Archive for the ‘Coursework’ Category

WWWTP? – Lab Decor Edition

Wednesday, October 19th, 2011

Today’s edition of What’s Wrong with this Picture? was sent in by an astute reader from Atlanta:

I’ve been a reader for a while, and when I saw these doors and signs on all of the chemistry labs at the new Undergraduate Learning Commons at Georgia Tech today, I immediately thought of your blog.

 

Incidentally, the missing “T” in the first picture is not the answer (the theft of “T”s from campus signs is a tradition at Georgia Tech). The problem, of course, is the myriad of Texas carbons in these Lewis structures. While I love the H2C= groups bonded directly to the benzene rings, what really gets me going are the triple bonds at the bridgeheads of the fused ring systems. Brilliant.

I think I’ll have to retire the WWWTP genre, because I can’t think of a worse place to post fakakta Lewis structures than the entrance of an orgo lab designed to teach undergrads to learn chemistry. This is the Sgt. Pepper’s of chemistry mistakes. Game over.

Do Starfleet Captains Really Need Orgo?

Monday, October 10th, 2011

Pre-meds often wonder whether they really need a year of organic chemistry, but what about prospective Starfleet officers? Will organic chemistry still be important for explorers in the 24th century?

Apparently not. (Skip to 7:45)

 

 

Mukaiyama Thioester Synthesis

Sunday, September 25th, 2011

I have made it a rule not to participate in blog carnivals. There is something disturbing about them. Perhaps it’s the association of carnivals with fun, which I try to limit in my life. Instead of organizing and participating in “carnivals”, I do exactly the same thing and call them “roundtables”. It’s so much more professional and so much less fun.

But ever since neutrinos decided to disobey the speed limit, I’ve been reconsidering my adherence to all of the rules in my life—including my self-imposed prohibition of carnivals. The good people at C&EN are hosting a blog carnival this month in honor of the International Year of Chemistry, and I feel strangely compelled to participate. The subject: “Your favorite chemical reaction”.

Fortunately, I didn’t need to conduct my usual 200 hours of background research to write this post, because I actually wrote it in January 2007. My favorite reaction is the same now as it was then:

 

I came across the above reaction while thumbing through a random issue of Chemical Reviews whilst consuming a carton of curry chicken from Yenching Restaurant. It looks like the reaction can be traced to this paper by Mukaiyama from 1970. Much like Charlie Brown’s obsession with a bit of cartoon strumpet known to him only as the little red-haired girl, I find myself in the predictament of having fallen in love with a reaction that has no name. But a reaction so lovely should not have to go nameless for a minute longer. Henceforth, the reaction shall be known as the Mukaiyama Thioester Synthesis in all lands and kingdoms for perpetuity. Go forth and spread the gospel. Yields are risen.

Here is what I believe to be the (shorthand) mechanism for this dandy:

What do I find so compelling about this beauty of a reaction? Perhaps it’s the involvement of my favorite compounds, thioesters? Perhaps it is the generation of a notoriously strong phosphorus-oxygen bond to serve as the driving force for the reaction? Perhaps it is the neat nucleophilic attack of the phosphine on the disulfide in a process that must be similar to thiol-disulfide interchange? Perhaps it is the fact that this single reaction has all of these things wrapped into one? I don’t know.

And that’s all I have to say about that.  Having looked over the other entries in the carnival, I find it unfortunate how far off-base the other contributors have been.  There is nothing about any other reaction that could justify its being someone’s favorite above Mukaiyama Thioester Synthesis. The reaction is clearly the greatest in history.

Back-to-School Trick Questions

Tuesday, September 14th, 2010

The kids are back in school, which means it’s time to mess with their heads.  Since the first week of undergrad orgo is usually devoted to a review of electronic structure and bonding, why not try this on for size:

Fake Problem Set #1.  (Insert fake instructions)  NOTE:  Draw all resonance structures where appropriate.

1)  The protons shown in green for 2,4-pentanedione (I) are roughly 10^40 times more acidic that those on n-pentane (II).  Provide an explanation. 

pentanedione and pentane

2)  The protons on benzene (III, C6H6) are roughly 10^7 times more acidic than those on n-pentane.  Provide an explanation.

benzene

3)  Boric acid (V) is a weak acid in water.  It is roughly a million times more acidic than methanol (IV).  Provide an explanation for the acidity of boric acid (by drawing chemical structures).

 boric acid and methanol

* All acidities based on pKa values in water (either measured or extrapolated) in  Evans’ pKa table.

Answers after the jump…

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I Judge People By Their Grammar and Knowledge of Phenol

Saturday, March 10th, 2007

Some commenters in a previous thread took umbrage at the fact that I admit to judging people by their grammar. Well, I do, and I’m not going to change anytime soon. I’ll put poor grammar on par with poor hygiene, dressing like a slob, and bad table manners—while they don’t automatically invalidate a person’s ideas, they will cause me to treat anything the person says with more skepticism than usual. With respect to the four errors I found in the first paragraph of this recent paper from Org. Lett., the misplaced apostrophe in “Evan’s” was the most aggravating. While the chemistry in the paper was good, as The Chem Blog has noted, the authors’ lack of attention to detail was borderline disrespectful. I expected more from one of the most storied labs in synthetic organic chemistry.

A lot of people will complain, “So what if I make a few mistakes? Why don’t you focus on the ideas?” That’s the thing: I want to focus on your ideas, so why don’t you stop whining and learn to write properly? The rules of grammar are not up for discussion—just follow them out of courtesy to your readers. Grammatical errors are distracting and will cause them to lose sight of what you’re writing. If you are someone who has no trouble reading documents riddled with mistakes, that’s great, but when you are writing, you aren’t writing for yourself.

While grammar shouldn’t be the sole criterion for evaluating intelligence, I will admit to judging some things by a relatively obscure set of criteria. For instance, I have a list of favorite subjects for judging textbooks and course packets. One of the first things I do to determine the quality of a sophomore organic textbook is to look in the index for phenol. As you all know, phenol is more acidic than “standard” aliphatic alcohols. If you took a survey, most people would ascribe this fact to a resonance effect by drawing the following structures:

There are a number of variations on this theme, including drawing out all of the unhybridized p orbitals and showing that an orbital on oxygen containing a lone pair can overlap with the pi system, thereby allowing for increased delocalization of the extra negative charge density.

It turns out that an inductive effect—not a resonance effect—is the predominant reason for the increased acidity of phenol relative to aliphatic alcohols. Whereas aliphatic alcohols have a C(sp3)—O bond, the carbon to which the hydroxyl group is bonded in phenol is sp2 hybridized. The increased s-character of the carbon orbital used to form the C—O bond makes it more electron withdrawing, which leads to greater stabilization of the conjugate base of the alcohol. For the purpose of comparison, look at the pKa of phenol compared to that of enol tautomer of acetone:

Even though you can only draw two resonance forms showing delocalization of the extra negative charge in the conjugate base of the enol (vs. four for phenol), the acidities of the two protons differ by less than an order of magnitude. For those interested, these data come from Evans’ Chem 206 lecture notes (Lecture 20, restricted access), where the point is hammered home in glorious detail. Professor Evans’ PowerPoint slides should be framed and displayed in the Smithsonian.

While we’re discussing phenol and errors, let me also use this example to illustrate one of the main problems with Wikipedia. Wikipedia is great, but it is home to a number of edit-happy users who think they know more than they actually do. If you look at the discussion page for phenol, someone actually addressed the resonance vs. inductive effect argument, but was unceremoniously (mis)corrected by another user, who references an incorrect explanation on the Internet. Thus, the main article (as of today) gives the incorrect (resonance > inductive) explanation:

Phenol has a limited solubility in water (8.3 g/100 ml). It is slightly acidic: the phenol molecule has weak tendencies to lose the H+ ion from the hydroxyl group, resulting in the highly water-soluble phenoxide anion C6H5O. Compared to aliphatic alcohols, phenol shows much higher acidity; it even reacts with NaOH to lose H+ whereas aliphatic alcohols do not. This is due to orbital overlap between the oxygen’s lone pairs and the aromatic system, which delocalizes the negative charge throughout the ring and stabilizes the anion. This effect is attenuated, however, due to oxygen’s relatively high electronegativity. [1]

God knows that we in the chemical blogosphere love the Wikipedia, but read it with skepticism.

This concludes today’s lesson. Your homework for the weekend is to find all of the grammatical errors in this post. For extra credit, find an error in a chemistry article on Wikipedia, fix it, and brag about having done so in the comments. Class dismissed.

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Trick Questions From Orgo

Monday, November 27th, 2006

Part of the fun of being a teaching assistant is getting to mess with undergrads’ heads. It’s more fun when the undergrads are pre-meds, and even more fun when they’re in the middle of their hardest course, organic chemistry. I was cleaning up my hard drive and came across three of my favorite trick questions, shown below. For best results, use them on exams rather than practice tests or problem sets.

1. Draw all resonance structures for deprotonated benzene (I).
2. Between II and III, which molecule has the larger dipole moment?

3. Show the products of the following three reactions assuming that one equivalent of methylmagnesium bromide is used in each:

 

Answers after the jump…

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