Org Prep Daily

June 14, 2007

We don’t need no orbitals

Filed under: Uncategorized — milkshake @ 9:48 am


Some organic chemistry textbooks like to give the student a ‘solid understanding’ of the theory of chemical bond before explaining any actual chemistry. If you are into this kind of thing, you can sink very deep into quantum chemistry. But you can be a just as productive synthetic chemist without bothering with the MO stuff. There are stereo-electronic effects that are influencing the product distribution or equilibrium in some commonly used reactions and systems – and you have to memorize that this is in fact what happens. You may be curious to learn the deeper explanation – but if not you can still use the reaction.

This orbital thing is actually not hard to learn – unless you want to do it on professional level, writing a quantum-computation-based modeling programs. It is just another qualitative and visually-helpful device, not much different from the sticks and balls approach, a device that reflects some aspect of the reality but is based on simplification and memorization (“this is how electron pairs in pi orbitals look like, trust me”). I don’t have a problem with MO’s – just with the educators who try to make it into a bigger science than it really is and to intimidate the unfortunate undergrads.

The MO-based approach to teaching organic chemistry reflects the hopes of 60’s and 70’s that organic chemistry can be neatly categorized and explained by few simple principles. Woodward-Hoffmann rules were a great breakthrough not necessarily for the synthetic chemistry (the electrocyclic reaction governed by these rules are not as frequently used as for example Pd- arylations) but for the self-confidence of organic chemists. This coincided with great advances in spectroscopy and computation that allowed to make a meaningful discussion about unstable intermediates, transition states and so on. The hope at that time was that a new fundamental understanding of entire classes of reactions would emerge, that  new synthetic reactions and retrosynthetic disconnecion schemes could be discovered through computation. Chemistry textbooks based on the  functional group transformations were abandoned in favor of textbooks based on reaction mechanism classifcations, sometimes to a terrible effect.

So if you are in early stages of learning organic chemistry and if you are being put off by MO diagrams, you can relax. Orbitals are helpful but they are not as deep or useful as some textbooks would make you believe – definitely not usefull on the level of collected procedures in Organic Syntheses or a handbook of protective groups. Teacher, leave the kids alone.


  1. I think the usefulness of orbital theory in teaching general, undergrad organic chemistry is in helping to truly understand the mechanism. Once I (finally) figured out that a carbocation was nothing more than an empty p-orbital, then things like eliminations, stereochemistry scrambling in SN1 reactions and the like became a lot more clear. It also helps to understand the roles of Lewis Acids.

    I’ve found that, in tutoring people in organic, that it’s hit or miss with the orbital theories. They might get it, but not TRULY get it, and if your prof isn’t making you learn the mechanisms (which is dumb in my opinion…why make someone learn a functional group transformation if you’re not going to show how it gets there), then there’s no point in going over orbital theory. In this aspect, I agree with you 100% in that the orbitals just get in the way and shouldn’t be mentioned other than “s and three ps come together and morph into four sp3 orbitals…which is why we have this shape to a methane molecule”. Depending on the depth of the teaching of the class, MOs should be used more as tools to support the ideas communicated during the lecture rather than as anything to terrify the students with and thus turn them off to the subject, at least in my opinion.

    Comment by Matt J. — June 14, 2007 @ 10:39 am

  2. I disagree. Perhaps if you view organic chemistry as a trade, in which one develops skills and obtains an intuition about reactivity, then MO diagrams are a waste of time. But organic chemistry is properly a *science* whose purpose should be to make sense of many apparently disparate observations. When the Woodward-Hoffman rules explained pericyclic reactions, I think that was an enormous triumph of the scientific method. I would argue that the fact that we don’t understand organic chemistry very well at all is an excellent reason to learn what we do understand. I challenge anyone who would argues that there is a solid mechanistic framework to organic chemistry at the present. Sure, you can push arrows, make models, and talk about orbital effects, but isn’t it curious how chemistry cannot be done by robots yet? It’s because tons of reactions which *should* work, *don’t* work. The “science” of methodology seems to involve screening tons of ligands, metals, and so forth, precisely because we don’t understand how it all works. Even when a reaction is “developed”, there is hardly ever any real understanding of what’s going on. I think David Collum’s work on lithium enolate aggregation shows very well how complicated something can be even when it looks very simple on paper. So I would argue for a much more rigorous and mechanistically based approach to organic chemistry teaching. And isn’t that a lot better than the typical US approach; i.e., memorizing a bunch of flashcards, and spilling them out onto a test?

    Comment by anon — June 14, 2007 @ 6:54 pm

  3. Yeah, but people who study chemistry are eventually going to use it for some practical ends – like making molecules. It is a bad thing to bully a kid into thinking that MO theory is fundamental for understanding chemistry and therefore essential for them to master. Because it it is not.
    I would rather teach the empirical facts about organic molecules first, like a stamp collection – and then go into stereoelectronic effects (Kirby is quite good, by the way). It may well be that some students will be then endeared by the orbitals “ah, now I understand why”. But I would keep it as an ingredient, I would not serve it as the whole dish. Especially not the first dish.

    Comment by milkshake — June 14, 2007 @ 7:28 pm

  4. Most people who take organic chemistry won’t be making molecules anyways. If you will be, then you will certainly take advanced courses, and get the MO theory anyways. I think it’s better to *not* treat organic chemistry as a “stamp collection”. In fact, I think that is why people, for the most part, hate organic chemistry. There is only a sort of masochistic and rough appeal to memorizing a big stack of reactions, compared to the elegance you can encounter by studying MO theory, or some other mechanistic success. Let’s teach people to think critically, using the scientific method, going from evidence, to hypotheses, and so forth. You wouldn’t argue that doctors shouldn’t be taught any biology and should be instead issued with charts which say what drug to give when, would you?

    I suppose the fundamental problem is a difference in opinion over what organic chemistry classes are for. If they’re for training people to do bench chemistry, then let’s throw MO theory out the window. If they’re for helping people understand what’s going on, then let’s keep it! Without MO theory, you are relegated to explaining everything with charges. Although that explains a lot of things, many other things don’t make sense.

    Just my two cents. I certainly understand and respect what you guys are saying…

    Comment by anon — June 14, 2007 @ 7:39 pm

  5. I second the recommendation for A. J. Kirby. His Oxford chemistry primer is a gem.

    Our undergrad inorganic lab had, on the reagent shelf, an empty glass jar labelled “vacant d orbitals”. An old joke but a good one. Seems to me like MO theory gives a more solid mechanistic framework in transition metals chem (not my field) rather than organic.

    Comment by Handles — June 14, 2007 @ 11:06 pm

  6. The “stamp collection” route is the surest way to alienate the largest group of non-chemistry majors from having even a passing interest in chemistry in the future, and is also the laziest/easiest approach to teaching organic. Milkshake, if you want students to pass exams and then forget most of the info they crammed into their heads then this approach is fine. If one expects an undergrad to actually understand (and hopefully master) the material presented to them, then a more rigorous view of structure, bonding and mechanism, such as MO, NBO etc. is vital. This goes for chem-majors, pre-meds and all points in between. I don’t believe that anyone “bullies” students into MO theory, its just that some TAS/profs have higher standards and expectations of students. Sure, there are teachers that have a hard-on for their own myopic view of a certain topic but I doubt that it is wide-spread. From my own experience, the more rigorous the course, the closer to the (current) truth it is. Ever noticed the fact that students fed a diet of simple VB and VSEPR get truly pissed off with Woodward-Hoffman rules, isolobal analogy etc? The “stamp collection” approach is the equivalent of using melting point and taste as characterization methods – they worked fine back then, but are laughably inept today.

    Then again, most TAs (and an alarming number of profs) can’t even draw the lone pairs on water correctly – the VB and VSEPR view still dominates textbooks. And don’t be too quick with the circle-jerk for Kirby – a lot of his explanations are fine on the surface but eventually turn out to be hand waving and often nonsense.

    Comment by Bad Cop — June 15, 2007 @ 12:43 am

  7. MOs, if explained well, are nice on paper but useless in the lab. Explained badly, they suck. I had a phys org class under a mediocre lecturer that would have had me changing majors if I weren’t so hardheaded.

    Comment by Ψ*Ψ — June 15, 2007 @ 3:51 am

  8. Fleming, Fleming, Fleming.

    Comment by Klug — June 15, 2007 @ 1:27 pm

  9. A couple of things to remember when you’re thinking about MOs are that they are not uniquely determined and they are intimately connected with each other. This means that it is usually meaningless to interpret an individual MO because you could just as easily use another equivalent set of MOs to describe the wavefunction. When someone draws an orbital picture to explain why something happens it is usually possible to counter with another picture why it shouldn’t. Visualizing MOs for small, symmetrical molecules can sometimes be useful although you need to look (as Woodward and Hoffmann did) at all the MOs rather than just picking your favourite one.

    This doesn’t mean that the MOs are completely random. They need to be mutually orthogonal, the electrons have to add up and energy of the system must be minimised. The connection between the orbitals lies partly in how interactions between electrons are modelled. Without going into too much detail, these interactions between electrons are what make QM methods computationally expensive. In effect, the interactions between electrons are ‘shared’ amongst the filled MOs. These interactions are usually ignored in introductory MO theory.

    When using QM methods in real applications, one can try to cast the problem into a form that involves calculating energies of molecular species that hopefully model the chemistry of interest. Sometimes a calculated property such as electrostatic potential is used to identify hot spots on the molecular surface and in some cases quantify the hotness of these spots. It’s worth bearing in mind that these calculations routinely use d-functions for first row elements and each p function is ‘split’ into two p-functions of different ‘sizes’ (this is 6-31G* that you may have encountered in the literature). I make this last point because it is also meaningless to interpret the coefficient of a particular atomic orbital.

    Comment by Great Molecular Crapshoot — June 16, 2007 @ 1:21 pm

  10. “s and three ps come together and morph into four sp3 orbitals…which is why we have this shape to a methane molecule”

    i was a little sad when i learned that hybrid orbitals were fiction

    Comment by squirmy — June 17, 2007 @ 1:45 am

  11. There is no god but the god of M.O.’s and Fleming is his Prophet.

    I spent many pointless hours as an undergrad doing the quantum mechanical derivations of M.O.s for my p-chem classes. Hey, you gotta use that ODE class we made you take for something, right? Then there were those horrible symmetry operators for M.O.s in inorganic chemistry. Can you see the S4?

    If you understand HOMO donates into LUMO to make a new bond, you’ve got all the MO knowledge an undergrad needs. Just don’t ask your professor about the photoelectron spectra of methane…

    Comment by Atompusher — June 19, 2007 @ 2:18 am

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