Category Archives: hot topics

Green Synthesis of Benzene and Pyridine Derivatives

In parallel to the discovery of new reactions there is also a need to develop a more “green attitude”. We, synthetic chemists are often too busy focused on our target molecules to pay much attention to the “costs” of our achievements. Synthesis frequently requires the use of relatively expensive and toxic transition-metals, large amounts of solvents and additives that lead to the generation of waste along with the desired products.

Going green also has an impact in economy. Industry expends important amounts of time (which means money) and money trying to remove metal catalysts and solvents. Some transition metals are toxic even at very low concentrations and that is obviously undesirable for pharma industry. Small amounts of metals can have an undesired influence in the colour or properties of an organic polymer.

It is important to invest time and resources in the development of metal free methodologies. In this post I want to highlight the work published in Green Chemistry by Wei Yi and co-workers toward the metal and solvent free synthesis of benzene and pyridine derivatives.


Pyridine and benzene derivatives are commonly found in organic molecules with interest in material or medicinal sciences. This new methodology describes the synthesis of benzene and pyridine derivatives from ready available ketones and amines using HOTf as catalyst. Wei Yi and co-workers remove any stochiometric or catalytic amounts of metals from the equation together with solvents.The reaction is performed in one pot with no need of other oxidants than air and features excellent yields, chemoselectivity and functional group tolerance.

If you want to know more why don’t you take a look to the original paper:

HOTf-Catalyzed Sustainable One-Pot Synthesis of Benzene and Pyridine Derivatives under Solvent-free Conditions. Xu Zhang, Zhiqiang Wang, Kun Xu, Yuquan Feng, Wei Zhao, Xuefeng Xu, Yanlei Yan and Wei Yib. Green Chem., 2016, Advance Article DOI: 10.1039/C5GC02747K

And my advice to all is that you consider GO GREEN:

12 Principles of Green Chemistry


Must Read Papers 2015. Part 2.

help 2At the end of 2015 I wrote a post (Must read papers 2015) including my favourite paper of the year and recommendations of a few nice reviews/highlights to read during Christmas. During 2015 I selected several papers I wanted to write about in the blog but unfortunately I have less time than I would like and I couldn’t write a line about many of them. Now 2015 is gone and I already have a few nice papers selected this year to comment in the blog. So all these nice papers are piling up and haunt me in my dreams because I don’t have enough time (or maybe because I’m just lazy).

To make a long story short I have decided to write a follow-up post of the Must read papers 2015 to comment a little bit on the best papers I selected during 2015 that for one reason or the other attracted my attention (click on the pictures if you want to go to the paper’s websites).

The first two papers of the post fit perfectly in the section Cool Synthesis under the topic Impossible Molecules. The Impossible Molecules topic is dedicated to molecules with exotic structures, elusive molecules and synthetically challenging molecules in general.  The first paper describes the first example of an amazing corannulene derivative bearing an internal heteroatom. The second paper describes a creative strategy to stabilise long cumulenes with a phenanthroline-based macrocycle.

1_ACIE_Benzene=Fused Azacorann

2_Cumulene rotaxanes

If you have ever read this blog before, you already know I’m a bit (just a bit) obsessed with halogenating reactions so you will find several posts on the topic. There are 2 papers I couldn’t write about during 2015 that I want to highlight. The first one describes a one-pot vicinal fluorination-iodination of arynes using the diphenyliodonium salt as a catalyst and CsF as a fluorine source. The second paper describes the synthesis of the molecules Halomon, Plocamenone and Isoplocamenone using a dihalogenating reaction I wrote about in a previous post.


3_sintesis total dihalogenacion

Another of my obsessions is the chemistry of Frustrated Lewis Pairs (FLP), and just as I said in one of my previous posts “This is not the first time and probably will not be the last time I post about Frustrated Lewis Pairs”. One of the papers I didn’t have time to write about is this nice contribution by Stephan’s group on the catalytic hydrogenation and reductive deoxygenation of ketones and aldehydes.

4_FLP reduction

The next paper is another creative contribution by Alcarazo and coworkers. The paper describes an interesting alternative to hipervalent iodine species, Dihalo(imidazolium)sulfuranes that are versatile electrophilic group-transfers reagents.

6_paper alcarazo

The last paper I want to mention in this post caught my attention because of the interesting fact that the selectivity of the two products obtained in a copper-catalysed arylation is controlled by the choice of the reaction vessel.

7_reaction vessel


Must read papers 2015

Now that 2015 is ending I remember a nice tradition we used to have in the research centre where I did my first postdoc. At the end of December we had a “Reaction of the year” seminar in which everyone of us had to present a paper we thought it was the most important contribution of the year.

I would like to use a similar idea in this post to open a discussion in which everyone can say their #favouritepaperof2015 and why. So I am going first…

Yeah, the main reason I liked so much this paper is that I may have a bit of an obsession with halogenation reactions in general. Anyway it is a must read paper in this year 2015, I’ve recently wrote a post about it if you are interested.

Besides my favourite paper of the year, for those who want to read a bit of chemistry during the Christmas break I would like to recommend you a couple of reviews and highlights on topics I really like and I hope you also enjoy (click on the pictures to go to the links).




asymmetric chlor

Top Drugs Academy Awards.

redcarpet awardBig Pharma companies invest billions of dollars every year for a very low rate of success and still all these efforts must pay off. Only a few drugs are accepted every year as they have to pass through innumerable tests in order to guarantee, for the most obvious reasons, the safety of patients-customers.

Last September C&EN released a supplement on The Top 50 Drugs of 2014. Something I see like the academy awards of drugs, a very interesting catalogue in which you can see the ultimate tendencies in drugs research and also the direction pharma companies are taking in terms of where to invest their money. The supplement analyses the top 50 drugs according to 3 different categories: The top 10 emerging blockbusters (drugs recently approved with $1 billion plus potential),  the top 10 drugs in development (most promising drugs still in the pipeline) and the 30 top-selling drugs on the market.

Apart from my curiosity as a chemist I wanted to know what are the diseases object of research for pharma companies. When you take a closer look to the diseases treated by the top selling drugs you see that the first and second are for the treatment of rheumatoid arthritis and the third top selling  drug is for asthma and chronic obstructive pulmonary disease. A bit unexpected I have to recognise, if I had to place a bet without all that information I would have said cancer, no doubt, is top 3. You see treatment for leukemia, a type of cancer, in the fourth position. Fifth position for the treatment of diabetes and at last cancer (used as a general term) appears in the sixth position. Then when you continue going down the list you see mainly cancer, HIV, respiratory problems and pain treatments. And it is quite clear that the treatment of pain has a big part in the whole business.

Concerning the top 10 emerging blockbusters and the top 10 drugs in development the tendency is similar. Predominantly cancer with a special mention to breast cancer, HIV, diabetes and in the top positions hepatitis C.

From a more synthetic point of view, there were a few things that caught my attention. First of all, where are all the super-big molecules from the literature in total synthesis? where are all these molecules isolated from plants and algae with medicinal properties? Instead of those, the vast majority of the drugs are small to medium size molecules. Molecules dominated by nitrogenated heterocyclic structures and in a great number of cases bearing fluor atoms or fluorinated functional groups. All these facts highlight the relevance of the development of the chemistry of heterocycles which are ubiquitous in nature. And also the increasing number of papers on fluorination methodologies in the literature as it is known that fluorine atoms often enhance the pharmacological properties of organic molecules.

And with all said, it only rests to congratulate the 2014 awardees. Nevertheless, my advice to all is try to keep yourselves healthy.

Frustrating Fuel Cells.

This is not the first time and probably will not be the last time I post about Frustrated Lewis Pairs (FLPs). Due to the unquenched acidity and basicity of FLPs, these systems present an extraordinary reactivity to the cleavage and activation of small molecules. Unarguably, the most important application is the activation of hydrogen, FLPs are capable to heterolitically cleavage the strong bond of the molecule of dihydrogen resulting in a hydride adduct of the Lewis acid and a protonated Lewis base at room temperature. From the point of view of a synthetic chemist, the activation of hydrogen with FLPs opens the door to a new class of metal-free hydrogenation reactions. However, creativity in the area of FLPs seems to be endless as shown in the great contributions by Andrew Ashley and Gregory G. Wildgoose groups from the Imperial College of London and the University of East Anglia towards the oxidation of hydrogen.

FLP Fuel Cell

In the search for alternatives to fossil fuels, hydrogen has raised as a promising and a clean source for the production of electricity from chemical energy with the use of fuel cell technology. In the absence of a catalyst, the necessary process of oxidation of hydrogen is slow and require large overpotentials. Here is where the FLPs play their role as they considerably reduce the voltage required for the hydrogen oxidation due to the generation of hydride intermediates that are easier to oxidise to protons. Ashley, Wildgoose and co-workers were able to stoichiometrically oxidise hydrogen using one of the most basic FLP system B(C6F5)3/P(tBu)3 but unfortunately the system is not robust enough to complete more than one catalytic cycle. Some improvements were made recently replacing B(C6F5)3 for a borenium cation as a Lewis acid although the system is still lacking enough stability to properly catalyse the oxidation. As a proof of principle, it is indeed possible to oxidise hydrogen with an electrochemical/FLP approach. FLP systems have the advantage of their inherent “tuneability”  and there is still plenty of room for improvement in the way to develop a FLP based fuel technology.

Do you want to know more? Here you are the original papers:

Elliot J. Lawrence, Vasily S. Oganesyan, David L. Hughes, Andrew E. Ashley, and Gregory G. Wildgoose. An Electrochemical Study of Frustrated Lewis Pairs: A Metal-Free Route to Hydrogen Oxidation. J. Am. Chem. Soc., 2014, 136 , 6031–6036.

Elliot J. Lawrence, Thomas J. Herrington, Andrew E. Ashley, Gregory G. Wildgoose. Metal-Free Dihydrogen Oxidation by a Borenium Cation: A Combined Electrochemical/Frustrated Lewis Pair Approach. Angew. Chem. Int. Ed. 2014, 53, 9922 –9925.

A NanoCar for NanoKid.

Molecular motors are biological molecular machines that convert energy into motion or mechanical work participating in many important processes such as muscle contraction, intracellular cargo transport or transcription of RNA from DNA. Thus, it is natural that these systems serve as an inspiration for chemists on the search for new and more complex synthetic machine-like functions.

In 1999 Feringa and co-workers at the University of Groningen (Netherlands) designed a synthetic molecular rotor, activated by ultraviolet light, capable of performing unidirectional 360o rotation and more recently in 2011 they took the concept one step further by synthesising a light-driven nanocar.


The car composed by a carbazole substituted diphenylbutadiyne chassis and 4 fluorene-based molecular motors acting as wheels can travel as far as 6 nm across a Cu(111) surface in 10 excitation steps. Movement requires that the adsorption energy of the molecule is less than the energy released in the isomerization step upon excitation and each cycle of unidirectional rotation takes 4 reaction steps: 1 double-bond isomerization induced by electronic excitation followed by 1 helix inversion induced by vibrational excitation and again 1 more double-bond isomerization and 1 more helix inversion to complete a 360o  rotation.

I can imagine  a teenager NanoKid, the kid-shaped organic molecule from the series of Nanoputians, asking his NanoDaddy to buy him the last model of NanoCar capable of running 6 nm in 10 electric bursts. Although, I don’t think NanoMum likes the idea…

Do you want to know more? Then, go directly to the sources:

Nagatoshi Koumura, Robert W. J. Zijlstra, Richard A. van Delden, Nobuyuki Harada, Ben L. Feringa. Light-driven monodirectional molecular rotor. Nature 401, 152-155 (9 September 1999).

Tibor Kudernac, Nopporn Ruangsupapichat, Manfred Parschau, Beatriz Maciá, Nathalie Katsonis, Syuzanna R. Harutyunyan, Karl-Heinz Ernst, Ben L. Feringa. Electrically driven directional motion of a four-wheeled molecule on a metal surface. Nature 479, 208–211 (10 November 2011).

What to Do with All That CO2 Stuff?

CO2_carpetThe Scripps Institution of Oceanography at UC–San Diego reported the past April 2014 a terrifying new milestone of 400 ppm of CO2 in the atmosphere. The accumulation of CO2 into the atmosphere is causing a growing reinforcement of the natural green house effect and is thus “extremely likely” causing the increase of average temperature in our planet. In other words, if we continue denying the evidence of a strong relationship between CO2 emissions and climate change we may reach a “no-return point”.

Let’s not be apocalyptic YET. There is a real concern about CO2 in the scientific community, research institutions and funding agencies are promoting a change of mentality towards bigger efforts on CO2 research. And here it comes the question, What to do with all the CO2? It is a tricky question with no easy answer as unfortunately there are many international conflicts of interests in terms of CO2 emission and climate change. From a scientific perspective there are a few strategies that can be followed to reduce, avoid and make a smart use of CO2.

-Smarter use of energy: an indirect way to reduce CO2 emissions. Invest and research in more efficient use of energy, insulation of buildings, fuel-efficient vehicles. For a higher effectiveness, all this must come along with educating people about a more conscious personal attitude toward energy use.

-Fuel shift from coal to gas: another way to reduce CO2 emissions. As simple as the amount of CO2 produced by burning gas is sensibly lower than by burning coal.

-Renewable sources of energy: such as sun, wind or geothermal. A field in continuous growing and development with the major drawback of reliability of supply as renewable energy often relies on weather and geographical location.

-Carbon  capture and storage: This technology with the focus of capturing and storing CO2 in huge amounts attracted the attention and enthusiasm of many. But there are also certain doubts as it can be seen as sweeping the CO2 under the carpet due to the uncertainty about the time permanence of stored CO2 and the possible impact on natural systems.

-And last but not least, Transform CO2 into chemicals. This is, no doubt, my favourite strategy, what did you expect? I’m a chemist. Transforming CO2 into chemicals is an indirect way to trap CO2 in a productive way and thus reducing the carbon footprint. CO2 has its most important application in the synthesis of urea for the industry of fertilizers and urea-formaldehyde resins, it is used in the synthesis of salicylic acid (the precursor of aspirin), the production of carbonates through direct reaction with epoxides and has many prospective applications in the area of polycarbonates and fuel production.

uses CO2

Production of chemicals with CO2 will pay off if two main objectives are accomplished. The first is that the amount of CO2 produced burning fuels for energy for a process must be lower than the CO2 transformed into a chemical. And the second is that the time CO2 stays as a chemical must be long enough to have an impact in the accumulation of CO2 into the atmosphere.

Do you want to know more? Here you are a couple of interesting reviews:

– Martina Peter, Burkhard Köhler1, Wilhelm Kuckshinrichs, Walter Leitner, Peter Markewitz, Thomas E. Müller. Chemical Technologies for Exploiting and Recycling Carbon Dioxide into the Value Chain. Chem. Sus. Chem. 2011, 9, 1216–1240.

– Michele Aresta, Angela Dibenedetto, Antonella Angelini. Catalysis for the Valorization of Exhaust Carbon: from CO2 to Chemicals, Materials, and Fuels. Technological Use of CO2. Chem. Rev., 2014, 114, 1709–1742.