10 Years of Blogging!
This week marks the 10th anniversary of this little blog! It’s crazy to think a pet project that I took on during my last year as a postdoc is still going on after a decade of recording the work of our group in computational chemistry and it is also a happy coincidence that this year is the centennial anniversary of IUPAC and the sesquicentennial anniversary of the Periodic Table, for which 2019 has been designated as the International Year of the Periodic Table. I will release various posts celebrating this first decade of blogging and some regarding the IYPT2019 as soon as possible, also some major changes in layout and look are coming. It has been suggested to me that setting a patreon.com account could help me raise some funding for assisting underprivileged students but I’m not so sure yet.
By 2009 the chemistry blogosphere was already in full swing, so I got to it a bit late. (Is commenting ‘First!‘ still a thing?) At the time my job future seemed a bit uncertain, I had already spent two years as a postdoc in Romania and prior to that I worked for a private company in their research center here in Mexico so I started to ramble here so in upcoming job interviews I could point to a resource which gathered my thoughts and some achievements in a more informal fashion than a CV or a resume. (Plus, I like writing about things other than chemistry just for myself, maybe someday I’ll start a blog with some fiction writings I have here and there.) Quite frankly I didn’t think I could go back into academia so I was mainly looking for jobs in the R&D departments of various chemical companies, particularly in the field of coatings which was the one I already had some experience.
I never imagined this little blog would gain any attention, I think I had something like 2,000 views on the first year, now it’s up to 1,500 views a week! One of the first posts that gained popularity quite quickly dealt with the calculation of SCRF calculations and some parameters we were struggling to get right. Once I found the best parameters for running them, my boss, the late Prof. Dr. Ioan Silaghi-Dumitrescu at Babes-Bolyai University, asked me to email them to the group and post them physically in the lab so we wouldn’t loose them; I thought it would be a better idea to have them on the blog so we all could access them easily and at the same time share our findings with whomever had the same issues. Turned out that many people struggled with these parameters for SCRF calculations in Gaussian and from that moment on that became one of the underlying principles of the blog: “any problem we face in the lab is definitely faced by someone else, so lets share our solution”; the other principle of course was my blatant self promotion.
One of the most rewarding aspects of having kept this blog going on for so long is knowing that it is a modest resource that some people has found helpful. Attending conferences and having people telling me they like my posts and have found help in them is extremely gratifying. Also, academically it has allowed me to meet wonderful people with whom I’ve established very interesting collaborations in various countries like Iran, US, Slovakia, Czech Republic, Chile, Bulgaria and many more.
Very early I started getting direct questions to specific problems and to the best of my abilities I’ve tried to answer them although I not always have the time to do so and for that I apologize to all the readers who didn’t get an answer; up until now keeping this blog has been a spare-time endeavor which not always gets the priority it deserves withing my academic tasks.
Thank you for reading, commenting and sharing these posts during this past decade! I truly appreciate it and it has been very important to me; I sometimes feel the posts go into the void but every now and then I’m approached by readers who have found the blog helpful and that is very rewarding. Here’s to ten more years!
Using PDB files for Electronic Structure Calculations
Quick Post on preparing Gaussian input files from PDB files.
If you’re modeling biological systems chances are that, more often than not, you start by retrieving a PDB file. The Protein Data Bank is a repository for all things biochemistry – from oligo-peptides to full DNA sequences with over 140,000 available files encoding the corresponding structure obtained by various experimental means ranging from X-Ray diffraction, NMR and more recently, Cryo Electron Microscopy (CEM).
The PDB file encodes the Cartesian coordinates for each atom present in the structure as well as their in the same way molecular dynamics codes -like AMBER or GROMACS- code the parameters for a force field; this makes the PDB a natural input file for MD.
There are however some considerations to have in mind for when you need to use these coordinates in electronic structure calculations. Personally I give it a pass with OpenBabel to add (or possibly just re-add) all Hydrogen atoms with the following instruction:
$>obabel -ipdb filename.pdb -ogjf -Ofilename.gjf -h
Alternatively, you can select a pH value, say 7.5 with:
$>obabel -ipdb filename.pdb -ogjf -Ofilename.gjf -h -p7.5
You may also use the GUI if by any chance you’re working in Windows:
This sends all H atoms to the end of the atoms list. Usually for us the next step is to optimize their positions with a partial optimization at a low level of theory for which you need to use the ReadOptimize ReadOpt or RdOpt in the route section and then add the atom list at the end of the input file:
Atomic coordinates
--blank line--
noatoms atoms=H
--blank line--
Finally, visual inspection of your input structure is always helpful to find any meaningful errors, remember that PDB files come from experimental measurements which are not free of problems.
As usual thanks for reading, commenting, and sharing.
Gustavo “Gus” Mondragón M.Sc. – Thesis Defense
We celebrate the successful thesis defense of Gustavo “Gus” Mondragón who has now completed his Masters degree and is now on to getting a PhD in our group. Gustavo has worked on the search for multiexcitonic states and their involvement in the excitonic transference between photosynthetic pigments, specifically between bacteriochlorophyll-d molecules (BChl-d) from the bchQRU chlorosome whose whole structure is shown in the gallery below. To this end, Gustavo has studied and implemented the Restricted Active Space method with double spin flip (RAS-2SF) with the use of QChem5.0, a method that has required the use and understanding of states with high multiplicities. Additionally, Gustavo has investigated the influence of the environment within the chlorosome by performing ONIOM calculations for the spectroscopic properties of a BChl-d dimer, finding albeit qualitatively a batochromic effect, probably an expected result but nonetheless an impressive feat for the level of theory selected.
BChQRU chlorosome. 600 Bchl-d molecules 
There’s still a lot of work to do in this line of research and although we’re eager to publish our results in this excitonic transference mechanism we want to be completely sure that we’re taking every possibility into consideration so we don’t incur into any inconsistencies.
Gustavo cultivates many research interests from excited states of these pigments to biochemical processes that require the use of various tools; I’m sure his permanence in our lab will bring lots of interesting results. Congratulations, Gus! Thank you for your hard work.
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.
- 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)
- 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.
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.
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!
XVII Mexican Meeting on Theoretical Physical Chemistry
The RMFQT meeting is a long standing tradition within the Mexican Comp.Chem. community; a tradition that is now transcending our borders as more and more foreign students and researchers take part of this party, for it is a festive occasion indeed. This was the first time the RMFQT was held at a private institute, The Monterrey Institute of Technology.
As in previous years, our lab contributed with a four posters and one talk by yours truly. The posters presented by Raul Torres, Raúl Márquez, Gustavo Mondragón and Dr. Jacinto Sandoval whose pictures you can spot below in the gallery.
My talk was on the collaborative nature of Comp.Chem. and our particular interactions with the organic synthesis lab of Dr. Moisés Romero. The published papers discussed in the talk can be found in Tetrahedron (post), PCCP (post), and some unpublished results that can be read as a preprint in preprints.org.
I had the pleasure to meet and interact with old friends and make new ones like Dr. Julio Palma from Penn State, whose work on molecular rectifiers is very interesting. Also, I got to interact with many wonderful students who apparently are aware of the existence of this blog. (A big shoutout to M. Joaquina Beltrán and Plinio Cantero, from Chile whose work on DNA mismatch sensors is quite interesting, I look forward to further interacting with their team of research.)
A particular reason for this meeting to be special for me is the fact that I have been now announced as part of the local organizing committee for the next edition in 2019 in Toluca. I was also asked to develop a centralized website and coordinate the social media communication related to the this and other events, starting with the creation of the official Twitter account for our network and the meeting. I’m working on a few ideas, but if you have any suggestions please send them in the comments section.
See you next year in Toluca!
Calculation of Intermolecular Interactions for Sensors with Biological Applications
Two new papers on the development of chemosensors for different applications were recently published and we had the opportunity to participate in both with the calculation of electronic interactions.
A chemosensor requires to have a measurable response and calculating either that response from first principles based on the electronic structure, or calculating another physicochemical property related to the response are useful strategies in their molecular design. Additionally, electronic structure calculations helps us unveil the molecular mechanisms underlying their response and efficiency, as well as providing a starting point for their continuous improvement.
In the first paper, CdTe Quantum Dots (QD’s) are used to visualize in real time cell-membrane damages through a Gd Schiff base sensitizer (GdQDs). This probe interacts preferentially with a specific sequence motif of NHE-RF2 scaffold protein which is exposed during cell damage. This interactions yields intensely fluorescent droplets which can be visualized in real time with standard instrumentation. Calculations at the level of theory M06-2X/LANL2DZ plus an external double zeta quality basis set on Gd, were employed to characterize the electronic structure of the Gd³⁺ complex, the Quantum Dot and their mutual interactions. The first challenge was to come up with the right multiplicity for Gd³⁺ (an f⁷ ion) for which we had no experimental evidence of their magnetic properties. From searching the literature and talking to my good friend, inorganic chemist Dr. Vojtech Jancik it was more or less clear the multiplicity had to be an octuplet (all seven electrons unpaired).
As can be seen in figure 1a the Gd-N interactions are mostly electrostatic in nature, a fact that is also reflected in the Wiberg bond indexes calculated as 0.16, 0.17 and 0.21 (a single bond would yield a WBI value closer to 1.0).
PM6 optimizations were employed in optimizing the GdQD as a whole (figure 1f) and the MM-UFF to characterize their union to a peptide sequence (figure 2) from which we observed somewhat unsurprisingly that Gd³⁺interacts preferently with the electron rich residues.
This research was published in ACS Applied Materials and Interfaces. Thanks to Prof. Vojtech Adam from the Mendel University in Brno, Czech Republic for inviting me to collaborate with their interdisciplinary team.
The second sensor I want to write about today is a more closer to home collaboration with Dr. Alejandro Dorazco who developed a fluorescent porphyrin system that becomes chiefly quenched in the presence of Iodide but not with any other halide. This allows for a fast detection of iodide anions, related to some gland diseases, in aqueous samples such as urine. This probe was also granted a patent which technically lists yours-truly as an inventor, cool!
The calculated interaction energy was huge between I⁻ and the porphyrine, which supports the idea of a ionic interaction through which charge transfer interactions quenches the fluorescence of the probe. Figure 3 above shows how the HOMO largely resides on the iodide whereas the LUMO is located on the pi electron system of the porphyrine.
This research was published in Sensors and Actuators B – Chemical.
Redox Allosteric Control – New communication in JACS
The Weak Link Approach (WLA) is a successful strategy for allosterically controlling the formation of cavities¹ and the access to them² through the action of reversible hemilabile-bond formation around an organometallic center. Thus far, the WLA has been used to mimic biological cavities whose access is controlled chemically as in the scheme shown below which belongs to a previous WLA work published in 2014, my first time involved in the calculation of bond energies for hemilabile groups.
Mendez-Arroyo et al. JACS (2014) 136, 10340-10348
Chiefly developed by the Chad Mirkin group at Northwestern, the WLA has now reached a new milestone in which the allosteric control is further coupled to a redox equilibrium which alters the strength of the hemilabile bonds. These findings are reported in JACS as a communication (DOI: 10.1021/jacs.8b09321). Previous efforts were unsuccessful due to the instability of the oxidized species, which makes regulation challenging. A ferrocenyl (Fc) group was attached to the hemilabile ligand to provide the redox center which can further assist and control the ring opening via an increment in the electrostatic repulsion of the two metallic centers. Thus, the weak-link is displaced by exogenous ligands only after the Fc group was oxidized.
Bond strengths for the hemilabile bonds were calculated at the ω-B97XD/lanl2dz level of theory upon optimized structures. Relative energies were calculated through the thermochemistry analysis (freq=noraman) made by Gaussian09 and the bond strengths were calculated with the NBODel procedure included in NBO3.1. In the open configurations we found that upon oxidation of Fc the exogenous ligand bond to Pt(II) strengthens by a few kcal/mol (2 – 10), however the Fe(III)-P distance increases and that can be observed via ³¹P NMR spectroscopy.
For the non-oxidized complexes, the HOMO’s are largely composed of the ferrocene highest energy orbitals, which is susceptible of being oxidized, whereas the LUMO’s are located throughout the organometallic fragment. When Ferrocene is oxidized to Ferrocenium, the situation is reversed and now HOMO’s are found spread over the organometallic fragment and the LUMO’s over ferrocenium; all of which is coherent with the idea of Fc now being able to be reduced. Plots for the HOMO LUMO orbitals for compound (6) in the Reduced (Fe2) and Oxidized (Fe3) states are shown (alpha and beta density are shown separately in the latter case).
-
- (6) Reduced HOMO
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- (6) Reduced LUMO
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- (6) Oxidized HOMO
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- (6) Oxidized LUMO alpha
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- (6) Oxidized LUMO beta
Thanks to Prof. Chad Mirkin, Dr. Andrea d’Aquino, and Edmund Cheng for letting me be a part of this project.
[1] D’Aquino, A. I., Cheng, H. F., Barroso-Flores, J., Kean, Z. S., Mendez-Arroyo, J., McGuirk, C. M., & Mirkin, C. A. (2018). An Allosterically Regulated, Four-State Macrocycle. Inorganic Chemistry, 57(7), 3568–3578.
[2] Mendez-Arroyo, J., Barroso-Flores, J., Lifschitz, A. M., Sarjeant, A. a., Stern, C. L., & Mirkin, C. a. (2014). A multi-state, allosterically-regulated molecular receptor with switchable selectivity. Journal of the American Chemical Society, 136(29), 10340–10348.
To Chem, or not “Too Chem”? That is the #ChemNobel Question
To chem or not -quite- too chem, that is the ChemNobel question:
Whether ’tis Nobeler in the mind to suffer
The curly arrows of organic fortune
Or to take rays against a sea of crystals
And by diffracting end them.Me (With sincere apologies to WS)
Every year, in late September -like most chemists- I try to guess who will become the next Nobel Laureate in Chemistry. Also, every year, in early October -like most chemists- I participate in the awkward and pointless discussion of whether the prize was actually awarded to chemistry or not. Indeed, the Nobel prize for chemistry commonly stirs a conversation of whether the accomplishments being recognized lie within the realm of chemistry or biology whenever biochemistry shows its head, however shyly; but the task of dividing chemistry into sub-disciplines raises an even deeper question about the current validity of dividing science into broad branches in the first place and then further into narrower sub-disciplines.
I made a very lazy histogram of all the 178 Laureates since 1904 to 2017 based on subjective and personal categories (figure 1), and the creation of those categories was in itself an exercise in science contemplation. My criteria for some of the tough ones was the following: For instance, if it dealt with phenomena of atomic or sub-molecular properties (Rutherford 1908, Hahn 1944, Zewail 1999) then I placed it in the Chemical Physics category but if it dealt with an ensemble of molecules (Arrhenius 1903, Langmuir 1932, Molina 1995) then Physical Chemistry was chosen. Some achievements were about generating an analysis technique which then became essential to the development of chemistry or any of its branches but not for a chemical process per se, those I placed into the Analytical Chemistry box, like last year’s 2017 prize for electron cryo-microscopy (Dubochet, Frank, Henerson) or like 1923 prize to Fritz Pregl for “the invention of the method of microanalysis of organic substances” for which the then head of the Swedish Academy of Sciences, O. Hammarsten, pointed out that the prize was awarded not for a discovery but for modifying existing methods (which sounds a lot like a chemistry disclaimer to me). One of the things I learnt from this exercise is that subdividing chemistry became harder as the time moved forward which is a natural consequence of a more complex multi- and interdisciplinary environment that impacts more than one field. Take for instance the 2014 (Super Resolved Fluorescence Microscopy) and 2017 (Cryo-Electron Microscopy) prizes; out of the six laureates, only William Moerner has a chemistry related background a fact that was probably spotted by Milhouse Van Houten (vide infra).
Figure 1 – Clik here for full scale version
Some of the ones that gave me the harder time: 1980, Gilbert and Sanger are doing structural chemistry by means of developing analytical techniques but their work on sequencing is highly influential in biochemistry that they went to the latter box; The same problem arose with Klug (1982) and the Mullis-Smith duo (1993). In 1987, the Nobel citation for Supramolecular Chemistry (Lehn-Cram-Pedersen) reads “for their development and use of molecules with structure-specific interactions of high selectivity.”, but I asked myself, are these non-covalent-bond-forming reactions still considered chemical reactions? I want to say yes, so placed the Lehn-Cram-Pedersen trio in the Synthesis category. For the 1975 prize I was split so I split the prizes and thus Prelog (stereochemistry of molecules) went into the Synthesis category (although I was thinking in terms of organic chemistry synthesis) and Cornforth (stereochemical control of enzymatic reactions) went into biochem. So, long story short, chemistry’s impact in biology has always had a preponderant position for the selection of the Nobel Prize in Chemistry, although if we fuse the Synthesis and Inorganic Chemistry columns we get a fairly even number of synthesis v biochemistry prizes.
Hard as it may be to fit a Laureate into a category, trying to predict the winners and even bet on it adds a lot of fun to the science being recognized. Hey! even The Simpsons did it with a pretty good record as shown below. Just last week, there was a very interesting and amusing ACS Webinar where the panelist shared their insights on the nomination and selection process inside the Swedish Academy; some of their picks were: Christopher Walsh (antibiotics); Karl Deisseroth (optogenetics); Horwich and Hartl (chaperon proteins); Robert Bergman (C-H activation); and John Goodenough (Li-ion batteries). Arguably, the first three of those five could fit the biochem profile. From those picks the feel-good prize and my personal favorite is John Goodenough not only because Li-ion batteries have shaped the modern world but because Prof. Goodenough is 96 years old and still very actively working in his lab at UT-Austin (Texas, US) #WeAreAllGoodEnough. Another personal favorite of mine is Omar Yaghi not only for the development of Metal-Organic-Frameworks (MOFs) but for a personal interaction we had twenty years ago that maybe one day I’ll recount here but for now I’ll just state the obvious: MOFs have shown a great potential for applications in various fields of chemistry and engineering but perhaps they should first become highly commercial for Yaghi to get the Nobel Prize.
W.E. Moerner and B.L. Feringa are now Nobel Laureates. Zare and Moerner have worked in spectroscopy whereas Feringa and Sonogashira are deep into synthesis
Some curiosities and useless trivia: Fred Sanger is the only person to have been awarded the Nobel Prize in Chemistry twice. Marie Curie is the only person to have been awarded two Nobel Prizes in different scientific categories (Physics and Chemistry) and Linus Pauling was awarded two distinct Nobel Prizes (Chemistry and Peace). Hence, three out of the four persons ever to have been awarded two Nobel Prizes did it at least once in chemistry – the fourth is John Bardeen two times recipient of the Nobel Prize in Physics.
Of course the first thing I’ll do next Wednesday right after waking up is checking who got the Nobel Prize in Chemistry 2018 and most likely the second thing will be going to my Twitter feed and react to it, hopefully the third will be to blog about it.
The announcement is only two days away, who is your favorite?
#WeAreAllGoodEnough
