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Showing posts with label Chemistry. Show all posts
Showing posts with label Chemistry. Show all posts

Tuesday, 10 March 2020

After 90 years, scientists reveal the structure of benzene

In 1825, the British physicist and chemist Michael Faraday isolates a particular compound in the residual liquid present in the bottom of lighting bottles: benzene. Suggested in 1861, the chemical structure of benzene was correctly described in 1933 by Linus Pauling. However, since its discovery, chemists have always wondered about its extremely complex electronic structure. And recently, a team of researchers finally described it in detail.

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Nearly 200 years after the molecule was discovered by Michael Faraday, researchers have finally revealed the complex electronic structure of benzene. This not only settles a debate that has been raging since the 1930s, this step has important implications for the future development of opto-electronic materials, many of which are built on benzenes.

The atomic structure of benzene is pretty well understood. It's a ring consisting of six carbon atoms, and six hydrogen atoms, one attached to each of the carbon atoms.

Benzene: a structure of 42 electrons described in 126 dimensions

Where it gets extremely tricky is when we consider the molecule's 42 electrons. "The mathematical function that describes benzene's electrons is 126-dimensional," said the chemist Timothy Schmidt of the ARC Centre of Excellence in Exciton Science and UNSW Sydney in Australia

"That means it is a function of 126 coordinates, three for each of the 42 electrons. The electrons are not independent, so we cannot break this down into 42 independent three-dimensional functions. The answer computed by a machine is not easy to interpret by a human, and we had to invent a way to get at the answer."

Structural portion of the benzene molecule modeled according to the Voronoi algorithm. (d): Voronoi website showing electronic spins. (d): cross section of the Voronoi site, showing the two electron spins of the CC bond (in blue and red). Credits: Yu Liu et al. 2020

So, that means mathematically describing the electronic structure of benzene needs to take 126 dimensions into account. As you can imagine, this is not exactly a simple thing to do. In fact, this complexity is why revealing the structure has remained a problem for so long, leading to debates about how benzene's electrons even behave. There are two schools of thought: that benzene follows valence bond theory, with localised electrons; or molecular orbital theory, with delocalised electrons. The problem is, neither really seems to quite fit.

Electronic dynamics much more complex than expected

"The interpretation of electronic structure in terms of orbitals ignores that the wavefunction is antisymmetric upon interchange of like-spins," the researchers wrote in their paper. "Furthermore, molecular orbitals do not provide an intuitive description of electron correlation."

The team's work was based on a technique they recently developed. It's called dynamic Voronoi Metropolis sampling, and it uses an algorithmic approach to visualise the wavefunctions of a multiple-electron system. This separates the electron dimensions into separate tiles in a Voronoi diagram, with each of the tiles corresponding to electron coordinates, allowing the team to map the wavefunction of all 126 dimensions. And they found something strange.

(a): Classic Kekule structures of the benzene molecule. (b): Structure proposed by the authors with the spins indicated in red and blue. Credits: Yu Liu et al. 2020

"The electrons with what's known as up-spin double-bonded, where those with down-spin single-bonded, and vice versa," Schmidt said in statement. "That isn't how chemists think about benzene."

The effect of this is that the electrons avoid each other when it is advantageous to do so, reducing the energy of the molecule, and making it more stable. "Essentially, this unites chemical thought, by showing how the two prevailing paradigms by which we describe benzene come together," he added.

"But we also show how to inspect what is called electron correlation - how the electrons avoid each other. This is almost always ignored qualitatively, and only invoked for calculations where only the energy is used, not the electronic behaviour."

In other words, this result describes the main effect of electronic correlation in benzene, and emphasizes that electrons are not paired in space when it is energetically advantageous.


The electronic structure of benzene from a tiling of the correlated 126-dimensional wavefunction

Yu Liu, Phil Kilby, Terry J. Frankcombe & Timothy W. Schmidt

Nature Communications

volume 11, Article number: 1210 (2020)

Saturday, 22 February 2020

For the first time, atoms have been individually manipulated and observed interacting

Understanding atomic interactions in detail is essential to refine the current chemical models concerning the construction and structuring of molecules. Until now, to study these interactions, chemists had to be content with groups of atoms in which they calculated and determined mean correlations, giving a vague idea of ​​the individual behavior of atoms during the formation of molecules. But recently, a team of researchers has developed a technique for manipulating individual atoms in order to observe them forming molecules.

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One way to analyze such exchanges is to grab single atoms with the equivalent of a tiny pair of tweezers, immobilize them, and record the changes as they meet. Fortunately, such a pair of tweezers exists. Made from specially aligned polarized light, these laser tweezers can serve as optical traps for tiny objects.

Manipulate individual atoms with optical tweezers

With sufficiently short light waves, an experimenter has a good chance of trapping something as small as an individual atom in these clamps. Of course, the atoms must first be cooled to make them easier to catch, and then separated in an empty space.

"Our method involves the individual trapping and cooling of three atoms to a temperature of about one millionth of a Kelvin using highly focused laser beams in a hyper-evacuated (vacuum) chamber, the size of a grid. -bread. We slowly combine the traps containing the atoms to produce controlled interactions which we measure”, explains the physicist Mikkel F. Andersen.

Experimental procedure for directly observing collisions of cold atoms. The researchers isolate three 85Rb atoms in separate optical tweezers and confirm their presence by fluorescence imaging. A collision and compression stage allows the atoms to interact. Credits; LA Reynolds et al. 2020

The atoms in this case were all rubidium atoms, which bond to form dirubidium molecules, but two atoms are not enough to achieve this. "Two atoms alone cannot form a molecule, you need at least three to do chemistry," says physicist Marvin Weyland.

Better understand the formation of molecules on the atomic scale

Modeling how it works is a real challenge. It is clear that two atoms must get close enough to be able to form a bond, while a third one tears off part of this bond energy to leave them connected. The three-body recombination between atoms should, in theory, force them out of their trap, which usually adds another problem to physicists trying to study the interactions between several atoms.

Rubidium atomic cloud cooled by laser and observed via the camera developed by the researchers. Credits: University of Otago

Using a special camera to amplify the changes, the team captured the moment the rubidium atoms moved closer together, revealing a different rate of loss than that predicted by the models. Indeed, it also means that molecules do not bind as quickly as existing models explain. The results were published in the journal Physical Review Letters .

"This is the first time that this basic process has been studied in isolation, and it turns out that it has produced several surprising results that were not expected from previous measurements in large clouds of atoms. With further development, this technique could provide a way to build and control unique molecules of particular chemicals,” says Weyland. Other experiments will help refine these models to better explain how groups of atoms work together to meet and bond under various conditions.


Direct Measurements of Collisional Dynamics in Cold Atom Triads

L. A. Reynolds, E. Schwartz, U. Ebling, M. Weyland, J. Brand, and M. F. Andersen

Phys. Rev. Lett. 124, 073401 –
Published 18 February 2020


Friday, 7 February 2020

In the liquid state, water molecules actually have two different structures

From the oceans to the cells passing through the atmosphere, water is omnipresent on Earth. In the liquid state, it is a solvent necessary for life. Which makes it one of the most studied molecules by chemists. However, there is still much to discover about it. By studying it through X-rays, a team of researchers recently discovered that water molecules adopt two different structures in the liquid state. A result that could have important implications in terms of biochemistry and industry.

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Researchers at the University of Tokyo have used calculation methods and analysis of recent experimental data to demonstrate that water molecules have two distinct structures in the liquid state.

The team studied the X-ray scattering through water samples and showed a hidden bimodal distribution under the first diffraction peak resulting from the tetrahedral and non-tetrahedral arrangements of the water molecules.

This work can have important implications in many scientific and technological fields, but especially with regard to living systems, such as proteins and cellular structures, which are strongly affected by the surrounding water molecules. Given the omnipresence of water on our planet and the central role it plays in all known life, it can be difficult to believe that there is still something to learn about this molecule.

An unusual liquid because of its structure and molecular arrangements

A simple molecule composed of only two atoms of hydrogen and one of oxygen, water still hides fundamental mysteries that remain to be elucidated. For example, water has unusually high melting and boiling points and expands even when it freezes (unlike most liquids that contract). These and other unusual properties make it very different from almost all other liquids, but also allow life as we know it to exist.

Water has a tetrahedral molecular arrangement where a molecule of H2O is linked to 4 other molecules via hydrogen bonds. Credits: Qwerter / Wikimedia Commons

The strangeness of water can be better understood by thinking of the unique interactions between H2O molecules - the hydrogen bond. Water tends to form four hydrogen bonds with its four neighbors, which leads to tetrahedral arrangements. Such arrangements can be largely deformed under thermal fluctuations. However, the question of whether the distortion leads to the coexistence of separate tetrahedral and non-tetrahedral arrangements has remained controversial.

Liquid water: X-rays reveal that it actually has two structures

Now, scientists at The University of Tokyo have combined computer simulations and the analysis of scattering experimental data to find the "structure factor" of water -- the mathematical function that represents the paths of dispersed X-rays when they scatter off the hydrogen and oxygen atoms. The analysis showed two overlapping peaks hiding in the first diffraction peak of the structure factor. One of these peaks corresponded to the distance between oxygen atoms as in ordinary liquids, while the other indicated a longer distance, as in a tetrahedral arrangement. "The combination of new computational methods and analysis of recent X-ray scattering data allowed us to see what was not visible in previous work," first author of the study Rui Shi explains.

Analysis of the X-ray diffraction by the oxygen and hydrogen atoms has shown a double peak indicating the existence of two distinct molecular structures. Credits: Rui Shi and Hajime Tanaka

One of these peaks corresponds to the distance between the oxygen atoms, as in ordinary liquids, while the other indicates a longer distance, as in a tetrahedral arrangement. This discovery can have enormous implications in many scientific fields. Knowing the exact structural order of water is essential for a complete understanding of molecular biology, chemistry and even many industrial applications.


Direct Evidence in the Scattering Function for the Coexistence of Two Types of Local Structures in Liquid Water

Rui Shi, Hajime Tanaka

J. Am. Chem. Sac

Publication Date:January 21, 2020

Thursday, 6 February 2020

A specific type of cancer treatment improves night vision, and we finally know why

Following a specific cancer treatment called photodynamic therapy, some patients have reported experiencing differences in their night vision, including the ability to see more clearly or to distinguish objects better in the dark. Photodynamic therapy uses light to destroy cancer cells, and its interaction with certain photosensitive proteins is believed to be the cause of this mysterious side effect.

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In a recent study, researchers show their understanding of what would be the cause of this photosensitivity change: rhodopsin, a light-sensitive protein in the retina, interacts with a photosensitive compound called chlorine e6, a crucial component of this type of cancer treatment.

The work is based on what scientists already know about the retinal organic compound, which is located in the eye and is generally not sensitive to infrared light. The results were published in the Journal of Physical Chemistry Letters .

An interaction between rhodopsin and chlorine e6

Visible light causes the rhodopsin to separate from the retina. This is then converted into electrical signals, which our brain interprets to form an image. Although little visible light is available overnight, it turns out that this mechanism can also be triggered with another combination of light and chemical reaction: under infrared light and with an injection of chlorine e6, the retina undergoes the same reactions as under visible light.

"This explains the increase in nighttime visual acuity," said chemist Antonio Monari, from the University of Lorraine in France, to CNRS. “However, we did not know precisely how rhodopsin and its active retinal group interacted with chlorine. It is this mechanism that we have now managed to elucidate via molecular simulation”.

Enhanced color scanning electron micrograph showing rods (in red) and human eye cones (x2500 magnification). Rods are long nerve cells that react to a small amount of light. Cones are shorter cells that detect color. Rods and cones transmit visual signals to the brain through the optic nerve. In theory, rods are not sensitive to infrared radiation, which predominates at night. Credits: Science Source / BSIP

Model the movements of individual atoms to understand the mechanism involved

In addition to certain chemical calculations, the team used molecular simulation to model the movements of individual atoms (in terms of respective attraction and repulsion), as well as the breaking or creation of chemical bonds.

The simulation, which is the subject of millions of calculations, lasted several months before being able to accurately model the chemical reaction caused by infrared radiation. In reality, this reaction would occur in a few nanoseconds.

Screen capture of the digital molecular simulation performed during these experiments. The chemical interaction between the chlorine e6 molecule used for phototherapy and the rhodopsin present in the receptors of the eye is visible. Credits: LPCT / University of Lorraine - CNRS

"For our simulation, we placed a virtual rhodopsin protein inserted into its lipid membrane in contact with several molecules of chlorine e6 and water, involving tens of thousands of atoms," said Monari.

As chlorine e6 absorbs infrared radiation, it interacts with oxygen in the eye tissue, transforming it into singlet oxygen (excited metastable state) very reactive and destroying cancer cells. Molecular simulation shows that singlet oxygen can also react with the retina and temporarily improve night vision.

Treating certain types of blindness or excessive sensitivity to light

Now that researchers are familiar with the chemistry behind this strange side effect, they may be able to limit the risk of this happening in patients undergoing photodynamic therapy, some of whom have reported seeing silhouettes and outlines otherwise. invisible in the dark.

This chemical reaction could also ultimately be used to help & treat certain types of blindness or excessive sensitivity to light. For the moment however, exploiting this still little understood phenomenon to offer a superhuman night vision is more than contraindicated…

"Molecular simulation is already used to shed light on fundamental mechanisms - for example, why certain DNA lesions are better repaired than others?" It also allows the selection of potential therapeutic molecules, by mimicking their interaction with a chosen target, "said Monari.


Induced Night Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

Marco Marazzi, Hugo Gattuso, Angelo Giussani, Hong Zhang, Miriam Navarrete-Miguel, Christophe Chipot, Wensheng Cai, Daniel Roca-Sanjuán, François Dehez, Antonio Monari

J. Phys. Chem. Lett. 2019, 10, 22, 7133-7140

Publication Date:October 25, 2019

Saturday, 25 January 2020

Researchers find way to harness the entire visible spectrum for energy production

For the very first time, scientists have demonstrated that it is possible to collect energy from the entire visible spectrum of sunlight and transform it quickly and efficiently into hydrogen. In fact, they have developed a single molecule that can efficiently absorb sunlight and also act as a catalyst to transform solar energy into hydrogen. A clean alternative to fossil fuels (for, in particular, motor vehicles).

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This new molecule collects energy from the entire visible spectrum and can harness more than 50% more solar energy than current solar cells. This discovery could well help humanity move from fossil fuels to energy sources that do not contribute to climate change.

“  The idea is to use the photons from the sun and transform them into hydrogen. Simply put, we collect energy from sunlight and store it in chemical bonds so it can be used later, "said Claudia Turro, professor of chemistry and director of the center at Ohio State University for chemical and biophysical dynamics (and who also directed this research). Namely, that photons are the elementary particles of light, and contain a certain amount of energy.

Thanks to this study, for the very first time, it has been demonstrated that it is possible to collect energy from the entire visible spectrum of sunlight, including low energy infrared ( part of the solar spectrum that had previously been difficult to collect) and transform it quickly and efficiently into hydrogen.

Hydrogen is a clean fuel, which means that it does not produce carbon or carbon dioxide as a by-product of its use. "  What makes it work is that the system is able to put the molecule in an excited state, where it absorbs the photon and is able to store two electrons to produce hydrogen. This storage of two electrons in a single molecule, as well as this use to produce hydrogen, is unprecedented,  ”said Turro.

Indeed, transforming the Sun's energy into fuel, for example to power a vehicle, first requires an energy collection mechanism. Then, this energy can be converted into fuel. The conversion requires a catalyst. In short: this is a device which accelerates a chemical reaction allowing the conversion of solar energy into a usable energy vector (in this case hydrogen).

Most of the previous attempts to collect solar energy and transform it into hydrogen have focused on higher energy wavelengths (like ultraviolet, for example). The latter have also relied on catalysts always involving two molecules (or more), which exchange electrons (energy) to produce fuel from solar energy. But a large part of this energy is lost in the exchange, which makes these multimolecular systems less efficient.

In addition, the few other attempts that relied on a single molecule catalyst were also ineffective "partly because they did not collect energy from the entire visible spectrum of the sun, and also because the catalysts themselves degraded quickly, "said Turro.

A system 25 times more efficient than current technologies

Now, Turro's research team has discovered how to make a catalyst from a single molecule, a form of rhodium (a chemical element), which means less energy is lost. The researchers also understood how to collect energy from the near infrared to the ultraviolet, more than the entire visible spectrum.

According to the researchers, the system they designed is nearly 25 times more efficient with low-energy near-infrared light than single-molecule systems operating with ultraviolet photons.

As part of this study, the researchers used LEDs to illuminate acid solutions containing the active molecule, and discovered that hydrogen was produced.

" I think the reason it works is because the molecule is difficult to oxidize,  " says Turro. "  And we have to have renewable energy. Just imagine, if we could use sunlight for our energy needs instead of coal, gas or oil, what we could do to fight climate change, ”added Turro.

But before the research team's results can be applied in the real world, "there is still a lot of work to do," admits Turro. Indeed, rhodium is a rare metal and the production of catalysts using it is expensive. The team is therefore working to improve this molecule to produce hydrogen over a longer period of time and to develop a catalyst exploiting less rare elements.


Article: Single-chromophore single-molecule photocatalyst for the production of dihydrogen using low-energy light

T. J. Whittemore, C. Xue, J. Huang, J. C. Gallucci & C. Turro

Nature Chemistry (2020)

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