fchk file errors (Gaussian) Missing or bad Data: RBond
We’ve covered some common errors when dealing with formatted checkpoint files (*.fchk) generated from Gaussian, specially when analyzed with the associated GaussView program. (see here and here for previous posts on the matter.)
Prof. Neal Zondlo from the University of Delaware kindly shared this solution with us when the following message shows up:
CConnectionGFCHK::Parse_GFCHK() Missing or bad data: Rbond Line Number 1234
The Rbond label has to do with the connectivity displayed by the visualizer and can be overridden by close examination of the input file. In the example provided by Prof. Zondlo he found the following line in the connectivity matrix of the input file:
2 9 0.0
which indicates a zero bond order between atoms 2 and 9, possibly due to their proximity. He changed the line to simply
2
So editing the connectivity of your atoms in the input can help preventing the Rbond message.
I hope this helps someone else.
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)
Fernando Uribe (Interaction energy calculations for non-canonical nucleotides)
Juan Guzmán (Reaction mechanisms calculations for catalyzed organic reactions)
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.
#MemeYourThesis #MemeYourResearch
As we were hanging out recently, the idea came to us at the lab to create memes in order to summarize our work. We should be writing articles but hey, we needed the break, and so we shared them with each other in our last group meeting along with a good laugh. Here are some of the funniest ones.
A fail safe method for Comp. Chem.
Having doughnuts during our weekly meetings has proven a huge success in itself:
Finding transition states for organic chemical reactions can be a bit frustrating at times:
Good old photosynthesis sparked a few realizations too:
We’re dealing with docking calculations for a massive number of molecules. This has sparked a few inside jokes too:
A conversation about heterocyclic nomenclature that sparked this other post:
Try your own and share. Thanks for reading.
A New Graduate Student!
Last Friday we had a new graduate student when our very own Marco Antonio Diaz defended his BSc thesis on the in silico design of drug carriers based on calix[n]arenes. During his thesis he performed around 160 different calculations regarding the interaction energy of our host-guest inclusion complexes, both using the supramolecular method and the NBODel procedure available in NBO3.1 as provided with Gaussian 09. One of the main targets of this work was to assess both methods -with the proper BSSE corrections- in their capabilities for the calculation of interaction energies.
We found that the NBODel method consistently generates interaction energies that are similar to those of the SM method + the BSSE correction (as opposed to SM – BSSE which is the proper correction). Marco and I are still in the process of writing the article so maybe it will be published in early 2018. In this case we’re using calixarenes to deliver three drugs: warfarine, furosemide, phenylbutazone to compite with ocratoxin-A (OTA) for the binding site in Human Serum Albumin (HSA).
This project is undertaken in collaboration with my good friend Dr. Sándor Kunsági-Máté in Pécsi Tudomanyegyetem in Hungary.
Congratulations to Marco from all of us here at the lab!
The Evolution of Photosynthesis
Recently, the journal ACS Central Science asked me to write a viewpoint for their First Reactions section about a research article by Prof. Alán Aspuru-Guzik from Harvard University on the evolution of the Fenna-Matthews-Olson (FMO) complex. It was a very rewarding experience to write this piece since we are very close to having our own work on FMO published as well (stay tuned!). The FMO complex remains a great research opportunity for understanding photosynthesis and thus the origin of life itself.
In said article, Aspuru-Guzik’s team climbed their way up a computationally generated phylogenetic tree for the FMO from different green sulfur bacteria by creating small successive mutations on the protein at a time while also calculating their photochemical properties. The idea is pretty simple and brilliant: perform a series of “educated guesses” on the structure of FMO’s ancestors (there are no fossil records of FMO so this ‘educated guesses’ are the next best thing) and find at what point the photochemistry goes awry. In the end the question is which led the way? did the photochemistry led the way of the evolution of FMO or did the evolution of FMO led to improved photochemistry?
Since both the article and viewpoint are both published as open access by the ACS, I wont take too much space here re-writing the whole thing and will instead exhort you to read them both.
Thanks for doing so!
Chemistry Makes the Chemical
The compound shown below in figure 1 is listed by Aldrich as 4,5,6,7-tetrahydroindole, but is it really?
Fig 1. An indole?
To a hardcore organic chemist it is clear that this is not an indole but a pyrrole because the lack of aromaticity in the fused ring gives this molecule the same reactivity as 2,3-diethyl pyrrole. If you search the ChemSpider database for ‘tetrahydroindole’ the search returns the following compound with the identical chemical formula C8H11N but with a different hydrogenation pattern: 2,3,3a,4-Tetrahydro-1H-indole
Fig 2. Also listed as an indole
The real indole, upon an electrophilic attack, behaves as a free enamine yielding the product shown in figure 3 in which the substitution occurs in position 3. This compound cannot undergo an Aromatic Electrophilic Susbstitution since that would imply the formation of a sigma complex which would disrupt the aromaticity.
On the contrary, the corresponding pyrrole is substituted in position 2
These differences in reactivity towards electrophiles are easily rationalized when we plot their HOMO orbitals (calculated at the M062X/def2TZVP level of theory):
If we calculate the Fukui indexes at the same level of theory we get the highest value for susceptibility towards an electrophilic attack as follows: 0.20 for C(3) in indole and 0.25 for C(2) in pyrrole, consistent with the previous reaction schemes.
So, why is it listed as an indole? why would anyone search for it under that name? Nobody thinks about cyclohexane as 1,3,5-trihydrobenzene. According to my good friend and colleague Dr. Moisés Romero most names for heterocyles are kept even after such dramatic chemical changes due to historical and mnemonic reasons even when the reactivity is entirely different. This is only a nomenclature issue that we have inherited from the times of Hantzsch more than a century ago. We’ve become used to keeping the trivial (or should I say arbitrary) names and further use them as derivations but this could pose an epistemological problem if students cannot recognize which heterocycle presents which reactivity.
So, in a nutshell:
Chemistry makes the chemical and not the structure.
A thing we all know but sometimes is overlooked for the sake of simplicity.
Mexico City Earthquake
Mexico City took a hard earthquake just a couple of weeks after the southern part of the country had another and 32 years to the day after the big one back in 1985 (I was seven back then).
If you wanna help this is a great place to do so. The Topos (Moles) Brigade is an elite rescue team that is taking out people from the rubble not just during this disaster but anywhere in the world where they’re needed.
Thanks
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).
See you all in 2020!
Photosynthesis and Singlet Fission – #WATOC2017 PO1-296
If you work in the field of photovoltaics or polyacene photochemistry, then you are probably aware of the Singlet Fission (SF) phenomenon. SF can be broadly described as the process where an excited singlet state decays to a couple of degenerate coupled triplet states (via a multiexcitonic state) with roughly half the energy of the original singlet state, which in principle could be centered in two neighboring molecules; this generates two holes with a single photon, i.e. twice the current albeit at half the voltage (Fig 1).
Jablonski’s Diagram for SF
It could also be viewed as the inverse process to triplet-triplet annihilation. An important requirement for SF is that the two triplets to which the singlet decays must be coupled in a 1(TT) state, otherwise the process is spin-forbidden. Unfortunately (from a computational perspective) this also means that the 3(TT) and 5(TT) states are present and should be taken into account, and when it comes to chlorophyll derivatives the task quickly scales.
SF has been observed in polyacenes but so far the only photosynthetic pigments that have proven to exhibit SF are some carotene derivatives; so what about chlorophyll derivatives? For a -very- long time now, we have explored the possibility of finding a naturally-occurring, chlorophyll-based, photosynthetic system in which SF could be possible.
But first things first; The methodology: It was soon enough clear, from María Eugenia Sandoval’s MSc thesis, that TD-DFT wasn’t going to be enough to capture the whole description of the coupled states which give rise to SF. It was then that we started our collaboration with SF expert, Prof. David Casanova from the Basque Country University at Donostia, who suggested the use of Restricted Active Space – Spin Flip in order to account properly for the spin change during decay of the singlet excited state. A set of optimized bacteriochlorophyll-a molecules (BChl-a) were oriented ad-hoc so their Qy transition dipole moments were either parallel or perpendicular; the rate to which SF could be in principle present yielded that both molecules should be in a parallel Qy dipole moments configuration. When translated to a naturally-occurring system we sought in two systems: The Fenna-Matthews-Olson complex (FMO) containing 7 BChl-a molecules and a chlorosome from a mutant photosynthetic bacteria made up of 600 Bchl-d molecules (Fig 2). The FMO complex is a trimeric pigment-protein complex which lies between the antennae complex and the reaction center in green sulfur dependent photosynthetic bacteria such as P. aestuarii or C. tepidium, serving thus as a molecular wire in which is known that the excitonic transfer occurs with quantum coherence, i.e. virtually no energy loss which led us to believe SF could be an operating mechanism. So far it seems it is not present. However, for a crystallographic BChl-d dimer present in the chlorosome it could actually occur even when in competition with fluorescence.
FMO Complex. Trimer (left), monomer (center), pigments (right)
BChQRU chlorosome. 600 Bchl-d molecules
I will keep on blogging more -numerical and computational- details about these results and hopefully about its publication but for now I will wrap this post by giving credit where credit is due: This whole project has been tackled by our former lab member María Eugenia “Maru” Sandoval and Gustavo Mondragón. Finally, after much struggle, we are presenting our results at WATOC 2017 next week on Monday 28th at poster session 01 (PO1-296), so please stop by to say hi and comment on our work so we can improve it and bring it home!
A New Graduate Student – Medicinal #CompChem on HIV-1
Last Friday Durbis Castillo-Pazos became officially a graduated chemist. His presentation about the in silico development of entry inhibtors for the HIV-1 virus was very clear and straightforward and he performed admirably during the examination for which he graduated with Honors from the Mexico State Autonomous University (UAEMex).
Ever since he came to my lab, Durbis was adamant to work in some project related to medicinal chemistry which is not really my thing. Still, we were able to take an old project related to the in silico design of entry inhibitors for the protein GP120 which is responsible for the entry of the HIV-1 virus into human T-cells; the very first stage of the HIV infection which leads to AIDS. The lengths to which Durbis took the project were remarkable but none of that would have been possible without the leadership of my good friend and colleague Dr. Antonio Romo from the Queretaro Autonomous University (UAQ) who not only guided us through the nuances of the field but also on the intricacies of working with Schrödinger Inc.’s software, MAESTRO.
Suffice it to say that based on a piperazine core and four thousand fragments with commercial pharmaceutical applications, Durbis built a 16.3 million compounds library from which a few candidates are selected as potential drug molecules after several docking steps at various precision levels and molecular dynamics simulations plus QSAR related analysis. More about the details in future posts.
The knowledge gained by Durbis allowed him to become a member of the QSAR team led by Dr. Karina Martinez, at the Institute of Chemistry UNAM which provides QSAR studies to various companies who want to submit this kind of studies for regulatory purposes. Durbis has his sight abroad and has been admitted to a prestigious graduate program where he will keep seeking to improve his knowledge on medicinal chemistry. I’m sure he will succeed in anything on which he sets his mind.
