#chemistry

waynerad@diasp.org

"Prickly paddy melon weed enzymes show potential as sustainable cement alternative." "An invasive weed that has long plagued the Australian agricultural industry could become a game-changing economic crop due to its potential to produce a cement alternative. Prickly paddy melon costs the agricultural industry around $100 million a year in lost grain yields, cattle deaths and control measures."

"But now researchers say enzymes produced by the paddy melon could be used to create a more sustainable form of cement and prevent soil erosion."

It took me a while to figure out what this was about. What it's about is a type of enzymes called urease enzymes. The reaction urease enzymes catalyze is urea + water = ammonia + carbon dioxide. What this has to do with concrete is there's this concept in concrete of "self healing" concrete, which works (to a limited extent) by having enzymes in the concrete that, when combined with water, precipitate calcium carbonate. Astute observers amoung you will at this point point out that calcium carbonate is not part of the chemical reaction that urease enzymes catalyze. Obviously you also need calcium present to precipitate calcium carbonate, but the real key is that the ph level is changed (more specifically increased, more specifically by the ammonia) such that dissolved calcium ions in the concrete will react with the carbon dioxide to precipitate calcium carbonate.

For those of you who like chemical formulas (helps me understand what's going on but I hear some people are scared off by formulas) , the reaction that the urease enzymes catalyze is:

(NH2)2CO + H2O -> 2NH3 + CO2

(that is, two of the (NH2) groups -- the lack of subscripts can be confusing).

And the formula for calcium carbonate is CaCO3.

What does all this have to do with the Australian weed prickly paddy melon? Apparently it's possible to produce these urease enzymes in massive quantities by extracting them from this plant.

I was disappointed by this as we humans consume crazy amounts of sand and are depleting the planet of sand for use in concrete, and I was hoping this would help with that. But no. In fact if you chase down the actual research paper (or the abstract, the full paper is paywalled), you'll find the researchers were primarily interested in urease enzymes for soil. Since ammonia increases pH, if a soil is acidic (remember, pH numbers under 7.0 are acidic, the lower the more acidic, while pH numbers above 7.0 are basic/alkaline, the higher the more basic/alkaline), adding these enzymes can reduce the acidity. Since ammonia is a nitrogen compound, it also helps to make nitrogen available for crops.

So, this won't help with concrete production from sand, and the article doesn't even try but instead talks about carbon footprint. Might be useful for limited "self-healing" concrete, and probably most useful for agricultural crop soil.

Prickly paddy melon weed enzymes show potential as sustainable cement alternative

#discoveries #chemistry #agriculture

waynerad@diasp.org

"Food and chemical companies are permitted to approve the use of new potentially harmful additives and other substances in snacks, drinks and more without the Food and Drug Administration's review and approval -- all thanks to a regulatory loophole known as the GRAS rule."

"GRAS, or 'generally recognized as safe,' is a food category created by Congress in 1958. The GRAS designation was intended to apply to ingredients widely recognized to be safe, such as salt, water, yeast and chicken breast."

"The GRAS rule, finalized in 1997, created a voluntary notification system that lets manufacturers bypass federal regulators' review. Companies can identify and use new GRAS ingredients but are not required to share this information with the FDA."

"Since 2000, food and chemical companies have used the GRAS loophole to approve 99 percent of new food chemicals, according to a 2022 EWG analysis. It leaves both the public and the FDA in the dark about the substances in our food."

"Experts estimate more than 1,000 GRAS substances have entered the food supply without FDA or public knowledge."

I never heard of this. Wonder if there is any connection with cancer rates in the population.

What is GRAS? - EWG

#chemistry #nutrition #regulation #fda

waynerad@diasp.org

East Germany during the cold war invented a "chemically hardened" glass. After the USSR collapsed and East Germany reunified with West Germany, the company, "Superfest Gläser", was closed. It turned out in the "capitalist" economy of the West, nobody wanted beer glasses that never break -- you make more money by selling glasses that do break.

There's a lesson there revenant to the future: understanding when the market lacks incentives for producing durable products, or actively favors its reverse, "planned obsolescence".

Apparently the East German Superfest Gläser chemically hardened glass was chemically different from Pyrex, the closest similar product we have in our economy. According to the article, the East German Superfest Gläser glass used a special potassium chloride solution that fused with the glass surface, filling in in micro ruptures within the glass structure, making the glass less prone to breaking. Pyrex, in contrast, is "borosilicate" glass, so called because it's made by combining regular glass with boric oxide. Pyrex's claim to fame isn't actually its hardness, it's its "low-thermal-expansion", making it ideal for measuring things with measurement lines that don't move around when the container is heated.

The East German glass was called "Ceverit".

"'Ce' stood for Chemisch (Chemically), 'ver' for verfestigt (hardened) and the 'it' stood for the silica component."

Superfest - The (almost) unbreakable East German glass

#chemistry #glass #plannedobsolescence

waynerad@diasp.org

Yvonne Burkart says the toxic load increases with each generation, causing disease to appear at younger ages. Toxins are in cosmetics, consumer products, fragrances, processed foods ("natural" flavoring does not prevent this), food packaging, water pollutants, air pollutants, and so on. Yvonne Burkart is a board-certified toxicologist.

The conversation is long and wide ranging, including such things as glutathione and microplastics and other endocrine disrupters, water and air filters, food choices, and so on.

"Cancer Is On The Rise!"- Toxicity Expert Shares The Everyday Products Linked To It | Yvonne Burkart - Dhru Purohit

#cancer #chemistry #toxicology

waynerad@diasp.org

New technique for killing cancer cells by getting them to vibrate in unison using light invented.

"The atoms of a small dye molecule used for medical imaging can vibrate in unison -- forming what is known as a plasmon -- when stimulated by near-infrared light, causing the cell membrane of cancerous cells to rupture. According to the study published in Nature Chemistry, the method had a 99 percent efficiency against lab cultures of human melanoma cells, and half of the mice with melanoma tumors became cancer-free after treatment."

"Near-infrared light can penetrate far deeper into the body than visible light, accessing organs or bones without damaging tissue." "Near-infrared light can go as deep as 10 centimeters (~ 4 inches) into the human body as opposed to only half a centimeter (~ 0.2 inches), the depth of penetration for visible light."

"The molecular jackhammers are aminocyanine molecules, a class of fluorescent synthetic dyes used for medical imaging."

"These molecules are simple dyes that people have been using for a long time. They're biocompatible, stable in water and very good at attaching themselves to the fatty outer lining of cells. But even though they were being used for imaging, people did not know how to activate these as plasmons."

"Due to their structure and chemical properties, the nuclei of these molecules can oscillate in sync when exposed to the right stimulus. I saw a need to use the properties of plasmons as a form of treatment and was interested in James Tour's mechanical approach to dealing with cancer cells. I basically connected the dots."

"The molecular plasmons we identified have a near-symmetrical structure with an arm on one side. The arm doesn't contribute to the plasmonic motion, but it helps anchor the molecule to the lipid bilayer of the cell membrane."

The paper is paywalled so I'm just going by what's in the press release.

Molecular jackhammers' 'good vibrations' eradicate cancer cells.

#discoveries #chemistry #medicine #cancer

waynerad@diasp.org

"MatterGen: a generative model for inorganic materials design".

So the approach taken here to "generating" materials is to use a diffusion model, except change it so it generates materials instead of images. Or at least, one specific subclass of materials, which is inorganic crystals.

With a diffusion model that generates images, the basic idea is that you take the process of adding noise to an image and reverse it. In other words, you train a model to remove noise from an image. And it has to remove noise in the direction of the text prompt that you gave it.

Here, we represent a crystal as a combination of atoms, a "lattice" that specifies what type of symmetry the crystal has, and coordinates for where the atoms are in the lattice. Then we come up with rules for adding "noise" to each of these. The neural network that gets trained learns to reverse this noise adding process. It learns a different way to reverse each of these three inputs: the atoms (elements, ions, covalent and ionic bonds), the lattice, and the positions of the atoms relative to the lattice. The coordinate system for the atoms is not relative to absolute 3D space (that is to say, Cartesian), it's relative to the lattice. The lattices have names like C2/m (monoclinic), P4/mbm (tetragonal), R3m (trigonal), P1 (triclinic), Pm3m (cubic), P63/mmc (hexagonal), Fm3m (cubic), and so on (3 dimensional space groups, see below).

Ok, now that you have the basic idea of the 3 types of diffusion the network uses: atom type diffusion, lattice diffusion, and coordinate diffusion relative to the lattice. The coordinate diffusion requires variance adjustment for atomic density to work properly. The lattice diffusion has some complications related to its rotation, and its mean and variance limits, which I would explain to you if I understood them. But I don't so we're going to skip that.

Ok, at this point you may be wondering: with an image diffusion model, it does reverse-diffusion in the direction of the text prompt you give it. But here, there's no text prompt. So what is there and what happens?

Instead of a text prompt, you specify what properties you want your material to have. And just as an image-based diffusion model has to be trained on a massive number of image-text pairs, this system has to be trained on a massive number of examples of materials-and-properties pairs. These come from 3 databases: the Materials Project database, the Alexandria database, and the Inorganic Crystal Structure Database (ICSD). These add up to 1,081,850 materials with up to 20 atoms.

This enables the system to "steer" the reverse diffusion towards the properties you say you desire. Generally you want stable properties, so the system starts with a stability calculation based on density functional theory (DFT) calculations. The system will filter out structures where the energy per atom after relaxation via DFT is above some threshold, below which it qualifies as "stable". The system checks that the bond lengths are reasonable. The system checks that the charges balance, so you don't have an ionic crystal that has an imbalance of ionic charges.

Once these checks are passed, it comes down to what you ask for. You can put limits directly on the structure, such as restricting what types of symmetry you can get in your lattice.

More commonly, though, you'll ask for magnetic, electronic, or mechanical properties. Examples of these would be magnetic density, or a target band gap, which affects the material's conducting or semiconducting properties.

You can ask for a certain bulk modulus. This has to do with how "elastic" a material is. It's a measure of a material's decrease in volume with increase in pressure.

There's even something called the Herfindahl-Hirschman index, which you may have heard of from the world of investing. Classically, it's a measure of the size of a company relative to the size of the industry it is in and the amount of competitiveness. Here, it measures the "supply chain risk" of a material.

"MatterGen: a generative model for inorganic materials design"

#solidstatelife #ai #chemistry

waynerad@diasp.org

Asteroid with elements beyond the periodic table. Well, apparently the asteroid 33 Polyhymnia, which is located in the main belt between Mars and Jupiter, isn't the only "compact ultradense object" that's been found, it's just the heaviest. According to this article, the densest stable element is osmium (element 76 on the periodic table). I did not know that. They key word is that sentence is "stable". The periodic table goes up to element 118, now called Oganesson, which is the heaviest element ever synthesized on Earth. But if density calculations on these "compact ultradense objects", including 33 Polyhymnia, are correct, then in order to be as dense as they are, have to contain heavier elements.

Osmium has a density of 22.59 g/cm^3, about twice that of lead. According to the article, the researchers made a mathematical model that suggests an element that would be element 164 on the periodic table would have a density between 36.0 and 68.4 g/cm^3.

But the asteroid 33 Polyhymnia has a density of about 75 g/cm^3.

I have to admit, I just don't see how this is possible. How does something as small as an asteroid have enough gravity to become compact enough to create these kinds of densities?

If you're wondering about the mathematical model, they say, "We solve numerically the relativistic Thomas-Fermi model of an atom."

I never heard of the Thomas-Fermi model so I looked it up. The basic idea is that instead of calculating the wave function for every electron, such you would do with the Schrödinger equation, you treat the electron density as a continuous distribution. As the number of electrons goes up, trying to calculate every electron, such as with the Schrödinger equation, gets harder and harder, but the Thomas-Fermi model actually gets more and more accurate. So it's the way to go for elements with boatloads of electrons. Accuracy is further improved by taking into account relativistic effects for fast-moving electrons.

Beyond the periodic table: Superheavy elements and ultradense asteroids

#astronomy #chemistry #quantumphysics

waynerad@diasp.org

"Over the past few decades, evidence has built that the Maya of Central America extensively used a mercury-containing compound for decoration and art. Mercury was so prevalent that archaeological sites are still heavily contaminated today. Tellingly, scientists reported that two water reservoirs in the heart of the ancient city of Tikal contained toxic levels of mercury, raising the possibility that the Maya suffered adverse health effects."

The "mercury-containing compound" they are referring to is cinnabar, which is mercury sulfide.

The Maya coveted mercury. It may have hastened their downfall.

#futurology #archaeology #chemistry #maya