I like to think that I understand organic chemistry on somewhat fundamental level, being able to talk, for not too long, about frontier molecular orbitals, conformational analysis and subtle structural features that influence peculiarities in chemistry of compounds in question. So now I've got the crystal structure of a compound which gives a ground to muse about all of the aforementioned stuff. And guess what? It brought more new questions than answers, having chosen to adopt an unexpected conformation that contradicts its reactivity observed in solution. Sometimes a hero in a role-playing game finds a relic plate armor — but he cannot put it on, for he lacks the skill 'plate armor'. It seems like calculations and advanced NMR experiments are required to properly understand what is going on with my chemistry... no time for that. The positive part is that we know most of what we need to for the first paper, but before it's out I'd like to say that I know the ways of our molecules...

  Reading this one raised controversial feelings in me. First, This paper is of little value and is not a JOC-level paper.

  1. Preparation of BODIPY dyes from pyrroles and aromatic aldehydes has been known for decades. What they published was preparation of 1 (one) "new" derivative, which is pretty damn far from causing gasps in the audience by being dramatically better.
  2. They published an OrgSyn procedure for the synthesis of 2,4-dimethyl-3-ethyl pyrrole (aka kryptopyrrole) as their own. With experimental details, in the format of full paper. Without citing anything. Sometimes people like to make mention of previous work, done by them or others, to fill the new paper with more material, which I'm fine with, unless it becomes too obvious and blatant like here. Not only this is an early 20th century name reaction (Knorr pyrrole synthesis), but the compound is commercially available and decently priced ($125/5g from Acros). "In keeping, compound [in question] turned into a thick blackish liquid." Now that's a discovery. Noone could ever imagine this may happen to an electron-plentiful pyrrole if one is going to keep the Acros bottle which says "refrigerate and store under inert atmosphere".

  However, this reminds me of all the troubles with looking for the procedures for syntheses of simple compounds, made long ago and published in the journals you may or may not find online. Sometimes it's even worse, when you have to follow a chain of two, three, or more references to track down the original procedure published somewhere of what even your librarian has never heard. So if I am to prepare something and cite a procedure source in my paper, I'd try to make sure that I'm not sending people too far. Otherwise, I'd just rewrite it, with or without modifications, with a reference to original paper. But I doubt it's worth doing to an Orgsyn procedure...

Are they being serious?


  1. LEWIS DOT STRUCTURES. Why do chemistry textbooks and Mendeleevists tell students that electrons are black dots, bonds are lines, and atoms are letters? It's a lie. X-ray crystallography and the Schrodinger equation prove that electrons are not black dots, bonds are not lines and atoms are not letters. Tell your teacher to: Teach the Lewis Dot Structure Controversy!"
  4. THE THIRD LAW OF THERMODYNAMICS. A perfect crystal at O Kelvin has zero entropy? Has anyone ever seen a perfect crystal? No! Is anything in the universe that cold? No! Who needs a Law about some twisted Mendeleevist fantasy. Teach the Third Law Controversy!

  Apparently, electrons, bonds, atoms and X-rays — that they have seen...
  via darth_vasya

  It is, I believe, the first time when I observe such serious discrepancy in physical properties of a compound in different sources. The density of propargylamine [CAS# 2450-71-7] is 0.803 in Aldrich and 0.86 in Acros, and if you google "2450-71-7 density" you'll see that people are confused. The compound, sadly, is absent in Merck Index and CRC Handbook and even in my obscure Russian sources. What's the big deal in 7% difference? Well, believe it or not, in the reaction that I've just ran the product is destroyed by excess of amine. I tend to blame the cruel world.

  Why wouldn't I just measure the damn density? Oh yes, sure, I would like to reserve this exciting field for myself. Preliminary results have shown that the density is closer to the Aldrich value (0.80), but additional experiments are required.

  BTW, according to Webster's, the radical is named propargyl because one of the hydrogens can be replaced by silver. Oookay, not a terribly logical move, but whatever. Allyl makes more sense — compounds alliin and allicin, found in garlic (Allium sativum), are responsible.

  (E)-cyclooctene is the smallest stable cyclic alkene with a double bond of trans-configuration. High level of strain leads to two distinct enantiomers of (E)-cyclooctene (the symmetry element is called chiral plane) and high inversion barrier (149 kJ/mol). This means that if you manage to separate the enantiomers, or to make it chiral through the asymmetric synthesis, you need to literally fry the poor molecule to achieve racemization. The strain also makes double bond unusually active, in particular, it readily forms complexes with silver(I). On this fact the purification procedure is based.

  Irradiation of olefins with UV-light is known to cause cis-trans-isomerization, and seems like the shortest route to (E)-cyclooctene from (Z)-cyclooctene. However, there are some problems, the biggest being low E:Z ratio at the photostationary state and poor photostability of the desired product. A neat way to overcome this problem is described in a recent JACS paper. The trick is to remove the product from the reaction mixture as it forms; this is achieved by continuously pumping the irradiated solution through a layer of silica impregnated with a silver salt. (E)-cyclooctene strongly binds to silver and stays; the other isomer goes through and returns under the tender rays of UV lamp. The product is liberated from the complex by a simple treatment of Ag-silica with aqueous ammonia.

  'Cause I'm holding a brand new BODIPY(624/636^[1]) in my lab coat pocket. It is the most far-red-absorbing compound I have ever made. It is blue by itself, but because of strong and EVIL red fluorescence it appears violet, and the color actually depends on how you look it at. I mean if you stare for it for exactly 6 hours and 66 minutes, you will start seeing hobbits BODIPY-shaped nanoputians creeping out, ready to take over.

  It is quite surprsing that there is no Wikipedia page for them, maybe I should work on that. But here is a nice review. The field is actually quite young. Here's a quote:

  4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (hereafter abbreviated to BODIPY) dyes tend to be strongly UV-absorbing small molecules that emit relatively sharp fluorescence peaks with high quantum yields. They are relatively insensitive to the polarity and pH of their environment and are reasonably stable to physiological conditions. Small modifications to their structures enable tuning of their fluorescence characteristics; consequently, these dyes are widely used to label proteins and DNA. However, these compounds also have some undesirable characteristics for many applications in biotechnology. For instance, most emit at less than 600 nm, and only a handful of water-soluble derivatives have been made. Thus, there is the potential that modifications to the BODIPY framework will lead to probes that can be used more effectively for imaging in living cells and whole organisms, but that is largely unrealized.

  Unusually small Stokes shift, which can be even lower than 10 nm, leads to quite unusual appearance. When you see something fluoresce green, you'd typically expect it to be yellow. Not often do you see red-green solutions. If, for some reason, absorption and emission are shifted to the red, the trend is preserved. This means that in the same solution, depending on the external illumination, you have two complementary colors. It's quite an amazing thing to my taste. Works great to impress girls, too.

  I also feel like backdating this so that I have an entry on Feb 29th.

  [1] — absorption/emission maxima, nm

  It is not a secret that chemists from any part of the world are usually suspicious when they have to follow a procedure published by some Asian group in some minor journal. This often comes in the form of weird reagents, reaction conditions, lack or absence of details in experimental procedures, microwave synthesis and so on. There should be a picture of chemist here, too. Anyway, sometimes such fears are well justified.

  He says a reviewer, a former student of his, pointed out that a Chiranjeevi submission on measurement of arsenic(III) was similar to a published paper from a Japanese group on chromium(III). In fact, Dasgupta says, but for the change in the name of the chemical being measured, the papers were identical. — and things like that in some 70 papers, published in a period from 2004 to 2007.

  Just in case, a quick intro to the world of color: all compound absorb electromagnetic radiation. The particular type of radiation, characterized by its wavelength, is known as light. From 400 to 700 nm we have visible light, and the compounds which do not absorb in this region are colorless, while those that do are colored. The fundamental Bouguer-Lambert-Beer law allows to relate the color intensity, or absorbance, to the properties of the material through which light is traveling: A=e*c*l [A = absorbance, e = extinction coefficient, a measure which is defined by the material itself, basically, it tells how colored the compound is, and l = light path length]. A nice experiment to make sure that absorbance actually depends on path length is to pour a colored solution (for example, potassium permanganate, if it's available to you) in a cylindric vessel. Watch from above while you dilute the solution - the color stays the same, but side view reveals that dilution actually occured.
  Absorbance is tied to the light path length, so to describe how colored the solution is the term optical density (OD) is used. OD=1 means that 90% of the light at given wavelength is absorbed and only 10% is transmitted. To the naked eye such solution will appear distinctly colored. 50% transmittance stands for OD of 0.3; for solutions with OD<0.1 it will be hard to notice the color without placing them in front of white background. If OD is greater than 10, your solution is brightly colored, if it's greater than 100, it's outrageously colored.

  With this not so quick and even somewhat comprehensive intro, let's talk about molar extinction coefficient, in particular, about the effects that chemists experience when log e is greater than 4.5 (e>30000), which is true for many common dyes. With a molecular mass of 500 and e of 50000, it takes only 100 mg/L (0.2 mM) to give us brightly colored solution. Thanks to their light-absorping properties, such compounds manifest themselves in very small concentrations. This property is certainly useful in many ways, but the whole purpose of this post is to point out that working with brightly-colored compounds raises the awareness of how difficult is it to make your glassware and workspace really clean. Say, usually I rinse the flask three times with acetone and consider it clean. Not true when dyes are involved. Especially if they are fluorescent, since the eye's sensitivity to fluorescence is even higher.

  A little bit of advice on handling the colorful spills from me, who had to clean up quite an amount of malachite green after a Dr. Sci. in biology, and a mess of saturated permanganate and a blown-up selenium dioxide reaction after himself. If the spill happens, clear the space and put everything else from the way before it gets stained, too. If the compound is a solid, do not try to wash it off all at once. As gently as you can, so as not to rub it into the surface, transfer it to your waste containter using a spatula or a piece of paper. Only when you're unable to go on this way use a solvent to clean up the rest. If it is liquid, my condolences. Do your best, try not to distribute.

  Finally, here's the compound from the previous post. Cheers to Kutti's screencast! I was lucky to stay clean, but I almost hated myself for being so cautious... I don't know the extinction coeffecient of this one, but I bet it's well above 100000. Credits to a colleague for the photo.

  To a stirred solution of 4-dimethylaminoazobenzene-4'-sulfonyl chloride (dabsyl* chloride) (324 mg, 1.00 mmol) and triethylamine (0.42 mL, 3 mmol, 3 eq) in dichloromethane (7 mL) under nitrogen was added toluene solution of 3-aminopropyl azide (ca. 0.8 M by NMR; 1.8 mL, 1.44 mmol, 1.44 eq) via syringe dropwise over 3 minutes. During the addition the color changed from deep blood-red to bright-orange. The reaction mixture was stirred overnight, washed with water (2x15 mL), dried (Na₂SO₄) and filtered through a 1-cm pad of silica with the aid of 10% methanol in dichloromethane (50 mL). Organic washings were concentrated to yield orange solid (ca. 500 mg), which was recrystallized from ethanol (20 mL) to give 322 mg (86%) of the product as sparkling red-orange flakes.
  NMR: (CDCl₃, 200 MHz) 7.94 (br s, 4H), 7.90 (d, 2H, J=9.2 Hz), 6.76 (d, 2H, J=9.2 Hz), 4.62 (t, 1H, J=6.3 Hz), 3.40 (t, 2H, J=6.3 Hz), 3.13 (s, 6H), 3.11 (m, 2H), 1.75 (quint, 2H, J=6.4 Hz); ESI-MS: [M+H]⁺ 388.1; R_f 0.60 (1:1 EtOAc:hexanes).

  Thou shalt expect colorful pictures in the next post.

  *There is some confusion in abbreviations. Dabsyl is a radical of sulfonic acid, while dabcyl is derived from the respective carboxylic acid.