Simulation of Raman Spectroscopy and crystal cell effects – Selenium Carboxylate Eur. J. Inorg. Chem.
Computing spectroscopic features of molecules is always an interesting challenge, specially when intermolecular contacts are into play. Take vibrational spectroscopy for instance, all the non-covalent interactions present in a solid will have an important effect on the the calculated frequencies and their intensities. However calculating the spectroscopical properties of a solid quickly becomes a daunting task.
My colleague and friend Dr. Vojtech Jancik asked me to calculate the Raman frequencies for a new compound: Selenoyl bis-carboxylate, which according to him was very hard to obtain due to the very nature of selenium. So we performed various calculations on the isolated molecule to reproduce the measured Raman spectrum but we soon realized that a calculation on the crystal cell was needed if we wanted to get a more thorough picture of the experiment.
The level of theory used was PBEPBE/LANL2DZ. Optimization of the title structure pointed to a low coordination capacity by carboxylate groups as evidenced by the longer Se -O-C=O distances and reduced Wiberg bond indexes. A blue shift was observed for all bands and so we calculated the Raman frequencies at the crystal structure which gave us a better correspondence between spectra. Finally we computed the Raman spectra for the full unit cell comprised of four molecules with which an excellent agreement was obtained (a scaling factor of 0.8 was used).
Unfortunately we failed to further extend this calculation to a larger system with four unit cells and 32 molecules apparently due to insufficient memory; the calculation just stalled and stopped without error after consuming its time in the queue. I’ll try to take a look into it some day.
You can read the whole story in: Synthesis and Crystal Structure of the First Selenonyl Bis(carboxylate) SeO2(O2CCH3)2
Lukas Richtera · Vojtech Jancik · Joaquín Barroso‐Flores · Petr Nykel · Jiri Touzin · Jan Taraba
Thanks for reading!
Last Monday the School of Chemistry at the National Autonomous University of Mexico celebrated 50 years of their modern graduate studies program; as part of the celebrations a formal investiture ceremony for those of us who got our PhD’s after 1990 was organized.
It was a great opportunity to reconect with old friends and teachers, I even got to meet my old high school chemistry teacher, Dr. Salvador Sánchez who in no little way helped me decide to follow chemistry as a career choice, and Dr. Raymundo Cea who was my first thesis director in the first years of this century. The University Rector, Dr. José Narro, gave a speech on the challenges of chemistry in the upcoming years, and Dr. Helgi Jung-Cook spoke about the challenges a PhD student faces and how much rewarding is to finish. Much is yet to be done for the advancement of science in the world and even more in Latin America, but even so UNAM is doing a great effort of keeping a strong base of scientists available for all branches of social development by continuosly supplying the much needed human resources with the highest standards.
In all it was an emotional and inspiring ceremony but above all a fun way to look back to those days in grad school when little happened outside our labs. Thanks to my parents, my sister and my lovely wife and unborn daughter for joining us all in this celebration of Mexican chemistry. (all photo credits: My Dad.)
It is with great pleasure that I announce the graduation of another member of our research group: Luis Enrique “Kike” Aguilar defended his BSc thesis yesterday and is now counting the days left for the Autumn when he’ll move to the Netherlands for a masters in computational chemistry.
Luis Enrique, Kike, calculated the interaction energies of 144 different inclusion complexes where calix and thia-calix[n]arenes were once again the chosen hosts (36 of them) and two drugs for the treatment of chronic myeloid leukemia (CML), namely Sorafenib and Bosutinib, were the guests.
The publication of the corresponding article in which we once again were fortunate enough to count with the collaboration of Dr. Rodrigo Galindo from Utah University in the molecular dynamics section, is still pending but we’re confident enough that it wont take much longer until it’s out there.
Kike is a very diligent student with great learning skills, I’m sure he’ll succeed in any enterprise he sets himself off. Congratulations, Kike! Thanks for being a part of our research but more importantly for being a part of our community.
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!
Editing large molecules on a seemingly simple visualizer as GaussView can be a bit daunting. I’m working on a follow up of that project we recently published in JACS but now we require to attach two macrocycles to the organometallic moiety; the only caveat is that this time we don’t have any crystallographic data with which to start. Generating a 3D model of this structure is already hard enough and even when you managed to do it there are many degrees of freedom that in some cases can lead to unrealistic geometries after optimization.
I recently came across a simple way to edit a large complicated molecule by optimizing the fragments separately and then joining them in a new molecule by using the clipboard. This rather simple method, that I for one had never exploited has just saved me a few good hours.
Copy a molecule (CTRL+C) and it will go to the clipboard as a molecular fragment for which you can define a new hot atom and thus bind it to the other fragment as you would with the regular builder. I strongly suggest to use a “New Molecule Group” instead of editing over an existing molecule. Also, if you are using the “paste” button, observe that it has three different options; you may want to use the last one “append to existing molecule” or you will have your fragments in different windows.
And remember, dihedral angles are your best friends.
Well, the title of this post is pretty self-explanatory as well as unrelated to computational chemistry. Yesterday here at CCIQS we received new equipment for supplying liquid nitrogen to our laboratories, especially to the NMR machines which consume it a lot, and also for the X-ray diffractometers which require cooling of crystals. This new compressor replaces the old one which has long overseen its useful life. So, anyway, I thought it would be a nice change for a post because I like bragging (or should I say ‘marketing’?) the equipment available here at CCIQS, and with the pending new grant we obtained for sustainable catalysis research, we’ll be seeing more of this shipments (including a small computer cluster for yours truly!). You can see my good friend, Dr. Vojtech “Beto” Jancik in the pictures (in short, a post about a joint paper will come out, stay tuned!).
It was your idea. You had it. Or did it have you? But suddenly, you see it wrapped around someone else’s words. You read and gasp in denying shock. This can’t be! You read again trying to find your mistake, it is clearly a mistake on your part; to find it, you search for differences, preferably major ones that reveal that the identity of this idea is different to yours. You hope to just be mistaking it for yours. The wording is different, of course, you would have emphasized it differently, the way it deserved to be emphasized. But nevertheless its a mistreated version of yours. No matter what, this was yours. Was. Heartbroken, you try to save some face, by treating it differently; by treating it better!; by tending to those bits this third party is neglecting; by dumping it and getting a new and better one. You were so close. All in vain, for the fact is that this idea is no longer just yours, it seduced someone else’s mind and got brought to life by swifter hands. Now forever they will remain bound together as two celestial bodies are bound by gravity in the marriage of scientific annals, under the complicit auspice of editors and reviewers. Yes. You were the last to know this went on. It once made you feel so special, proud of your sparkling originality and your long hard work, brilliant even, but now you feel idle and exposed while in the dark.
You wish that at least you were perceived as a fool, as a laughing stock or even as an intellectual cuckold! But you are left worse than that: You are left with nothing. Empty handed. A runner up at best or part of the despised ‘me-too‘ kind, but only if you manage to get something out there at which the public scrutiny can roll their eyes. Still, that would be indeed better than having nothing to show for after all those long hours of shared intimacy with this idea. Angrily, you decide to blame others: technicians for delaying experiments; your collaborators for delaying revisions; your students for delaying data, and even the head of the department, maybe just for being other than yourself. You read again. The idea, no longer yours alone, stares back at you; no amount of hatred can change that. And then you wonder if you could have possible been on the other side before? You hope you have, for that means you are ahead in the game, but like in any game, sometimes you loose. Could your mind have been the seducing one before? You hope it has, for if it hasn’t it means you are playing alone in a corner of no interest to anyone, and what fun is that? What fun is a game in which you cannot win?
You mend fences. You accept that for this time someone was lucky but soon luck will come back and you will seduce other ideas; your hands will bring them to life and you will successfully collect the recognition for it, no matter how little the victory. Affairs with new ideas will come. Luck will come back. And it will come back to find you busily working or will not come back at all.
Pauli’s Exclusion Principle is a paramount concept in Quantum Mechanics which has implications from statistical mechanics to quantum chemistry, consequently, there are many different statements to summarize it depending on the forum. I occasionally joke with my students about how we learnt it in kindergarten an how we state it now at the end of our computational chemistry course.
So, are you a toddler or high up there with W. Pauli predicting the existence of sub-atomic particles at CERN? Which statement of Pauli’s Exclusion Principle sounds more familiar to you?
LOL just feeling a little humorous this morning!
As we approach to the end of another year, and with that the time where my office becomes covered with post-it notes so as to find my way back into work after the holidays, we celebrate another paper published! This time at the Journal of Physical Chemistry A as a follow up to this other paper published last year on JPC-C. Back then we reported the development of a selective sensor for Hg(II); this sensor consisted on 1-amino-8-naphthol-3,6-disulphonic acid (H-Acid) covalently bound to a modified silica SBA-15 surface. H-Acid is fluorescent and we took advantage of the fact that, when in the presence of Hg(II) in aqueous media, its fluorescence is quenched but not with other ions, even with closely related ions such as Zn(II) and Cd(II). In this new report we delve into the electronic reasons behind the quenching process by calculating the most important electronic transitions with the framework laid by the Time Dependent Density Functional Theory (TD-DFT) at the PBE0/cc-pVQZ level of theory (we also included an electron core potential on the heavy metal atoms in order to decrease the time of each calculation). One of the things I personally liked about this work is the combination of different techniques that were used to assess the photochemical phenomenon at hand; some of those techniques included calculation of various bond orders (Mayer, Fuzzy, Wiberg, delocalization indexes), time dependent DFT and charge transfer delocalizations. Although we calculated all these various different descriptors to account for changes in the electronic structure of the ligand which lead to the fluorescence quenching, only delocalization indexes as calculated with QTAIM were used to draw conclusion, while the rest are collected in the SI section.
Thanks a lot to my good friend and collaborator Dr. Pezhman Zarabadi-Poor for all his work, interest and insight into the rationalization of this phenomenon. This is our second paper published together. By the way, if any of you readers is aware of a way to finance a postdoc stay for Pezhman here at our lab, please send us a message because right now funding is scarce and we’d love to keep bringing you many more interesting papers.
For our research group this was the fourth paper published during 2014. We can only hope (and work hard) to have at least five next year without compromising their quality. I’m setting the goal to be 6 papers; we’ll see in a year if we delivered or not.
I’d like to also take this opportunity to thank all the readers of this little blog of mine for your visits and your live demonstrations of appreciation at various local and global meetings such as the ACS meeting in San Francisco and WATOC14 in Chile, it means a lot to me to know that the things I write are read; if I were to make any New Year’s resolutions it would be to reply quicker to questions posted because if you took the time to write I should take the time to reply.
I wish you all the best for 2015 in and out of the lab!
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.Sc. 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 synthesis 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.