Working with some nitrogen compounds

I always laugh whenever I see a new paper (JACS or Angewandte Chemie notwithstanding) describing the synthesis of and/or new/novel nitrogen compounds that are either some kind of superfuel (read: large ∆G) or so rare that precious little previous literature can be found on them.

There are reasons why you hardly read about them or why they are not in widespread use in industry already.

The reason that one gets our attention is that compounds with lots of nitrogens in them – more specifically, compounds with a high percentage of nitrogen by weight – are a spirited bunch. They hear the distant call of the wild, and they know that with just one leap of the fence they can fly free as molecules of nitrogen gas. And that’s never an orderly process.

...And thermodynamically, there aren't many gently sloping paths down to nitrogen gas, unfortunately. Both enthalpy and entropy tilt things pretty sharply. - Derek Howe

I like Ancient Hacker's summary on slashdot:

Rocket fuel was a big research area in the 1950's. Dozens of very good chemists spent a whole load (hundreds of millions of 1950-size dollars) trying to make better rocket fuels.

( One of them wrote a informative and funny book about that time and place ).

The short summary is: Yes, you can make higher oomph rocket fuels and oxidizers with more oxygen in them.

But a lot of the formulas are impractical as:

(0) They were already discovered years ago, and discarded, but chemists don't like to write up their failures, and researchers don't like to read old moldy research summaries anyway.

(1) They're waaay too expensive to make, even for military uses.

(2) They are highly toxic, even more toxic than the widely-used hydrazines, which can kill you in several interesting ways.

(3) They're so unstable, you have to keep them under impossible conditions, like no sound, no vibrations, no light, and under a part per million of crud in the perfectly-smooth and unscratched nickel-plated tanks.

(4) They can't be stored for more than a day or so before the fuel or oxidizer starts decomposing itself or the tank walls.

(5) Too many of the researchers were vaporized while handling the stuff. Literally. Truly. Completely. That tends to make it hard to find substitute researchers to continue working with the same stuff.

(6) For military applications, you need a fuel that can be handled by raw recruits, stored for many months, be pumped quickly into not always totally clean rocket tanks, kept in those loaded rockets for days to months, and tolerate wide temperature swings. These requirements alone disqualify a large percentage of really zippy fuels and oxidizers.

The odds are pretty high against this "new" compound being all that new, or it passing the basic requirements for fuel or oxidizer.

One of my side projects in Grad School was funded by NASA and we were handling hydrazine to test their viability for use in micro-reactors. That was one nasty little guy to deal with on a daily basis, and we all had to wear dosimeter badges on our lab coats in addition to two layers of gloves, sleeve protectors and rubber boots. And yes, the whole setup was inside a fume hood with the sash lowered all the time.


Be grateful this isn't your PhD project.

Oh, and Merry Christmas to those of you celebrating the Yuletide holiday. Stay warm and safe!

Edit (25 Dec): A nice youtube video of shock sensitive nitroglycerin:

The truth about doing research in Grad School and beyond

Credit: Boingboing and Chemistry Blog.

The term "lab rats" doesn't come out of nowhere. Again, it is very important to choose the right adviser.

The cartoon below would be a good response to the last part of Carreira's letter:



Afterall, Guido seems to be doing well at Novartis after leaving Caltech.

Edit (30 June): A Boston Globe reporter spoke with Erick (Now at ETH-Zurich). He now claims that is a joke.

Reached by email at the Swiss Federal Institute of Technology, where he runs a lab, Carreira said that the letter has been circulating for a dozen years, and he expressed frustration that it has surfaced again in such a public way. It has caused him to receive "many e-mails that have been threatening and downright inhumane," he wrote. In response to questions about the letter's authenticity, and a request for a more general comment, he forwarded an email that he had sent to an earlier correspondent. It said, in part:

"I wonder whether you would think it fair to be judged on the basis of a letter 14 years old, especially when the comments and rash judgments are made without knowledge of the context or the circumstances surrounding the individuals involved. Indeed how does anyone out who is so quick to pass judgement and who is coming to conclusions know that it is not part of a 14-year old joke (or satire as you state) that backfired? ...


I am quite sure everyone has at some time or another an e-mail, photo, letter, note, or comment that when taken out of context can be used to create whatever monster one wishes to envisage. After all no one is perfect. Is it really fair to be haunted by these endlessly? I do not know how old you are, but can you really say you have done nothing you would rather forget about and not be reminded of 14 years later? I like to think people grow and change."

In this note and in a shorter one to me, Carreira said that he had been advised by a lawyer not to comment on the validity or the context of the letter. (I asked him a follow-up question about the oblique suggestions that the letter was some kind of joke, but he has not yet replied.)

I certainly don't think any person on the receiving end of such a letter will think it is satire, or funny at all.

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Another one (Bob Tjian was then a professor in biochemistry at Berkeley when this memo was circulating amongst the grad students in the department in the mid-90s):

To: All Lab Members
Fm: Robert Tjian
Re: Dismal Attendance at Group Meetings and Slack Work Ethics

From now on, I or someone designated by me will take attendance at group meetings starting at 9:10 am. If you are not there, I will not sign your salary sheets. Also, if you haven't noticed the number of people working on weekends and nights in the lab is the worst I've seen in my 17 years. The frequency of vacation, time taken off and other non-lab activities is bordering on the ridiculous. In case you forgot, the standard amount of time you are supposed to take is 2 weeks a year total, including Christmas. If there isn't a substantial improvement in the next few months, I'll have to think of some draconian measures to "motivate" you. I also want to say that the average lab citizenship and community spirit of keeping the lab in functioning order is at an all-time low. Few people seem to care about fixing broken equipment and making sure things in the lab run smoothly. If the lab were extremely productive and everyone was totally focused on their work, I might understand the slovenliness but productivity is abysmal and if we continue along this path we will surely reach mediocrity in no time.
Finally, those of you who are "lame ducks" because you have a job and are thinking of your own nibs, so long as you are here you are still full-fledged members of this lab, which means participating in all aspects of the lab (i.e. group meetings, Asilomar, postdoc seminars, etc.)
I realize that this memo won't solve all the problems. so I am going to schedule a meeting with each one of you starting this Saturday and Sunday and continuing on weekends until I've had a chance to speak with everyone and to give you a formal evaluation. Sign up for an appointment time on the sheet outside my door.
This is the first time I've had to actually write a memo of this type and I hope
it's the last time.

Robert Tjian

Two more letters from Paul Gassman and Albert Meyers, with excellent information about standard expectations of grad students and postdocs.

Selecting undergraduates to mentor

A few weeks ago, I made the decision to take in a couple of undergrads and have them work directly under me in the lab. Regular readers of this blog might be able to guess my reason for doing so. It is not altrusic intent on my part, although I must state that this arrangement will be a win-win situation for all of us involved (if the research results and their lab performance turn out well). They will get the research experience along with strong recommendation letters for grad school and a small stipend, and I will get some help in my experimental work and substantially more to write about in my Teaching Statement. I am fortunate the advisor is agreeable and supportive of my decision, and sees this as a necessary step for my professional development as a future faculty.

That said, I set a relatively high bar for my applicants. I did not want any average Joe or Jane - I used the GPA (imperfect as it may be) as the first cut-off, basically restricting myself to the top 20% or so of the cohort. This group is also the one which is most likely to get admitted to the top-ranked departments. Then, to sieve out those who weren't serious about working or putting on their thinking caps in the lab, my applicants had to submit and complete a written exercise along with a resume listing the relevant coursework taken and grades obtained. Finally, they had to pass my interview. I focused on their academic ability, motivation, and commitment to put in time and effort in their work. I want them to succeed, and their success will reflect my success as a mentor.

A fellow postdoc friend in the neighboring lab thought I was crazy to set so many conditions. He operates on more of an open-door policy - basically allowing any interested undergraduates (GPA > 3.0) to volunteer in his lab for a few weeks and then offering those who do a good job the option to get research credits or for a lucky few - to become paid undergraduate research assistants. "You won't get anyone!" he howled, but I got the students who met my criteria within a week of putting out the advertisement. Too many in fact, and I had to reject some excellent candidates. I felt weird to be sitting on the other side - deciding on who gets into the group or not.

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Many moons ago, I worked in an organic chemistry group in my undergraduate institution for 3 semesters. The postdoc I worked under was a hard driver. I remember spending my first few months in the lab just washing glassware, and this was a few years before Philip Yeo's now infamous comment that people with basic science degrees would qualify only as test-tube washers in A*star. I progressed from just doing the washing to doing the grunt work in mixing reactant solutions, preparing suspensions, purifying and separating intermediates using a rotovap and packed silica columns, and analysing the samples using TLC and 1H NMR. In return for my (hard) work, I got an A for the research credits that counted towards my major GPA, strong recommendations for grad school and a stint in another university for a summer of more research work.

Part of my labor went into a Science paper that the postdoc published with the professor a year after I graduated. There were just the 2 of them in the list of authors. My name did not even appear in the 'Acknowledgement' section, although to be fair I did not make any intellectual contribution to the publication. I was just a 'lab tech' following the postdoc's instructions.

Sometimes I look back and wonder - I was this close in getting my name to a Science paper as an undergraduate.

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Note: To those of you who have never heard of Nature or Science, Jorge Cham does a good job illustrating scientists' obsession with having at least one paper published in either one: I, II, III.

Tales from the Lab III

Someone stuck this bumper sticker to the lab door's window:

Biodiversity is Nature's way of telling us it's OK to be different.

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My lab has an Aldrich bottle labelled "Synthetic Sea Water". I am more familiar with seeing "Distilled water" or "Deionized water" bottles lying around.

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A couple of grad students and postdocs in my department and allied ones are starting an "Organic Reaction Mechanisms" club.

Dear colleagues,

In order to keep our synthetic chemistry skills sharp, Dr. X is going to start a mechanism club. The point is to broaden our synthesis knowledge through mechanisms. It will be an informal thing, and we will try to make it fun. If necessary, we may even lure you with beer.

Several of you have already expressed interest, and I would like to invite all of you to join. It seems that Wednesday evening would be a good day/time, but I encourage input from all of you. Please let me know if you are interested, and if Wed. evening would work for you (of course I'm not talking about tomorrow). I know that there are people that I forgot to include, so feel free to tell your coworkers.

Thanks,

Imagine that. A group of students and postdocs starting a club that attempts to make understanding reaction mechanisms fun. Talk about having geeky fun.

Woohooo!

Diet Coke and Mentos: Soda-Candy Explosions

Tonya Coffey and her students reported "an experimental study of the Diet Coke and Mentos reaction (made famous in a 2006 Mythbusters episode), and consider(ed) many aspects of the reaction, including the ingredients in the candy and soda, the roughness of the candy, the temperature of the soda, and the duration of the reaction." (Am. J. Phys., 2008, 76(6), 551 - 557)

Basically,

1. The Mythbusters correctly identified potassium benzoate and aspartame as key ingredients in the Diet Coke–Mentos reaction. (Static water) Contact angle measurements were used to show that these ingredients reduce the work required for bubble formation, allowing carbon dioxide to rapidly escape from the soda. The small amount of caffeine in Diet Coke is unlikely to contribute significantly to the reaction.

2. The Mythbusters also correctly identified the roughness of the samples as one of the main causes of the reaction. The importance of sample roughness was shown by comparing SEM and AFM images of the samples to the explosive power of the reaction. Increased surface roughness implies a higher surface area to volume ratio, meaning that more growth sites should be present on per unit volume.

3. Samples which encounter less viscous drag and hence fall more quickly through the soda will cause a more explosive reaction. Also, for the same amount of mass lost, the eruption will be more dramatic when the reaction takes place over a shorter time.

4. Finally, hotter beverages result in a more explosive reaction. (A direct illustration of Henry's law and Le Chatelier's Principle)

The kinds of things researchers do...like popping candy into sodas and watching them fizzle and frazzle.