Tag Archive | azides

Tetrazole synthesis, Part II: Harnessing the tetrazole-azidoazomethine equilibrium

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 tetrazole-azidoazomethine equilibrium

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:

Routes to azidoazomethines

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.

BMS discovery route using Duncia's method for tetrazole synthesis

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.

BMS's Process for Tetrazole Synthesis on Large Scale

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 :

Amidrazone route to 5-substituted tetrazoles

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.

McKee and Montgomery fused tetrazole synthesis

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 Purine Synthesis by shifting the tetrazole-azidoazomethine equilibrium

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.

Tetrazole synthesis, Part I: Azide-based methods and dealing with the danger of hydrazoic acid

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.

Tetrazole flavors

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.

Types of tetrazoles under consideration

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.

Novartis/Cambridge example of the reaction of a  nitrile with sodium azide to produce a tetrazole

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.

Merck Frosst Discovery Chemistry Route

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!

Sharpless and Merck Frosst Modifications

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.

Valsartan synthesis

Next:  The tetrazole-azidomethine equilibrium and its use in tetrazole synthesis.

Toward the ideal reaction – Part 2

Toward the Ideal Reaction – Part 2

In Part 1, the concept of an ideal reaction for biomolecule labeling was outlined:  One step, no protecting groups, fast, efficient, specific, no catalyst or reagents, no external stimulus, and easy cleanup.  Jäschke’s work on oligonucleotide labeling via the inverse-demand Diels-Alder cycloaddition of tetrazines with norbornenes was featured.

Let’s look at some other chemistry and invite an expert guest, Jack Hodges, to chime in.  He also has a few things to say about big pharma versus small companies.

What about click chemistry?  Well, about that copper…

When one thinks of simple addition reactions for biomolecule labeling, click chemistry comes to mind.  Sharpless’s copper-catalyzed dipolar cycloaddition of azides with alkynes to produce triazoles is the de facto standard click reaction, but, well, it uses copper.  Not ideal.  Plus, the copper may cause problems in the applications we’re focusing on.

Naturally, ingenious chemists have jumped on that problem.

Copper-free click reactions – dial in some strain, maybe change the dipole

How do you speed up dipolar cycloadditions to alkynes without using copper?

You can fool around with the electronics of the alkyne, but then you run the risk of making it susceptible to unwanted reactions.

Alternatively, it’s well-known that dipolar cycloadditions are faster with strained dipolarophiles.  Bertozzi harnessed this effect for click chemistry via cyclooctynes (so-called SPAAC reactions, for strain-promoted alkyne-azide cycloadditions).  Others have joined the fray.

Another approach is to swap out the azide for a speedier nitrone dipole (SPANC reactions), as reported by the groups of van Delft and McKay.

Here’s an example of what we’re talking about, using van Delft’s bicyclononynes (BCNs):

Insights from a guest expert:  Dr. Jack Hodges

To give us an inside look at the state of the art in this area, we have with us my colleague Jack Hodges, ex-WLPD/Pfizer, who now leads the chemistry effort at Berry & Associates, Inc. (B&A), a firm that specializes in nucleic acids chemistry.  Some of you may recall Jack’s prominence in the early days of combinatorial chemistry, where he published seminal articles on the use of polymer-supported scavengers.  He has recently negotiated a scientific and business relationship between B&A and SynAffix, B.V. to provide a line of SPAAC reagents for the oligonucleotide field that are derived from van Delft’s BCN.

Will Pearson:  Jack, what are some of the challenges of using click chemistry in the oligonucleotide field?  

Jack Hodges:  There are plenty of examples of people who have used Cu-catalyzed Click reactions on oligonucleotides but there are also other examples where the Cu(I) catalyst has been reported to cause partial degradation of the oligo.  The partial degradation paper we always note in our product literature is Kanan, M.W., et al., Nature, 2004, 431, 545-9.  There are probably other similar reports.  This problem doesn’t seem too surprising to me since both Cu(I) and Cu(II) can coordinate to heteroatoms, and nucleic acids are full of heteroatoms.  Whether or not you believe Cu(I) is a serious problem around oligos, my feeling is that if you don’t need it, why bother?  There are numerous recipes for making Cu(I) in-situ for traditional Click reactions and often it takes a fair amount of investigation to find the one that will work for your application.  The Cu-free approach does away with all that.  Just put the strained alkyne and the azide together and the triazole forms.  The old fashioned expression is “dump and stir”.  Somehow “dump and stir” doesn’t have as nice a connotation as “Cu-free Click” or the sound of the quirky acronym “SPAAC” (short for strain-promoted azide/alkyne cycloaddition), but in practice it is just that simple.

WP:  For copper-free click reactions of azides with alkynes, there are quite a few competing techniques.  Would you please tell us about your path to selecting van Delft’s BCNs, giving us a little perspective on the various technologies that are available?  What made BCNs your top choice for commercialization?  (B&A also sells compounds based on Schultz & Pigge’s MFCOs.)

JH:  There are two things that attracted us to BCN.  First the BCN synthesis looks attractive from a commercial standpoint.  It starts with 1,5-cyclooctadiene (which is about as cheap an 8-membered ring compound as one can buy) and requires relatively few synthetic steps, each of which look to be scalable.  Second, BCN has the lowest calculated LogP value among the other popular cyclooctynes in the literature.  This makes BCN desirable in terms of maintaining the viable biological properties for oligos and other biological macromolecules to which it is attached.  DIFO is pretty close to BCN in terms of LogP but it is much harder to synthesize.  To be fair, BCN-OH is still hugely more lipophilic than propargyl alcohol.  So if you absolutely need to avoid lipophilicity, maybe the traditional Cu-catalyzed Click is your best bet.

WP:  What should we know about IP and licensing in this field?

JH:  So far as I am aware, the only issued US Patent for Cu-free Click reagents and methods belongs to UC Berkeley (US 7,807,619).  There are other published patent applications that may well lead to additional patent coverage in this field.  It seems pretty clear that SPAAC reagents and methods fall outside the broad coverage of the Scripps patents that cover Sharpless’s Cu-Catalyzed Click methodology.

WP:  The classic ways to attach things to oligonucleotides involve amine acylation or thiol alkylation.  Besides click chemistry, what other bioorthogonal conjugation methods do you believe are useful for the modification of oligonucleotides?

JH:  Another Click reaction, oxime formation, is gaining steam with oligos.  B&A now sells some oxyamine and aldehyde reagents that can be incorporated during oligo synthesis or via post-synthetic modification.  Based upon their current popularity, we will be expanding our oxyamine product offerings.

WP:  While I’ve got you here, is there anything you’d like to say about your experience of working in a small chemistry company versus your time in big pharma?

JH:  On the whole both experiences have been very positive.  I had a great run in the pharma industry when it was still a vibrant place for doing top notch research.  For most of my 22-year career in pharma, drug companies embraced the financial risk of drug discovery.  That made it fun to be a chemist working in big pharma.  I don’t think the same fun is there today because drug companies got too big via mergers.  As they grew, the lower productivity of research staff that occurred while they were distracted immediately following a merger (when there is an inevitable re-evaluation, repositioning, and reorganization of research endeavors) somehow became part of the justification for the industry to reduce the overall amount of research investment.  To me, pharma companies today have all caught the same disease.  They all seem downright fearful of research investment.  To the scientists in the trenches, it can appear as if their management puts as high a priority on trying to minimize risk as it does trying to discover drugs.  Perhaps Bruce Roth’s recent article in C&E News says it better than I do here. (WP:  Links here and at Chemjobber here; see also Firestone’s perspective here and at In the Pipeline here.)

Today, I am very happy working in a privately-held specialty chemical company.  The ‘you eat if you can sell it’ attitude of small company life certainly keeps a scientist’s daily activities interesting, especially in a world where foreign competitors seem to always have a lower labor cost.  This environment drives Berry & Associates to work on the most difficult problems of our customers.  There we can provide products of tremendous value to cutting edge biological technologies.  To highly educated and experienced chemists, such work is as fun as it is profitable.

WP:  You’ve been working with heterocycles for most of your career.  Looking back so far, what accomplishment in that field do you feel is most significant?

JH:  Ten years later, I still get inquiries about my lithiooxazole paper that was published in JOC in 1991.  It didn’t feel like super-remarkable chemistry at the time but people still read that paper.  Editorially speaking, I guess that is a darn good reason to publish results that initially surprise you.  You can save others from the same surprises!