Using math in synthesis

Synthetic chemists do not use a lot of math. We rely on it, there is no question about it, especially when it comes to our daily NMR experiments. Indeed, there is just so much math in the FID treatment alone. It just does not seem to affect our hypothesis-generating abilities, so we do not have a need to worry about all those complexities.

When I was doing my protein experiments with Elena Dobrovetsky during my sabbatical stay at SGC, it seemed that the “C1V1 = C2V2 (C: concentration, V: volume)” equation ruled our days. I suppose this one simple relationship is the most widely used piece of math when you need to prepare your 142nd buffer of the day.

But what is the single most important mathematical equation every organic chemist should know? In my personal view, it is the one describing the relationship between temperature, energy, and the ratio of two molecular entities expressed as K:


We normally refer to K as the equilibrium constant, but I wish we had a more generic term. This is because the value of the equation is in that it relates the difference in energy barriers to the ratio of products or transition states. Thus, the equation covers the domains of both thermodynamics and kinetics. Below you will see that equation again, this time rewritten in a more palatable way for quick calculations at room temperature. An immediate consequence is that each factor of 10 between the respective ratios of A and B (these could be ground or transition states) translates into a free energy change of about 1.4 kcal / mole.


Simple tools are often better

I am continuing my second year organic chemistry class, and although I am now covering NMR spectroscopy, the material of last week stirred some more “infrared memories”. I want to come back to the glory of this kind of spectroscopy and make it even more exciting… What if we want to see a situation where a unique reactivity insight is offered by way of analyzing an IR spectrum? This is different from the example I discussed in my last week’s post, in which the isocyanide functional group was distinguished from its cyanide counterpart through a shift in the wavenumber. This was more about functional group characterization. Now we want to shed light on reactivity preferences.


Above is a classic aziridine paper from Stamm and co-workers. Due to their substantial strain (about 27 kcal/mol), aziridines are different from other amines because aziridine nitrogen is much more pyramidal (which is to say that its barrier to inversion is high). Stamm’s experiments suggest that there is a marked difference between the chemistry of cis- and trans-acyl aziridines shown. You can see that the cis-isomer has a stronger C=O bond (reflected in the higher wavenumber). Interestingly, the cis-aziridine was found to preferentially react with nucleophiles (there were several nucleophiles and these details are beyond the scope of this post) at the carbonyl carbon, whereas the trans-aziridine preferentially reacted just like an epoxide. What might be the reason for this peculiar dichotomy? The IR spectra provide valuable clues. Apparently, the equalized steric environments of the top and bottom faces in the trans- case contribute to more efficient conjugation between the nitrogen lone pair and the carbonyl group. The trans-aziridine reacts as strained heterocycles normally do: the three-membered ring pops open. In contrast, in the cis-aziridine case, the acyl substituent prefers to occupy the less hindered face of the molecule. The nitrogen center is substantially more pyramidalized, which is reflected in less extensive conjugation and, hence, lower wavenumber. This explains why the carbonyl carbon is now preferentially attacked by the nucleophile. The Stamm study clearly shows the strong dependence of acyl aziridine reactivity on the nitrogen pyramid. In closing, IR can be really useful and full of insights.

Twisting and turning: small molecule ligands in bound states

The protein database ( is a wonderful resource that provides plenty of ideas for structural biologists and chemists alike. While the value of pdb is self-explanatory when it comes to structural biologists, it is not that clear-cut as far as organic chemists is concerned. I do think we should all use this important and searchable resource. There are many reasons to like it and one of them is that you can get some interesting ideas about molecular design. Today I will discuss torsional preferences in protein-bound small molecules. Entropic tricks used by chemists allow one to narrow down conformational freedom that is accessible for a given small molecule and, regardless of your view on the entropy/enthalpy compensation (this should be a separate topic for a post), small molecules likely engage their targets by involving a “quantized” set of functional group orientations. But do these correspond to energy minima? For instance, what if you look at the diarylamine fragment shown below and ask a question about statistical analysis of all pdb instances where it appears bound to a protein? Might there be a preferred abc dihedral angle? If yes, what is it?


In this regard, I will post two important papers today. The first one is rather controversial. It has seen a fair amount of criticism in the literature. This work by Perola shows that over 60% of the ligands do not bind to their targets in a local minimum conformation ( The criticism directed against this work questions the validity of geometrical parameters of small molecules determined by protein crystallographers (remember my old posts – these guys are a different breed when compared to chemistry-oriented crystallographers). The controversy here is connected to the age-old problem of resolution, I suppose. The second paper is by Hao and co-workers ( ). This work is about accessible ranges of geometrical parameters for functional groups in small molecule ligands. Figure 1 of this paper is really cool: it shows the conformational histogram derived from PDB X-ray structures as a bar diagram. The authors superimpose the number of occurrences of a given torsional motif with the potential energy calculated using DFT. This paper suggests that the most probable values of the torsion angles agree well with the calculated global energy minima. I think there are creative ways of using these kinds of findings in efforts to design constrained ligands.

Old habits and common sense: a case of desulfurization

In our group meetings I always lament on how reluctant we are to change our set ways of running a given synthetic operation. I understand the argument of sticking to what works, but I just don’t get it when we are reluctant to give a chance to superior methodology, especially when it represents a synthetic operation that might be superior to our favorite tool. For instance, in our peptide work, we often run reductions of C-SH bonds into C-H bonds. What do we use in order to effect this transformation? We typically use Raney nickel… My main “beef” with this substance is its poor safety profile. The misery this reagent can bring when mishandled is considerable. Given the emphasis on safe laboratory operations these days, pyrophorics should be the first chemicals to be careful about. Yet, we continue to rely on that Raney nickel concoction. In this regard, Danishefsky’s radical desulfurization mediated by trialkylphosphites provides a marvelous and significantly safer alternative. Below is its mechanism and a paper that appeared some time ago.


In my view, one of the goals of modern chemistry research should be to replace hazardous reagents with alternatives that accomplish the same objective while minimizing risks. While technical expertise is a reliable antidote against mistakes in the lab, complacency and routine are among the dangers affecting everyone. And routine is the worst of them, a real bane of laboratory practice. Even experienced chemists may fall into this trap… A given reaction would go safely and without a glitch 100 times, but might abruptly fail without an apparent reason on the 101st attempt.

Azetes and their reasons to exist

Here is a heterocycle we do not hear a whole lot about these days: azete. Once you wonder about this kind of molecule, you will find yourself at the outskirts of organic chemistry! Azetes do not get mentioned at all when we teach sp2-rich nitrogen heterocycles (such as pyridine and pyrrole). However, they do exist and are isolable, despite being antiaromatic. I am always reminded of Alan Marchand’s instructive remark that one should not incorporate thermodynamically controlled steps when building strained molecules. Accordingly, azetes are made by a thermal decomposition of the cyclopropenyl azide (see below). The very existence of azetes is clearly kinetic in origin, which is to say that these four-membered rings can be obtained once a sufficient barrier preventing their decomposition has been secured. In the language of those brave souls who consider making molecules of this kind, successful isolation of an azete can be achieved once several tert-butyl groups are placed at the periphery of the molecule. The NMR of tris(tert-butyl)azete is the most interesting part of the classic Angewandte paper by Regitz (link below). There are only two groups of signals corresponding to tert-butyl groups, which means that the molecule is a time-averaged form of the two structures shown in the magenta rectangle below. It is as if the atoms are dancing around and the molecule keeps distorting itself…


Why am I bringing up this obscure heterocycle? As I teach my CHM 249 class, I always contemplate really weird things. I feel a need to mention this sort of stuff as it makes me feel particularly good to be a synthetic chemist. What can be better? We create our own subject, the stuff that often has no business being stable, let alone found in nature. Just think about it: have you ever heard of synthetic astronomy? Nope. But synthetic chemistry – by all means! Synthetic biology seems to be emerging, though.

Housekeeping and vacuum cleaners

How do we get students interested in chemistry? There are many ways of achieving this goal and some of them work better than others, depending on a particular individual. I recall being interested in fundamentals and mechanism. For instance, the first time I heard about benzene ring and its electron cloud, I was awestruck for a while. Some people prefer to see parallels with macroscopic objects. What works for them are “molecular rulers”, “molecular robots”, and so on… All of these cases involve reductionist approaches to a particular action or an object that is familiar to everyone. Nowadays, people do less of this sort of blue-sky science.

Now… What if we think about a vacuum cleaner? What would be a molecular-level analogy in this case? Does it exist? I was just thinking about it today and I have to say that this is not a stretch at all. We do not need to create anything artificial in this case as there is something we all have in us and it works pretty well. Hydrophobic vacuum cleaners perform vital roles in cells. Consider molecules such as p-glycoprotein (or p-gp). The role of p-gp is to pump out all manner of hydrophobic molecules out of cells. While this function is critical when toxins are considered, one would actually want to minimize the premature “suction” of life-saving therapeutic agents. The reason I thought about this problem today is due to our long-standing interest in peptide macrocycles. We have some cool recent results pointing to a correlation between certain structural aspects of our macrocycles and their cellular influx. But what about efflux, which is the opposite process? The following paper by Chang and co-workers came out in Science several years ago: It serves as a reminder that nature has its clever ways of dealing with almost anything we throw at it. Alas, we can spend tremendous efforts designing macrocycles for a particular function, but p-gp will have its final say… What you see in the graphic below (I made it using PyMol) is molecular-level view of a selenium-containing macrocycle that has been co-crystallized with the molecule of p-gp. The bad news (for those of us who care about molecular design of bioactive molecules) is that there is a large hydrophobic cavity in p-gp that is geared to accept all sorts of “cargo”, ultimately removing molecules from cells. Remarkably, the enantiomer of the macrocycle you see also got co-crystallized with the protein. The position of the enantiomeric molecule is different from its mirror image, but as far as p-gp is concerned, the score is p-gp – 2: selenium macrocycle – 0! As an aside – check out the C-Se-C angles…


Watching paint dry

My distinguished colleague, Professor Mitch Winnik, used to give a really interesting talk entitled “Watching paint dry”. This slightly facetious title is meant to represent a popular belief that watching paint dry is one of the most boring things known to man. If you know something about colloidal chemistry, you would quickly realize that this complex and multifaceted process is anything but boring.

Today I want to talk about infrared (IR) spectroscopy. Does this sounds boring? I think the majority of organic chemists look at IR spectroscopy as the chore of compound characterization. I think you will all agree that synthetic organic students rarely use IR in order to answer questions pertaining to mechanism and/or compound characterization (unless they are putting together their theses or supplementary materials for papers). There is indeed something to be said about other methods that provide way more information and are almost as fast (eg NMR). Accordingly, there are more streamlined means to ascertain product purity and identity, unless you are an inorganic chemist studying the structure of antimony pentachloride. In this case you have no choice but to use IR…

This week I started teaching my second year organic chemistry class (CHM 249), which is one of my favourite courses. I always start with spectroscopy and my first week is all about IR. I asked myself if I can think of an example where IR has enabled structural assignment and led to a valuable insight. I did not have to go far in order to dig out an example… When compared to cyanides, isocyanides are distinguished by a shift in the characteristic CN absorbance of about 100cm-1 in their IR spectrum. Here is a classic paper from the 1960’s that takes advantage of this difference:!divAbstract. In it, Booth and Frankiss showed a very peculiar property of trimethylsilyl cyanide. This molecule is in equilibrium with its isocyanide form, albeit the latter accounts for a very small percentage of the mixture. Curiously, the composition is pressure-dependent and the amount of the isocyanide component increases with pressure (someone should use this property, by the way).


The relatively small amount of the isocyanide form in TMSCN did not prevent Hulme and co-workers from using this reagent in a multicomponent reaction:

Balancing reaction “coolness” with selectivity

Over the Christmas break, I wrote about my long-standing interest in electrochemistry. Indeed, many interesting things are possible on electrode surfaces. But let’s not forget that there are some aspects of electrosynthesis that are exceptionally challenging. The biggest one of all lies in the difficulty to control the fate of electrogenerated intermediates. For instance, you can create some really neat radical cations using anoxic oxidation, yet their diffusible nature renders them tough to control. Unless one of the reagents is used in large excess or the reaction is intramolecular, alternate pathways can take over the reaction landscape. It’s no wonder that metal catalysis continues to be the go-to source for achieving selective transformations in chemistry: bond-forming events tend to take place within the metal coordination sphere, which helps achieve control over reactive intermediates.

Now let’s consider photochemistry. Photochemical transformations have a lot in common with electrochemistry in that it is often difficult to control the pathways accessible to photoexcited states. Yet, there are marvelous examples that enable rapid increase in molecular complexity despite the low isolated yields. Witkop reaction is one such process. This transformation has been expertly reviewed by Gaich and co-workers in Angewandte Chemie ( The Witkop reaction is believed to proceed through intramolecular photon-induced electron transfer from the excited state of the indole chromophore to the chlorocarbonyl group. Subsequent loss of the chloride anion leads to a diradical cation, which ultimately gives the substitution product shown below. As the authors point out, average yields range from 30 to 55% (with by-products rarely reported, which is too bad…). However, the utility of this reaction in complex molecule synthesis proves its value relative to cumbersome alternatives to achieve the same objective.


A call to arms: ligand efficiency

Happy New Year, everyone!

As our lab opens a new chapter in its quest for bioactive macrocycles, I thought it would be fitting to dedicate the first post of 2014 to the concept of ligand efficiency. We all know that there is a “size continuum” when it comes to biologically active molecules. Everything under the sun has been engaged in drug discovery efforts – from small molecules that “poke” targets using a handful of contacts to antibodies that employ multivalent interactions. It is also known that, during the process of optimizing a clinical candidate, a compound typically increases in molecular weight. This makes sense because legions of medicinal chemists throw everything they have learned in grad school in efforts to improve the compound potency. Not surprisingly, potency within a chemical series is often strongly correlated with molecular weight. This was noted by luminaries such as Chris Lipinski at Pfizer as well as by researchers at other pharmaceutical companies.

Here is an interesting fact, though: despite the rise in the molecular weight of clinical candidates, the mean molecular weight of drugs in clinical development declines in each subsequent stage to market ( Isn’t that interesting?

It is at this stage that we need to consider the concept of ligand efficiency. The latter is quite intuitive: it represents the binding free energy for a ligand divided by its molecular size. In this regard, the following paper by Reynolds and co-workers is significant: Upon examination of thousands of examples, the authors came to the conclusion that ligand efficiency increases rapidly up to 20 heavy atoms, but reaches plateau beyond 25 heavy atoms. This “magical number” 25 roughly corresponds to the size of a tripeptide sequence. In fact, there is an awesome paper in J. Med. Chem. that discusses “privileged” sequences of amino acids. This manuscript stresses the significance of tripeptide motifs due to the maximal ligand efficiency achieved at around 25 heavy atoms (

RGD (Arginine-Glycine-Aspartic acid) is the proverbial example of a privileged tripeptide motif. Discovered by Erkki Rouslahti (now at UCSB) using phage display, RGD is a protrusion on the surface of fibronectin (shown below). This area of fibronectin mediates its interactions with integrin receptors. As you might know, the RGD sequence has found numerous applications in the area of cyclic peptides. Nature is really telling us something with this loop and suggests cyclization as a means of designing peptidomimetics. But let’s think about it: how many other, undiscovered, RGD-like sequences are lurking out there? I will bet that there are many… We need to find them.