Blog Archives

Internal Symposium at CCIQS – 2016 edition

Having a symposium right after the winter holidays is a great way to get back in touch with colleagues and students; we get to hear how their work is progressing and more importantly I get forced to become focused once again after a few weeks of just not paying much attention to anything related to work.

This year our group has happily gained some additions and sadly seen some others leave in search of a better future. María Eugenia “Maru” Sandoval gave a talk on the work she did on Singlet Fission (SF) in the Fenna-Matthews-Olson (FMO) complex during a three month stay at the Basque Country University in Spain under the supervision of Dr. David Casanova. Aside her calculations regarding Förster theory and a modification to Marcus’ equation, Singlet Fission was explored by her as a possible mechanism in which the Photosynthetic complex FMO might transfer solar energy from the antennae to the reaction center; one that might explain the high efficiency of it.

SF is a fascinating phenomenon: So you get an excited state S1 for a molecule1 that has been struck with a suitable photon; this excited state can either radiate back to the ground state (S0) but if there were two degenerate and coupled triplets whose energies are similar to half the S1 energy then the excited state might decay into [TT]1, hence singlet fission. In some cases (e.g. polyacene crystals) one of these triplets might be located in an adjacent molecule, this creates a hole in a second molecule due to the same single photon! This means creating twice the current albeit at half the voltage in photovoltaic materials. Maru has explored the possibility of SF occurring in natural systems and we think we might be on to something; she will defend her masters thesis any day now and we should see a publication later on this year. After that, she is pondering a few interesting options for her PhD.

On the poster session, our lab was represented by Marycarmen Reséndiz, Gustavo Mondragón and Guillermo Caballero. Durbis Pazos just now joined our group so he didn’t have to present a poster but nevertheless showed up gladly to support his colleagues. Gustavo will work on other aspects regarding the photochemistry of the FMO complex while Marycarmen is working on calculating the electronic interactions of chemically modified nucleotides when incorporated into DNA strands. Guillermo had a poster on his calculations for another reaction mechanism that caught his eye while still working with the experimentalists. I’m pleased to say that Guillermo is close to being published and also close to leaving us in order to get a PhD in a prestigious university that shall remain unnamed.

Thank you guys for keeping up the good work and maintaining the quality of the research we do, here is to a year full of success both in and out of the lab! Any success this lab has is due to you.

New Liquid Nitrogen Plant at CCIQS

Well, the title of this post is pretty self-explanatory as well as unrelated to computational chemistry. Yesterday here at CCIQS we received new equipment for supplying liquid nitrogen to our laboratories, especially to the NMR machines which consume it a lot, and also for the X-ray diffractometers which require cooling of crystals. This new compressor replaces the old one which has long overseen its useful life. So, anyway, I thought it would be a nice change for a post because I like bragging (or should I say ‘marketing’?) the equipment available here at CCIQS, and with the pending new grant we obtained for sustainable catalysis research, we’ll be seeing more of this shipments (including a small computer cluster for yours truly!). You can see my good friend, Dr. Vojtech “Beto” Jancik in the pictures (in short, a post about a joint paper will come out, stay tuned!).

Internal Symposium at CCIQS – 2014 edition

Once again as every year we celebrate our internal symposium here at CCIQS, and like every year, my students presented some of their progress with their research projects. This time, three students, from three different levels, present posters regarding some of the data they’ve obtained.


María Eugenia ‘Maru’ Sandoval presented a poster regarding the molecular dynamics simulations performed for the drug Imatinb and a family of calix- and thia-calix[n]arenes as published here and reported in this blog here. ‘Maru’ is now a first year grad student at the National University, UNAM, after spending a year working for a pharmaceutical company. Her research in the realm of photosynthesis has only begun recently, that is why we had to rely on some other data.


Luis Enrique Aguilar is researching cation-π interactions within the aromatic cavities of calix[n]arenes in order to find suitable leads among these, our favorite macrocyles, for designing extraction agents of heavy (toxic) metals. Luis Enrique is an undergrad student here at the State University who should finish this year and has shown some interest (threatened us) in writing his dissertation thesis in our research group.


Monserrat Enriquez is a PhD student at CINVESTAV under the joint supervision of Dr. Eddie López-Honorato and myself (Dr. Eddie is her principal advisor), her research project involves both theoretical calculations and synthesis of the leads for extraction agents for several Arsenic species. For the time being, Monserrat is here with us, far from her home on the north side of the country, for this semester in which we have to finish with the theoretical section of her work. Besides her research concerning calixarenes she is also running calculations on the interactions between graphene oxide and the aforementioned As species. We are very excited about working with such a complex yet simple material that has such an exciting electronic structure.

This symposium is always interesting and important in bringing our research projects closer to all the comunity of this center. And since symposium comes from the Greek meaning ‘drinking together‘, then lets raise our glasses and toast for the data to come!



The Nobel Prize in Chemistry 2013

I’m quite late to jump on this wagon but nonetheless I’m thrilled about this year’s Nobel Prize in Chemistry being awarded to three awesome computational chemists: Martin Karplus (Harvard), Michael Levitt (Stanford) and Arieh Warshel (USC) for the development of computational models at the service of chemistry; most prominently, the merging of computations both at the classical . and quantum levels, the former allows for a computationally feasible calculation while the latter provides the needed accuracy for the description of a chemical process.

Nobel Laureates in Chemistry 2013 (source:

Nobel Laureates in Chemistry 2013 (source:

As a computational chemist myself I must say that, at some level, it feels as some sort of vindication of the field, which makes me wonder if it indeed needs it, I don’t think so but maybe some might. Last week, Nobel week, I attended a symposium on the Advances in Quantum Chemical Topology where big names such as Paul Ayers, Paul Popelier and Chérif Matta among many others participated along with my friends and colleagues from CCIQS, Fernando Cortés (whom actually organized the whole thing! Kudos, Fer!) and Vojtech Jancik who contributed to the experimental (X-ray diffraction methods) part of the symposium. Surprisingly nobody at the conferences mentioned the Nobel Prize! Not even during the round table discussion titled “The Future of Quantum Chemical Topology“. At some point during this discussion the issue of usefulness came out. I  pointed out chemists have this inherent need of feeling useful, including computational chemists, as opposed to physicists of any denomination. Computational or theoretical chemists try to be like physicists yet still have chemistry behavior baggage. Even more baffling is the fact that at such an abstract conference usefulness is discussed, yet those theoretical chemists who do not develop new methods, nor dwell into equations or propose new Hamiltonians, but rather make use of well established methodologies for tackling and solving particular problems in chemistry become somewhat ostracized by the theoretical chemistry community*.

Much controversy among the comp.chem. community was aroused by this much deserved award (try reading the comment section on this post by the great Derek Lowe at In The Pipeline). Here in Mexico we have a saying: “Ni son todos los que están ni están todos los que son” which is hard to translate given the two different meanings of the verb To Be, but it can be roughly translated as “Not all the ones who should be are present, nor the ones that are present are all that should be“, or something like that. Of course there are many other computational chemists that are left behind from this prestigious prize, but the contributions of Karplus, Levitt and Warshel to chemistry through the use of computational chemistry can be denied. In fact this does vindicate the field of comp.chem. by acknowledging the importance of modelling in molecular design and reactivity understanding.

Congratulations from a Mexican fan to Professors Karplus, Levitt and Warshel for the most deserved Nobel Prize in Chemistry 2013!

PS a much better post on this topic can be found at the curious wavefunction.

Thanks for reading, liking, rating and commenting

*Of course this is just my opinion and views (which is redundant to state since this is my very own blog!)

Summer internships are Over

For the last five weeks we had guests in our lab coming from different places of the country: Tepic (west), León (Center) and Mexico City (Right in the middle!). During those five weeks they worked in the field of computational chemistry helping our research efforts with a couple of drug carrying molecules. They learned about computational chemistry and drug design; about wavefunctions and density functionals; about population analysis and vibrational frequency analysis. Dead hours were a bit complicated to handle because the convergence of each calculation takes some time and, as opposed to a wet-chemistry lab, I couldn’t just ask them to purify starting materials or distillate solvents. A question to other theoretical/computational chemists: What could I have asked young undergrad students (with backgrounds ranging from engineering to pharmacy) to do during those dead hours? What did I do wrong? Anyway, they manage to spend a good time since they all got along quite well.

Now they are back to their hometowns getting ready for the congress, hosted by the same organization that awarded them the stipend to come and spend their summer with us (The Dolphin Program / Programa Delfín) as well as to going back to school in a few more weeks. I asked* them to write a guest post for the blog telling their experience, which is presented below. Thanks to you all for choosing our lab to get your internship this summer!

Javier Camacho (Mexico City)

Javier_Delfin_2013Hi, I’m Javier from ESIQIE-IPN
The dolphin program has given me the opportunity to experience how is to be in a high-level scientific research. Login to CCIQS next to the imminent Dr. Joaquin Barroso Flores, left me a pleasant experience. The great contribution that gives this line of research has allowed me to meet new horizons, beyond the area of engineering, to which I belong.
The theoretical chemistry and computational chemistry together, are a great weapon to develop virtual optimizations that allow us to find drug transport agents, without making the vast amount of laboratory tests that are required. Explaining that this is one of the many applications that can be used.
To undertake this experience has left me very satisfied, be guiding a person who likes his work and want to show what he knows, it makes me very happy. After these long weeks of work and perseverance, with certainty affirm the interesting and productive it is to be part of the investigation in Mexico.
I thank the Dolphin Program, gives CCIQS the UAEM-UNAM and Dr. Joaquin for opening the doors to this great opportunity to start my story as a researcher.


Paulina Pintado (Tepic, Nayarit)

la fotoHi my name’s Paulina and I came as part of Dolphin Research Program that gives the opportunity of participates in a real work of investigation with a professional at the topic. In this occasion I came to work with Ph.D. Joaquin Barroso in a small project of his line of research; namely theoretical drug carriers design. In this six weeks besides to learn more aspects about my career, in this case Theoretical Chemistry applied to pharmaceutical industry; I tested the experience of travel to another town just by myself, live with people from different parts of the country with distinct customs and visit few places of the town.
This summer will always be memorable ‘cause this internship is an important event for my professional experience and also for my personal development and I hope many others students have the courage to try get into the world of scientific research.
So just remains for me to thank to Ph.D. Joaquin Barroso for giving me the chance to do this internship in his lab I hope you continue having success in your work, I feel pretty glad to met him and my others research’s mates.



Daniel Carteño (Mexico City)

Ey my name’s  Daniel and this summer of  2013  i had been the opportunity to do a research  internship in Toluca under P.H.D. Joaquin Barroso, and during this period of time I´ve learnt a bit about His research work, not only this is  an important experience for my educational history, but it also is for my personal life. Learnt about theoretical chemistry open my vision of this discipline, because when I thought about chemistry I´ve never imagine a computational laboratory, this the most important part, nowadays the researches have been removed due to  they are so expensive and finally the conclusion  is not expected, when you use a super computer like me and my work team used, it doesn’t matter if you have a mistake  or do something wrong, only you have to write again the keywords and the only thing you spend is time. Even in Mexico theoretical chemistry is not famous in my opinion is a useful work tool. This research internship was highly satisfactory and hope do it again i´m glad

*Their contributions were completely voluntary and no editing of their original texts has been made.

First graduated student!

Today is truly a landmark in our lab because on this day, María Eugenia “Maru” Sandoval-Salinas has defended her thesis and has thus obtained her B. Sc. in Chemistry. She is the first student under my supervision to achieve this goal, and I hope it won’t be long until we get some more, although now the bar has been set quite high. For the time being, Maru is pursuing a career in the pharmaceutical industry but has every intention of coming back to the lab for her Masters degree; she has a reserved spot here with us at CCIQS.

Hard work pays off - We wait for you to come back for your Masters Degree!

Hard work pays off – We wait for you to come back for your Masters Degree!

Maru’s thesis deals mainly, but not exclusively, with calculating the interaction energies of calix- and thia-calix[n]arenes with the tyrosine kinase inhibitor Imatinib, which is widely used in the treatment of Chronic Myeloid Leukemia (CML), in order to rationally design a drug delivery agent for this drug. Her work is (a huge) part of an article currently under revision that I only wish had been published before her defense. Still, we await for that paper to be published in the next few weeks.

Throughout her stay at our lab, Maru was a dedicated student willing to learn new skills every time. As she replied today to one of the questions: “it’s not so much how many calculations I got right, but how many I got wrong!“. I find deep meaning in this sentence, perhaps deep enough as to consider it an aphorism, because indeed the more we try the more we fail, and the more we fail the more we learn and the closer we get to success.

Congratulations, Maru! I personally thank you for all the hard work invested in your thesis, all the long hours in front of the computer and your disposition to learn and work during the last 1.5 years. I’m certain you’ll find success in any venture you undertake; and I’m certain of it because you never stop trying.

Taking the Oath after being unanimously approved

Taking the Oath after being unanimously approved

XIth Mexican Reunion on Theoretical Physical Chemistry

For over a decade these meetings have gathered theoretical chemists every year to share and comment their current work and to also give students the opportunity to interact with experienced researchers, some of which in turn were even students of Prof. Robert Parr, Prof. Richard Bader or Prof. Per Olov Löwdin. This year the Mexican Meeting on Theoretical Physical Chemistry took place last weekend in Toluca, where CCIQS is located. You can find links to this and previous meetings here. We participated with a poster which is presented below (in Spanish, sorry) about our current research on the development of calixarenes and tia-calixarenes as drug carriers. In this particular case, we presented our study with the drug IMATINIB (Gleevec as branded by Novartis), a powerful tyrosinkynase inhibitor widely employed in the treatment of Leukaemia.

The International Journal of Quantum Chemistry is dedicating an issue to this reunion. As always, this meeting posed a great opportunity to reconnect with old friends, teachers, and colleagues as well as to make new acquaintances; my favourite session is still the beer session after all the seminars! Kudos to María Eugenia “Maru”  Sandoval-Salinas for this poster and the positive response it generated.

CONACyT funding was approved!

A couple of months ago, maybe a little bit more, I got the news that the project I submitted to the National Council for Science and Technology (CONACyT) was approved! Now we only have to wait for the money to actually show up and that might take a while – a long while! Nevertheless this is always very good news and we are very excited about it because this means more money for research, specifically on the electronic molecular pathways of photosynthesis.

When I submitted the project I wrote a little post about the funding scheme which seemed, if not unfair, at least flawed, and I still believe in what I wrote. To be honest I thought it wouldn’t be funded but it turns out it was but I still think the reviewing process could be better.

There is a lot of research to do – too little time to do it.

www.CCIQS; The (not-quite) official website

The Joint Center for Sustainable Chemistry Research (Centro Conjunto de Investigación en Química Sustentable) was born in 2008 as a project between the Institute of Chemistry from the National Autonomous University of Mexico and the Chemistry School from the Mexico State Autonomous University aimed to the development of research in green and sustainable chemistry as well as that of human resources trained in the same areas.

I have found through the statistics page in this blog that CCIQS is a somewhat popular search term but unfortunately there is still no website available due to some technical dificulties. Therefore I here upload the link to our proto-website (only Spanish for the time being, sorry)

I hope this helps people find some info about what we do and how to get in touch with us. Opportunities for scholarships are available both for graduate and undergraduate students. If you are interested in working with us, please get in touch with the researcher of your choice and ask for any available positions; we look forward to having more students to interact with!

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