Category Archives: Computational Chemistry

Two more students graduated!

It is with great pleasure that I’d like to announce the thesis defense of Guillermo “Memo” Caballero and Howard Diaz who in past days became the second and third students, respectively, to get their B.S. degrees with theses completed at our lab. I want to publicly thank them for their hard work which hasn’t only contributed with a thesis to our library but will soon contribute with research papers to our count.

Guillermo “Memo” Caballero worked on the calculation of a reaction mechanism that cannot happen. He started as a synthetic chemist and when he hit a wall at the lab he thought computational chemistry might help him get on the right direction. He has proven now that the aromatization process of a substituted glutarimide into the corresponding pyridine can only proceed only if substituents with a very strong electron withdrawing effect are used. For two reaction mechanisms proposed, both of them intramolecular rearrangements and only one of them concerted, the calculated energy barriers to reach for the corresponding transition states (QST2 and QST3 methods used) are higher than a pyrolitic decomposition. Memo found also that the delocalization of the pi electron system and its extent goes a long way into the stabilization of the non-aromatic analogue. At first we wanted to treat this problem as a tautomeric equilibrium but since we cannot observe the aromatic tautomer there is no equilibrium and hence no tautomerism. We are still thinking how to name this correspondence between the two compounds when we submit the corresponding paper. It must be said that Guillermo graduated with the highest honors in a most deserved way.


Howard Diaz worked on the design of molecular blockers for the entrance process of the HIV-1 virus into lymphocytes through the GP120 protein. Six known blockers based on phenyl-indoyl-urea were assessed through docking, the binding site of the GP120 protein was described in terms of the interactions formed with each on these compounds and that served as the basis for what in the end came up to be a 36 compound library of blockers, whose structures were first optimized at the B3LYP/6-31G** level of theory. All the 42 blockers were docked in the binding site of the protein and a thorough conformational search was performed. From this set, lead compounds were selected in terms of their binding energies (first calculated heuristically) and further studied at the Density Functional Theory, B97D/cc-pVTZ in order to study the electronic structure of the blocker when interacting with a selection of residues at the binding site. Interaction energies calculated at the quantum level are consistent with the complex formation but since we had to cut the protein to only a few residues little correlation is found with the first calculation; this is fine and still publishable, I just wish we had a more seamless transition between heuristics and quantum chemical calculations. Wiberg indexes were very low, as consistent with a hydrophobic cavity, and delocalization energies calculated with second order perturbation theory analysis on the Natural Bond Orbitals revealed that the two most important interactions are C-H…π and Cl…π, these two were selected as key parameters in our design of new drugs for preventing the HIV-1 virus to bind lymphocytes-T; now we only need to have them synthesized and tested (anyone interested?).

Thank you guys for all your hard work, it has truly payed off. I’m completely certain that no matter what you do and where you go you will be very successful in your careers and I wish you nothing but the very best. This lab’s doors will always remain open for you.


Physical Chemistry Meeting and CCIQS Symposium

Materials Research Institute at Morelia Michoacan (southern Mexico)

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

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

“Kike” Aguilar – Calix[n]arenes as drug carriers for Bosutinib and Sorafenib

Thanks a lot for your efforts; they are paying good results to your ca

The boys from the lab

The boys from the lab

reers and the advancement of our research group. Now back to work, guys!


Atoms in Molecules (QTAIM) – Flash lesson

As far as population analysis methods goes, the Quantum Theory of Atoms in Molecules (QTAIM) a.k.a Atoms in Molecules (AIM) has become a popular option for defining atomic properties in molecular systems, however, its calculation is a bit tricky and maybe not as straightforward as Mulliken’s or NBO.

Personally I find AIM a philosophical question since, after the introduction of the molecule concept by Stanislao Cannizzaro in 1860 (although previously developed by Amadeo Avogadro who was dead at the time of the Karlsruhe congress), the questions of whether or not an atom retains its identity when bound to others? where does an atom end and the next begins? What are the connections between atoms in a molecule? are truly interesting and far deeper than we usually consider because it takes a big mental leap to think about how matter is organized to give rise to substances. Particularly I’m very interested with the concept of a Molecular Graph which in turn is concerned with the way we “draw lines” to form conceptual molecules. Perhaps in a different post we can go into the detail of the method, which is based in the Laplacian operator of the electron density, but today, I just want to collect the basic steps in getting the most basic AIM answers for any given molecule. Recently, my good friend Pezhman Zarabadi-Poor and I have used rather extensively the following procedure. We hope to have a couple of manuscripts published later on. Therefore, I’ve asked Pezhman to write a sort of guest post on how to run AIMALL, which is our selected program for the integration algorithm.

The first thing we need is a WFN or WFX file, which contains the wavefunction in a Fortran unformatted file on which the Laplacian integration is to be performed. This is achieved in Gaussian09 by incluiding the keyword output=wfn or output=wfx in the route section and adding a name for this file at the bottom line of the input file, e.g.


(NOTE: WFX is an eXtended version of  WFN; particularly necessary when using pseudopotentials or ECP’s)

Analyzing this file requires the use of a third party software such as AIMALL suite of programs, of which the standard version is free of charge upon registration to their website.

OpenAIMStudio (the accompanying graphical interface) and select the AIMQB program from the run menu as shown in figure 1.


Figure 1

Figure 1

Select your WFN/WFX file on which the calculation is to be run. (Figure 2)


Figure 2

Figure 2

You can control several options for the integration of the Laplacian of the electron density as well as other features. If your molecules are simple enough, you may go through with a successful and meaningful calculation using the default settings. After the calculation is finished, several result files are obtained. We’ll work in this tutorial only with *.mpgviz (which contains information about the molecular graph, MG) and *.sum (which contains all of  needed numerical data).

Visualization of the MG yields different kinds of critical points, such as: 1) Nuclear Attractor Critical Points (NACP); 2) Bond Critical Points (BCP); 3) Ring CP’s (RCP); and 4) Cage CP’s (CCP).

Of the above, BCP are the ones that indicate the presence of a chemical bond between two atoms, although this conclusion is not without controversy as pointed out by Foroutan-Njead in his paper: C. Foroutan-Nejad, S. Shahbazian and R. Marek, Chemistry – A European Journal, 2014, 20, 10140-10152. However, at a first approximation, BCP’s can help us to explore chemical interactions.

Now, let’s go back to visualizing those MGs (in our examples we’ve used methane and ethylene and acetylene). We open the corresponding *.mpgviz file in AIMStudio and export the image from the file menu and using the save as picture option (figure 3).

Figure 3

Figure 3

The labeled atoms are NACP’s while the green dots correspond to BCP’s. Multiplicity of a bond cannot be discerned within the MG; in order to find out whether a bond is a single, double or triple bond we have to look into the *.sum file, in which we’ll take a look at the bond orders between pairs of atoms in the section labeled “Diatomic Electron Pair Contributions and Delocalization Data” (Figure 4).

Figure 4

Figure 4

Delocalization indexes, DI’s, show the approximate number of electrons shared between two atoms. From the above examples we get the following DI(C,C) values: 1.93 for C2H4 and 2.87 for C2H2; on the other hand, DI(C,H) values are  0.98 for CH4, 0.97 in C2H4 and 0.96 in C2H2. These are our usual bond orders.

This is the first part of a crash tutorial on AIM, in my opinion this is the very basics anyone needs to get started with this interesting and widespread method. Thanks to all who asked about QTAIM, now you have your long answer.

Thanks a lot to my good friend Dr Pezhman Zarabadi-Poor for providing this contribution to the blog, we hope you all find it helpful. Please share and comment.

New paper in JACS

Well, I only contributed with the theoretical section by doing electronic structure calculations, so it isn’t really a paper we can ascribe to this particular lab, however it is really nice to see my name in JACS along such a prominent researcher as Prof. Chad Mirkin from Northwestern University, in a work closely related to my area of research interest as macrocyclic recognition agents.

In this manuscript, a calix[4]arene is allosterically opened and closed reversibly by coordinating different kinds of ligands to a platinum center linked to the macrocycle. (This approach has been referred to as the weak link approach.) I recently visited Northwestern and had a great time with José Mendez-Arroyo, the first author, who showed me around and opened the possibility for further work between our research groups.

(Ligands: Green = Chloride; Blue = Cyanide)

Closed, semi-open and fully open conformations; selectivity is modulated through cavity size. (Ligands: Green = Chloride; Blue = Cyanide)

Here at UNAM we calculated the interaction energies for the two guests that were successfully inserted into the cavity: N-methyl-pyridinium (Eint = 57.4 kcal/mol) and Pyridine-N-oxide (Eint = +200.0 kcal/mol). Below you can see the electrostatic potential mapped onto the electron density isosurface for one of the adducts. Relative orientation of the hosts within the cavity follows the expected (anti-) alignment of mutual dipole moments. At this level of theory, we could easily be inclined to assert that the most stable interaction is indeed the one from the semi-open compound and that this in turn is due to the fact that host and guest are packed closer together but there is also an orbital issue: Pyridine Oxide is a better electron acceptor than N-Me-pyridinium and when we take a closer look to the (Natural Bonding) orbitals interacting it becomes evident that a closer location does not necessarily yields a stronger interaction when the electron accepting power of the ligand is weaker (which is, in my opinion, both logic and at the same time a bit counterintuitive, yet fascinating, nonetheless).

Electrostatic potential mapped onto the electron density surface of one of the aducts under study

Electrostatic potential mapped onto the electron density surface of one of the adducts under study

All calculations were performed at the B97D/LANL2DZ level of theory with the use of Gaussian09 and NBO3.1 as provided within the former. Computing time at UNAM’s supercomputer known as ‘Miztli‘ is fully acknowledged.

The full citation follows:

A Multi-State, Allosterically-Regulated Molecular Receptor With Switchable Selectivity
Jose Mendez-Arroyo Joaquín Barroso-Flores §,Alejo M. Lifschitz Amy A. Sarjeant Charlotte L. Stern , and Chad A. Mirkin *

J. Am. Chem. Soc., Article ASAP
DOI: 10.1021/ja503506a
Publication Date (Web): July 9, 2014

 Thanks to José Mendez-Arroyo for contacting me and giving me the opportunity to collaborate with his research; I’m sure this is the first of many joint projects that will mutually benefit our groups. 


Some .fchk files wont open in GaussView5.0 (Update)

A couple of weeks ago I posted a solution for a common error regarding .fchk files that will display the error below when opened with GaussView5.0. As I expected, this error has to do with the use of diffuse functions in the basis set and is related to a change of format between Gaussian versions.

Missing or bad data: Alpha Orbital Energies
Line Number 1234

Although the method described in the previous post works just fine, the following update is a better approach. Due to a change of spelling between G03 and G09 (which has been corrected for G09 but not available for GV versions prior to 5.0.9) one must change “independent” for “independant

To make the change directly from the terminal the following command is needed:

sed -i 's/independent/independant/g' file.fchk

Alternatively you can redirect the output to a new file

sed -e 's/independent/independant/g' file.fchk > newfile.fchk

if you want to keep the old version and work with a new one.

Of course this edition can be performed manually with any text editor available (for example if you work in Windows) but solutions from the terminal always seem easier and a lot more fun to me.

Thanks to Dr. Fernando Cortés for sharing his insight into this issue.

If a .fchk file wont open in GaussView5.0

I’ve found the following error regarding the opening of .fchk files in GaussView5.0.

Missing or bad data: Alpha Orbital Energies
Line Number 1234

The error is prevented to a first approximation (i.e. it at least will allow GV to open and visualize the file but other issues may arise) by opening the file and modifying the number of basis functions to equal the number of independent functions (which is lower)

FOpt RM062X 6-311++G(d,p) 
Number of atoms I 75
Info1-9 I N= 9
 163 163 0 0 0 110
 2 18 -502
Charge I 0
Multiplicity I 1
Number of electrons I 314
Number of alpha electrons I 157
Number of beta electrons I 157
Number of basis functions I 1199
Number of independent functions I 1199
Number of point charges in /Mol/ I 0
Number of translation vectors I 0
Atomic numbers I N= 75
... ...
... ...

Once both numbers match you can open the file normally and work with it. My guess is this will continue to happen with highly polarized basis sets but I need to run some tests.

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!

New paper in Computational and Theoretical Chemistry

I always get very happy to have a new paper out there! I find it exciting but most of all liberating since it makes you feel like your work is going somewhere but most of all that it is making its way ‘out there'; there is a strong feeling of validation, I guess.

Two very different families of calix[n]arenes (Fig 1) were tested as drug carriers for a very small molecule with a huge potential as a chemotherapeutic agent against Leukemia, namely, 3-phenyl-1H-[1]benzofuro[3,2-c]pyrazole a.k.a. GTP which has proven to be an effective in vitro Tyrosine Kinase III inhibitor. Having such a low molecular weight it is expected to have a very high excretion rate therefore the use of a carrier could increase its retention time and hence its activity. This time we considered n = 4, 5, 6 and 8 for the size of the cavities and R = -SO3H and -OEt as functional groups on the upper rim as to evaluate only a polar coordinating group and a non-polar non-coordinating one since GTP offers two H-bond acceptor sites and one H-bond donor one along the π electron density that could form π – π stacking interactions between the aromatic groups on GTP and the walls of the calixarene.

Fig 1. Calixarenes under study and their complexes with GTP

Fig 1. Calixarenes under study and their complexes with GTP

Once again calculations were carried out at the B97D/6-31G(d,p) level of theory along with molecular dynamics simulations for over 100 ns of production runs. NBO Deletion interaction energies were computed in order to discern which hosts formed the most stable complexes.

NBO Del interaction energies B97D/6-31G(d,p)

NBO Del interaction energies B97D/6-31G(d,p)

You may find a link to the ScienceDirect website for downloading the paper from this link. Last, but certainly not least, I’d like to thank all coauthors for their contributions and patience in getting this study published: Dr. Rodrigo Galindo-Murillo; Alberto Olmedo-Romero; Eduardo Cruz-Flores; Dr. Petronela M. Petrar and Prof. Dr. Kunsági-Máté Sándor. Thanks a lot for everything!


Donor and acceptor H-bond sites increases the probability of keeping the drug in place for a higher retention rate

Donor and acceptor H-bond sites increases the probability of keeping the drug in place for a higher retention rate

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!




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