Check out the International Society of Heterocyclic Chemistry’s New Website

Dave Williams (yes, that Dave Williams), the Secretary of the International Society of Heterocyclic Chemistry, has put together a new web site for the Society as part of a thrust to energize this long-standing organization (founded in 1968!):

I’d recommend checking it out and supporting the Society. Individual membership is quite inexpensive. There’s also the opportunity for company sponsorship.

The ISHC has quite a bit to offer, including …

• A Biennial Congress on Heterocyclic Chemistry at locations around the world. The 26th ISHC Congress will be held in Regensburg, Germany in the summer of 2017.

• The review publication Progress in Heterocyclic Chemistry, free with membership.

The ISHC Bulletin, featuring recent publications of ISHC Members.

• Stewardship of the E.C. Taylor Senior Award in Heterocyclic Chemistry and the A.R. Katritzky Junior Award in Heterocyclic Chemistry.

One of Dave’s initiatives is to curate useful information on heterocyclic chemistry, so stop by the web site and take a look around. What resources do you know of that might find a home there?

Thanks to Dave, Oliver Reiser (ISHC President), Fredrick Luzzio (ISHC Treasurer), Dan Comins (ISHC Past President), and the members of the Advisory Board for their efforts to keep the Society alive and relevant.

On a personal note: The Heterocyclist, whose name derives in part from his love of bicycling, has been slow in posting for a while, in part due to a rather nasty bicycle accident. Think titanium hardware. He’s been keeping up with the literature as he recovers, and intends to get back in the saddle soon, blog-wise if not bike-wise.

Regioselective synthesis of 3- and 5-aminopyrazoles

Just a bit of sodium ethoxide does the trick …

The Knorr pyrazole synthesis, broadly defined, involves the condensation of hydrazines with 1,3-dielectrophiles, e.g., 1,3-diketones, beta-ketoesters, alpha-cyanoketones, beta-alkoxyacrylonitriles, alkoxymethylenemalonates, etc. When a nitrile electrophile is involved, an aminopyrazole typically results, producing compounds that are very useful in the pharmaceutical field. The first two equations in the general scheme below use hydrazine as the dinucleophile, but what happens when an unsymmetrically-substituted hydrazine is involved?  Wouldn’t it be nice to be able to produce either the 3- or 5-aminopyrazole regioisomer in a selective fashion?

Pyrazole introduction

This problem has been kicking around the literature for a long time. The 5-aminopyrazole is generally the major product, leaving the 3-aminopyrazole as a useful-yet-expensive poor cousin. Much effort has been spent trying to rationalize and predict the outcome of these processes, so a recent paper from Fandrick, et al., from Boehringer Ingelheim is a most welcome arrival.

Heating the nitrile 3 with the alkyl-substituted hydrazine 4 in ethanol produces the 5-aminopyrazole 7, presumably through the adduct 5, a result that is consistent with the prior literature. At first glance, this should be rather surprising, since it is known that alkylhydrazines are more nucleophilic at the most substituted nitrogen, i.e., k1 should be larger than k2, thus producing adduct 6 and the 3-aminopyrazole 8. (Arylhydrazines are different; they are generally more nucleophilic on the unsubstituted nitrogen, though it depends on the nature of the arene.) Fandrick and co-workers proposed that 6 is indeed the kinetically-formed adduct, but its cyclization to 8 (under typical neutral conditions) is slower than isomerization to the more stable adduct 5, producing 7 instead.

Fandrick work

In order to obtain the more rare and often desirable 3-aminopyrazole 8, Fandrick simply introduced sodium ethoxide to the mix with the idea that the kinetically favored 6 might be transformed to 8 before it can isomerize to 5. It worked, producing 3-aminopyrazoles with selectivities of up to 99:1 depending on the exact example.

Increasing the size of the alkyl group on the hydrazine should erode the selectivity for 8 in the kinetically-controlled ethoxide reaction, since the internal nitrogen of the hydrazine, while electronically more nucleophilic, is less accessible due to steric hindrance. Indeed, moving to cyclohexylhydrazine and then t-butylhydrazine leads to diminished and even reversed selectivities of 72:28 and 5:95 for 8:7. Under neutral thermodynamic conditions, cyclohexyl- and t-butylhydrazine gave >99:1 ratios of 7:8, as expected.

Arylhydrazines are known to highly favor 5-aminopyrazoles, which was supported by the current work when employing neutral (thermodynamic) conditions. Interestingly, reasonable quantities of 1-aryl-3-aminopyrazoles 8 were formed under kinetically-controlled (ethoxide) conditions. Hence, with phenylhydrazine, a 1:1 ratio of 8:7 was formed, indicating that a good deal of 6 was formed kinetically. Using the more electron-rich p-methoxyphenylhydrazine under kinetically controlled conditions produced even more of the 3-aminopyrazole, giving a 78:22 ratio of 8:7. This presumably reflects and increase in the nucleophilicity of the internal hydrazine nitrogen due to the resonance donating effect of the p-methoxy substituent.

Conditions-based regiocontrol in metal-catalyzed arylations of heteroaromatic C-H bonds

This is a follow-up to a previous post on the regioselectivity of C-H arylation reactions of heteroaromatic compounds.  

The direct C-H functionalization of aromatic compounds (including heterocycles) via transition metal catalysis has emerged as a powerful alternative to electrophilic (or nucleophilic) aromatic substitution and transition metal-catalyzed cross coupling reactions.  If you’re looking for an overview, Jie Jack Li has edited an excellent book on the general subject of C-H bond functionalization entitled C-H Bond Activation in Organic Synthesis. Heterocyclist readers are directed to Chapter 10 by Donna A. A. Wilton for a treatment of C-H activation in heteroaromatic compounds.

In a previous post, we considered the regioselectivity of C-H arylation reactions of heteroaromatic compounds, focusing on substrate-based regiocontrol, i.e., factors in the heteroaromatic compound that influence the site of C-H functionalization.

In this post, we consider emerging examples of conditions-based regiocontrol, i.e., modifying the reaction conditions, including the catalyst itself, to direct the regioselectivity of heteroaromatic C-H arylation reactions.  While there is little in the way of a satisfying mechanistic rationale for these results, it’s a promising synthetic approach. For entry into the relevant literature on this strategy, take a look at Engle and Yu’s JOC Perspective and Neufeldt and Sanford’s review in Accounts.

First up is an early report of conditions-based regiocontrol by Lapointe, Fagnou, and coworkers.  Conditions for selecting electron-rich (indole) or electron-poor (pyridine N-oxide) sites were explored using chemistry from various labs:

Conditions-based control

Next up, in very recent work by Bedford, Durrant, and Montgomery (U Bristol and Vertex), regiocontrol in the palladium-catalyzed arylation of pyrazolo[1,5-a]pyrimidine was achieved by tuning the catalyst.  The presence of a phosphine ligand directed arylation to C-7, the most acidic C-H as determined by NaOD exchange. In contrast, phosphine-free conditions favored arylation at C-3, the most electron-rich carbon as determined by calculations.  The two processes are believed to involve different mechanisms, though the details are not yet known.  The SPhos ligand system was homogeneous. Deuterium labeling studies showed that coordination to palladium was followed by a slower deprotonation that was still not the rate-determining step.  The phosphine-free system was heterogeneous and proceeded with a protracted induction period via two discrete catalytically-active species.



Bedford 2

Finally, consider the promising work of Yu and co-workers on the arylation of pyridines.  Six-membered-ring heteroaromatics are still relatively rare substrates for C-H functionalization because of the basic nitrogen, which tends to bind to the metal.  Most examples rely on making the N-oxide to circumvent this problem (e.g., the Fagnou example above), but Yu has been able to arylate simple pyridines by adding 1,10-phenanthroline, which competes well for the palladium, allowing the pyridine substrate to enter into the activation cycle.


Further advances in the understanding of substrate-control of regioselectivity combined with efforts at conditions-based control will surely elevate C-H functionalization to a new level of predictability and utility.

Update: Hong, et al. (KAIST), have recently published a nice paper on catalyst-controlled divergent C4/C8 regioselective C-H acylation of isoquinolones. Aryliodoinium salts were used as the aryl donors. C4 selectivity was achieved via an electrophilic palladation pathway; C-8 arylation was performed using an Ir(III) catalyst.

“Glass Microbiology” sculptures are beautiful

Off topic, but worth it:  UK artist Luke Jerram, in consultation with U of Bristol scientists, has made some incredible 1,000,000x scale glass sculptures of viruses, bacteria, and other tiny critters.  Check out a gallery of his Glass Microbiology sculptures, then take a look at his other work, which includes live arts projects, large-scale public engagement artwork, etc.   This guy has range!

SARS Coronavirus

SARS Coronavirus

Enterovirus 71, a causative agent for hand, foot, and mouth disease (HFMD)

Enterovirus 71, a causative agent for hand, foot, and mouth disease (HFMD)

Escherichia coli

Escherichia coli

Pd(II)-Catalyzed Dehydrogenative Cyclizations of N-Allylimines

Near-simultaneous reports of an interesting new pyrrole (and dihydropyrrole) synthesis have appeared recently from the labs of Frank Glorius (Westfälische Wilhelms-Universität Münster) and Naohiko Yoshikai (Nanyang Technologial University, Singapore).  Optimization of the additives, solvent, and temperature led to essentially the same conditions from each laboratory.  A balloon of oxygen is preferred: yields are much lower when air is used.  A Heck-type mechanism is shown, but a Wacker-type mechanism involving nucleophilic attack of an enamine onto a Pd-complexed alkene could not be ruled out.


The scope of the reaction is decent, as indicated below.  Failures include R3 = CF3 or cyclopropyl and R2 = Ph.  N-Homoallylic and N-cinnamyl imines were also unsuccessful.


Specific examples are shown below:


Short Course: “Heterocyclic Chemistry – A Drug-Oriented Approach”

Interested in having a short course on Heterocyclic Chemistry at your company?

In late 2011, I put together a new two-day short course entitled “Heterocyclic Chemistry – A Drug-Oriented Approach” to present at companies.  In a nutshell, it’s an intensive, preparatively-oriented course on the synthesis of the types of molecules encountered in the pharma and agricultural endeavors.  There is a heavy focus on practical, proven methodology that people actually use.  I keep it updated with lots of current chemistry.

Beyond the two days of instruction at your company, participants are left with a great resource:  A book of over 500 slides of information, nicely organized, well-referenced, and containing many specifics on the best ways to make heterocycles.

I’m booking courses for 2013 and early 2014.  Learn more by checking out the course web site, where you’ll find more on what the course covers.  You can also download a two-page summary of the course to pass around to your colleagues.  If you know of other chemists who might be interested in the course, I’d appreciate passing this along.  You can reach me at will at pearsonchemsolutions dot com.

Sample Slides:

Sample Slide 1Sample Slide 2

Just look at the structure of this alkaloid!

Sometimes you just have to step back and marvel at the structures that are found in nature.  Check out zamamiphidin A, a new manzamine alkaloid isolated from an Okinawan sponge by J. Kobayashi and co-workers (Organic Letters).  Heptacyclic.  Quaternary ammonium.  Massively bridged.  Well done, sponges!

Zamamiphidin A