Some time ago I noticed that Mother Nature, despite its amazing virtues, does not know how to make C-N bonds by oxidation. Think about it: there are so many C-N bonds out there (in DNA, in alkaloids, you name it), yet none of them are made using oxidative enzyme machinery. If you are thinking about C-O bonds, then there are many examples of their construction using oxidative enzymes such as p450’s and others. However, all C-N bonds have reduction as their origin or are made using carbonyl condensation reactions. One might speculate as to why this might be the case. From Mother Nature’s standpoint, the most plausible reason would be “why bother?”. The metal-based nitrogen oxidants are inherently more difficult to produce compared to their oxygen counterparts (for example, metal nitrenes vs metal oxo species), so there is no evolutionary reason to go high in energy if the key bond-forming events can be accomplished using simpler means. The key factor is that molecular oxygen is our readily accessible terminal oxidant and there is just no nitrogen analog that is similarly abundant. We later wrote a short commentary in Nature Chemical Biology discussing this problem. This paper continues to be well cited (primarily by synthetic folks who need a believable justification for why synthetic nitrogen transfer systems are cool):

http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio0606-284.html

Now it turns out that chemists can teach Mother Nature some new tricks. Take a look at the paper by Bollinger and co-workers in Nature Chemical Biology:

http://www.nature.com/nchembio/journal/v10/n3/full/nchembio.1438.html

The α-ketoglutarate/iron-dependent dioxygenases and halogenases are typically recruited to run a wide range of enzymatic reactions ranging from hydroxylation to halogenation. Despite this useful palette of reactions, no C-N coupling by this class of enzymes has previously been reported. Bollinger et al. discovered that an αKG/Fe-dependent halogenase, SyrB2, can catalyze aliphatic nitration and azidation reactions. I am showing the azidation process above, which takes place when excess sodium azide is fed to the enzyme (thus, azide anions outcompete chloride anions). Despite the fact that chemical yields in the present version of the process are still very low, this study opens up new possibilities for nitrogen transfer by selective enzymatic C-H activation. It is conceivable that engineering of substrate specificity through directed evolution might be achieved in the future iterations of this system.

I already mentioned a sustained current interest in flow chemistry. I am a believer in this method. It is interesting to see reports where chemistry is run in thin capillaries where residence time rules. This parameter is unheard of in our typical “flask-based” reactions. Of particular significance to me is the paper by my former PhD student, Zhi He, who is now doing his postdoctoral work with Tim Jamison at MIT. Zhi’s manuscript, which just came out in Angewandte, documents a flow approach to phenols starting from Grignard reagents. This work serves as an example of an economical approach to phenol synthesis, whereby aryl Grignard reagents are directly oxidized using compressed air in “continuous gas-liquid segmented flow system”. Many functional groups are tolerated in this process. What’s interesting is that the determined reaction profile prescribes the optimal region of pressure/temperature around -25 ^oC and 200 psi. An opportunity to quickly scan the 2D pressure/temperature grid is powerful. The concept of residence time is critical to the success of flow approaches and, given the importance of kinetics in chemistry, there is potential to look at space/time control of REALLY exotic intermediates.

http://onlinelibrary.wiley.com/doi/10.1002/anie.201310572/abstract

In vivo, in vitro, in silico… How about in fluo? After all, “fluo” is the Latin for flow. Have you heard anyone refer to flow synthesis this way? I just thought about this term now, but there are probably precedents of its use out there.

Great job, Zhi!

Nerve agents are scary molecules. Thankfully, there is an antidote for pretty much anything, but only if taken at the right time (recall all those old Hollywood action movies…). There is a very interesting Swedish structural biology paper that describes molecular-level interactions between a series of nerve agents and their target – acetylcholinesterase (AChE). Nerve agents are fairly simple organophosphorous compounds that wreak havoc by covalent modification of Serine-203 in the active site of AChE. HI-6 is an oxime-containing antidote for several types of phosphorous-containing nerve agents. This oxime is remarkably efficient, acting as a competing nucleophile that reacts with the phosphorus center of the modified AChE, thereby restoring its normal enzyme activity. Is there a better way to demonstrate the marvels of chemistry? Everything here makes sense from the standpoint of simple polar interactions. Below I am showing a crystallographic view of Russian VX-modified AChE as well as the reaction of HI-6 that restores enzyme activity. The paper is remarkable because it also provides evidence why HI-6 fails with certain kinds of nerve agents such as tabun (tabun-modified Serine-203 is shown in the box). Apparently, the Phe338/His447 array close to Serine-203 reduces the conformational mobility in the tabun-AChE complex. The steric interactions interfere with the approach of oxime-pyridinium group of HI-6 to the phosphorus atom of the adduct. The kinetics of reactivation are thereby significantly slower and other (smaller) antidotes need to be designed.

http://www.sciencedirect.com/science/article/pii/S0006295213000531

I want to talk about an interesting parallel between Olympics and research in graduate school. You are probably thinking: “What on Earth is he talking about now?”…

I follow the updates from Sochi and, once in a while, tune in to see some of the events. The athletes do mind-boggling tricks and I constantly hear about medal counts. I respectfully disagree with the notion that getting a medal is the only way to evaluate a given athlete’s success. I think that the concept of personal best is equally important, especially in the events where execution over a defined period of time counts for success. When I look at athletes who do not end up reaching the podium, I catch myself thinking that they often demonstrate tenacity and hunger to improve over their past accomplishments. To me, this is what Olympics should be all about, but personal best metrics of success are not often mentioned.

I also think that in graduate research, each student should strive to achieve his or her personal best. This is naturally accomplished by improving on the number and quality of papers compared to what he or she had published the year before. Striving for a paper in Nature, Science, or other type of high impact journal, is probably akin to getting some sort of a medal. These are great goals to have, but we all know that such papers are rare and are not entirely under student control due to a number of complicating factors (politics, etc). On the other hand, if a student publishes a couple of papers in a given year, the following year should be an improvement: how about three papers, or two papers in the same level of journal and one in a higher impact journal? This way one’s personal best is established and there is definite progress.

Conformations of complex molecules such as cyclic peptides are tough to decipher. What a truism! I have mentioned this many times on this blog. Every now and then, I am forced to ask myself: how much effort do we really want to spend studying these complex systems? At times it feels as if we have a good grip on a given molecule, only to be disappointed by some capricious twist that throws all of our theories down the drain. The main reason things are difficult lies in the effects of media and additives, which can turn into the frustrating end of science. There are just so many geometrical variables a peptide of some complexity possesses that it is no surprise that things aren’t simple.

There are some monumental teachings from the past that suggest there is light at the end of the tunnel. Slowly but surely, I am compiling a list of additives with demonstrable ability to affect conformations as well as biological properties of cyclic peptides. One of these days I am going to publish a paper on this subject. For now, I just want to draw your attention to Dan Rich’s JACS paper from 1992 (the year I started graduate school, by the way). Cyclosporine A (shown below) is a known immunosuppressant that binds to cyclophilin (which is cyclosporine’s protein target). The trouble is, if the Leu-Leu amide bond in cyclosporine A is in its cis state, the molecule is biologically inactive. Dan Rich’s contribution demonstrates that the addition of LiCl to cyclosporine A in THF shifts the cis/trans equilibrium towards the bioactive trans form. What’s remarkable here is that the authors did not stop at evaluating the NMR spectra with and without LiCl, but convincingly demonstrated that the LiCl perturbation method works to alter the biological properties of cyclosporine A. According to the authors, a significantly more potent inhibition of cyclophilin is recorded in the presence of LiCl. Now – how about the effect of LiCl on the cellular permeability of cyclic peptides?

http://pubs.acs.org/doi/abs/10.1021/ja00033a047

I remember Kevin Moeller’s instructive paper in Tetrahedron, where he showed that, in order to run complicated electroorganic experiments, all you need is a simple Lantern battery from Home Depot. While fancy set-ups with high precision capabilities are available, good experimentalists who lack access to complex set-ups always find a way around the problem:

http://www.sciencedirect.com/science/article/pii/0040403996019466

These days, many of our students are attracted to flow synthesis. We recently had a nice departmental seminar on this subject by Thomas Johnson, one of Mark Lautens’ PhD students. I think chemists relate to the idea that new ways of improving mass transport can accelerate the rate of a given reaction, dramatically improving its efficiency. One of my former PhD students, Zhi He, is now heavily involved in flow synthesis in the lab of Prof. Tim Jamison at MIT. While I see the virtues of flow synthesis, I wonder: what can a lab with no access to microfluidics do in order to run reactions in flow? In short: be resourceful (just like Kevin Moeller). Here is a link to a great recent paper in J. Chem. Ed. by Prof. Thomas Wirth. Thomas was a visiting scholar at the University of Toronto several years ago and taught organic chemistry to our graduate students. The point of this work is to show that one can reap the benefits of flow set-ups and do it in an undergraduate lab using inexpensive syringes and glass tubes.

http://pubs.acs.org/doi/abs/10.1021/ed3006083

By the way, you can get glass reactors for these kinds of experiments from a cool German company by the name of “Little Things Factory”:

http://www.ltf-gmbh.com/index.html

Earlier today I was very sad to find out about the passing of Professor Alan Katritzky of the University of Florida. He is one the legends of chemistry with countless contributions to the field.

This giant of heterocyclic chemistry has always struck me as someone with remarkable clarity of thought when it came to teaching the fundamentals of heterocycle construction. I think that his legacy will live on, and this is not a cliché: Katritzky’s teachings are engrained in our understanding of heterocycles. I myself learned an important and simple lesson about nitrogen chemistry from Professor Katritzky. Shown below are the three kinds of nitrogen one might expect in heterocycles. Despite the mind-boggling diversity of nitrogen-containing structures, there are only three ways of having nitrogen within the frameworks of heterocycles. This concept is both powerful and simplifying. In my own classes, I have always observed that this simple concept really helps students in their efforts to navigate the treacherous and often confusing concepts of heterocycle synthesis.

I wondered what would be the best way to pay a tribute to the legacy of Professor Katritzky and realized that there could be nothing better than an example from his own work. I chose his regioselective synthesis of pyrazoles. In this process, Katritzky used benzotriazole, one of his favourite tools. In the regioselective pyrazole synthesis shown below, the Bt-reagent condenses with an aldehyde, which is followed by another condensation with a substituted hydrazine. Subsequent alkylation and extrusion of the elements of benzotriazole produces the pyrazole ring as a single regioisomer. This powerful condensation/alkylation/elimination method of preparing polysubstituted pyrazoles has been used countless times in medicinal chemistry. The wonderful world of Katritzky’s synthetic tools will continue to provide versatile solutions to the synthesis of small molecules.

http://pubs.acs.org/doi/abs/10.1021/jo0101407