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DFT beyond academia


Density Functional Theory is by far the most successful way of gaining access to molecular properties starting from their composition. Calculating the electronic structure of molecules or solid phases has become a widespread activity in computational as well as in experimental labs not only for shedding light on the properties of a system under study but also as a tool to design those systems with taylor-made properties. This level of understanding of matter brought by DFT is based in a rigorous physical and mathematical development, still–and maybe because of it–DFT (and electronic structure calculations in general for that matter) might be thought of as something of little use outside academia.

Prof. Juan Carlos Sancho-García from the University of Alicante in Spain, encouraged me to talk to his students last month about the reaches of DFT in the industrial world. Having once worked in the IP myself I remembered the simulations performed there were mostly DPD (Dissipative Particle Dynamics), a coarse grained kind of molecular dynamics, for investigating the interactions between polymers and surfaces, but no DFT calculations were ever on sight. It is widely known that Docking, QSAR, and Molecular Dynamics are widely used in the pharma industry for the development of new drugs but I wasn’t sure where DFT could fit in all this. I thought patent search would be a good descriptor for the commercial applicability of DFT. So I took a shallow dive and searched for patents explicitly mentioning the use of DFT as part of the invention development process and protection. The first thing I noticed is that although they appear to be only a few, these are growing in numbers throughout the years (Figure 1). Again, this was not an exhaustive search so I’m obviously overlooking many.

Figure 1 – A non-exhaustive search in a patents database

The second thing that caught my attention was that the first hit came from 1998, nicely coinciding with the rise of B3LYP (Figure 2). This patent was awarded to Australian inventors from the University of Wollongong, South New Wales to determine trace gas concentrations by chromatography by means of calculating the FT-IR spectra of sample molecules (Figure 3), so DFT is used as part of the invention but I ignore if this is a widespread method in analytical labs.

Figure 2 – B3LYP cited in scientific publications

While I’m mentioning the infamous B3LYP functional, a search about it in patents yields the following graph (Figure 4), most of which relate to the protection of photoluminescent or thermoluminescent molecules for light emitting devices; it appears that DFT calculations are used to provide the key features of their protection, such as HOMO-LUMO gap etc.

Figure 4 – Patents bearing B3LYP as part of their invention

So what about software? Most of the more recent patents in Figure 1 (2018 – 2022) lie in the realm of electronics, particularly the development of semiconductors, ceramical or otherwise, so it was safe to assume VASP could be a popular choice to that end, right? turns out that’s not necessarily the case since a patent search for VASP only accounts for about the 10% of all awarded patents (Figure 5).

Figure 5 – VASP in patents

I guess it’s safe to say by now that DFT has a significant impact in the industrial development, one could only expect it to keep on rising, however the advent of machine learning techniques and other artificial intelligence related methods promise an accelerated development. I went again to the patents database and this time searched for ‘machine learning development materials‘ (the term ‘development’ was deleted by the search engine, guess found it too obvious) and its rise is quite notorious, surpassing the frequency of DFT in patents (Figure 6), particularly in the past 5 years (2018 – 2022).

Figure 6 – The rise of the machines in materials development

I’m guessing in some instances DFT and ML will tend to go hand in hand in the industrial development process, but the timescales reachable by ML will only tend to grow, so I’m left with the question of what are we waiting for to make ML and AI part of the chemistry curricula? As computational chemistry teachers we should start talking about this points with our students and convince the head of departments to help us create proper courses or we risk our graduates to become niche scientists in a time when new skills are sought after in the IP.

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Thanks again to Prof. Juan Carlos Sancho García at the University of Alicante, Spain, who asked me talk about the subject in front of his class, and to Prof. José Pedro Cerón-Carrasco from Cartagena for allowing me to talk about this and other topics at Centro Universitario de la Defensa. Thank you, guys! I look forward to meeting you again soon.

Exciton Energy Transfer-Talk at the Virtual Winter School of Comp.Chem. 2022


I’m very honored to have been invited to this edition of this long standing event, the Virtual Winter School of Computational Chemistry. In this talk I walk through the basics of what are excitons and how do they move or transfer across matter; and of course, a primer on how to calculate the energy transfer with Gaussian.

This is a very basic introduction but I hope someone finds it useful. Thanks to Henrique Castro for inviting me to take part of this experience and to all the professors and students involved in the organization. Don’t forget to go and check all the other fantastic talks, including one by Nobel Laureate and chemistry legend Prof. Roald Hoffmann, at the Virtual Winter School’s website: https://winterschool.cc/

XVIII RMFQT


It was my distinct pleasure for me to participate in the organization of the latest edition of the Mexican Meeting on Theoretical Physical Chemistry, RMFQT which took place last week here in Toluca. With the help of the School of Chemistry from the Universidad Autónoma del Estado de México.

This year the national committee created a Lifetime Achievement Award for Dr. Annik Vivier, Dr. Carlos Bunge, and Dr. José Luis Gázquez. This recognition from our community is awarded to these fine scientists for their contributions to theoretical chemistry but also for their pioneering work in the field in Mexico. The three of them were invited to talk about any topic of their choosing, particularly, Dr. Vivier stirred the imagination of younger students by showing her pictures of the times when she used to hangout with Slater, Roothan, Löwdin, etc., it is always nice to put faces onto equations.

Continuing with a recent tradition we also had the pleasure to host three invited plenary lectures by great scientists and good friends of our community: Prof. William Tiznado (Chile), Prof. Samuel B. Trickey (USA), and Prof. Julia Contreras (France) who shared their progress on their recent work.

As I’ve abundantly pointed out in the past, the RMFQT is a joyous occasion for the Mexican theoretical community to get together with old friends and discuss very exciting research being done in our country and by our colleagues abroad. I’d like to add a big shoutout to Dr. Jacinto Sandoval-Lira for his valuable help with the organization of our event.

XXVIII International Materials Research Congress


I just came back from beautiful Cancun where I attended for the third time the IMRC conference invited by my good friend and awesome collaborator Dr. Eddie López-Honorato, who once again pulled off the organization of a wonderful symposium on materials with environmental applications.

Dr. López-Honorato and I have been working for a number of years now on the design application of various kinds of materials that can eliminate arsenic species from drinking water supplies, an ever present problem in northern Mexico in South West US. So far we have successfully explored the idea of using calix[n]arenes hosts for various arsenic (V) oxides and their derivatives, but now his group has been thoroughly exploring the use of graphene and graphene oxide (GO) to perform the task.

Our joint work is a wonderful example of what theory and experiment and achieve when working hand-in-hand. During this invited talk I had the opportunity to speak about the modeling side of graphene oxide, in which we’ve been able to rationalize why polar solvents seem to be -counterintuitively- more efficient than non-polar solvents to exfoliate graphene sheets from graphite through attrition milling, as well as to understand the electronic mechanism by which UV light radiation degrades GO without significantly diminishing there arsenic-adsorbing properties. All these results are part of an upcoming paper so more details will come ahead.

Thanks to Dr. Eddie López for his invitation and the opportunity provided to meet old friends and make new ones within the wonderful world of scientific collaborations.

XVI Mexican Meeting on Phys.Chem.


A yearly tradition of this Comp.Chem. lab and many others throughout our nation is to attend the Mexican Meeting on Theoretical Physical Chemistry to share news, progress and also a few drinks and laughs. This year the RMFQT was held in Puebla and although unfortunately I was not able to attend this lab was proudly represented by its current members. Gustavo Mondragón gave a talk about his progress on his photosynthesis research linking to the previous work of María Eugenia Sandoval already presented in previous editions; kudos to Gustavo for performing remarkably and thanks to all those who gave us their valuable feedback and criticism. Also, five posters were presented successfully, I can only thank the entire team for representing our laboratory in such an admirable way, and a special mention to the junior members, I hope this was the first of many scientific events they attend and may you deeply enjoy each one of them.

Among the invited speakers, the RMFQT had the honor to welcome Prof. John Perdew (yes, the P in PBE); the team took the opportunity of getting a lovely picture with him.

Here is the official presentation of the newest members of our group:

Alejandra Barrera (hyperpolarizabilty calculations on hypothetical poly-calyx[n]arenes for the search of NLO materials)

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Fernando Uribe (Interaction energy calculations for non-canonical nucleotides)

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Juan Guzmán (Reaction mechanisms calculations for catalyzed organic reactions)

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We thank the organizing committee for giving us the opportunity to actively participate in this edition of the RMFQT, we eagerly await for next year as every year.

 

WATOC 2017


Last week the WATOC congress in Munich was a lot of fun. Our poster on photosynthesis had a great turnout and got a lot of positive feedback as well as many thought provoking questions. One of the highlights of my time there was seeing my former students and knowing they’re all leading successful and happy grad-student lives in Europe, I’m so very proud of them. It was great to connect with old friends and making new ones; a big thank you to all the readers of this little blog who took the time to come and say hi, I’m very glad the blog has been helpful to you.

Better recounts of WATOC 2017 can be found in the great Rzepa’s blog here and here.

Below there is an image of our poster (some typos persist).

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See you all in 2020!

Internal Symposium at CCIQS – 2016 edition


Having a symposium right after the winter holidays is a great way to get back in touch with colleagues and students; we get to hear how their work is progressing and more importantly I get forced to become focused once again after a few weeks of just not paying much attention to anything related to work.

This year our group has happily gained some additions and sadly seen some others leave in search of a better future. María Eugenia “Maru” Sandoval gave a talk on the work she did on Singlet Fission (SF) in the Fenna-Matthews-Olson (FMO) complex during a three month stay at the Basque Country University in Spain under the supervision of Dr. David Casanova. Aside her calculations regarding Förster theory and a modification to Marcus’ equation, Singlet Fission was explored by her as a possible mechanism in which the Photosynthetic complex FMO might transfer solar energy from the antennae to the reaction center; one that might explain the high efficiency of it.

SF is a fascinating phenomenon: So you get an excited state S1 for a molecule1 that has been struck with a suitable photon; this excited state can either radiate back to the ground state (S0) but if there were two degenerate and coupled triplets whose energies are similar to half the S1 energy then the excited state might decay into [TT]1, hence singlet fission. In some cases (e.g. polyacene crystals) one of these triplets might be located in an adjacent molecule, this creates a hole in a second molecule due to the same single photon! This means creating twice the current albeit at half the voltage in photovoltaic materials. Maru has explored the possibility of SF occurring in natural systems and we think we might be on to something; she will defend her masters thesis any day now and we should see a publication later on this year. After that, she is pondering a few interesting options for her PhD.

On the poster session, our lab was represented by Marycarmen Reséndiz, Gustavo Mondragón and Guillermo Caballero. Durbis Pazos just now joined our group so he didn’t have to present a poster but nevertheless showed up gladly to support his colleagues. Gustavo will work on other aspects regarding the photochemistry of the FMO complex while Marycarmen is working on calculating the electronic interactions of chemically modified nucleotides when incorporated into DNA strands. Guillermo had a poster on his calculations for another reaction mechanism that caught his eye while still working with the experimentalists. I’m pleased to say that Guillermo is close to being published and also close to leaving us in order to get a PhD in a prestigious university that shall remain unnamed.

Thank you guys for keeping up the good work and maintaining the quality of the research we do, here is to a year full of success both in and out of the lab! Any success this lab has is due to you.

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.

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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

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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?

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

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

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“Not!”

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.

Symposium at IQ-UNAM 2015


Earlier this week we had at our annual symposium at the institute of chemistry where we had distinguished international visitors such as Prof. Theodor Agapie, Prof. Lanny Liebeskind (associate editor of Organometallics), Prof. Marc Petit and Prof. Francois Gabbaï (associate editor of Organometallics), as well as our very own colleagues like Dr. Fernando Cortés who presented a recent paper published on Nucleic Acids Research, and Vojtech Jancik who talked about the high resolution crystallography performed at CCIQS. One of the presentations I liked the most was the one by Dr. Abel Moreno who is now doing some research on the proteins that crystallize calcium carbonate in the formation of egg-shells; Dr. Moreno recently got some 70 million years old fossilized dinosaur egg-shells, from which he is expecting to isolate some samples! Very exciting! I visited Dr. Moreno’s lab to take a look at this fossils and forgot to take a picture of them but trust me they were very cool to look at.

Our lab contributed with a poster by ´Maru´Sandoval (pictures below) in which she presented her research on the excited states of bacteriochlorophyll molecules present in the Fenna-Matthews-Olsen (FMO) complex of photosynthetic bacteria, and more importantly on the excitonic transference between them with the use of the singlet fission model.

These are great opportunities to establish collaborations and get new ideas for future work. Kudos to the organizers and administrative staff for keeping the academic life of our institute to high standards!


      

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