Now, I’ve worked with light-sensitive reagents (like the iodomethane and methallyl iodide) before, so I’m comfortable turning off the light and covering the reaction with foil to keep out extraneous photons.  That’s not so bad, because when the reaction’s done, you can flip on the light to work up the reaction.

Not so when the product is light sensitive.  Gotta keep the light off.  Gotta extract in the dark.  Gotta dry the organic layer with foil around the flask.  Gotta rotovap in the dark with foil around the flask.  Worst of all, gotta run a column in the dark.  For that, I cut off some of the sides of a cardboard box and used them as a shield to block the light and holed myself up in the dark corner of my hood to run the column.  Then gotta rotovap the fractions corresponding to product in the dark in foil.  Take the mass in the dark…  Ugg.  Pain all around.  Oh yeah, I forgot I gotta keep the NMR samples in the dark while I acquire the spectra, too.

Plus, gotta keep the product away from light until I set up the next reaction (which is going on right now)… and that’s gotta be in the dark.  At least when this reaction’s done, I can turn the lights back on.

Fortunately, the first reaction worked quite well.  I ran two multi-gram reactions side by side in the dark and got quantitative yield on both.

So while I run off to find some vitamin D supplements, tell me what the most operationally painful experiment you’ve set up is.  I’m sure many of you have stories that make mine seem trivial.  What experiment’s the biggest pain to run?  I think any reaction involving FOOF (the most awesome, most onomatopoeic molecular formula evah) has to be up there.

Now students have probably been complaining about textbooks since time immemorial. Aristotle probably complained that his scribe made spelling mistakes in his copy of The Republic. Most of the time our bellyaching is justified. Not only do textbooks cost a lot, but there is often a gross amount of errors in them. Everyone knows that the first time you find a caption or answer wrong, it makes the rest of the book suspect. Also, these errors give the publishers a reason to release a next edition…that never seems to fix even half of the errors. However, they do switch around problem numbers, add a few pages of new content, and possibly even rearrange chapters. So now the professors lesson and homework plan, that goes by chapter numbers, page numbers, and problem numbers, is moot. And the student is effectively forced to buy the new edition (price “adjusted for inflation”) or suffer some inconveniences. Most choose to simply buy the new edition since tracking down the old one can be difficult and you have to be quick. Also, sometimes bookstores won’t buy back the old edition so if you had it, and an edition switch occurred before you finished your course track, you are up the creek.

Some of these issues can be addressed with online textbooks. The idea of supplementing physical texts with online modules has been around and implemented by publishers for many years. However, I’ve yet to see a good entirely online chemistry textbook. The advantages of online texts are of many: accessible anywhere you get 3G or Wi-Fi and have your mobile device, interactive learning capabilities, easy distribution, instant update/revision, and low cost publishing (server fees). Of course this won’t necessarily result the publisher make more money, but at 4 billion (yea, you read that correctly, billion) dollars a year, the industry doesn’t really need much help.

The student, however, does. We need these online textbooks, not just to save our wallet, but also to help prevent being stuck with an expensive and lousy text for a year that does a poor job of explaining the material. That expensive O-Chem book I bought really was terrible and it forced my professor to do a lot of extra work in teaching us not to follow the book’s direction of simply memorizing 500 reactions, but to see the patterns and the underlying physical explanations. In the end, we learned from his powerpoints and I paid $215 for a glorified reference book.

Well, some people are pioneering an effort to create an “Open Access Textbook”. In a perfect example of “chem 2.0″, UC Davis Professor Delmar Larsen is the project director of the ChemWiki, a truly free online textbook written by everyone, for everyone. In an absolutely Herculean effort, the developers and Larsen (Mary Obrien, Ron Rusay, Brent Krueger, Michelle McCombs) are trying to create a free and complete, as in covering all branches, chemistry textbook using a community of students, faculty, and outside experts from around the world. Of course they aren’t there yet, and there is still a long way to go but hey, their text literally gets better everyday.

Now I know you probably have a lot of questions: what about correctness and plagiarism? Could such a thing ever be considered an Authority? What do the publishers say? Does anyone actually use the thing? Well, it just so happened that a couple of weeks ago, I was at Davis for the Borge fellowship visitation and I had a chance to talk with professor Larsen who agreed to answer some of these questions for me. In a couple of days, I’ll post the interview here. For now, I suggest you go and check out http://chemwiki.ucdavis.edu/ and browse not just through the core, but the wikitexts and community as well.

A graduate student at the University of Wisconsin-Madison suffered burns and the loss of their favorite chair due to a fire that was started in the lab. A small lab fire usually wouldn’t make for interesting news, but see if you can spot something strange in the redacted narrative from the Madison Fire Department.

E4 found dry chem extinguisher activated, smoke, dry chem created haze on fire floor. found burned cushion chair in stairwell that was pushed there from room where reportedly students were working with chemicals that were spilled on to a chair that then started on fire. students came up with the idea to use a dry chem extinguisher as well as push the burning chair down the hallway to the stair well. It was reported to us that (deleted) was one of the students who was already at the UW hosp being treated for burns to his hand. E4 saw no one on the fire floor upon arrival.

The student took a burning item out of the laboratory and put it in the stairwell. A follow up revealed the student was worried about other chemicals in the lab catching on fire, but to the best of my knowledge most laboratories are designed to contain a lab fire. If the fire had gotten further out of control and caught the hallway and stairwell on fire, Madison might be missing a building today.

For future reference young graduate students the correct method for dealing with a burning chair in lab is the following. Rush to the safety shower and turn the flow of water on, then with a non-flammable object push the chair under the shower. Do not transport flaming objects outside the lab!

The chemical that started the fire was ethanol. Apparently the student was cleaning a pipette with an open flame nearby. As the student was shaking the pipette dry, a few drops of ethanol landed onto the chair and caught on fire.

The fire department received the call at 11:17 pm.

More media coverage: UW student burned in lab fire (The Cap Times)

Mitch

Carl “Dan” Fish, a worker at the DuPont plant in Belle West Virginia, died this past Sunday due to phosgene exposure. Only scant details about the incident have been released by DuPont thus far, but this is what we have been told.

On Saturday afternoon a site employee was exposed to Phosgene from a leaking transfer hose. The hose was not in service when the leak occurred but did contain a small amount residual Phosgene from an earlier use. The employee was transported to the hospital by the Kanawha County Ambulance Authority for treatment and observation as part of the standard protocol for exposure to this material.

Unlike previous chemistry related deaths this has gotten the attention of Washington. Senator Rockefeller (D-WV) released a statement Monday, Rockefeller Statement on Incidents at DuPont Chemical Plant, calling for a thorough investigation of the incident. Since Rockefeller is the chairman of the Senate Commerce Committee, the committee with oversight of the facility, and being a senator from West Virginia Dupont can look forward to being under intense scrutiny.

Update 1: The senior senator from West Virginia, Robert Byrd (D-WV), has released his own statement: Byrd statement on incident at DuPont chemical plant

Update 2: It took DuPont 20 minutes to identify the chemical exposure to Metro 911 services after the initial call for an ambulance: DuPont calls: ‘Can you give me some more information?’
Audio Files: 1st Call from Dupont Advising Medical Emergency, Cpt Wallace Contacting Dupont for more info (The Charleston Gazette)

Update 3: The U.S. Chemical Safety Board voted to investigate the incident that caused a braided steel hose connected to a one-ton capacity phosgene tank to suddenly rupture. The lead investigator will be Johnnie Banks and the CSB team will arrive Tuesday at DuPont: Board Votes to Initiate Investigation on Accidents at DuPont Chemical Facility in Belle, West Virginia (CSB)

Update 4: Obituary

Update 5: From an anonymous source that I can not verify.

From what I’m told, he and another employee were walking by the tube when he heard it getting ready to bust and he shoved the other employee out of the way and he took the full brunt of it to the face and chest himself. I’m surprised they don’t mention those heroics in their statements. BTW, he was in his 50’s. He worked at that plant for 32 yrs.

Update 6: Senator Rockefeller called for a full CSB investigation into DuPont’s safety infrastructure and the facility’s compliance with emergency notification requirements to Metro 911 and federal agencies. In addition he asked for $1.6 million to create a new CSB team to alleviate the current workload and allow a concentrated effort for CSB to examine DuPont: Chemical Safety Board Must Have Resources To Review and Investigate All Current Cases Simultaneously (Press Release, Jan 27th 2010)

Update 7: “[During a briefing at a Charleston hotel] CSB lead investigator Johnnie Banks said the hose that sprayed phosgene onto Fish showed signs of “fraying” and “wear.” …another Kanawha Valley chemical company that uses phosgene, Bayer CropScience, utilizes only solid steel piping for transfers of the chemical. Banks described the hose as an 18-inch-long quarter-inch hose, with woven stainless steel on the outside and Teflon inside. It was damaged badly enough that investigators could see its Teflon lining through a small hole”. From: CSB: DuPont phosgene hose showed signs of ‘fraying’ (The Charleston Gazette, Jan 28th 2010)

Mitch (Our best thoughts from everyone at Chemistry Blog goes to his family and friends at this time)

Pronounciation and Origins
Curriculum is Latin for course. Vitae is Latin for life (technically the plural of life, unless you’re in second declension genitive). Put it together and it translates to course of life. As vitae is loaned from Latin it can be very confusing to pronounce. Dictionary.com has the correct pronunciation of vitae as vigh-tee. This is a little irking since scientists know how to pronounce Latin words and in Latin vitae would be pronounced vee-tigh (more-or-less).

Now to the point. It would be great if there was a place online for the chemical class to keep their CVs. As you develop more work experience it would be nicer to update one centralized CV than to update your word file and then redistribute your CV. Imagine having a link to your CV on your business card, it would be more employer friendly than having them hold onto your business card + several printed pages of CV. To that end, I made a website for that purpose.

I have been using it solely for my personal use, but if there was interest from other chemists I’ll be willing to open it up to a larger audience. Link below…

Mitch’s CV: chemicalvitae.com/mitch

The template is based on Paul Bracher’s CV template that he posted about oh-so many years ago. As I alluded to above, if you want one leave a comment and if there is enough demand I’ll open it up to public registrations. If demand is but a twinkle, I’ll setup the site with a lot less bells-and-whistles and keep registration limited only to the commenteers.

For those chemists that are worried about having too much information about themselves visible on the internet, I can block search-engines from visiting/indexing your profile. So only the people that you have given a link to your CV will be able to find it. Let me know what you guys think.

Mitch

Edit: Fixed some Latin grammar.

Lesson #1
The one thing that was never made clear to me is that you should have an hour long talk ready to go. I was asked the night before my interview if I would be willing to give an institute wide 1-hour seminar while I was there. Unfortunately for my own professional development I politely chickened-out; I have some ACS talks of 20-25 min length but nothing prepared that would tell a cohesive story for a whole hour. Other postdocs that I have seen interview at Berkeley usually give talks to the group they want to join and not the big seminar talk.

Lesson #2
The interview is all day long. My day started at 9:00 am with a meeting with the professor I contacted, followed by a presentation to his research group of my thesis work. Afterwards it was 1-on-1 talks with his postdocs and a lunch with the group. Which is what I expected. After lunch came meetings with the other professors in the department, an aspect of the process that I was not expecting and was more under prepared then I would have liked to be. The final meeting of the day was with the professor I initially contacted followed by more specifics on what aspects of his work was most interesting to me. The whole process ended after 5:00 pm with an early dinner.

Lesson #3
You need to wear a suit. Fortunately my friends got that into my head before the interview.

Lesson #4
The last step in the process is getting the funds. I need to apply for a fellowship to get started, but as the institute manages the fellowship program I am applying to, I was told not to worry about getting it.

The whole day went well, and I look forward to that next step in academia. If anyone else has gone through this process please share your experience in the comments.

Mitch

The machine that eats human bodies

Want a solution to cremation pollution? In the 9th annual “Year in Ideas” issue, the New York Times Sunday Magazine covers a new Scottish company that wants people to “resomate” human remains as opposed to traditional cremation.

The company’s web site mentions that resomation “uses less energy than cremation and produces significantly less CO2 and avoids putting mercury and other harmful contaminants into the atmosphere.”

How does this work? According to the NYT: “The corpse is placed in a pressurized chamber. The vessel is then filled with water and potassium hydroxide, creating a highly alkaline solution, and heated to 330 degrees. After about three hours, all that’s left are a soft, white calcium phosphate from bone and teeth and a light brown primordial soup of amino acids and peptides.”

Huh. Even though it’s kinda grody, I have to say that it makes a lot of sense. Will alkaline hydrolysis be your body’s ultimate fate?

I will finally finish my first semester of grad school in a week. It’s weird to think that I had just driven cross country to this cluster of red brick buildings in the middle of a corn field not too long ago. Today I did my first synthesis in grad school, which earned today a blog post of its own.

Here are some of my random thoughts and lesson learned from my first couple of months of grad school:

1. The midwest: I was and probably always will be a Cali girl. But so far, the lack of a coastline, mountains,  or any civilization beyond the city limit really haven’t bothered me yet. I love the humidity in the summer and watching the leaves turn color.
2. Classes: This semester, I took advanced group theory and a matsci class. I find these interesting but not very difficult (probably true: MS = More of the Same). Taking graduate-level courses in my senior year definitely helped. I probably didn’t spend nearly as much time on these as…
3. Teaching! I teach an honors genchem course. I love my students (all 80 of them!… ok, most of them)  and it’s a ton of fun to teach. I like that I can be a teacher and a mentor, since most of them aspire to do something relating to chemistry. I also learned that I should never have children of my own. Why bother when I can have college-aged ones that I can return to their respective parents when I get sick of them?
4. Research: We spent a lot of our first semester getting tours and meetings to decide whose research group we will be married to for the foreseeable future. I haven’t gotten to do a lot of work in lab yet, but so far I think what I saw in undergrad and a little bit of the post-bac life about grad school is rather accurate.
5. Stipend: If I haven’t griped to you about this already, here it is– many of you know that I took a pretty significant pay cut (I get paid about 2/3 less now than my previous job) to go to grad school. The thing about not living in California though… I live very comfortably on my paycheck. If anyone is thinking about grad school, that should be a major consideration to make (cost of living vs stipend).

Take home lesson to those of you who are thinking about graduate school: observe grad students and ask questions. Do the math on your budget. There is more to it than the ranking. After all, you are putting 6 years of your early 20s on the table, wouldn’t you expect a little more from yourself in return?

Happy first synthesis day to myself. A glass of Livermore Valley merlot for the many more reactions to come and fires to put out.

Noel

For those of you who have not yet been summoned, I’ll share with you a general description of my experience. The first step is to wait. I sat in a room with a few hundred other people for five hours before I, along with 60 other people, were called to a courtroom to begin the selection process.

Inside the courtroom sat the potential jurors, the prosecution/defense, the suspect, judge, bailiff and court reporter. They observed while I and the other potential jurors swore to answer all questions truthfully. Twenty of us, (everyone is assigned and referred to by a number. I was ten) were called to the jury box. The case involved a driving under the influence (DUI) charge and one by one the jurors were required to answer a series of general questions (Do you know anyone in law enforcement? What is your occupation? Do you have any strong feelings about the charges? Etc.). When asked my occupation I responded that I was a graduate student in chemistry.

After the general questions both the prosecution and defense asked additional questions, some directed to particular individuals. The questions attempted to uncover the jurors preconceived notions about the suspect and crime. One question asked by the defense sparked my attention. The attorney asked, “Does anyone know how breathalyzer works?”

Although a simple concept that can be grasped by any general chemistry student, the most common portable breathalyzer is actually a very clever use of electrochemistry. Inside of the device is an electrochemical cell operating at a constant potential:

At the cathode, oxygen is reduced in the presents of water to produce hydroxide ions.

O₂ + 2H₂O + 4e^- –> 4OH^-

At the anode, the ethanol in your breath is oxidized to acetic acid.

CH₃CH₂OH + 4OH^- –> H₃CCOOH + 3H₂O + 4e^-

Because this is a well defined 4 electron process, the current produced can be used to determine the amount of ethanol in your breath.

In response to the defense attorney’s question, I raised my hand, prepared to explain the chemistry behind the device. Unexpectedly, the lawyer turned to me and, as if already aware of my answer, dismissively said, “I will get back to you later.”

After 10 minutes the defense lawyer returned to me and delivered the following two questions:

1)  “It is the responsibility of a juror to leave any expertise at the door and make their decisions based only on what is presented by witnesses called during the trial.  This also includes not discussing your external knowledge with fellow jurors. Can you, even if you know the testimony of one of the experts is wrong, make your decision based only on what is presented?”

My answer: Yes. (Internal monologue: I can but I would lose sleep at night knowing I allowed a potentially innocent person to be punished.)

2)  “While hearing a testimony that contains information you know to be false you might instinctively think “that is wrong and this is why.”  Can you stop yourself from having these thoughts?”

My answer: No. (Internal monologue: Is that even possible?)

Following a meeting between the judge, prosecution and defense, the first three jurors were dismissed. I was one of them, along with a man who could not speak English and a woman whose best friend had been killed by a drunk driver.

In retrospect, it appears that I was dismissed from the jury because I am a chemist/scientist.  Despite not being selected, my jury summons provided a thought provoking experience and left me with several questions. I will now pose these questions to you, my fellow members of the scientific community.

1) Could you convict someone of a crime knowing that it is based on incorrect testimony?

2) We have spent years training our brains to critically analyze everything we think and hear. Can you shut that off on request?

3) In a system where those who testify swear under oath to tell the truth, is it hypocritical to expect those making the decision to suppress what they know to be true?

4) Why wouldn’t you want additional expertise on a panel of individuals deciding the outcome of a trial? Aren’t they the most qualified and as a result most likely to make the correct decision?