Welcome to the second part of our Tour de Tetrazoles. In Part I, we saw that tetrazoles, particularly 5-substituted versions, are often made from nitriles and an azide source. Toxic and explosive hydrazoic acid can be formed in this chemistry, but we saw that there are ways to minimize its production.
Now let’s take a look at another general approach to tetrazoles, namely the concerted electrocyclic ring-closure of azidoazomethines. This chemistry will allow us to access a variety of tetrazoles, including fused-bicyclic versions, often under azide-free (and hydrazoic acid-free) conditions.
The tetrazole-azidoazomethine equilibrium
Azidoazomethines, also known as imidoyl azides, can undergo a concerted electrocyclization reaction to tetrazoles:
The position of the equilibrium depends on the nature of the substituents: electron-withdrawing groups on the azomethine nitrogen favor the open form, whereas hydrogen and normal organic substituents favor the tetrazole (leading reference and theoretical studies).
Fascinating, but there’s more: This equilibrium is an excellent entry point for tetrazole synthesis. Anything you can do to make the azidoazomethine will, with the right substituents, lead to the tetrazole.
Accessing azidoazomethines, and thus tetrazoles
If you can make the azidoazomethine, you’ll get the tetrazole. So, how does one make azidoazomethines? There are two primary methods, namely (1) the use of an activated amide to acylate sodium azide and, (2) the diazotization of amidrazones, themselves available by acylation of hydrazine with an activated amide:
Notice that the amidrazone method doesn’t require sodium azide or its equivalents, prompting some to call this an “azide-free” method. A word of caution, though: It’s conceivable that the azidoazomethine could eliminate azide, so hydrazoic acid may still be lurking. Use caution.
Example: Azidoazomethines (and thus tetrazoles) by Duncia’s method
John Duncia at du Pont reported a nice way to access azidoazomethines (and thus tetrazoles) from amides and TMSN3 using diethyl azodicarboxylate and triphenylphosphine. Shown below is a more recent application of Duncia’s method by discovery chemists Li, Tino, and co-workers at Bristol-Myers Squibb, who synthesized BMS-317180, a GHS agonist.
The Process R&D group at BMS later felt that the issues of high exothermicity, TMSN3 safety, and PPh3PO removal warranted another approach to the tetrazole for scale-up.
Example: Azidoazomethines (and thus tetrazoles) from amidrazone diazotization
The BMS process group ultimately decided to avoid azide chemistry altogether by using amidrazone diazotization chemistry. Hydrazinolysis of the oxazoline shown below gave an amidrazone that was then diazotized to give the azidoazomethine (not shown) and thus the tetrazole on a 40 kg scale. Superb.
By the way, you can also make 5-substituted tetrazoles from amidrazones, though it’s not as common as the nitrile/azide method discussed in Part I of this post. Here’s an example :
Fused bicyclic tetrazoles: An ideal application of the azidoazomethine-tetrazole equilibrium
Azidoazomethines where the azomethine (imine) is part of a ring, e.g. 2-azidopyridines and 4-azidopyrimidines, undergo electrocyclization to provide fused bicyclic tetrazoles. Historically, this is where the azidoazomethine-tetrazole chemistry began, with work by Bülow (1909; azidopyrimidines), Benson (1954, azidopyrimidines), Boyer (1959, azidopyridines), and McKee (1962, azidopyrimidines). The following example is from McKee’s lab at UNC and Montgomery’s lab at SRI (see also here). Both the azide and diazotization methods were used successfully.
Finally, remember that the position of the azidoazomethine-tetrazole equilibrium depends on the electron density around the tetrazole? McKee used that knowledge to develop a new purine synthesis: Converting the above amine (electron donor) to the imidate shown below (electron acceptor) caused the azidoazomethine-tetrazole equilibrium to shift to favor the latter, which upon heating gave a purine. There’s some great stuff in the old literature.
McKee, by the way, was the professor that got me interested in heterocyclic chemistry… see an earlier post for that story.
I hope you’ve enjoyed this Tour de Tetrazoles. I know there are some tetrazole experts out there, so please share some of your knowledge in the Comments.
Azaphiles, unite! Azaphobes, run! It’s time to delve into the synthesis of tetrazoles (review) in this two-part post. Whatever you think you know about making these hard-core heterocycles, I’ll wager you’ll still find something interesting here. Are you thinking that all tetrazoles are made with azide chemistry and thus you’ll lose a limb to an explosion? Read on.
Full disclosure: I love molecules with several nitrogens in a row. My graduate work involved adding organometallics to azides to produce triazenes and a good deal of my group’s research at the University of Michigan involved azides, triazoles, triazolines, etc. Good times.
When considering tetrazoles, most organic chemists will likely think first of 5-substituted tetrazoles, long known to be good carboxylic acid biomimetics/bioisosteres in the drug discovery endeavor, their acidity being much the same as those of carboxylic acids (see Meanwell’s excellent review). But there are other important types of tetrazoles that are nonacidic, e.g., disubstituted tetrazoles and fused bicyclic tetrazoles.
In the current post, we’ll consider making 5-substituted tetrazoles using azide chemistry. Online IR studies by the process R&D group at Merck Frosst are instructive in dealing with the dangers of hydrazoic acid.
In the next post, we’ll look at the tetrazole-azidoazomethine equilibrium for the synthesis of disubstituted and fused-bicyclic tetrazoles, where we’ll find that one can avoid sodium azide and hydrazoic acid issues entirely. Well, almost entirely.
5-Substituted tetrazoles – dealing with the dangers of hydrazoic acid
A popular procedure for making 5-substituted tetrazoles is the reaction of sodium azide with a nitrile, often in the presence of an ammonium salt. The example shown below is from Organic Syntheses (Novartis Process R&D and Ley’s group at Cambridge), providing the useful enantiocatalyst shown on an 80 mmol scale. The excess sodium azide was destroyed with sodium nitrite and sulfuric acid, which converts hydrazoic acid into nitrogen and nitrous oxide gases.
While the above procedure may be popular, any time you use sodium azide you should be thinking, “hydrazoic acid can be generated, it’s explosive and toxic, and I need to take the appropriate safety precautions.” That’s precisely what happened during some recent process R&D work at Merck Frosst on the steroyl-CoA desaturase inhibitor MK-8245. The discovery chemistry route used NaN3/pyridinium chloride as shown below, but the process group felt that the potential for significant amounts of hydrazoic acid generation was too high.
Armed with the ability to detect hydrazoic acid in the headspace above the reaction mixture using online IR, the Merck Frosst researchers surveyed alternatives. Sharpless’s zinc bromide procedure, proposed to minimize hydrazoic acid formation by control of the pH, led to a reading of 2000 ppm of HN3 in the headspace, which is below the detonation threshold of 15,000 ppm but was still felt to be undesirable. In their own survey of conditions, the Merck Frosst scientists found something quite new and significant: Reaction with sodium azide in the presence of a catalytic amount of zinc oxide in aqueous THF (pH 8) proceeded efficiently, and most notably, with only 2 ppm of HN3 in the headspace! They were able to make 7 kg of the tetrazole in one run in nearly quantitative yield. Nice!
I’d be remiss if I didn’t mention Bu3SnN3 and Me3SiN3/Cu(I) as sodium azide surrogates, sometimes used on large scale. Shown below is an application to valsartan (see here and here) with recycling of the tin by-products. The intermediate stannyl tetrazole and leftover Bu3SnN3 were converted with HCl to Bu3SnCl, which was then converted to the fluoride, which was removed by filtration and recycled to Bu3SnCl.
Next: The tetrazole-azidomethine equilibrium and its use in tetrazole synthesis.
It’s time for some “oldie-but-goodie” heterocyclic chemistry, namely the Knorr pyrrole synthesis. What’s left to be said about this venerable route to pyrroles? Well, I’d like to point out that it should probably be termed the Knorr pyrrole syntheses (plural). As usual with chemistry, things are more complex than they first appear.
Here’s the upshot: There are two fundamentally different pyrrole connectivities that are produced under the Knorr umbrella. Let’s look at what they are and then delve a little deeper into the connectivity that is often overlooked.
What is the conventional Knorr synthesis?
If you were to consult a reference source or ask someone to describe “the Knorr pyrrole synthesis,” you’d probably find something like this:
The Knorr is usually considered to be the condensation of an α-aminocarbonyl compound with another carbonyl compound, typically an active methylene compound such as a β-ketoester, in the fashion shown above, generally proceeding by (i) condensation of the amine with the other carbonyl compound and (ii) an intramolecular aldol (Knoevenagel) condensation. Using an organizational system that I employ in my heterocyclic chemistry course, it’s a [3+2]-a,c approach, i.e., it makes the bonds at the “a” and “c” faces of the pyrrole by combining a three-atom component and a two-atom component.
Getting specific, one of my favorite examples is Hamby and Hodges’ 1993 work at Parke-Davis, featuring a Weinreb amide approach to the α-aminocarbonyl compound and reductive deprotection to the amine in the presence of the β-ketoester:
Most [3+2]-a,c Knorr examples produce pyrroles with an electron-withdrawing group (EWG) at the 3-position, but there are examples without it.
The Fischer-Fink variant of the Knorr pyrrole synthesis
If you look a bit further into the Knorr synthesis, you find examples that I would classify as [3+2]-a,d variants. Here, the α-aminocarbonyl compound contributes two pyrrole atoms rather than three; the other carbonyl compound (typically a 1,3-diketone) contributes three atoms rather than two. These reactions proceed by (i) condensation of the amine with the other carbonyl compound to form bond a and (ii) an intramolecular aldol condensation to form bond d. If the amine bears two electron-withdrawing groups (as it does in much of the early work), one is lost during the reaction.
This variant of the Knorr synthesis is perhaps best termed the Fischer-Fink variant after the discoverers of traces of these compounds in traditional Knorr syntheses that employ ethyl acetoacetate (H. Fischer and E. Z. Fink, Hoppe-Seyler’s Z. Physiol. Chem. 1944, 280, 290 and 1948, 283, 152 and this link).
It was Kleinspehn in 1955 who figured how to obtain a majority of the [3+2]-a,d connectivity: simply use diethyl malonate rather than ethyl acetoacetate. Paine and Dolphin later improved Kleinspehn’s method by preforming the amine rather than carrying out an oxime reduction in situ. The Paine/Dolphin method is notable in that it works regioselectively with unsymmetrical 1,3-diketones and has found wide application in porphyrin synthesis.
Let’s look at a couple of my favorite examples of the Fischer-Fink variant of the Knorr pyrrole synthesis.
Elliott and co-workers at BioCryst used an α-cyano aldehyde rather than a 1,3-diketone, producing a 2-carboxy-3-aminopyrrole, an intermediate in their synthesis of some PNP-inhibitory pyrrolopyrimidinones (9-deazaguanines):
Prashad and co-workers in the process group at Novartis later used the Elliott chemistry to prepare a related PNP-inhibitor. Both the BioCryst and Novartis groups used cyanamide as the cycloguanidinylating agent to produce the pyrrolopyrimidinones, a method that can be traced back to the work of my early mentor Robert McKee at UNC-CH, the subject one of my earlier posts.
The Fiesselmann-type modification of the Fischer-Fink variant
Okay, that’s a mouthful, but I think it’s worth treating this [3+2]-a,d method separately. In the Fischer-Fink chemistry, a 2-aminomalonate is used, one of the esters being lost in the cyclization reaction. Starting in the 1980s, examples began to appear where a simple glycinate is used; the second ester is omitted. Thus, the condensation of simple α-amino esters with 1,3-diketones or their equivalents produces 2-carboxypyrroles as shown in the following example by Mataka (Synthesis, 1983, 157-159):
As far as I can tell, there isn’t a standard way to refer to these reactions. They remind me of the Fiesselmann thiophene synthesis, which involves the condensation of α-mercaptoacetates with 1,3-diketones and their equivalents, so I’ll call these Fiesselmann-type modifications of the Fischer-Fink variant of the Knorr pyrrole synthesis.
Here are a few more examples of the Fiesselmann-type pyrrole syntheses. Note the complementary regiochemistry of the last two examples.
The greater Knorr synthesis umbrella produces two basic connectivities resulting from [3+2]-a,c or [3+2]-a,d constructions.
Knorr-o-philes please weigh in.
[Jan. 21, 2012: Edited Fischer-Fink citation to include earlier work.]
In principle, the acid-catalyzed cyclodehydration of amino alcohols is an attractive way to make saturated nitrogen heterocycles since it avoids having to make the alcohol into a leaving group such as a halide or sulfonate. And acid is cheap.
Unfortunately, this reaction doesn’t work well for underivatized amines because the amine is converted to a non-nucleophilic ammonium salt.
Enter the Mitsunobu reaction, which works quite well with simple amino alcohols (despite their low pKa) as well as their derivatives (amides, sulfonamides, etc.) The literature is filled with examples of such intramolecular Mitsunobu reactions.
However, if you play your cards right, acid-catalyzed cyclodehydrations can be practical and even preferred over the Mitsunobu method. The rule of thumb is that the alcohol should be able to form a reasonable carbocation. Park and co-workers recently published a nice example that compares these two methods in the context of 2,3-disubstituted indoline synthesis.
An attempted Mitsunobu reaction on the amido alcohol shown gave the indoline in low yield; the major product was elimination of water. Resorting to aqueous HCl in dioxane afforded the desired indolines in good yield with a small amount of elimination. Inversion at the secondary alcohol was observed. Substrates with a secondary benzylic or allylic alcohol worked, whereas those with a secondary alcohol (or an electron-poor benzylic alcohol) failed.
The authors propose a rather implausible nitrogen-complexed cation intermediate and don’t speculate on the why acid catalysis beats the Mitsunobu reaction. I suspect it’s related to leaving group ability and subtleties wherein the amide carbonyl oxygen is involved in a balancing act between assisting the departure of the leaving group by neighboring group participation (for hydronium ion) and acting as an internal acceptor of the benzylic proton in an E2-like mechanism (for oxyphosphonium ion). Your thoughts?
The starting materials were made by a diastero- and enantioselective reaction of the sparteine-complexed dianion shown below. While the authors don’t show it this way, I’ve taken the liberty of drawing the organolithium as internally complexed. It is believed that the benzylic organolithium equilibrates to the most stable diasteromeric sparteine complex, which then reacts with inversion of configuration with aldehydes to give the desired secondary alcohols in good yield with high er and dr. As a reminder, most configurationally stable organolithiums react with retention of configuration, but it’s not a certainty; there are numerous examples where inversion is observed.
In summary, if your alcohol is reasonably capable of ionization, the acid-catalyzed method is worth a shot. Otherwise, the Mitsunobu is generally a nice way to make saturated nitrogen heterocycles. Of course, classic chemistry involving halides and sulfonates is also viable if you don’t mind the extra work.
The aminomethylation of arenes and electron-rich aromatic heterocycles typically involves iminium ion chemistry, i.e., Mannich-type reactions. But when the heterocycle is electron-poor, what then? Recent work offers an attractive approach involving nucleophilic α-amino radicals.
David Mitchell and co-workers at Lilly recently published the scaleup of LY2784544, a JAK2 inhibitor. Their paper is chock-full of interesting chemistry and is highly recommended for a read, but let’s look at just one slice: the installation of the morpholinomethyl group using a radical addition reaction.
In a first-generation approach, the intermediate shown below was subjected to Minisci’s method for radical alkylation. Phthalimide-protected glycine was used as a source of pthalimidomethyl radicals. Around 3.5 kg of the CH substitution product was obtained, but the route was abandoned due to reproducibility problems, relatively low regioselectivity, insoluble by-products, and the need for large amounts of silver nitrate.
In a second-generation route, iminium ion chemistry was explored, but none of the desired material was formed. In their survey of iminium ion techniques, however, the Lilly group found one outlier: Hwang and Uang’s method using N-methylmorpholine-N-oxide and VO(acac)2. In the Uang work, electron-rich arenes such as phenols and naphthols were aminomethylated; there were no examples of electron-deficient heterocycles. Nonetheless, after some optimization, the Lilly group was able use the Uang method to produce the desired aminomethylated material shown above in good yield on a 44 kg scale.
Mechanistically, Mitchell and co-workers believe the Uang chemistry is substrate-dependent. For electrophilic substrates such as the current imidazopyridazine, the reaction proceeds by a radical mechanism involving the addition of a relatively nucleophilic α-amino radical to the pyridazine ring. With electron-rich systems such as those found in Uang’s work, an iminium ion mechanism is probably operational. Further mechanistic work is underway.
For those of you in drug discovery, do you think it would be interesting to carrying out such radical aminomethylations on existing drugs or related compounds? I’m reminded of the recent bevy of direct trifluoromethylation reactions by Baran, MacMillan, and Qing, featured at C&EN and In The Pipeline. Yes, aminomethyl groups and trifluoromethyl groups serve greatly different ends, but direct introduction of the former at rather unreactive sites would seem to be a nice option.
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.
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!