Monthly Archives: December 2018

Estimation of pKa Values through Local Electrostatic Potential Calculations


Calculating the pKa value for a Brønsted acid is very hard, like really hard. A full thermodynamic cycle (fig. 1) needs to be calculated along with the high-accuracy solvation free energy for each of the species under consideration, not to mention the use of expensive methods which will be reviewed here in another post in two weeks time.

Thermodynamic_Cycle
Fig 1. Thermodynamic Cycle for the pKa calculation of any given Bronsted acid, HA

Finding descriptors that help us circumvent the need for such sophisticated calculations can help great deal in estimating the pKa value of any given acid. We’ve been interested in the reactivity of σ-hole bearing groups in the past and just like Halogen, Tetrel, Pnicogen and Chalcogen bonds, Hydrogen bonds are highly directional and their strength depends on the polarization of the O-H bond. Therefore, we suggested the use of the maximum surface electrostatic potential (VS,max) on the acid hydrogen atom of carboxylic acids as a descriptor for the strength of their interaction with water, the first step  in the deprotonation process. 

We selected six basis sets; five density functionals; the MP2 method for a total of thirty-six levels of theory to optimize and calculate VS,max on thirty carboxylic acids for a grand total of 1,080 wavefunctions, which were later passed onto MultiWFN (all calculations were taken with PCM = water). Correlation with the experimental pKa values showed a great correlation across the levels of theory (R2 > 0.9), except for B3LYP. Still, the best correlations were obtained with LC-wPBE/cc-pVDZ and wB97XD/cc-pVDZ. From this latter level of theory the linear correlation yielded the following equation:

pKa = -0.2185(VS,max) + 16.1879

Differences in pKa turned out to be less than 0.5 units, which is remarkable for such a straightforward method; bear in mind that calculation of full thermodynamic cycles above chemical accuracy (1.0 kcal/mol) yields pKa differences above 1.0 units.

We then took this equation for a test with 10 different carboxylic acids and the prediction had a correlation of 98% (fig. 2)

47051619_1824157374360101_2244437569725005824_n
fig 2. calculated v experimental pKa values for a test set of 10 carboxylic acids from equation above

I think this method can really catch on for a quick way to predict the pKa values of any carboxylic acid imaginable. We’re now working on the model extension to other groups (i.e. Bronsted bases) and putting together a black-box workflow so as to make it even more accessible and straightforward to use. 

We’ve recently published this work in the journal Molecules, an open access publication. Thanks to Prof. Steve Scheiner for inviting us to participate in the special issue devoted to tetrel bonding. Thanks to Guillermo Caballero for the inception of this project and to Dr. Jacinto Sandoval for taking the time from his research in photosynthesis to work on this pet project of ours and of course the rest of the students (Gustavo Mondragón, Marco Diaz, Raúl Torres) whose hard work produced this work.

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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!

Computational Chemistry from Latin America


The video below is a sad recount of the scientific conditions in Mexico that have driven an enormous amount of brain power to other countries. Doing science is always a hard endeavour but in developing countries is also filled with so many hurdles that it makes you wonder if it is all worth the constant frustration. 

That is why I think it is even more important for the Latin American community to make our science visible, and special issues like this one from the International Journal of Quantum Chemistry goes a long way in doing so. This is not the first time IJQC devotes a special issue to the Comp.Chem. done south of the proverbial border, a full issue devoted to the Mexican Physical Chemistry Meetings (RMFQT) was also published six years ago.

I believe these special issues in mainstream journals are great ways of promoting our work in a collected way that stresses our particular lines of research instead of having them spread a number of journals. Also, and I may be ostracized for this, but I think coming up with a new journal for a specific geographical community represents a lot of effort that takes an enormous amount of time to take off and thus gain visibility. 

For these reasons I’ve been cooking up some ideas for the next RMFQT website. I don’t pretend to say that my colleagues need any shoutouts from my part -I could only be so lucky to produce such fine pieces of research myself- but it wouldn’t hurt to have a more established online presence as a community. 

¡Viva la ciencia Latinoamericana!

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