Tag Archives: molecules

‘Golden’ protein crystals

Yet another use for gold. From a March 14, 2017 news item on Nanowerk (Note: A link has been removed),

Scientists from the London Centre for Nanotechnology (LCN) have revealed how materials such as gold can help create protein crystals. The team hope their findings, published in the journal Scientific Reports (“Protein crystal nucleation in pores”), could aid the discovery of new medicines and treatments. The Lead author; Professor Naomi Chayen states that “Gold doesn’t react with proteins, due to its inert nature, which makes it an ideal material to create crystals”.

Image: Crystals of an antibody peptide complex related to AIDS research Courtesy: LCN

A March 14, 2017 (?) LCN press release, which originated the news item, expands on the theme,

Proteins are crucial to numerous functions in the body – yet scientists are still in the dark about what most of them look like. This is because the most powerful way of revealing the structure of proteins is to turn them into crystals, and then analyse these with X-rays. However, persuading proteins to turn into useful crystals is notoriously difficult. All crystals start from a conception stage when the first molecules come together; this is called nucleation. But reaching nucleation is often difficult as it requires a lot of energy – and many proteins simply can’t overcome this barrier. Scientists also struggle to create medicines that bind to particular proteins – for instance a protein involved in cancer formation, if they don’t know the protein’s structure.

“How can you target a protein if you have no idea what it looks like? It’s like recognising a face in a crowd – you need a picture,” explained Professor Naomi Chayen, lead author of the research.

Forcing molecules together with gold

One technique for allowing proteins to reach their nucleation point is to trap them in tiny holes. This forces the molecules together, which helps them overcome the energy barrier needed to trigger the first crystal. One material that scientists have found to be effective at growing crystals is gold. Creating many holes in the metal creates a substance called porous gold, which acts as a perfect environment for growing crystals, explained Professor Chayen: “Gold doesn’t react with proteins, due to its inert nature, which makes it an ideal material to create crystals. Creating holes in the metal enable it to act a bit like coral, with each hole providing an ideal environment to harbour crystals.”

Creating crystals

In the latest research, the team investigated the best size hole needed to create crystals. They found that a variety of different sized holes produced the highest quality crystals. Most holes were around 5-10nm, just slightly larger than the width of a human hair. Professor Chayen explained: “Imagine walking down a street with many potholes – some of the holes will be big enough for me to step out of, while some will be too small for my foot to fall into. “However, some will be the exact size of my foot, and will trap me in them. This is the same principle as having different pore sizes – it allows us to trap different size protein molecules, enabling them to form crystals.”

She added that the findings which give a simple explanation of why, and under what conditions porous materials can induce protein crystal nucleation may help scientists design porous materials that would produce the highest quality crystals.

Here’s a link to and a citation for the paper,

Protein crystal nucleation in pores by Christo N. Nanev, Emmanuel Saridakis & Naomi E. Chayen. Scientific Reports 7, Article number: 35821 (2017) doi:10.1038/srep35821 Published online: 16 January 2017

This is an open access article.

Explaining research into matching plasmonic nanoantenna resonances with atoms, molecules, and quantum dots

There’s a very nice explanation of the difficulties associeated with using plasmonic nanoantennas as sensors in a March 21, 2016 news item on phys.org,

Plasmonic nanoantennas are among the hot topics in science at the moment because of their ability to interact strongly with light, which for example makes them useful for different kinds of sensing. But matching their resonances with atoms, molecules or so called quantum dots has been difficult so far because of the very different length scales involved. Thanks to a grant from the Engkvist foundation, Timur Shegai, assistant professor at Chalmers University of Technology, hopes to find a way to do this and by that open doors for applications such as safe long distance communication channels.

A molecule being illuminated by two gold nanoantennas. By: Alexander Ericson Courtesy: Chalmers University of Technology

A molecule being illuminated by two gold nanoantennas. By: Alexander Ericson Courtesy: Chalmers University of Technology

The image, looking like a stylized butterfly or bow tie, above accompanies Karin Weijdegård’s March ??, 2016 Chalmers University of Technology press release, which originated the news item, expands on the research theme,

The diffraction limit makes it very hard for light to interact with the very smallest particles or so called quantum systems such as atoms, molecules or quantum dots. The size of such a particle is simply so much smaller than the wavelength of light that there cannot be a strong interaction between the two. But by using plasmonic nanoantennas, which can be described as metallic nanostructures that are able to focus light very strongly and in wavelengths smaller than those of the visible light, one can build a bridge between the light and the atom, molecule or quantum dot and that is what Timur Shegai is working on.

“Plasmonic nanostructures are themselves smaller than wavelengths of light, but because they have a lot of free electrons they can store the electromagnetic energy in a volume which is actually a lot smaller than the diffraction limit, which helps to bridge the gap between really small objects such as molecules and the larger wavelengths of light,” he says.

Matching the harmonic with the un-harmonic

This might sound easy enough, but the problem with combining the two is that they behave in very different ways. The behaviour of plasmonic nanostructures is very linear, like a harmonic oscillator it will regularly move from side to side no matter how much energy or in other words how many excitations are stored in it. On the other hand, so called quantum systems like atoms, molecules or quantum dots are very much the opposite – their optical properties are highly un-harmonic. Here it makes a big difference if you excite the system with one or two or hundreds of photons.

“Now imagine that you couple together this un-harmonic resonator and a harmonic resonator, and add the possibility to interact with light much stronger than the un-harmonic system alone would have allowed. That opens up very interesting possibilities for quantum technologies and for non-linear optics for example. But as opposed to previous attempts that have been done at very low temperatures and in a vacuum, we will do it at room temperature.”

Communication channels impossible to hack

One possible application where this technology could be useful in the future is to create channels for long distance communications that are impossible to hack. With the current technology this kind of safe communication is only possible if the persons communicating is within a distance of about one hundred kilometres from each other, because that is the maximum distance that an individual photon can run in fibres before it scatters and the signal is lost.

“The kind of ultra small and ultra fast technology we want to develop could be useful in a so called quantum repeater, a device that could be installed across the line from for example New York to London, that would repeat the photon every time it is about to be scattered,” says Timur Shegai.

At the moment though, it is the fundamental aspects of merging plasmons with quantum systems that interest Timur Shegai. To be able to experimentally prove that the there can be interactions between the two systems, he first of all needs to fabricate model systems at the nano level. This is a big challenge, but with the grant of 1,6 million SEK over a period of two years that he just received from the Engkvist foundation, the chances of success have improved.

“Since I am a researcher at the beginning of my career every person is a huge improvement and now I can hire a post doc to work with my group. This means that the project can be divided into sub parts and together we will be able to explore more possibilities about this new technology.”

Thank you Karin Weijdegård for the explanation.

Gold atoms: sometimes they’re a metal and sometimes they’re a molecule

Fascinating work out of Finland shows that a minor change in the number of gold atoms in your gold nanoparticle can mean the difference between a metal and a molecule (coincidentally, this phenomenon is alluded to in my April 14, 2015 post (Nature’s patterns reflected in gold nanoparticles); more about that at the end of this piece. Getting back to Finland and when gold is metal and when it’s a molecule, here’s more from an April 10, 2015 news item on ScienceDaily,

Researchers at the Nanoscience Center at the University of Jyväskylä, Finland, have shown that dramatic changes in the electronic properties of nanometre-sized chunks of gold occur in well-defined size range. Small gold nanoclusters could be used, for instance, in short-term storage of energy or electric charge in the field of molecular electronics. Funded by the Academy of Finland, the researchers have been able to obtain new information which is important, among other things, in developing bioimaging and sensing based on metal-like clusters.

An April 10, 2015 news release (also on EurekAlert) on the Academy of Finland (Suomen Akatemia) website, which originated the news item, describes the work in more detail,

Two recent papers by the researchers at Jyväskylä (1, 2) demonstrate that the electronic properties of two different but still quite similar gold nanoclusters can be drastically different. The clusters were synthesised by chemical methods incorporating a stabilising ligand layer on their surface. The researchers found that the smaller cluster, with up to 102 gold atoms, behaves like a giant molecule while the larger one, with at least 144 gold atoms, already behaves, in principle, like a macroscopic chunk of metal, but in nanosize.

The fundamentally different behaviour of these two differently sized gold nanoclusters was demonstrated by shining a laser light onto solution samples containing the clusters and by monitoring how energy dissipates from the clusters into the surrounding solvent.

“Molecules behave drastically different from metals,” said Professor Mika Pettersson, the principal investigator of the team conducting the experiments. “The additional energy from light, absorbed by the metal-like clusters, transfers to the environment extremely rapidly, in about one hundred billionth of a second, while a molecule-like cluster is excited to a higher energy state and dissipates the energy into the environment with a rate that is at least 100 times slower. This is exactly what we saw: the 102-gold atom cluster is a giant molecule showing even a transient magnetic state while the 144-gold atom cluster is already a metal. We’ve thus managed to bracket an important size region where this fundamentally interesting change in the behaviour takes place.”

“These experimental results go together very well with what our team has seen from computational simulations on these systems,” said Professor Hannu Häkkinen, a co-author of the studies and the scientific director of the nanoscience centre. “My team predicted this kind of behaviour back in 2008-2009 when we saw big differences in the electronic structure of exactly these nanoclusters. It’s wonderful that robust spectroscopic experiments have now proved these phenomena. In fact, the metal-like 144-atom cluster is even more interesting, since we just published a theoretical paper where we saw a big enhancement of the metallic properties of just a few copper atoms mixed with gold.” (3)

Here are links to and citation for the papers,

Ultrafast Electronic Relaxation and Vibrational Cooling Dynamics of Au144(SC2H4Ph)60 Nanocluster Probed by Transient Mid-IR Spectroscopy by Satu Mustalahti, Pasi Myllyperkiö, Tanja Lahtinen, Kirsi Salorinne, Sami Malola, Jaakko Koivisto, Hannu Häkkinen, and Mika Pettersson. J. Phys. Chem. C, 2014, 118 (31), pp 18233–18239 DOI: 10.1021/jp505464z Publication Date (Web): July 3, 2014

Copyright © 2014 American Chemical Society

Copper Induces a Core Plasmon in Intermetallic Au(144,145)–xCux(SR)60 Nanoclusters by Sami Malola, Michael J. Hartmann, and Hannu Häkkinen. J. Phys. Chem. Lett., 2015, 6 (3), pp 515–520 DOI: 10.1021/jz502637b Publication Date (Web): January 22, 2015

Copyright © 2015 American Chemical Society

Molecule-like Photodynamics of Au102(pMBA)44 Nanocluster by Satu Mustalahti, Pasi Myllyperkiö, Sami Malola, Tanja Lahtinen, Kirsi Salorinne, Jaakko Koivisto, Hannu Häkkinen, and Mika Pettersson. ACS Nano, 2015, 9 (3), pp 2328–2335 DOI: 10.1021/nn506711a Publication Date (Web): February 22, 2015

Copyright © 2015 American Chemical Society

These papers are behind paywalls.

As for my April 14, 2015 post (Nature’s patterns reflected in gold nanoparticles), researchers at Carnegie Mellon University were researching patterns in different sized gold nanoparticles when this was noted in passing,

… Normally, gold is one of the best conductors of electrical current, but the size of Au133 is so small that the particle hasn’t yet become metallic. …

The birth of a molecule

This research comes from Korea’s Institute of Basic Science in a Feb. 27, 2015 news item on Azonano,

The research team of the Center for Nanomaterials and Chemical Reactions at the Institute for Basic Science (IBS) has successfully visualized the entire process of bond formation in solution by using femtosecond time-resolved X-ray liquidography (femtosecond TRXL) for the first time in the world.

A Feb. 18, 2015 IBS press release, which originated the news item, provides more details,

Every researcher’s longstanding dream to observe real-time bond formation in chemical reactions has come true. Since this formation takes less than one picosecond, researchers have not been able to visualize the birth of molecules.

The research team has used femtosecond TRXL in order to visualize the formation of a gold trimer complex in real time without being limited by slow diffusion.

They have focused on the process of photoinduced bond formation between gold (Au) atoms dissolved in water. In the ground (S0) state, Au atoms are weakly bound to each other in a bent geometry by van der Waals interactions. On photoexcitation, the S0 state rapidly converts into an excited (S1) state, leading to the formation of covalent Au-Au bonds and bent-to-linear transition. Then, the S1 state changes to a triplet (T1) state with a time constant of 1.6 picosecond, accompanying further bond contraction by 0.1 Å. Later, the T1 state of the trimer transforms to a tetramer on nanosecond time scale, and Au atoms return to their original bent structure.

“By using femtosecond TRXL, we will be able to observe molecular vibration and rotation in the solution phase in real time,” says Hyotcherl Ihee, the group leader of the Center for Nanomaterials at IBS, as well as the professor of the Department of Chemistry at Korea Advanced Institute of Science and Technology.

Here’s a link to and a citation for the paper,

Direct observation of bond formation in solution with femtosecond X-ray scattering by Kyung Hwan Kim, Jong Goo Kim, Shunsuke Nozawa, Tokushi Sato, Key Young Oang, Tae Wu Kim, Hosung Ki, Junbeom Jo, Sungjun Park, Changyong Song, Takahiro Sato, Kanade Ogawa, Tadashi Togashi, Kensuke Tono, Makina Yabashi, Tetsuya Ishikawa, Joonghan Kim, Ryong Ryoo, Jeongho Kim, Hyotcherl Ihee & Shin-ichi Adachi. Nature 518, 385–389 (19 February 2015) doi:10.1038/nature14163 Published online 18 February 2015

This paper is behind a paywall although there is a free preview via ReadCube access.