Category: Post-lecture

I have retired from the Reed College faculty, effective Sept 1, 2021. This Chem 201 site hosts materials that I created for the classes I taught between Fall 2008-2019. If you are looking for a current version of the Chem 201 materials, this is the wrong place to look. You need to consult the current instructors, Prof. Arthur Glasfeld + Dr. Alicia McGhee for Fall ’21.

I taught organic chemistry at Reed for 32 years (1989-2021) and at Pomona College for 4 years before that. Chem 201 was always a ‘big lift’ for me each year and I know that I demanded an equally big effort, if not more so, from the huge number of students who took the class. It was stressful and demanding for everyone involved. Even so, organic chemistry or ‘o chem’, (or ‘orgo’, if you insist) has been my favorite area of chemistry ever since my sophomore year of college (1972-73) and I have always looked forward to the opportunity to introduce a new crop of students to something that I had devoted so much of myself to. Thank you, students!!! You gave me everything you could and no o chem prof could have ever found a better set of comrades.

I also want to send a big “Thank You” to my colleagues in the Reed chemistry department who supported me in ways large and small, and to my colleagues in the IT/AV departments who supported our web sites and computer+projection systems over the years. I asked for a lot from all of you and you delivered. <3

Finally, I owe a very special “Thank You” to Tony Moreno, Digital Project Manager. This version (and many previous versions) of the Chem 201 and Chem 201-202 web sites would never have existed without Tony’s contributions. Tony, I see your creativity and thoughtfulness everywhere I look. =)

Understanding what molecules look like, how they move, what relationships exist between atoms, are all challenging mental tasks. Here are two tools that might help.

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The discovery of the electron in 1897 was followed just 14 years later by the discovery of the atomic nucleus in 1911. In 1913 Bohr proposed a model of the hydrogen atom in which the electron made perfectly circular orbits around the newly discovered nucleus (proton) only to see his theory replaced by Schrödinger’s more general theory, wave mechanics, in 1926. Wave mechanics has dominated the thinking of chemists ever since, but it has hardly been the last word on the matter. More subatomic particles have been discovered, and other forms of quantum mechanics have been suggested over the years (matrix mechanics, density functional theory, …) including theories (quantum electrodynamics, quantum chromodynamics, …) that go far beyond the simplistic thinking of chemists.

So what really happens when two electrons, or perhaps an electron and a positively charged nucleus, get really, really close to each other? Wave mechanics turns to Coulomb’s law for help, and Coulomb states that the force between these particles varies inversely with the square of the distance between them, that is, the force is proportional to 1/r^2. This would imply that the force (and the potential energy associated with it) approaches infinity as r approaches zero. This can lead to disturbing thoughts (what keeps electrons from ‘falling into’ the nucleus?) and disturbing mathematical problems (how do I work with a formula that busts its way to infinity?).

Nautilus recently emailed me an old article (“The Trouble with Theories of Everything”, 1 Oct 2015) that looks into these disturbing corners of science and concludes, “There is no known physics theory that is true at every scale—there may never be.” Coulomb’s law, wave mechanics, you name it – are designed to explained certain phenomena that appear on certain scales of time, space, energy, and so. It may be possible to extrapolate them to other scales successfully, but there are no guarantees. Caveat extrapolator!

Carbon, C

Show-stealing diva,

throw yourself at anyone,

decked out in diamonds.

And that pretty much sums it up. Carbon is awesome.

Interested in seeing how the other elements fare when filtered through haiku paper? Check out Elemental Haiku (Science, 4 Aug 2017) or, even easier, find them in this interactive periodic table.

Note: element 119 has not been synthesized yet so the poet has already gone where no scientist has been (yet).

What’s so special about the sunlight during an eclipse? Isn’t it the same old sunlight we see the rest of the time?

Yes, it is, but because the event is so interesting to look at, and because the normally blinding solar disk is partly blocked out, the temptation is to look, and look, and look. See “Chemistry explains why you shouldn’t stare at the solar eclipse without proper protection” (C&ENews, print 21 Aug 2017, online 14 Aug 2017).

The article explains the photochemical events that trigger retinal damage (the “heat” of the sunlight is not to blame) and it describes several options for safe viewing of the Sun. Here’s a bit from the article: (more…)

Predicting the outcome of an “opposite side attack” SN2 reaction can be confusing at first, but animations can help. Check out the SN2 animation at chemtube3D.com. To operate the animation, find the drawing of the chemical reaction and click on the forward reaction arrow.

Try to understand the simple reaction from multiple perspectives: 1) the C seems to push its way through its 3 H neighbors to get from leaving group to nucleophile, OR 2) the 3 H neighbors seem to back away from the approaching nucleophile and move to the leaving group’s side of the molecule. You can rotate the animation as it plays so that you can see it from different angles.

Another SN2 animation to watch: HS(-) + (S)-PhCHClCH3

The web is loaded with videos explaining optical activity and demonstrating polarimeters of various types (see Sorrell, Fig. 4.3, p. 114). Here are two SHORT clever videos from David Whyte (and his cheeky daughter?):

1. Home made polarimeter by David Whyte. (https://youtu.be/HP14LAEy9BY) Modern computer displays rely on liquid crystals and the light emitted by an LCD is polarized. David displays a yellow rectangle on his laptop screen so the yellow light emitted by the screen is a good approximation of polarized monochromatic (single wavelength) light. Next he loads some syrup (sucrose + water) into a transparent can on top of the screen. Finally, he films the screen+syrup setup through some polarized sunglasses and rotates the glasses back and forth. Things to notice:
   1. When he films the screen+syrup setup without the glasses in place, everything looks yellow and equally bright. You can’t see any effect of sucrose on the angle of polarization because your eyes are not sensitive to polarization angles.
   2. The first time he puts the sunglasses between the camera and the setup (0:31), the syrup goes black while the screen stays bright. Clearly, the syrup is rotating the plane of polarization, i.e., the light coming out of the syrup has a different angle from the rest of the screen. The syrup looks black because the light coming out of the syrup is rotated 90º from the sunglasses’ polarization.
   3. Three seconds later (0:34) he has rotated the sunglasses so that the screen goes black and the syrup is light. Again, this proves that the syrup is rotating the plane of the polarized light coming out of the screen. If the syrup were not optically active, the syrup and the screen would all go black simultaneously.
2. Home made polarimeter, #2 by David Whyte. https://youtu.be/CJS6CwL2eQU The previous video showed that syrup (sucrose) rotates plane-polarized light. This video shows that the angle is correlated with the path length of the solution. The same basic setup is used: computer screen (light source + polarizer #1) + sample + sunglasses (polarizer #2), but there are four samples: W (pure water), 1 (short layer of syrup), 2 (medium layer of syrup), 3 (tall layer of syrup). Also, in this video he holds the sunglasses steady and rotates the screen. Things to notice:
   1. Pure water, W, is achiral and optically inactive. Notice that the color and brightness of W matches that of the surrounding screen. Water has no effect on the angle of polarization.
   2. Syrup is optically active, but the amount of optical activity (the amount the sucrose sample rotates the plane of polarization) depends on the amount of sucrose in the light beam. The longest (tallest) sample, 3, deviates the most from pure water, i.e., it has the greatest effect on the plane of polarization. The shortest sample, 1, behaves almost identically to pure water. 2, as you might expect, falls in between.
   3. This video looks at a full 360º rotation of the screen polarization relative to the sunglasses. The screen should go dark twice during a full rotation: once when the light hitting the sunglasses is polarized 90º from the sunglasses’ polarization, and again when the light is polarized 270º from the sunglasses’ polarization. See if you can spot these two “go black” spots for each sample. (Hint: use the arrow that Whyte has drawn on the screen to read the angle; you should see a sample go black a second time when the arrow has reversed its direction from the first time the sample went black).