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Mexican Phys.Chem. Meeting XVth edition 

For the fifth year in a row my research group has participated in this traditional meeting on theoretical and computational chemistry, now at the beautiful city of Merida in southeastern Mexico.

Several distinguished international guests included Profs. Jose Luis Mendoza (Florida State University), Adrián Roitberg (University of Florida), Vincent Ortiz (Auburn University) and Paul Ayers (McMaster U. Canada); Their contributions rounded up nicely those of household names like Drs. Alberto Vela, Gabriel Merino (CINVESTAV) (the latter was also the main organizer), Jesus Hernández-Trujillo (UNAM), Jose Luis Gazquez (UAM-I), Óscar Jimenez (Guanajuato), and so many others who were also present.

My students presented four posters summarized below:

1) Maru Sandoval and Gustavo Mondragón on Photosynthesis, particularly the search for exciton transference mechanisms in both natural and theoretical arrangements of photosynthetic pigments. Some very exciting results have been observed; their publication is really near.

2) Raúl Torres and Gustavo Mondragón presented their work on arsenic removing calixarenes, published earlier this year, and the extension of said work to As(III) acids. Graphene oxide is now considered in our simulations as per the experimental work of our colleagues, Prof. Reyes Sierra and Prof. Eddie Lopez-Honorato.

3) Marco Diaz, Guillermo Caballero, Gustavo Mondragón and Raúl Torres had this poster on the calculation of sigma holes as descriptors for predicting pka values in organic acids. Their +1600 calculations project has found the best levels of theory (and ruled out some like B3LYP, of course) with some nice correlations. Yet, much work is still to be done but we’re on the right track.

4) Durbis Castillo presented his work on molecular docking and dynamics of a large library of HIV-1 entry inhibitors for which he uses the suite MAESTRO as a continuation of another project of ours. His enormous library is now in the hundredths of thousands and although we’re facing some technical difficulties, Durbis is thriving in his search. This is our first serious attempt towards a more mature drug discovery project; a manuscript should be ready in the first part of next year.

This guys and the rest of the lab who weren’t present are the ones who make our research flourish and they’ve all earned a day or two at the beach!

Here’s to fifteen more years of RMFQT!

XIV Mexican Reunion on Theoretical Physical Chemistry

Each year the Mexican community who works in the realm of computational and theoretical chemistry gathers to share the most recent work done around our country. This year, I tried to live Tweet the event and although I failed miserably in doing so -as well as in convincing others to join me- I’m trying to put together the things that caught my attention. I also tried to Storify it but I cannot embed the result here in WordPress.

María Eugenia “Maru” Sandoval just came back from a short stay in Spain where she worked with Prof. David Casanova on Singlet Fission theory applied to her work on photosynthesis. Here work was presented as a poster although we would have preferred she gave a talk.


Also, Guillermo “Memo” Caballero presented his recent developments in reaction mechanisms.   

Below there is a list of Tweets from the conference. If you are interested in any of these items please contact me for further information, or just, you know, google the people mentioned in each Tweet, it shouldn’t be too hard.



Of course when you have a large meeting with so many people working with and on Density Functional Theory (DFT) you know that Perdew’s suggested ‘Jacob’s ladder’ of functional quality for chemical accuracy is bound to show up a few times.
I actually wrote a post that gravitates around this issue but using figurative painting as an analogue. You may find it here






That is Pt “double bond” Sn. By no means I’m equating platinum to tin. No sir. Mulliken’s population analysis should not even been brought up anymore, should it?



If there is water and ice on Mars then most definitely should be clathrates. (Please excuse the misspelling throughout, though.)


The rest are the previous announcements which were aimed to generate the momentum for the live tweeting thing.



I hope I can make this a thing next year during the 15th edition of RMFQT. I had the honor to be the first speaker and I will upload my presentation soon.

Physical Chemistry Meeting and CCIQS Symposium

Materials Research Institute at Morelia Michoacan (southern Mexico)

Materials Research Institute at Morelia Michoacan (southern Mexico)

So many events going on and so little time to blog about.
Two weeks ago, four members of this group traveled to Morelia in southern Mexico to present their research at the XIII Mexican Physical Chemistry Meeting. The next week after that, they all brought their posters back to Toluca for the internal symposium at CCIQS, where a masters student, María Eugenia, gave a small talk about her research project concerning photosynthesis in bacteria. Below, a short description of their projects is presented in order of seniority.

María Eugenia “Maru” Sandoval
Maru is working in photosynthesis of green sulfur bacteria. Her research deals with the excited states calculations at the Time Dependent DFT level for describing the first stages of photon interaction in antennae complexes of the photosystem II, namely the Fenna-Matthews-Olsen (FMO) complex, which was selected due to its relative structural simplicity over that of more evolved organisms. Maru also gave a talk at the internal Symposium back in Toluca the very next week where she got a positive feedback which will be used in her project.

Howard Diaz
One of the many strategies out there for treatment of HIV-1 infections is to block those proteins used to anchor the virus to a healthy cell. Sort of getting the virus’ hands busy so they can’t attach to a host. 60+ new compounds derived from thiourea were screened and assessed in their interactions with protein GP120, the protein to which the attachment is made, through docking and DFT calculations. Lead compounds are reported. It must be stressed that Howard got an award at CCIQS for having one of the best posters out of 70 in the entire symposium. Kudos and thanks to you, Howard! We now have some MD simulations in order.

Howard Diaz -  GP120 blockers for HIV-1

Howard Diaz – GP120 blockers for HIV-1

Guillermo “Memo” Caballero
His project has some nice philosophical implications if you ask me. Memo started as an experimental chemist and when he ran into a wall trying to obtain a pyridine from the non-aromatic analogue (glutarimide), he came to our group to run some calculations and find out how to force the aromatization process, or at least rationalize if it could be performed at all. Two mechanisms were proposed and now we know that even when the reaction should be quite exothermic, the reaction barriers are too high to be overcome by conventional methods. We now need to find a way to decrease those barriers (cue transition metal simulations). So in a way we are dealing here with the mechanism of a reaction that never happens (at least in an intramolecular way), leading to a reverse reductio ad absurdum reasoning – we assumed the reaction(s) did happen and we found out why is it impossible for them to happen.

No pic. available as of yet

Luis Enrique “Kike” Aguilar
Luis continues to work with calix(n)arenes, this lab’s first love, in drug delivery systems. He is working with two drugs at once: Bosutinib and Sorafenib, second generation drugs for the treatment of Chronic Myeloid Leukemia in cases were resistance to Imatinib has been developed. One of his main goals is to find a calixarene system which is able to discriminate between Bosutinib and pseudo-bosutinib, a commercial isomer which has incorrectly been available for a few years now.

"Kike" Aguilar -  Calix[n]arenes as drug carriers for Bosutinib and Sorafenib

“Kike” Aguilar – Calix[n]arenes as drug carriers for Bosutinib and Sorafenib

Thanks a lot for your efforts; they are paying good results to your ca

The boys from the lab

The boys from the lab

reers and the advancement of our research group. Now back to work, guys!


XIIth Mexican Reunion on Theoretical Physical Chemistry

As every year this month we had the yearly Mexican Reunion on Theoretical Physical Chemistry organized by prominent researchers in the field, such as Dr. Emilio Orgaz (UNAM), Dr. Alberto Vela (CINVESTAV) and many other. Over 150 different works were presented during this edition which took place in Juriquilla, Querétaro at one of the many campuses of the National Autonomous University of Mexico scattered all around the country. Below you can see some pictures from the talks and the first poster session.


This time we contributed with a small poster on a mechanism proposed by Howard Diaz (an undergrad student from UAEM) on the equilibrium transformation of dihydrocinolines into 1-amino-indoles by an intramolecular rearrangement. May this post also serve as the starting point of a -mini-tutorial on how to evaluate a mechanism theoretically using QST3 and IRC in implicitly solvated environments (PCM)


Howard Diaz posing next to his poster

The equilibrium under study and the proposed mechanism  by which it occurs, originally proposed by Frontana-Uribe et al. looks a bit like this:


Dihydrocinolines in equilibrium with 1-aminoindole


Mechanistic proposal by Frontana-Uribe et al.

The energy profile, in which all transition states were calculated with the QST3 method, is presented below, calculated at various levels of theory. Also, the Internal Reaction Coordinate (IRC) connecting both states was calculated and is shown further below in the full poster.

Energy Profile

Energy Profile

From this results we believe that a new mechanistic proposal is needed since the energy barrier for the first step is quite high (~60 kcal/mol) and hence a bit unlikely to occur through that transition state. Nevertheless this is a first approach to elucidating a mechanism and the more knowledge about it the higher the control will be on this chemical transformation.

A full version of the poster is shown below for your convenience (Spanish). See you all at the next RMFQT in Morelia 2014!

Full Poster

Full Poster

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.

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