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NNadir

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Driving through NE PA, Trump country, I saw a great anti-Trump sign.

It read, "Make Orwell fiction again."

It may be my favorite.

I also saw a quite impressive numer of Biden signs, quite impressive given the area.

I feel better politically than I have in years.

The Chairwoman of the SUNY Stony Brook Chemistry Dept Running Against a Trumper...

...for Congress.

This is a note in the high impact scientific journal Science: In New York, chemist Nancy Goroff is battling a Trump loyalist for a seat in Congress

It should be open sourced, as it's a news item.

An excerpt:

Her opponent calls her a “radical professor.” But Nancy Goroff says her scientific expertise is exactly what Congress needs to deal effectively with climate change, the COVID-19 pandemic, and a host of other issues.

A physical organic chemist and longtime faculty member at Stony Brook University, Goroff will face off in November against Representative Lee Zeldin (R–NY), a lawyer seeking his fourth term. If she wins, Goroff would become the first female Ph.D. scientist to serve in Congress.

Running in a Long Island district that voted for Donald Trump in 2016 after twice backing Barack Obama for president, the first-time candidate is touting her scientific credentials.

“As a scientist, I look at things differently than the way politicians do,” Goroff says in one ad. Referring to the pandemic, she adds, “I’m running for Congress to use my science to lead us out of this crisis...”

...Along with many of her academic peers, Goroff stepped up those advocacy efforts after Trump took office in January 2017. She participated in both the Women’s March the day after his inauguration and the People’s Climate March in April, although professional obligations prevented her from attending the March for Science 1 week earlier. But she didn’t join the cluster of scientists running as part of what turned out to be a successful attempt by Democrats to regain control of the U.S. House of Representatives.

“I had just started as department chair [in January 2017] after stepping down as interim dean of the graduate school, and I was focused on how to make the university a better place,” she says.

Still, she didn’t like where Trump was taking the country, and she was also troubled by the growing power of social media to amplify false messages and distort civic discourse. In the aftermath of the November 2018 midterm elections, she says, “I felt that it was time to put in a full effort and try to be part of the solution...”


It was my privilege here in New Jersey to have a scientist as a Congressperson, Representative Dr. Rush Holt, until he retired. He was, by far, the best congressperson I have ever had in my entire life, and not just because he was a scientist, but because he was also an outstanding human being. I didn't agree with every position he took, but I always felt that his positions were considered and honorable. He was an (unsuccessful) pioneer in addressing the rising issue of election integrity when he was in Congress.

I grew up in Suffolk County, on Long Island. It's suburban redneck country, fairly right wing, although there is some potential for decency there, and a few times, I recall that Democrats actually won a few elections, not many but a few.

SUNY Stony Brook is a fairly decent university, not quite the UC Berkeley it was founded to be, but a pretty good school over all.

I wish Professor Goroff all the success in the world. May she succeed in her effort to win the election.


I've been sleepwalking, trying to take what's lost and broke And make it right

Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry

The paper I'll discuss in this post is this one: Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry (Wołos et al., Science 369, 1584 (2020) eaaw1955.

I was inspired to spend some time with this (full) paper by another post in this group, specifically this one: A New Chemical 'Tree of The Origins of Life' Reveals Our Possible Molecular Evolution (ScienceAlert) (Thank you eppur se muova!)

When I was a kid, planning an organic synthesis was largely a "seat of the pants" undertaking; one would look at a structure, and try to figure a series of disconnections that were available to bond formation using synthetic reactions of various types - the more you knew, the better you were able to plan these things - and one would talk to friends, advisors, bosses and also spend a long time in the library in the complex pathways to various leather bound "chemical abstracts" and their various kinds of indexes, find the relevant abstract, then search for the bound issue of the journal, only, often, to find that the particular paper was not the one you actually needed to accomplish the task. You'd work your way back until you had a plan using readily available starting materials.

Sometimes, your plan would actually work so far along the line, and you'd get ambitious and scale up, and then a flask would break, and boom...the pain...the pain...the pain...

You really had to think a lot in those days, and also consider the risks of wasting valuable materials.

You really had to think, and certain things had to be second nature.

Here's a problem, I pulled out of an old "exercise book," Ranganathan and Ranganathan, Academic Press, 1980, for problem 124. pg 42, on my bookshelf: The problem asked to propose a mechanism for the reaction that converted compound #4 into compound #10:





The paper, Chemistry of Santonic Acid. Oxidative and Reductive Modifications (Hortmann and Daniel, J. Org. Chem. 1972, 37, 26, 4446–4460) of course, gives an answer to the problem, a mechanism that seems quite reasonable, but the point of the exercise is to work it out yourself before being prodded by the paper.

Imagine someone asked you to make compound 10 with almost no information, other than what you learned in school? It's not too obvious...

This nice presentation, from K.C. Nicolaou shows classic "disconnection" thinking: [link:https://nicolaou.rice.edu/ppt_lectures/12_GERMANY_GENERAL.pdf|Total Synthesis of Natural Products of Biological
and Medicinal Importance]

It's been 30 years, maybe, since I planned a full synthesis; my career took a different path, but those were the "good old days." (Obviously not Lindsay Graham "Good Old Days" Up yours Lindsay.)

But when I was a kid, we used to go, like kids going to a big rock concert, to lectures by E.J. Corey, or D.H.R Barton, or Barry Trost, or K.C. Nicolaou or Roald Hoffman...

...sigh... Life is fun and then you die.

There are now, I'm sure a large number of computational programs to help design syntheses, and in fact, the paper referenced above, is about prebiotic chemistry, where the starting materials are simply the common "prebiotic" molecules spread across space. These programs probably use connectivity matrices of some kind or another - I don't know - my knowledge of programming is primitive at best, and to be honest, it's been decades since I thought about connectivity matrices.

I'm not sure if the link give more than the simple abstract or what is called the "structured abstract," to non-subscribers but the "structured abstract" has this conclusion:

CONCLUSION
Computer-generated reaction networks are useful in identifying synthetic routes to prebiotically relevant targets and are indispensable for the discovery of prebiotic chemical systems that are otherwise challenging to discern. As our network continues to grow by means of crowd-sourcing of newly validated prebiotic reactions, it will allow continued simulation of chemical genesis, beginning with molecules as simple as water, ammonia, and methane and leading to increasingly complex targets, including those of current interest in the chemical and pharmaceutical industries.


So there you have it...

The "structured abstract" includes this graphic:



The caption:

Network of prebiotic chemistry.
Computer simulation of plausible prebiotic reactions creates a network of molecules that are synthesizable from prebiotic feedstocks and establishes multiple unreported—but now experimentally validated—syntheses of prebiotic targets as well as self-regenerating cycles. In this schematic illustration, light blue nodes represent abiotic molecules, dark blue nodes represent molecules along newly discovered prebiotic syntheses of uric and citric acids, and red nodes represent other biotic molecules.


From the introduction:

Research on the chemical origins of life (OL) is coming of age. The pioneering efforts of Miller (1), Oparin (2), Oró (3, 4), and Orgel (5) by the 1960s; Eschenmoser (6) in the 1990s; and Sutherland (7, 8), Carell (9), Moran (10), and others (11–15) in recent years have systematized the knowledge about reactions that can be performed under consensus prebiotic conditions, as well as the plausible synthetic routes leading to life’s key molecules. On the other hand, we still have only a fragmentary understanding of whether and how other types of molecules formed on primitive Earth and how this entire prebiotic molecular space evolved into systems of chemical reactions (12, 16) and compartments (17, 18) housing them. Such analyses require consideration of very large numbers of putative reaction pathways but are finally becoming possible, owing to recent advances in the study of chemical reaction networks and computer-assisted organic synthesis (19, 20). In this study, we use such large-scale in silico network analyses to map the space of molecules synthesizable from basic prebiotic feedstocks, quantifying the structure of this space as well as the abundances and thermodynamic properties of its members. We then demonstrate three notable forms of chemical emergence: (i) that the molecules created within the network can themselves enable new types of prebiotic reactions, including multicomponent transformations that lead to complex and useful organic scaffolds; (ii) that within just a few synthetic generations, simple chemical systems (such as self-regenerating cycles) begin to emerge; and (iii) that the network contains prebiotic routes to surfactant species (both peptide-based and long-chain carboxylic acids), thus outlining a path to biological compartmentalization. We support these results by experimental validation of previously unappreciated prebiotic syntheses (e.g., of acetaldehyde, diglycine, as well as malic, fumaric, citric, and uric acids) and entire reaction systems—notably, we demonstrate a self-regenerating cycle of iminodiacetic acid (IDA) that complements prebiotic autocatalysis on the basis of the formose cycle (21). The web application underlying our calculations is made freely available to the community (https://life.allchemy.net) in the hope that synthetic network analyses will become a useful addition to the toolkit of OL research by supporting accelerated discovery of prebiotic routes, including environmentally friendly syntheses of useful targets from basic feedstocks.

Allchemy’s “Life” module uses 614 reaction rules (“transforms”) involving C, O, N, S, and P elements, grouped within 72 broader reaction classes. Inclusion of these rules in our set is contingent on the existence of literature-described examples that document their execution under generally accepted prebiotic conditions...


The authors, however, dodge the elephant in the room, chirality:

Our transforms account for reaction by-products and specify the scope of admissible substituents, structural motifs incompatible with a given reaction (some 400 potentially conflicting groups are considered for each reaction), typical conditions accepted in prebiotic chemistry, solvents, temperatures, and more. They do not consider stereochemistry [because homochirality probably appeared as a result of chemical evolution of racemic mixtures (25)] or reaction kinetics [because kinetic data are only sparingly reported in the studies of prebiotic chemistries (26)]. On the other hand, yields for each type of reaction are approximated on the basis of statistics collected from relevant publications and are categorized as trace (≤3%), low (>3% to ≤10%), moderate (>10% to and high (≥80%) (SM section S2).


The authors begin their task by running the alchemy program for two hours on a "standard laptop computer," using a network of reactions that involved only carbon, hydrogen, oxygen, and sulfur and which limited the molecules "discovered" in silico to those with a molecular weight of less than 300 Daltons. This generated tens of thousands of molecules, 82 of which were "biotic," which they define as consisting of the following classes of molecules: "...amino acids and peptides, nucleobases and nucleosides, carbohydrates, and metabolites..."

Again, to beat a dead horse, lacking chirality, the molecules are only weakly "biotic" in nature as I see it, and remain so without the spontaneous generation of chirality through either kinetic or other means.

In this paper, the captions are rather long and pretty much tell much of the story:

Fig. 1 Biotic and abiotic molecules in the networkof prebiotic chemistry:



The caption:

(A) Scheme illustrating the synthetic algorithm in which SMARTS-coded (22) reaction transforms act on the current pool of reactants to produce the next generation of compounds. Afterward, these products are combined with original reactants and the procedure repeats until a user-specified number of generations is reached. (B) Six generations of a synthetic network originating from six primordial substrates—H2O, N2, HCN, NH3, CH4, and H2S—and leading to possible biotic products [amino acids and peptides, nucleobases and nucleosides, carbohydrates, and metabolites found in living organisms (28); red circles] and abiotic products [other small molecules; blue circles] with molecular mass not exceeding 300 g/mol. Circle size corresponds to the molecule’s incoming connectivity, kin (i.e., the number of reactions that produce this molecule as product). (C) Forty-one biotic molecules within the network’s seven generations [six generations are shown in (B); for the full network with all seven generations, see https://tol.allchemy.net]. Of the biotic class, glycine is in the second generation (G2); urea, adenine, butenedioic acid, and oxalic acid are in G3; glyceraldehyde, isoguanine, aspartic acid, hypoxanthine, cytosine, phenylalanine, succinic acid, malic acid, glyoxylic acid, and aldotetrose are in G4; xanthine, alanine, serine, guanine, uracil, lactic acid, oxaloacetic acid, and aldohexose are in G5; malonic acid, pentofuranose, glycerol, pyruvic acid, cytidine, and ketoheptose are in G6; and ketohexose furanose, threonine, methionine, proline, glutamic acid, citric acid, acetic acid, thymine, adenosine, guanosine, uridine, and uric acid are in G7. Various di-, tri-, and tetrapeptides are also present within G4 to G7 (fig. S55). In addition, histidine is in G8, arginine in G11, valine in G12, and leucine in G16. The molecules shown are colored according to the lowest-yielding step within the shortest pathway: Red, at least one step is predicted to generate only traces of product (≤3%); orange, at least one step is low yielding (≤10%); and green, all steps are predicted to proceed in moderate or high yields. (D) Allchemy’s screenshot of the G4 tree, with the two shortest prebiotic synthesis pathways of succinic acid and of glycine colored according to the yields of individual steps [color coding as in (C)]. (E) Schemes of the pathways. Numbers below reaction arrows correspond to the transform labels in SM section S2; this section also contains details of prebiotically plausible reaction conditions (e.g., CuCN, KCN, H2O, and irradiation for conversion of hydrogen cyanide into formaldehyde), along with pertinent literature references. Raw Allchemy screenshots of the pathways are provided in SM section S4. If two numbers are given below a single arrow, it means that the software recognizes the product of the first reaction as highly reactive and prone to the second reaction in a tandem sequence [e.g., hydrolysis of a nitrile to a carboxylic acid (#38) creates 2-aminomalonic acid, which readily undergoes elimination of carbon dioxide (#2) under hydrolysis conditions; formation of imines (#10) creates methyleneamine, which then undergoes addition of cyanide (#18)].


Another graphic:

Fig. 2 The network’s molecular content and synthetic connectivity.



The caption:

(A) Distribution of biotic (blue markers) and abiotic (gray markers) molecules in a plane defined by molecular mass and heat of formation calculated using the PM6-D3H4X (66) semiempirical method implemented in the MOPAC2016 software (67). To simplify presentation, abiotic compounds were clustered into 1202 groups according to their structural similarity (quantified by Tanimoto coefficients between molecules’ ECFP4 fingerprints). Each cluster is represented by a circle of diameter proportional to the number of members, and position is determined by the group’s centroid (i.e., a group’s “representative” molecule, defined as the molecule with maximum average Tanimoto similarity to other members of the cluster). A similar correlation is observed when larger and unclustered samples of abiotic compounds are considered (see fig. S11 for distributions of >11,000 compounds; also see table S1 for additional thermodynamic considerations). (B) Distribution of biotic and abiotic compounds in a plane defined by the logP values calculated from Wildman and Crippen’s method (32) and the number of hydrogen bond acceptors. Biotic compounds are, on average, less hydrophobic than abiotic compounds for a given number of hydrogen bond acceptors. Further details of the underlying feature selection are described in the SM section S6.2. (C and D) Graphical illustration of condition changes along synthetic pathways leading to 30 randomly chosen (C) biotic versus (D) abiotic compounds in the G7 network. The horizontal axes quantify the numbers of steps in each pathway: For an n-step synthesis, the first step will correspond to location 1/n, the second step to 2/n, and the final step to n/n = 1 (i.e., all pathways stop at the scale’s value of 1). Conditions on the vertical axis: A, acidic; MA, moderately acidic; N, neutral; MB, moderately basic; and B, basic. (E and F) Full condition variability statistics are summarized in histograms for the syntheses of (E) 82 biotic molecules and (F) 36,603 abiotic molecules. The difference in the two distributions is statistically significant with P value < 0.001, as evaluated by χ2, Kolmogorov-Smirnov, and bootstrap tests (SM section S6.1). (G) Distribution of node degrees (k) for G5, G6, and G7 networks. Connectivity of a given node is the sum of the numbers of its incoming and outgoing connections (k = kin + kout; for distributions of kin and kout, see fig. S58). Linearity of these dependencies shown on the doubly logarithmic scale indicates a power law —P(k) ∝ k^(−γ ), where γ ~ 1.8—and a scale-free network architecture. (H) Cumulative distribution of Π (k)=∑kki=0 versus k provides evidence for preferential attachment. In this expression, denotes the average increase of the degrees of nodes with k = i between the fifth and sixth generations (green curve) and between the fifth and seventh generations (blue). The plot traces such evolutions of all nodes present in the network’s fifth generation (compounds in G5 with only a single incoming connection are not considered). The linearity of the dependence on the doubly logarithmic scale indicates another power law, Π (k)=kα, and an exponent greater than unity (α ~ 1.6 to 1.8) confirms preferential attachment. Notably, the slopes of both power laws are close to the values we previously found (35) for the scale-free network of all organic chemistry, indicating that prebiotic and modern organic syntheses are both governed by the same rules of synthetic reactivity.


The authors note that the elimination of some classes of reaction classes does not necessarily preclude arriving at the full or nearly full set of biotic molecules as a generated in the full sized class reactions, whereas removing sets of reaction classes has a fairly profound effect on the the number of abiotic molecules generated.

Interestingly, the software is said to find new pathways to biotic molecules.

Because the individual reaction rules used to generate the network are derived from the OL literature, we trivially expect the network to contain the known prebiotic pathways leading to all of these biotic compounds. Indeed, all such syntheses are present in the network, as illustrated in Fig. 3, A and B, for adenine, a popular target of prebiotic studies (for syntheses of other targets, see SM section S4). Notably, in addition to cataloging known routes, the network also contains previously unreported syntheses of biotic molecules. As a case in point, consider a computer-generated subnetwork of reactions leading to succinic acid and also involving syntheses of lactic, pyruvic, malic, fumaric, and glyoxylic acids (all biotic molecules are depicted in green in Fig. 3C). Analysis of the network in comparison with known literature reveals that most routes to these biotic molecules are a patchwork of steps reported in different publications (corresponding to different colors of the arrows), some of which are not concerned with OL issues (steps marked as NOL for non-OL), but all performed under prebiotic conditions.


Fig. 3 Examples of known and newly identified syntheses within the network of prebiotic chemistry.



A) Ten prebiotic synthetic pathways leading to adenine, all previously described in the OL literature, are highlighted in the network (for clarity, only a subnetwork of C-, O-, and N-based chemistries up to G4 is shown). Identical synthetic connections common to several pathways are indicated by arcs of different curvatures. (B) Chemical schemes of adenine’s prebiotic syntheses, along with those from pertinent literature (3, 49, 61, 69–77). Colored circles over the arrows correspond to the colors of pathways shown in (A). Circle segments are used to indicate to which multiple pathways a given step belongs. The first (trimerization of HCN) and last (formation of amides, imides, amidines, or guanidines followed by cyclization) steps are common to all pathways. There are three main strategies in the syntheses of adenine; formamidine (1) and formamide (2) participate as second substrates in three key, two-component reactions. hν, light. (C) Subnetwork of reactions that lead to succinic acid and involve syntheses of lactic, pyruvic, malic, fumaric, and glyoxylic acids (biotic molecules are in green). Previously unreported connections now verified by experiment are denoted with red arrows. Previously reported connections share the same color if they come from the same source publication. NOL indicates reactions reported outside of origins research but performed under prebiotic conditions. (D to F) Syntheses of (D) citric acid, (E) diglycine, and (F) uric acid. Gray arrows and structures denote reactions that have been described previously [the fourth reaction in (D), hydrolysis of malonitrile, is described in (C)]; black structures and red arrows represent the software-predicted reactions that we verified experimentally. When several reactions were performed in one pot, some intermediates were not isolated (but were still confirmed spectroscopically); these are enclosed in square brackets. For all experimental details, see the main text and experimental procedures in SM sections S7 to S12. rt, room temperature.


Now it gets interesting, because was is discussed is an abiotic example of something that characterizes many metabolic processes, cyclic reactions, the most famous of which is the citric acid (Krebs) cycle.

Turning our attention to other classes of prebiotic chemistry, we considered the synthesis of citric acid (CA), illustrated in Fig. 3D. Recently, a prebiotic mimic of the CA cycle was reported (10), but it contained only analogs of CA and not CA itself. Our network analysis suggested that CA could emerge under prebiotic conditions in water from two equivalents of oxaloacetic acid [the synthesis of which has already been reported in the OL literature (10)] via a tandem aldol self-condensation (H2O, pH 7.5, 4°C) and decarboxylation sequence followed by a second decarboxylation. This second decarboxylation, promoted by either 0.054 or 0.081 M FeCl3, worked better at room temperature than at 70°C, the temperature used for related compounds in previous work (10). Under our milder conditions, we obtained CA in ~5% yield, whereas under harsher conditions, the citroylformic acid substrate gradually decomposed, reducing the yield to ~2% (table S8).


Reference 10 is this paper:

Synthesis and breakdown of universal metabolic precursors promoted by iron. (Muchowska, K.B., Varma, S.J. & Moran, J. Nature 569, 104–107 (2019))

And finally, there is the issue of catalysis, which, to return to a point I made earlier, may include asymmetric catalysis.

Emergence of catalysts and reaction types

We first discuss the finding that compounds created within the network can themselves act as catalysts of additional chemical reactions, all operative under prebiotic conditions, thereby substantially expanding the accessible prebiotic chemical space. To show this, we queried the network for known organocatalysts or bi- and tridentate metal chelators capable of binding metal cations present on primitive Earth [e.g., Cu(II), Zn(II), and Mn(II) (40)] and also used in modern organometallic catalysts. Figure 4A lists eight such catalysts enabling different reaction types and collectively more than doubling the size of the network. All of these reactions were previously carried out under prebiotic conditions (41–48), but their relevance to OL was unnoticed.

Fig. 4 Chemical emergence in the network of prebiotic chemistry.


The caption:

A) (Left) Eight types of chemical reactions enabled by seven molecules created in the original G7 network (note that OAc and IDA repeat twice in nine entries shown). These molecules are either organocatalysts or components of catalytic complexes with prebiotically plausible metal cations [e.g., Zn(II), Cu(II), and Mn(II)]. All of the reactions shown had been previously performed under prebiotic conditions, but their relevance to origins research was not noted. (Middle) Colored arrows illustrate how many additional compounds can be created in our prebiotic network upon addition of each of the reactions shown. There is one arrow for entries 4 and 5 because two different catalysts enable the same reaction type (A3 coupling). (Right) Examples of molecules that are made synthesizable via these reactions. The gray part of the arrow at the bottom indicates the sum of these molecules (21,529), and its green extension represents the additional 34,957 molecules that are created when all of the reactions (1 through 9) are added to the generative set simultaneously. (B) The red arrow corresponds to the selective hydrolysis of 2-aminopentanedinitrile to 2-amino-4-cyanobutanamide catalyzed by formaldehyde, a reaction proposed by the software and validated experimentally. The remaining steps illustrate how the software navigated the synthesis of the aminopentanedinitrile substrate from the HCN primordial feedstock. These steps are shown in gray to indicate that they have already been executed by others and described in the OL literature. (C) The red arrow corresponds to the synthesis of 1-(1H-imidazol-4-yl)ethane-1,2-diol from ketotetrose, ammonia, and formaldehyde catalyzed by copper(II) acetate. This transformation was proposed by the software and chosen for experimental validation because it establishes an unreported prebiotic route to the histidine amino acid. All downstream and upstream steps (in gray) have been described earlier in OL literature. Previously, histidine was generated along an inefficient bypass (also shown in the scheme) from aldotetrose and formamidine (50).


IDA here is imidodiacetic acid, which is a derivative of the simplest amino acid, glycine, a "Siamese" glycine if you will. This molecule is an excellent chelator of metals, and as such, can coordinate metals which may act as catalysts.

The cyclic reaction detailed in the next figure, includes IDA in its pathway.

Fig. 5 Emergence of self-regenerating cycles within the network of prebiotic chemistry.



The caption:

(A) Self-regenerating cycle in which one molecule of IDA (orange) can produce up to two copies of itself. When the cycle was executed experimentally under prebiotic conditions (indicated next to the arrows), and upon pH changes from basic to slightly acidic to basic, it regenerated 126% of the IDA substrate, confirming autocatalysis. Dashed arrows trace the bypass route (through 4 and 5) that may also be used to regenerate IDA. (B) Plot quantifying the experimentally observed cycle yields for different combinations of the key parameters: the concentration ratio of the IDA and NCA reagents used in the first aminolysis step, the pH during the Strecker reaction, and the concentration of NaOH used for the final hydrolysis [5 M is not a likely prebiotic condition and actually produced suboptimal yield (table S13), but we tested it solely to map the phase space of the cycle]. Circle color corresponds to the yield scale on the right. For all experimental details, see SM section S9. (C) Another noteworthy cycle candidate pending experimental validation and producing up to three copies of each incoming (2-cyanoethyl)glycine molecule (orange). For an average 80% yield of each step, the overall cycle yield would still be ~114%.

The final piece of the puzzle is lipids, which of course make up cellular membranes, both for cells themselves and for intracellular organelles.


The caption:

Emergence of surfactants
Finally, the third class of emergence was the formation of surfactant molecules capable of spontaneously forming vesicles that could potentially house reactions and systems such as those described above. As illustrated in Fig. 6A, straight-chain saturated fatty acid and α-hydroxy acid surfactants can form through repeated four-step cycles of aldehyde homologation. Breaking the cycle, the last step of fatty acid synthesis, may then occur via nitrile or thioamide hydrolysis to carboxylic acid. The aldehyde homologation cycle was proposed by Patel et al. (8) as a prebiotic method to make hydrophobic amino acids, but its straightforward extension to fatty acid surfactants was not noted in that report. In another and synthetically much shorter approach, peptide surfactants with variable glycine or alanine tails and aspartic acid head groups are available within only a few synthetic generations. Previously, such peptides had been synthesized by modern, nonprebiotic synthetic methods and had been shown (in the context of nanotechnology, not OL research) to form nanotubes and nanovesicles (64).


Fig. 6 Biomimetic routes to surfactants and additional pharmaceutically relevant scaffolds.



The caption:
(A) Prebiotic synthesis of fatty acid and α-hydroxy fatty acid surfactants by iteration of a known prebiotic sequence of four reactions homologating an aldehyde [for reactions 1 to 4, see (8)] followed by a previously unidentified breaking of the cycle via straightforward nitrile or thioamide hydrolysis. (B) A much shorter (i.e., fewer reaction steps) synthesis of peptide surfactants with variable glycine or alanine tails and aspartic acid head groups via sequential addition of Leuchs’ anhydride. (C) Implications of recently reported (78) prebiotically plausible methyl isocyanide formation from HCN, ultimately allowing for Passerini-type reactions (black arrows). Addition of methyl isocyanide to our reaction set substantiates prebiotically plausible syntheses of some useful scaffolds (red arrows): α-acyloxycarboxamides via a classic Passerini reaction (3-CR, three-component reaction), peptide mimics via the four-component Ugi reaction, or heterocyclic derivatives of pyrazine via a less obvious three-component reaction, which has been reported in non-OL literature under prebiotic conditions (79). In the schemes shown, R1, R2 = alkyl, aryl, or hydrogen; R3 = any carbon; R4 = alkyl, aryl; and R5 = alkyl, aryl. AMP, adenosine monophosphate.


The authors consider, in conclusion that their work may not only assist in approaching the intellectually satisfying question of the origins of life, but may well have practical import as well.

Taken together, the above analyses and synthetic examples lead us to suggest that computational reaction network algorithms are useful for identifying new synthetic routes to prebiotically relevant targets and indispensable for the discovery of prebiotic chemical systems that are otherwise challenging to discern. Naturally, the prebiotic reaction networks should and will grow as distinct prebiotically plausible transformations are experimentally validated. As such transformations are added to our generative set (by means of the crowd-sourcing module illustrated in fig. S5, panel xii), we expect that network analyses will be able to trace prebiotic syntheses starting from primitive feedstocks to increasingly complex scaffolds, including those found in modern drugs (e.g., Fig. 6C). In other words, we envision a fruitful junction between prebiotic chemistries, performed in water and often under environmentally friendly conditions, and environmentally friendly pharmaceutical synthesis…

I voted. It feels good to get it done, even if my son is going to "cancel my vote."

One of my happiest memories as a child is when my parents would drive back from voting - they always took me along - and my mother, a swing voter, would tell my father that she "canceled his vote," by voting for the Democrat.

In the good old family tradition, my oldest son announced he would be "cancelling my vote."

All three of us here at home, and the son away who will be voting in PA, are voting straight Democratic for all candidates, from Biden/Harris on down, but I voted against all three ballot initiatives on the NJ ballot, including the one that would legalize marijuana.

I don't believe that people should go to jail for possessing, smoking or even (privately) growing it, but I don't want legal pot stores here.

My son was a little upset with me and gave me the "alcohol is worse than pot" lecture that one hears, and while I'm not sure that the premise of that argument is wrong, I retorted that pancreatic cancer is worse than breast cancer, but this doesn't support an argument to make breast cancer easier to get. (To my knowledge, he has never smoked pot, but I don't want to make it easier for him to try.)

(He didn't like that.)

But the important point is that both my wife and dropped our ballots in the special drop boxes NJ has distributed, and there's two more votes for Joe and Kamala, and for the rest of the Democratic ticket, and two more to go from my family, my vote cancelling son and my "no pot on the ballot" son in PA.

I feel great!

Editors of the prestigious scientific journal Nature endorse Joe Biden!

Nature has been very active recently - for a very clear reason - in encouraging scientists to get political. Now there's this, another unprecedented US Presidential endorsement from a major scientific journal, following NEJM:

Why Nature supports Joe Biden for US president.

We cannot stand by and let science be undermined. Joe Biden’s trust in truth, evidence, science and democracy make him the only choice in the US election.

On 9 November 2016, the world awoke to an unexpected result: Donald Trump had been elected president of the United States.

This journal did not hide its disappointment. But, Nature observed, US democracy was designed with safeguards intended to protect against excesses. It is founded on a system of checks and balances that makes it difficult for a president to exercise absolute power. We were hopeful that this would help to curb the damage that might result from Trump’s disregard for evidence and the truth, disrespect for those he disagrees with and toxic attitude towards women.

How wrong we turned out to be.

No US president in recent history has so relentlessly attacked and undermined so many valuable institutions, from science agencies to the media, the courts, the Department of Justice — and even the electoral system. Trump claims to put ‘America First’. But in his response to the pandemic, Trump has put himself first, not America.

His administration has picked fights with the country’s long-standing friends and allies, and walked away from crucial international scientific and environmental agreements and organizations: notably, the 2015 Paris climate accord; the Iran nuclear deal; the United Nations’ science and education agency UNESCO; and even, unthinkable in the middle of a pandemic, the World Health Organization (WHO).

Challenges such as ending the COVID-19 pandemic, tackling global warming and halting the proliferation and threat of nuclear weapons are global, and urgent. They will not be overcome without the collective efforts of the nation states and international institutions that the Trump administration has sought to undermine.

On the domestic front, one of this administration’s most dangerous legacies will be its shameful record of interference in health and science agencies — thus undermining public trust in the very institutions that are essential to keeping people safe...

...Joe Biden must be given an opportunity to restore trust in truth, in evidence, in science and in other institutions of democracy, heal a divided nation, and begin the urgent task of rebuilding the United States’ reputation in the world.


I'm quite sure it's open sourced, and the full endorsement can be read at the Nature website.

The outcome of world history very much depends on this election. As the job of the scientist is to engage with reality, to analyze it, to report it, and indeed to predict outcomes, these actions by the premier journals of the scientific community are of paramount importance.

A comprehensive quantification of global nitrous oxide sources and sinks

The paper I'll discuss in this post is this one: A comprehensive quantification of global nitrous oxide sources and sinks (Tian, H., Xu, R., Canadell, J.G. et al. Nature 586, 248–256 (2020))

Nitrous oxide, N2O, laughing gas, has always been a part of the nitrogen cycle, but with the invention of the Haber-Bosch process in the early 20th century, on which our modern food supply depends, the equilibrium has been severely disturbed. Since, like CFC's, nitrous oxide is both a greenhouse gas and an ozone depletion agent. I'm sure I've written in this space and elsewhere about this serious environmental issue, since it worries me quite a bit. So this paper in Nature caught my eye. The authors are a consortium of scientists from around the world, who have assembled what may be the most detailed account of accumulations of this gas in the atmosphere.

The abstract is open sourced, and may be found at the link in the paper. It is worth pointing out the cogent portions of it however:

Analysis of process-based model estimates reveals an emerging N2O–climate feedback resulting from interactions between nitrogen additions and climate change. The recent growth in N2O emissions exceeds some of the highest projected emission scenarios3,4, underscoring the urgency to mitigate N2O emissions.


From the introduction to the paper:

Nitrous oxide (N2O) is a long-lived stratospheric ozone-depleting substance and greenhouse gas with a current atmospheric lifetime of 116 ± 9 years1. The concentration of atmospheric N2O has increased by more than 20% from 270 parts per billion (ppb) in 1750 to 331 ppb in 2018 (Extended Data Fig. 1), with the fastest growth observed in the past five decades5,6. Two key biochemical processes—nitrification and denitrification—control N2O production in both terrestrial and aquatic ecosystems and are regulated by multiple environmental and biological factors including temperature, water and oxygen levels, acidity, substrate availability7 (which is linked to nitrogen fertilizer use and livestock manure management) and recycling8,9,10. In the coming decades, N2O emissions are expected to continue to increase as a result of the growing demand for food, feed, fibre and energy, and an increase in sources from waste generation and industrial processes4,11,12. Since 1990, anthropogenic N2O emissions have been reported annually by Annex I Parties to the United Nations Framework Convention on Climate Change (UNFCCC). More recently, over 190 national signatories to the Paris Agreement have been required to report biannually their national greenhouse-gas inventory with sufficient detail and transparency to track progress towards their nationally determined contributions. However, these inventories do not provide a full picture of N2O emissions owing to their omission of natural sources, the limitations in methodology for attributing anthropogenic sources, and missing data for a number of key regions (for example, South America and Africa)2,9,13. Moreover, a complete account of all human activities that accelerate the global nitrogen cycle and that interact with the biochemical processes controlling the fluxes of N2O in both terrestrial and aquatic ecosystems is required2,8. Here we present a comprehensive, consistent analysis and synthesis of the global N2O budget across all sectors, including natural and anthropogenic sources and sinks, using both bottom-up and top-down methods and their cross-constraints. Our assessment enhances understanding of the global nitrogen cycle and will inform policy development for N2O mitigation, which could help to curb warming to levels consistent with the long-term goal of the Paris Agreement.


The authors refer to "bottom up" analyses, which consists basically of multiple source terms such as known emissions, modeling of agricultural inputs based on field measurements, etc., and "top down" analyses which consist of measurements coupled to transport flux modeling. The utilize 43 N2O "flux estimates" 30 of which are "bottom up," 5 of which are "top down" and 8 models.

They write:

With this extensive data and bottom-up/top-down framework, we established comprehensive global and regional N2O budgets that include 18 sources and various different chemical sinks. These sources and sinks are further grouped into six categories (Fig. 1, Table 1): (1) natural sources (no anthropogenic effects) including a very small biogenic surface sink; (2) perturbed fluxes from ecosystems induced by changes in climate, carbon dioxide (CO2) and land cover; (3) direct emissions from nitrogen additions in the agricultural sector (agriculture); (4) other direct anthropogenic sources—including fossil fuel and industry, waste and waste water, and biomass burning; (5) indirect emissions from ecosystems that are either downwind or downstream from the initial release of reactive nitrogen into the environment—including N2O release after transport and deposition of anthropogenic nitrogen via the atmosphere or water bodies as defined by the Intergovernmental Panel on Climate Change (IPCC)14; and (6) the atmospheric chemical sink, for which one value is derived from observations and the other is derived from the inversion models


This cartoon figure gives a feel for sources:

Fig. 1: Global N2O budget for 2007–2016.



The caption:

The coloured arrows represent N2O fluxes (in Tg N yr−1 for 2007–2016) as follows: red, direct emissions from nitrogen additions in the agricultural sector (agriculture); orange, emissions from other direct anthropogenic sources; maroon, indirect emissions from anthropogenic nitrogen additions; brown, perturbed fluxes from changes in climate, CO2 or land cover; green, emissions from natural sources. The anthropogenic and natural N2O sources are derived from bottom-up estimates. The blue arrows represent the surface sink and the observed atmospheric chemical sink, of which about 1% occurs in the troposphere. The total budget (sources + sinks) does not exactly match the observed atmospheric accumulation, because each of the terms has been derived independently and we do not force top-down agreement by rescaling the terms. This imbalance readily falls within the overall uncertainty in closing the N2O budget, as reflected in each of the terms. The N2O sources and sinks are given in Tg N yr−1. Copyright the Global Carbon Project.


A Tg - terragram - is, of course, a million metric tons.

Isotopic analyses can show the sources, by the way, of N2O. For example, N2O in the troposphere is slightly enriched in the O17 isotope, which is believed to be connected with interactions of atmospheric ammonia and the dangerous fossil fuel combustion waste NO2. The origin of the anomalous or “mass‐independent” oxygen isotope fractionation in tropospheric N2O (Crutzen, et al., Geophys. Res. Lett. Volume 28, Issue 3 1 February 2001 Pages 503-506)

In the paper under discussion there is a rather large table l will not reproduce here that breaks down various source inputs and outputs, natural and anthropogenic. The mean value for concentrations of nitrous oxide in the atmosphere have risen from a mean value of 1,462 Tg, 1.462 billion tons, to a mean value in the period between 2007 and 2016 of 1,555 Tg, 1.555 billion tons, an increase of 93 million tons.

A breakdown of inputs represented graphically:

Fig. 2: Regional N2O sources in the decade 2007–2016.



The caption:

The Earth’s ice-free land is partitioned into ten regions: North America, South America, Europe, Middle East, Africa, Russia, East Asia, South Asia, Southeast Asia and Oceania. Each subplot shows the emissions from five sub-sectors using bottom-up approaches, followed by the sum of these five categories using bottom-up approaches (blue) and the estimates from top-down approaches (yellow). Bottom-up and top-down estimates of ocean emissions are shown at the bottom left (from bottom to top, lighter to darker, the contributions from the 30°–90° N, 30° S–30° N and 90°–30° S regions). Error bars indicate the spread between the minimum and the maximum values. The centre map shows the spatial distribution of 10-year average N2O emissions from land and ocean based on the land and ocean models. Per capita N2O emission (kg N per capita per year) during 2007–2016 is shown in Supplementary Fig. 2. The map was created using ESRI ArcMap 10.4.1.


Fig. 3: Ensembles of regional anthropogenic N2O emissions over the period 1980–2016.



The caption:

The bar chart in the centre shows the accumulated changes in regional and global N2O emissions during the study period of 1980–2016. Error bars indicate the 95% confidence interval for the average of accumulated changes. The Mann–Kendall test was performed to examine a monotonic increasing or decreasing trend in the estimated ensemble N2O emissions globally and for each region over the period 1980–2016. The accumulated changes were calculated from the linear regressed annual change rate (Tg N yr−2) multiplied by 37 years. All regions except Southeast Asia show a significant increasing or decreasing trend in the estimated ensemble N2O emissions during the study period . *P < 0.05.


Predictions:

Fig. 4: Historical and projected global anthropogenic N2O emissions and concentrations.



a–d, Global anthropogenic N2O emissions (a, b) and concentrations (c, d) compared to the four RCPs in the IPCC assessment report 5 (a, c; ref. 2) and the new marker scenarios based on the SSPs used in CMIP6 (b, d; ref. 48). The historical emissions data are represented as the mean of the bottom-up and top-down estimates of anthropogenic N2O emissions, whereas the historical atmospheric concentration data are from the three available observation networks: AGAGE, NOAA, and CSIRO. Top-down anthropogenic emissions were calculated by subtracting natural fluxes derived from bottom-up approaches. To aid the comparison, the four RCPs were shifted down so that the 2005 value is equal to the 2000–2009 average of the mean of top-down and bottom-up estimates. The SSPs are harmonized3 to match the historical emissions used in CMIP649; Extended Data Fig. 10 shows the unharmonized data.


These IPCC reports by the way, are bitterly comical in all of their optimistic scenarios, "RCP" Representative Concentration Pathways. Things are not even "business as usual" as described in the early editions. Things are worse than business as usual.

This is true here. The authors write:

Observed atmospheric N2O concentrations are beginning to exceed predicted levels across all scenarios. Emissions need to be reduced to a level that is consistent with or below that of RCP 2.6 or SSP 1−2.6 in order to limit warming to well below the 2 °C target of the Paris Agreement. Failure to include N2O within climate mitigation strategies will necessitate even greater abatement of CO2 and methane. Although N2O mitigation is difficult because nitrogen is the key limiting nutrient in agricultural production, this study demonstrates that effective mitigation actions have reduced emissions in some regions—such as Europe—through technological improvements in industry and improved efficiency of nitrogen use in agriculture.


Nitrous oxide will support combustion; it is an oxidizing gas. In theory it would be reduced by fire, but in general, combustion also generates significant higher nitrates, NO and NO2 which are ultimately transformed into N2O.

The main sink is photolytic, at wavelengths below 230 nm, which is in the UV range. Singlet oxygen, a high energy state of oxygen gas, also can destroy N2O. It is also generated by radiation, as well as some chemical means.

In recent years, I have come to think of air as a working fluid in Brayton cycle/combined cycle power plants. I've returned to an old idea about which I thought much in the 1990s and early 2000's - although they were not directed at that time to Brayton cycles, but rather as Rankine cycles, which is to use highly radioactive materials as heat transfer agents, in those days, salts in the liquid phase, in these days salts and metals in the vapor phase. Under these circumstances, new sinks for highly stable or highly problematic greenhouse and ozone depleting agents, as well as particulates, might represent a new sink for not just nitrous oxide, but others.

I trust you are enjoying a safe, productive, and enjoyable weekend.

Electrochemical oxidation of 243Am(III) in nitric acid by a terpyridyl-derivatized electrode.

The paper I'll discuss in this post came out about 5 years ago, but somehow I missed it. The paper is: Electrochemical oxidation of 243Am(III) in nitric acid by a terpyridyl-derivatized electrode (Christopher J. Dares1, Alexander M. Lapides1, Bruce J. Mincher2, Thomas J. Meyer1,* Science Vol. 350, Issue 6261, pp. 652-655).

I've written several times about the element amercium, in this space, most recently about its separation from its f-series cogener, europium.

Liquid/Liquid Extraction Kinetics for the separation of Americium and Europium. The process described therein is a solvent based process, but utilizes specialized membranes. As I noted at that time, there are several drawbacks to the process.

However americium is potentially valuable fuel, particularly because of its nonproliferation value, since burning it will generate the heat generating isotope plutonium 238, (via the decay of Cm-242, formed from the decay of Am-242) which when added to other plutonium isotopes, can make them all useless in nuclear weapons.

It turns out, on further inspection, that Am-242 and its nuclear isomer Am-242m - both of which are highly fissionable - are among the best possible breeder fuels, having a high neutron multiplicity, meaning they can serve to transmute uranium into plutonium, greatly expanding the immediate availability of nuclear energy while avoiding isotope separations.

Here is the plot of the neutron multiplicity for the fission of Am-242(m):



Evaluated Nuclear Data File (ENDF) Retrieval & Plotting ("Neutron induced nubar." )

This spectrum, which is from the ENDF nuclear data files is clearly not highly resolved, to be sure, and surely represents a kind of average. It is undoubtedly difficult to obtain highly purified Am-242m for experimental verification. An interesting approach to obtaining it in high isotopic has been proposed, owing to its possible utility in making very small nuclear reactors for medical or space applications: Detailed Design of 242mAm Breeding in Pressurized Water Reactors (Leonid Golyand, Yigal Ronen & Eugene Shwageraus, Nuclear Science and Engineering, 168:1, 23-36 (2011)). To my knowledge, however, this proposal has never been reduced to practice.

There are very few nuclei that exhibit this high a multiplicity, over 3 neutrons per fission at any incident neutron energy. To my immediate knowledge, the only such nuclei is plutonium-241, and this over a fairly narrow range of incident neutron energies in the epithermal region.

I also discussed the critical masses of americium isotopes in this space: Critical Masses of the Three Accessible Americium Isotopes. In a fast nuclear spectrum, americium-241, the common americium isotope produced in the common thermal nuclear reactors that dominate the commercial nuclear industry, particularly in used fuel that has been stored for decades without reprocessing, is fissionable and thus is a potential nuclear fuel in its own right.


A "refinement" of some nuclear physics parameters relevant to the use of americium as a nuclear fuel was published about 13 years ago as of this writing, by scientists at Los Alamos: Improved Evaluations of Neutron-Induced Reactions on Americium Isotopes (P. Talou,*† T. Kawano, and P. G. Young, Nuclear Science and Engineering 155, 84–95 2007).

In a fast nuclear reactor, neutrons have an energy of 1 to 2 MeV whereas in a thermal reactor, the neutron speed is taken to be the kinetic energy of molecules in air, generally taken as 0.0253 eV, almost 100 million times lower energy. Thermalized neutrons tend to be absorbed without fission in americium-241, whereas at higher energy, they tend to fission. The following graphics from this paper show that for a region of neutrons well above the thermal region, but in the general region with the fission to capture ratio climbs:





The next graphic, from the same paper, shows that the neutron induced fission of americium-241, like its capture product, americium-242(m), has a very high neutron multiplicity, meaning that it is also an excellent breeder fuel under these conditions:



Even limited to the left most region of this graphic, which is actually the region in which "fast" reactors work, the multiplicity is shown to be above 3 neutrons/fission. The graph indicates that were the fusion people ever able to run a fusion reactor, where neutrons emerge with an incredible 14 MeV energy, and chose to use a hybrid approach fusion/fission approach to solve the unaddressed problem of heat transfer, americium could provide very high neutron fluxes to do incredible amounts of the valuable work that neutrons can do.

The next question is "How much Americium is Available?"

Kessler - who writes frequently on the subject of denaturing nuclear materials to make them useless for weapons applications - addressed this issue about 12 years ago in this paper: G. Kessler (2008) Proliferation Resistance of Americium Originating from Spent Irradiated Reactor Fuel of Pressurized Water Reactors, Fast Reactors, and Accelerator-Driven Systems with Different Fuel Cycle Options, Nuclear Science and Engineering, 159:1, 56-82.

According to the IAEA calculations he referenced in this paper, as of 2005, there were about 106 MT in used nuclear fuel all around the world. During storage of used nuclear fuel, especially MOX fuel, but not limited in any sense to it, the amount of americium rises because of the decay of its precursor, plutonium-241, Pu-241, which has a half-life of 14.29 years, and which invariably accumulates as a nuclear reactor operates. Ten years after removal from an active core, about 61.6% of the Pu-241 in the fuel will still be present, with the balance having decayed to Am-241. Because of anti-nuclear fear and ignorance, which is quite literally killing the world we know and love, we now have unprocessed used nuclear fuel that has been stored for 40 years or more, without having been processed, albeit this without killing anyone. Forty year old used nuclear fuel will still contain 14.4% of the Pu-241 originally in it, but will obviously have more americium than it did when it was removed from the reactor. (The half-life of Am-241 is 432.6 years.) It seems reasonable to me that we may have more than 200 MT of americium available. This is not a lot of material, but it is significant. The energy content of this much americium, fully fissioned, is very roughly equal to about 10% to 20% of the annual energy demand of the United States. This much americium is certainly not enough to address any more than a tiny fraction of the completely unaddressed climate crisis, but on the other hand, the high neutron multiplicity can certainly accelerate the rate at which we can accumulate fissionable nuclei that are the only viable option for doing anything about climate change. (And let's be clear. Right now we are doing less than nothing to address climate change.) The amount of americium available to use is certainly enough to run 10 to 20 nuclear reactors running exclusively on americium.

Kessler's paper offered some calculations of the isotopic vectors of the Americium available in different fuel scenarios and presented them graphically. In connection with the thermal neutron spectrum graphics he writes:

Figure 2 shows the isotopic ratios of 241Am, 242mAm, and 243Am for a variety of different fuel cycle options in the spent-fuel elements of a modern PWR for a cooling time of 10 yr after discharge.18–24 Options A and B represent low-enriched-uranium LEU fuel after a burnup between 33 and 50 GWd/t…

...In options C, D, and E, either reenriched reprocessed uranium ~RRU! ~option C! or natural uranium or RRU both together with plutonium options D and E! are used…

...In options F and G, RRU or thorium is mixed with plutonium and MAs in order to incinerate both plutonium and MAs in PWRs.


Figure 2:



The graphic refers to a 10 year cooling period, and again, many used nuclear fuels are much older, with the result that the percentage of Am-241 in these cases would be more enriched in Am-241 with respect to the other isotopes.

Kessler offers similar analysis in various fast neutron cases which I will not discuss here. Very few of these types of reactors have operated commercially, although the advent of small modular "breed and burn" reactors, which Kessler does not address, will likely change this. Kessler also doesn't address a case which in my imagination would be superior to all solid fuel cases, specifically liquid metal fuels, a case that was abandoned in the 1960s because of the relatively primitive state of materials science in those days but is certainly worth reexamining 60 years later, given significant advances in that science.

Anyway, in writing this post, and researching it, I have convinced myself once in for all, that my previous feeling that it was a disgrace to let Pu-241 decay into Am-241 was wrong. I have changed my mind: Am-241 is more valuable than Pu-241, even accepting the high value of Pu-241.

This brings me to the Science paper referenced at the outset of this post:

Americium in its chemistry is dominated by the +3 oxidation state, and in this state, it behaves very much like the lanthanide f elements. Significant quantities of the lower lanthanide f elements are formed via nuclear fission, from lanthanum itself up to and including gadolinium.

The process described in the above referenced Science paper uses electrochemistry to make americium behave more like uranium, neptunium, and plutonium, in exhibiting oxidation states higher than +3, and thus having far different properties than the lanthanides.

From the paper's introduction:

Nuclear energy continues to be an attractive large-scale energy source due to its high power density and lack of carbon emissions (1). However, there are drawbacks to its expanded use, including the management of used fuel and high-level waste (HLW) (2, 3). The presence of the minor actinide americium in the nuclear waste stream greatly limits the storage capacity of geologic repositories due to heat production, especially from 241Am, which is a major contributor to the long-term radiotoxicity of HLW. Closed nuclear fuel recycling schemes that improve uranium efficiency and minimize the volume of HLW are under development in nuclear energy programs worldwide. In these schemes, Am must be separated from the lanthanides before transmutation because their high-neutron cross sections would otherwise disrupt the fission efficiency of the recycled fuel. Some schemes also separate Am from curium to facilitate radiologically safe fuel fabrication (4).

Partitioning of Am from the lanthanides is arguably the most difficult separation in radiochemistry. The stable oxidation state of Am in aqueous, acidic solutions is Am(III). With its ionic radius comparable to the radii of the trivalent lanthanide ions, its coordination chemistry is similar, leaving few options for separation. One approach is the use of soft donor ligands that exploit the slightly more diffuse nature of the actinide 5f-orbitals over the harder lanthanide 4f-orbitals. This provides a stronger, more covalent bond between actinides and N-donor ligands. Notable progress has been made in complexation-based strategies, but considerable challenges have been encountered when attempting to adapt their narrow pH range requirements for process scale-up, stimulating efforts to find alternatives. Another approach is oxidation and separation using the higher oxidation states of Am (5, 6). Unlike the lanthanides, with the exception of the ceric cation, Am(III) can be oxidized and forms [AmVO2]+ and [AmVIO2]2+ complex ions in acidic media. The high oxidation state ions could be separated from the lanthanides by virtue of their distinct charge densities using well-developed solvent extraction methods (4)...


Although solvent extraction method are in fact, well developed, it does not follow that they are the best approach to separations of the elements in used nuclear fuel. If I were to look at electrochemical oxidation of americium, I would also look at electrochemical based separation, including an analogue to the separation of nucleic acids and proteins, electrophoretic migration through gels, or liquid/liquid, gel, or solid based ion selective membranes.

The beauty of electrochemistry is that it avoids the use of reagents. the wide use of primitive solvent extraction methods in the mid to late 20th century led to problematic situations like the Hanford tanks about which very stupid anti-nukes carry on endlessly even as they completely ignore, with contempt for humanity, the millions upon millions of people killed every damned year, at a rate if about 19,000 human beings per day, from dangerous fossil fuel waste.

More excerpts of text in the paper:

Penneman and Asprey first reported the generation of Am(V) and Am(VI) in the 1950s (7). Determination of the formal reduction potentials has relied on both direct electrochemical measurements and indirect calorimetry. Formal potentials for the Am(IV/III) couple were evaluated in the 1960s and 1970s in concentrated phosphoric acid solutions (≈2 to 15 M) with Am(IV) stabilized and Am(V) destabilized by phosphate coordination, decreasing the driving force for disproportionation (8–12). Am(IV) is also stabilized in mildly acidic, concentrated fluoride solutions (13). Reported values for the Am(IV/III) potential have varied from as low as 2.2 V to as high as 2.9 V, with the standard value of 2.62 V versus the saturated calomel electrode (SCE) in 1 M perchloric acid...

...Oxidizing Am(III) in noncomplexing media is hampered by the high potential for the intermediate Am(IV/III) couple (Fig. 1) (15). Only a limited number of chemical oxidants, including persulfate and bismuthate, have been explored for this purpose (16). Oxidation by persulfate gives sulfate as a by-product, which complicates subsequent vitrification of the waste (17). Bismuthate suffers from very low solubility, necessitating a filtration step that complicates its removal (16). Adnet and co-workers have patented a method for the electrochemical generation of high-oxidation-state Am in nitric acid solutions (18), based on earlier results by Milyukova et al. (19, 20), who demonstrated Am(III) oxidation to Am(VI) in acidic persulfate solutions with Ag(I) added as an electron transfer mediator with Eo[Ag(II/I)] = 1.98 V versus SCE...


The fact that the authors are embracing the cultural mentality of so called "nuclear waste," rather than the recovery of valuable nuclear materials, has no bearing on the quality of their science. I just have to say that.

The redox potentials of americium:



The caption:

Fig. 1 Latimer diagram for Am in 1 M perchloric acid. Potentials listed are V versus the SCE.


The authors proposed the use of a new type of electrode, an organic/indium tin oxide electrode, to oxidize americium. Here is a a cartoon representation of this electrode:



The caption:

Fig. 2 Molecular structure of p-tpy on the surface of an ITO particle with the protonation state depicted as expected in neutral pH.

(Left) A simple molecular illustration. (Right) A density functional theory–optimized p-tpy structure with pyridine rings oriented to show the potential tridentate bonding motif, ideally placed on a surface.


A word on indium tin oxide: This compound is found in pretty much every touch screen in the world. It is also widely used in some types of solar cells. In the past, at DU, I used to engage a dumb "renewables will save us" anti-nuke in discussion of the fact - facts matter - that the world supply of indium is limited, and therefore any so called "renewable energy" technology based on it is, um, well, not in fact "renewable." Ultimately this person bored me to death, and I put him or her on my lovely "ignore" list, since there is no value in engaging people who simply repeat distortions and outright lies over and over, in a Trumpian fashion. The fact remains supplies of indium are limited. It is considered a "critical material" of concern to people who study such things. The world does risk running out of it. The difference, of course, between cell phones and solar cells and nuclear fuel reprocessing plants do not require large amounts of mass, since the environmental superiority of nuclear fuel to all other energy forms derives entirely from its enormous energy to mass ratio. In fact, indium is a minor fission product found in used nuclear fuel, and more than enough can easily be recovered from such a fuel to make these electrodes. I am not endorsing these particular types of electrodes by the way; I'm not sure that nitric acid solutions are in fact the best approach to nuclear fuel reprocessing; there are strong arguments that they are not. The point is, that in comparison to the requirements of solar cells and cell phones, the requirement for indium in this case, were it to go commercial - and it never may do so - is trivial.

Some graphics on the electrochemical results obtained in working with the electrode:



The caption:

Fig. 3 Electrochemical oxidation of 0.43 mM Am(III) in 0.1 M nitric acid with 0.9 M sodium nitrate using a p-tpy–derivatized ITO electrode.

(Left) Am speciation measured by visible spectroscopy in a 1-cm cuvette at an applied potential of 1.8 V versus SCE. The appearance of Am(V), concurrent loss of Am(III), and overall mass balance are plotted. (Right) Electrochemical Am oxidation scheme involving a p-tpy–derivatized electrode.


The authors remark on the effect of radiation on these solutions:

Autoreduction by radiolytic intermediates provides an explanation for only partial oxidation of Am(III) to Am(V) and Am(VI) at the electrolysis steady state, as observed here. Quantitating the extent of autoreduction and its role in defining the electrolysis steady state are important elements in possible electrochemical/separation schemes for Am. Compared with chemical oxidation, the electrochemical procedure offers the advantage of avoiding complications from oxidizing agents and their reduced forms (16).

Radiolysis of water by Am generates one-electron reducing agents such as H atoms and two-electron reducing agents such as hydrogen peroxide, as well as other redox transients (35). The concentration of radiolysis products varies linearly with total Am concentration, with zero-order reduction kinetics observed for the appearance or disappearance of Am species. Under these conditions, rate constants for these Am species during autoreduction can therefore be derived from the slopes of concentration-time plots (36, 37).

Radiolytically produced one-electron and two-electron reductants provide independent pathways for Am(VI) reduction, with an overall rate constant for Am(VI) loss of 23.4 × 10−6 s−1 (fig. S10). The Am(IV) produced from the two-electron reduction of Am(VI) by radiolytic intermediate or intermediates, presumably H2O2, rapidly disproportionates to Am(V) and Am(III). The reduction of Am(V) to Am(IV) or Am(III) is slow on this time scale (fig. S10).


It seems to me, perhaps naively, that this issue might be addressed by continuous separation, by methods to which I alluded above, to continuous separations, driving the equilibrium. Part of the problem might be addressed by putting beta emitting species - which in real life would be present anyway - in the solution, but no matter.

Some more commentary:

Electrolysis of an 84 μM solution of Am(III) at 2.25 V, 130 mV below the Am(IV/III) couple, gives Am(V) and Am(VI), both of which grow linearly in concentration with time (Fig. 4). After 1 hour, the increase in Am(VI) remains linear but with a noticeable decrease in rate. The growth in Am(V) also slows after 1 hour, eventually leveling off to reach a steady-state concentration of 30 μM. After 13 hours of electrolysis, the composition of the solution was 9 μM (11%) Am(III), 45 μM (54%) Am(V), and 30 μM (36%) Am(VI).


Figure 4:



The caption:

Fig. 4 Electrochemical oxidation of 84 μM Am(III) in 0.1 M nitric acid with 0.9 M sodium nitrate using a p-tpy–derivatized ITO electrode at an applied potential of 2.25 V versus SCE.

(Left) Am speciation as measured by visible spectroscopy in a 50-cm waveguide. (Right) Visible spectra of species before controlled potential electrolysis and after 13 hours of electrolysis with highlighted speciation changes.


The authors conclude:

Our results demonstrate low-potential oxidation of Am(III) to Am(VI) in noncoordinating solutions at high-surface-area metal oxide electrodes derivatized with a surface-bound terpyridine ligand. The mechanism appears to involve surface binding of Am(III) and oxidation to Am(IV) followed by further oxidation to Am(V) with release as [AmO2]+. Electrochemical oxidation is in competition with autoreduction by radiolysis intermediates, with Am(VI) more susceptible to reduction than Am(V).


This is an interesting little paper. I very much enjoyed going through it as well as thinking a little more deeply about the entire subject of americium, which might prove a valuable tool in saving the world via the use of nuclear energy.

While considering all of this, I have to say what's always on my mind:

To my way of thinking, opposition to nuclear energy - even though such opposition appears often on my end of the political spectrum - is criminally insane.

Right now, hurricanes are marching, year after year, all over the United States and other parts of the world. Vast forests, farms and homes have burned all over the Western United States this year, droughts are destroying crops as are things like derechos. We do not record the number of people killed by extreme heat events, but the scientific literature suggests these numbers are rather large, and we have seen the most extreme temperatures ever recorded in 2020. Insects that spread infections are appearing at ever higher latitudes...

The list of the scale of what we are experiencing from climate change goes on and on and on...

And yet...and yet...and yet...I hear from people that "nuclear power is too dangerous." Compared to what?

Let's be clear on something, OK? Opposition to nuclear energy is as ridiculous and as absurd as refusing to wear masks in the Covid-19 epidemic because of political orthodoxy; similarly it kills people. Many of us on the left should examine and confront our own anti-science political orthodoxy, much as old white men like myself need to examine and confront our suppressed racist rationalizations.

Questioning ourselves is something we all must do; because we cannot hope to struggle to achieve the status of being moral human beings without doing so.

Nuclear energy need not be entirely risk free to be vastly superior to everything else; it only needs to be vastly superior to everything else, which it is. It is immoral to oppose nuclear energy.

I trust that you will have a safe, yet rewarding weekend.

How Trump damaged science -- and why it could take decades to recover.

This is a news item in the current issue of the scientific journal Nature: How Trump damaged science — and why it could take decades to recover. (Jeff Toleffson, Nature News October, 6, 2020)

I don't believe a subscription is required.



Some excerpts from this rather long news story, necessarily long since so much damage has been done.

Some excerpts:

People packed in by the thousands, many dressed in red, white and blue and carrying signs reading “Four more years” and “Make America Great Again”. They came out during a global pandemic to make a statement, and that’s precisely why they assembled shoulder-to-shoulder without masks in a windowless warehouse, creating an ideal environment for the coronavirus to spread.

US President Donald Trump’s rally in Henderson, Nevada, on 13 September contravened state health rules, which limit public gatherings to 50 people and require proper social distancing. Trump knew it, and later flaunted the fact that the state authorities failed to stop him. Since the beginning of the pandemic, the president has behaved the same way and refused to follow basic health guidelines at the White House, which is now at the centre of an ongoing outbreak. As of 5 October, the president was in a hospital and was receiving experimental treatments.

Trump’s actions — and those of his staff and supporters — should come as no surprise. Over the past eight months, the president of the United States has lied about the dangers posed by the coronavirus and undermined efforts to contain it; he even admitted in an interview to purposefully misrepresenting the viral threat early in the pandemic. Trump has belittled masks and social-distancing requirements while encouraging people to protest against lockdown rules aimed at stopping disease transmission. His administration has undermined, suppressed and censored government scientists working to study the virus and reduce its harm. And his appointees have made political tools out of the US Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA), ordering the agencies to put out inaccurate information, issue ill-advised health guidance, and tout unproven and potentially harmful treatments for COVID-19.

“This is not just ineptitude, it’s sabotage,” says Jeffrey Shaman, an epidemiologist at Columbia University in New York City, who has modelled the evolution of the pandemic and how earlier interventions might have saved lives in the United States. “He has sabotaged efforts to keep people safe.”

The statistics are stark. The United States, an international powerhouse with vast scientific and economic resources, has experienced more than 7 million COVID-19 cases, and its death toll has passed 200,000 — more than any other nation and more than one-fifth of the global total, even though the United States accounts for just 4% of world population...

...As he seeks re-election on 3 November, Trump’s actions in the face of COVID-19 are just one example of the damage he has inflicted on science and its institutions over the past four years, with repercussions for lives and livelihoods. The president and his appointees have also back-pedalled on efforts to curb greenhouse-gas emissions, weakened rules limiting pollution and diminished the role of science at the US Environmental Protection Agency (EPA). Across many agencies, his administration has undermined scientific integrity by suppressing or distorting evidence to support political decisions, say policy experts.

“I’ve never seen such an orchestrated war on the environment or science,” says Christine Todd Whitman, who headed the EPA under former Republican president George W. Bush.


This is from Christie Todd Whitman, who in the Bush administration was certainly a previous "worst ever" administrator of that agency, refusing to do a damned thing about climate change. Even a Republican with as a pathetic view of environmental issues can be outraged by Trump.

...All the while, the president has peddled chaos and fear rather than facts, as he advances his political agenda and discredits opponents. In dozens of interviews carried out by Nature, researchers have highlighted this point as particularly worrisome because it devalues public trust in the importance of truth and evidence, which underpin science as well as democracy.

“It’s terrifying in a lot of ways,” says Susan Hyde, a political scientist at the University of California, Berkeley, who studies the rise and fall of democracies. “It’s very disturbing to have the basic functioning of government under assault, especially when some of those functions are critical to our ability to survive.”...


There's plenty here, read it and weep...


Why Nature needs to cover politics now more than ever

An Editorial in Nature has recently discussed why scientists must be politically engaged: Why Nature needs to cover politics now more than ever.

It's open sourced; no subscription is required.

For convenience, some excerpts:

Since Nature’s earliest issues, we have been publishing news, commentary and primary research on science and politics. But why does a journal of science need to cover politics? It’s an important question that readers often ask.

This week, Nature reporters outline what the impact on science might be if Joe Biden wins the US presidential election on 3 November, and chronicle President Donald Trump’s troubled legacy for science. We plan to increase politics coverage from around the world, and to publish more primary research in political science and related fields.

Science and politics have always depended on each other. The decisions and actions of politicians affect research funding and research-policy priorities. At the same time, science and research inform and shape a spectrum of public policies, from environmental protection to data ethics. The actions of politicians affect the higher-education environment, too. They can ensure that academic freedom is upheld, and commit institutions to work harder to protect equality, diversity and inclusion, and to give more space to voices from previously marginalized communities. However, politicians also have the power to pass laws that do the opposite.


The coronavirus pandemic, which has taken more than one million lives so far, has propelled the science–politics relationship into the public arena as never before, and highlighted some serious problems. COVID-related research is being produced at a rate unprecedented for an infectious disease, and there is, rightly, intense worldwide interest in how political leaders are using science to guide their decisions — and how some are misunderstanding, misusing or suppressing it...

...Perhaps even more troubling are signs that politicians are pushing back against the principle of protecting scholarly autonomy, or academic freedom. This principle, which has existed for centuries — including in previous civilizations — sits at the heart of modern science.

Today, this principle is taken to mean that researchers who access public funding for their work can expect no — or very limited — interference from politicians in the conduct of their science, or in the eventual conclusions at which they arrive. And that, when politicians and officials seek advice or information from researchers, it is on the understanding that they do not get to dictate the answers...

... Last year, Brazil’s President Jair Bolsonaro sacked the head of the country’s National Institute for Space Research because the president refused to accept the agency’s reports that deforestation in the Amazon has accelerated during his tenure. In the same year, more than 100 economists wrote to India’s prime minister, Narendra Modi, urging an end to political influence over official statistics — especially economic data — in the country.

And just last week, in Japan, incoming Prime Minister Yoshihide Suga rejected the nomination of six academics, who have previously been critical of government science policy, to the Science Council of Japan. This is an independent organization meant to represent the voice of Japanese scientists. It is the first time that this has happened since prime ministers started approving nominations in 2004...

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