Khan Academy for Organic Chemistry – Part 2

by James

in Alkanes, Conformations, Organic Chemistry 1, Stereochemistry, Teaching

Khan Academy for Organic Chemistry, Part 2: Bonding, Conformations, and Stereochemistry

This second  installment of the guide to Khan Academy organic chemistry videos covers videos 13 to 26, covering the topics of chemical bonding, conformational analysis, and stereochemistry. It also goes into the naming conventions for alkenes.

Video #13
Title: “sp3 Hybridized Orbitals And Sigma Bonds”
Length: 16:23
Summary: Introduction to orbitals. The electron configuration of carbon is drawn [ 1s22s22p2].   The drawing of orbitals and bonding in methane is shown.  Everything is drawn really well actually. Methane (CH4) is drawn and the concepts of hybridization and sigma bonding are introduced.
Key Concepts/Skills: Introduction to how orbitals fill up for carbon, and how the tetrahedral structure for methane is explained by the concept of valence repulsion of orbitals. The equality of each of the C-H bonds is explained by hybridization. The concept of “sigma bonding” is introduced, where end-on-end overlap of orbitals provides bonding.
Nitpicky criticisms: In this video it’s not actually explained *why* CH4 is tetrahedral; quickly reviewing this would be helpful.

 Video #14
Title: “Pi bonds and sp2 hybridized orbitals”
Length: 14:13
Summary: Introduction to pi bonds. The sigma and pi orbitals are drawn out showing the bonding in ethene.
Key concepts/skills: How to draw sigma and pi bonds. Pi bonds are orbitals with “side on side” overlap. Why we can’t have rotation around pi bonds? Because this would result in breaking the “side on side” overlap.  Again, he is very good at drawing.
Nitpicky criticisms:  draws out dashes and wedges for the first time, without explicitly introducing what this notation means. Also, it would be helpful to draw out the second pi bond for ethyne.

Video #15
Title: “Newman Projections”
Length: 14:22
Summary: The structure of methane is drawn, and then ethane. Then ethane is drawn in 3-D with a ball and stick model, followed by a sawhorse projection. Then, this drawing is rotated to show the Newman projection of ethane. The “staggered” and “eclipsed” forms of ethane are drawn, and their energies are compared.
Key concepts/skills: The concept of conformations as being 3-D structures of different shape arising from bond rotations. How to do simple bond rotations.  “Eclipsed” and “staggered” conformations, and why “staggered” is more stable. How to draw simple Newman projections. The concept of “dihedral angle”.
Criticisms: none
Other comments: He mentions “torsional strain” as being like when you wind up a spring, and it naturally wants to return back to its original form, which is a good analogy.

Video #16
Title: “Newman projections 2”
Length: 11:12
Summary: The Newman projection of butane is drawn, and the different conformations are explored. The terms “anti”, “syn”, and “gauche” are introduced.
Key concepts/skills: how to go from a “ball and stick” model to a Newman projection. How to rotate a Newman projection.  Introduction of the terms “anti”, “gauche”, and “syn”; the concept that bulky groups “syn” to each other have higher potential energy (less stable).
Criticisms: None
Other Comments: Going from a line diagram to a “ball and stick” diagram, followed by an “angled” ball and stick, to a Newman is an effective way to show the progression.

Video #17
Title: “Chair and Boat Shapes for Cyclohexane”
Length: 12:29
Summary: Khan draws flat cyclohexane and demonstrates that it doesn’t accurately portray the tetrahedral nature of carbon.  Cyclohexane is then drawn out in the chair conformation, identifying the axial and equatorial hydrogens. The boat form of cyclohexane is also drawn with all its hydrogens. Finally, cyclohexane is shown in equilibrium between its two chair conformations and it is demonstrated that all axial hydrogens become equatorial and vice versa.
Key concepts/skills: Cyclohexane chair conformation; axial and equatorial; chair flips; how a chair interconverts all “axial” groups to become “equatorial” positions.
Nitpicky criticisms: When putting the hydrogens on the chair for the first time, Khan could be more explicit in saying that the axial hydrogens alternate “straight up” with “straight down”, while equatorial alternate “somewhat up” and “somewhat down”; this is more informative than saying “like that”. At 8:20 when the energies of the chair and boat conformations are being compared, only the “flagpole” interactions are considered; it should also be mentioned that all of the C-H bonds in the cyclohexane are staggered, whereas the boat has eclipsing interactions.  Finally it could be very helpful to show a chair flip “in action” and how it occurs through the twist-boat conformation.
Red Flags: The word “configuration” is used instead of “conformation” in this video.

Video #18
Title: “Double Newman Diagram for Methylcyclohexane”
Length: 14:38
Khan draws “flat” methylcyclohexane and then both “chair” forms for methylcyclohexane, and mentions that the methyl group is less stable in the axial position. The Newman projections of both chair forms are drawn and it is shown that the chair form with axial methyl has an extra gauche interaction that is not present when methyl is equatorial.
Key concepts/skills: axial position is less stable than equatorial position; how to draw the Newman projection of a cyclohexane.
Nitpicky criticisms: None
Red Flags: Just the incorrect continuation of “configuration” as above.

Video #19
Title: “Introduction to Chirality”.
Length: 6:46
Summary: A left hand and a right hand are drawn, and it’s shown that these are non-superimposable mirror images, and therefore “chiral”.  There are two concepts for chemistry: chiral molecules and chiral atoms. Chiral molecules  are not superimposable on their mirror image. Chiral atoms have carbons bonded to 4 different groups. Draws the two mirror images for 1-bromo-1-fluoroethane and shows that they are not superimposable. It is therefore a chiral molecule with a chiral center.
Key concepts/skills: Chiral centers; chiral molecules as having “non-superimposable mirror images”.
Criticisms: None

Video #20
Title: “Chiral Examples 1”
Summary: The molecules chlorocyclopentane, bromochlorofluoromethane, and 1-bromo-1-chloro-2-fluoroethane are drawn and the chirality of each of these molecules is compared.
Key concepts/skills: Planes of symmetry; enantiomers; stereoisomers
Nitpicky criticisms: It might have been faster to point out the plane of symmetry in chlorocyclopentane instead of rotating. Around 5:50 it might be better if the “rotated” molecule is shown so that we can see why it’s not superimposable on its mirror image. At 6:20 says that these molecules “sometimes have different chemical properties” but doesn’t say when [this will be confusing, because enantiomers only have different chemical properties when in a chiral environment].  It’s strange that “enantiomers” is brought up as a topic before the subject of “constitutional isomers” has been mentioned.  The discussion on “stereoisomers” from 6:50 to 7:30 is really muddled until it’s finally mentioned that stereoisomers have the same connectivity but different arrangement in space. At 8:00 there is a mea culpa for the “configuration” mistakes of the previous videos.
Red Flags: Around 10:30, since the 3-D structure of the molecules is not drawn, it is not clear that they are actually enantiomers.

Video #21
Title: “Chiral examples 2”
Length: 10:19
Summary: The molecules 2-hydroxyhexane and 1,3-difluorocyelopentane are drawn out and their chirality is discussed.
Key concepts/skills: Chiral centers, chiral molecules, planes of symmetry. How to identify chiral centers.
Nitpicky criticisms:  One of the problems with drawing chains with substituents pointing straight up and straight down is that you have to redraw them if you want to show stereochemistry [thinking of the second example here].
Red flags: For 1,3-difluorocyclopentane, Khan doesn’t show the stereochemistry on the ring. Therefore it’s not proper to assert that the molecule lacks a plane of symmetry. While cis-1,3-difluorocyelopentane has a plane of symmetry, trans-1,3-difluorocyclopentane is actually chiral. This should be corrected.


Video #22
Title: “Cahn-Ingold-Prelog System for Naming Enantiomers”
Length: 11:02
The two enantiomers of 1-bromo-1-fluoroethane are drawn and they are named as R and S.
Key concepts/skills: The Cahn-Ingold-Prelog naming system; how to apply this to naming molecules.
Nitpicky criticisms: At 2:37 he says that they “polarize light differently” ; this should be corrected to say “rotate plan-polarized light in different directions” and expanded on a little bit.

Video #23
Title:  “R,S (Cahn-Ingold-Prelog) Naming System Example 2”
Length: 11:08
Summary: The first ~4 minutes is just naming the molecule. Then, it goes through how to assign R and S to 1-bromo-3-fluoro-2,3-dimethylbutane.
Key concepts/skills: Assigning R/S to stereocenters; rotating molecules;
Nitpicky criticisms: None

Video #24
Title: “Stereoisomers, Enantiomers, Diastereomers, Constitutional Isomers, and Meso Compounds”
Length: 13:36
Summary:  This video compares 1-cylobutanol and tetrahydrofuran (constitutional isomers); (S)-1-bromo-1-fluoroethane  (2 versions of the same molecule); 2-chloro-4-fluoropentane (R and S enantiomers),  2 diastereomers of 2-bromo-4,6-dichloroheptane, and cis-1,2-dibromocyclohexane (a meso compound).
Key concepts/skills: Recognizing relationships between types of isomers through doing bond rotations (enantiomers, diastereomers, or the same); meso compounds
Nitpicky criticisms:  My main criticism of this video is that the method isn’t very general and the chosen molecules are very simple.  It takes a long time to rotate molecules. It’s easier to determine R/S for two given molecules and then compare them to tell you whether they are enantiomers, diastereomers, or the same. Also, through the video (especially 4 minutes through 6 minutes) he struggles with the right terms for describing stereoisomers. Should be: “same connectivity, different arrangement in space”.

Video #25.
Title: “Cis trans and E-Z Naming Scheme for Alkenes”
Length: 4:56
Summary: The cis and trans isomers of 2-butene are drawn and alternatively named as Z and E 2-butene respectively.
Key skills/concepts: The terms “cis” and “trans” for alkenes.
Nitpicky criticisms: It might be helpful to point out that these molecules are diastereomers and that they have different physical properties (melting points, boiling points) as well as different chemical properties. Also it is better to call the methyl groups “substituents” rather than “functional groups”.

Video #26
Title: “Entgegen-Zusammen Naming Scheme for Alkenes Examples”
Length: 6:04
Summary: The alkenes (Z)-4-methylheptene and (E)-3-bromo-oct-3-ene are named.
Key concepts/skills: Using the Cahn-Ingold-Prelog system to assign  (E) or (Z) to alkene isomers.
Nitpicky criticisms:  Again I would say “substituent” instead of “functional group” here.

My overall impression is that these videos are an OK introduction to these subjects, if lacking in detail.  Khan is quite talented at drawing and his somewhat spontaneous style is compelling, if not always precise. Of these videos I think the two sections that need the most work are those on 1) converting a flat cyclohexane to its chair forms, and 2) distinguishing molecules as enantiomers, diastereomers, or the same. These are two of the core skills of first-semester organic chemistry and they are not taught with sufficient detail to be truly useful for someone taking a course. Also, it would have been good to include a section on constitutional isomers before stereochemistry was introduced.   However, as a series of videos to give a general overview of the subject, these videos are fine and generally free of glaring errors.

Next Post – Khan Academy Videos For Organic Chemistry, Part 3

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{ 5 comments… read them below or add one }


“enantiomers only have different chemical properties when in a non-chiral environment”

Think you mean ‘in a chiral environment’



oops. Thanks for the spot – fixed!



I really like this series, James. I’ve heard more than a few organic chemists complain about these videos, but it’s good to see a thorough analysis.



Thanks Mike. If this is useful to people, I’m happy.


Med School Odyssey

I found that the videos on the calculus sequence were rather disappointing as well. But, it probably helps a lot of people that would otherwise have gotten left behind in their normal class.


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