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Dr. Joaquin Barroso's Blog

Scientific log of a computational chemist - "Make like a molecule and React!"
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On Friday May 30th, my good friend Dr. Josefina Aldeco, my wife and I, visited a children’s home in Querétaro (central Mexico) and brought them a few cool chemistry experiments for a short show. This event was promoted by a non-profit organization called “ Anímate a estudiar ” (Dare to study), namely by Mrs.

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A couple of weeks ago I posted a solution for a common error regarding .fchk files that will display the error below when opened with GaussView5.0. As I expected, this error has to do with the use of diffuse functions in the basis set and is related to a change of format between Gaussian versions.

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I’ve found the following error regarding the opening of .fchk files in GaussView5.0. CConnectionGFCHK::Parse_GFCHK() Missing or bad data: Alpha Orbital Energies Line Number 1234 The error is prevented to a first approximation (i.e. it at least will allow GV to open and visualize the file but other issues may arise) by opening the file and modifying the number of basis functions to equal the number of independent functions (which is lower)

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So many things have happened since I last updated this blog but I will come to write on them when appropriate. Right now I’d like to share an invitation by Prof. Ponnadurai Ramasami from the University of Mauritius to the upcoming Virtual Conference on Computational Chemistry from the 1st to the 31st of August.

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I always get very happy to have a new paper out there! I find it exciting but most of all liberating since it makes you feel like your work is going somewhere but most of all that it is making its way ‘out there’; there is a strong feeling of validation, I guess.

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Once again as every year we celebrate our internal symposium here at CCIQS, and like every year, my students presented some of their progress with their research projects. This time, three students, from three different levels, present posters regarding some of the data they’ve obtained.

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Sciencebase.com This is a guest post from Samantha Morra of EdTechTeacher.org, an advertiser on FreeTech4Teachers.com. Augmented Reality (AR) blurs the line between the physical and digital world. Using cues or triggers, apps and websites can “augment” the physical experience with digital content such as audio, video and simulations.

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eutactic I have written a bit of code lately which automates the process of constructing chemical reaction energy level diagrams rather well. It’s called rxnlvl . It’s written in Python, outputs to SVG (Scalable Vector Graphics) and is GPL3. I’m not a ninja programmer by any stretch of the imagination, however the program is basically functional, and in my estimation yields quite attractive results.

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Happy new year to all my readers! Having a new paper published is always a matter of happiness for this computational chemist but this time I’m excedingly excited about anouncing the publishing of a paper in the Journal of Chemical Theory and Computation, which is my highest ranked publication so far!

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Another year is almost done and as I write my annual report I realize this year has had several milestones for me as a researcher, most of which got recorded in this blog. I published three papers in peer reviewed journals, one of which actually made the cover of J. Inclusion Phenomena , the other two were published in J. Phys. Chem. C and Eur. J. Inorg.

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Theoretical evaluation of a reaction mechanism is all about finding the right transition states (TS) but there are no guarantees within the available methods to actually find the one we need. Chemical intuition in the proposal of a mechanism is paramount. Let’s remember that a TS is a critical point on a Potential Energy Surface (PES) that is a minimum in every dimension but one.