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New paper in Tetrahedron #CompChem “Why U don’t React?”

Literature in synthetic chemistry is full of reactions that do occur but very little or no attention is payed to those that do not proceed. The question here is what can we learn from reactions that are not taking place even when our chemical intuition tells us they’re feasible? Is there valuable knowledge that can be acquired by studying the ‘anti-driving force’ that inhibits a reaction? This is the focus of a new manuscript recently published by our research group in Tetrahedron (DOI: 10.1016/j.tet.2016.05.058) which was the basis of Guillermo Caballero’s BSc thesis.



It is well known in organic chemistry that if a molecular structure has the possibility to be aromatic it can somehow undergo an aromatization process to achieve this more stable state. During some experimental efforts Guillermo Caballero found two compounds that could be easily regarded as non-aromatic tautomers of a substituted pyridine but which were not transformed into the aromatic compound by any means explored; whether by treatment with strong bases, or through thermal or photochemical reaction conditions.


These results led us to investigate the causes that inhibits these aromatization reactions to occur and here is where computational chemistry took over. As a first approach we proposed two plausible reaction mechanisms for the aromatization process and evaluated them with DFT transition state calculations at the M05-2x/6-31+G(d,p)//B3LYP/6-31+G(d,p) levels of theory. The results showed that despite the aromatic tautomers are indeed more stable than their corresponding non-aromatic ones, a high activation free energy is needed to reach the transition states. Thus, the barrier heights are the first reason why aromatization is being inhibited; there just isn’t enough thermal energy in the environment for the transformation to occur.


But this is only the proximal cause, we went then to search for the distal causes (i.e. the reasons behind the high energy of the barriers). The second part of the work was then the calculation of the delocalization energies and frontier molecular orbitals for the non-aromatic tautomers at the HF/cc-pVQZ level of theory to get insights for the large barrier heights. The energies showed a strong electron delocalization of the nitrogen’s lone pair to the oxygen atom in the carbonyl group. Such delocalization promoted the formation of an electron corridor formed with frontier and close-to-frontier molecular orbitals, resembling an extended push-pull effect. The hydrogen atoms that could promote the aromatization process are shown to be chemically inaccessible.


Further calculations for a series of analogous compounds showed that the dimethyl amino moiety plays a crucial role avoiding the aromatization process to occur. When this group was changed for a nitro group, theoretical calculations yielded a decrease in the barrier high, enough for the reaction to proceed. Electronically, the bonding electron corridor is interrupted due to a pull-pull effect that was assessed through the delocalization energies.

The identity of the compounds under study was assessed through 1H, 13C-NMR and 2D NMR experiments HMBC, HMQC so we had to dive head long into experimental techniques to back our calculations.

The ‘art’ of finding Transition States Part 1

Guillermo CaballeroGuillermo Caballero, a graduate student from this lab, has written this two-part post on the nuances to be considered when searching for transition states in the theoretical assessment of reaction mechanisms. He’s been quite successful in getting beautiful energy profiles for organic reaction mechanisms, some of which have even explained why some reactions do not occur! A paper in Tetrahedron has just been accepted but we’ll talk about it in another post. I wanted Guillermo to share his insight into this hard practice of computational chemistry so he wrote the following post. Enjoy!


Yes, finding a transition state (TS) can be one of the most challenging tasks in computational chemistry, it requires both a good choice of keywords in your route section and all of your chemical intuition as well. Herein I give you some good tricks when you have to find a transition state using Gaussian 09 Rev. D1

METHOD 1. The first option you should try is to use the opt=qst2 keyword. With this method you provide the structures of your reagents and your products, then the program uses the quadratic synchronous transit algorithm to find a possible transition state structure and then optimize it to a first order saddle point. Here is an example of the input file.

link 0
--blank line--
#p b3lyp/6-31G(d,p) opt=qst2 geom=connectivity freq=noraman
--blank line--
Charge Multiplicity
Coordinates of reagents
--blank line--
Charge Multiplicity
Coordinates of products
--blank line---

It is mandatory that the numbering must be the same in the reagents and the products otherwise the calculation will crash. To verify that the label for a given atom is the same in reagents and products you can go to Edit, then Connection. This opens a new window were you can manually modify the numbering scheme. I suggest you to work in a split window in gaussview so you can see at the same time your reagents and products.

The keyword freq=noraman is used to calculate the frequencies for your optimized structure, it is important because for a TS you must only observe one imaginary frequency, if not, then that is not a TS and you have to use another method. It also occurs that despite you find a first order saddle point, the imaginary frequency does not correspond to the bond forming or bond breaking in your TS, thus, you should use another method. I will give you advice later in the text for when this happens. When you use the noraman in this keyword you are not calculating the Raman frequencies, which for the purpose of a TS is unnecessary and saves computing time. Frequency analysis MUST be performed AT THE VERY SAME LEVEL OF THEORY at which the optimization is performed.

The main advantage for using the qst2 option is that if your calculation is going to crash, it generally crashes at the beginning, in the moment of guessing your transition state structure. Once the program have a guess, it starts the optimization. I suggest you to ask the algorithm to calculate the force constants once, this generally improves on the convergence, it will take slightly more time depending on the size of your structure but it pays off. The keyword in the route section is opt=(qst2,calcfc). Indeed, I hardly encourage you to use the calcfc keyword in any optimization you want to run.

METHOD 2. If method 1 does not work, my next advice is to use the opt=ts keyword. For this method, the coordinates in your input file are those for the TS structure. Here is an example of the input file.

link 0
--blank line--
#p b3lyp/6-31G(d,p) opt=ts geom=connectivity freq=noraman
--blank line--
Charge Multiplicity
Coordinates of TS
--blank line--

The question that arises here is how should I get the coordinates for my TS? Well, honestly this is not a trivial task, here is where you use all the chemistry you know. For example, you can start with the coordinates of your reagents and manually get them closer. If you are forming a bond whose length is to be 1.5Å, then I suggest you to have that length in 1.6Å in your TS. Sometimes this becomes trial and error but the most accurate your TS structure is, based on your chemical knowledge, the easiest to find your TS will be. As another example, if you want to find a TS for a [1,5]-sigmatropic reaction a good TS structure will be putting the hydrogen atom that migrates in the middle point through the way. I have to insist, this method hardly depends on your imagination to elucidate a TS and on your chemistry background.

Most of the time when you use the opt=ts keyword the calculations crashes because of an error in the number of eigenvalues, you can avoid it adding noeigen to the route section; here is an example of the input file, I encourage you to use this method.

link 0
--blank line--
#p b3lyp/6-31G(d,p) opt=(ts,noeigen,calcfc) geom=connectivity freq=noraman
--blank line--
Charge Multiplicity
Coordinates of TS
--blank line--

If you have problems in the optimization steps I suggest you to ask the algorithm to calculate the force constants in every step of the optimization opt=(ts,noeigen,calcall) this is quite a harsh method because will consume long computing time but works well for small molecules and for complicated TSs to find.

Another ‘tricky’ way to get your coordinates for your TS is to run the qst2 calculation, then if it fails, take the second- or the third-step coordinates and used them as a ‘pre-optimized’ set of coordinates for this method.

By the way, here is another useful trick. If you are evaluating a group of TSs, let’s say, if you are varying a functional group among the group, focus on finding the TS for the simplest case, then use this optimized TS as a template where you add the moieties and use this this method. This works pretty well.

For this post we’ll leave it up to here and post the rest of Guillermo’s tricks and advice on finding TS structures next week when we’ll also discuss the use of IRC calculations and some considerations on energy corrections when plotting the full energy profile. In the mean time please take the time to rate, like and share this and other posts.

Thanks for reading!


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!


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