Archive for the ‘Organic’ Category

Orgo Thursdays

Monday, August 10th, 2015

ed_academic_bigOne of the nice things about being a professor is that you have the agency necessary to successfully garner support for causes you feel are worthwhile. Earlier this year, I brought to SLU something that I had sorely missed from my time as an undergrad at NYU: organic division problem sessions. These were held once a month during the school year and worked as follows:

Each organic group took turns hosting the sessions. The hosts would be responsible for bringing pizza, beer, and 3 or 4 hard, graduate-level organic problems. The organic students and faculty would gather at 6 pm, eat, drink, and work the problems. Volunteers would put up their answers, the audience would nitpick and argue, the faculty would weigh in with suggestions, and if no one could figure them out, the people who brought the problems would set us straight.

The attendance of organic graduate students was expected, and undergraduates were welcome to attend. In something of a paradoxical twist, I think these sessions were instrumental in both (i) making me appreciate that organic chemistry is hard and (ii) making me feel like organic chemistry was something I could do.

At Harvard, I attended Christina White’s monthly organometallic sessions, even though I was the dumbest participant by far. Each person was responsible for bringing one slide that summarized a recent paper from the literature. While these weren’t problems, there was a fair amount of arguing over mechanisms. The White Lab’s departure to Illinois marked the end of these sessions for me. It’s kind of unfortunate that Harvard had nothing else—that I know of—considering the rich history of late-night organic chemistry seminars at Harvard led by Woodward.

Earlier this year, I decided to champion these blasts from the past and start one at SLU.

On the third Thursday of every month, I host a voluntary organic problem session. I bring pizza and three graduate-level problems, and the students work them over, present ideas, and face my ridicule—or occasionally, approbation. Usually I steal problems from texts, but if I’m feeling saucy, I’ll write them based on interesting papers I’ve come across and stashed away.

While attendance at Orgo Thursdays is completely voluntary—except for my grad students, for whom the session replaces group meeting that week—we’ve averaged 12 participants over the first seven sessions. That’s makes the sessions just a shade smaller than those at NYU, and isn’t too shabby given the size of our department.

Now that I’ve seen these sessions from both sides of the table, I am convinced of their value in a number of areas:

1. For any skill, if you don’t use it, you lose it. The problems keep students and me thinking about fundamental course material long after final grades are in the books. The continued practice is going to help our grad students become better teachers and perform better on their comprehensive exams, which are taken in the summer between their second and third year.

2. There is something to be said for placing students in uncomfortable situations where they have to think on their feet and be brave. This is a life skill that classes often don’t focus on developing.

3. These sessions are a great opportunity for everyone to interact with people from other research groups. I believe strongly that departments should actively foster wide collegiality, where students and faculty have meaningful interactions not only with their labmates, but with people in other labs. Such an environment is so much more enjoyable and supportive than when each group is an island.

4. These sessions help me get to know our students better. It’s never a good situation when a professor has to write a ‘third’ rec-letter for a student he hasn’t talked to since a class four years ago.

5. The problem sessions give undergrad students an opportunity to stay involved in organic chemistry after their sophomore classes in the subject are done. Undergrads also get a taste for what graduate school is like, given they are working graduate-level problems alongside our graduate students. When I was an undergrad, it was empowering to participate in these sessions.

My plan is to keep hosting Orgo Thursdays until I run out of problems or money to buy pizza. So long as people keep coming, I assume they see value in the activity too.

Textbooks Make Me Feel Dirty

Monday, August 3rd, 2015

ChemBark Ed on Dollar BillWe’re three weeks away from the start of the semester at SLU, and this time of year always brings the first wave of e-mails from the next class of students. While these messages vary in length and tone, they can generally be distilled to one question: “Professor, what do I really need to buy for your course?”

Can I use the previous edition of the text? Do I really need a model kit? Do I really need the model kit on sale in the bookstore? Can I share my model kit with a friend? Do I have to buy the subscription for the online homework?

Whenever I read these e-mails, a part of me dies inside. I feel their pain. They’ve just paid their bills for thousands of dollars in tuition, with two more years of it to go. And now, after absorbing that massive hit, they’ve got to scrounge up another $375 dollars for my coursepack. It’s a slap in the face.

The cost of these materials makes me sick, and the prices are rising at an astounding rate. For my college organic text, I paid less than half of what students are asked to pay today. Are today’s books really worth double my book, which remains a valued reference on my office bookcase? Has our understanding of introductory organic chemistry really changed that significantly in the last 15 years? No.

I’ll be teaching Organic Chemistry I for Majors again and using the same coursepack we did when I arrived at SLU.  It contains: (i) the textbook, (ii) the solutions manual, (iii) a plastic model kit, and (iv) a subscription to the online homework assignments. That all costs about $375 when purchased together.

Three hundred and seventy-five American dollars!

While I could easily point the finger at the publishing companies as the villains that they are, ultimately, they are not the problem—I am. After all, I’m the one who assigns the books for my course. And for that, I’m truly sorry, but allow me to explain:

While there are a dozen good organic texts, I think we can all agree that it makes sense for a class to adopt a single textbook. As a teacher, I literally want everyone on the same page, with a precise understanding of what information everyone is responsible for. In the absence of a strong external force, inertia will govern this decision. It makes sense for an instructor or department to stick with the book it used the previous year, because the switching costs of an instructor having to rework the syllabus, slides, and order of practice problems can introduce a lot of unnecessary work. And there are benefits to students when we use the same book as the year before, because they can buy a used version. Furthermore, they can get something out of borrowing their friends’ old notes and exams.

Now, here’s where the publishing industry appears and sinks in its fangs. The used-book market poses a serious threat to their revenue stream, because they only make money by selling new copies. It’s the bookstores and old students who make money from the used-book market. So, what do the publishers do? Release a new edition! By releasing a new edition, the publishers can (i) find professors to drive orders of new books and (ii) stop printing the old edition so colleges can’t find enough used copies of it, forcing adoption of the new edition.

These new editions usually contain few or no substantive changes relative to the previous edition. It can be as silly as shuffling content between chapters, renumbering the practice problems, and adding a few new photos. Case in point is the 4th edition of the text I use now. Anyone with the 3rd edition would have no problem following my class, because hardly anything changed.

Another thing that burns me up is that by the 4th edition of a text, you’d expect all of the errors would have been ferreted out and corrected by now. Have they? No. I maintain a list of errata in the text on my webpage and use it to show my students that organic chemistry must be hard—not even the textbook’s author can get it right.

Textbook publishers erode the used-book market to drive the sale of expensive new editions, but professors are complicit in maintaining this skewed market. Why? Because we are the ones that assign these textbooks as required course materials. And you know why professors don’t especially care? Because we get our textbooks for free. The publishers will just give away a $250 text to us because they want us to force 200 students to buy it. They’ll even sweeten the deal by giving us free lecture slides that correspond to the text. The sales technique is brilliant: make life as easy as possible for the professors and give them free stuff so that they will force their students to buy your product. While it’s not exactly a kickback, it’s not terribly far from it.

So, the textbook market is not a fair one as far as students are concerned. Students can’t shop around for the highest quality book at the best price; they are essentially required to buy whatever textbook their professor decides at whatever price the publisher is charging. And as if that wasn’t enough to make you sick, publishers send instructors e-mails like the one I received a month ago:

From: <Textbook Publisher>
Subject: When it’s required, they’re prepared required_advert_450Disgustingly shameless. I feel gross just reading it.

Hey, instructor buddy! You want your students to learn? Well, then you need to *require* them to purchase our expensive online add-on! And don’t worry—we’ll give instructors free access to the system, of course!

Don’t get me wrong. I recognize that authors and publishers perform a valuable service. While our understanding of first-year organic chemistry hasn’t changed in 30 years, our ability to make instructive figures has certainly improved to the point that no one would choose a text from the 1980s over those offered today. So yeah, publishers should be compensated for the materials they produce. But at the same time, there is a limit to what is reasonable. Issuing a ‘new’ edition every three years at $375 a pop is ridiculous.

So, students, please forgive me. I know the system is unfair, but there really isn’t a good alternative at the moment. I would much rather you spend $375 on a nice iPad and download the coursepack for free. Unfortunately, the free organic texts in existence pale in comparison to the expensive texts out there, and the time required for a professor to produce all of the necessary materials for a class is too much to do in one shot. I hope you will believe me when I say that I’m working on it, but it’s going to take some time. Every year I produce a little more material and build towards the goal of obviating the need for an expensive text. Give me 20 years and that should become reality. I hope someone else beats me to it.

My Design for Organic Exams

Tuesday, October 21st, 2014

ed_academic_bigIt’s fall semester at SLU, and I’m teaching organic chemistry for our majors once again. Last year, I was focused on just getting through the course. I was so consumed by producing slides, homework assignments, practice exams, and real exams on a tight schedule that I didn’t get to think hard about the finer points of design until the class was over. Now, on the second pass, I can focus on making improvements rather than creating everything from scratch.

At SLU, instructors don’t get assigned TAs for proctoring and grading unless the class has greater than 30 students. In the spring, the majors’ class fell below this number and I had to think about designing exams to make grading as efficient as possible without eroding their effectiveness as tools for teaching and thoughtful evaluation. The system I settled on was different from my experience in both college and grad school, so I thought I’d share.

I’ve settled into a system in which quizzes and exams generally have four or five sections/problems picked from the following varieties: multiple choice, mechanism, synthesis, A+B reactions, explanations, and calculations. While I’ve never been a huge fan of multiple choice, it allows me to test a variety of straightforward points without the strain of having to grade a wide assortment of free-response questions. My multiple-choice questions are typically five choices, with students getting +5 points for a correct response and +2 points for leaving a question intentionally blank. This scoring system introduces a penalty for guessing; students need to recognize that sometimes the best option in life is to admit “I don’t know.”

In my system, if there is an exam on Wednesday, the students have a quiz due on the previous Friday that covers the same material. Each quiz contributes 2% to the final grade in the course, while each exam contributes 20%. The quiz has the same length, format, and answer sheet as the exam, except the problems are harder to compensate for the fact that I give students 48 hours for the quiz and allow them to talk with each other about the answers. I like how this approach requires the class to be familiar with the exam material almost a full week before the exam, and that students have an incentive to form study groups and debate answers to hard problems. I never learned as much in organic chemistry as when I was trying to defend my proposed answers to classmates. Finally, having what is essentially a hard practice exam due on the Friday before the “real” exam means that I can return it graded and marked with comments by Monday. In many cases, these quizzes serve as wake-up calls to students while there is still time to fix issues that need attention.

In every chemistry class I’ve taken, students either wrote their exam answers directly on the problem booklet or in small blue exam books. I find these response media are murder to grade because you spend so much time flipping through pages, hunting for answers, and flipping back to write the subtotal for that problem on the cover page. And, of course, there are always two or three students who get creative and write their answers out of order or on the back side of pages.

To solve this problem, I started writing exams such that students have to place all of their answers on a single letter-sized piece of paper. I draft an answer sheet for each exam on which it is clear where each answer should be written. When the answer is a single word or structure, I’ll typically draw a box for it. The use of a single sheet minimizes the burden of flipping, while the answer boxes (located at the same spot for every student) minimize the burden of hunting. Here’s a sample answer sheet typical of one of my orgo exams:


I copy answer sheets onto 65-lb. card stock so that both sides of the sheet can be used without the pen ink bleeding through to the other side. I find that the smooth sheets sold under the Neenah brand are better than sheets of the less expensive Staples brand, which have an annoying coarse texture on one side. The card stock also gives a regal quality to the answer sheets. These puppies are suitable for framing and will withstand decades of wear if pinned to the refrigerator door of a proud parent.

Another nice thing about having students limit their answers to a single sheet is that the entire stack for the class can be scanned without hassle. Most modern office copiers are capable of sheet-feed scanning, so if your exams have no staples, you can scan the entire stack of paper all at once and e-mail the data to yourself as a single PDF. What a wonderful miracle of technology.

I scan the entire set of answer sheets both before and after I’ve graded them. In doing so, I have a permanent record of performance that I can access for eternity. If there is an issue over improper grading or a student attempting to cheat by altering answers upon return of the graded copy, I can refer to the electronic file. If a student needs a letter of recommendation two years down the road, I can open up the file and make specific comments about his/her performance. And if I want to mine data in the future for some pedagogical purpose or project, all of the data will be available for analysis.

A final important feature of each answer sheet is that I have a line for students to write their names at the top of the back side. This makes returning exams very simple, because I can fan them in columns in alphabetical order on a table and have students come in groups to pick them up. With only the top inch of the back page of each sheet exposed, students cannot see each other’s grades. Of course, as the columns thin out, I adjust the sheets to prevent greater exposure.

As I discussed before, I allow students to bring handwritten notes into exams. They serve to emphasize that organic chemistry is about analysis—not memorization. Also, having students organize the information of each unit onto a single sheet of paper forces them to make connections about the material in their minds ahead of the exam. This semester, I’ve started collecting, scanning, and returning these note sheets as well. I am fascinated at how students organize their thoughts, and I plan to use this information in my future letters of recommendation when appropriate. How an individual organizes her thoughts on paper gives you an interesting window into her mind.

So, that’s the system. Are there drawbacks? Yes. I tend not to write long mechanisms or synthesis problems that go over four steps, because there isn’t enough space to do so. With that said, I’m not sure if these problems offer much added benefit relative to alternatives with more concise answers.

One thing that I’ve found surprising is that even though the answers for the exam all fit on one page, there are students who still feel they need three hours to finish. I thought that offering four shorter exams instead of three longer ones would make time a non-factor, but often at the end of two hours, I still find myself nagging for all of the papers to be turned in.

Anyway, I like how this system works and will continue to modify it to work better for both the students and me. It is ironic that as a teacher, I feel that I am the one in the classroom who has the most to learn.

UCLA Professor Patrick Harran Strikes Deal with Prosecutors

Sunday, June 22nd, 2014

BulldoodyPatrick Harran, the UCLA professor who faced four felony counts in connection with the death of Sheri Sangji in a laboratory fire, has struck a deal with prosecutors that allows him to avoid charges in exchange for a $10,000 fine, 800 hours of community service, and running a lab free of safety violations. So long as Harran completes his end of the terms of the agreement, he will avoid trial and have an untarnished criminal record.

What a relief!

As an assistant professor in charge of a research lab, I could not be happier with this outcome. I have a lot of stuff to worry about, and ensuring the safety of my students cannot be allowed to get in the way of important things like finding consulting gigs, collecting awards, traveling to international conferences, and stealing ideas for grants. All of those OSHA rules are meant for industry, not academia. The bar for what passes as safe in academic labs is clear, and people who want to work under moderately safe conditions know better than to go to graduate school. The government simply can’t expect me to be responsible for what happens in my lab, which is well over 50 feet from my office and not even the same direction as the restroom. I’m happy to buy enough safety goggles and almost enough lab coats to outfit my students, but the rest is up to them. If Aldrich has written a technical note on their hazardous experiment, my students know not to bother me.

The most important aspect of the Harran deal is how it extends the long, proud tradition of excusing PIs of any professional responsibility for their work. Society recognizes that professors are only supposed to have good things happen to them. We get the lion’s share of credit for papers, not the students or postdocs. We get the big salaries, not the students or postdocs. We get the awards, not the students or postdocs. On the flip side, professors must be protected from negative consequences at all costs. If an accident happens in one of our labs, that’s the students’ fault. If multiple papers from one of our labs contain fabricated data, that’s the students’ fault as well. Clearly, professors are not responsible for supervising their groups for integrity or safety. We know this because Dalibor Sames and Patrick Harran are still in charge of their labs. I applaud Columbia and UCLA for recognizing that you can’t discriminate against professors for trivial things like irresponsibility and incompetence. Anyway, it’s the competent professors you need to watch—lightning never strikes twice, right?

Of course, I realize that there should be some consequences when something truly horrible happens. In these situations, professors must arrange for perfunctory punishments that allow all of the parties charged with oversight to save face. That’s what we saw here: UCLA threw some money at a scholarship in the victim’s name and at establishing a safety program it should have had in the first place. Personally, Harran was forced to donate money to the hospital where his student died. Incidentally, I think $10,000 was way too much; the man only earns $301,000 a year. How is he going to make ends meet with just $291,000? At least Harran’s lawyers were clever in how they disguised the 800 hours of community service as a major inconvenience instead of court-mandated preparation for the Broader Impacts section of Harran’s next NSF proposal. Killing two birds with one stone is exactly why good lawyers get paid the big bucks.

In all seriousness, I think the deal agreed to by prosecutors is a grave injustice, but one that comes as no surprise in today’s legal system. Without any changes to the material facts of the case, how does the DA go from charging someone with four felony counts to striking a deal that allows Harran to have a spotless record with a payment, community service, and actually doing his job of running a lab free of safety violations? Note that this was not a plea bargain; Harran pleaded guilty to nothing—not a misdemeanor, or even an infraction.

The game plan of Harran’s legal defense was quite effective: delay, delay, and delay. They gummed up the works with continuance after continuance and motion after motion. In the end, it appeared the prosecutors were willing to do anything just to clear the case. I mean, was this deal what the prosecutors were holding out for all of these years? What makes it all the more worse is that the original deal called for 400 rather than 800 hours of community service. The judge had to step in and double it.

My heart goes out to Sheri’s family for their loss. While I think our legal system has denied them justice, my hope is that the field of chemistry does not forget what happened to her. I hope UCLA’s reported new-and-improved safety culture persists, and I hope the rest of the world of academic chemistry also strives to do a much better job regarding safety than it has in the past. At the very least, I can guarantee you that Sheri’s death has had an indelible, positive effect my approach to safety and how I manage my lab and students.


For more coverage: C&EN’s Jyllian Kemsley and Michael Torrice have done a fantastic service for the community in covering the case, and Chemjobber has been curating links to coverage on his site.

Some Very Peculiar NMR Spectra in Organic Letters

Monday, August 19th, 2013

A close examination of the Supporting Information attached to this paper from 2011 in Organic Letters reveals some pretty interesting NMR spectra:


(compound 5dfull spectrum)

Hmmmmm. I have collected hundreds of NMR spectra, and I can’t ever recall seeing a spectrum in which intensity was not a reasonably continuous function of chemical shift. That is, values of chemical shifts had only one associated intensity each, and no spectra had missing chunks of signal.

Here are some other interesting pieces of spectra from the same paper:

compound3j_hnmr_zoom(compound 3jfull 1H NMR spectrum)


compound3j_cnmr_zoom(compound 3jfull 13C NMR spectrum)


compound_7c_zoom  (compound 7cfull spectrum)

You can check out all of the spectra in the SI for yourself—the file is open access.

So, what is going on here? One explanation is that we’re seeing something very scientifically interesting. I hope this is the case. Another explanation could be user error, or a malfunction on the part of the instrument and/or software used to collect and analyze the data.

Yet another explanation could be that unexpected or undesired peaks (e.g., those corresponding to impurities in the samples) have been erased from the spectra. Some of you might think this suggestion is outlandish—why would a chemical researcher manipulate spectral data in this regard?—but I cannot take credit for conceiving of this idea. I believe the first time I was alerted to this (highly unethical) practice was by the Editor-in-Chief of the journal in which this work appears.

Organic chemists and readers of this blog will recall that earlier this summer, Amos B. Smith III—the Editor-in-Chief of Organic Letters—penned an editorial documenting that he hired a data analyst to examine spectra and other data submitted to the journal for possible manipulation. The editorial included the statement:

I write to alert the organic chemistry community to a serious problem related to the integrity of data being submitted for review and publication by Organic Letters and to outline steps that the Journal is taking to address this concern. Recently, with the addition of a Data Analyst to our staff, Organic Letters has begun checking the submitted Supporting Information more closely. As a result of this increased scrutiny, we have discovered several instances where reported spectra had been edited to remove evidence of impurities. Such acts of data manipulation are unacceptable. Even if the experimental yields and conclusions of a study are not affected, ANY manipulation of research data casts doubts on the overall integrity and validity of the work reported.

I wish to reiterate that I have no definitive idea of what happened in the production of the spectra in this paper; this post only notes that they don’t look normal. In an effort to ascertain more about the spectra, five days ago, I reached out by e-mail to the first author, corresponding author, and Editor-in-Chief of the journal.

Dr. Bruno Anxionnat, the first author of the paper, did not respond. His former PI and the corresponding author on the paper, Professor Janine Cossy, replied with the following statement:

Dear Professor Bracker

There is probably a mistake as I know that the 1st supporting information with some spectra were wrong and I asked an other student to reproduce the experiments and sent back an other SI with the right spectra, may be the 1st SI was not changed by the right one.

Right now, I am abroad and can not check but I am going to check with the Organic Letters editorial office and I will tell theñm to contact you

Sincerely yours
Janine Cossy

I will note that Professor Cossy is an Associate Editor of the journal in addition to being corresponding author on the paper. You may recall that Smith’s editorial in Org. Lett. addressed the responsibilities of corresponding authors quite clearly:

In some of the cases that we have investigated further, the Corresponding Author asserted that a student had edited the spectra without the Corresponding Author’s knowledge. This is not an acceptable excuse! The Corresponding Author (who is typically also the research supervisor of the work performed) is ultimately responsible for warranting the integrity of the content of the submitted manuscript.

The responsibility to foster a research environment where all involved can confidently present their results, even if they are not optimal, resides with each research supervisor and Corresponding Author. At times, the inherent power of a research advisor’s position can create an atmosphere that leads some to embellish results.

In my e-mail to Professor Smith seeking comment, I made sure to mention his recent editorial. He sent back the following note:

Dear Bracher,

Thank you for bringing these discrepancies to my attention. As with any allegation concerning published articles, we have shared your concerns with the author, who is as you note an Associate Editor. Organic Letters has standard procedures for handling inquiries regarding the content reported in published articles, which are in play here.  As you may be aware, COPE ( provides  journal editors and publishers with guidelines for handling such issues.  Speculation and comment are premature at this time.

ACS and ACS Editors hold the conviction that the observance of high ethical standards is vital to  the entire scientific enterprise. Guidelines for a course of conduct by  those engaged in the publication of chemical research, specifically, editors, authors, and manuscript reviewers are set forth in ACS Ethical Guidelines to Publication of Chemical Research

Amos Smith

So, there you have it. The matter is being examined more closely, and it would appear the ball is in Organic Letters’ court. Interestingly, there are a few more papers (listing Anxionnat as first author and Cossy as corresponding author) where you might notice similar-looking spectra:

Anxionnat, B.; Pardo, D.G.; Ricci, G.; Cossy, J. Eur. J. Org. Chem. 2012, 4453–4456. (paper, SI)

Anxionnat, B.; Robert, B.; George, P.; Ricci, G.; Perrin, M.-A.; Pardo, D.G.; Janine Cossy. J. Org. Chem. 2012, 77, 6087–6099. (paper, SI)

Go have a look and judge for yourself.