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Gustavo “Gus” Mondragón M.Sc. – Thesis Defense

We celebrate the successful thesis defense of Gustavo “Gus” Mondragón who has now completed his Masters degree and is now on to getting a PhD in our group. Gustavo has worked on the search for multiexcitonic states and their involvement in the excitonic transference between photosynthetic pigments, specifically between bacteriochlorophyll-d molecules (BChl-d) from the bchQRU chlorosome whose whole structure is shown in the gallery below. To this end, Gustavo has studied and implemented the Restricted Active Space method with double spin flip (RAS-2SF) with the use of QChem5.0, a method that has required the use and understanding of states with high multiplicities. Additionally, Gustavo has investigated the influence of the environment within the chlorosome by performing ONIOM calculations for the spectroscopic properties of a BChl-d dimer, finding albeit qualitatively a batochromic effect, probably an expected result but nonetheless an impressive feat for the level of theory selected.

There’s still a lot of work to do in this line of research and although we’re eager to publish our results in this excitonic transference mechanism we want to be completely sure that we’re taking every possibility into consideration so we don’t incur into any inconsistencies.

Gustavo cultivates many research interests from excited states of these pigments to biochemical processes that require the use of various tools; I’m sure his permanence in our lab will bring lots of interesting results. Congratulations, Gus! Thank you for your hard work.


Dr. Gabriel Merino wins The Walter Kohn Prize 2018

Just as I was thinking about the state of Mexican scientific environment in the global scale, Prof. Dr. Gabriel Merino from CINVESTAV comes and gets this prize awarded by the International Center for Theoretical Physics (ICTP) and the Quantum ESPRESSO Foundation, showing us all that great science is possible even under pressing circumstances. 

Prof. Dr. Gabriel Merino at CINVESTAV Mérida, Yucatán, MEXICO

This prize is awarded biennially to a young scientist for outstanding contributions in the field of quantum-mechanical materials and molecular modeling, performed in a developing country or emerging economy,and in the case of Dr. Merino it is awarded not only for his contributions to theory and applications but also by his contributions to the prediction of novel systems that violate standard chemical paradigms, broadening the scope of concepts like aromaticity, coordination and chemical bond. The list of his contributions is very long despite his young age and there are barely any topic in chemistry or materials science that escapes his interest.

Gabriel is also one of the leading organizers of the Mexican Theoretical Physical Chemistry Meeting, an unstoppable mentor with many of his former students now leading research teams of their own. He is pretty much a force of nature. 

Congratulations to Dr. Gabriel Merino, his team, CINVESTAV and thanks for being such an inspiration and a good friend at the same time.

¡Felicidades, Gabriel!

A New Graduate Student!

Last Friday we had a new graduate student when our very own Marco Antonio Diaz defended his BSc thesis on the in silico design of drug carriers based on calix[n]arenes. During his thesis he performed around 160 different calculations regarding the interaction energy of our host-guest inclusion complexes, both using the supramolecular method and the NBODel procedure available in NBO3.1 as provided with Gaussian 09. One of the main targets of this work was to assess both methods -with the proper BSSE corrections- in their capabilities for the calculation of interaction energies.

We found that the NBODel method consistently generates interaction energies that are similar to those of the SM method + the BSSE correction (as opposed to SM – BSSE which is the proper correction). Marco and I are still in the process of writing the article so maybe it will be published in early 2018. In this case we’re using calixarenes to deliver three drugs: warfarine, furosemide, phenylbutazone to compite with ocratoxin-A (OTA) for the binding site in Human Serum Albumin (HSA).


This project is undertaken in collaboration with my good friend Dr. Sándor Kunsági-Máté in Pécsi Tudomanyegyetem in Hungary.

Congratulations to Marco from all of us here at the lab!

Some Comp.Chem. Tweeps

Out of some +1000 twitter accounts I follow about a quarter are related computational chemistry. The following public list isn’t comprehensive and prone to errors and contains researchers, programmers, students, journals, products and companies who gravitate around the use of in silico methods for the understanding and design of chemical and biochemical compounds.


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!)

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