Tuesday, July 26, 2016

Maoecrystal V, or I how I learned to cope with my mediocrity

   Greetings and salutations ladies and gentlemen! Our total synthesis of maoecrystal V has been published in JACS recently. It is a fascinating molecule, in my opinion, with a beautiful array of densely interlocked rings, myriad of quaternary carbons, and an intriguing bioactivity profile to back it up (or not). It is no wonder, that it received so much attention from synthetic community, especially in the first five years after its publication in Org Lett. But don’t be fooled by that pretty face, this molecule is a demon in disguise! Making it in the lab is like having a crush on that popular girl in high school: no matter what you do or how much you try, the only thing you are going to get is a beat down by her much more handsome and stronger boyfriend. This pretty much sums up my experience working with this molecule.

   On the very first day in the Baran Lab, I decided to go for the baddest molecule in town, perhaps out of shear arrogance, or maybe stupidity, but most likely a combination of both. At that time, at least in my eyes, such molecule was maoecrystal V. This decision took me on a hell of journey, a roller-coaster ride if you will, full of adventure and unexpected outcomes, that changed me as person and a semi-scientist. But that is the beauty of total synthesis, in my opinion, it pushes you to your very limits and that is when you truly realize what you can and can’t do.

   The journey began with making the bicyclic ketone 5a or 5b, which turned out to be far from a trivial task. I am embarrassed to admit that it took me six months to actually make it. I have no excuse for that. The figure below summarizes some of the early failed approaches.

The Journey Begins
   When the route to 5a had finally been developed (described in the paper), the stage was set to explore the key addition/pinacol rearrangement sequence. At this point, Phil probably thought, “Yea... this Cernijenko guy needs all the help in the world and then some”, so I was joined by an awesome post-doc Rune Risgaard. We actually made a really good and productive team because we were quite different and complemented each other really well. United by misery and failure, fueled by unhealthy obsession (both of us really really wanted to make this damn molecule) we became good friends and marched on to the battlefield. We had absolutely no clue what was awaiting us.

   The pinacol rearrangement and hydroxymethylation is pretty well covered in the paper and there is additional information regarding these steps in the Supporting Information. Unfortunately, my therapist has forbidden me to discuss these steps to prevent further damage. Consequently, I will skip straight to the installation of the last carbon of the molecule. The cyanide was perfect for our purposes since it was a nucleophilic source of carbon that had the same oxidation sate as the ester and seemed small enough to react with a hindered C-8 ketone. The Figure below summarizes our attempts to accomplish this task.

A small glimpse of the challenge
   To sum up, the reactivity was not the problem. Most of time time the yields were very good, stereocontrol, on the other hand, was an issue. The cyanide was always coming from the undesired face giving us exclusively undesired diastereoisomer. We tried different CN sources, Lewis and Bronsted acids, solvents, and additives. The outcome was the same in almost every case. Interesting example is the reaction mediated by I2 where CN approached from the desired face but attacked the more hindered bis-neopentyl ketone to give 28. I was very surprised to see the X-ray crystal structure and to this date I still have no clue how I2 completely switched the chemoselectivity of this reaction. Other nucleophiles such as vinyl lithium, furanyl lithium, lithium 1,3-dithianes, corresponding Grignard and organocerium reagents did not solve this problem. We also tried blocking the undesired face by epoxidizing the C-15/16 alkene, but CN still approached from the undesired face. However, a very important result for us was the formation of 29 mediated by Zn(OTf)2 because it is the only example where we achieved the desired stereo- and chemoselectivity. The compound itself was synthetically useless but it made us realize that if we form the THF ring first, CN might approach from desired face. Interestingly, that hypothesis lead to the synthesis that was published today. In total synthesis things can go from terrible to great in just one reaction.

   Lastly, I would like to discuss the very last reaction in synthesis. It is quite strange to eliminate iodide with Oxone. Initially, we tried to engage iodo ketone 18 (formed as ~15:1 mixture of iodo epimers 18a (major) and 18b (minor)) in classic base promoted E2 type elimination. But not even a trace of maoecrystal V was formed despite myriad of conditions examined. We believe that there was simply no antiperiplanar hydrogen available for the desired elimination to take place. While the minor 18b iodo ketone, in principle, should have underwent E2 elimination, we think that the chair conformation with axial iodide is highly disfavored due 1,3-diaxial strain. As a result, 18b' is probably more accurate representation of its conformation, where iodide is pseudoequatorial on a boat.

The Iodide Elimination
   This is where we got quite lucky. After oxidation of the iodohydrin with one of the commercial bottles of DMP, iodoketone was formed in excellent yield along with 2-4% of maoecrystal V as a by-product. The relevant portion of crude NMR is attached below.

MCV hiding in the weeds
   How did it form? Freshly made DMP or other bottles of commercial DMP did not give any traces of maoecrystal V. It was just that one bottle that consistently yielded small amounts of maoecrystal V. What was in it? Long story short, we suspected that maybe it was contaminated with Oxone (which is used to make DMP) since oxidative elimination of iodide with m-CPBA was known in the literature (this reaction was very messy and low yielding in my crooked hands). Indeed, simply adding buffered aq. solution of Oxone to the reaction mixture resulted in very clean elimination of iodide to finally give maoecrystal V. That was a very good day in the lab.

   We were able to make decent amount of this natural product using this route, as a result, we had the chance to explore its bioactivity profile with different collaborators. Unexpectedly, it turned out that synthetic maoecrystal V was not active in any of the cancer cell lines (even HeLa) tested. Our dreams of curing cervical cancer were shattered, but we received a lot of valuable lessons from this synthetic campaign. That was a hell of a ride! R.I.P MCV, I hope we will never meet again.

-Art

Friday, June 10, 2016

Tales from the Trenches: Pallambins


Our total synthesis of Pallambins C and D is out today in JACS. We have placed a summary of our failed approaches and strategies in the supporting information to give the reader a glimpse of what went into developing our synthetic route. Here we highlight a few reactions and problems encountered during this work.  Our early approach began with the gamma-arylation of a beta,gamma-unsaturated ketone. We found these conditions worked well, but as the synthesis progressed and more material was required to keep the synthesis moving forward we noted severely decreased yields as the scale of the reaction increased. Careful observation of the reaction mixture itself revealed that the catalyst, ligand and base created a heterogeneous solution which clumped up and accumulated at the liquid/gas interface of the round bottom flask. This clumping limited the reaction to 2 mmol scale before seeing a steep drop in yield from ca. 70% to ca. 20%. We resorted to setting up many 2 mmol scale reactions in parallel, but this was a cumbersome and not very efficient work around the issue.
A Morton flask may have been a solution to this problem, but we did not have one available in lab and purchasing one would not solve all the issues with this approach. The cost of 3-bromofuran was high (to begin a synthesis from), the stoichiometric use of Cs2CO3 was necessary (we examined various bases) but not ideal and the enone delivered from this method lacked an alpha-methyl group. The sum of these issues led us to examine an alternative Robinson annulation disconnection of the enone revealing ethyl vinyl ketone and a furanoaldehyde. This aldehyde could arise from a Claisen rearrangement of the corresponding allyl vinyl ether.
Although the aldehyde was known in the literature, we found the reported 20% yield of the product to be an unbreakable barrier for the classic Claisen rearrangement despite our best attempts at catalysis and variation of reaction conditions. Ultimately the Eschenmoser-Claisen rearrangement emerged as the superior reaction, but instead delivered an amide rather than the desired aldehyde necessitating a reduction. Surprisingly, DIBAL reduction of the amide was sluggish and only reached 50% conversation. This was both frustrating and frightening as we did not have a way to adequately supply material to the front line of the synthesis. Fortunately, an examination of various reported methods led us to the use of tetramethyldisiloxane (TMDS) in the presence of Ti(OiPr)4 to achieve the desired reduction of the amide to an aldehyde in the same pot as the Eschemoser-Claisen rearrangement in 75% overall yield.

Why isn’t the Robinson annulation asymmetric?
We examined various options in pursuit of an asymmetric synthesis with little success. Although we were able to achieve some degree of asymmetric induction using phenylalanine, the yield of the reaction remained low despite optimization efforts. The use of asymmetric phase transfer conditions increased the yield of the desired enone, but we observed a large drop in ee.
Although phase transfer conditions did not deliver the level of ee we desired, the increased yield was welcomed as the previous conditions for the Robinson annulation used LiOH in isopropanol to deliver the enone in ca. 50%. We briefly revisited Buchwald’s gamma-arylation conditions in our quest for ee. Sadly, after a small ligand screen it became apparent that this would be a lengthy and rather expensive endeavor leading to the abandonment of an asymmetric synthesis all together. Steps 3-11 are discussed to some degree in either the text or supporting information and we are more than happy to answer any question you may have regarding these steps in the comments.

Selenophenol (things I had to work with)
As many of you know Derek Lowe’s In The Pipeline blog sometimes features “Things I Won’t Work With”.  One particular entry describes  selenophenol (PhSeH) in all of its stinky glory. After the failure of several endgame strategies we considered a radical cyclization approach to D-ring formation. Attempts to install various radical precursors at the anomeric position were surprisingly unsuccessful except for one, PhSeH. Completion of the synthesis seemed so close at the time that we decided to go ahead and use PhSeH. Unfortunately, installation of the selenoacetal required the use of PhSeH as a solvent in the presence of ZnI2. We attempted to use PhSeH in quantities up to a 1:1 solvent mixture with MeCN with no success, leaving no option other than using PhSeH as the solvent. The selenoacetal was installed on a model substrate (the Claisen rearrangement yield problem had not been solved at this point) followed by installation of an alkynoate. Treatment of the alkynoate model substrate with Bu3SnH and AIBN resulted in formation of the desired [3.3.0]furanofuranone system on the model substrate in good yield.
To our dismay, the success of this radical cyclization on the model substrate did not translate to the pallambin system. We explored various methods for radical generation, reaction concentration, rate of addition and everything else we could try to reproduce the result of the model substrate over the course of 2 months with no positive result. This was very tough and stinky time in lab.
Generation of PhSeH from PhSeSePh and the subsequent distillation was a nightmare! The smell of PhSeH is something along the lines of a dumpster filled with rotting skunks set on fire. One afternoon while working with PhSeH a drop of the disgusting liquid fell on one of my gloves unnoticed. I briefly removed my hand from the fume hood and passed it near my face while reaching for something and my head was instantly knocked back by the apocalyptic smell of PhSeH. This small but concentrated exposure resulted in the complete loss of my sense of smell for about 10 days. This was the absolute final straw for PhSeH and the approach was abandoned altogether. It was quite terrifying once I passed the 7 day mark with no sense of smell. I felt like I had made an irreversible mistake that would effect the rest of my life. Fortunately, my sense of smell returned over the course of 3 weeks, but even a year later I’m still haunted by phantom PhSeH smells.

-Luisruben P. Martinez