Organic Chemistry Study Tips

By James Ashenhurst

Instructor’s “kludges” of organic chemistry

Last updated: October 6th, 2022 |

A kludge, as commonly defined, is a workaround – an inelegant,  quick and dirty solution to a problem.

Miles Glacier Bridge Damage (and kludge) 1984 -(Wikipedia)

When I’m teaching a reaction or a new concept to students, I’m focused on getting them to understand the core idea. In the process of doing so, there will often be little obstacles that stand in the way (more often than not, they are acid-base reactions).

As much as I might want to stop and point out the finer points of the reaction, we’re always dealing with constraints: time and attention. So I say to myself, “we can always go back to this later – let’s focus on the big picture”.

That’s when I break out the kludge. I don’t necessarily like it, but it’s usually the best choice under the circumstances.

Here are four common instructor’s kludges in organic chemistry.

1. H3O+ .

What we’re saying when we use H3O+ is, “basically, we’re adding acid to the product of this reaction, and the identity of the acid doesn’t matter so much.” Technically I hate using H3O+, since it ignores the counterion. Sometimes I’ll just say “acid” instead. But it’s so prevalent and widespread that it isn’t going away any time soon.

2. The magic wand of proton transfer.

I’ve mentioned the magic wand of proton transfer before. We need to move a proton from one atom to another. There are probably 5 different ways to write the mechanism that would be perfectly acceptable. But writing out one mechanism would exclude the others. So we often just write” proton transfer”. Magic!


3. The base in the E1 reaction (and others).

In this reaction, the acid (HI) in this case protonates the alcohol to give H2O(+), which then leaves to form a carbocation. Here comes the judgement call. There’s an iodide I(-)  ion floating around. The most natural thing to do is to show I(-) acting as a base, regenerating HI. Most of the time, this is what I find myself teaching. However, this is not strictly correct! Iodide is a considerably weaker base than water.

Is it worth the extra time to teach this? I think it largely depends on the student and the course. My personal preference is for the student to just understand the reaction first. If they get it fairly quickly, I’ll add in the extra layer of detail.

4. [1,4] versus [1,2] addition.

This one often stumps me as an instructor. Most students learn that Grignard reagents add to the carbonyl carbon, but Gilman reagents (organocuprates) add to the alkene. The hard question to answer is “why” ? If you haven’t gone over the concept of hard and soft acids and bases (or even molecular orbital theory) this is a tough concept to explain without throwing up your hands and saying “just memorize this”.

What say you, instructors of organic chemistry? Any other kludges you use in your daily practice?


Comment section

14 thoughts on “Instructor’s “kludges” of organic chemistry

  1. New organic teacher here (completed my first semester teaching in July). In order of the questions:

    1) I use H3O+ willy-nilly, but I do spend a solid week on acid-base chemistry to try to ensure that everyone knows that it is the species produced by any sufficiently strong acid in water. I also have observed that students never place the same weight on things you say out loud as they do on stuff you write on the board, so I will say “You can work this up with any acid, HCl is probably the easiest thing to use because it’s common.” That way they know “H3O+ = generic strong acid” and know HCl is a good choice but don’t get confused if I use H2SO4 for some reason.

    2) In sophomore organic, I never use “proton transfer,” but always show it explicitly. Similarly to above, if I see a step that can be done multiple ways, I say “Okay, I’m going to show water taking off this proton, but you could use another molecule of starting material as well and that would be valid.” Out loud, not on the board.

    3) I usually use your same kludge. Actually, when I’m writing on the board, I do it like this:

    Me: Okay, so now we have a leaving group, this protonated alcohol, what’s going to happen next:

    Students: (dead silence)

    Me: Don’t make me use the awkward silence on y’all again.

    Student: It’ll…leave?

    Me: Yeah. How?

    Smart student who has known the answer the whole time, kind of: That hydrogen will go.

    Me: Right…this hydrogen? So you need a base to do that, right?

    Students: *headbob*

    Me: What bases do we have around?

    Smart student: Iodide?

    Me: Yeah, although water is a good choice too.

    I haven’t done conjugate addition yet. We’ll get that in orgo 2.

  2. I loathe Kludge #3. I absolutely do not let my students get away with using Br-, Cl-, or HSO4- as a base in any proton transfer reaction. And when water’s not around to be that nice mild base, or if we haven’t added pyridine to be a proton sponge, I’ll make them use another molecule of starting material to keep the catalytic cycle going.

    Kludge #1 I do use. Except when we get deeper into enolate chemistry. H3O+ is no good anymore for arbitrarily quenching an aldol addition. NH4Cl is acidic enough to quench the aldol addition, but mild enough not to lead to elimination. H3O+ (or HCl or something more explicit) is only used if the aldol elimination is wanted. Otherwise, I let them know H3O+ is general, NH4Cl is more specific (and actually commonly used in actual labs), then I use the two interchangeably.

    For Kludge #2, I allow the intramolecular proton transfer. Yeah, that’s probably not what’s happening, but those acidic acyl substitution mechanisms are long enough as it is. As long as they’ve got the arrows going in the right direction, I’ll allow it.

    For Kludge #4, I go back to The Lies We Tell and use my stock phrase ‘for our purposes, this is what we need to know. They ‘why’ is a bit beyond the scope of the course…’ or some such phrase. I have given a 5-min overview of HSAB Theory… but I suspect they don’t digest much of that.

    The other Kludge I try not to use, but often find myself falling back on is having H2SO4 protonate an alkene, or carbonyl, or some such lewis base while the reaction is run in a perfectly good protic solvent. Alkene additions is one of the first mechanism chapters we cover first semester, and I definitely make sure that they know the first and fastest reaction is protonation of ROH by H2SO4 to give ROH2+ (R = H, C). THEN the alkene can be protonated by ROH2+. By the time we get to carbonyls second semester, I usually relax that requirement because, again, the mechanisms are long enough as it is.

    1. I see a lot of instructors use H3O(+) more or less interchangeably with H2O/H2SO4, especially in the context of addition of H2O to alkenes. H2SO4 seems to be the acid of choice for elimination of alcohols to give alkenes, since it’s taught that the HSO4 anion is “non-nucleophilic” and “non-basic”.
      The “for our purposes” line is something I will be using a lot more of.
      If I have to show proton transfer, I always draw it as an intermolecular reaction, and point out that we could show a few other equally valid mechanisms.

    1. i agree with u completely here it helps only with klude 4 but at rest of the times in kludges 1,2,3 it just creates more confusion when the detail is not present

  3. I agree wholeheartedly with azmanam on Kludge #2.

    As far as proton transfer, I prefer to just use H+. It’s simple, easy to write and all my students know what a good source of H+ is. If a base is needed later on, I allow them to use the generic “B” or “B-“.

    I don’t worry about totally balancing reactions, and that is something most of my students get. I will, in lecture, often ask “what do we need to balance this?” and most students quickly answer “chlorides!” or something along those lines.

  4. Here are my thoughts after 15yrs doing this…
    (1) H3O+ is it a kludge ? Isn’t it the most common acid species present in an aq. solution of a strong acid ? And if the A- is irrelevant, then isn’t H3O+ a simple species to use ?

    (2) H+ transfer… I always show the steps and not just intramolecularly (a partial kludge embedded in this one?)

    (3) I often use “B” as the base in mechanisms…..then at the end I always go back and make sure I identify what B could be… make a list of them…. gives a chance to mention the factors

    (4) Fortunately we are now spared this one in our intro course and leave it to a more advanced course.

    1. Thanks!
      H3O(+) is the dominant acid species present in aqueous solution, but part of me hates the imprecision that comes with leaving out the counterion. I realize that A- is not part of the reaction but still, to leave the charges unbalanced like that came as a bit of a surprise to me in Org 1 after being forced to balance everything in gen chem. The other two are judgement calls, I can certainly see the benefits/costs of using either method.

      1. Net ionic equations are written in second semester gen chem without using spectator counterions for redox reactions/electrochemistry. I don’t think that’s a big deal, so long as students understand counterions are present.

  5. I don’t like kludge #2 because it requires a 4-membered transition state. I require my students to deprotonate with water and then re-protonate using H3O+ (assuming the reaction is happening in an aqueous solution).

    1. But if we’re dealing with a proton (which only has an s-orbital, after all) is a 4-membered transition state so bad? Look at hydroboration for example.

      I’d be curious if it’s possible to model what % of the reaction is intramolecular and what % is intermolecular.

  6. For 4, I use a combination of arguments including LG ability (Nu: will add reversibly to C=O bonds… if they they can leave) and bond strength (C-C sigma and pi vs C-O sigma and pi) to argue that C=C addition (1,4) is generally favored. Why do a limited number go 1,2? That is a kinetic argument. I hint at MO but mostly lean on their knowledge of experimental conditions (mild acid/temps for C=O hydration; harsh acid/high temps for C=C hydration). I think ~15-20% get it.

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