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To Chem, or not “Too Chem”? That is the #ChemNobel Question


To chem or not -quite- too chem, that is the ChemNobel question:
Whether ’tis Nobeler in the mind to suffer
The curly arrows of organic fortune
Or to take rays against a sea of crystals
And by diffracting end them.

Me (With sincere apologies to WS)

Every year, in late September -like most chemists- I try to guess who will become the next Nobel Laureate in Chemistry. Also, every year, in early October -like most chemists- I participate in the awkward and pointless discussion of whether the prize was actually awarded to chemistry or not. Indeed, the Nobel prize for chemistry commonly stirs a conversation of whether the accomplishments being recognized lie within the realm of chemistry or biology whenever biochemistry shows its head, however shyly; but the task of dividing chemistry into sub-disciplines raises an even deeper question about the current validity of dividing science into broad branches in the first place and then further into narrower sub-disciplines.

I made a very lazy histogram of all the 178 Laureates since 1904 to 2017 based on subjective and personal categories (figure 1), and the creation of those categories was in itself an exercise in science contemplation. My criteria for some of the tough ones was the following: For instance, if it dealt with phenomena of atomic or sub-molecular properties (Rutherford 1908, Hahn 1944, Zewail 1999) then I placed it in the Chemical Physics category but if it dealt with an ensemble of molecules (Arrhenius 1903, Langmuir 1932, Molina 1995) then Physical Chemistry was chosen. Some achievements were about generating an analysis technique which then became essential to the development of chemistry or any of its branches but not for a chemical process per se, those I placed into the Analytical Chemistry box, like last year’s 2017 prize for electron cryo-microscopy (Dubochet, Frank, Henerson) or like 1923 prize to Fritz Pregl for “the invention of the method of microanalysis of organic substances” for which the then head of the Swedish Academy of Sciences, O. Hammarsten, pointed out that the prize was awarded not for a discovery but for modifying existing methods (which sounds a lot like a chemistry disclaimer to me). One of the things I learnt from this  exercise is that subdividing chemistry became harder as the time moved forward which is a natural consequence of a more complex multi- and interdisciplinary environment that impacts more than one field. Take for instance the 2014 (Super Resolved Fluorescence Microscopy) and 2017 (Cryo-Electron Microscopy) prizes; out of the six laureates, only William Moerner has a chemistry related background a fact that was probably spotted by Milhouse Van Houten (vide infra).

Some of the ones that gave me the harder time: 1980, Gilbert and Sanger are doing structural chemistry by means of developing analytical techniques but their work on sequencing is highly influential in biochemistry that they went to the latter box; The same problem arose with Klug (1982) and the Mullis-Smith duo (1993). In 1987, the Nobel citation for Supramolecular Chemistry (Lehn-Cram-Pedersen) reads “for their development and use of molecules with structure-specific interactions of high selectivity.”, but I asked myself, are these non-covalent-bond-forming reactions still considered chemical reactions? I want to say yes, so placed the Lehn-Cram-Pedersen trio in the Synthesis category. For the 1975 prize I was split so I split the prizes and thus Prelog (stereochemistry of molecules) went into the Synthesis category (although I was thinking  in terms of organic chemistry synthesis) and Cornforth (stereochemical control of enzymatic reactions) went into biochem. So, long story short, chemistry’s impact in biology has always had a preponderant position for the selection of the Nobel Prize in Chemistry, although if we fuse the Synthesis and Inorganic Chemistry columns we get a fairly even number of synthesis v biochemistry prizes.

Hard as it may be to fit a Laureate into a category, trying to predict the winners and even bet on it adds a lot of fun to the science being recognized. Hey! even The Simpsons did it with a pretty good record as shown below. Just last week, there was a very interesting and amusing ACS Webinar where the panelist shared their insights on the nomination and selection process inside the Swedish Academy; some of their picks were: Christopher Walsh (antibiotics); Karl Deisseroth (optogenetics); Horwich and Hartl (chaperon proteins); Robert Bergman (C-H activation); and John Goodenough (Li-ion batteries). Arguably, the first three of those five could fit the biochem profile. From those picks the feel-good prize and my personal favorite is John Goodenough not only because Li-ion batteries have shaped the modern world but because Prof. Goodenough is 96 years old and still very actively working  in his lab at UT-Austin (Texas, US) #WeAreAllGoodEnough. Another personal favorite of mine is Omar Yaghi not only for the development of Metal-Organic-Frameworks (MOFs) but for a personal interaction we had twenty years ago that maybe one day I’ll recount here but for now I’ll just state the obvious: MOFs have shown a great potential for applications in various fields of chemistry and engineering but perhaps they should first become highly commercial for Yaghi to get the Nobel Prize.

simpson_betting_poll_-_h_-_2016

W.E. Moerner and B.L. Feringa are now Nobel Laureates. Zare and Moerner have worked in spectroscopy whereas Feringa and Sonogashira are deep into synthesis

Some curiosities and useless trivia: Fred Sanger is the only person to have been awarded the Nobel Prize in Chemistry twice. Marie Curie is the only person to have been awarded two Nobel Prizes in different scientific categories (Physics and Chemistry) and Linus Pauling was awarded two distinct Nobel Prizes (Chemistry and Peace). Hence, three out of the four persons ever to have been awarded two Nobel Prizes did it at least once in chemistry – the fourth is John Bardeen two times recipient of the Nobel Prize in Physics.

Of course the first thing I’ll do next Wednesday right after waking up is checking who got the Nobel Prize in Chemistry 2018 and most likely the second thing will be going to my Twitter feed and react to it, hopefully the third will be to blog about it.

The announcement is only two days away, who is your favorite?

#WeAreAllGoodEnough

 

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Fluorescent Chemosensors for Chloride in Water – Sensors and Actuators B: Chemical


A new publication is now available in which we calculated the binding properties of a fluorescent water-soluble chemosensor for halides which is specially sensitive for chloride. Once again, we were working in collaboration with an experimental group who is currently involved in developing all kinds of sustainable chemosensors.

The electronic structure of the chromophore was calculated at the M06-2X/6-311++G(d,p) level of theory under the SMD solvation model (water) at various pH levels which was achieved simply by changing the protonation and charges upon the ligand. Wiberg bond indexes from the Natural Population Analysis showed strong interactions between the chloride ion and the chromophore. Also, Fukui indexes were calculated in order to find the most probable binding sites. A very interesting feature of this compound is its ability to form a cavity without being a macrocycle! I deem it a cavity because of the intramolecular interactions which prevent the entrance of solvent molecules but that can be reversibly disrupted for the inclusion of an anion. In the figure below you can observe the remarkable quenching effect chloride has on the anion.

Sensors

A quick look to the Frontier Molecular Orbitals (FMO’s) show that the chloride anion acts as an electron donor to the sensor.

Frontier Molecular Orbitals

Frontier Molecular Orbitals

If you are interested in more details please check: Bazany-Rodríguez, I. J., Martínez-Otero, D., Barroso-Flores, J., Yatsimirsky, A. K., & Dorazco-González, A. (2015). Sensitive water-soluble fluorescent chemosensor for chloride based on a bisquinolinium pyridine-dicarboxamide compound. Sensors and Actuators B: Chemical, 221, 1348–1355. http://doi.org/10.1016/j.snb.2015.07.031

Thanks to Dr. Alejandro Dorazco from CCIQS for asking me to join him in this project which currently includes some other join ventures in the realm of molecular recognition.

A new chemist is graduated


It is with great pleasure that I announce the graduation of another member of our research group: Luis Enrique “Kike” Aguilar defended his BSc thesis yesterday and is now counting the days left for the Autumn when he’ll move to the Netherlands for a masters in computational chemistry.

Luis Enrique, Kike, calculated the interaction energies of 144 different inclusion complexes where calix and thia-calix[n]arenes were once again the chosen hosts (36 of them) and two drugs for the treatment of chronic myeloid leukemia (CML), namely Sorafenib and Bosutinib, were the guests.

The publication of the corresponding article in which we once again were fortunate enough to count with the collaboration of Dr. Rodrigo Galindo from Utah University in the molecular dynamics section, is still pending but we’re confident enough that it wont take much longer until it’s out there.

Kike is a very diligent student with great learning skills, I’m sure he’ll succeed in any enterprise he sets himself off.  Congratulations, Kike! Thanks for being a part of our research but more importantly for being a part of our community.


    

Symposium at IQ-UNAM 2015


Earlier this week we had at our annual symposium at the institute of chemistry where we had distinguished international visitors such as Prof. Theodor Agapie, Prof. Lanny Liebeskind (associate editor of Organometallics), Prof. Marc Petit and Prof. Francois Gabbaï (associate editor of Organometallics), as well as our very own colleagues like Dr. Fernando Cortés who presented a recent paper published on Nucleic Acids Research, and Vojtech Jancik who talked about the high resolution crystallography performed at CCIQS. One of the presentations I liked the most was the one by Dr. Abel Moreno who is now doing some research on the proteins that crystallize calcium carbonate in the formation of egg-shells; Dr. Moreno recently got some 70 million years old fossilized dinosaur egg-shells, from which he is expecting to isolate some samples! Very exciting! I visited Dr. Moreno’s lab to take a look at this fossils and forgot to take a picture of them but trust me they were very cool to look at.

Our lab contributed with a poster by ´Maru´Sandoval (pictures below) in which she presented her research on the excited states of bacteriochlorophyll molecules present in the Fenna-Matthews-Olsen (FMO) complex of photosynthetic bacteria, and more importantly on the excitonic transference between them with the use of the singlet fission model.

These are great opportunities to establish collaborations and get new ideas for future work. Kudos to the organizers and administrative staff for keeping the academic life of our institute to high standards!


      

New paper in JPC-A


As we approach to the end of another year, and with that the time where my office becomes covered with post-it notes so as to find my way back into work after the holidays, we celebrate another paper published! This time at the Journal of Physical Chemistry A as a follow up to this other paper published last year on JPC-C. Back then we reported the development of a selective sensor for Hg(II); this sensor consisted on 1-amino-8-naphthol-3,6-disulphonic acid (H-Acid) covalently bound to a modified silica SBA-15 surface. H-Acid is fluorescent and we took advantage of the fact that, when in the presence of Hg(II) in aqueous media, its fluorescence is quenched but not with other ions, even with closely related ions such as Zn(II) and Cd(II). In this new report we delve into the electronic reasons behind the quenching process by calculating the most important electronic transitions with the framework laid by the Time Dependent Density Functional Theory (TD-DFT) at the PBE0/cc-pVQZ level of theory (we also included an electron core potential on the heavy metal atoms in order to decrease the time of each calculation). One of the things I personally liked about this work is the combination of different techniques that were used to assess the photochemical phenomenon at hand; some of those techniques included calculation of various bond orders (Mayer, Fuzzy, Wiberg, delocalization indexes), time dependent DFT and charge transfer delocalizations. Although we calculated all these various different descriptors to account for changes in the electronic structure of the ligand which lead to the fluorescence quenching, only delocalization indexes as calculated with QTAIM were used to draw conclusion, while the rest are collected in the SI section.

jpca

Thanks a lot to my good friend and collaborator Dr. Pezhman Zarabadi-Poor for all his work, interest and insight into the rationalization of this phenomenon. This is our second paper published together. By the way, if any of you readers is aware of a way to finance a postdoc stay for Pezhman here at our lab, please send us a message because right now funding is scarce and we’d love to keep bringing you many more interesting papers.

For our research group this was the fourth paper published during 2014. We can only hope (and work hard) to have at least five next year without compromising their quality. I’m setting the goal to be 6 papers; we’ll see in a year if we delivered or not.

I’d like to also take this opportunity to thank all the readers of this little blog of mine for your visits and your live demonstrations of appreciation at various local and global meetings such as the ACS meeting in San Francisco and WATOC14 in Chile, it means a lot to me to know that the things I write are read; if I were to make any New Year’s resolutions it would be to reply quicker to questions posted because if you took the time to write I should take the time to reply.

I wish you all the best for 2015 in and out of the lab!

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