Monthly Archives: November 2016

Finite Element(s) Chemistry

(Ah! Mathematicians, did you see what I did there?)

There are a number of appalling videos on line in which iPhones are destroyed by various means. From a chemist standpoint, the reason why I’m so disgusted with them is the waste of rare elements which go into the making of their components: From Neodymium to Indium, most of these metals come from conflict zones in which they are extracted in the most precarious conditions imaginable, but furthermore, they are so scarce the production of electronics is almost unsustainable. I wont post any links to these infuriating videos so as to not direct traffic to any of them, instead I will direct your attention to a wonderful book titled The Elements of Power: Gadgets, Guns, and the Struggle for a Sustainable Future in the Rare Metal Age by David S. Abraham. (Sheesh! Nobody uses short titles anymore? Can you imagine Nabokov writing Lolita: A little girl with a not so little mind and the professor who picked up on that? I digress.) It is hard not to read this long-titled book and feel a tad guilty; it is in fact a bit blackmailing but above all, realizing what a wasteful society (ugh! I hate that word) we are makes a strong wake up call to the future of sustainability. I would never claim that the solution is renouncing to technology but instead to find a sustainable technology within the framework of current technology. Easier said than done -of course- but stopping waste of such precious resources should be the first step in everyones mind, and don’t even get me started on balloons filled with He! In all fairness, one can also find a lot of scary articles on line from dubious to respectful on how smartphones and other rare-metals-containing gadgets are damaging the Earth.

Last year I enjoyed reading Andy Weir’s novel The Martian (later a major motion picture from Alien’s director Ridley Scott), in which an astronaut is stranded in Mars -left for dead by his crewmates, with nothing but the finite supplies of the station and his knowledge of chemistry, botany and engineering, all of which allows him to survive by extending, but above all reusing, those resources which included not only food but O2, H2O and even hydrazine, H2N2 originally intended for fuel but from where he now gets H2 for synthesizing a larger supply of water by reacting it with the O2 pulled out of the CO2-filled Martian atmosphere. I’m pretty sure Weir didn’t intend this novel to be a metaphor but it definitely works well as one of the limited resources available on Earth and the necessity of optimizing their use, collecting and disposal. Resources on Earth seem infinite, or they at least they did back when the industrial revolution started.

I guess the point is that sustainability goes hand in hand with using the least resources to get new ones as well as with avoiding their waste. I think one must agree that Chemistry, like no other science, has shaped our world for better and worse.

I haven’t rambled on sustainability in a while. Feels bad. Must be the winter.

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!

Tribology – New paper in JPC A

Tribology isn’t exactly an area with which us chemists are most familiar, yet chemistry has a great impact on this branch of physics of high industrial importance. Tribology is basically the science which studies the causes and consequences of friction between surfaces. 

The plastic bag industry requires the use of chemical additives to reduce the electrostatic adherence between sheets of plastic. My good old friend Dr. Armando Gama has studied through Dissipative Particle Dynamics (DPD) coarse-grained simulations the friction coefficients of having two slightly different molecules: erukamide and behenamide, which only differ in the presence of a double bond between carbon atoms 12 and 13 (Fig1).


Fig 1

In order to study the electronic aspects that give rise to different tribological effects in these very similar molecules, four chains of each kind were bounded to a frozen graphene surface (four bonds apart to prevent steric crowding) and were optimized at the B97D/6-31G(d,p) level of theory.



Double bonds in erukamide pile together through pi-pi stacking interactions (Fig2) which are absent in behenamide which is why these last ones are able to slide better between each other (Fig3). Interaction energies calculated for the inner chains at the same level of theory are 44.21 and 34.46 kcal/mol for erukamide and behenamide, respectively. As per the suggestion of a referee we extended the calculations to a 2D system by placing seven molecules on graphene, which once again was kept at the optimized geometry of its isolated state, at four bonds of separation in order to prevent steric crowding (Fig 4).


Fig 4

This calculations clearly represent a limit case with a high density covering of the surface, but they nevertheless reflect the observed trend that behenamide works better than erukamide in reducing the static friction coefficient between sheets.

The paper is now available at JPC-A. Thanks to Dr. Gama for this great opportunity to work with his team, I know it wont be the last.

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