About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

Chemistry and Drug Data: Drugbank
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
Not Voodoo

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
Realizations in Biostatistics
ChemSpider Blog
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Eye on FDA
Chemical Forums
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa

Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
Gene Expression (I)
Gene Expression (II)
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net

Medical Blogs
DB's Medical Rants
Science-Based Medicine
Respectful Insolence
Diabetes Mine

Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem

Politics / Current Events
Virginia Postrel
Belmont Club
Mickey Kaus

Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« Zafgen's Epoxide Pays Its Way | Main | Where's the Widest Variety of Chemical Matter? »

June 25, 2014

That's Just Too Colorful

Email This Entry

Posted by Derek

orange%20compound.jpgI have just made the most eyewateringly fluorescent orange compound of my entire chemical career. It's not in a structural class that normally I would be exploring, but it's been a while since I was on a normal project, so that's fine. But this thing - yikes. I keep telling myself "It's a probe, it's a tool, don't worry", as all my med-chem instincts tell me that a compound like this, whose color would blend in only with a pile of nasturtiums, cannot be clean. But it is. And those same instincts keep telling me that a compound this wildly colorful can never, ever be of any use in a biological setting. It's an irrational prejudice, but it dies hard.

Comments (57) + TrackBacks (0) | Category: Life in the Drug Labs


1. CanuckGradStudent on June 25, 2014 8:38 AM writes...

What about isatins? They've been investigated for every medicinal property under the sun and they're the brightest compounds I've ever worked with. They're so highly colored we materials chem folk now co-opt them to build solar cell dyes?

Actually the brightest orange I've seen is just plain old isatin.

Permalink to Comment

2. Charlie Abrams on June 25, 2014 8:43 AM writes...

Color me confused: Azo? Methylene blue? Prontosil?

Permalink to Comment

3. Virgil on June 25, 2014 8:44 AM writes...

I guess the classic example of colored drugs gone bad would be dinitrophenol for weight loss. If IIRC it was the first ever drug banned by the FDA. In addition to having the rather undesirable side effect of death, the users steadily turned bright orange over time.

Permalink to Comment

4. Hap on June 25, 2014 8:57 AM writes...

Well, they did lose weight...even if having the thinnest corpse in the funeral home wasn't exactly what they wanted.

If it's an isatin, there's plenty of derivatization papers out there - throw in a carbonyl compound and a cinchona alkaloid, and something will probably happen. The product probably won't be colorful, though.

Permalink to Comment

5. Lias Balbes on June 25, 2014 9:00 AM writes...

Post a picture, please!

Permalink to Comment

6. Vader on June 25, 2014 9:06 AM writes...

What Charlie and Lias said.

Permalink to Comment

7. Anonymous on June 25, 2014 9:14 AM writes...

bright orange? Mutagen!

Permalink to Comment

8. MolecularGeek on June 25, 2014 9:31 AM writes...

You ought to be able to sell it to the microscopy and imaging crowds as a dye, if nothing else.

Permalink to Comment

9. pharmacologyrules on June 25, 2014 9:36 AM writes...

#3--do you think John Boehner takes diNO2phenol?

Permalink to Comment

10. MAZ on June 25, 2014 9:38 AM writes...

Oxindole RTK inhibitor?

Permalink to Comment

11. newnickname on June 25, 2014 9:38 AM writes...

#2 asked about Prontosil. Not only is the chemical a red color, but it turned the patients red! ... while also saving their lives as a side effect.

Permalink to Comment

12. Hap on June 25, 2014 9:45 AM writes...

Other than the yellow solution, it looks like a fruit-tomato juice hybrid. It's pretty, though.

Permalink to Comment

13. dlib on June 25, 2014 9:47 AM writes...

Now is the time to don the white coat, put it in a flask, light up the bunsen burner and call the marketing department's photographer ;-)

Permalink to Comment

14. TX raven on June 25, 2014 9:54 AM writes...

"It's an irrational prejudice..."

I thought they called these things "guidelines"


Permalink to Comment

15. Anonymous on June 25, 2014 9:55 AM writes...

Isn't this the stuff they put in Berocca that makes your wee fluorescent yellow?

Permalink to Comment

16. Helical Investor on June 25, 2014 10:05 AM writes...

Doc - I have some good news and bad news for you.

Patient - What's the good news?

Doc - We have an effective way of treating your ailment.

Patient - And the bad news?

Doc - Your future career opportunities may be limited to 'Oompa Loompa'.

Permalink to Comment

17. anon the II on June 25, 2014 10:05 AM writes...

Thanks for the picture. How 'bout a structure to boot?

Permalink to Comment

18. Chrispy on June 25, 2014 10:17 AM writes...

This is the kind of compound that can really show you how good your flash chromatography technique is. Nice, compact band migrating down the column? Good! Streaky, irregular glob? not so good...

Does it fluoresce as well?

Permalink to Comment

19. Hap on June 25, 2014 10:18 AM writes...

"To boot" would probably be right...I'd like to continue reading this blog, and if Dr. Lowe's unemployed, he won't have as much to blog about, and/or it would speed adoption of the "Do you like my writing? Please pay me to do it so I don't have to get out my change cup and sit in Harvard Square" blogging model.

Permalink to Comment

20. Contrarian on June 25, 2014 10:18 AM writes...

Cisplatin, doxorubicin, riboflavin, cobalamins, carotenoids, iodine, chloroquine, prussian blue, methylene blue, selenium sulfide...

Permalink to Comment

21. Vaudaux on June 25, 2014 10:22 AM writes...

Doxorubicin? Bright red in the IV tubing on the way in, also bright red on the way out an hour later.

Rifampin is pretty bright too

Permalink to Comment

22. PJ Hansen on June 25, 2014 10:29 AM writes...

If the compound a tool, and clean, then it looks like you've made enough to screen for target binding against all compounds in anyone's library. Until the end on time.

Permalink to Comment

23. CMCguy on June 25, 2014 10:35 AM writes...

Irrational or not even if biology turns out OK would suggest increases certain risks in the Clinical and Marketing aspects. Several actual drugs have been mentioned by commentators however would guess most encountered added hurdles not typically present with white crystalline products. You can always claim revisiting older classical medchem approach which was partly born out testing compounds from the dye industry.

Permalink to Comment

24. Erebus on June 25, 2014 10:37 AM writes...

Coenzyme Q10 is just slightly less orange than the stuff in the pictures. Isatin is pretty bad, itself. And emodin is basically the same sort of orange color... to say nothing of the other anthraquinones I've seen, which are all various shades of bright yellow to bright orange...

Permalink to Comment

25. Hap on June 25, 2014 10:42 AM writes...

All the cyanine dyes and dipyrroloboroles have to be colored too, so I don't imagine the color is a problem for a tool compound.

If it's bright enough, perhaps they can license it to OH for improvement of their construction signs - "Look, they're luminescent! Our drivers can't miss these, right?"

Permalink to Comment

26. Semichemist on June 25, 2014 10:46 AM writes...

I think I'm in tune with your instincts, seeing you hold a vial of something that colorful without gloves on is making me physically uncomfortable...

Permalink to Comment

27. David Formerly Known as a Chemist on June 25, 2014 10:46 AM writes...

I remember back in graduate school working for a short period on synthesizing hypericine (look it up), which was being explored by NIH as a lead for HIV (awww, the 80s, when even brick dust like hypericine could garner attention). A couple milligrams dissolved in a liter of acetone looked like whole blood.

Permalink to Comment

28. Secondaire on June 25, 2014 10:48 AM writes...

Beautiful. I was in a group that got a compound into Phase I for various stubborn cancers a while back, and that thing (with lots of conjugated heterocycles) was brown as a solid, and a lovely purple-magenta in solution.

Permalink to Comment

29. Jade_Nekotenshi on June 25, 2014 11:05 AM writes...

Doxorubicin and mitoxantrone come to mind, but then, those are really quite nastily toxic. They're just somewhat *more* toxic to the tumor than to everything else.

Permalink to Comment

30. Curryworks on June 25, 2014 11:14 AM writes...

looks like curcumin

Permalink to Comment

31. a. nonymaus on June 25, 2014 11:30 AM writes...

Bright colors, no problem. Long-lived luminescence, on the other hand... That's a good way to end up with singlet-oxygen phototoxicity. (unless you're trying to do that with some photodynamic therapy)

Permalink to Comment

32. oldnuke on June 25, 2014 11:30 AM writes...

Maybe a replacement for Red Dye No 2? gr

I'll never forget when my Dad discovered that the local market was using Red Dye #2 in their ground beef! The first clue was our Schnauzer's beard was slowly turning red.

Dad was not pleased and reported them to the USDA and State Health Dept. Fortunately, Snoopy's beard recovered. gr

Permalink to Comment

33. Derek Freyberg on June 25, 2014 11:31 AM writes...

Cyanocobalamin (injectable vitamin B-12) is a nice red.
And for orange, there are the CT scan contrast agents, which are iodinated something-or-others. Granted they put the oral one in Tang, which itself is orange, but you do pee orange as the agent makes its way through your system.

Permalink to Comment

34. Anonymous on June 25, 2014 11:34 AM writes...

Sutent is a yellow color - and also quite toxic

Permalink to Comment

35. A. Nonny Mouse on June 25, 2014 12:03 PM writes...

If it's not toxic, try dying material (or hair) with it. You could make a fortune if you've found a new family of dyes.

Permalink to Comment

36. John Wayne on June 25, 2014 12:58 PM writes...

@13 - Yeah, where are the lab tours when somebody makes something colorful?

Best be careful Derek; when this baby hits the clinic they are going to have to ground up skittles to make the placebo tablet the same color as the API.

Permalink to Comment

37. nachtmystium on June 25, 2014 1:15 PM writes...

Nasturtium would make a good metal band name...

Permalink to Comment

38. Anonymous on June 25, 2014 1:54 PM writes...

By measuring the absorption spectrum from the photo, and deconvoluting this into absorption and emission spectra of the compound, I think I've figured out that the molecular structure contains *at least* one aromatic group. Maybe more.

Permalink to Comment

39. Keiran Lee on June 25, 2014 2:14 PM writes...

@38 Dork

Permalink to Comment

40. Anonymous on June 25, 2014 2:59 PM writes...

OK I'm going to have to throw the rifamycins out there.

Permalink to Comment

41. Anonymous on June 25, 2014 4:33 PM writes...

Having worked in a manufacturing site that made large quantities of Sutent, epirubicin and doxorubicin the colour came in handy for proving product containment (or lack thereof)!

Permalink to Comment

42. Anonymous on June 25, 2014 5:16 PM writes...

Whatever the pigments are in the nasturtium are biologically relevant :)

Last year I grew nasturtiums. They taste VERY good. Kind of spicy and tangy. Intense. Great in salads.

Permalink to Comment

43. Jacob from Upstate NY on June 25, 2014 7:16 PM writes...

Back at the very beginning of my career, in my first semester in graduate school, I was sent off to make derivatives of perylene tetracarboxylic dianhydride as fluorescent probes for various things. I made one of these things and it barely dissolved in any NMR solvent except acetone-D6 and DMSO-D6. The solution was very similar in color to the red part of your picture there. So I finally got my spectra and I tossed the tube in a beaker in my cabinet and went home. The next morning, the rising sun shine into my cabinet, which lit up with an eerie green glow: that was the most fluorescent thing I've ever seen.
I then became more interested in the fluorescence than the synthesis, switched to a physical chemistry program, and became a physical inorganic chemist with a specialty in solid state NMR of aluminosilicate zeolites.
Go figure.

Permalink to Comment

44. Anonymous on June 26, 2014 1:55 AM writes...

Strongly fluorescent? Quantum yield please, 0.8-0.9 or bust.

Permalink to Comment

45. Anonymous on June 26, 2014 1:56 AM writes...

Strongly fluorescent? Quantum yield please, 0.8-0.9 or bust.

Permalink to Comment

46. elperrogrande on June 26, 2014 4:32 AM writes...

Gloves? (-;

Permalink to Comment

47. DrSnowboard on June 26, 2014 5:18 AM writes...


Permalink to Comment

48. Nekekami on June 26, 2014 6:35 AM writes...

Here's an experiment for you, Derek...

Will the smoke have that pretty orange if it goes boom?

Permalink to Comment

49. lol on June 26, 2014 11:57 AM writes...

Did you realize we can read your notebook from the reflection in that window!!! no but be careful.

Permalink to Comment

50. asd on June 26, 2014 8:57 PM writes...

Coming from a different chem background and not med chem, why is everyone worried about a little color?

Permalink to Comment

51. geekosaur on June 27, 2014 10:46 AM writes...

As a non-chemist: bright color usually means lots of electrons floating around loose, which usually means it reacts with anything it gets too close to. This is usually a liability in med chem, where off-target effects mean potential for nasty side effects.

Permalink to Comment

52. Another Kevin on June 28, 2014 12:12 PM writes...

Isn't phenazopyridine about that colour? It's even sold OTC...

Permalink to Comment

53. sepisp on June 30, 2014 6:01 AM writes...

Physically, color means that the compound has a conjugated system, and some of the resonance transitions this system has have an energy coincidentally in the visual range. For pure hydrocarbons, you need pretty big systems for this to happen, as in for instance beta-carotene. There is also a good explanation why heteroatoms can induce this even with rather small number of bonds - I've seen the article, but I'm not a quantum chemist so I can't explain it properly. It has something to do how the system is "squeezed" relative to an alkene. E.g. you get a much richer set of resonances with an azo compound vs. just an alkene. This is why you can get intense colors with something as small as a reductic acid, isatin or quinone.

Permalink to Comment

54. Cymantrene on July 2, 2014 2:20 AM writes...

My colleagues are working on a magenta dye used in printers. In solution and in thin layer it is magenta as one would expect, but in crystalline form it's metallic green with a golden hue, just like rose chaffer. It's astonishingly beautiful :-)

Permalink to Comment

55. Anonymous on July 6, 2014 12:34 AM writes...

@30 yep, I was going to say it looked like curcumin. One guy in my lab is synthesizing tetrazine compounds, which are fabulously colored: Neon red, fire engine red, orange, barbie pink, yellow; and they fluoresce yellow and orange.

Permalink to Comment

56. Gin on July 9, 2014 3:05 PM writes...

@29: mitoxantrone is a boring dark blue at physiologic pH. I've never altered pH to see if it turns orange, though.

An off the wall guess - cytochrome C? It is also beautifully orangish-red colored, although it is useful biologically so it can't be the answer.

Permalink to Comment

57. Shushu on October 15, 2014 10:12 PM writes...

I don't think that's what this is, but the coloration and its intensity looks almost exactly like the Petasis reagent in solution (

"orange colored" doesn't do it justice. even dilute solutions of this stuff are intensely vibrant

Permalink to Comment


Remember Me?


Email this entry to:

Your email address:

Message (optional):

The Last Post
The GSK Layoffs Continue, By Proxy
The Move is Nigh
Another Alzheimer's IPO
Cutbacks at C&E News
Sanofi Pays to Get Back Into Oncology
An Irresponsible Statement About Curing Cancer
Oliver Sacks on Turning Back to Chemistry