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.

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.

I just came back from beautiful Cancun where I attended for the third time the IMRC conference invited by my good friend and awesome collaborator Dr. Eddie López-Honorato, who once again pulled off the organization of a wonderful symposium on materials with environmental applications.

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.

The format of a research paper hasn’t changed much throughout history, despite the enormous changes in platforms available for their consumption and the near extinction of the library issue. Convenient electronic files such as PDFs still resemble printed-and-bound-in-issues papers in their layout instead of exploiting the seemingly endless capabilities of the electronic format. For instance, why do we still need to have page numbers?

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

“Well, where else were they supposed to appear?” I was sent this error along with the previous question for a failed optimization.

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 […]

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.

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.

Calculating the p K a 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.