Tag Archives: Opinion

A research project true story

INTRO FARGO_4

LUVERNE, MINNESOTA, JULY 1986

Lorne Malvo, a young and ambitious postdoc, joins the lab of rising star Dr. Lou Solverson at the University of Luverne in Minnesota. Within Dr Solverson’s group, Lorne starts an industrially funded project on the Haber-Bosch process toward the artificial nitrogen fixation for the production of ammonia. The Haber-Bosch process is typically conducted at 150–250 bar and between 400–500 °C but recently in 1985 it was published a patent using a new family of iron catalysts that, according to the patent, were capable to substantially reduce the ranges of pressure and temperature with no loss of efficiency. The sponsors of the project wanted Dr Solverson and Lorne to investigate the validity of the results published in the patent and further investigate new catalysts to improve the Haber-Bosh process.

The results published in the patent lacked lots of information related to the synthesis and characterization of the catalysts used, experimental procedures and catalysis conditions were poorly described. So the initial step of reproducing published results turned into a big challenge.

LUVERNE, MINNESOTA, SEPTEMBER 1987

After more than one year of tests and catalyst screening Lorne and Dr. Solverson were not capable to reproduce the results published in the patent and started to question its veracity. Still all this work was very useful to learn about all the difficulties of the process itself and produced enough relevant data for a publication. Solverson and Malvo were aware of the difficulty of publishing a paper based on someone else’s results but also assumed the responsibility of sharing with the catalysis community their results which questioned an accepted patent. Under the title “Reinvestigation of new iron catalysts for the Haber-Bosch process” Solverson and Malvo submitted a paper to the journal Catalysis & Chemistry (from the Editorial Fargo) with an impact factor of 5.04.

LUVERNE, MINNESOTA, OCTOBER 1987

Solverson and Malvo received comments from the referees:

-Referee one considered the paper could be published in Catalysis & Chemistry because of the interest to the catalysis community and wanted to include a few more references (probably this referee’s work)

-Referee two did not accept the paper arguing that Malvo and Solverson’s contribution was only a reproduction of the work published in the patent.

Referee two was what Malvo and Solverson were most afraid of, someone that did not understand the aim of the paper which was a warning to the community about a patent that at first seemed promising. After a few unsuccessful attempts to convince referee two, Malvo and Solverson decided to submit their work to the journal Chemistry of Catalysis (Bo Munk Editorial) with an impact factor of 4.7.

LUVERNE, MINNESOTA, DECEMBER 1987

Malvo and Solverson’s paper was accepted with minor revisions in Chemistry of Catalysis. A few days before the paper was in press Malvo realised that impact factors had changed and now Chemistry of Catalysis had an impact factor of 5.426 (Previously 4.7) and Catalysis & Chemistry had an impact factor of 4.556 (Previously 5.04).

SOME YEARS AFTER THAT…

Dr Solverson was awarded with a prestigious grant and was promoted to Full Professor, he continues producing high quality research but the events occurred during 1987 made him very sceptical about the peer-review system.

Lorne Malvo could not take it anymore and lost all faith in the peer-review system, he quitted science and currently survives as soldier of fortune. If you have a problem, if no one else can help, and if you can find him, maybe you can hire him.

A couple of interesting papers on the Haber-Bosh process:

Lessons learned and lessons to be learned for developing homogeneous transition metal complexes catalyzed reduction of N2 to ammonia. Chinnappan Sivasankar, Sambath Baskaran, Masilamani Tamizmani, Kankanala Ramakrishna. Journal of Organometallic Chemistry, Volume 752, 2014, Pages 44–58.

Exploring the limits: A low-pressure, low-temperature Haber–Bosch process. Aleksandra Vojvodica, Andrew James Medfordb, Felix Studta, Frank Abild-Pedersena, Tuhin Suvra Khana, T. Bligaarda, J.K. Nørskov. Chemical Physics Letters, Volume 598, 2014, Pages 108–112.

To understand better this post you may want to take a look to these links:

Fargo_(TV_series)

Fargo (film)

 

 

 

 

 

 

Advertisements

Quick guide to get your synthetic methodology in a top journal

Nowadays thousands of “gurus” share their expertise to offer guidance in topics ranging from beauty and health to how to succeed in life. Chemistry of course is not an exception, we have our own gurus to seek for a piece of advice on many chemistry-related topics. Well, I am not a guru but still for my post today I would like to write a few lines on how I think you can improve your chances to get your synthetic methodology published in a good journal. I have also included one beautiful Yes-No flow diagram so my post is taken more seriously.

get published

Even in the case you have developed a new methodology to solve a very challenging synthetic problem, you may not get your results published in the top journals if you don’t include all the relevant information. For example, sometimes including a mechanism proposal is as important as getting excellent yields. I have considered two main scenarios:

Your synthetic methodology is new: The best scenario possible. You are the first one that solved the puzzle, but make sure the problem you are working in has relevance. And make sure that you are the first, so you did a good and meticulous literature research. Let’s say your method is good and your research is relevant, now is time to be creative. Select challenging and varied substrates and explore functional groups tolerance. If you are using a catalyst or a reagent developed by you it has to be fully characterized, an X-Ray structure can make the difference to get to the top journals. A new methodology might mean new reaction pathways or mechanisms. In my opinion at least a mechanism proposal should be always included. More and more often publications in synthetic methodology include now theoretical calculations to support mechanistic proposals.

Your methodology is not new but is way better than the others: Now is time to show your muscles. Besides being creative with substrates, having a full characterization or good mechanistic studies, now more than ever you have to include “extra toppings” to strengthen your chemistry. Stablish clear comparisons between your methodology and current methods using tables, explore recyclability or robustness of your catalyst, reagent or conditions. In other words try to highlight all your methodology’s strengths. Show off, put some efforts trying to scale-up to multi-gram levels “I synthesised 500 g at once, why? Because I can”. Apply your methodology to the synthesis of products of interests.

To conclude this post what could be better than showing a very good example of how to get your synthetic methodology in a good journal? This great work by Snyder and co-workers (click the link) speaks for itself: Et2SBr⋅SbCl5Br: An Effective Reagent for Direct Bromonium-Induced Polyene Cyclizations (Angew.Chem.Int.Ed.2009,48, 7899 –7903). In their paper, Snyder and co-workers describe a new reagent for well known reactions of bromocyclization. They describe the synthesis of their reagent with a full characterization including an X-Ray structure and more importantly they don’t hesitate to show muscle. They compare their reagent with the existing methods at that time to clearly show their reagent is in general better than the others, they also explore the scaleability of their methodology and apply it to the synthesis of natural products.

Celebrities, Pharaohs and Chemists.

“When kids look up to great scientists the way they do to great musicians and actors, civilization will jump to the next level”                                                                                                                                                                   –Brian Greene-

fameThe recent release of Stephen Hawking’s biopic “The theory of everything” along with others like Alan Turing’s “The Imitation game” have helped to revive debates in social media about celebrity scientists. By the way, both are great movies. It turns out that nowadays science is sexy, wasn’t it always? And no doubt that the TV show “The Big Bang theory” had a great deal in catalysing these events. Recently it was brought to my attention a post called Who’s the world’s greatest living chemist? And I started to think if maybe any of my contemporary fellow chemists could be in that list in 30-40 years. People whose work I read every day in the journals or people that work in the same department. This is somewhat exciting and scary at the same time, some of the guys I know are brilliant but won’t make it to their 50s drinking so much beer.

I have always been a great fan of the Authors Profile section of the Journal Angewante Chemie International Edition. ACIE grants chemists, who have recently published their 10th, 25th, 50th or 100th, with a profile consisting on a series of question about themselves. The questions are not always the same but many of them are repeated in several profiles. You can find a lot of interesting, surprising and sometimes odd details about your “chemistry idols”. I learnt about the profiles section during my last year of PhD when I was thinking of sending applications for prospective postdoctoral stays.

Everyone knows about the topics in chemistry they like the most, but if you are moving to another research centre for a couple of years and that is likely to be in a different country you better like both the chemistry and the people you are working with/for. I was very interested about the reasons why my chemistry idols and other big names in chemistry decided to be chemists. I found answers that were not new to me and at the same time were comforting, the kind of: “I was motivated by a teacher”, “it is fun”, “everything around us is chemistry”, “I love working in the lab”, “I like creative challenges”. And I say comforting when other may say boring because I found others answers like “God directed me this way” and  “the registered mail with my application to study biology never arrived at central admissions” you can take your own conclusions on those last ones. It would take many hours to analyse all the profiles published so far. I might do it sometime, but if someone else out there has the time and the dedication I am not claiming the rights for the idea. Just one additional comment/thought about one of the answers given to “if I could be anyone for a day, I would be…” that intrigued me the most, I saw in a few profiles answering that they would be Pharaoh Cheops and a my follow up question to them would be: Is it because you want your legacy to be comparable to the pyramids or because the number of postdoc-slaves you want?

5 Simple Organic Chemistry Reactions that “Saved My Life”.

ORGANIC CHEMISTRYGet ready for a tips-that-saved-my-life type of post for this one. Not with the idea to disappoint you, but this post will not help you to lose weight, improve your relationship with your boss or save your marriage. Rather than all that I have selected a “Top 5” of very simple organic chemistry reactions that at some point were crucial to the progress of my research projects.

Mitsunobu Reaction. Discovered by Oyo Mitsunobu. This reaction can be a very useful and straightforward alternative to nucleophilic substitutions and as in the case of SN2 it proceeds with inversion of configuration.

mitsunobu

The Mitsunobu reaction allows the direct reaction of primary and secondary alcohols with acidic nucleophiles to afford products such as esters, ethers and amines among others. One of the reagents employed in the reaction, DEAD, (diethylazodicarboxylate) can be substituted by its cousin DIAD (diisopropylazodicarboxylate) if you are superstitious.

Sonogashira Coupling. In my opinion every single synthetic chemist must have cross-coupling reactions in their “synthesis toolbox”. Palladium catalysed cross-coupling reactions are unarguably of most relevance as reflected by the 2010 awarded chemistry nobel prize.

sonogashira

Discovered by Kenkichi Sonogashira, Sonogashira reaction allows the coupling of terminal alkynes with aryl or vinyl halides with a palladium catalyst, a copper(I) cocatalyst, and an amine as base.

Wittig reaction. Discovered by Georg Wittig, for which he was awarded the nobel prize in chemistry in 1979. The Wittig Reaction is probably the preferred method for synthetic chemists for making alkenes. The reaction allows the preparation of alkenes by the reaction of an aldehyde or ketone with the ylide generated from a phosphonium salt.

wittig

Triphenylphosphine oxide is generated in the process as a byproduct and sometimes it can be difficult to separate from the desired products. If you are sick of seeing that annoying triphenylphosphine oxide in your Wittig reactions you might want to take a look to the alternative proposed by O’Brien and co-workers from the University of Texas.

Selenoxide elimination. Another useful method for the synthesis of alkenes. Selenoxides decompose to the corresponding alkenes at mild temperatures and can be readily prepared from nucleophilic carbonyl derivatives by reaction with selenylating reagents such as PhSeCl in the presence of a base.

selenoxide

It is for this reason that selenoxide elimination has grown into a general method for the preparation of α,β-unsaturated carbonyl compounds.

Electrophilic aromatic halogenation. Electrophilic aromatic substitution is a general type of reactions you find in the first chapters of all organic chemistry books and you learn during the first semester of organic chemistry. Rule of thumb, electron-donor groups promote substitution at the ortho and para positions while electron-withdrawing groups promote the meta position.

halogenating

In particular electrophilic halogenation is a very useful method to introduce diversity in the molecules as the aromatic halides generated can be easily modified for example with the use of cross-coupling reactions. Electrophilic aromatic halogenation can be performed in the presence of strong halogenating reagents in some cases although the use of Lewis acids is typically required.

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 on 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.

You Know Nothing Jon Snow.

Jon snowI think that Socrates with his “One thing only I know, and that is that I know nothing” and Ygritte from the popular Game of Thrones with her “You know nothing Jon snow” were both right. This of course needs further explanation, recently it was brought to my attention an article published in Journal of Cell Science in 2008 with the catching title “The importance of stupidity in scientific research“. The main conclusion I extract from the article is the good of stupidity, understood as ignorance by choice, for the progress of science. In other words, if you don’t feel “stupid”, meaning that you don’t have questions to answer related to your research project, either the problem you are trying to solve is just trivial or you are not  trying hard enough. In the article it is also discussed the fact that teaching  at universities may not be effective enough as students are not aware of how difficult research is and do not learn how to use their so-called “stupidity” in a productive way.

There is something else I would like to discuss in this post. I enjoyed the concept of “productive stupidity”. But, what if there were no more questions what if you reach the point when you solve the riddle, not just the one but all, I rather die. There is one more important point I do agree with in the article, we (scientists) start loving what we do at first because we are good at science then it comes more (at least that happened to me), we need the knowledge, to solve the puzzle and there is never enough. Knowledge has been my driving force since I remember, to the point that when I master a topic I need to refresh and search for more challenging things. So I hope I can always feel “stupid” and know nothing and have always someone around me able to tell: you know nothing.

 

“I love it when a plan comes together” didn’t work for me.

I-love-it-when-a-plan-comes-together

If you were a kid in the 80’s (as I was) you have probably recognised the quote in the title “I love it when a plan comes together” from the leader of The A team Hannibal Smith. And now you are picturing Hannibal (I am) saying his quote while lighting a big cigar. Well, I have to say that things didn’t work for me that way but I’m not less happy because of that.

I guess that many people, scientists (yes, scientists are people after all) or more specifically chemists like me make a lot of plans with lots of time in advance imaging how their careers in science will be. I decided I wanted to be a chemist at the age of 16. So, there I was collecting all type of information on “how to become a chemist” and I started to write my own script , my own pathway to become a chemist.  Study hard, get good marks, go to university, study hard, get good marks, get a Ph.D. fellowship, publish a lot in good journals, go abroad for a couple of years as post-doc, work hard, publish a lot, get permanent position and live happily ever after doing chemistry stuff. It wasn’t that difficult, was it?

First year at the university studying chemistry, everything goes as planned, I am happy there are no surprises so far, I am on my way to become a chemist so I only have to stick to the plan. Time goes by, I fall in love with organic chemistry and I get my degree, and now what? Let me check the script, yes of course now is time for a Ph.D. Perfect then, bullet point under the section “start my  Ph.D.”

-Go to see supervisor to discuss about the best options to get funding for my Ph.D.

That was the exact moment my script started to have major failures, my supervisor changed everything when he recognised to me that I would have more opportunities in a better chemistry group. He knew how much I wanted to do a Ph.D. and took the liberty to contact one of his colleagues from probably one of the best groups in organic chemistry at that time in Spain. This is what it was going on, my supervisor was “plotting against me” he was making plans behind my back, he dared to change my script, the script  I had been writing for years. The morning I went to my supervisor’s office with the idea to talk about fellowships he had set me up with a phone interview for a Ph.D. position. Guess what, I got a Ph.D. position in an interview I had not included in my career plans. That moment definitely changed my life and my career.

That was only the beginning, as I was writing the post I realised it was going to be too long and that I should write a bit more on “plan changes” in my next posts.   Life has made many plans on my behalf and I had to re-write my script many times.

Thanks Javier I will never be able to thank you enough.