July 3, 2008 at 12:52 pm | | everyday science, great finds, science@home, tutorial

I’m on vacation with my financier fiancée for a week in South Carolina: a few days at our friends’ wedding, a few days at Hilton Head, and a few days with my soon-to-be in-laws. The weather has been beautiful: heat and humidity reminding of my UNC days. The shark that swam past me gave me the creeps, but otherwise Hilton Head was perfect.

One strange event: a friend got a sunburn and a strange rash. The dermatologist asked if she had been making Mojitos or drinking Coronas. Huh? Diagnosis: Phytophotodermatitis. This is really cool: limes (and various other plants) contain furocoumarins (particularly psoralen, structure below), coumarin-type chromophores that absorb strongly in the UV.

Psoralens act as photosensitizers: absorbing UV light and releasing reactive triplets or radicals. With fluorescence quantum yields only around 1-2%, psoralens transition to the triplet state (via El-Sayed’s rule, I expect, from the Jablonski diagram below) and phosphoresce strongly. Chromophores stuck in their triplet state can return to the singlet ground state by coupling with triplet O2, producing a highly reactive singlet O2 species. This may be one mechanism of the photosensitizing properties of psoralens. Alternatively, a psoralen molecule in its triplet state can react directly with DNA or other biomolecules with electron-donating capability. Various other photosensitizing reactions are discussed in an interesting review (Kitamura, N.; Kohtani, S.; Nakagaki, R. J. Photochem. Photobiol. C 2005, 6, 168-185).

So, basically, my friend was spraying tan accelerator on her skin, then sitting in the sun for hours! That equals strangely shaped splotches of sunburn. In fact, psoralens have been used in photochemotherapy (also called PUVA) for certain skin ailments, such as eczema and psoriasis. So be careful squeezing limes on the beach, or picking parsnips or playing with celery in the sun.

Check out some doctory stories in this article: Weber, I. C.; Davis, C. P.; Greeson, D. M. J. Emer. Med. 1999, 17, 235-237.

Fuel Economy and A/C

May 18, 2008 at 11:48 am | | everyday science, news, science and the public

So, I’ve heard from several people over the course of my life that it is more fuel efficient to run a car with the windows down rather than use the A/C.

However, a new article on Fuel Economy Myths from CNN-Money suggests that this isn’t so at high speeds.

There’s no question air-conditioning makes extra work for the engine, increasing fuel use. But car air conditioners are much more efficient today than they used to be. In around-town driving, using the A/C will drop fuel economy by about a mile a gallon.

Meanwhile, driving at higher speeds with the windows down greatly increases aerodynamic drag. As speed increases, drag becomes more of an issue, making A/C use the more efficient choice at high speeds.

At most speeds and in most vehicles, A/C use drains slightly more fuel than driving with the windows down, contends David Champion, head of auto testing for Consumer Reports. “My final take on is that it’s very close,” says Phil Reed, consumer advice editor for “It’s hard to measure the difference and every vehicle is different.”

The best choice—if temperature and humidity allow—is to keep the windows rolled up and to turn the A/C compressor off. You can keep the fans running to blow in air from the outside, but your car will be as aerodynamic as possible while still letting you breathe. You will save gas, but the fuel economy improvement will be slight.

Other myths include the idea the Premium gas gives you better gas mileage (false in modern cars – the car’s computer can tell the density of the fuel and adjusts the spark plug timing. Lower-octane fuel “slightly” decreases horsepower, but has negligible effect on fuel economy), and that over-inflating tires increase fuel economy (obviously true – less friction, but dangerous due to braking and turning issues).


Stanford Professors Speak Out about Bush’s Climate Strategy

April 17, 2008 at 4:04 pm | | conferences, everyday science, news, science and the public, science community

A few Stanford profs that were attending the GCEP workshop on Carbon Management in Manufacturing are featured in an ABC 7 News story.  This includes one chemistry professor interviewed, and another makes a cameo at the very end.  It’s only 2 minutes long and worth watching.

Watch News Story Here

(If anyone knows how to embed this rather than just linking to it, please let me know).

a vial and a laser, part II

April 9, 2008 at 10:41 am | | everyday science

Some people enjoyed the last installment, at 488 nm. Now we have another picture with a 532-nm, diode-pumped, frequency-doubled Nd:YAG laser:

The red fluorescence in the cuvette comes from a red-emitting DCDHF fluorophore (the last one was a green-emitting version).

a vial and a laser

April 3, 2008 at 12:49 pm | | everyday science

I always like seeing a laser pass through a vial of fluorophores.

This is the 488-nm line of an Ar-ion laser passing through a DCDHF fluorophore in water.

FRETing about forster vs. fluorescence

March 2, 2008 at 7:19 pm | | everyday science, open thread, tutorial

fret-plot.jpgUntil recently, I thought FRET stood for “Förster resonance energy transfer”; I figured that “fluorescence resonance energy transfer” was a bastardization used by biologists. But a friend challenged me on that point, claiming that fluorescence was more specific and meaningful than Förster. I was all confused.

My reasoning was this: Förster’s equation for long-range dipole-dipole nonradiative energy transfer is a specific case of RET; other cases (e.g. Dexter electron exchange) have different mechanisms and follow different scaling laws. Moreover, because fluorescence is not necessary in the FRET mechanism, I thought it was misleading.

But how true is all that? Does Dexter ET count as RET? Is FRET the only way to transfer the potential to fluoresce from one molecule to another? My friend claimed that Dexter should not be called RET, because it is electron exchange instead of Coulombic.

So I refer to the experts.

Bernard Valeur, in Molecular Fluorescence, says:

The term resonance energy transfer (RET) is often used. In some papers, the acronym FRET is used, denoting fluorescence resonance energy transfer, but this express is incorrect because it is not the fluorescence that is transferred but the electronic energy of the donor. Therefore, it is recommended that either EET (excitation energy transfer or electronic energy transfer) or RET (resonance energy transfer) are used.

That doesn’t help solve the Förster vs. fluorescence dilemma, but instead adds another term (EET, gross) to throw into the mix. But I think this sorta supports my using “Förster” because “fluorescence” is misleading and too broad. Anyway, good ol’ Bernard goes on to carefully describe the different RET mechanisms and formulas.

So what does Joseph R. Lakowicz say? First, he calls it “fluorescence resonance energy transfer,” but then echoes Valeur that RET is a preferable term because “the process does not involve the appearance of a photon.” But Lakowicz also differentiates RET and Dexter electron exchange (because the latter is purely quantum-mechanical).

In Turro’s Modern Molecular Photochemistry, the energy-transfer chapter starts right in with a “Golden Rule” for the transitions between states, and demonstrates that the probability includes an exchange term and a Coulombic term. (Valeur’s book also includes a nice mathematical explanation of the two terms; it might even be in Lakowicz somewhere!)

So now I’m mostly reconvinced that FRET should be Förster resonance energy transfer, not fluorescence. That is, RET is the general term for nonradiative excitation-energy transfers, and FRET is a specific mechanism—the specific mechanism applied in practically all biophysical measurements using RET to study distances.

What do you think? Am I way off?

UPDATE: IUPAC says I’m right.

do not unplug that fridge

February 13, 2008 at 5:38 pm | | everyday science, hardware

You can tell that someone had an unfortunate day when they opened the fridge and found all their samples ruined:

fridge-sign1.JPG fridge-sign2.JPG fridge-sign3.JPG

Who would unplug a fridge, anyway? Ridiculous. I think it was the people putting a new ventilation system in the room, a few years ago.

(My camera has been broken for the last few months. Now that it’s fixed, I hope to post more photos!)

irradiating a cuvette

February 12, 2008 at 1:54 pm | | everyday science

Just a nice picture of a cuvette in diffuse 407-nm laser light:


Don’t look at it for too long or you’ll burn your corneas.

pretty picture for a friday

January 25, 2008 at 3:32 pm | | cool results, everyday science

Just a picture of my nice column (thanks for the help and the hood-space, Nick):


Some photoproducts of a cool reaction that I’ll tell you about when it’s published.

strange ice

January 17, 2008 at 5:35 pm | | EDSELs, everyday science, grad life

edsel.jpgToday, I became the senior graduate student in my lab. Which is scary, because who do I go to when I have questions?!?! The new students joining the lab tend to come to me with a lot of questions. I’m sure the other senior lab members get a lot of questions, too; and it’s fun to watch the now-second years get all the same questions that they asked me when they joined. I really like helping people with science questions, and I want the new members of the lab to benefit from me just as much as I benefited from my seniors when I joined. But then there are those other questions…

This EDSEL goes for the Best Question from a New Lab Member of 2007. Runner-up is “What is the phone number here in lab?” My answer: “Um, it’s written right there on the phone.” The winner goes to this conversation:

Post Doc: I just got a package that had ice in it to keep the sample cold. What do I do with the ice?

Sam: You can put ice in the sink. It’s just water, so it’s OK to go down the drain.

PD: But it’s strange ice.

Sam: What do you mean, “strange”? Is it dry ice?

PD: I dunno.

Sam: You know, dry ice: solid carbon dioxide?

PD: I dunno.

Sam: Hrumph. Is it smoking?

PD: Yes.

Sam: That’s dry ice. Just leave it in the box and it will sublime.


Now, the post doc isn’t from the US, so maybe he couldn’t remember the word for dry ice. But I thought the “frozen CO2” description would help. I guess not. I’d ask him to post his side of the story, but he’s no longer in the lab.

“Post Doc,” if you’re reading this: Congrats! You won an EDSEL.

scifinder scholar 2007: finally online

January 7, 2008 at 3:36 pm | | everyday science, literature, software, wild web

Here at Stanford Chemistry, we just got access to Scifinder Scholar 2007 … the online version. Cool! Finally, web-access to CAS searching. I decided to try it out and give a little review.

First, I’ll say that I actually like the little stand-alone SFS program: I find it quite user friendly and versatile. But a version accessible via the web is nice (and inevitable). The online version has kept most of the same interface and function, with a web style.

Other databases, notably ISI Web of Science, are really great at finding H-index values or citation trends. But, when I really want to do a lit search on a topic or reaction, SFS is always my first choice (maybe after just typing it into Google). CAS has a nice Flash demonstration and screen shots here. Here are some on my own screen shots (click on them for full images).

A fruitless search:

And the result. Or a reaction search:


Another cool new feature in SFS (web or software version), is the “keep me posted” button: You can follow up on searches or results. Currently, I have alerts from ISI sent to my RSS reader; I’ll have to explore this new SFS feature to see if it’s better.

A couple bad things about the new web version of SFS. It can be a little slow loading the Java and Javascript pages. More importantly, it does not include the ever-so-helpful “remove duplicates” feature. (UPDATE.) I hope this latter problem can be corrected, because I hate seeing the same paper listed millions of times!

I think I’ll use SFS web, especially when I’m using a computer that doesn’t have the software installed. Overall rating: super rad cool.

fun to look in a microscope

October 26, 2007 at 3:03 am | | cool results, everyday science

Sometimes it’s just entertaining to look into a microscope. I like this pic I took the other day:

It looks like a tiny sun. But it’s just a fluorophore solution that has dried up and left some large aggregates (which emit at a longer wavelength—the green is the normal emission—maybe Excimer will like this, at CBC’s new website).

You can also see a bleached region in the middle of the green from the peak of the laser excitation region, and a swath of bleached dye where I moved the stage up and down before the picture. You might even make out some single molecules in the center. Quite impressive for a simple digital camera!

This was actually before I aligned the beam for real experiments, so all the ring patterns are actually interference due to poor alignment. I just thought that the misalignment made it pretty, so I took a color picture.


October 19, 2007 at 2:51 pm | | everyday science, literature, science community

Initialisms and acronyms pervade science. I mean, they’re pervasive everywhere, but scientists use them a lot. And each field and subfield and subsubfield has its own set of acronyms.

I can be sorta a snob when it comes to grammar and acronyms; I like sentences that I can understand. So I decided to set down some guidelines for making a good acronym. Now these are neither exhaustive nor necessary: I’m sure I forgot some rules and I know that some good acronyms fail some of the rules. I just wanted to get something down on epaper; maybe y’all can help me flesh out the list.

Guidelines for Introducing a New Acronym in a Paper (GINAP)

  1. First off, for new compounds, basically anything goes as long as the acronym is simpler than the IUPAC name.
    Of course, you should check whether the chemical or a similar structure has already published with an acronym. If it hasn’t, then just choose the major letters and make an acronym so you can refer to it throughout the paper and other papers. For instance, 6-propionyl-2-dimethylaminonaphthalene (PRODAN) is a great acronym; it has the added bonus that once can pronounce the word. It could also have been PPDMAN: not as sexy but it would accomplish the purpose.
  2. Ask yourself, Does this method/system/etc. need a new acronym? Does it deserve one?
    Not all new ideas necessitate a new word. Not all ideas you publish will be new. For these reasons, it’s important to question how important it is to introduce a new acronym in the first place. If your method is a slight variation on a common practice, or a common practice applied to a new system, maybe you don’t need a new acronym. Moreover, if you can describe what you are doing with a few words (or in a few sentences one time in the methods section), then there’s another reason not to come up with a new acronym. This guideline has two goals: (a) to avoid further obfuscating the terminology in your field and (b) to avoid taking credit for a whole method if you only contributed a minor part. For instance, polarized radiation imaging of single-molecules (PRISM) would be a fun acronym, but people have been doing that for decades without naming it.
  3. Don’t try to be too cute
    Acronyms are best justified by making sentences more clear. So come up with an acronym that makes sense, not one that is catchy.
  4. Make the acronym descriptive and meaningful
    If an informed person knows what each letter of the acronym stands for, they should understand the method (or system or instrument or whatever). For instance, TEM stands for transmission electron microscopy; a reasonable scientist could understand that this refers to a microscopy technique that involves transmitting electrons through a sample. But what does mean cleverly harnessing the absorption of single molecules (CHASM) mean? (OK, I made that one up.)
  5. Make the acronym unambiguous
    I think that each letter should be unambiguous: if a letter could easily stand for two opposites, then clarify by adding another letter. For instance, “I” could stand for “inter-” or “intramolecular,” so for excited-state proton transfers, ESIPT could be ESInterPT or ESIntraPT. Another example is Förster resonant energy transfer (FRET): because the ambiguity with the “F,” the first word is often referred to as “fluorescence,” which is wrong. (My favorite exception to this rule is laser. Laser is one of the best acronyms ever, but the “s” could easily stand for “stimulated” or “spontaneous,” the two types of emission. If you know how a laser works, it’s obvious that it’s amplification by stimulated emission, but the acronym doesn’t necessarily help someone who doesn’t know.)
  6. Be consistent
    Be consistent in which letters you use. For instance, GINAP above uses each capitalized letter when in title case (it skips the prepositions and articles). PRODAN isn’t consistent because “pro” comes from “propionyl.” FlAsH (Fluorescein Arsenical Hairpin binder) is not consistent, but the capitalization indicates that.

OK, what else did I forget? Or what are your favorite acronyms? Does anybody know of a good list of bad scientific acronyms out there? (NMR acronyms don’t count because they’re all bad. COSY. Pffft!)

pretty bubbles

September 10, 2007 at 4:54 pm | | cool results, everyday science

No, not these.



Another, and the setup:

bubble_bleach1.jpg bubble_bleach_setup1.jpg bubble_bleach_setup2.jpg

It’s a pretty simple experiment: bleaching a vial of dye to determine what the fluorophore photodegrades into. I bubbled some air to make sure I get the reaction with oxygen.

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