Tuesday, July 9, 2019


We came across an interesting compound in Natural Product Reports Hot off the Press today:

 This rather precarious-looking [3.2.2] bicyclic compound was originally isolated from Bacillus sp., in a 2015 report, and the same compound was re-isolated separately from Melocanna baccifera in a new 2018 publication. Curious about this unique structure, we did what any good chemist would do, and attempted to build a model of it. After breaking some plastic we quickly realized that this compound, if it existed, would have to adopt a bent-arene conformation wherein the pi-system of the arene is bent out of conjugation (see haouamine for an example of a real cyclophane that exhibits this behavior).
 Seeming to contradict this unconjugated structure were the reported 13C NMR shifts (published earlier by Zeng et al), which were within the expected range of an unstrained para-substituted phenol. Additionally, the reported HMBC data reported by Zeng and coworkers lacked any correlations spanning across the supposed ethereal oxygen (e.g., between C-5 and H-3), which would have provided key evidence for the bicyclic structure. The reported mass [M+H] = 121.0645 is consistent with an [M+H] ion of the disclosed structure; however, it would also be consistent with an [M - H2O] ion from 4-hydroxyphenethyl alcohol…

Fortunately, we had a bottle of the latter compound hanging around the lab. A quick NMR confirmed our suspicions – the proton and carbon chemical shift data (see below) for this primary alcohol are exactly the same as those reported by the authors for the "bicyclic" compound. Furthermore, after shooting our commercial material on the LCMS we observed a major ion peak at 121.1 ([M - H2O]), with none of the 139.0754 one would expect for M+H of 4-hydroxyphenethyl alcohol. (EDIT: A kind reader pointed out to us that the much larger peak observed at 107.1 corresponds to [M - MeOH], via C-C bond homolysis to give the benzylic radical cation)
Further, a careful observer of the MS data could have known this off-the-bat: In the 2018 report, the authors ionize the compound on negative mode, and see a large peak at 137.06, corresponding to [M-H] of the (correctly assigned) compound.
Here's our data for commercial 4-hydroxyphenethyl alcohol:

We thus reassign the proposed structure to the much simpler 4-hydroxyphenethyl alcohol.
Our conclusion? If something looks really unusual, check all the reasonable hypotheses before you propose something exotic. Sometimes, things are zebras, but if you hear hoofbeats...it's probably a horse.

– Kyle M. and Sol

Monday, April 1, 2019

You heard it here first

La Jolla, California -- Sources close to Professor Phil "Strongman" Baran inform us that he his quietly announced his surprise early retirement. Says Baran, "I'm really tired of organic chemistry, and want to move forward in pursuing my passion project -- artisanal organic free-range grass-fed bodybuilding supplements. Given the immense responsibility of running an ethically-sourced supplement company, I just can't juggle being a PI any more."

Analysts at BBT (Baran Bodybuilding Technologies) announce their excitement about the newly-developed supplements: "We've developed a secret formula that maximizes development of so-called vanity muscles (pecs, biceps, and abs), while minimizing any undesired hypertrophy of annoying functional muscles (e.g., quads). Finally practitioners can achieve that 'ripped-torso, chicken-legs' look that everyone strives for."

Baran doesn't have an estimate of when his product will go to market, saying, "I've got to graduate all these pesky PhD candidates in my lab first. Then, the real work can begin."

You heard it here first, folks.

Happy April 1.

Thursday, February 21, 2019


Our work on electrochemical Birch reduction was published today. In case you don't want to read the manuscript, here's the Cliff notes:

  • Pfizer approached us, saying traditional Birch is bad news for med chemists (alkali metals are spooky; condensing ammonia is gross; the whole thing is a lot of effort). They asked us to make a better Birch.
  • We developed some conditions to effect the Birch transformation with electrochem. Basically, the conditions are mix substrate, LiBr, electricity, DMU, a key phosphoramide additive (TPPA), and THF. No ammonia, no alkali metals, no cryogenics.
  • Intuitively, one might naively assume that what's going on here is that the LiBr is reduced to Li(0), and from there the reaction goes through a standard chemical Birch mechanism. We assumed that, naively (at first).
  • Turns out, that mechanism is not at all the case, as demonstrated by much experimental and computational mechanistic study. Instead, the substrate is reduced directly on the electrode. Further, Li(0) is never generated at all. Safe stuff. Cool beans.
  • We went back to Pfizer with this. They seemed pretty happy.
  • Oh, also the reaction works in flow, on >100 g scale.
  • Oh, also, the key phosphoramide additive, that makes everything work, came from the Li-ion battery literature.
A huge shout-out has to go to our collaborators: Shelley Minteer and her group (led on the student side by postdoc David) for electroanalytical work, Matt Neurock and his group (led on the student side by grad student Sagar) for computational work, and our longtime buddies at Asymchem (led by Longrui) for scaleup and flow work. We should also note that this whole collaboration is driven by the CCI electrochemistry consortium, which has been a tremendous way to put people from various subfields of electrochemistry in touch with one another.

Anyway, normally, this is the part of the blog where we'd tell some funny anecdotes about the project. Unfortunately, the whole team is way too excited to get back in the hood for subsequent projects, so we didn't write anything. In lieu of anecdotes, please accept a few vaguely-electrochemical-Birch-related poems:


We set out to Birch some arenes;
to make a scary reaction more clean.
It turned out lack of lithium
gave us complete freedom
to safely Birch on our Electrosyeeeens


Birch in Winter frost
with Electrochemistry
No lithium, good.


Poor Arthur Birch
did much research.
He was always sad,
for his reaction was bad.
Now we made it better
but alas, he is deader.

Oh, also we made a video, objectively comparing the time it takes to run a classical, chemical Birch, to the new electrochemical protocol. We hope you enjoy it:

- Electrochemical Birch team

Monday, January 14, 2019

Technique primer: Test tube columns

As many of you remember, a little over a year ago Phil did a AMA on reddit. On that AMA, a bunch of people requested that we do a post on how to build/run disposable test tube columns:

Well, writing up this blog post somehow slipped through the cracks for a year (Sorry!!), but without further delay, here's how we do the technique.

Step 1: Building the glassware. 

We use these columns on crude reaction mixtures from ~10 to ~500 mg scale. For smaller scale than this, we use prep TLC; larger, just a standard reusable column.

To build the column, for 10-50 mg, we just use a Pasteur pipette as the column. For 50-200 mg, we build it out of a 16 X 150mm tube. For 200-500 mg, we build it out of a 25 X 150 mm tube.

For the latter two, the first step is to pull a bottom spout from the test tube. Basically, you heat the tube with a Benzomatic torch, until you see the bottom glow orange and "wilt" slightly. At this point, you grab the glass with a pair of tweezers and steadily pull to make a long stem. It's hard to explain, but easy to demonstrate:

It's a bit tricky the first time, but gets simple with practice.

After letting the tube cool to rt, snapping off the bulk of the stem gets you a nice looking column:

(If you're using a Pasteur pipette, you get to skip to this stage)

Step 2: Building/running the column.

From here, it's just a matter of packing a small chunk of Kimwipe into the bottom, and tamping it down, followed by adding a bit of sand, and then silica gel. With modern silica gel, we have found that even <3" column height is still plenty to do reasonable separations. After equilibrating with a column volume or two of solvent, here's what it looks like, ready to load and use as usual:

One nice thing about the column sizes is that the 16mm tube (loosely) accommodates a 14/20 inlet adapter, while the 25mm tube (loosely) takes a 24/40 adapter. This way, you can run it with positive air pressure exactly as you would any other flash column. This is a 16mm tube, and as you can see, the small inlet adapter fits it nicely:

When the column is finished, here at Scripps, our EH&S allows us to dispose of the whole thing, tube and all, into our silica waste stream. Check with your EH&S for what to do at your institution.

Regardless, the best part of this technique is there are no dishes to wash!

Hope that this helps aspiring chromatographers,

Baran Lab

Sunday, January 13, 2019

11-Step Total Synthesis of Teleocidins B-1–B-4

Our paper describing the total synthesis of Teleocidins B-1–B-4 is now published in JACS! I started working on this project in November 2017 and completed the synthesis in June 2018. I then spent another 6 months optimizing the route to increase the yield and decrease the step count.

In the biosynthesis of these molecules the indolactam core is transformed into Teleocidin by a Friedel-Crafts type reaction with a terpene fragment. However, nature’s synthetic strategy provides a mixture of Teleocidins B-1-B-4 which is something we wanted to avoid. When I started to evaluate our own synthetic strategy, I immediately identified the introduction of the two quaternary carbons to the indolactam core in a stereocontrolled fashion as the major challenge (even one sterically hindered quaternary carbon can be difficult!). I knew we would have to establish the relative stereochemistry independently because the terpene fragment and amino acid moieties are quite distal. 

I also realized we needed to install a functional handle on the indole moiety in a highly regioselective fashion to facilitate coupling with the terpene fragment.With a bit of luck (and a lot of hard work) we were able to overcome these challenges and you can find the details in the paper/SI. I wanted to use this blog post to provide further insight into some of the key reactions which led us to success.

In the beginning, we had to fight against nature…

The first step in our synthesis is an electrochemical amination between our indole scaffold and valine. After optimization, I tried to scale up the reaction using some conventional large glassware which I bought from our local Japanese supermarket. However, almost no desired product was observed and even worse, I lost 6 grams of starting material along with the nickel, ligand and my time. I was so shocked that I couldn't even find my tongue! Phil suggested to try again but this time using the ElectraSyn carousel. The switch in setup facilitated reactivity and with a little optimization the desired product was formed in 51% yield.

I also want to highlight one of the unexpected problems we faced in this synthesis which is not described in the paper. While the desired indolactam is commercially available, it costs $274 per mg (Sigma) so it was a bit outside of our budget! We first tried to make the 9-membered ring by hydrolysis of the valine methyl ester followed by condensation using HATU, but the desired product was isolated in just 19% yield. However, after plenty of screening we found that the use of LDA was crucial for this reaction and we managed to obtain 2.1 grams of the protected indolactam! That was a really great day in the lab.

In April 2018 I was joined by Kosuke, a very talented visiting student from Osaka (Japan), who really helped me to optimize the route to what is now shown in the paper. Yuzuru, an amazing graduate student, also helped me by optimizing a key reaction and preparing a late-stage intermediate. I want to thank the team and especially Phil who was always ready with a lot of suggestions. I can definitely say he never compromises in the quest for an ideal total synthesis. 

Hugh and Teleocidin team

Thursday, January 3, 2019

Decarboxylative carboxylation: radiolabeling carboxylic acids the easy way

Our latest paper, which arose from a collaboration with the radiochemistry team at BMS, describes a new approach to carbon-14 radiolabeling and is now published in JACS (after previous submission to the ChemRxiv). I began working on this project as a visiting student in October 2017 and it has been an amazing learning experience with some tough challenges and valuable lessons. In this blog post I want to discuss some of the interesting problems we encountered upon diving into the field of radiochemistry.

To summarize, our synthetic approach consists of the formation of a redox-active ester followed by a chemoselective nickel-catalyzed decarboxylative carboxylation to reintroduce the (now radiolabeled) carboxylic acid. That carbon-14 label is a useful tool for radiochemists to perform the absorption, distribution, metabolism, excretion and toxicity studies required for drug development. Our method has some nice advantages including the two-step degradation-reconstruction synthetic approach (starting from the unlabeled product which is usually available in plentiful supply) and the use of [14C]-CO2, the cheapest and most common carbon-14 reagent.

During the initial reaction development, we successfully performed the desired decarboxylative carboxylation sequence using 50 psi of [13C]-CO2. Although this procedure allowed us to test the scope of the reaction (scheme 2 in the paper), our collaborators let us know the pressure and use of excess labeled reagent were big problems when it came to translating to radiolabeled [14C]-CO2.  

We first considered limiting the stoichiometry of the [14C]-CO2 to about 10 equivalents while maintaining the pressure in the system. Several options were considered included pressurizing with an inert gas (discounted due to the dependency of the concentration of CO2 on its partial pressure, rather than the overall pressure), pressurizing with unlabeled CO2 (avoided because it would dilute the radiolabel too much) or using amine additives to sequester the CO2 into solution and promote reactivity (no reaction observed presumably due to coordination to/deactivation of the catalyst). Thinking further about the factors which influence the concentration of a gas in solution we realized it may be possible to accomplish our goal by simply cooling the reaction down. Gases are more soluble at colder temperatures (when most gases dissolve in solution the process is exothermic, an increased temperature causes an increase in kinetic energy which promotes gas escape from solution). Through use of Henry’s law, the concentration of CO2 in solution under the pressurized [13C]-CO2 conditions was estimated. With this figure as a target, the temperature required to obtain a similar concentration at atmospheric pressure of CO2 was calculated to be about -25 °C. 

Running the reaction at -25 °C gave, perhaps unsurprisingly, only partial conversion of the starting material to the product. Using 10 equivalents of CO2 at atmospheric pressure and maintaining the cryogenic period for just one hour then sealing the vessel, warming to room temperature and stirring overnight gave full conversion of the sm with efficient isotopic incorporation (see the SI S12-S14 for further details)! The BMS team were now satisfied with this procedure and after making a few minor adjustments, they produced a working carbon-14 setup using standard radiochemical glassware and techniques. Upon testing the method with [14C]-CO2 we observed isotope incorporations suitable for use in all preclinical and clinical ADME studies and the project could be called a success. All in all, application of the method to the strict requirements of carbon-14 setting led us to some fun and interesting challenges and provided the answer to the age-old question…


Although we think Breeder Steve may have been considering one particular decarboxylation process, we can conclusively say the answer is yes #chemistrygoals! I would like to thank everyone in the lab for all their help on this project and please check out the complementary carbon isotope exchange methods just published by the Shultz group at Merck and the Audisio group at Universit√© Paris-Saclay.

Cian Kingston
La Jolla, CA
January, 2019

Friday, December 21, 2018

Simply Strained: Total Synthesis of Herqulines

Our recent syntheses of herqulines B and C have been published today in JACS. While the paper describes the direct nature of our final approach towards these highly strained alkaloids and even hints at some of the difficulties encountered along the way, the truth is that the journey towards the herqulines was a two-year campaign plagued by failure and confusion. There were many lows along the way, but there were also some highs that made it all worth it. In the end, I learned many lessons about chemistry, but more broadly about science, problem solving, time management, and the formula for a truly winning team (huge shoutout to my partner in crime, Chi He). As I’m sure many of you know, what is reported in a synthesis paper is most likely the end result of many more lessons learned that are not visible in a short communication. Thus, I hope to convey a sense of this in the space below.

I was first introduced to the herqulines in the fall of 2016 as part of a thought experiment that we lovingly refer to in the Baran Lab as synthesis “boot camp.” In contrast to some of the other targets pursued in our lab, these tiny alkaloids don’t look like more than a simple reduced dipeptide upon initial inspection of the two-dimensional structure. It wasn’t until I built a plastic model of herquline B that I realized what a beast this thing truly is (late-stage x-ray structure pictured, gives one a decent idea what we’re dealing with). Strained is an understatement when describing the herquline core. The piperazine ring sits at the base of the macrocycle, with two six-membered rings flanking each side of the heterocycle in a
bowl shape. Throw in a pair of weird skipped enones and a 1,4-dicarbonyl at the strained ring juncture and you’ve got yourself one unhappy customer. The structural features, it turns out, were just the beginning of challenges involved when dealing with these alkaloids. As I would come to appreciate in short order, strained diamines are not only very challenging to handle from analytical and purification standpoints, but are also exquisitely unstable when the wrong transformation is applied at the wrong stage of the synthesis. In short, this was a proper adventure in total synthesis. So let’s get down to the nitty gritty. Let’s get the show on the road...

Our first approaches were predicated on the (spoiler alert: incorrect) precedent that Birch reduction of a strained biaryl was not a viable strategy towards our target. I’ll spare you from the gory details, but well over a year was spent perusing a host of strategies that ultimately led us back to the strategy in the paper, in which the macrocycle is built as a biaryl DKP.
Our task was simply to defy all precedent and reduce two aromatic rings and a DKP all within a highly strained, unstable core. Initially, I set out to reduce the DKP, while Chi fearlessly embarked on a quest to perform the first Birch reduction. For the DKP reduction, most common hydride reducing conditions resulted in either decomposition or monoreduction of the tertiary amide. One standout example, however, was Brookhart’s Ir-catalyzed amide reduction mediated by diethylsilane. However, the resulting biaryl diamine was highly unstable in our hands, and could not be isolated. It seemed that the strain was just too much and thus one of the aromatic rings needed to be reduced first.

To that end, Chi had screened a range of Birch conditions and protecting group swaps and was beginning to see some potential (see figure).

While the regioselectivity was incorrect, it nonetheless proved that this strategy could potentially be fruitful. The true complexity of the situation was soon realized when we discovered that when the DKP nitrogens are both N– H, the regioselectivity flipped and it matched our product’s requirements! This was a truly exciting day but much work still needed to be done, as the natural product of course has one methylated nitrogen.

We quickly prepared the asymmetric DKP macrocycle found in the herqulines (up until that pointN-methylation was somewhat of an afterthought) only to find that the regioselectivity was again incorrect. To complicate matters further, the resulting styrenyl position readily was reduced under most Birch conditions screened, and we even saw some elimination of methanol and additional styrene reduction.

screening all known metals, solvents, temperatures, concentrations, and 
additives, we had only proton sources to screen before giving up on yet another strategy. We screened a bunch of proton sources which all gave the same negative result, with the exception of 2,2,2-trifluoroethanol, which cleanly delivered the desired regioisomer! This breakthrough was the result of empirical observation and to this day the mechanistic underpinnings of this selectivity are at best conjecture.

Recalling our above efforts to effect DKP reduction, Brookhart’s Ir-catalyzed amide reduction again reduced both amides to the corresponding piperazine. We were now one Birch reduction away from the promised land and excitement was brewing.

Of course, the synthesis gods were not ready to smile upon 
us yet, as every Birch condition screened resulted in either no reaction, or reduction of either homobenzylic position prior to any reduction of the second aromatic ring. We were back in the familiar position of despair, beginning to think that at this advanced stage we would ultimately fail once again, when it occurred to us that ketalization may be a viable workaround, given its ability to relieve strain (two more spcarbons), alter the conformation, and remove a double bond (improving selectivity).

After some screening, the ethylene glycol ketal proved a competent substrate and the second Birch proceeded cleanly, 
with the correct regioselectivity. Simple hydrolysis delivered herquline C, which, after a few days in CDCl3, equilibrated to an approximately 1:1 mixture with its more stable congener, herquline B. Treatment of herquline C (or this mixture) with DBU in toluene brought about clean conversion to pure herquline B, thus wrapping up an adventure that we will not soon forget. In the end, the simple, direct approach panned out. When I look at this route now, this pathway even seems obvious, but if you’ve read this far (sorry if I got a bit long-winded), you’ll know that this route was the result of much experimentation and intimate understanding of the reactivity and stability of every intermediate along the way. In short, this was a hell of an adventure in total synthesis. Thanks for reading!

Tom Stratton
La Jolla, CA 

December, 2018

p.s. See also the Wood group's elegant synthesis of the same molecules!