Blog Archives
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.
G. Merino et al. Degenerate carbocations account for automerization for bi-tri-cyclic C cmpds. #mechanisms #RMFQT15 #CompChem
— Joaquin Barroso (@joaquinbarroso) November 20, 2015
//platform.twitter.com/widgets.js
Calculating Redox potentials with DFT. Carlos Amador-UNAM wB97XD/sdd cc-pvtz. Best LOT for Born Haber cycle 4 Ferrocene #RMFQT15 #CompChem
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
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
Jacobs ladder showed up quite late this year at the #RMFQT15 check new PBE modifications by Crisostomo from @Cinvestav_IPN wait 4 the paper
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
Jacobs ladder showed up quite late this year at the #RMFQT15 check new PBE modifications by Crisostomo from @Cinvestav_IPN wait 4 the paper
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
non requested advice 2 young Comp.Chem.students:don’t waste skills on over studied systems. methods r the same 4 old&new reactions. #RMFQT15
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
Ramiro Quijano. Yucatán U. Study antraquinones. tautomerization of quinones. In Drug Design Tautomers matter #RMFQT15
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
Instituto Tecnológico de Tlanepantla. Pt=Sn for EtOH cracking. Why is Mulliken still a thing? #RMFQT15 #CompChem #CannotLiveTweet
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
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?
A very thorough investigation of CH4 water clatrates. Will be a great paper! Rubicelia Vargas & Jorge Garza from UAM #RMFQT15
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
Clatrates. Non-covalent interaction index. CH4 is weakly bound by water when forced inside the cage – Rubicelia Vargas #RMFQT15 #CompChem
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
If there is water and ice on Mars then most definitely should be clathrates. (Please excuse the misspelling throughout, though.)
Clatrates in Mars? Stochastic map of water around CH4 2.5m structures only a 303 cages – Rubicelia Vargas UAM #RMFQT15 #CompChem
— Joaquin Barroso (@joaquinbarroso) November 19, 2015
//platform.twitter.com/widgets.js
The rest are the previous announcements which were aimed to generate the momentum for the live tweeting thing.
Mexican Drs. [Alberto Vela, JL Gazquez, M. galvan, etc.] studied/worked with Prof. R. Parr. All 2B present at #RMFQT15 Guadalajara next week
— Joaquin Barroso (@joaquinbarroso) November 16, 2015
//platform.twitter.com/widgets.js
Next week: Mexican Meeting on Theoretical Physical Chemistry. Follow the #CompChem work in Mexico through #RMFQT15. Will live tweet
— Joaquin Barroso (@joaquinbarroso) November 16, 2015
//platform.twitter.com/widgets.js
“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.
Singlet Fission in the Fenna-Matthews-Olson Complex – A Talk
Last week at the congress of the Mexican Society of Chemistry I presented some of our results in the study of photosynthesis. Below I embeded the talk. Unfortunately for the wider audience of this blog, the talk is in Spanish (if anyone out there is willing to make subtitles for it I’ll hire you on the spot!)
The slides are also in Spanish although they should be easier to follow for non-Spanish speakers and they are uploaded in SlideShare at this link.
A big thank you to Maria Eugenia “Maru” Sandoval for all the hard work and time invested in this project!
Thanks for clicking!
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!
Physical Chemistry Meeting and CCIQS Symposium
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
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](https://joaquinbarroso.files.wordpress.com/2014/11/img_20141107_184857_856.jpg)
“Kike” Aguilar – Calix[n]arenes as drug carriers for Bosutinib and Sorafenib
The boys from the lab
reers and the advancement of our research group. Now back to work, guys!
WATOC 2014 – Virtual edition
I had a blast last week at WATOC2014 in Santiago de Chile! It was a wonderful opportunity to find old friends, meet new ones and listen to some exciting research done around the world, as well as some of the classics such as Pekka Pyykkö, who was awarded the Schrödinger medal. I decided to share my talk on SlideShare.com but also here because I found at WATOC that many many people seem to like this little space of mine! I was shocked, flattered but mostly happy to know that this little blog of mine is well regarded.
So, without further ado, here is my presentation at WATOC2014, please read the captions on each image for context. Feel free to make any comments, sharing or liking. Thanks for clicking!
Self explanatory 🙂
Administration of a drug follows one of these two extreme pharmacokinetic pathways. Either way, drugs accumulate in non-target tissues, are wasted and cause undesired secondary effects.
Ideally, a drug should arrive to the target tissue. Several polymolecular drug carriers have been developed.
In terms of monomolecular carriers, cyclodextrines have shown moderate success.
Calixarenes offer a more chemically-tunable alternative.
We decided to go with drugs for the treatment of chronic myeloid leukemia
.
Interaction energies were calculated with the NBODel approach, in which elements of the Fock Matrix common to two molecular fragments are deleted
This deletion yields a new Fock matrix which is re-diagonalized; the increase in energy is ascribed to the interaction between both fragments.
GTP was a small place to start (chemical space blocked due to animation lost in translation)
Interaction energies obtained
Hydrogen bonds and pi – pi interactions account for the large interaction energies
Detail of the interactions in some of the obtained geometries
MD simulations show the progress of the “release” process.
So we moved to a larger drug with more degrees of freedom (and a comercial one too)
Chemical space increased regard to the one used with GTP.
In both cases, two insertion modes were considered.
Some results…
100ns of MD show three kinds of structures (inserted, partially released and totally released)
PMF US – the profile of release tells us if the carrier is way too strong to be a carrier at all.
Where do we go from here?
Second generation CML drugs; however Bosutinib poses a funny challenge
A comercial error has released two isomers to the market, only one of them actually works. CAN WE GENERATE A RECOGNITION AGENT??
I know, some results need some attention, I know, trust me.
Also, Imatinib is cardiotoxic. We research now the competence between allegedly affected enzymes and the carriers to at least delay the toxic effect.
.
.
Thanks to all of these wonderful guys who made all publications possible (and also those who gave the money)
(The view from my office in Toluca, Mexico) ANY QUESTIONS? Write it in the comments section!
If you made it this far, let me tell you that this is also available at Slideshare.com 🙂
Thanks for reading, commenting and sharing!
WATOC 2014
I inexcusably forgot to write about my visit to WATOC2014 but as they say it’s better late than never. I’ve been here in Santiago de Chile for a day and a half now attending mostly to session 5 “applications to compelling problems”. WATOC (World Association of Theoretical and Computational Chemists) is probably the largest conference in our speciality and some of the big names are here which makes me very nervous to present my talk!
My talk will be very similar to the one presented in the last ACS meeting in San Francisco, in silico design of monomolecular drug delivery agents based on calix[n]arene macrocycles.
I wont try to report from WATOC, I’m not any good at that but will for sure be available if anyone wants to contact me.
Visit to ‘Universidad de la Cañada’ in Oaxaca, Mexico
A couple of weeks ago I was invited to give a talk to a small university in southern Mexico called ‘Universidad de la Cañada‘ in the state of Oaxaca, one of the most underprivileged states in our nation. This institution is a rather small one but the work they are doing over there with as little resources as they have is truly remarkable . UNCA offers degrees in pharmacy, pharmacology, food sciences, clinical chemistry and other topics that aim to supply the needed human resources for the various industries that are settled in the region. There is a true feeling of togetherness at UNCA since they have little pieces of equipment yet they are all fully shared among researchers regardless of who received the finance to acquire them. Last year, two of their students came for a two months stay, after which, Alberto and Eduardo got their names on a publication of our research group. It was nice to see them again and even nicer to learn they are about to finish their studies and that they will come back again to our lab in late July.
Every year at UNCA there is a Pharmacology Day on which the students show the results to their research projects during a poster session and listen to lectures by guest speakers from various universities around Mexico. Most of their projects were aimed to the isolation of natural products from local resources and their usage in several kinds of consumer products. UNCA is in a very small town, village I might say, surrounded by mountains and vegetation; the view was spectacular as you may see from the pictures below. Thank you very much to my good friend Dr. Carmen Hernández-Galindo for inviting me to participate and share our work with their students, I hope we may go back again and keep a fruitful exchange between our groups.
-
- UNCA
-
- Me, Eduardo, Alberto
-
- Some arachnids
-
- Dr. Carmen Hernández and I
-
- Grasshoppers. A delicacy in Oaxaca
During this talk, I took the opportunity to talk about the aforementioned paper in the context of molecular recognition and their in silico design but I think I should have talked more about the computational strategies that are most employed in the pharmaceutical industry. Never mind. I hope I get the opportunity to right this wrong. Still it was nice to give Alberto and Eduardo the opportunity to brag a little about being published authors.
Kudos to Rola Aburto, Dr. Margarita Bernabé, Dr. Rocío Rosas, and all the academic staff at UNCA for their invaluable dedication to teaching science against all odds, I can testify, through the hard work of their students, hat their effort is paying off.
Virtual Conference in Computational Chemistry VCCC-2014 (1st call)
So many things have happened since I last updated this blog but I will come to write on them when appropriate. Right now I’d like to share an invitation by Prof. Ponnadurai Ramasami from the University of Mauritius to the upcoming Virtual Conference on Computational Chemistry from the 1st to the 31st of August. Deadlines can be consulted here and the most important is the abstract submission on June 30th. This conference is part of the official celebrations of the International Year of Crystallography so talks involving experimental determination of electron densities will be well suited.
I participated in the latest edition and I must say it was a very enriching opportunity to learn from so many other researchers from across the world without leaving my desk. I already know what my talk will be about, now that we are so close to finish and submit a paper on the absence of reactivity for an anti-aromatic set of molecules. (I think I’ll call it “The reactivity of molecules that never existed [but that maybe should have.].) All talks are sent either as pdf, powerpoint presentations, youtube videos, etc. and Q&A are done over e-mail.
So this is a calling to other computational chemists out there who want to participate in this virtual conference. Kudos to Prof. Ponnadurai Ramasami and lets hope we can crystallize his visit to Mexico during 2014 the International Year of Crystallography (pun intended) and here’s to me going sometime to Mauritius!
Internal Symposium at CCIQS – 2014 edition
Once again as every year we celebrate our internal symposium here at CCIQS, and like every year, my students presented some of their progress with their research projects. This time, three students, from three different levels, present posters regarding some of the data they’ve obtained.
María Eugenia ‘Maru’ Sandoval presented a poster regarding the molecular dynamics simulations performed for the drug Imatinb and a family of calix- and thia-calix[n]arenes as published here and reported in this blog here. ‘Maru’ is now a first year grad student at the National University, UNAM, after spending a year working for a pharmaceutical company. Her research in the realm of photosynthesis has only begun recently, that is why we had to rely on some other data.
Luis Enrique Aguilar is researching cation-π interactions within the aromatic cavities of calix[n]arenes in order to find suitable leads among these, our favorite macrocyles, for designing extraction agents of heavy (toxic) metals. Luis Enrique is an undergrad student here at the State University who should finish this year and has shown some interest (threatened us) in writing his dissertation thesis in our research group.
Monserrat Enriquez is a PhD student at CINVESTAV under the joint supervision of Dr. Eddie López-Honorato and myself (Dr. Eddie is her principal advisor), her research project involves both theoretical calculations and synthesis of the leads for extraction agents for several Arsenic species. For the time being, Monserrat is here with us, far from her home on the north side of the country, for this semester in which we have to finish with the theoretical section of her work. Besides her research concerning calixarenes she is also running calculations on the interactions between graphene oxide and the aforementioned As species. We are very excited about working with such a complex yet simple material that has such an exciting electronic structure.
This symposium is always interesting and important in bringing our research projects closer to all the comunity of this center. And since symposium comes from the Greek meaning ‘drinking together‘, then lets raise our glasses and toast for the data to come!
Cheers!
