2943: Unsolved Chemistry Problems

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Unsolved Chemistry Problems

Title text: I'm an H⁺ denier, in that I refuse to consider loose protons to be real hydrogen, so I personally believe it stands for 'pretend'.

Explanation

This explanation may be incomplete or incorrect: Created by a caffeinated biochemist - Please change this comment when editing this page. Do NOT delete this tag too soon. If you can address this issue, please edit the page! Thanks.

Every field of research has unsolved problems considered "important" or "significant" that motivate continued research. The scientists at what is apparently the "grand opening" of their new chemistry lab list several real chemistry problems, followed by one also-unsolved-but-less-scientific problem (the p in pH)

Arbitrary Enzyme Design:

Enzymes are catalytic proteins. Enzyme catalysis is often unique in comparison with other catalysis methods as it is highly specific, or tailored to a specific reaction. As such, enzyme catalysis, besides being the basis of all biochemical processes, is becoming increasingly relevant to industrial synthesis processes. As enzymes can easily be produced synthetically through recombinant gene technology, being able to design an arbitrary enzyme for any reaction would mean that effectively any reaction could be relatively easily catalyzed, revolutionizing the chemical synthesis industry.

Protein Folding:

Proteins are large molecules that consist of chains of amino acids. These amino acid chains become folded in extremely complex ways to form intricate 3D structures, and the way a protein is folded is of critical importance to its function. Because of the huge importance of proteins to biological life, biologists have devoted significant attention over many decades to the problem of protein structure prediction. This refers to the ability to predict the 3D structure of a protein based on the amino acid sequence, and remains one of the most important problems in computational biology. The ability to predict protein structure purely from amino acid sequence — the so-called "de novo" prediction — is known in computational biology as an unusually difficult problem due to the complexity of amino acid chains. Known as "Levinthal's paradox," the number of possible conformations from the backbone conformations alone is estimated to be in the ballpark of 10^300. Despite this, protein folding occurs extremely quickly in reality. Because of this difficulty in sampling conformations, even with optimization, such as secondary structure prediction and Monte Carlo simulation, a "true" accurate simulation is extremely computationally expensive. Because of this, the most accurate solutions, such as AlphaFold, utilize a combination of homology modeling (sampling experimentally determined proteins with similar sequences to infer structural motifs and similarities) and deep learning to accurately guess protein structure. See also 1430: Proteins.

Depolymerization:

Polymers are very large molecules formed out of repeating subunits called monomers. Monomers are molecules, typically organic in nature, that can bond with at least one other molecule, with two or more making long chains or networks called polymers. That process is known as polymerization. Depolymerization is breaking polymers down into the small molecules they were originally made from. This is done through a variety of processes, such as radiation, electrolysis, adding chemicals, and other means. Plastics are the best-known polymers, but cellulose, proteins, and DNA are also technically polymers. The huge number of varieties and mixtures in plastics makes recycling them a huge challenge, and there is increasing concern about plastic waste damaging the environment.

Polymerization is usually exothermic, releasing energy as heat. To reverse this would require adding energy in a targeted way. Simply destroying a polymer — by means of highly-reactive chemicals, heat, or radiation — doesn't generally release the monomer molecules to a significant degree; most of the reaction products are highly degraded. Most polymers are made by a process of catalysis, with the small monomer molecules interacting via a catalyst structure, often in liquid form, and the eventual product is usually solid. To reverse this would require getting the catalyst to interact in a very precise way with the solid polymer, and it's relatively difficult for the catalyst structure to get into the proper configuration with the solid tangled polymer molecules.

Another highly-desired depolymerization process would be to convert cellulose into its component glucose molecules. That glucose could then be used for a variety of different purposes, including fermentation to alcohol to use as a fuel. Currently, when plants are grown, much of the solar energy and carbon dioxide they absorb ends up in the form of cellulose rather than as starch, sugar, protein, or other substances that we find useful. Our being able to make use of the cellulose would make farming much more energy-efficient. Some organisms are able to depolymerize cellulose by means of enzymes, but our ability to use similar processes on an industrial scale is still limited. (Those organisms use a complex multi-step biochemical process which essentially "invests" energy into splitting off a glucose molecule, then recoups the investment by metabolizing the glucose.) It's also possible to depolymerize cellulose at high temperature and pressure using nothing more than water and acid, but that process is energy-intensive. It might be possible to do it with a solar-heated reactor.

What the “p” in pH stands for:

“p” shows up in pH, pK_a, pK_b, and other things related to the concentration of H+ ions and OH- ions. The meaning of the "p" in "pH" has been the subject of much dispute. It is sometimes referred to as "power of Hydrogen", perhaps related to the fact that pH is a logarithmic scale, and the logarithm is the inverse of the exponented function and, in all three languages that pH was first published in, the word for "potency" is used for exponents. The term pH was introduced by Søren Peter Lauritz Sørensen, who did not publish his results in English, and more accurately translates as "hydric exponent". The letter p could stand for, in the languages in which Sørensen published: the French 'puissance', German Potenz, or Danish potens, all referring to the concept of the "exponent" in exponential functions.

Title Text: Hydrogen Denier

In the title text, Randall claims to be an H⁺ denier by refusing to consider loose protons to be hydrogen atoms, and as such, the “p” stands for pretend. Part of the joke is Randall's implication that this is a well-known conspiracy theory that he personally buys into (it isn't). The word "denier" is often used as shorthand for other conspiracy theories, such as a "climate change denier" or a "moon landing denier."

Here's a breakdown of this joke:

• H⁺ is the chemical symbol for a positively-charged atom of hydrogen, the smallest atom on the Periodic Table. Since hydrogen is normally just one proton and one electron, when you take the electron away, you make it positively charged (the + sign in the superscript) and you effectively end up with just a single loose proton. So the shorthand for "loose proton" is to refer to it as an H⁺ ion.

• pH is taught in high school science class to essentially measure the concentration of extra loose protons in, say, an aquarium. (Different fish prefer slightly different pH levels/alkalinity.) As mentioned earlier, you can interpret the term "pH" to be referring to the "p" of "H" -- the power/potency of H⁺ ions.

(Note that in reality, lone H+ ions do not exist in water, and instead they glom onto H₂O molecules to form H₃O⁺ and H₅O₂⁺/(H₂O--H--OH₂)⁺ due to intermolecular hydrogen bonding. If you don't know what these chemical symbols mean, don't worry about it.)

But as an H⁺ denier, Randall doesn't consider loose protons to be hydrogen atoms. He has a purist's view of hydrogen, that it is just "pretending" to be hydrogen as soon as it loses an electron. As a denier, he interprets the term "pH" as referring to the concentration of "pretend Hydrogen".

Transcript

[Hairbun stands behind a lectern on a podium speaking into a microphone on the lectern. A Cueball like guy stands to the left and another Cueball like guy and Megan stand to the right. There is a large sign hanging in the background along with some ornaments.]

Sign: Grand Opening

Hairbun: Our lab will be working on chemistry's top unsolved problems: arbitrary enzyme design, protein folding, depolymerization, and, of course, the biggest one of all:

Hairbun: Figuring out what the "p" in "pH" stands for.

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Discussion

P stands for poncentration, SMH my head 😒 --172.70.162.211 21:22, 7 June 2024 (UTC)

You may find this helpful: RAS syndrome Trogdor147 (talk) 22:25, 8 June 2024 (UTC)

Oh, that was intentional, my friend. (Also, I believe you meant RAS syndrome.) --162.158.74.48 07:34, 10 June 2024 (UTC)

I think p stands for "pitch", because people start pitching random numbers when they are supposed to calculate a pH (or even an pOH) from given concentrations.Tier666 (talk) 09:54, 10 June 2024 (UTC)

Is 'depolymerization' in this context referring to means of chemically recycling plastics? As I understand it, we basically just do recycling of thermoplastics at the moment by physically melting them, whereas being able to split a plastic apart into its component monomers would in principle enable a completely closed loop lifecycle for plastics, easing the strain on dwindling oil reserves and landfills and whatnot. Since these are supposed to be important unsolved problems, I feel like it probably is a reference to this, but I'm not a chemist and there may be something else which makes more sense. 162.158.33.134 22:37, 7 June 2024 (UTC)

In a chemistry context, depolymerization is simply the process of breaking down polymers into monomers. Plastic recycling is one potential application. Another is production of biofuels. It's a well understood process (usually just heat it up enough and/or apply the proper chemical treatment). Getting the desired outputs in an efficient manner is, in some cases, an unsolved problem. 172.69.246.150 16:05, 8 June 2024 (UTC)

i've always been taught that the p stood for "parts". youtu.be/miLcaqq2Zpk 04:01, 8 June 2024 (UTC)

In chemistry, I was taught that it was "potential". I didn't even know this was in dispute. L-Space Traveler (talk) 04:54, 8 June 2024 (UTC)

P does not stand for anything. Originally, it was contrasted with q. Sørensen was performing electrochemical experiments and contrasted the reference electrode q with the hydrogen electrode p. Using p and q like this is common, like using x and y, u and v, or m and n. It's not an abbreviation, just a variable name. He recommended normalizing the concentration of hydrogen ions (i.e. dividing it by 1 mol/l) and calling the result Cₚ or C_q (depending on the electrode). Then each of these tends to be a small number, which we could write as 10^(-p) or 10^(-q). The number p⁺_H then represented the negative log of the normalized concentration of hydrogen cations at the hydrogen electrode. You can read about it in "The origin and the meaning of the little p in pH" by Jens G. Nørby, published in Cell. The associations with words like "power" and "potential" are now widely considered urban legends. 172.70.134.39 04:55, 8 June 2024 (UTC)

My chemistry teacher at school taught us that pH stands for Latin "pondus hydrogenii", meaning "weight of hydrogen". I never questionned this, until today. 162.158.111.178 19:20, 8 June 2024 (UTC)

My high school chemistry teacher, who was also a French teacher, told us it was for pouvoir hydrogène, meaning “to be able to hydrogen”—I think? I never questioned this, until today. At least it's close to the puissance theory in the article—it's the infinitive-verb form. P₁h₃r₁e₃d₁₃ (talk) 17:18, 10 June 2024 (UTC)

Added some stuff concerning the biochem part, since that's my field of expertise. I recently personally felt the problem of the protein folding problem trying to get supercomputer time to simulate a protein I was studying! Also, given that antibody-antigen generation is still extremely faulty I highly highly doubt arbitrary enzyme design will be solved anytime soon, even though great leaps in protein folding have been made. 172.70.39.40 02:13, 9 June 2024 (UTC) caffeinated biochemist

THe issue with loose protons is not ib being or not being atoms. Loose protons have no electrons at all, and thus cannot do Pauli repulsion, and thus cannot do regular chemistry - "should" burrow too much into electron density. The former, however, is not true, because loose protons attach themselves to lone pairs and thus get eletrons and thus can do regular chemistry. This duality is the source of the "proton controversy". In water, for instance, lone H+ do not exist and form H3O+ and H5O2+ /(H2O--H--OH2)+. 162.158.172.4 09:25, 9 June 2024 (UTC)

I've always heard it described as "parts hydrogen", which seems simple enough. Surprised this isn't yet mentioned in the explanation. PotatoGod (talk) 19:47, 10 June 2024 (UTC)

Seriously guys, read the Nørby paper. It's good. It is also irrefutable. p did not originally stand for anything. Or if it did, you will have to explain what q stood for. This is like insisting the a, b, and c in the Pythagorean Theorem must stand for something in some language. It's just factually, provably not the case. We don't have to keep adding speculations about what it might have meant when there is no mystery. 172.70.230.193 05:57, 13 June 2024 (UTC)

"ρ operator"

I'm not finding any mention of the "ρ operator" in a Google search. Is this section just fiction? The author has no prior contributions to this wiki. BunsenH (talk) 22:42, 9 June 2024 (UTC)

As this operator isn't even mentioned in the comic the section is irrelevant, fiction or not. Trivia at best. I removed that part Elektrizikekswerk (talk) 09:52, 10 June 2024 (UTC)

I assume that it was intended to "explain" the origin of the 'p', as derived from 'ρ'. But I'm reasonably certain that the whole thing was just made up. BunsenH (talk) 15:55, 10 June 2024 (UTC)

Protein folding is biophysics (or rather computational biophysics if you’re doing it in a worthwhile way - Alphafold 2 anyone?), I’m genuinely mad about this. NavieredAndStoked (talk) 19:45, 30 July 2024 (UTC)NavieredAndStoked