I assembled a list of journal articles reporting total syntheses of natural products based on suggestions from several people on Twitter. In addition to their subject matter, they are considered to be eloquently written. Read them to see if you agree or even make your own suggestion.
The post is actually on Storify at the following URL:
Nothing incites apoplexy in your favorite peptide chemist like mentioning how “real” synthetic chemists are dismissive of the challenges that can arise, from time to time, in the formation of amide bonds. C’mon. How hard can it really be? Activate an acid using your favorite alphabet soup reagent and allow an amine nucleophile to take it from there. Done…. But sometimes things get complicated. Sarah Reisman’s#^ hot-off-the-presses Angewandte Chemie communication reporting the syntheses of (-)-lansai B (1) and the “no cardio required” (+)-nocardioazines A & B (2 & 3) reveal that even a card-carrying synthetic chemist can be stymied by amide bond formation, for a while. As it turns out, the forces of amide bond formation were used for good – in the macrocyclization of (+)-nocardioazine B.
This post is the second installment of an annual exercise for my organic synthesis class where I try to deconstruct a total synthesis communication paragraph by paragraph. The strategy and execution of the writing are put on equal footing with that of the chemistry. Our goal is to understand how the manuscript – both its text and its graphics – communicates the ideas behind the science and the agenda/priorities of the author. It is a case study in synthesis AND manuscript writing. The discussion of the manuscript in class emphasizes active reading and what behaviors active reading entails.
So there’s no better place to start than at the beginning. The title “Enantioselective Total Synthesis of (-)-Lansai B and (+)-Nocardioazines A and B” and abstract are straightforward stylistically and they give clear clues about the story that will unfold in the manuscript. Three words/phrases do the work that is needed here. 1 – The term “enantioselective” indicates how the chirality of the natural products will be introduced in the molecule: via chiral catalysts in enantioselective reactions in the synthetic sequence. 2 – “Formal [3+2] cycloadditions” refers to a new and powerful reaction introduced earlier by the group for formation of pyrroloindolines. 3 – By noting that macrocyclization occurred by “intramolecular diketopiperazine formation” the authors tip their hand on the ultimate route for the synthesis of nocardioazine A. Now to the manuscript proper.
Paragraph 1: The introduction is textbook for a synthesis paper. It gives a quick one-two punch in the form of biological activity (1, 2, and 3 in Figure 1 are potential antibacterial and anticancer agents.) and a description of the structure (They are bis(pyrroloindolines) linked via a diketopiperazine.). It then back-fills with some details for each point. First, the star compound, (+)-nocardioazine A (2), is a P-glycoprotein inhibitor. P-glycoprotein is an efflux pump central to multi-drug resistance resistance in several cancers. The remainder of the paragraph points out the subtleties of the structures, especially the stereochemical relationship between the group at the C3 of the pyrroloindoline unit and the carboxamide, giving rise to the exo- and endo- nomenclature throughout the paper. (-)-Lansai B (1) is constructured of two exo pyrroloindolines in the same enantiomeric series, whereas nocardioazines A (2) and B (3) are made from one endo- and one exo- pyrroloindoline of opposite enantiomeric series. Compounds 4–7 in Figure 1 nicely illustrate the relationships. Reisman emphasizes that these precursors make “appealing synthetic targets for asymmetric catalysis where selection of the appropriate enantiomer of the catalyst dictates the absolute stereochemistry of the pyrroloindoline building block.” That’s a great sentence. She’s building up the value of their approach before she fully reveals it. The paragraph closes by noting that there is one reported synthesis of 3 and none of 1 and 2.
Paragraph 2: Some readers may have realized already that this synthesis will showcase the formal (3+2) cycloaddition methodology based on the hints (really statements) in the abstract and first paragraph. The pyrroloindoline natural product targets in the this paper, among others, likely motivated the development of the transformation. That’s a standard argument made by organic chemists for the development of new reactions. If you didn’t see it coming, it becomes explicit in the first sentence of this paragraph. The method for enantioselective synthesis of pyrroloindolines (box in Figure 1) is a major component of their retrosynthetic analysis. In fact, that IS their retrosynthetic analysis as shown in the figure. Reisman trusts that you can make the DKP disconnection and, if you don’t see it now, she’ll walk you through it shortly. “Utility” in the last sentence of the paragraph rings in your ears – this report on total syntheses exclaims the utility of the formal (3+2) methodology.
Despite the centrality of the reaction to the syntheses, it gets a mere mention and a call of Figure 1 but that’s nearly it as far as explanation. The reader must work through the figure and, if necessary, revisit reference 4a, which is the JACS communication that describes the reaction. The reaction uses C3 substituted indoles and 2-amidoacryates in the presence of SnCl4 and catalytic (R or S) BINOL to deliver pyrroloindolines with high enantioselectivity. Note the cis relationship between the R1, H, and carboxylate groups in structure 10 of Figure 1; this is the exo- relationship defined earlier. The reaction is formally equivalent to a (3+2) cycloaddition where the two olefinic carbons and the nitrogen of the amidoacrylate are the “3” and the two carbons of the indole are the “2”. Scheme 1 from the JACS communication gives some insight into the transformation and to the origin of the enantioselectivity. Conjugate addition by the indole onto the amidoacrylate is followed by protonation of the resulting enolate followed by ring closure. With regard to selectivity, Reisman speculates in the JACS communication, “[conjugate addition] occurs with modest levels of catalyst control, whereas the enolate protonation step occurs with high levels of catalyst control. In effect, the catalyst-controlled protonation step serves to resolve the mixture of enantiomeric intermediates.”
With that, they’re finished with introductions and on to the business of the syntheses.
Paragraph 3: Like a lion after a young gazelle, Reisman aims for (-)-lansai B (1) as her first target. Here she provides a little more detail on the retrosynthesis by stating that formation of the DKP would be the way to unite the two pyrroloindoline fragments, 4 and 5, via “sequential amide bond formation.” Simple. She finishes the paragraph by calling the starting materials for the synthesis of 4 and 5, indoles 13 and 16, both of which are in Scheme 1. If you wondered where the indoles themselves came from, reference 4a is there to guide you. The SI of that paper shows a tandem amination-Heck reaction with substituted bromo-iodo-benzenes and allyl amine to deliver the indoles.
From here, the organization of the paragraphs communicating the syntheses of 1–3 largely follows the synthetic strategy. That is, Reisman walks the reader through pyrroloindoline synthesis using the formal (3+2) method and then make use of those advanced intermediates in the formation of DKPs to complete the syntheses. As always, there are minor twists and turns in the storyline though.
Paragraph 4: This paragraph takes the reader through the synthesis of two pyrroloindolines, 15 and 18, from the corresponding indoles. Again calling Scheme 1, the paragraph starts by describing a Suzuki-Miyaura reaction that installed the prenyl group on intermediate 15. To be clear, this group is the only difference in the two pyrroloindoline units in (-)-lansai B (1). “Subjection” of 13 to the cycloaddition reaction provided 14 in 85% yield, 14:1 dr, and 92%ee. An aside: Subjection is a great word – it’s perfectly descriptive but it bears a tinge of that, “Is it really a word?” feel to it. Anyway, on scale up (> 1.0 mmol), she notes that lower yields were obtained and that a scan of protic additives showed that addition of 2,6-dibromophenol maintained yield and selectivity. They suggest that, “…2,6-dibromophenol facilitates turnover of the chiral catalyst, but is not reactive enough to protonate the transient enolate directly in a nonselective fashion.” It’s like a goldilocks acid in a milieu of acids in the cycloaddition reaction. This observation underscores the complexity of the reaction mechanism. Thankfully, the results are easily understood and useful. Conversion of 16 to 17 follows the same protocol (79%, 12:1 dr, 93% ee). The paragraph continues on with some deprotections to end with intermediates 15 and 18. (-)-Lansai B (1) is about to yield DKP formation.
Paragraph 5: The concession paragraph. The plan was to finish (-)-lansai B (1) through DKP formation by sequential amide bond formation. Preparation of intermediate 19 in Scheme 1 was to be the first of the two amide bond forming reactions. Despite scanning a “wide variety of peptide coupling conditions” – queue visions of alphabet soup – they did not see coupling but only decomposition of 18. Reisman then recalls a successful coupling of exo-pyrroloindolines by Danishefsky and coworkers in their synthesis of amauromine. There both nitrogens were protected as t-butyl carbamates whereas 18 has one N-alkyl and one N-trifluoracetamide. She comments, “these findings reveal that the N substitution of the exo- pyrroloindoline significantly influences the stability of the activated ester under peptide coupling conditions.” So peptide chemistry can pose challenges. They then present an alternative strategy involving the completely deprotected amino acids 20 and 21 (Scheme 2). The plan is to take a hit on yield and mix 20 and 21 to form three DKPs in one reaction; in their estimation this was more efficient that several protecting group manipulations. Coupling using BOPCl gave the two homodimers, each in 20% yield, and (-)-lansai B (1) in 38%; the synthesis was six steps with an overall yield of 20%. In hindsight, the concession was a small one and they learned a little about the amide couplings along the way.
Paragraph 6: On to the nocardios! Paragraph 6 revisits Figure 1 as it presents the retrosynthesis of 2 and 3 in greater detail. Again the strategy makes use of DKP formation but now targets the more complicated pyrroloindolines 6 and 7 as key intermediates. Compound 6 is the sole endo– configured pyrroloindoline in the paper. Note that its C2 and C3 positions are of the same enantiomeric series as 4 and 5, though. Access to it will require cycloaddition as before followed by epimerization of the carbon a- to the carboxylate. Exo-pyrroloindoline 7, on the other hand, is of the opposite enantiomeric series relative to 4 and 5 and it contains an allyl group (rather than methyl) at C3. Its synthesis will be a real test of the formal (3+2) cycloaddition methodology. The paragraph continues down the forward synthetic path by presenting the cycloaddtion reaction of 22 (Scheme 3) with 2-amidoacrylate 9a to give 23. For the preparation of 23, S rather than R-BINOL is used; this is exactly the point of using asymmetric catalysis and nicely illustrates the power of the cycloaddition. They take a bit of hit on yield for this transformation though. They obtain 23 in 52% yield, 19:1 dr, and 90% ee. The modest yield is attributed to an unwanted side product that results from allyl migration (from C3 to C2 of the indole) under the reaction conditions. However, the presence of the allyl group challenges the scope of the cycloaddition beyond what was done previously and fares well overall. Deprotection of the TFA group then gives one coupling partner, exo-24.
Paragraph 7: Paragraph 7 contains more pyrroloindoline synthesis. This time it’s N-allyl-C3-methyl-indole 25 that is the starting material; this indole is also a little more complicated than the models used in the development of the method. Of note is that 9b, the benzyl ester version of the 2-amidoacrylate, is used in the cycloaddition reaction (Scheme 3). This is the only instance among the four cycloadditions that uses this acrylate. It’s not discussed, but in the methodology paper, this acrylate gave the best combination of yield, dr and ee. It is up to the reader to surmise that despite the modest yield (due to lower diastereselectivity in this case), 9b must have given better results than 9a for the transformation. Transesterification, the need for which is not really explained, sets up the epimerization of the carbon alpha to the carboxylate of 26. Cleavage of the methyl ester then reveals acid endo-27 which is ready for amide bond formation.
Paragraph 8: The nocardio A/B synthesis is now at the stage where pyrroloindolines 24 and 27 are “poised” for DKP formation. Coupling in this case using BOPCl was successful. The product, 28 (Scheme 3), was isolated in 84% yield. A footnote directs the reader to the SI for details of the optimization of the yield of the reaction at this point. Inspection of the SI shows that the base, equivalents of amine (24), and rate of addition of acid (endo-27) to the mixture were optimized. She then pays additional homage to the amide bond by comparing the failure to couple 15 and 18 with the success with 24 and 27, writing, “…in addition to the N-substituents, the relative stereochemistry of the pyrroloindoline coupling partners is determinate of the ease of peptide formation.” A saponification-acidification sequence closes the DKP to give 29 (74%). Removal of the N-allyl group then provides 30, a versatile intermediate common to both nocardio A and B. The paragraph ends with the efficient cross methathesis of 30 and 2-methyl-2-butene. The reaction completes the (+)-nocardioazine B (3) synthesis; their route delivered it in 21% overall yield in 9 steps. Modestly, the paper defers the opportunity to compare this synthesis of 3 to the one reported by the group of Ye (10 steps, 12%).
Paragraph 9: Reisman’s attention now turns to (+)-nocardioazine A (2). The plan is to advance compound 30, the penultimate intermediate in the synthesis of (+)-nocardioazine B (3). Cross metathesis of 30 with methacrolein, Luche reduction, and mesylation-chlorination proceed without incident to give 33 (Scheme 4). “Gratifyingly,” (Another great word, although I would have stolen a Wood/Stoltz gem, “To our delight,”) macrocyclization via N-alkylation was also successful, giving 34 in 73% yield. This intermediate is so close to the target itself; it is amongst those “lofty heights of an advanced intermediate”. All that’s left is a seemingly mundane epoxidation that should be quite diastereoselective based on the shape of the macrocycle. The writing seems down right despondent when it lists the epoxidation conditions that yielded little more than the unstable N-oxide 35. Upon inspection of the solid state structure of 34, the recalcitrance of the trisubstituted double bond toward epoxidation was argued not to be steric, but rather resulted from the “electron-withdrawing nature of the allylic nitrogen.” No citation, no further explanation. The lack of additional discussion here leaves the reader grasping for a complete understanding of the lack of reactivity.
Paragraph 10: This paragraph details one last gasp to push intermediate 34 over the line to (+)-nocardioazine A (2). Dihydroxylation and chemoselective mesylation followed by intramolecular epoxidation delivered the C2’’-epi-nocardioazine A (37). Ultimately this was a dead end and Reisman moves on without any additional comment. Damn.
Paragraph 11: But then she fires it up one more time. Paragraph 11 walks through a revised synthesis of (+)-nocardioazine A (2) in Scheme 5. They intercept an early intermediate from the previous (attempted) route, pyrroloindoline 23, and proceed with a cross metathesis using methacrolein, Luche reduction and then Sharpless epoxidation on the resultant allylic alcohol giving intermediate 40. This was converted to the corresponding mesylate (41) in anticipation of the upcoming alkylation. Compound 43 is the amine nucleophile for the alkylation. It was prepared from 42 via de-allylation. Although not numbered there, 42 was also an intermediate in Scheme 4. The conversion of 26 to endo-27 entailed transesterification, epimerization, and demethylation to reveal the acid. Drop the last (demethylation) step and you’ve got 42. Alkylation of 41 with 43 then proceeds efficiently and without incident. Saponification of the methyl esters and hydrolysis of the trifluoroacetamides of 44, the product of the alkylation, gave 45. Lofty heights. “We were pleased to find that subjection of 45 to PyBroP in DMF promoted intramolecular DKP formation to afford (+)-nocardioazine A (2).” [YAWP! Mic drop.] Rather than exclaim, Reisman chooses to be understated, cool. She moves on to reassign the stereochemistry of 2 relative to the isolation paper; the reassigned structure of 2 is consistent with Ye and coworker’s reassignment of 3. The paragraph ends with the usual metrics (nine linear steps, 11% overall yield) and the observation that the macrocyclization by DKP formation was effective.
Paragraph 12: The wrap up hits the points that have been collected along the manuscript. 1 – We made the three related bis(pyrroloindoline) DKP natural products. 2 – The enantioselective formal (3+2) cycloaddition is useful to total synthesis. And finally, validation their respect for the amide bond. 3- “In addition, subtle changes in the relative stereochemistry and nitrogen substitution patterns of pyrroloindolines were shown to significantly influence the ability to prepare bis(pyrroloindolines) by DKP formation.” This finish signals Reisman’s appreciation of the amide bond as a worthy adversary.
¶Thanks to Sarah E. Reisman for sharing ChemDraw versions of the figures and schemes from the Angewandte paper.
# Professor Reisman has a tenuous connection to UConn Chemistry. Timo Ovaska, her undergrad research advisor, earned his PhD with Bill Bailey in our department. She then traveled west to New Haven to work in John Wood’s lab when he was still at Yale. Though Sarah isn’t a native nutmegger, we’d gladly claim her as our own; the (+)-nocardioazine B synthesis shows a good bit of Yankee ingenuity.
^ Although this post has been written as though Professor Reisman is the sole researcher and writer, it has been done for clarity only. It’s safe to say that she, like all faculty, values the scientific collaboration and training with post-docs, grad students, and undergrads as the most enjoyable part of the job.
It was an international roller coaster ride. There were ups and downs. The time went faster than I expected. I returned to the place where I started. I want to do it all again. My Fulbright experience during the spring and summer of 2013 in Barcelona played a transformative role in my life, both personally and professionally. I have returned to my “normal” life with a broader perspective on my research and with a profound appreciation of place, history and especially interpersonal relationships that I had previously dismissed. In much the same way I packed a bit of eastern Connecticut to share with Barcelona, I’ve returned with my story about Catalunya that must be told.
Initially it was a maelstrom of sensations, impressions, and emotions: new sights, new smells, city life, commuting as a contact sport, late lunch and later dinner, Catalan in my ears that was close to the familiar Castilian Spanish but not quite intelligible, the kindness of the locals, joyous solitude filled with reading, writing and thinking, wretched solitude away from my family. My host and his lab were one constant during this time. I had chosen to work at the Chemistry Institute of Sarria (Instituto Quimico de Sarria, or simply IQS) with Professor Antoni Planas. Science is inherently international. Chemical reactions follow the laws of Nature so the lab was a logical place to connect with something that was familiar to me. I had also rented an apartment before I arrived in Barcelona through a company on the internet. I lived in a furnished third floor apartment in a neighborhood called the Eixample near the Diagonal and Passage of San Joan. The Eixample, literally ‘extension’, covers a huge swath of Barcelona. It was created as part of a huge expansion of the physical layout of the city that occurred in the 19th century. As with similar urban expansions of the time (e.g. NYC) the Eixample was laid out in a very logical grid pattern. With the most important locations of the city – my lab and my apartment – organized, I began to fill in the corridor between the two. Within a couple of weeks I had established a daily routine and had the physical lay of the land in my head. I could traverse the route from apartment to lab (by train) without conscious effort. I had coffee at Mr. Pan on most mornings. I did Saturday morning shopping at several stalls in the Market of the Conception near my house. I knew to get to the Poll Bo before three o’clock on Sunday if I wanted a chicken for lunch. The most basic challenges of day-to-day living had been overcome; I was on top of it all. I began to feel like l was really a local.
Research Collaboration: Let’s get the proteins to do the work.
Toni Planas, my host at IQS, is the Chair of the Department of Bioengineering. Work in his lab ranges from fundamental enzymology to the engineering of algae to overproduce beneficial fish oils. He is world-famous for being amongst the original developers of glycosynthase technology. Glycosynthases are engineered proteins that have their origins in sugar metabolism. One type of carbohydrates, the cellulose that makes up paper, for example, are linear polymers of individual sugar monomers. An easy analogy is to beads on a string – the beads are the sugar monomers and the bits of string between are the bonds that link together the monomers. There are enzymes – an enzyme is a protein that lets a chemical reaction occur more rapidly – in all living organisms that break the bonds between those monomers. Enzymes that break down the bonds in sugar polymers are called glycosidases. As Toni was studying the atomic details of how glycosidases actually speed up the cleavage reaction, he realized that a specific amino acid in the protein was critical for activity. More importantly, he reasoned if that you switched that amino acid so it couldn’t break the bond, maybe the enzyme could form the bond rather than break the bond – the enzyme would run “in reverse”. Given the appropriate conditions, these enzymes are remarkably efficient at making the bonds between sugar monomers. In effect, you could build the string of beads rather than tear it apart. The term glycosynthase was coined to indicate that the enzymes could use sugars (“glyco”) to synthesize (“synthase”) polymers.
Glycosynthases caught my eye because my research group makes artificial sugar compounds that contain an extra atom in the monomer ring. We’ve investigated how to synthesize these sugars and characterized how they are bound by proteins. Before the Fulbright investigation, we used a different type of protein called a lectin whose regular function is simply to bind sugar molecules. Our expanded sugars compete with natural sugars for the binding pockets of lectins – this could have implications for preventing bacterial infections, among other applications. Our question was whether glycosynthases could utilize our expanded sugars in their reactions. This question is more complex because the protein must bind AND then perform the bond forming reaction (They “do chemistry.”).
Once in the lab, I felt like I was a post-doc again. I was quickly reunited with an envelop of sugar samples I had sent from my lab before my departure. With my graduate student mentor, Hugo Aragunde-Pazos, I expressed and purified both a glycosidase and glycosynthase we had identified as the first candidates for our investigation. Some of the techniques I learned were completely new; others were old-hat. Hugo and the rest of my labmates were remarkably helpful and patient. I had many many interactions with the students that introduced me to a different perspective on how to think about science and research. Dealing with language slowed me down relative to how quickly I may have worked in a lab where English was the primary language. My lab technique was a little rusty too, I must admit. Despite the fact that the students were happy to speak Castilian Spanish (and when really pressed, English) in place of Catalan, I spent significant mental energy on simple communication. Language barriers may have initially slowed my work, but it went away after a few weeks. Those weeks I felt stressed and apprehensive because of the challenges language presented. The experience made a strong impression on me that I will never forget. I have more respect for all the international students and post-docs I’ve ever known and I will understand and anticipate this emotion in others when they’re in the same position.
It’s not breaking news to report that the mid-day meal is the main meal of the day in Spain. Lunchtime brought a special opportunity to me in addition to nourishment. It was a relaxed, informal atmosphere to discuss just about anything. My regular lunch group was composed of the people with whom I shared desk space: two of the advanced graduate students Victoria Codera and Sergi Abad, and two of the scientists Teresa Pellicer and Patricia Torruella Barrios. This group instantly became my logistical, social and cultural advisors on Barcelona and all of Catalunya. They taught me some Catalan. They explained how things worked within IQS, within Barcelona/Catalunya and within Spain. They kept me up-to-date on Spanish current events, like a brief hubbub surrounding subsidized cocktails in the Spanish parliament. The most productive lunches were when we planned activities for me to do with my family when they eventually joined me in Barcelona. These conversations were a fertile ground for me to get to learn about Catalan food, history, geography, everything. We determined early on that we could easily plan a year’s worth of weekend excursions, but we would have to concentrate that down to a solid month of touring.
Life Outside the Lab: Diversions
I also did extensive “field work” – aka sight-seeing – in Barcelona and Catalunya to prepare for the arrival of my family. I spent a couple of hours waiting in line one Saturday night to see a landmark Gaudí building, “Casa Milà” better know as “La Pedrera”. Entrance was free because it was the “Night of the Museums,” an event sponsored by the Catalan government and local companies. The line wrapped around three sides of a city block; that alone was sight to see. In between occasional forays on the internet afforded by free wifi hotspots, I actually chatted with some of the people who were in line with me. They provided support for my decision on which museum to visit that night (We didn’t actually get into La Pedrera until about midnight.), but they were happy to show their pride in their city and try out a little English too. Once inside I was struck with the brilliance of Gaudí; the attic of the building collects maquettes of several of his other works to showcase his design philosophy. His ability to harness natural themes – even abstractions such as conic sections – into the design of objects is a hallmark. To Gaudí form had to follow function in a way that uplifts one’s human spirit. Occasionally, a one or two of my labmates would join me on an excursion. The most noteworthy of these was a day trip to the Costa Dorada beach town of Sitges. I joined Victoria and her boyfriend Frances along with Anabella, a group alumni from Guatemala who happened to be visiting. We went to Sitges on Corpus Christi, a Catholic holiday in the spring, to see the “carpets of flowers” that are laid out in the streets. The carpets are designed and executed by neighborhood groups and some are really sophisticated. It’s kind of a stationary Rose Parade. The most interesting part comes during the afternoon when series of 8-10 foot puppets “gigantes” dance through the streets while simultaneously destroying the carpets. Victoria and Frances couldn’t explain why the gigantes had to destroy the flower creations, but it seemed symbolic. Regardless, we, along with the other kids and adults watching, shrieked with delight as the gigantes passed by.
Once they arrived in Barcelona, my family and I roamed around Catalunya as unapologetic tourists. We visited the Gothic quarter, the Magic Fountain on Montjuic and all the Gaudí spots like Parc Guell, Sagrada Familia, La Pedrera and Casa Batllo. All of these sights were in the city itself. We also went further afield in Catalunya to Montserrat, the Codorniu vineyards in Sant Sadurní d’Anoia, the beach at Vilanova i la Geltru, and the town of Figueres which is Salvador Dali’s hometown. We would take “breaks” in between excursions that would allow me to catch up on work and let them catch up on sleep. My one-bedroom apartment seemed palatial for two months became cramped when the four of us were living there together. Throughout our journeys my appreciation of the history, culture and people of Catalunya deepened. I was proud to claim temporary residency there.
Food is an essential component of culture and relationships. The dish most often thought of as the national dish of Spain is paella. In its simplest form it is yellow rice colored by saffron with shellfish cooked in a tomato and seafood broth. There are many, many variations but I staunchly defend my mother-in-law’s version as the world’s best. Paella was both the food and the entertainment at a party in honor of my host Toni who had just received the Fischer Prize at the 2013 European Carbohydrate Symposium. It was also a fortunate coincidence that the party was held as my family arrived in Barcelona. It was a perfect opportunity to introduce them to my new friends and colleagues. Preparing the paella was one of the main activities at the party. Three teams cooked one paella each; this was sufficient to serve everyone at the party. My family and I were happily only spectators for the cooking but participants in the eating. There was drama, trash-talking, some minor sabotage and all-out fun afoot as the paella was being cooked. The noted Catalan “gastronomy as performance art” couldn’t hold a candle to Fischer Prize party. Afterward we consumed the mountains of paella, there was a premier viewing of a video prepared in honor of Toni as Fischer Prize winner. It was a music video parody “Planas Style” a Catalan rendition of PSY’s “Gangnam Style” that included some embarrassing singing and dancing by everyone in the lab. While paella may be the national dish of Spain, the staple of the Catalan diet is bread with tomato, pa amb tomaquet in Catalan. It is one of those foods that is deceptively simple. It is the simplicity that requires using the best possible ingredients: bread (often toasted but not always), ripe tomatoes, olive oil and salt. Raw garlic is also used in the most traditional version. At a restaurant, the ingredients are delivered to your table for you to assemble. Start with the toast and rub it with a clove of raw garlic. Add olive oil and salt. Then take a fresh tomato cut horizontally, not longitudinally, and rub it onto the toast leaving only the tomato skin behind. Part of the attraction to me is the ritualistic nature of the preparation. It brings out my inner alchemist.
The Heart of the Matter
In the spirit of the Fulbright program, I arranged interviews with a few scientists in Barcelona whose research interests are similar to mine. Interviews were extracurricular; they were done outside my lab schedule. I originally had high hopes of doing several interviews, but in the end was able to do only three. In hindsight I wish I had made time for more. I caught up with my friend Xavi Salvatella, who had returned to Barcelona from a post-doc in England since I last spent time with him. I also interviewed Ernest Giralt who was an informal advisor to me as a graduate student. I also met Lluis Ribas, a scientist and entrepreneur working on developing new antibiotics. All three of these researchers work at the Institute for Research in Biomedicine (IRB) in Barcelona. In the he interviews I asked about their latest research results and I also asked how they got to the IRB and what it meant for them to be doing research in Barcelona. The latter part of the interviews revealed more about Catalunya than I had expected they would. A theme centered on the importance of relationships with family and friends emerged as they recounted their decision to live and work in Barcelona. Each one is emotionally connected to Catalunya. Their identity as Catalans was clearly distinct from their identity as Spaniards. It struck me that these things – identification with ‘home’ and close personal relationships – make any group unique but it also common to all groups. What makes us different makes us the same. For me this was both profound and bittersweet. Profound because I realized that these were the same reasons that my brothers would have cited if I had asked them why they chose to live and work in the town where we grew up. And bittersweet because I’ve underemphasized those factors in my own career choices. The realization has kindled a desire in me to remember the importance of people and place.
Looking back on my short residence in Barcelona, the ups and downs seem a little less dramatic now than they were along the ride. All of my experiences there have provided valuable lessons and memories. The scientific work was rewarding and productive. Beyond that, I now have a deeper understanding of how Catalans see the world and themselves. I am attached to both the specifics of this perspective – in terms of their uniqueness in the context of Spain – and the broader concept that emphasizes relationships. I hope that I have revealed some small insights of my Nutmegger’s perspective of the world to my new friends and colleagues in Barcelona. I eagerly anticipate my next ‘ride’ there.
Note: Many, many thanks go to Jeff Winkler for looking over the post and also sharing an original copy of the manuscript.
Reading a research article is an active process. It’s completely different from leisure reading like a novel or magazine. It’s more like a special – extreme – case of textbook reading. The information has to be unpacked, worked-over and constantly grappled with. During the first meeting of my Organic Synthesis class this year, my students and I worked through the Winkler synthesis of Ingenol. The objectives of the activity were three-fold: 1 – I wanted to compare the strategy used by Winkler to that the recent Baran synthesis. (Which was itself spurred by Carmen Drahl’s reporting on Baran’s synthesis.) 2 – I wanted to analyze how the authors used text and figures to relay the information about natural product synthesis. This helps me develop dos and don’ts for my own writing and a strategy I wanted to share with my students. 3 – I wanted to illustrate how much work an “active” reading of a manuscript should actually be. Below is a play-by-play of the manuscript. It analyzes how Winkler et al. communicated their results in the manuscript and how the reader should interact with the text.
Paragraph 1: Straightforward opening for a total synthesis paper. The authors mention the textbook reasons of “biological activity” and “structural complexity” that inspired their efforts. The inside-outside, C8/C10 trans intrabridgehead stereochemistry linking the BC rings is the most noteworthy feature. Structure 16 is also identified as an important intermediate in this paragraph. It is likely singled out because its preparation completes the carbon skeleton of Ingenol 1, a milestone in the synthesis.
Paragraph 2: This paragraph details the retrosynthetic strategy of the authors and is accompanied by Scheme 1. “Dioxenone photoaddition-fragmentation product 2” is the first intermediate offered in the retrosynthesis. The authors don’t elaborate on what is required to convert 2 to 1, so it is up to the reader to work it out. Inspection of the structures shows that, regardless of order, that: • the A ring of must be methylated at C2 and the C1-C2 alkene must be formed; • both C4 and C5 must be oxygenated; • the C6-C7 alkene must be formed; and • the ester attached to C6 must be reduced down to the corresponding alcohol. Additionally, the authors’ description of 2 leaves a little bit to be desired. It describes how the intermediate was prepared, but little else. To understand, the active reader has to look forward to Scheme 2 to see the intermediates 13/14 to see the photoaddition product and also back at the earlier work from the laboratory where the tandem photoaddition-fragmentation strategy was developed. Once the reader is familiar with the two-step sequence, intermediate 3 becomes a logical precursor for 2. The dioxenone unit in 3 can be simplified to the keto unit in 4 via a retro-carboxylation and enolization process. Reductive enolate formation and alkylation of 5 would lead to 4. The origins of enone 5 are not completely explained in the main text, but reference 6 states, “We thank Professor Phil Eaton (Univeristy of Chicago) for providing an unpublished procedure for the conversion 6 to 5.” Compound 6 is the deoxygenated version of 5; it lacks Ingenol’s C3 hydroxy group. The note in reference 6 points the reader in the right direction, but it still requires work to understand where 6 itself came from. In this case, reference 4 leads the way. Tetrahedron 1968, 24, 553 (ref 4c) shows that 6 can be synthesized via elimination and acylation of lactone X or its corresponding hydroxy acid using polyphosphoric acid. The precursors were probably prepared from beta-keto ester Y and methyl/ethyl methacrylate based on the J. Org. Chem. 1999,64, 3770 reference (4a).
Paragraph 3: The forward synthesis of intermediate 16 from 5/6 depicted in Scheme 2 begins here. The paragraph is dedicated to one reaction in the synthesis: the reductive alkylation of 6 using methyl crotonate as the electrophile. In the reaction, three contiguous stereocenters are set including a quaternary center right in the middle. Two relative stereochemical relationships arise from the three centers. The authors deal with each separately. The cis relationship between the bridgehead carbons in 7/8 is because the beta face of the enolate is less sterically hindered than the alpha face. This argument should probably conjure an image of a bis-envelope conformation of a cis-[3.3.0]bicyclooctane. The C10-C11 stereochemistry requires transition state structures to rationalize the diastereoselectivity. Figure 1 shows transition states, labeled A and B, and they are “called” in the paragraph; that is, the writing makes specific reference to the items in the figure by name or letter. This connection between text and figures is common and effective technique to facilitate reader understanding. Figure 1 uses arrows to draw attention to the interaction that disfavors TS B; it’s the C4 methine and the alpha hydrogen of crotonate (both TS have a gauche interaction between the electrophile and the enolate). This paragraph is a good example of using a figure to rationalize a key principle that supplements the reaction sequence presented in a scheme. A structure for the product of alkylation discussed in paragraph 3 is not actually shown in Scheme 2. Instead, the product of a two-step sequence, alkylation and silyl enol ether formation, is shown. When 6 was used as the starting material of the sequence, 7 was the product. The sequence yielded a mixture of diastereomers in a 14:1 a:b (C11 methyl) ratio.
Paragraph 4: If the same two-step sequence was conducted on the more highly functionalized enone 5, an unacceptably low yield and diastereoselectivity was obtained. The authors consequently elected to continue forward from compound 7. The paragraph continues on to describe the reactions that converted 7 first into ketone 9 and ultimately to dioxenone. Conversion of 9 to 10 included carboxylation of an in situ generated lithium enolate with Mander’s reagent. This reagent gave the beta keto (methyl) ester as the product. It is converted to the PMB ester in the proceeding step before dioxenone formation without explanation. We reasoned that the transesterification was necessary (Why else would they add a step?) and that it implicated the ester oxygen as a nucleophile in the dioxenone formation. In the case of a PMB ester, the resulting carbocation would be relatively stable especially when compared to a methyl carbocation. The paragraph ends with the formation of compound 10. This makes good sense because they have taken the starting material forward to an intermediate that secures the functionality (the dioxenone) of one half of the photocycloaddition reaction.
Paragraph 5: The manuscript switches focus to the other end of the molecule that will participate in the upcoming photocycloaddition. They install a hydroxyl group onto C14 of 10 by an allylic oxidation to give compound 11. One unanswered question is why that couldn’t have been done earlier, perhaps before the sequence that formed dioxenone 10. The allylic oxidation is necessary to introduce functionality into this segment of the molecule that can be parlayed toward the cyclopropane unit of Ingenol. Photocycloaddition of 10 was low yielding so they refunctionalized to the corresponding allylic chloride. The chloride was considerably more efficient in the cycloaddition, providing 14 in 60% yield. Compound 14 is the first of the two showcase reactions that will ultimately deliver the carbon skeleton of Ingenol. The enthusiasm of the authors is apparent by the exclamation point used to finish the sentence, “…we were delighted to find that photocycloaddition of the derived allylic chloride 12 proceeded in 60% yield to give the desired photoadduct 14, accompanied by the C13 chloro-isomer (5:2 ratio)!” They are pleased with the reaction. In reference 8 they also promise to explain the origins of the C13 chloro isomer, which here goes without further comment.
Compound 14 is amongst the “perilous heights of an advanced intermediate” as has been stated about so many compounds in natural product synthesis. There is an abundance of functionality waiting to be unleashed en route to key intermediate 16. The cyclobutane, just formed in the cycloaddition, will be unraveled in the formation of the challenging inside-outside bicycle ring junction between rings B and C. The carboxylate will eventually become the C6 hydroxymethyl group. The C14 chloride will enable the cyclopropanation via the intermediacy of the alkene. Based on the group’s previous work and the enthusiasm about the success of the cycloaddition, they are confident that the fragmentation would be successful. They give the fragmentation a clause and then continue tidying up the structural elements until they arrive at 15. In the footnotes there is the comment on the C6 stereochemistry – remember that that gives an indication of the electron motion of the fragmentation.
Stylistically, it may have been nicer to highlight the two-step sequence by making them the sole subjects of one paragraph. Perhaps paragraph 4 could have simply ended with the synthesis of the chloride, 12. I would have relegated the cycloaddtion of 11 to the notes and then let paragraph 5 shine in the brilliance of the photocycloaddition-fragmentation sequence.
Paragraph 6: The key steps necessary for the synthesis of the carbon skeleton of Ingenol are now behind them. A dihalocyclopropanation of alkene in 15 is followed by bis-alkylation with methyl cuprate to give the landmark intermediate 16. This paragraph wraps up the presentation of Scheme 2. To get to this point in the synthesis, there have been 18 linear steps.
Comparing structure 2 and 16 shows that they are very similar. The main differences are the oxygenation at C3 and the redox state of the group attached to the C6 carbon. It could even seem that the rest of the synthesis is endgame.
Paragraph 7: The payment for using 6 in place of 5 has come due. In paragraph 7, the authors quickly move through a series of transformations that convert 16 to 22. The key player that enables these transformations is the hydroxymethyl group attached to C6. Oxidation of that group to the corresponding aldehyde allows sequential eliminations that create the diene in 22. The authors report flatly in this paragraph that the seven steps reported are “to introduce the A ring functionality present in ingenol”. They don’t put emphasis on it, but it’s logical to think that they’d have preferred to carry an oxygenated C3 up to this point and done only one or two steps to be in a much better position than they presently are. So it goes.
Paragraph 8: The alkenes have been introduced into 22 so they can be oxygenated. It must be a “controlled burn”, however. They first reduce the aldehyde attached at C6 and then do a dihydroxylation on the C5-C6 alkene. The regioselectively is ascribed to greater steric accessibility of this alkene relative to the C3-C4 alkene. Similarly, the beta selectivity is also due to the steric accessibility of reagents from the beta face according to the authors. Building a model is an obvious way to get a sense of the 3D shape of the molecule as well as the associated selectivities of reactions associated with intermediates along the way. Unfortunately it’s not always put into practice. It definitely counts as “active” reading and will help understanding.
Paragraph 9: This paragraph finishes up the B ring synthesis. Dihydroxylation of the C3-C4 alkene and protection of the secondary hydroxyl as the benzoate give 28 and set up the linkage of the two tertiary alcohols into cyclic sulfate, 29. Elimination of the cyclic sulfate to provide the C6-C7 alkene was based on previous work in a closely related system. The remainder is some typical plug-and-chug to get to structure 31. As the authors write at the end of the paragraph, “it remained only to introduce the requisite A ring functionality to complete the synthesis of Ingenol.”
Paragraph 10: Structurally the paragraphs in the manuscript are a little clunky. They seem to tease the subject of the proceeding paragraph at the end of a given paragraph and then jump straight into the details at the start of that next paragraph. I don’t know if it’s accidental or by design. The authors walk the reader through C4-C5 diol protection, oxidation, Pd(0) beta-keto ester formation, alkylation, decarboxylation/oxidation to give enone 35. Whew. Steppy? They follow with Luche reduction of the enone and deprotections to ultimately deliver the title compound, Ingenol 1. They remind the reader that this was a racemic synthesis by reporting that the material prepared by them was identical to an authentic sample except for optical rotation.
Paragraph 11: The wrap-up. The synthesis was 43 steps from 6 with an average yield of 80%. That’s an 0.0068% overall yield using their numbers. It would be nice to have the authors report that number themselves. They complete the paragraph with the highlights of the synthesis. The best of these highlights is the penultimate sentence, “The establishment of the C8/C10 trans intrabridgehead stereochemistry serves as a testament to the utility of the intramolecular dioxenone photoaddition-fragmentation approach to the synthesis of structurally and stereochemically complex natural products.” Agreed. This paper showcases that tandem approach to the carbon skeleton AND continues to complete the total synthesis of Ingenol 1.
Atoms at specific “key” positions along the ring of a group of -membered ring macrocycles can govern its shape, or “topology”. The driving force for the organization of the structures is the minimization of steric strain on groups attached to the key atoms. When the key atom is a stereocenter, a macrocycle with planar chirality is observed. The key positions can work in a coordinated fashion to guide one topology over another. X-ray crystal structures of representative -macrodiolides served as the basis of the structural observations made. The results provide a framework for the design of new macrocycles with well-defined structures as well as for understanding some general principles that influence the topology of natural product macrocycles.