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Science

Machine learning solves the who’s who problem in NMR spectra of organic crystals

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Probabilistic assignment of the 13C NMR spectrum of crystalline strychnine. Credit: @EPFL Manuel Cordova

Solid-state nuclear magnetic resonance (NMR) spectroscopy—a technique that measures the frequencies emitted by the nuclei of some atoms exposed to radio waves in a strong magnetic field—can be used to determine chemical and 3D structures as well as the dynamics of molecules and materials.

A necessary initial step in the analysis is the so-called chemical shift assignment. This involves assigning each peak in the NMR spectrum to a given atom in the molecule or material under investigation. This can be a particularly complicated task. Assigning chemical shifts experimentally can be challenging and generally requires time-consuming multi-dimensional correlation experiments. Assignment by comparison to statistical analysis of experimental chemical shift databases would be an alternative solution, but there is no such database for molecular solids.

A team of researchers including EPFL professors Lyndon Emsley, head of the Laboratory of Magnetic Resonance, Michele Ceriotti, head of the Laboratory of Computational Science and Modeling and Ph.D. student Manuel Cordova decided to tackle this problem by developing a method of assigning NMR spectra of organic crystals probabilistically, directly from their 2D chemical structures.

They started by creating their own database of chemical shifts for organic solids by combining the Cambridge Structural Database (CSD), a database of more than 200,000 three-dimensional organic structures, with ShiftML, a machine learning algorithm they had developed together previously that allows for the prediction of chemical shifts directly from the structure of molecular solids.

Initially described in a Nature Communications paper in 2018, ShiftML uses DFT calculations for training, but can then perform accurate predictions on new structures without performing additional quantum calculations. Though DFT accuracy is attained, the method can calculate chemical shifts for structures with ~100 atoms in seconds, reducing the computational cost by a factor of as much as 10,000 compared to current DFT chemical shift calculations. The accuracy of the method does not depend on the size of the structure examined and the prediction time is linear in the number of atoms. This sets the stage for calculating chemical shifts in situations where it would have been unfeasible before.

In the new Science Advances paper, the team used ShiftML to predict shifts on more than 200,000 compounds extracted from the CSD and then related the shifts obtained to topological representations of the molecular environments. This involved constructing a graph representing the covalent bonds between the atoms in the molecule, extending it a given number of bonds away from the central atoms. They then brought together all the identical instances of the graph in the database, allowing them to obtain statistical distributions of chemical shifts for each motif. The representation is a simplification of the covalent bonds around the atom in a molecule and doesn’t contain any 3D structural features: this allowed them to obtain the probabilistic assignment of the NMR spectra of organic crystals directly from their two-dimensional chemical structures through a marginalization scheme that combined the distributions from all the atoms in the molecule.

After constructing the chemical shift database, the scientists looked to predict the assignments on a model system and applied the approach to a set of organic molecules for which the carbon chemical shift assignment has already, at least in part, been determined experimentally: theophylline, thymol, cocaine, strychnine, AZD5718, lisinopril, ritonavir and the K salt of penicillin G. The assignment probabilities obtained directly from the two-dimensional representation of the molecules were found to match the experimentally determined assignment in most cases.

Finally, they evaluated the performance of the framework on a benchmark set of 100 crystal structures with between 10 and 20 different carbon atoms. They used the ShiftML predicted shifts for each atom as the correct assignment and excluded them from the statistical distributions used to assign the molecules. The correct assignment was found among the two most probable assignments in more than 80% of cases.

“This method could significantly accelerate the study of materials by NMR by streamlining one of the essential first steps of these studies,” Cordova said.

AI and NMR spectroscopy determine atoms configuration in record time

More information:
Manuel Cordova et al, Bayesian probabilistic assignment of chemical shifts in organic solids, Science Advances (2021). DOI: 10.1126/sciadv.abk2341. www.science.org/doi/10.1126/sciadv.abk2341
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Ecole Polytechnique Federale de Lausanne

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Machine learning solves the who’s who problem in NMR spectra of organic crystals (2021, November 26)
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Technology

Ghost of Tsushima: Director’s Cut Solves PS5 Save Transfer Woes

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We’d had some indication from the likes of Star Wars Jedi: Fallen Order and Saints Row The Third Remastered that Sony had solved the PlayStation 5’s curious save transfer system, but Ghost of Tsushima: Director’s Cut puts any scepticism beyond doubt. In order to move your progress from the PS4 version to its next-gen counterpart, you’ll simply need a save stored locally on your system.

So, for example, if you’ve played Ghost of Tsushima through backwards compatibility in the past, then you don’t need to do anything: just boot the Director’s Cut and select Transfer PS4 Console Save. That’s it: you’ll load into your game exactly where you left of – and, yes, all of the Trophies that you’ve unlocked previously will pop.

If, however, you last played Jin’s heroic adventure on a PS4, then all you need to do is download your data from the PS Plus cloud onto your PS5. And if, of course, you don’t have Sony’s subscription, then you can just use a USB stick to move the data to your new console. But that’s it: you don’t need to install your PS4 copy and upload your save data within the game or anything like that.

Sony was roundly criticised at launch for its complicated save transfer procedures. Effectively, the PS5 couldn’t read PS4 save data, so the only solution was for developers to implement upload protocols into their last-gen games, so that the information could be unpacked and then converted online. This wasn’t ideal because it meant installing the PS4 game just to transfer the data.

But that problem, like many other PS5 teething troubles, appears to be a thing of the past. It’s not ideal that the console launched in somewhat of a half-baked state, but the most important thing is that these issues are being eradicated relatively promptly. Hopefully we never have to deal with this particular drawback again.



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Science

Hubble telescope solves mystery of star’s dimming

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New findings from NASA’s Hubble Space Telescope have helped astronomers to solve the mystery of why Orion’s bright red supergiant Betelgeuse dramatically faded for a period of weeks last year. 

In examining the massive red hypergiant VY Canis Majoris, astrophysicists from NASA and the University of Minnesota, Minneapolis found that the same processes are occurring on a much larger scale.

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The observation was published in the Feb. 4, 2021 edition of The Astronomical Journal, where the authors wrote that imaging and spectroscopy confirm a “record of high mass-loss events over the past few hundred years.”

“The similarity of this correspondence in VY [Canis Majoris] with the remarkable recent dimming of Betelgeuse and an outflow of gas is apparent,” they said. “The evidence for similar outflows from the surface of a more typical red supergiant suggests that discrete ejections are more common and surface or convective activity is a major source of mass loss for red supergiants.”

In a Thursday press release from NASA, the University of Minnesota’s Distinguished Professor Roberta Humphreys explained that Hubble data showed VY Canis Majoris behaving like Betelgeuse “on steroids.” 

This artist’s impression of the hypergiant star VY Canis Majoris reveals the star’s large convection cells and giant arcs. Credits: NASA, ESA, and R. Humphreys (University of Minnesota), and J. Olmsted (STScI)

In the case of the smaller star, researchers say that the dimming was due to an outflow of gas that may have formed dust which temporarily obstructed some of the star’s light. 

“I think the big takeaway about these results, is that the massive ejections or outflows from the star observed in the [Hubble] images and measured in the spectra are correlated with periods of great variability and deep minima in its light observed over two centuries,” Humphreys told Fox News on Friday. 

“We think this is due to activity or convection on the surface responsible for massive gaseous ejections,” she continued. “For example, we know that the sun has flares and outburst of flows of gas we see as prominences.”

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“In VY Canis Majoris — 30 [times the] mass of [the] sun and 300,000 more luminous — this is much more extreme,” she said. “These gaseous outflows may be as much as 10 times the mass of Jupiter.”

Arcs of plasma surround VY Canis Majoris, appearing to have been cast out from it by distances that are thousands of times farther away than the Earth is from the sun and over the past several hundred years.

However, other structures close to the millions of years-old star — which look like knots — are relatively compact and scientists working with Humphrey were able to date more recent eruptions to the 19th and 20th centuries when VY Canis Majoris faded to one-sixth of its original brightness.

The release notes that the hypergiant loses 100 times as much mass at Betelgeuse and is now only visible using a telescope.

“This is probably more common in red supergiants than scientists thought and VY Canis Majoris is an extreme example,” she said in the release. “It may even be the main mechanism that’s driving the mass loss, which has always been a bit of a mystery for red supergiants.”

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The future of the start is uncertain, but Humphreys said that the star is “obviously unstable.”

“This high mass loss will determine its eventual fate either as a supernova or black hole,” she said.

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Science

Maarten Schmidt solves the puzzle of quasars | Space

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Maarten Schmidt via Caltech.

Today in science: On February 5, 1963, Dutch astronomer and Caltech professor Maarten Schmidt had a eureka moment when studying a quasi-stellar radio source, or quasar, that had profound implications for how scientists would view the universe. Schmidt was studying a quasar known as 3C273 that was starlike in appearance with the addition of a mysterious jet. But even stranger was its spectrum. Astronomers examine the spectrum, or range of wavelengths of light, that a star emits in order to decipher the object’s composition. But the emission lines of 3C273’s spectrum didn’t match any known chemical elements. Schmidt had a sudden realization that 3C273 contained the very ordinary element hydrogen. It was just tricky to identify because the spectral lines of hydrogen didn’t appear where expected; instead they were highly shifted toward the red end of the spectrum. Such a large redshift could occur if 3C273 were very distant, about 3 billion light-years away.

Dr. Schmidt recalled the excitement of his revelation to EarthSky. He said:

This realization came immediately: my wife still remembers that I was pacing up and down much of the evening.

The implications were just this: For the quasar to be so far away and still visible, 3C273 must be intrinsically very bright and very powerful. It’s now thought to shine with the light of two trillion stars like our sun. That’s hundreds of times the light of our entire Milky Way galaxy. Yet 3C273 appears to be less than a light-year across, in contrast to 100,000 light-years for our Milky Way.

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The quasar 3C273 is not only distant. It is also exceedingly luminous, implying powerful energy-producing processes unknown in 1963. Schmidt announced his revelation about quasars in the journal Nature on March 16, 1963.

Maarten Schmidt is a Dutch astronomer who, in 1963, recognized that quasars are located in the very distant universe, and therefore must be extremely powerful energy sources.

X-ray image of 3C273 and its jet. Today, this quasar is known to lie at the center of a giant elliptical galaxy. Image via Chandra X-ray Observatory.

Today, hundreds of thousands of quasars are known, and many are more distant and more powerful than 3C273. It’s no exaggeration to say they turned the science of astronomy on its ear. Why, for example, are these powerful quasars located so far away in space? Light travels at a finite speed (186,000 miles per second), and we only see quasars in distant space and therefore in the distant past. These strange objects only existed in the early universe and no longer exist in the present universe. Why?

In the 1960s, 3C273 and other quasars like it were strong evidence against Fred Hoyle’s Steady State theory, which suggested that matter is continuously being created as the universe expands, leading to a universe that is the same everywhere. The quasars showed the universe is not the same everywhere and thus helped usher in Big Bang cosmology.

But the Steady State theory had been losing ground even before 1963. The biggest change caused by Maarten Schmidt’s revelation about the quasar 3C273 was in the way we think about our universe.

In other words, the idea that 3C273 was extremely luminous, and yet occupied such a relatively small space, suggested powerful energies that astronomers had not contemplated before. 3C273 gave astronomers one of their first hints that we live in a universe of colossal explosive events – and extreme temperatures and luminosities – a place where mysterious black holes abound and play a major role.

According to a March 2013 email from Caltech:

In 1963, Schmidt’s discovery gave us an unprecedented look at how the universe behaved at a much younger period in its history, billions of years before the birth of the sun and its planets. Later, Schmidt, along with his colleague Donald Lynden-Bell, discovered that quasars are galaxies harboring supermassive black holes billions of light-years away, not stars in our own galaxy, as was once believed. His seminal work dramatically increased the scale of the observable universe and advanced our present view on the violent nature of the universe in which massive black holes play a dominant role.

What are quasars? Astronomers today believe that a quasar is a compact region in the center of a galaxy in the early universe. The compact region is thought to surround a central supermassive black hole, much like the black hole thought to reside in the center of our own Milky Way galaxy and many (or most) other galaxies. The powerful luminosity of a quasar is thought to be the result of processes taking place in an accretion disk, or disk of material surrounding the black hole, as these supermassive black holes consume stars that pass too near. These sorts of activities happen during galaxy mergers, which peaked in the early universe.

ULAS J1120+0641 was the farthest quasar known in 2011. The quasar appears as a faint red dot close to the center. Composite image created from the Sloan Digital Sky Survey and the UKIRT Infrared Deep Sky Survey, via Wikimedia Commons.

The Chinese-born U.S. astrophysicist Hong-Yee Chiu coined the name quasar in May 1964 in the publication Physics Today. He wrote:

So far, the clumsily long name ‘quasi-stellar radio sources’ is used to describe these objects. Because the nature of these objects is entirely unknown, it is hard to prepare a short, appropriate nomenclature for them so that their essential properties are obvious from their name. For convenience, the abbreviated form ‘quasar’ will be used throughout this paper.

Currently, the farthest known quasar is ULAS J1342+0928, but it could get dethroned at any time. It has a redshift of z=7.54 and existed when the universe was about 690 million years old, just 5% of its current age.

Bottom line: Today in science, on February 5, 1963, Maarten Schmidt unraveled the mystery of quasars and pushed back the edges of our cosmos. His insight into the most distant and luminous objects known has changed the way scientists view the universe.

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