaccine target

Respiratory virus study points to likely vaccine target

The work provides a promising route for designing a vaccine effective against a broad range of RSV strains, which cause serious respiratory disease in infants and older adults.

Respiratory syncytial virus (RSV) causes 118,000 deaths in young children each year worldwide and 57,000 hospitalizations of children each year in the United States alone. Attempts to develop a vaccine—at first based on inoculations with inactivated virus, and then targeting a key viral surface protein (RSV F)—have failed. Recent studies, however, suggest that a second viral surface protein (RSV G) is a promising target.

In one earlier study, elevated concentrations of antibodies targeting both RSV F and RSV G were associated with lower clinical disease severity scores, despite a substantially lower absolute abundance of anti-G antibodies. Another study found that higher levels of maternal anti-G antibodies correlated with less severe disease in infants (up to 4-6 months of age), even though anti-G antibodies were again found in lower concentrations.

While the RSV F surface protein allows the virus to enter a host cell, RSV G is what allows the virus to stick to lung cells and distort immune responses. This disruption of the immune response by RSV G might explain why vaccines based on RSV F have failed. Thus, a protective antibody response that blocks RSV G activity could be more effective, but scientists didn’t know how antibodies target RSV G at the molecular level.

>Read more on the ALS website.

Image: Stanislav Fedechkin and Rebecca DuBois.
Credit: C. Lagattuta/UC Santa Cruz

Scientists find a new way to make novel materials by ‘un-squeezing’

Scientists find a new way to make novel materials by ‘un-squeezing’

Like turning a snowball back into fluffy snow, a new technique turns high-density materials into a lower-density one by applying the chemical equivalent of ‘negative pressure.’

Some materials can morph into multiple crystal structures with very different properties. For instance, squeezing a soft form of carbon produces diamond, a harder and more brilliant form of carbon. The Kurt Vonnegut novel “Cat’s Cradle” featured ice-nine, a fictional form of water with a much higher melting point than regular ice that threatened to irreversibly freeze all the water on Earth.

These materials are called polymorphs, and they’re commonly made by applying pressure, or squeezing. Scientists looking for new materials would also like to do the opposite – apply “negative pressure” to stretch a material’s crystal structure into a new configuration. In the past, this approach seemed to require negative pressures that are difficult if not impossible to achieve in the lab, plus it risked pulling the material apart.

Now researchers at the Department of Energy’s National Renewable Energy Laboratory (NREL) have found a way to create the equivalent of negative pressure by mixing two materials together under just the right conditions to make an alloy with an airier and entirely different crystal structure and unique properties.

>Read more on the SSRL website

Image: SLAC staff scientists Laura Schelhas and Kevin Stone at an experimental station at the Stanford Synchrotron Radiation Lightsource, where they used X-rays to measure the structure of a novel ‘negative pressure’ material created at NREL.
Credit: Matt Beardsley/SLAC National Accelerator Laboratory
Study suggests water may exist in Earth’s lower mantle

Study suggests water may exist in Earth’s lower mantle

Water on Earth runs deep – very deep. The oceans have been measured to a maximum depth of 7 miles, though water is known to exist well below the oceans. Just how deep this hidden water reaches, and how much of it exists, are the subjects of ongoing research.

Now a new study suggests that water may be more common than expected at extreme depths approaching 400 miles and possibly beyond – within Earth’s lower mantle. The study, which appeared March 8 in the journal Science, explored microscopic pockets of a trapped form of crystallized water molecules in a sampling of diamonds from around the world.

Diamond samples from locations in Africa and China were studied through a variety of techniques, including a method using infrared light at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). Researchers used Berkeley Lab’s Advanced Light Source (ALS), and Argonne National Laboratory’s Advanced Photon Source, which are research centers known as synchrotron facilities.

>Read more on the Advanced Light Source website

Photo: Oliver Tschauner, professor of research in the Department of Geoscience at the University of Nevada, Las Vegas, holds a diamond sample during a recent round of experiments at Berkeley Lab’s Advanced Light Source.
Credit: Marilyn Chung/Berkeley Lab

Stressing over new materials

Stressing over new materials

Titanium is a workhorse metal of the modern age. Alloyed with small amounts of aluminum and vanadium, it is used in aircraft, premium sports equipment, race cars, space craft, high-end bicycles, and medical devices because of its light weight, ability to withstand extreme temperatures, and excellent corrosion resistance. But titanium is also expensive. Metallurgists would love to understand exactly what makes it so strong so that they could design other materials with similarly desirable properties out of more common, less expensive elements. Now, researchers utilizing the U.S. Department of Energy’s Advanced Photon Source (APS) have used high-intensity x-rays to show how titanium alloy responds to stress in its (until now) hidden interior. Eventually, the researchers believe they will be able to predict how strong a titanium part such as an aircraft engine will be, just by knowing how the crystals are arranged inside of it. And materials scientists may be able to use such a computational model to swap in atoms from different metals to see how their crystalline structures compare to that of titanium.

>Read more on the Advanced Photon Source website

Figure: (extract) (A) A computational model of crystals inside a block of titanium, (B) includes effects noticed during the experiment to place permanent deformations (the darkened areas,) [not visible here, entire picture here]  while (C) models permanent deformations without incorporating the diversity of load seen in the experiment.