Category Archives: Computational Chemistry

Locked out of your Linux Session

Funny enough I was unable to log into my Linux (Ubuntu) session and I realized this might be a more common problem that it seemed. So, if you keep getting redirected to the login screen after typing your correct password over and over (and over and over), there’s no need to panic.

This usually has to do with the .Xauthority file, so from the login page press Ctrl+Alt+F1 which will bring you to the command line where you can login with your usual credentials. Once logged in, search for the .Xauthority file and check that it is owned by you and not the root

ls -l ~/.Xauthority 
-rw------ 1 root root 1 feb 11 13:13 /home/joaquin/.Xauthority

Use the following command to change ownership

chown group:username ~/.Xauthority

in my case both group and username are joaquin. You may need to ‘sudo’ it. If that doesn’t work try deleting the file altogether, upon login it will be created again.

rm -rf ~/.Xauthority

In any case, if any of these solutions worked, press Ctrl+Alt+F7 to go back to the login screen and now you should be able to get in.

These solutions are quite straightfoward but if the problem persist you may need to update the system or downright install it again from the command line we opened at the begining.

Good Luck to Dr. Jacinto Sandoval

We’re sad to begin this year by saying farewell to Dr. Jacinto Sandoval-Lira who held a postdoc position in our lab for two years with a DGAPA – UNAM scholarship, a very competitive and highly sought-after position here in Mexico. Dr. Sandoval will now relocate to the Technological Institute of San Martín Texmelucan in Puebla, Mexico, whose students will be fortunate to have him as a tutor and a teacher of chemistry in the environmental engineering department.

During the past two years we’ve worked together in various projects, mainly the excitonic transference between photosynthetic pigments but also in calculating reaction mechanisms and solving chemical equilibria problems with various computational approaches, but apart from the research Dr. Sandoval was also a co-organizer of the past Meeting on Physical Chemistry, organized a local course on the use of Dens Tool Kit (DTK), as well as our weekly lab seminars and taught various graduate and undergraduate courses on molecular modeling, chemoinformatics and computational chemistry, not too mention all the collaborations he has brought to our lab in the field of organic chemistry of which I regard him as an expert. He really has been a force of nature!

Aside from a brilliant scientist and a hard working one, Jacinto is an exceptional human being and a great friend. His attention to detail, his drive, and his willingness to help others reach their full potential make him an ideal colleague and an ideal professor. I don’t wish you luck, Jacinto, you don’t need it: I wish you success!

The International Year of the Periodic Table #IYPT2019 and the Tie that Binds

This time I try delivering a personal video post to close this #IYPT2019 celebrations. I hope you find it interesting.

I invite you all to always imitate molecules and react!


It was my distinct pleasure for me to participate in the organization of the latest edition of the Mexican Meeting on Theoretical Physical Chemistry, RMFQT which took place last week here in Toluca. With the help of the School of Chemistry from the Universidad Autónoma del Estado de México.

This year the national committee created a Lifetime Achievement Award for Dr. Annik Vivier, Dr. Carlos Bunge, and Dr. José Luis Gázquez. This recognition from our community is awarded to these fine scientists for their contributions to theoretical chemistry but also for their pioneering work in the field in Mexico. The three of them were invited to talk about any topic of their choosing, particularly, Dr. Vivier stirred the imagination of younger students by showing her pictures of the times when she used to hangout with Slater, Roothan, Löwdin, etc., it is always nice to put faces onto equations.

Continuing with a recent tradition we also had the pleasure to host three invited plenary lectures by great scientists and good friends of our community: Prof. William Tiznado (Chile), Prof. Samuel B. Trickey (USA), and Prof. Julia Contreras (France) who shared their progress on their recent work.

As I’ve abundantly pointed out in the past, the RMFQT is a joyous occasion for the Mexican theoretical community to get together with old friends and discuss very exciting research being done in our country and by our colleagues abroad. I’d like to add a big shoutout to Dr. Jacinto Sandoval-Lira for his valuable help with the organization of our event.

Non-canonical Base Pairs show Watson-Crick pairing in MD simulations

Elucidating the pairing of non-hydrogen bonded unnatural base pairs (UBPs) is still a controversial subject due to the lack of specificity in their mutual interactions. Experimentally, NMR is the method of choice but the DNA strand must be affixed on template of sorts such as a polymerase protein. Those discrepancies are well documented in a recent review which cites our previous computational work, both DFT and MD, on UBPs.

Since that last paper of ours on synthetic DNA, my good friend Dr. Rodrigo Galindo from Utah U. and I have had serious doubts on the real pairing fashion exhibited by Romesberg’s famous hydrophobic nucleotides d5SICS – dNaM. While the authors claim a stacked pairing (within the context of the strand in the KlenTaq polymerase enzime), our simulations showed a Watson-Crick-like pairing was favored in the native form. To further shed light on the matter we performed converged micro-seconds long simulations, varying the force field (two recent AMBER fields were explored: Bsc1 and OL15), the water model (TIP3P and OPC), and the ionic compensation scheme (Na+/Cl or Mg2+/Cl).

In the image below it can be observed how the pairing is consistently WC (dC1′-C1′ ~10.4 A) in the most populated clusters regardless of the force field.

Also, a flipping experiment was performed where both nucleotides were placed 180.0° outwards and the system was left to converge inwards to explore a ‘de novo’ pairing guided solely by their mutual interactions and the template formed by the rest of the strand. Distance population for C1′ – C1′ were 10.4 A for Bsc1 (regardless of ionic compensation) and 9.8 A for OL15 (10.4 A where Mg2+ was used as charge compensation).

This study is now published in the Journal of Biomolecular Structure & Dynamics

Despite the successful rate of replication by a living organism -which is a fantastic feat!- of these two nucleotides, there is little chance they can be used for real coding applications (biological or otherwise) due to the lack of structural control of the double helix. The work of Romesberg is impressive, make no mistake about it, but my money isn’t on hydrophobic unnatural nucleotides for information applications 🙂

All credit and glory is due to the amazing Dr. Rodrigo Galindo-Murillo from the University of Utah were he works as a developer for the AMBER code among many other things. Go check his impressive record!

Useful Thermochemistry from Gaussian Calculations

Statistical Mechanics is the bridge between microscopic calculations and thermodynamics of a particle ensemble. By means of calculating a partition function divided in electronic, rotational, translational and vibrational functions, one can calculate all thermodynamic functions required to fully characterize a chemical reaction. From these functions, the vibrational contribution, together with the electronic contribution, is the key element to getting thermodynamic functions.

Calculating the Free Energy change of any given reaction is a useful approach to asses their thermodynamic feasibility. A large negative change in Free Energy when going from reagents to products makes up for a quantitative spontaneous (and exothermic) reaction, nevertheless the rate of the reaction is a different story, one that can be calculated as well.

Using the freq option in your route section for a Gaussian calculation is mandatory to ascertain the current wave function corresponds to a minimum on a potential energy hypersurface, but also yields the thermochemistry and thermodynamic values for the current structure. However, thermochemistry calculations are not restricted to minima but it can also be applied to transition states, therefore yielding a full thermodynamic characterization of a reaction mechanism.

A regular freq calculation yields the following output (all values in atomic units):

Zero-point correction=                           0.176113 (Hartree/Particle)
 Thermal correction to Energy=                    0.193290
 Thermal correction to Enthalpy=                  0.194235
 Thermal correction to Gibbs Free Energy=         0.125894
 Sum of electronic and zero-point Energies=           -750.901777
 Sum of electronic and thermal Energies=              -750.884600
 Sum of electronic and thermal Enthalpies=            -750.883656
 Sum of electronic and thermal Free Energies=         -750.951996

For any given reaction say A+B -> C one could take the values from the last row (lets call it G) for all three components of the reaction and perform the arithmetic: DG = GC – [GA + GB], so products minus reagents.

By default, Gaussian calculates these values (from the previously mentioned partition function) using normal conditions, T = 298.15 K and P = 1 atm. For an assessment of the thermochemistry at other conditions you can include in your route section the corresponding keywords Temperature=x.x and Pressure=x.x, in Kelvin and atmospheres, respectively.

(Huge) Disclaimer: Although calculating the thermochemistry of any reaction by means of DFT calculations is a good (and potentially very useful) guide to chemical reactivity, getting quantitative results require of high accuracy methods like G3 or G4 methods, collectively known as Gn mehtods, which are composed of pre-defined stepwise calculations. The sequence of these calculations is carried out automatically; no basis set should be specified. Other high accuracy methods like CBS-QB3 or W1U can also be considered whenever Gn methods are too costly.

Failure Reading NMR data in GaussView

There was this following message on a GIAO calculation when trying to open the file in GaussView5.0 (it opens successfully in ChemCraft)

Failure reading NMR data 
Line Number 2414

When you go to said line (line 2414) you find the following string:

Eigenvalues:-12345.6789 -12345.6789 -12345.6789

Which belong to the eigenvalues of the SCF NMR GIAO shielding tensor. The problem lies with the space missing between the colon sign ‘:’ and the ‘-‘ sign of the first eigenvalue. You can fix it either by hand with an editor but GV only warns you about the first instance so there may be others and you need to repeat the procedure. It is probably best to fix them all in one go with the following command from the terminal:

sed -i ‘s/Eigenvalues:-/Eigenvalues: -/g’

It is good to be back in Romania at the UBB writing these posts where this blog began. Thanks to my good friend Dr. Alexandru Lupan for pointing out this error.

Atom specifications unexpectedly found in input stream.

“Well, where else were they supposed to appear?”

I was sent this error along with the previous question for a failed optimization. Apparently there is no answer in the internet (I quickly checked) so here it is:

Gaussian is confused about finding atomic coordinates because there is also a geom=check instruction placed in the route section, i.e., it was told to retrieve the atomic coordinates from a checkpoint and then it was given those atomic coordinates within the input so it doesn’t know what you mean and exits.

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.

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.

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