Wikipedia:Reference desk/Archives/Science/2020 November 16

= November 16 =

Thermodynamic force for synthesis of alkyl halides from alcohols
It's my fifth year of tutoring organic chemistry for the bread and yet something bugs me about the traditional explanations for synthesis of alkyl halides from alcohols. I'm a nontraditional premed / healthcare worker so I've always been more interested in the biochemical applications of organic chemistry rather than its industrial applications; nevertheless in my lessons I strongly emphasize "real life". Sometimes in the problem sets given by my students' professors where they have only learned how to use haloacids rather than say thionyl chloride or phosphorus tribromide (especially in abridged courses), I am forced to repeatedly re-explain why using haloacids work despite my discomfort.

It doesn't help that many of my students' professors set problems where the solvent is missing, the reaction conditions are missing and I do not know how the product is being distilled or how product is being removed. I also have never chlorinated or brominated an alcohol in the lab. Here is the thing that bugs me: carbon-halogen bonds are weaker than carbon-oxygen bonds. Why then is the formation of alkyl halides via SN2 more sluggish for chlorides versus bromides? The C-Cl bond is stronger than the C-Br bond. In polar aprotic solvent chloride should be a stronger nucleophile than bromide (if I am dissolving the alcohol in say carbon tetrachloride -- I suppose if one uses the alcohol as the solvent, sure). Thermodynamically, alcohols can be protonated but alkyl halides cannot. In addition, water as a leaving group can never deprotonate and re-form a hydroxide nucleophile. Hence, acidic conditions favor the alkyl halide but basic conditions favor the alcohol (ignoring elimination). Thermodynamically, how can I rationalize this?

Let's propose we chlorinate or brominate butanol:


 * Primary R-OH: +110 kcal/mol
 * Primary C-Cl: -85 kcal/mol (C-Br: -67 kcal/mol)
 * H-OH: -110 kcal/mol
 * H-Cl: +103 kcal/mol (H-Br: +87 kcal/mol)
 * dH: +18 kcal/mol (+20 kcal/mol for bromination instead of chlorination)

I'm aware these are homolytic cleavage tables not heterolytic cleavage, but still Hess' law should still apply. I am not sure how this plays into the qualitative reversibility of the reaction (surely if the H-Cl bond is stronger than C-Cl, we should be able to protonate the C-Cl bond to allow for a reversible reaction?) What's the real answer? I am tired of undergraduate lies to children. Yanping Nora Soong (talk) 02:26, 16 November 2020 (UTC)


 * You are exactly right that you can propose a simple equilibrium of the overall reaction:
 * RCH2–OH + H–Cl RCH2–Cl + H–OH
 * and think about the relative bond-strengths and microscopic reversibility and energetics of each step of the reaction mechanism.
 * Some thoughts that don't make a complete answer but do highlight some important ideas. The average bond-energy of a bond-type in a molecule is not the same as the bond dissociation energy of one such bond or if the substrate is quite different. The one that caught my eye was water. The average H–O energy in the H–O–H molecule is around –110 kcal/mol, but the first H–O bond losing one H) is around –119 kcal/mol. Similarly, I'm not sure the "pure" H–Cl bond-energy is relevant when one is considering protonating C–Cl (the Cl–H bond-strength is surely different in C–Cl+–H).
 * And as you note, there may be heterolytic differences--that introduces solvent effects and substantially different values in some cases. Those might not be important in a Hess's law cycle if you have really high temperature and lots of excess reagents (to overcome any activation barrier and don't have to worry about loss of reactant by secondary reaction with the product). And you also need a mechanism to get the reaction to work.
 * The easy way to rationalize when teaching is "in the given example, there are a ton of unstated variables. The fact that it does work means it's easy to pick variables that overcome (for example) reversibility. Therefore, the first step is to recognize even what could happen before designing an experiment to make it a likely high yield of what would happen." There is no one protocol that works for all substrates, and you can't start by teaching "every substrate is different, every product has different volatility and solubility, so let's learn every reaction as a practical example to optimize." POCl3 and SOCl2 are nice because their very nature drives the reaction so easily and you don't need to worry about equilibrium effects.
 * Regarding the Cl vs Br rate, there is the preliminary step of protonation of the alcohol prior to the SN2 mechanistic step itself. If HBr is a stronger acid than HCl, then that first-step equilibrium shifts more towards products. How does that affect the rate of the two-step process? DMacks (talk) 04:33, 16 November 2020 (UTC)
 * The easy way to rationalize when teaching is "in the given example, there are a ton of unstated variables. The fact that it does work means it's easy to pick variables that overcome (for example) reversibility. Therefore, the first step is to recognize even what could happen before designing an experiment to make it a likely high yield of what would happen." There is no one protocol that works for all substrates, and you can't start by teaching "every substrate is different, every product has different volatility and solubility, so let's learn every reaction as a practical example to optimize." POCl3 and SOCl2 are nice because their very nature drives the reaction so easily and you don't need to worry about equilibrium effects.
 * Regarding the Cl vs Br rate, there is the preliminary step of protonation of the alcohol prior to the SN2 mechanistic step itself. If HBr is a stronger acid than HCl, then that first-step equilibrium shifts more towards products. How does that affect the rate of the two-step process? DMacks (talk) 04:33, 16 November 2020 (UTC)
 * Regarding the Cl vs Br rate, there is the preliminary step of protonation of the alcohol prior to the SN2 mechanistic step itself. If HBr is a stronger acid than HCl, then that first-step equilibrium shifts more towards products. How does that affect the rate of the two-step process? DMacks (talk) 04:33, 16 November 2020 (UTC)
 * Regarding the Cl vs Br rate, there is the preliminary step of protonation of the alcohol prior to the SN2 mechanistic step itself. If HBr is a stronger acid than HCl, then that first-step equilibrium shifts more towards products. How does that affect the rate of the two-step process? DMacks (talk) 04:33, 16 November 2020 (UTC)


 * So something I would point out to my students is that these reactions consume the acidic species (in the case of favoring the alkyl halide) or consume the basic species (in the case of favoring the alcohol), as distinct from the acid-catalyzed or base-catalyzed additions/substitutions they will later learn where the presence of water strongly must be accounted for (driven off/added). By a similar thermodynamic principle, water must be driven off to drive acid-catalyzed esterification to completion, but this is not required in saponification, which consumes the base rather than borrowing it for catalysis. So perhaps it is not C-X or C-OH bond strengths per se driving the reaction after all, but the chemical potential of the acidic or basic species? After all, the acidic species or the basic species are typically used in excess. In large enough excesses (1M or more), the activity coefficient of their chemical potentials would readily increase (opposite the Debye-Huckel trend for more dilute charges). By sliding the pH up and down, I alter the position of the equilibrium, which makes sense in part because water is a less reactive Bronsted-Lowry acid compared to HX but the alkyl halide is a more reactive Lewis acid than alcohol. Is this closer to a more enlightening approach?


 * The other issue is that in looking at BDE I am only looking at enthalpy rather than change in free energy. (It is a bit easier to teach changes in enthalpy than account for both dH and dS in an organic reaction in solvent.) In the dissociation of haloacids, dH is negative and dS is negative (which would be against intuitition from how I conceive of dissolving most solutes, were I not reminded that adding water to strong acid readily generates steam). Are there any worked examples for this particular case? It is such a basic topic in organic chemistry that I cannot seem to find suitably rigorous thermodynamic treatment for. I would like to follow the rigorous treatment myself so I can pick and choose which intuitive or qualitative explanations are best for a given situation (my students may not spontaneously ask to be "put through the rigors" but they often readily raise their own objections). Yanping Nora Soong (talk) 05:36, 16 November 2020 (UTC)

Where does the natural typical smell of urine come from?
Where does the natural typical smell of urine come from? (I'm not asking about the pathological smell, but the typical one the most of the people have it physiologically), which substance/es cause it? --ThePupil (talk) 08:44, 16 November 2020 (UTC)
 * You can find the answer in Wikipedia. See Urine.--Shantavira|feed me 10:20, 16 November 2020 (UTC)
 * Actually, the querant cannot. That article section only talks about how the "normal" odor can be affected by disease or by the consumption of certain foodstuffs. It doesn't explain what gives rise to the "normal" odor in the first place.
 * Unfortunately, a cursory websearch only seems to find items which similarly offer explanations for "non-normal" odors, although some mention that ammonia is a contributor to the "normal" smell and can sometimes seem stronger than usual.
 * Perhaps a biochemist (for example) will notice this query and be able to give, or track down, an explanation, and perhaps even be willing to add the missing information to our article. {The poster formerly known as 87.81.230.195} 90.197.26.5 (talk) 11:49, 16 November 2020 (UTC)


 * (ec) That section only lists causes for atypical odours. A source I found is this rather old textbook, which describes the odour of "fresh normal urine" as being "due to the organic acids of the aromatic series". It is not immediately clear to me which group of acids this refers to; both the aromatic amino acids and the phenolic acids are both organic and aromatic. Uric acid belongs to neither of these groups. The textbook later mentions "aromatic ethyl-sulphuric acids" among the normal constituents of urine. Perhaps others more versed in organic chemistry can translate this into current terminology. --Lambiam 12:15, 16 November 2020 (UTC)

Why does feces odor smell good if strength is low enough?
Sagittarian Milky Way (talk) 12:00, 16 November 2020 (UTC)


 * Which sense of "Why"?. One answer is, "by definition", provided we define the strength of the odour of faeces to be "low enough" if it smells good. --Lambiam 12:43, 16 November 2020 (UTC)

Boiling sugar
I've found what look to be two contradictory statements, but I'm probably misunderstanding something. How can one boil sugar if it doesn't even melt? This is the 18th century, so they probably didn't have convenient access to other kinds of sugars. Nyttend backup (talk) 18:54, 16 November 2020 (UTC)
 * Thomas Telford: "Being a pioneer in the use of cast-iron for large scaled structures, Telford had to invent new techniques, such as using boiling sugar and lead as a sealant on the iron connections."
 * Sucrose infobox: Melting point — "None; decomposes at 186 °C (367 °F; 459 K)"
 * The statement in the Telford article about "using boiling sugar and lead as a sealant" is NOT in the citation at the end of the paragraph where you have the above quote. You are safe to remove the statement entirely with the edit summary "This statement is not in the citation at the end of the paragraph".  -- Jayron 32 19:04, 16 November 2020 (UTC)
 * Ever made toffee? Sugar solution boils. One then dips Welsh flannel in it and uses this to caulk the joints. DuncanHill (talk) 19:07, 16 November 2020 (UTC)
 * That would be boiling sugar-water, though, not boiling sugar. --Trovatore (talk) 19:37, 16 November 2020 (UTC)
 * (e/c) "Boiling sugar" is perfectly normal English. DuncanHill (talk) 22:23, 16 November 2020 (UTC)
 * In the sense of sugar-water, really? Seems at the very least imprecise, and I'm not personally familiar with that usage.  Could be a specialized usage in candy-making, maybe? --Trovatore (talk) 22:29, 16 November 2020 (UTC)
 * Perhaps this is a cultural difference. I grew up in a culture where making sweets, jam, preserves, etc was a normal part of life. DuncanHill (talk) 22:38, 16 November 2020 (UTC)
 * The sentence says "sugar and lead," so it already isn't just sugar... --OuroborosCobra (talk) 22:22, 16 November 2020 (UTC)
 * The sentence in the Thomas Telford was originally added by this edit with no cite. Our Pontcysyllte Aqueduct article says "Welsh flannel and a mixture of white lead and iron particles from boring waste", cited to a Royal Commission on the Ancient and Historical Monuments of Wales ref that states "a mixture documented to be of flannel, white lead and iron borings". So please update the Telford article and add the ref. DMacks (talk) 23:58, 16 November 2020 (UTC)
 * The claim of using sugar can also be sourced, e.g. from this Guardian article that predates the edit adding the claim to the article. Just a wild guess: perhaps Telford experimented not only with basic lead carbonate but also with lead acetate, another lead salt for which an old-fashioned name is lead sugar, and someone misinterpreted a phrase such as "a lead-sugar concoction" as denoting a mixture of lead and sugar, after which the error kept getting copied. --Lambiam 10:32, 17 November 2020 (UTC)
 * A 1985 book source mentions "Welsh flannel and lead dipped in boiling sugar". There has to be some older, original source for this sweet story. --Lambiam 11:05, 17 November 2020 (UTC)
 * Good find (and detail about old names)! DMacks (talk) 12:31, 17 November 2020 (UTC)
 * There's another, more precise comment about joints in the Pontcysyllte Aqueduct:
 * "The joints were made watertight using welsh flannel dipped in boiling sugar, after which the joints were sealed with lead."

- Pontcysyllte Aqueduct in Science Photo Library, https://www.sciencephoto.com/media/174860/view/pontcysyllte-aqueduct


 * which seems to separate the lead's role from sugar. Alas, it's not sourced. --CiaPan (talk) 12:50, 17 November 2020 (UTC)


 * This says "a strange combination of Welsh flannel and a lead, iron and sugar concoction", this says "Welsh flannel and a mixture of white lead and iron particles from boring waste". Haven't found anything we could really use as a source yet, but a mixture of white lead, iron filings, and boiling sugar (pace those who have never made toffee) slathered over some good flannel could perhaps be viable. DuncanHill (talk) 13:14, 17 November 2020 (UTC)
 * Just for the record, as to what adding sugar to molten iron would have done, would be to create a crude form of steel. Sugar, a carbohydrate, is basically "carbon + water" and at those temperatures in a relatively low-oxygen environment, you would drive off water and be left with just carbon.  Carbon + iron = steel, so I suspect the "boiling sugar (implied solution) added to the mixture or iron and lead would have formed some type of lead-steel-like alloy.  Unless, of course, someone somewhere in the chain of misinterpretations has read misread something like "sugar of lead" or "sugared lead" or some such phrase which may have been lead sugar, which of course, contains no actual sugar.  But those are only a few different possibilities, and unless we have the original source from Telford's own writing (rather than the nth-generation misreading of that source) it's still really hard to say.  -- Jayron 32 13:45, 17 November 2020 (UTC)
 * And in today's "What's old is new again", 2007 patent "Production of Iron Using Environmentally-Benign or Renewable Reducing Agents". DMacks (talk) 20:30, 17 November 2020 (UTC)