Chemistry Blog

Mar 19

ACS – San Francisco Meet Up

There have been discussions about doing a meet up at ACS-SF again. The last time the bloggers tried this we got a pretty good showing in 2006 (embarrassing link to my drunken write-up).

If you are in town for the conference and want to meet up to get some food and drinks here is the plan. Fellow bloggers from coronene and everyday scientist will be in the bar at Chevy’s on Monday. We’ll meet there at 6:30 pm and be done before SCI-Mix begins at 8pm.

Restaurant/Bar: Chevys Fresh Mex
Address: 201 3rd Street, San Francisco, CA 94103-3154
Time: Monday 6:30 pm to 8:00pm (March 22nd)
Map: From Google, it is literally across the street from Moscone.
If you can’t find us, my cell number is (510)684-8092.

Maz and I will get there early, look for two brown kids with press passes.

If you can’t make it to the meet-up you can still trust Chemistry Blog to give you all the highlights from the ACS conference. For more coverage check out the C&EN blog as well.


Mar 18

ACS Mobile

Credit: Linda Wang/C&EN

ACS has released an app that streams new ACS graphical abstracts to your iphone. Unfortunately you have to pay $2.99 for the app. A free alternative I wrote can be found at the mobile site for ChemFeeds.

The nice thing about my version is it works for any mobile device that gets internet and not just iphones. It also covers RSC and Elsevier journals in addition to ACS. You can email article links to yourself for later reading and even leave comments on the abstracts. Admittedly the ACS version looks sleek, but iphones only apps are worthless for us Android users.

Link to C&EN’s ACS Mobile coverage: ACS Publications Go Mobile

Link to ChemFeeds Mobile:

Note: If you are not a member of the smart phone community yet, you can still get your graphical abstracts fix at the regular ChemFeeds website:


Mar 17

Scientific shopping

In the process of explaining the process of buying scientific equipment to a layperson, I was struck that I could not adequately explain Sigma-Aldrich’s role in the market.

If you take two extremes of retail shopping, there’s WalMart (broad selection, low prices, relatively few outlets) and there’s 7-11 (narrow selection, relatively high prices, lots of corner outlets). With 7-11, you presumably pay a little more for a little more convenience.

To the organic chemist, Aldrich is convenient (free shipping!), it’s typically high cost and the quality ranges for completely satisfactory to below average. The convenience and the high cost = 7-11; the extraordinarily broad selection of compounds, a little more WalMart-like. My experience with the customer service has been pretty good, actually.

So what is Aldrich? I think it’s more like a department store than anything (you can buy Aldrich brand glassware, not that I know a lot of people who do.) What do you all think? Do you have any favorite suppliers? (Seeing as how Acros is an advertiser, I have nothing but good to say about them.) What store do you equate with your favorite supplier?

Mar 15

Hydrogen Sulfide Suicide

I woke up this morning to Breaking News on my local morning news.  Police responded to a suspicious vehicle call around 10pm, where they found a woman slumped over in her car.  Police opened the door, whereupon they discovered a bucket with chemicals on the front seat.  The officer was overcome with the fumes and treated at the hospital for burning in his throat.  His condition is as yet unknown (update: he was released).

The regional hazmat team evacuated the surrounding neighborhood while they attempted to remove the woman from the car.  The woman did not survive.

The police are not releasing details of the chemical used, but it appears to be related to a similar suicide on the other side of town in February.  In that case, the victim left notes all over the car saying, “Do not open!!! poison gas!!! hydrogen sulfide.”  Another note, in part, read “hazmat team needed.”  When hazmat crews opened the car in that case, they measured levels of hydrogen sulfide more than 3 times the lethal limit.

Hydrogen sulfide (HS) (MSDS) is a colorless, highly flammable gas.  Humans can detect hydrogen sulfide at low concentrations, where it smells like rotten eggs.  Higher levels (~40 ppm) can irritate mucous membranes and cause headache, fatigue, dizziness, and even memory loss and bronchitis on repeated exposure.  At concentrations 50-400 ppm, can produce cough, dyspnea, hemoptysis, cyanosis, agitation, vertigo, confusion, nausea and vomiting, tremulousness, cardiac arrhythmias, hypertension, and, possibly, loss of consciousness.  According to one source, “just 2-3 breaths of HS at >700 ppm can cause immediate death.”  Most notably, prolonged exposure quickly leads to “olfactory fatigue” whereupon you can no longer smell hydrogen sulfide and can no longer detect its presence.

The mode of action is as follows: “The major route of toxicity for HS is by inhalation. At lower doses, local irritant effects predominate. At higher exposures, cellular respiration may cease as HS forms a complex bond to the iron ion in mitochondrial cytochrome oxidase, arresting aerobic metabolism in an effect similar to cyanide toxicity and affecting all organs, particularly the nervous system.”

It’s no secret that chemicals can be used for nefarious purposes.  Perhaps the most familiar is death by cyanide poisoning, with perhaps the most infamous case being the suicide of graduate student Jason Altom at Harvard in 1998.  Atropine, adrenaline, carbon monoxide, chloroform, and even the bizarre UK case of assassination by polonium.  The educated chemist has only a thin line to cross when reaching across the chemical shelf.  A good dose of respect with a large side of humility is in order as we remember the power of the knowledge we have attained.

Suicide by hydrogen sulfide was new to me.  But a wave of this type of chemical suicide swept Japan beginning in 2008.  A USA Today article written in July 2008 noted over 500 deaths so far that year from hydrogen sulfide.  One teen, who released the gas in her apartment, sickened more than 80 people throughout the complex as the gas spread from unit to unit.  Isolated cases have appeared throughout the United States in the past few years, including these two around me in the last 3 weeks.

Fortunately, emergency management teams have produced a number of documents to aid emergency responders.

  • Very detailed CDC bulletin on hydrogen sulfide with sections for on-site medical care as well as information for long-term care
  • St. Louis University bulletin on the dangers of and treatment for hydrogen sulfide inhalation
  • Shelby County (KY) EMS presentation on hydrogen sulfide

Other Chemistry Blog posts on suicides in chemistry.

On behalf of the Chemistry Blog community, anyone struggling with thoughts of suicide – especially anyone who came to this page today for that reason – is urged to call 911, your local emergency response number, or any of the numerous national and local suicide hotlines available.  The comments of this post will be closely monitored.  Anyone attempting to post recipes for the generation of hydrogen sulfide gas will have their comments removed immediately.

Update: Chemjobber sends along an article from The Atlantic magazine talking in sometimes raw emotion about the suicide mentality that seems to be problematic in parts of Japan.

Update2: An updated list of places to contact if you are contemplating suicide today.  Please talk to someone.

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Mar 09

Photophobic Chemistry

Ugg… what a pain.  The reaction I’m doing today produces a low molecular weight, light-sensitive α,β-unsaturated ketone as a product.  It’s a derivative of methyl vinyl ketone.  Not only is it low-boiling, it also polymerizes upon standing in light.  Ugg…

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.

Mar 03

Online Textbooks: ChemWiki Part 1

I remember buying my first O-chem books back when I was attending DVC (Diablo Valley College), a not-so-little community college here in the Bay Area. At first I checked the bookstore and lost my lunch when I saw the price of the new books. The text was $215, the lab manual was another $70, and the solutions manual was $100. Unfortunately, a new edition had been released that year, so even though the professor said that we could use older editions, many of the problem sets wouldn’t match up, so we’d have to get the problems from our classmates. In the end, the cheapest and most convenient route was to go online and buy the international editions. Even after extending the method to all my other classes, I still paid almost $500 for books that semester. Now I attended DVC before California went belly-up, so my classes were still a great bargain at $18 a unit. Since I usually took ~19 units, my total tuition cost was around $350 a semester. The cost of the books were actually greater than my cost of tuition. The sad thing is, this wasn’t an unusual case. Luckily this wasn’t too much of a hardship for me; I had a job on campus and money saved up. However, I knew a lot of students for whom the beginning of the semester meant not eating lunch in order to save up gas money.

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 and browse not just through the core, but the wikitexts and community as well.

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