Tag Archive | indoles

On the regioselectivity of metal-catalyzed functionalizations of heteroaromatic C-H bonds

The direct functionalization of aromatic heterocycles at ring C-H bonds via transition metal-catalyzed processes has become a powerful alternative to electrophilic aromatic substitution.  Arylation, benzylation, alkenylation, and amination of aromatic heterocycles are possible, largely via palladium or copper catalysis.  There are hundreds of papers describing the functionalization of both five- and six-membered ring heteroaromatics, but here’s the rub:  How can one predict the regioselectivity of these reactions?  A recent paper by Daniel Ess and co-workers at BYU (Organic Letters) moves us closer to that goal.

Let’s say you’re in the drug discovery business and would like to snap a bunch of different arenes onto a core structure.  Where will they go?  Regioselectivity is often high (c.f. the example from Lapointe, Fagnou, and co-workers below), but how can we rationalize and predict the regioselectivity, especially in cases where there is no directing group present?

Ess and co-workers summarized the work that has been done so far on rationalizing the regioselectivity of these reactions.  I would also suggest looking at the Lapointe/Fagnou paper cited above, which focuses on the same issue.  C-H bond acidity, carbon center nucleophilicity, steric and stereoelectronic effects, activation-strain analysis, etc., have all been posited.  If you have the software, know-how, and patience to calculate the geometries and energies of all of the relevant transition states, go for it.  In that vein, I’ve shown an exemplary transition state from Ess’s (that’s a lot of esses!) paper below, which features the widely accepted six-membered ring CMD (concerted metalation-deprotonation) mechanism.  Shown is the transition state for the reaction of pyrazine-N-oxide with PhPd(PMe3)OAc.

But who wants to calculate transition states?  Well, Ess has uncovered an attractive shortcut:  He and his co-workers, upon noting that the CMD step is inherently endothermic and thus has a late transition state, postulated that all you really need to know are the relative thermodynamic stabilities of the palladium aryl intermediates.  After all, in a late transition state, the C-Pd bond is well along the way to being formed, so a higher C-Pd bond strength should be correspond to a lower TS energy.  Indeed, after adjusting for some hydrogen bonding effects in certain substrates, they found that the regioselectivity of fourteen out of fourteen examples were correctly rationalized by estimating the thermodynamic stability of the palladium aryl intermediates, a much easier task than TS calculation.

Ess and co-workers also proposed another way to get at this problem:

…the strongest C-H bond (in the substrate) will be preferentially activated since it will lead to the most stable Pd-C bond.  Indeed, for arenes and heteroarenes 1 – 14 the strongest C-H bond generally has the lowest activation energy.

Now the task becomes a “comprehensive thermodynamic analysis of palladium aryl bonding,” which “will be the subject of a future detailed study.”  Add in an understanding of C-H bond strength in heteroaromatics and these reactions will be even more attractive.

A final note.  Focusing on the substrate alone is only part of the picture.  In the Lapointe/Fagnou work, conditions-based site-selectivity was also found to be important:



[EDIT: A follow-up to this post was published July 7, 2015, focusing on conditions-based regioselectivity.]

Fluorescent Indocyanines for Color-Coded Surgery

I always get excited when I see an unexpected glowing spot on a TLC plate.  Fluorescence!  I’ve sent many a graduate student on a wild goose chase to try to identify the source of that glow.

My curiosity about these compounds blossomed during my time in industry, where we worked on fluorescent compounds and quenchers of fluorescence.  Adding to the fun was the fact that most small-molecule fluorophores (as opposed to materials like quantum dots) are heterocyclic compounds.

Let’s look at a current application of fluorescent heterocycles and then a bit of chemistry.

Color-Coded Surgery

Check out this recent TEDMED talk by Quyen T. Nguyen, M.D., a Professor of Surgery at UCSD, who gives an entertaining talk on the use of fluorescent dyes to aid in finding and removing every last bit of a tumor.  Her collaborator, Roger Tsien, received the Nobel Prize in Chemistry in 2008 for his work on green fluorescent protein (GFP).

In this work, cell-penetrating peptides (CPPs) composed of polycationic sequences of 6-12 consecutive arginines are covalently attached to a fluorophore (Cy5, more on that later).  These labeled CPPs can penetrate into pretty much any mammalian cell without requiring specific receptors.  To target them to the tumor, they make activatable CPPs (ACPPs).  Generalized cellular uptake of the CPPs is blocked by fusing them to a polyanionic peptide domain (featuring glutamates) via a protease-cleavable linker, neutralizing the polycation domain via the formation of an intramolecular hairpin.  For specificity, the linker is designed so that it is cleaved by certain matrix metalloproteinases that are overexpressed in tumors.  After injection, the ACPPs travel to the tumor, are cleaved by the proteinases, and accumulate in the adjacent tumor tissue.  Shine some light on the area and you can see the tumor, including the normally difficult-to-find margins.  Great stuff!

What are the fluorescent dyes being used?

Nguyen and Tsien use indocyanines (or simply “cyanines” for our purposes), which have been long-known for their fluorescent properties and are popular for photography, laser printing, non-linear optical materials, and of course labeling biomolecules.  They have the typical push-pull electronic structure of many fluorophores; the conjugated system has an electron donor at one end and an acceptor at the other.

Back to Nguyen and Tsien:  Take a look here and here for some of their work.  For many of their applications, they use Cy5 (originally Pharmacia Biotech, now GE Healthcare), a pentamethine cyanine dye shown in the scheme below, which absorbs at 650 nm and emits at 670 nm in the red region of the visible spectrum.  This is well beyond the region of background fluorescence that is found in tissue, so the signal-to-noise is good.  They’re also quite bright.  Another advantage of these long-wavelength emitters is that the light can travel through quite a bit of tissue.

Structurally, an interesting feature is the presence of the geminal dimethyl groups, which not only dictate the landscape of the conjugated pi-system, they keep the dye molecules from stacking, which would allow energy transfer and thus quenching of fluorescence.  One can vary the number of methine groups in the central conjugated region to tune the wavelengths of absorption and emission (Cy3, Cy7, etc.)

How are cyanine dyes made?

The venerable Fischer indole synthesis is used to make the 2,3,3-trimethyl-(3H)-indole starting materials.  N-alkylation with an alkyl halide produces a salt, which is used in an aldol-like double condensation reaction with 1,1,3-trimethoxy-2-propene, an equivalent of malondialdehyde.

If you would like to learn more about the chemistry of cyanine dyes, take a look at Mojzych and Henary’s review on the synthesis of cyanine dyes, or if you can’t access that, download the thesis of Jamie Gragg, who has a nice historical overview of the discovery and development of cyanines.

If fluorescent heterocycles interest you, check back here for occasional posts; there will be more!