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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).

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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!

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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.

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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: NBC.com)

Nobel Laureates in Chemistry 2013 (source: NBC.com)

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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