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When we're reasoning about chemical reactions and their mechanisms (in organic chemistry in particular), the way we model the behaviour of molecules is almost in a “common sense” way. In terms of tracing their trajectories, steric effects, positive and negative charges behaving how point charges would. The treatment to me feels very different to how we think about electrons, for example.

Is this because reactions occur in the bulk, and even though we are thinking about what is happening in terms of the behaviour of individual molecules, that molecule actually represents some sort of average behaviour of the bulk, and so quantum effects/weirdness are being averaged out and we can think of them acting in a more “common sense” way?

Of course I understand that the actual bonding and our understanding of chemical structures and things like that comes from QM based models.

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    $\begingroup$ Molecules are a good deal heavier than electrons. $\endgroup$ Commented Nov 28, 2022 at 9:54
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    $\begingroup$ Quantum and relativistic effects fortunately tend to be pretty subtle in case of most molecules' reactions. Still there's QM/MM used sometimes. In general, one models stuff as crudely as it's still viable. $\endgroup$
    – Mithoron
    Commented Nov 28, 2022 at 14:38
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    $\begingroup$ I think you need to define "quantum effects" more precisely. For example, organic mechanism are often explained conceptually in terms of orbital interactions, and orbitals can only exist because of QM, so is that a "quantum effect" or not? $\endgroup$
    – Andrew
    Commented Nov 28, 2022 at 18:08
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    $\begingroup$ @IvanNeretin - I largely agree, but protons are also small enough that proton tunneling effects can also be relevant to chemical reactions, for example giving classically impossible isotope effects $\endgroup$
    – Andrew
    Commented Nov 28, 2022 at 18:10
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    $\begingroup$ The most common (and fairly useful) treatment of reactions is in the Born-Oppenheimer framework, ie assuming nuclei are slow and follow classical movement while electrons are treated with quantum mechanics. When you write reactions on paper the bond breaking-bond forming process is a quantum process, but the regular electron counting methods give generally a good guess about them. The BO approximation goes to the toilet eg when light atoms tunnel (PCET and similar cases) or in case of many photochemical reactions. The diagrammatic versions are sill a good first guess, though. $\endgroup$
    – Greg
    Commented Nov 30, 2022 at 4:20

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The answer in short is Born Oppenheimer Approximation (I'm a physics grad student, by the way), and the fact that electrons are much lighter, or "more quantum", than atom nuclei.

In more details: Given nuclei are much heavier than electrons, and given typical temperature and pressure in chemistry. It turns out one can use Born Oppenheimer Approximation to treat electron quantum mechanically (using orbitals, for instance) while treating nuclei classically, and still get good enough results (for reaction barrier, for instance). Under Born Oppenheimer Approximation, the energy of a system, given a specific nuclei configuration, is given by electrons energy and electron-nuclei-interaction-energy calculated by quantum mechanics (assuming classical nuclei position) + nuclei energy calculated classically (assuming classical nuclei position).

There are a few cases where Born Oppenheimer Approximation fails in chemistry. For instance, proton transfer (movement of hydrogen) often need quantum mechanical treatment (like tunneling rate) if one wants to get good result (for reaction barrier or reaction rate, for instance) since hydrogen is the lightest of nuclei. Chemistry in astronomy and laboratory with extreme pressure and temperature might require quantum mechanical treatment of nuclei (for instance, superliquidity of Helium 3 requires quantum mechanical treatment of nuclei). Zero-point energy of nuclei vibration also require quantum mechanical treatment of nuclei.

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    $\begingroup$ When you mean proton transfer what exactly are you talking about? Would acid/base reactions count here? $\endgroup$
    – xasthor
    Commented Nov 30, 2022 at 8:19
  • $\begingroup$ @xasthor I'm not totally sure. I do know that {low barrier, long distance} reaction doesn't necessarily require quantum tunneling of H because thermal energy is enough to go over the barrier. {high barrier, short distance} reactions are strongly affected by tunneling because tunneling rate decay over distance quickly... continuing $\endgroup$
    – Bohan Xu
    Commented Nov 30, 2022 at 8:59
  • $\begingroup$ @xasthor I'm more of a physicist than chemist, but I feel acid base reaction tend to have {low barrier, long distance} (low enough for thermal energy to go over the barrier), especially when facilitated by coordination of water around ions. I have only read about how quantum tunneling of H matters in the context of tautomerization-like reactions where H is moving within the same molecule while breaking covalance bond {high barrier, short distance} $\endgroup$
    – Bohan Xu
    Commented Nov 30, 2022 at 9:13
  • $\begingroup$ If I understand you correctly, you are implying that in acid-base reactions, there is necessarily an intermediate phase where the H+ ion is solvated in water and this is transported over a distance, which isn't the case. Consider the acid-base reaction between HCL and NH3 for example. I don't think this would qualify as a "long distance" reaction $\endgroup$
    – xasthor
    Commented Nov 30, 2022 at 10:52
  • $\begingroup$ @xasthor I didn't say it well. I probably should leave the {especially when facilitated by coordination of water around ions} out of my explanation since it is not always the case and it fundamentally doesn't solve the problem. I should have said that typical acid base reaction tend to have low energy barrier (you can google "acid base reaction, typical energy barrier"), so it is not necessary to use tunneling to judge whether the reaction will happen or not. This is what I know for sure. $\endgroup$
    – Bohan Xu
    Commented Nov 30, 2022 at 14:38
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Quantum effects most definitely are important in chemistry,and can easily be observed even in bulk samples, such as the photoelectric effect. Put $\ce{H2}$ and $\ce{Cl2}$ in a flask (in a dark room), and nothing happens immediately because the activation energy to dissociate $\ce{Cl2}$ has not been reached. Hit the flask with a bright red light, and still nothing. Use even a weak UV source, though, just a single near-UV LED, and BANG. Not rocket science, but certainly quantum chemistry, worth a Nobel prize for Einstein in '21.

See a demo of the reaction. If you want to try it, enough UV can go through an ordinary borosilicate test tube to work. Caveat: Both $\ce{Cl2}$ and the resultant $\ce{HCl}$ are somewhat poisonous, and, with the bang, the glass container can shatter!

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    $\begingroup$ This reaction has radical mechanism, no kicking out electrons, like in photoelectric effect. $\endgroup$
    – Mithoron
    Commented Nov 28, 2022 at 22:14
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    $\begingroup$ @Mithoron, it is the same phenomena: wavelength longer than needed for activation has insufficient energy, no matter how many photons. Whether ionized, or moving to a higher energy level, e = hν is a quantum effect. Each photon is a quanta of energy. $\endgroup$ Commented Nov 29, 2022 at 1:42
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    $\begingroup$ Note for kiddies : "in '21" refers to 1921, not 2021. :-) $\endgroup$ Commented Nov 29, 2022 at 1:59
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    $\begingroup$ I agree that molecules absorbing specific frequencies is not the photoelectric effect and calling it so might be misleading to student (though both share the same underlying quantum mechanism). $\endgroup$ Commented Dec 1, 2022 at 21:36
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When we're reasoning about chemical reactions and their mechanisms (in organic chemistry in particular), the way we model the behaviour of molecules is almost in a “common sense” way.

When the reasoning happens in our heads and on paper, it is easier to use heuristics than quantum mechanics. The chemical reactions are governed by quantum mechanics, of course, but you can predict quite a bit through analogies to known reactions in your head without doing a quantum chemical calculation.

This works particularly well in organic chemistry because many reactions involved functional groups of a limited set of atoms (C, H, O, N, ...). Of course, organic chemists use almost the entire periodic table when it comes to reagents, but those are a given for a type of reaction, and you ask whether you can apply them to a new organic molecule, having tried them for a lot of cases already.

Is this because reactions occur in the bulk, and even though we are thinking about what is happening in terms of the behavior of individual molecules, that molecule actually represents some sort of average behavior of the bulk, and so quantum effects/weirdness are being averaged out and we can think of them acting in a more “common sense” way?

No, each single molecule has to react independently, so it does not help that the molecules are present in bulk (like it does for equilibrium thermodynamics). In fact, the "cheaper" computational methods such as molecular dynamics are not so helpful when trying to predict chemical reactions.

Of course I understand that the actual bonding and our understanding of chemical structures and things like that comes from QM based models.

Traditionally, QM was used to study very simple systems (dihydrogen reacting with proton, for example), and you had to extrapolate to more complicated systems. This is changing as methods and hardware become more powerful. Once you have a handheld device that can do a full QM calculation on the reaction you are attempting in the lab, I'm sure chemists in the lab will do a quick QM calculation before starting the wet chemistry, but we are not quite there yet.

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I think you say why don't we use quantum mechanics to calculate e.g., the trajectories of the molecules of a gas.

We could write a single wavefunction for all the molecules of the gas but remember since the Schrödinger equation is a partial differential equation, it gets very complicated.

So we use some approximation, which is not 'correct' but it is still a good approximation for our experiment e.g., when the # of molecules gets so big in thermal equilibrium we can say that the direction of the motion of the particles is random. That's why statistical mechanics was created in the first place.

Conversely some processes cannot be explained using only classical mechanics and these processes were unexplainable before QM. So yes, we look for a model that is close to the outcomes of the experiments and we can use it to make predictions for what will happen if we change the setup of the experiments a little bit. And if we don't push these models to the limit of their range then we can use them to understand better chemistry.

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