UVeh-Vis v1.1 is now available
Dr. Joaquin Barroso's Blog
by joaquinbarroso
6M ago
This new version of UVeh-Vis contains modifications of the graphical properties of the output plot: Font type, font size, legend style and widow size corrections. Now, the discontinuity of the plot at the start and the end of the plot is fixed, so the plot is now completely continuous With some more technical features such as: CSV file generations of your plot coordinates with the command “-csv”, file that will be saved in your path of execution as “output.csv”. ex: “$ UVeh-Vis file1.out file2.out -wl 200,800 -csv” Lorentzian adjustment is now available using the “-ltz” command. ex: “$ UVeh-V ..read more
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The X-Mas ‘Chemistree’ that came from Mexico – Prof. Jaime Keller
Dr. Joaquin Barroso's Blog
by joaquinbarroso
7M ago
One of the first things I remember learning about chemistry in middle school (back in the early nineteen nineties) was how to write the electronic configuration of atoms using a sort of arcane code of numbers and letters in a weird progression hard to be rationalized, if not for a diagonal scheme that showed the precise way to fill orbitals with electrons as you moved forward the other big diagram of chemistry, the Periodic Table. It was a pointless lesson at the time, but nonetheless made me feel like I was into the secret complex language of scientists. It was only decades later that I lea ..read more
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Predicting the ChemNobel 2023 – A C&EN conversation
Dr. Joaquin Barroso's Blog
by joaquinbarroso
10M ago
Last week I wasn’t invited by CNN to participate in a webinar to talk about who might win this year‘s Nobel prize for Chemistry. Aside from addressing who our favorite candidates were we also talked about how polymathy seems to be a common thread in a creative job such as being a scientist. Listen to us talk about not-so-hidden talents, overlooked laureates, ancient interactions, and 3-D printed Nobel medals. I’ll make an edit in less than 24 hours after we finally learned who will be 2023 Nobel laureates in chemistry. CLICK HERE to watch the video at the c&en website ..read more
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Azahomocubanes – A New Paper in RSC Advances
Dr. Joaquin Barroso's Blog
by joaquinbarroso
10M ago
Cubane (C8H8) and homocubane (C9H10) are very strained molecules. Substitution of a carbon atom for a nitrogen one to reduce the tension in homocubane has been elusive until recently (Fahrenhorst-Jones et al. 2022). In contrast to cubane, substitution of C by N can occur at four different positions, so the obvious question is which one would be the most stable. Geometry optimizations at the M06-2X-D3/def2-TZVP level of theory and energy refinement on those structures at the CCSD(T)/aug-cc-pVTZ level were carried out to assess their electronic structures. Their Gibbs free energy differences (k ..read more
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Plotting UV-Vis spectra from QChem 5.0 calculations (UVeh-Vis)
Dr. Joaquin Barroso's Blog
by joaquinbarroso
11M ago
Undergraduate students in our lab shown in the picture above, Emanuel Contreras (right) and Humberto Estrada (left), just added a python-based code to our GitHub page, with which you can automatically plot UV-Vis spectra obtained from excited state calculations such as TD-DFT, CCSD, RAS, etc. made with QChem5.x (Gaussian16 availability coming soon!). You can choose the wavelength range and the band with, and use it to compare as many files simultaneously as you may want. UVeh-Vis (eh from Emanuel and Humberto, of course) requires updated versions of Python 3 and Matplotlib. You start by clonin ..read more
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Is your Wavefunction stable?
Dr. Joaquin Barroso's Blog
by joaquinbarroso
1y ago
So you optimized your molecule, you found all real frequencies, you’re done! right? Well, maybe not. When molecules are well-behaved you probably can either use a restricted or an unrestricted method to find the optimized wavefunction and derive as many properties as you want from it; this occurs for most organic molecules and to some extent to main group elements with little to no radical character. But from time to time, it just so occurs that the wavefunction stemming from your calculation is not the most appropriate to describe your electronic structure. This analysis allows you to quickly ..read more
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Undefined symbol, angle beta, card X
Dr. Joaquin Barroso's Blog
by joaquinbarroso
1y ago
I kept getting this pesky error, with no apparent solution found online. It happened when copy-pasting coordinates from files in different platforms. I edited the input file many many times in Linux but only when I got to look at it in a Windows Notepad was that I saw the following lines: 6 0.000000000 0.000000000     -0.030561000 Where the “” symbols had to be removed by deleting every apparently empty space between coordinates. So, this error: Undefined symbol, angle beta, card X where X is the atom number line where the error is found ..read more
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Calculating chemical descriptors with Mordred
Dr. Joaquin Barroso's Blog
by joaquinbarroso
1y ago
QSA(P)R and Machine Learning methods rely on finding correlations between molecular properties of known values for a given set of molecules in order to predict the properties of another set of molecules closely related to the former. These molecular properties to be correlated are known as ‘descriptors’, which are values that can be measured (pKa, refraction index, boiling point, etc.) or calculated (HOMO/LUMO gap, polarizbility, electronic energy, etc.) and depend on the structure of a molecule. Sometimes descriptors can be very abstract features with little to no physicochemical meaning, but ..read more
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Dr. Gustavo Mondragón PhD – A new graduate from the lab!
Dr. Joaquin Barroso's Blog
by joaquinbarroso
1y ago
It is my distinct pleasure to share the news of Gustavo “Gus” Mondragón obtaining his PhD degree in Theoretical Chemistry. Today he defended his thesis admirably, on his work related to excitonic transfer mechanisms between photosynthetic pigments; part of his results, those related to the dynamical red-shifting absorption Qy bands for Blastochloris viridis were published in the Journal of Chemical Theory and Computation, the rest of his research is, as of now, pending publication in two further papers. Gustavo arrived to the lab back in 2014 as an undergraduate student and simply just stayed ..read more
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What do we talk about when we talk about Empty Orbitals?
Dr. Joaquin Barroso's Blog
by joaquinbarroso
1y ago
My biggest pet peeve regarding the perception of experimental chemists about theoretical chemistry relates to the physical interpretation of orbitals. Every now and then there’s a serious claim about having atomic/molecular orbitals experimentally observed (read: Can Orbitals Be Directly Observed? in this blog for more.) But the discussion becomes even more esoteric when we talk about the existence (potential observation?) of unoccupied orbitals. Are you there empty orbital? It’s me, Joaquin *sigh* So, are orbitals there when no electrons ‘inhabit’ them? The rules of quantum mechanics yield a ..read more
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