Khan Academy for Organic Chemistry – 3

by James

in Teaching

For the previous videos in this series, see Part 1 and Part 2

In this segment we’ll walk through videos 27-37 of Khan Academy for organic chemistry, covering mostly substitution reactions.

Video #27: Introduction to reaction mechanisms
Length: 11:22
The video shows the reaction of H-Br with 1-pentene to form 2-bromopentane.
Key concepts/skills: Arrow pushing, electronegativity as a factor determining electron density.
Nitpicky criticisms: It would have been good to start with the reaction of a different alkene (say, ethene) where Markovnikoff’s rule does not come into play. Here, there’s some question as to why the bromine ends up on the most substituted carbon. Also, if I say I don’t like referring to molecules as “guys”, do I sound like too much of a grump?
Red flags:  In textbooks and courses across North America (and the world), curved arrows show the movement of a pair of electrons in reactions. However, in these videos, Khan depicts curved arrows as showing the motion of a single electron. For example, in the first reaction, the arrow is showing the movement of a single electron from the double bond to the hydrogen of H-Br. The arrow is just meant to show the movement of the electron from the “far” carbon of the alkene to be donated to the hydrogen. The electron that is part of the “near” carbon stays in the same place. Hence, we have a lone pair of electrons bonded to hydrogen; the “far” carbon has lost a carbon, leading to the formation of a carbocation, the “near” carbon retains its electron, the hydrogen receives an electron from the “far” carbon and has an electron “stolen” from it by the bromine, which becomes Br(-).

While this might sometimes be a good way of keeping track of charges, it’s going to lead to major headaches later on when reactions that truly do deal with the motion of single electrons (radical reactions) arise.

Why does this matter? It’s true that arrow-pushing is a convention to show the movement of electrons, and in that sense, is somewhat arbitrary. However, if you’re learning conventions from a textbook or course on one hand, and Khan Academy on the other, this is going to lead to considerable confusion. I don’t think it’s a good idea to present a series of videos where a convention is used in a different way to the way it’s conventionally used.

 Video #28: Markovnikov’s Rule and Carbocations
Length: 9:09
Summary: The reaction of 1-pentene with H-Br to give 1-bromopentane is shown, and it is asked why this is not formed as the major product instead of 2-bromopentane. It is shown that this is due to the preferential stability of secondary carbocations versus primary carbocations, leading to the distribution of products we know as “Markovnikov’s rule”.
Key concepts/skills: Markovnikov’s rule, carbocation stability (tertiary > secondary > primary). Introduction of the terms primary, secondary, tertiary.
Nitpicky criticisms: Instead of saying that it “comes from Markovnikov’s rule” (5:43), I would say it “expresses something known as Markovnikov’s rule”. The product distribution is actually a result of carbocation stability.
Red flags: Just the arrow pushing.


Video #29: Addition of Water (Acid catalyzed) mechanism
Length: 13:23
Summary: The reaction of 2-methyl 2-pentene with H3O(+) to give 2-methyl-2-pentanol is shown (addition, and then proton transfer). Key concepts/skills: Markovnikov’s rule, arrow pushing,  deprotonation.
Nitpicky criticisms:  At 2:50 it’s said that “oxygen doesn’t like having this positive charge”. There’s a missed opportunity here to say that the formal charge is on oxygen, but the actual positive charge is on hydrogen.  I wouldn’t say “the carbocation attacks that oxygen” (7:05).
Red flags: Just the arrow pushing, but here it shows an example of how the arrow pushing can lead to confusion. When it’s said (5:56)  that “this was the electron it always had, and this is the one it just got back from the hydrogen”, it might give the viewer the impression that electrons have labels – which they do not. They’re indistingushable. I hope students don’t end up worrying about “which” electron to move.
“Attaboy”: Good to show the equilibrium arrows for protonation/deprotonation.

Video #30: Polymerization of Alkenes With Acid
Length: 12:04
Summary: The polymerization of vinyl chloride to form a tetramer is shown.
Key concepts/skills: Polymerization, Markovnikoff’s rule, arrow pushing.
Nitpicky criticisms: None
Red flags: Just the arrow pushing.


Video #31 SN2 Reactions
Length: 11:31
Summary: The reaction of bromoethane with hydroxide ion is shown. The transition state with partial bonds is also drawn.
Key concepts/skills: Substitution reactions, the SN2 reaction, nucleophiles, leaving groups, transition states.
Nitpicky criticisms: Rather than saying that a nucleophile “likes other people’s nucleuses”, it’s better to say it “donates a lone pair of electrons” – this way you can tie it back to Lewis basicity. Would be good to show partial charges on the C and Br. Showing HO(-) forming from H2O is not impossible, but improbable; usually we get OH(-) just from adding NaOH or a similar species. It would be good to answer the question – “what makes Br(-) a good leaving group here?”.
Red flags: Just the arrow pushing.


Video #32 Introduction to SN1 reactions
Length: 12:02
Summary: The SN1 reaction of 2-bromo-2-methyl propane with water is shown.
Key concepts/skills: The SN1 reaction, substitution, carobcations, water as a weak nucleophile.
Nitpicky criticisms:  It would be good to show that the carbocation is flat, this way you can say that the nucleophile can come in from either side. It would also not hurt to say more explicitly that the reaction is fastest for tertiary, followed by secondary and slowest for primary, and this is because of carbocation stability.
Red flags: Just the arrow pushing.


Video #33 Steric hindrance
Length: 10:20
Summary: The rates of reaction between iodide ion and methyl fluoride, ethyl fluoride, isopropyl fluoride, and tert-butyl fluoride are compared, and it is stated that the SN2 will be fastest with methyl fluoride due to less steric hindrance.
Key concepts/skills: steric hindrance
Nitpicky criticisms: It might be good to mention that the reason we have to have a backside attack is because there is an empty orbital there which the nucleophile can donate to. The discussion at 9:07 is kind of tautological.
Red flags: Fluoride as a leaving group. This is a serious error. Fluoride is essentially never a leaving group in SN2 reactions, because it forms unusally strong bonds. This should be fixed. Perhaps use iodide as the leaving group, and have the nucleophile as HO(-) or CN(-). But this should be fixed as soon as possible. [Edit, March 13/2013 – this has been fixed, follow this link

Video #34 SN2 stereochemistry
Length: 10:01
Summary: This video shows the reaction of 2-bromobutane with hydroxide ion, and it is shown that the reaction proceeds with inversion of stereochemistry. 
Key concepts/skills: Inversion of stereochemistry, the SN2
Nitpicky criticisms: Nothing major.
Red flags: Arrow pushing. At 0:23 it’s implied that hydroxide ion is a much weaker nucleophile than iodide, which isn’t true.


Video #35  Solvent Effects on SN1 and SN2 reactions
Length: 14:14
Summary: The SN1 and SN2 reactions are compared, using generic substrates, nucleophiles, and leaving groups
Key concepts/skills: Solvents (polar protic, polar aprotic), SN1, SN2, inversion
Nitpicky criticisms: Diethyl ether (Et2O) isn’t the best choice as a polar aprotic solvent (it’s borderline nonpolar). A better choice would be acetonitrile or DMSO. Also, protic solvents are defined as something that “in solution some of its protons might get knocked off”. It would be better to mention hydrogen bonding – this is also why nucleophilicity is decreased in polar protic solvents. Finally, it would be good to show a mixture of retention and inversion for the SN1 case.
Red flags: Just the usual.


Video #36 Nucleophilicity (Nucleophile Strength)
Length: 13:54
Summary: The nucleophiles I(-), F(-), H2O, and HO(-) are compared; polar protic solvents water and alcohols are compared with polar aprotic solvents (diethyl ether).
Key concepts/skills: Nucleophilicity, the effect of solvent on nucleophilicity, polar vs. polar aprotic solvents
Nitpicky criticisms: Right off, it would be good to say precisely that a nucleophile donates an “electron pair”, not “extra electrons”. Also when we say that a nucleophile gives away protons to a “nucleus”, be careful, because H+ is a nucleus, and when a lone pair gives electrons to H+, it’s called a “base”. At 5:00 there’s an opportunity to say that protic solvents have hydrogen bonds. I’m not sure that it’s clear from the discussion around 11 minutes that fluoride forms stronger hydrogen bonds, and therefore will be less reactive.
Red flags: None


Video #37: Nucleophilicity Vs. Basicity
Length: 12:47
Summary: The hydrogen bonding network around fluoride is shown. Ions are ranked according to basicity [HO-, F-, Cl-, Br-, I-] and their nucleophilicity in polar protic [I-, OH-, F-] and aprotic [OH-, F-, I- ] solvents. It’s also shown that hydroxide ion is a better nucleophile than a bulky alkoxide due to steric hindrance.
Key concepts/skills: Basicity, nucleophilicity; how nucleophilicity is affected by steric hindrance.
Nitpicky criticisms: Where does the ranking of nucleophilicity I- > OH(-) > F(-) in a polar protic solvent come from? It would be good to mention the trends with nucleophlicity, how it changes as you go across and down the periodic table.
Red flags:  More than most videos in this series, the discussion here is really not clear. It’s said that nucleophiles are “good at reacting”. What does this mean, exactly?  How is this different from basicity?What’s missing here is a clear discussion. What’s I’d say is this: Both nucleophiles and bases donate a lone pair of electrons. In the special case where the lone pair is donated to a proton, we say it’s acting as an “acid” .In all other cases, we say it’s acting as a “nucleophile”. Because acid-base reactions are frequently reversible, we can measure equilibria. However, many reactions of nucleophiles with atoms other than protons (e.g.) carbon are not reversible; so we measure according to rate instead. Nucleophilicity increases as an atom can give up its electrons more easily, hence it increases going to the left and down the periodic table; however, in polar aprotic solvents, the trend down the periodic table is reversed.


I thought the first 26 videos (mostly on nomenclature) were fine, but videos 27-37 have serious problems. It’s not clear to me from the videos that a full understanding of key concepts like nucleophilicity and leaving group ability are properly conveyed. Furthermore, the system of arrow pushing is very different than that used in standard textbooks and in organic chemistry courses. I’m looking forward to future videos from Khan Academy which improve on these, especially video #33.


Next Post – Khan Academy Videos For Organic Chemistry, Part 4


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{ 3 comments… read them below or add one }


Whoa, things are getting juicy now… :-)

On the curved arrows issue, I think I see the spirit of his approach—he’s trying to exhaustively illustrate the fate of every electron in the intro video. This spirit is misguided, IMO. Aside from dangerous intermingling with the “true” convention (which does have deeper meaning, insofar as curved arrows represent orbital interactions), I feel like this approach is missing the forest for the trees. Focusing in so closely on single electrons promotes tunnel vision.

On fluoride as a leaving group…WTF?! Of all the possible leaving groups in the world…a freaking iodonium salt would’ve been a better choice. Yikes.



I agree that the convention has deeper *meaning*, it’s just that the convention chosen – “arrows” – is artibrary. But perhaps I’m splitting hairs….
Agree that trying to keep track of every single electron is ultimately an exercise in futility.


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