"Two lifeforms merge in once-in-a-billion-years evolutionary event."

"Last time this happened, Earth got plants."

"The phenomenon is called primary endosymbiosis, and it occurs when one microbial organism engulfs another, and starts using it like an internal organ."

The article says the first time was 2.2 billion years ago when mitochondria went from free-standing bacteria to internal organelles of archaea, eventually to become the mitochondria in animals and in us, and the second time was 1.6 billion years ago when free-standing cyanobacteria became organelles of plants called chloroplasts. This time we have a cyanobacterium called UCYN-A that can do nitrogen fixation becoming an organelle of a species of algae called B. bigelowii

What mitochondria do is take energy in the form of sugar (glucose) or ketones derived from fat and turn it into ATP (adenosine triphosphate), which is the chemical form it needs to be in to power the activity of the cell.

What chloroplasts do is photosynthesis, turning sunlight into the energy-storage molecule glucose.

What nitrogen "fixation" is all about -- strange term, I know -- it doesn't mean the nitrogen is "broken", it means the nitrogen is unavailable to biological systems before it gets "fixed" -- don't ask me why people use this term -- is converting atmospheric nitrogen (N2) to a form biological organisms can use. You see, the air we breathe is about 70% nitrogen, but these N2 molecules have a triple bond that is hard to break, so atmospheric N2 basically doesn't react with anything. You breath it in, you breathe it out, nothing happens. You get the nitrogen you need for your cells elsewhere.

And biological cells do need nitrogen. It's a key element in amino acids, the building blocks of protein. It's also part of nucleic acids -- DNA and RNA. You get yours from your food, primarily from the protein. But where does your food get it? It has to come from the atmosphere somewhere along the line. There has to be something analogous to how chloroplasts pull CO2 out of the atmosphere and use it to make glucose.

To get bioavailable nitrogen, cyanobacteria with special cells and enzymes convert atmospheric nitrogen to ammonia (NH4). (Equation below -- I'm going to skip here.) The special enzymes are an enzyme complex called the "nitrogenase complex". The special cells are called heterocysts. The reason the special cells are necessary is the nitrogenase complex enzymes don't work in the presence of oxygen. Heterocysts have extra thick cell walls to keep oxygen out.

The simple way to think of this is as an exchange of N (nitrogen) for C (carbon): The cyanobacteria provides the N and the algae provides the C. The two do an exchange as a symbiotic relationship. And apparently they've taken the next step and merged into a single organism, rather than remaining free-standing symbionts.

Now, the researchers here have not proven unequivocally that such a merger has happened -- for that they would need to prove gene migration between the two organisms. That may be done in time. For now, they have provide pretty compelling evidence: size ratios and synchronized cell division. The article talks about size ratios and that's because the sizes of the two organisms usually move in lockstep after they merge. They show a tight coupling for three sublineages of UCYN-A (called UCYN-A1, UCYN-A2, and UCYN-A3). This makes sense when you consider both want to optimize the underlying metabolic interconnection.

They've also synchronized their cell division, so they reproduce in lockstep. Another hallmark of endosymbiotic merger.

Two lifeforms merge in once-in-a-billion-years evolutionary event

#discoveries #biology #chemistry

"Are large language models superhuman chemists?"

So what these researchers did was make a test -- a benchmark. They made a test of 7,059 chemistry questions, spanning the gamut of chemistry: computational chemistry, physical chemistry, materials science, macromolecular chemistry, electrochemistry, organic chemistry, general chemistry, analytical chemistry, chemical safety, and toxicology.

They recruited 41 chemistry experts to carefully validate their test.

They devised the test such that it could be evaluated in a completely automated manner. This meant relying on multiple-choice questions rather than open-ended questions more than they wanted to. The test has 6,202 multiple-choice questions and 857 open-ended questions (88% multiple-choice). The open-ended questions had to have parsers written to find numerical answers in the output in order to test them in an automated manner.

In addition, they ask the models to say how confident they are in their answers.

Before I tell you the ranking, the researchers write:

"On the one hand, our findings underline the impressive capabilities of LLMs in the chemical sciences: Leading models outperform domain experts in specific chemistry questions on many topics. On the other hand, there are still striking limitations. For very relevant topics the answers models provide are wrong. On top of that, many models are not able to reliably estimate their own limitations. Yet, the success of the models in our evaluations perhaps also reveals more about the limitations of the exams we use to evaluate models -- and chemistry -- than about the models themselves. For instance, while models perform well on many textbook questions, they struggle with questions that require some more reasoning. Given that the models outperformed the average human in our study, we need to rethink how we teach and examine chemistry. Critical reasoning is increasingly essential, and rote solving of problems or memorization of facts is a domain in which LLMs will continue to outperform humans."

"Our findings also highlight the nuanced trade-off between breadth and depth of evaluation frameworks. The analysis of model performance on different topics shows that models' performance varies widely across the subfields they are tested on. However, even within a topic, the performance of models can vary widely depending on the type of question and the reasoning required to answer it."

And with that, I'll tell you the rankings. You can log in to their website at ChemBench.org and see the leaderboard any time for the latest rankings. At this moment I am seeing:

gpt-4: 0.48

claude2: 0.29

GPT-3.5-Turbo: 0.26

gemini-pro: 0.25

mistral_8x7b: 0.24

text-davinci-003: 0.18

Perplexity 7B Chat: 0.18

galactica_120b: 0.15

Perplexity 7B online: 0.1

fb-llama-70b-chat: 0.05

The numbers that follow the model name are the score on the benchmark (higher is better). You'll notice there appears to be a gap between GPT-4 and Claude 2. One interesting thing about the leaderboard is you can show humans and AI models on the same leaderboard. When you do this, the top human has a score of 0.51 and beats GPT-4, then you get GPT-4, then you get a whole bunch of humans in between GPT-4 and Claude 2. So it appears that that gap is real. However, Claude 2 isn't the latest version of Claude. Since the evaluation, Claude 3 has come out, so maybe sometime in the upcoming months we'll see the leaderboard revised and see where Claude 3 comes in.

Are large language models superhuman chemists?

#solidstatelife #ai #genai #llms #chemistry

"Xaira, an AI drug discovery startup, launches with a massive $1B, says it's 'ready' to start developing drugs."

$1 billion, holy moly, that's a lot.

"The advances in foundational models come from the University of Washington's Institute of Protein Design, run by David Baker, one of Xaira's co-founders. These models are similar to diffusion models that power image generators like OpenAI's DALL-E and Midjourney. But rather than creating art, Baker's models aim to design molecular structures that can be made in a three-dimensional, physical world."

Xaira, an AI drug discovery startup, launches with a massive $1B, says it's 'ready' to start developing drugs

#solidstatelife #ai #medicalai #drugdiscovery #chemistry

"In a series of painstakingly precise experiments, a team of researchers at MIT has demonstrated that heat isn't alone in causing water to evaporate. Light, striking the water's surface where air and water meet, can break water molecules away and float them into the air, causing evaporation in the absence of any source of heat."

"The effect is strongest when light hits the water surface at an angle of 45 degrees. It is also strongest with a certain type of polarization, called transverse magnetic polarization. And it peaks in green light -- which, oddly, is the color for which water is most transparent and thus interacts the least."

They go on to say:

"The astonishing new discovery could help explain mysterious measurements over the years of how sunlight affects clouds, and therefore affect calculations of the effects of climate change on cloud cover and precipitation. It could also lead to new ways of designing industrial processes such as solar-powered desalination or drying of materials."

Does this effect from barely-absorbed visible light really have enough energy for high-performance water desalination driven by solar energy? The paper is paywalled so I guess I'll have to take them at their word.

How light can vaporize water without the need for heat

#discoveries #chemistry #evaporation

Plastics. We think so much about the exponential growth of computer technology that we forget about other things growing exponentially.

It's like that line from the 1967 movie, "I just want to say one word to you... just one word: Plastics."

We may be paying more attention to computers, but plastics haven't gone away. They've kept growing exponentially.

I'm going to quote a boatload of stuff from this PlastChem report, but, in actuality it's going to look like a lot but in reality it's about 2 pages from an 87-page report. Actually once you add in all the appendices it's a 181-page report. And I'm going to quote these parts rather than summarize because I can't think of a way to compress this down much further, so since I can't do a better job of it myself I'm just going to present the choice quotes from the report. Here we go:

"The plastics economy is one of the largest worldwide. The global plastic market was valued at 593 billion USD in 2021. In the same year, the global trade value of plastic products was 1.2 trillion USD or 369 million metric tons, China, the USA, and European states are the major plastic-producing countries with emerging economies experiencing a rapid expansion of local production capacities. The plastics economy is tightly embedded in the petrochemical sector, consuming 90% of its outputs to make plastics. This, in turn, creates strong linkages with the fossil industry, as 99% of plastic is derived from fossil carbon, production mostly relies on fossil energy, and the plastic and fossil industries are economically and infrastructurally integrated."

"Plastic production increases exponentially. The global production of plastics has doubled from 234 million tons in 2000 to 460 million tons in 2019 and its demand grows faster that cement and steel. On average, production grew by 8.5% per year from 1950-2019. Business-as-usual scenarios project that plastic production will triple from 2019 to 2060 with a growth rate of 2.5-4.6% per year, reaching 1230 million tons in 2060. By 2060, 40 billion tons of plastic will have been produced, with about 6 billion tons currently present on Earth."

"The projected increase in plastic use is driven by economic growth and digitalization across regions and sectors. China is expected to remain the largest plastic user, but plastic demand is expected to grow stronger in fast-growing regions, such as Sub-Saharan Africa, India, and other Asian countries. Plastic use is projected to increase substantially across all sectors until 2060, and polymer types used in applications for packaging, construction and transportation make up the largest share of the projected growth.14 Importantly, the OECD predicts that petroleumbased, non-recycled plastics will continue to dominate the market in 2060. Single-use plastics, currently 35-40% of global production, are expected to grow despite regional phase-outs."

"Globally, seven commodity polymers dominate the plastics market. These include polypropylene (PP, 19% of global production), low-density polyethylene (LDPE, 14%), polyvinylchloride (PVC, 13%), high-density polyethylene (HDPE, 13%), polyethylene terephthalate (PET, 6%), polyurethane (PUR, 6%), and polystyrene (PS, 5%). Over 80% of Europe's total polymer demand is met by these, mostly in virgin form). Their usage varies by sector, with HDPE, LDPE, PET, and PP mainly being applied for packaging, and PS and PVC in construction."

"Plastic waste generation is expected to almost triple by 2060. In line with the growth in plastic use, the future plastic waste generation is projected to almost triple, reaching 1014 million tons in 2060. Waste generated from short-lived applications, including packaging, consumer products and textiles, and plastic used in construction are expected to dominate. The latter is relevant because long-lived applications will continue to produce 'locked-in' plastic waste well into the next century. Despite some improvements in waste management and recycling, the OECD projects that the amount of mismanaged plastic waste will continue to grow substantially and almost double to 153 million tons by 2060."

"The scale of plastic pollution is immense. The OECD estimates that 22 million tons of plastic were emitted to the environment in 2019 alone.14 While there are uncertainties in these estimates, they illustrate the substantial leakage of plastics into nature. Accordingly, approximately 140 million tons of plastic have accumulated in aquatic ecosystems until 2019. Emissions to terrestrial systems amount to 13 million tons per year (2019), but the accumulating stocks remain unquantified due to data gaps. While mismanaged waste contributes 82% to these plastic emissions, substantial leakages originate further upstream and throughout the plastic life cycle, such as from the release of micro- and nanoplastics. While the latter represent a relatively small share in terms of tonnage, the number of these particles outsizes that of larger plastic items emitted to nature."

"Plastic pollution is projected to triple in 2060. A business-as-usual scenario with some improvement in waste management and recycling predicts that the annual plastic emissions will double to 44 million tons in 2060. This is in line with other projections which estimate annual emissions of 53-90 million tons by 2030 and 34-55 million tons by 2040 to aquatic environments. According to the OECD, the accumulated stocks of plastics in nature would more than triple in 2060 to an estimated amount of 493 million tons, including the marine environment (145 million tons, 5-fold increase) and freshwater ecosystems (348 million tons, 3-fold increase). Since the impacts of plastic pollution are diverse and occur across the life cycle of plastics, the OECD concludes that 'plastic leakage is a major environmental problem and is getting worse over time. The urgency with which policymakers and other societal decision makers must act is high.'"

"Plastic monomers (e.g., ethylene, propylene, styrene) are mainly derived from fossil resources and then reacted (or, polymerized) to produce polymers (e.g., polyethylene, polypropylene, and polystyrene) that form the backbone of a plastic material. A mixture of starting substances (i.e., monomers, catalysts, and processing aids) is typically used in polymerization reactions. To produce plastic materials, other chemicals, such as stabilizers, are then added. This creates the so-called bulk polymer, usually in the form of pre-production pellets or powders. The bulk polymer is then processed into plastic products by compounding and forming steps, like extrusion and blow molding. Again, other chemicals are added to achieve the desired properties of plastic products, in particular additives. Importantly, such additives were crucial to create marketable materials in the initial development of plastics, and a considerable scientific effort was needed to stabilize early plastics. Throughout this process, processing aids are used to facilitate the production of plastics."

"At the dawn of the plastic age, scientists were unaware of the toxicological and environmental impacts of using additives in plastics. Their work to make plastic durable is essentially what has made plastics both highly useful, but also persistent and toxic."

"The growth in additives production mirrors that of plastics. The amount of additives in plastics can significantly vary, ranging from 0.05-70% of the plastic weight. For example, antioxidants in PE, PS, and ABS (acrylonitrile butadiene styrene) account for 0.5-3% of their weight. Light/UV stabilizers in PE, PP, and PVC constitute 0.1-10% by weight. Flame retardants can make up 2-28% of the weight, while plasticizers in PVC can be as high as 70% by weight. About 6 million tons of additives have been produced in 2016 and the annual growth rate is 4% in the additives sector. Accordingly, additive production can be expected to increase by 130-280 thousand tons per year. By 2060, the joint production volume of a range of additive classes is the projected to increase by a factor of five, closely mirroring the growth in overall plastic production."

"Plastics also contain non-intentionally added substances. Non-intentionally added substances include impurities, degradation products, or compounds formed during the manufacturing process of plastics, which are not deliberately included in the material. Examples include degradation products of known additives (e.g., alkylphenols from antioxidants) and polymers (e.g., styrene oligomers derived from polystyrene). Unlike intentionally added substances (IAS), which are in principle known and therefore can be assessed and regulated, non-intentionally added substances are often complex and unpredictable. Thus, their identity remains mostly unknown and these compounds, though present in and released from all plastics, cannot easily be analyzed, assessed, and regulated. Despite these knowledge gaps, non-intentionally added substances probably represent a major fraction of plastic chemicals."

"The number and diversity of known plastic chemicals is immense. A recent analysis by the United Nations Environment Programme suggests that there are more than 13 000 known plastic chemicals, including polymers, starting substances, processing aids, additives, and non-intentionally added substances. The main reason for such chemical complexity of plastics is the highly fragmented nature of plastic value chains that market almost 100 000 plastic formulations and more than 30 000 additives, 16,000 pigments, and 8000 monomers. While this represents the number of commercially available constituents of plastics, not necessarily the number of unique plastic chemicals, it highlights that the diversity of the plastics sector creates substantial complexity in terms of plastic chemicals."

"A full overview of which chemicals are present in and released from plastics is missing, mostly due to a lack of transparency and publicly available data. Nonetheless, the available scientific evidence demonstrates that most plastic chemicals that have been studied are indeed released from plastic materials and products via migration into liquids and solids (e.g., water, food, soils) and volatilization into air. Additional chemical emissions occur during feedstock extraction and plastic production as well as at the end-of-life (e.g., during incineration). This is problematic because upon release, these chemicals can contaminate natural and human environments which, in turn, results in an exposure of biota and humans."

"Most plastic chemicals can be released. The release of chemicals from plastics has been documented in a multitude of studies, especially in plastic food contact materials, that is, plastics used to store, process or package food. A systematic assessment of 470 scientific studies on plastic food packaging indicates that 1086 out of 1346 analyzed chemicals can migrate into food or food simulants under certain conditions. Accordingly, 81% of the investigated plastic chemicals are highly relevant for human exposure. Newer research with advanced methods to study previously unknown plastic chemicals illustrates that this probably represents the tip of the iceberg. Studies using so-called nontargeted or suspect screening approaches show that commonly more than 2000 chemicals leach from a single plastic product into water. While less information is available on non-food plastics, this highlights two important issues. Firstly, plastics can release a large number of chemicals which, secondly, then become relevant for the exposure of biota, including humans (termed 'exposure potential' in this report)."

"Many plastic chemicals are present in the environment. Upon release, plastic chemicals can enter the environment at every stage of the plastic life cycle. Accordingly, plastic chemicals are ubiquitous in the environment due to the global dispersal of plastic materials, products, waste, and debris. For instance, a recent meta-analysis suggests that more than 800 plastic chemicals have been analyzed in the environment. However, this evidence is fragmented, and a systematic assessment of which compounds have been detected in the environment is lacking. Yet, the evidence on well-studied plastic chemicals indicates that these are present in various environments and biota across the globe, including remote areas far away from known sources. Examples include many phthalates, organophosphate esters, bisphenols, novel brominated flame retardants, and benzotriazoles. Based on the existing evidence on well-researched compounds, it is prudent to assume that many more plastic chemicals are omnipresent in the natural and human environment, including in wildlife and humans."

"Humans are exposed to plastic chemicals across the entire life cycle of plastics. This ranges from the industrial emissions during production, affecting fence line communities, to the releases during use, affecting consumers, and at the end-of-life, including waste handling and incineration. These releases have resulted in extensive exposures of humans to plastic chemicals. For example, many phthalates, bisphenols, benzophenones, parabens, phenolic antioxidants as well as legacy brominated and organophosphate flame retardants have been detected in human blood, urine, and tissues in different global regions. Humans can be exposed to plastic chemicals directly, such as phthalates and other additives leaching from PVC blood bags used for transfusion or leaching into saliva in children mouthing plastic toys. Indirect exposure occurs through the ingestion of contaminated water and foodstuffs that have been in contact with plastics (e.g., processing, packaging). The inhalation and ingestion of plastic chemicals from air, dust and other particulate matter are other important routes of exposure. Importantly, research shows that women, children, and people in underprivileged communities often have higher levels of exposure."

"Non-human organisms are exposed to plastic chemicals. The scientific literature provides rich information on the exposure of wildlife to plastic chemicals, in particular on bisphenols and phthalates in terrestrial and aquatic ecosystems as well as persistent organic pollutants, and antioxidants in marine environments. The United Nations Environment Programme highlights a global biomonitoring study which showed that seabirds from all major oceans contain significant levels of brominated flame retardants and UV stabilizers, indicating widespread contamination even in remote areas. Beyond seabirds, various other species are exposed to plastic chemicals according to the United Nations Environment Programme, such as mussels and fish containing with high levels of hazardous chemicals like HBCDD (hexabromocyclododecane), bisphenol A, and PBDEs (polybrominated diphenyl ethers), suggesting plastics as a probable source. Land animals, including livestock, are exposed to chemicals from plastics, such as PBDEs in poultry and cattle. and phthalates in insects. Importantly, plastic chemicals can also accumulate plants, including those for human consumption. This highlights a significant cross-environmental exposure that spans from marine to terrestrial ecosystems and food systems. However, while research on plastic chemical in non-human biota is abundant, it remains fragmented and has not been systematically compiled and assesses thus far."

"Endocrine disrupting chemicals in plastics represent a major concern for human health. The plastic chemicals nonylphenol and bisphenol A were among the earliest identified compounds that interfere with the normal functioning of hormone systems. These findings marked the beginning of a broader recognition of the role of plastic chemicals in endocrine disruption and dozens have since been identified as endocrine disrupting chemicals. This includes several other bisphenols, phthalates (used as plasticizers), benzophenones (UV filters), and certain phenolic antioxidants, such as 2,4-ditertbutylphenol. For example, strong scientific evidence links bisphenols to cardiovascular diseases, diabetes, and obesity. Accordingly, there is a strong interconnection between plastic chemicals and endocrine disruption."

"Additional groups of plastic chemicals emerge as health concern. The Minderoo-Monaco Commission's recent report comprehensively assesses the health effects of plastics across the life cycle, including plastic chemicals. In addition to phthalates and bisphenols, the report highlights per- and polyfluoroalkyl substances (PFAS) widely utilized for their non-stick and water-repellent properties. PFAS are strongly associated with an increased risk of cancer, thyroid disease, and immune system effects, including reduced vaccine efficacy in children. Additional concerns pertain to their persistence and their tendency to bioaccumulate in humans. In addition, brominated and organophosphate flame retardants have been linked to neurodevelopmental effects and endocrine disruption, adversely affecting cognitive function and behavior in children, as well as thyroid and reproductive health. Several other plastic chemicals are known to cause harm to human health, for example because they are mutagens (e.g., formaldehyde) or carcinogens with other modes of action, like melamine."

"Plastic chemicals also impact human health when released from production and disposal sites. These more indirect effects include the contribution of plastic chemicals to water and air pollution across the life cycle. For instance, chlorofluorocarbons, previously used as blowing agents in plastic production, can deplete the stratospheric ozone layer and thereby indirectly affect human health. Other issues include the promotion of antimicrobial resistance due to the dispersion of biocides transferring from plastics in the environment and the release of dioxins and PCBs from the uncontrolled burning of plastic wastes. The latter are especially toxic and persistent, and accumulate in the food chain, leading to increased human exposure."

"The health impacts of well-researched plastic chemicals are established. Arguably, there is a large body of evidence that links certain groups of plastic chemicals to a range of adverse health effects. These include but is not limited to bisphenols, phthalates, PFAS, and brominated and organophosphate flame retardants. Research focusses particularly on their endocrine disrupting effects, include adverse impacts on reproduction, development, metabolism, and cognitive function. However, it should be noted that research into other groups of plastic chemicals and other types of health effects remains largely fragmented and has rarely been systematically assessed. Here, initiatives such as the Plastic Health Map75 can support a more strategic approach."

"Plastic chemicals exert a host of adverse impacts on wildlife. This includes both acute and chronic toxicity in individual organisms and populations, as well as indirect effects across food webs. Ecotoxicological effects of heavy metals, such as cadmium and lead, as well as endocrine disrupting chemicals used in plastics, such as bisphenols, phthalates, and brominated flame retardants, have received the most research attention to date. Oftentimes, these endocrine disrupting chemicals induce environmental impacts at very low concentrations."

Jumping to page 24 for "Key Findings" of Part II of the report, "What is known about plastic chemicals":

"There are at least 16,000 known plastic chemicals. The report identifies 16,325 compounds that are potentially used or unintentionally present in plastics."

"There is a global governance gap on plastic chemicals. 6% of all compounds are regulated internationally and there is no specific policy instrument for chemicals in plastics."

"Plastic chemicals are produced in volumes of over 9 billion tons per year. Almost 4000 compounds are high-production volume chemicals, each produced at more than 1000 tons per year."

"At least 6300 plastic chemicals have a high exposure potential. These compounds have evidence for their use or presence in plastics, including over 1500 compounds that are known to be released from plastic materials and products."

"Plastic chemicals are very diverse and serve multiple functions. In addition to well-known additives, such as plasticizers and antioxidants, many plastic chemicals often serve multiple functions, for instance, as colorants, processing aids, and fillers."

"Grouping of plastic chemicals based on their structures is feasible. Over 10,000 plastic chemicals are assigned to groups, including large groups of polymers, halogenated compounds, and organophosphates."

Jumping to page 28, they have a visualization of the number of different plastic chemicals by use category:

3674 Colorants
3028 Processing aids
1836 Fillers
1741 Intermediates
1687 Lubricants
1252 Biocides
959 Monomers
897 Crosslinkers
883 Plasticizers
862 Stabilizers
843 Odor agents
764 Light stabilizers
723 Catalysts
595 Antioxidants
478 Initiators
389 Flame retardants
215 Heat stabilizers
205 Antistatic agents
128 Viscosity modifiers
103 Blowing agents
83 Solvents
74 Other additives
56 NIASs (non-intentionally added substances)
47 Others
31 Impact modifiers

On page 30 they have a table that gives you numbers by chemical category (with many groups missing because apparently there is a "long tail" of categories with fewer than 10 members that they didn't bother to include):

802 Alkenes
443 Silanes, siloxanes, silicones
440 PFAS (per- and polyfluoroalkyl substances)
376 Alkanes
202 Carboxylic acids salts
140 PCBs (polychlorinated biphenyls)
124 Aldehydes simple
89 Azodyes
75 Dioxines and furans
66 Alkylphenols
61 Ortho-phthalates
52 Aceto- and benzophenones
50 Phenolic antioxidants
45 PAHs (polycyclic aromatic hydrocarbons)
34 Bisphenols
29 Iso/terephthalates and trimellitates
28 Benzotriazoles
25 Ketones simple
24 Benzothiazole
22 Aromatic amines
20 Alkynes
20 Alkane ethers
18 Chlorinated paraffins combined
15 Aliphatic ketones
14 Aliphatic primary amides
11 Salicylate esters
10 Parabens
10 Aromatic ethers

Page 57 has a table of the number of chemicals by category considered hazardous. Page 61 has a table of the number of chemicals considered hazardous by usage category instead of chemical structure.

Last section is policy recommendations.

The report is 87 pages, but the document is 181 pages. The rest is a series of appendices, which they call the "Annex", which has the glossary, abbreviations, and detailed findings for everything summarized in the rest of the report.

https://plastchem-project.org/

#discoveries #chemistry #health #environment

Optical Tweezers Investigate Tiny Particles

#laserhacks #biology #chemistry #colloid #diffraction #dvdburner #glycerol #laser #opticaldrive #opticaltweezers #tweezers #hackaday
posted by pod_feeder_v2

Sheets of gold that are one atom thick have been synthesized.

They're calling it "goldene", to make you think of "graphene," "the iconic atom-thin material made of carbon that was discovered in 2004."

"Since then, scientists have identified hundreds more of these 2D materials. But it has been particularly difficult to produce 2D sheets of metals, because their atoms have always tended to cluster together to make nanoparticles instead."

"Researchers have previously reported single-atom-thick layers of tin and lead stuck to various substances, and they have produced gold sheets sandwiched between other materials. But 'we submit that goldene is the first free-standing 2D metal, to the best of our knowledge', says materials scientist Lars Hultman at Linköping University in Sweden."

"The Linköping researchers started with a material containing atomic monolayers of silicon sandwiched between titanium carbide. When they added gold on top of this sandwich, it diffused into the structure and exchanged places with the silicon to create a trapped atom-thick layer of gold. They then etched away the titanium carbide to release free-standing goldene sheets that were up to 100 nanometres wide, and roughly 400 times as thin as the thinnest commercial gold leaf."

"That etching process used a solution of alkaline potassium ferricyanide known as Murukami's reagent. 'What's so fascinating is that it's a 100-year-old recipe used by Japanese smiths to decorate ironwork,' Hultman says. The researchers also added surfactant molecules -- compounds that formed a protective barrier between goldene and the surrounding liquid -- to stop the sheets from sticking together."

"Light can generate waves in the sea of electrons at a gold nanoparticle's surface, which can channel and concentrate that energy. This strong response to light has been harnessed in gold photocatalysts to split water to produce hydrogen, for instance. Goldene could open up opportunities in areas such as this, Hultman says, but its properties need to be investigated in more detail first."

Meet 'goldene': this gilded cousin of graphene is also one atom thick

#chemistry

Don't know much about #Chemistry ...

#humor #lol #taste #joke #just4fun #fun #funny

---

♲ anarcho-catgirlism - 2024-04-16 15:16:20 GMT

#shitpost

"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

"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

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

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

Leveraging large language models for predictive chemistry | #llms #compchem #chemistry #generativeai

Reverse Engineering Smart Meters, Now with More Fuming Nitric Acid

#reverseengineering #chemistry #decapping #destructive #fna #fumingnitricacid #micropositioning #microscopy #smartmeter #hackaday
posted by pod_feeder_v2

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

Darkroom Robot Automates Away the Tedium of Film Developing

#mischacks #35mm #arduino #c41 #chemistry #darkroom #developing #film #processing #sousvide #hackaday
posted by pod_feeder_v2

"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

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

Custom Fume Hood for Safe Electroless Plating

#chemistryhacks #air #chemistry #corrosion #electrolessplating #exhaust #fumehood #safety #hackaday
posted by pod_feeder_v2

RAAC crisis map. I stumbled across this map not knowing what the "RAAC crisis" was. Turns out it's buildings collapsing because of a type of concrete called RAAC.

RAAC crisis map

#architecture #chemistry