<Joaquin | Barroso>
@joaquinbarroso.bsky.social
š¤ 796
š„ 512
š 84
CompChemist. Baseball fanatic. Casual cyclist. Dad.
#CompChem
->
https://joaquinbarroso.com
This is great news! The 25th edition of the Mexican Meeting on Theoretical Physical Chemistry (RMFQT) is in one year and getting closer! A special number at Theoretical Chemistry Accounts is currently accepting contributions. Let's celebrate the
#CompChem
Fiesta!
link.springer.com/collections/...
add a skeleton here at some point
10 days ago
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In photo physics (as in photosynthesis) calculating emission spectra is as-if not more-important as calculating absorption. A new guest blog post on how to do it in Gaussian 16 by @gustavmondragon
#CompChem
#TDDFT
#EmissionSpectra
#Spectroscopy
joaquinbarroso.com/2026/03/30/a...
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Absorption and Emission Spectra with Gaussian 16
In photosynthesis research, emission spectraāparticularly chlorophyll fluorescenceāare not merely complementary to absorption measurements but are often more informative. While absorption spectra iā¦
http://joaquinbarroso.com/2026/03/30/absorption-and-emission-spectra-with-gaussian-16/
about 2 months ago
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Calculating emission spectra with Gaussian16
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Absorption and Emission Spectra with GaussianĀ 16
In photosynthesis research, emission spectraāparticularly chlorophyll fluorescenceāare not merely complementary to absorption measurements but are often more informative. While absorption spectra indicate which wavelengths are harvested, emission spectra reveal the fate of that energy, providing direct insight into its partitioning between photochemistry, heat dissipation, and fluorescence. In this way, they serve as sensitive probes of energy transfer efficiency among pigments and of the functional state of the photosystems.
http://joaquinbarroso.com/2026/03/30/absorption-and-emission-spectra-with-gaussian-16/
about 2 months ago
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Can Frustrated Lewis Pairs Really Split Water? A New Paper in Inorg.Ā Chem. Obtaining hydrogen from water is one of those topics that attracts lots of attention from many fronts in chemistry; on paper, it can be clean, elegant, and deceptively simple. In practice, however, water is stubborn andā¦
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Can Frustrated Lewis Pairs Really Split Water? A New Paper in Inorg.Ā Chem.
Obtaining hydrogen from water is one of those topics that attracts lots of attention from many fronts in chemistry; on paper, it can be clean, elegant, and deceptively simple. In practice, however, water is stubborn and breaking it apart requires catalysts, large energy inputs, or clever chemistry that juggles thermodynamics and kinetics. Among the many clever ideas proposed over the last decade, …
http://joaquinbarroso.com/2026/01/13/can-frustrated-lewis-pairs-really-split-water-a-new-paper-in-inorg-chem/
4 months ago
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One electron C-C bond or Weak Interaction? New paper inĀ PCCP The compound spiro-dibenzocycloheptatriene (figure 1) made headlines a year ago by claiming that the ipso carbon atoms across the molecule were bound together by a single electron Ļ bond. This is truly a seductive idea: that somewhereā¦
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One electron C-C bond or Weak Interaction? New paper inĀ PCCP
The compound spiro-dibenzocycloheptatriene (figure 1) made headlines a year ago by claiming that the ipso carbon atoms across the molecule were bound together by a single electron Ļ bond. This is truly a seductive idea: that somewhere out there, in the shadows of open-shell aromatics, carbon atoms might form a single-electron Ļ-bond ā a unicorn of bonding, indeed. Since bold claims require bold scrutiny, we went ahead and dissected the electronic structure of the radical molecule in question with all the tools at our disposal; We also analyzed that of the neutral complex from where it was derived and also the double cation to analyze the consequences of removing the alleged electron holding such an unusual interaction, for if this C-C bond truly exists, it should alter the interaction energy between the fragments in a way consistent with a real Ļ bond.
http://joaquinbarroso.com/2025/12/10/one-electron-c-c-bond-or-weak-interaction-new-paper-in-pccp/
5 months ago
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I've been struggling with some calculations for a couple of days now only to find the solution in my own blog *sigh* Should I be glad I made a sort of note for my future self or should I be concerned about getting older?
6 months ago
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/home/myself/manuscript_submitted be like: manuscript.docx manuscript_rev1.docx manuscript_rev1_comments.docx manuscript_rev2_notracks.docx manuscript_rev3_1_final.docx manuscript_refs1_1_final_final_notracks.pdf re_manuscript_4_2_3_1_referees_final_comments_annotated.docx
7 months ago
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Bond Dissociation Energy withĀ Gaussian16 The strength of a chemical bond can be defined as the change in enthalpy when a bond is homolytically broken into two radicals. Bond dissociation energy is thus the measure of the strength of a bond and, while it is temperature dependent, it can beā¦
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Bond Dissociation Energy withĀ Gaussian16
The strength of a chemical bond can be defined as the change in enthalpy when a bond is homolytically broken into two radicals. Bond dissociation energy is thus the measure of the strength of a bond and, while it is temperature dependent, it can be calculated by DFT or ab initio methods. In this tutorial we're going to calculate the C-H bond dissociation energy (BDE) in the methane (CH4) molecule, one of the strongest aliphatic bonds in organic chemistry.
http://joaquinbarroso.com/2025/10/22/bond-dissociation-energy-with-gaussian16/
7 months ago
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#IYQ2025
Are the 2 electrons in a covalent bond 'entangled'? I mean, in the sense of 'Einstein's spooky action at distance'. If so, what would that imply for a homolytic cleavage? Would both mol fragments be entangled? Is electron correlation somehow related to that entanglement?
7 months ago
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reposted by
<Joaquin | Barroso>
Nature Reviews Chemistry
8 months ago
Congratulations to this morning's Nobel prize winners. If you'd like to read a little more about one of them - Omar Yaghi - then do check out this recent Q&A we published ahead of his 60th birthday earlier this year.
rdcu.be/eJ3vj
#ChemNobel2025
#chemsky
š§Ŗ
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The man of MOFs and more
Nature Reviews Chemistry - Ahead of his 60th birthday, Omar Yaghi discussed his life in science so far and where he believes is the exciting space for future developments.
https://rdcu.be/eJ3vj
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Si thrilled to finally see Prof. Omar Yaghi getting a most deserved Nobel prize!
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8 months ago
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Chemists west of the Atlantic Ocean: Are you in Alfred Nobelās Good or Naughty list? Go to bed now.
#ChemNobel
8 months ago
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How appropriate that this Intl. year of the quantum sciences, the Nobel Prize in Physics is awarded to Macroscopic Quantum Tunneling Effect. Paraphrasing Sabina Hossenfelder: "Thanks to this, we can keep discussing the interpretation of Quantum Mechanics, but now inside a clean room." š§Ŗ
#IYQ2025
add a skeleton here at some point
8 months ago
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Fortunately, the news tunneled its way to the recipient.
add a skeleton here at some point
8 months ago
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reposted by
<Joaquin | Barroso>
Benjamin Pope
8 months ago
it's actually not two Nobels for Josephson junctions, just one that tunnelled over a gap of 52 years
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If not thought-provoking, at least I hope it's talk-provoking. A new blog post on Quantum Chemistry and the interpretations of Quantum Mechanics.
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Is Quantum Chemistry aligned with the Copenhagen or the Many Worlds interpretation of QuantumĀ Mechanics?
2025 was declared by UNESCO as the International Year of Quantum Sciences, bringing a lot of celebrations, however much of the discourse is dominated by physicists and quantum technologists, some of which proclaim the dawn of the new "quantum revolution". Yet, amid the excitement, I can't help but notice that quantum chemistry remains underrepresented, despite being the discipline that has arguably done the most to turn quantum mechanics into a practical, predictive science.
http://joaquinbarroso.com/2025/10/02/is-quantum-chemistry-aligned-with-the-copenhagen-or-the-many-worlds-interpretation-of-quantum-mechanics/
8 months ago
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reposted by
<Joaquin | Barroso>
Laura Howes
8 months ago
This is happening in an hour, join me to talk all things
#chemnobel
add a skeleton here at some point
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Unrecognized potential number 6 inĀ GetPot Unrecognized potential number 6 in GetPot A rather silly error in Gaussian, but one that seems to be common and to which I haven't found any posted solutions, so here goes mine. This error shows up when reading an external basis set and looks like thisā¦
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Unrecognized potential number 6 inĀ GetPot
Unrecognized potential number 6 in GetPot A rather silly error in Gaussian, but one that seems to be common and to which I haven't found any posted solutions, so here goes mine. This error shows up when reading an external basis set and looks like this (color emphasis mine): Rotational constants (GHZ): 0.0492351 0.0073969 0.0065324 Leave Link 202 at Tue Sep 30 16:14:43 2025, MaxMem= 104857600 cpu: 1.5 elap: 0.2 (Enter /tmpu/scunam/7/gaussian-2016.C01/g1/g16/l301.exe) General basis read from cards: (5D, 7F) ====================================================================================================== Pseudopotential Parameters ====================================================================================================== Center Atomic Valence Angular Power Number Number Electrons Momentum of R Exponent Coefficient SO-Coeffient ====================================================================================================== Unrecognized potential number 6 in GetPot.
http://joaquinbarroso.com/2025/09/30/unrecognized-potential-number-6-in-getpot/
8 months ago
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#CompChem
in the
#Postseason
be like
8 months ago
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#ChemNobel
season is upon us. Which flavor of chem do you think will be recognized this year? Comment tour top picks. Phys/Theo Org Inorg Med/Bio
8 months ago
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La pasión por la ciencia nunca le cupo en el pecho. Por eso la derramó sobre todos los que la conocimos. DEP Dra. Julieta Fierro Gossman
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Julieta Fierro: "La ciencia nos demuestra que no tenemos la verdad"
YouTube video by Aprendemos juntos Mex
https://youtu.be/01hMSGUa_ms?si=Ug9NX2dhoNV2QfAC
8 months ago
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Fui invitado a Sensacional de CientĆficos para hablar sobre el aƱo de las Ciencias CuĆ”nticas VĆ©anlo completo en YouTube o escĆŗchenlo en su podcasteria favorita YouTube:
youtu.be/2Mul2CMUJLk
Spotify:
shorturl.at/fQLZb
Apple Podcasts:
shorturl.at/CwKpf
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9 months ago
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Using DensToolKitViewer to get the bestĀ viewpoint In this tutorial, we shall prepare a figure using DensToolKitViewer 2.1.0 (or later) to select the viewing angle of the molecule, for whenever the default view isn't the optimal viewpoint or to get various for comparison. Installation and mainā¦
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Using DensToolKitViewer to get the bestĀ viewpoint
In this tutorial, we shall prepare a figure using DensToolKitViewer 2.1.0 (or later) to select the viewing angle of the molecule, for whenever the default view isn't the optimal viewpoint or to get various for comparison. Installation and main controls were already covered in a previous post, as well as an update for ease of use. We use the file…
http://joaquinbarroso.com/2025/08/27/using-denstoolkitviewer-to-get-the-best-viewpoint/
9 months ago
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Installing and uninstallng DensToolKitViewer The new DensToolKitViewer just got even better! So, if you want to update DTKViewer to make the most of the new features, in this tutorial we shall compile and install DensToolKitViewer. We provide the explicit steps to compile under Ubuntu and underā¦
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Installing and uninstallng DensToolKitViewer
The new DensToolKitViewer just got even better! So, if you want to update DTKViewer to make the most of the new features, in this tutorial we shall compile and install DensToolKitViewer. We provide the explicit steps to compile under Ubuntu and under MacOSX. We will assume that the git repo is cloned in /home/your_username/Downloads. For this, execute the following commands…
http://joaquinbarroso.com/2025/08/25/installing-and-uninstallng-denstoolkitviewer/
9 months ago
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We think of
#quantum
entanglement as exotic, but from a bottom-up perspective it's the rule. What if the exotic thing is the classical limit, where this network of correlations collapses? Is our reality the true exotic thing?
#IYQ2025
#QuantumMechanics
9 months ago
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Wouldn't Thermodynamics guarantee that if someone is hotter than me, I'm cooler than them? š¤
9 months ago
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30 years ago today I got into chemistry school at UNAM. Itās been 30 years in which Iāve thought about atoms and molecules every single day. Itās been a great thirty years and hereās to thirty more.
9 months ago
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Something becomes canon in Academia when you no longer need to cite the original source, i.e. Newton's laws. That said, DFT theorems (and the most popular functionals for that matter) are canon, right? Right? Here's looking at you
#reviewer2
.
#CompChem
#ProfLife
9 months ago
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Getting Images with DensToolKitViewer2.0 ā AIM withĀ DTK2.0 Preparing publication quality images from your calculations is essential. To pre-visualize images to get the best orientations of your molecule, DTK2.0 includes two options: a new GUI called DensToolKitViewer and DTKQDMol. To installā¦
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Getting Images with DensToolKitViewer2.0 ā AIM withĀ DTK2.0
Preparing publication quality images from your calculations is essential. To pre-visualize images to get the best orientations of your molecule, DTK2.0 includes two options: a new GUI called DensToolKitViewer and DTKQDMol. To install DensToolKitViewer, you need CMake and the QT-5 libraries all of which you can install in the following way (Ubuntu): ~$sudo apt install -y qtbase5-dev qt5-qmake cmake freeglut3-dev qtdeclarative5-dev ~$cd /path-to-denstoolkit/src/dtkview ~$mkdir build ~$cd build ~$cmake ..
http://joaquinbarroso.com/2025/06/26/getting-images-with-denstoolkitviewer2-0-aim-with-dtk2-0/
11 months ago
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This is the first post of a new tutorial series on working with DensToolKit (DTK) for analyzing electron density through various scalar fields. In this post, installation and NCI plotting. Stay tuned for more!
#CompChem
#DTK
#DensToolKit
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DensToolKit 2.0 (DTK) is now available!
DensToolKit2 is a versatile open-source, cross-platform, suite of programs for analyzing electronic densities calculated from various sources and getting cool plots for some of the most popular scaā¦
https://joaquinbarroso.com/2025/06/17/denstoolkit-2-0-dtk-is-now-available/
11 months ago
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Even though the deadline hadn't passed yet, by the time I tried to register for
#WATOC2025
, it was already full. I'm suffering from severe FOMO :_(
11 months ago
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Nothing helps me learn more about a computational chemistry technique I don't master than referee number 2.
11 months ago
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A wonderful review on how theory has lead the way in chemistry!
add a skeleton here at some point
12 months ago
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Later means never whenever in a sentence of the structure āto be {any-verb} later.ā
about 1 year ago
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What if you asked AI for a self portrait?
about 1 year ago
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Not too long ago I was talking to my kids about self driving labs worked by robots. Today, my 9yo daughter gave me this drawing. āDaddyās future self-sting labā š„²
about 1 year ago
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A new Blog Post regarding our latest paper in Nature Comms. on the Halide effect on pre-organization of diasteroselective Grignard reactions
joaquinbarroso.com/2025/02/19/d...
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Diasteroselective Grignard Reaction ā New paper in Nature Communications
The Grignard addition is one of those reactions you learn during your first year of Organic chemistry and probably the last you forget when you become a computational chemist. It was Victor Grignarā¦
https://joaquinbarroso.com/2025/02/19/diasteroselective-grignard-reaction-new-paper-in-nature-communications/
over 1 year ago
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It's fascinating to learn new things from old reactions! Halide and preorganization effects in Grignard reactions for the synthesis of non-canonical nucleotides. A new collaboration with the group of R. Britton in Nature Communications.
www.nature.com/articles/s41...
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Unmasking the halide effect in diastereoselective Grignard reactions applied to C4Ā“ modified nucleoside synthesis - Nature Communications
The Grignard reaction represents one of the most powerful carbon-carbon bond forming reactions and is the subject of continual study. Here, the authors report a halide effect on the diastereoselectivi...
https://www.nature.com/articles/s41467-025-56895-7
over 1 year ago
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From curiosity thereāll be amazement. For all.
#11F
#WomenInSTEM
#GirlsInSTEM
#IDWGS2025
over 1 year ago
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A new graduate student from our lab! Weāre proud of Humberto Estrada who admirably defended his thesis on photosynthesis today. The future of quantum biology research is in good hands!
#IYQ
Ad astra, Humberto!
over 1 year ago
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Yes, I had to do it and jump on the bandwagon. How can
#DeepSeek
help revolutionize computational chemistry research and education, now in the blog.
#CompChem
joaquinbarroso.com/2025/01/28/h...
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How DeepSeek Can Revolutionize Computational Chemistry Research and Education
Computational chemistry is a field that thrives on innovation, precision, and the ability to tackle complex problems. With the rise of artificial intelligence (AI) and machine learning (ML), tools ā¦
https://joaquinbarroso.com/2025/01/28/how-deepseek-can-revolutionize-computational-chemistry-research-and-education/
over 1 year ago
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This morning I realized Iāve lived longer in the 21st century than in the 20th. It left me feeling strangely homesick.
over 1 year ago
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Calculating pka values for inorganic acids (arsonic acids); DFT and Machine Learning are not the whole story! A cool collaboration showing the power of contrasting many models when calculating physicochemical properties. A new post in my blog:
joaquinbarroso.com/2025/01/22/p...
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pka values for Arsonic Acids ā New paper in ACS Omega
Calculating reaction constants, in the correct physical way, requires accurate thermodynamic calculations involving solvation/desolvation energies at high levels of theory, because free energy deviā¦
https://joaquinbarroso.com/2025/01/22/pka-values-for-arsonic-acids-new-paper-in-acs-omega/
over 1 year ago
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Today we said goodbye to Claudia Torres who will pursuit a masters degree in Germany; her research on polaron and bipolaron calculations on conducting polymers, is soon to be published! Ad astra, Claudia! We wish you the very best!
over 1 year ago
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More on how to calculate pka values, now for inorganic (As) compounds. Thanks to Miroslava Nedyalkova for instigating this collaboration. Comparative Analysis of pKa Predictions for Arsonic Acids Using DFT & ML approaches New paper in ACS Omega
pubs.acs.org/doi/full/10....
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Comparative Analysis of pKa Predictions for Arsonic Acids Using Density Functional Theory-Based and Machine Learning Approaches
Arsonic acids (RAsO(OH)2), prevalent in contaminated food, water, air, and soil, pose significant environmental and health risks due to their variable ionization states, which influence key properties such as lipophilicity, solubility, and membrane permeability. Accurate pKa prediction for these compounds is critical yet challenging, as existing models often exhibit limitations across diverse chemical spaces. This study presents a comparative analysis of pKa predictions for arsonic acids using a support vector machine-based machine learning (ML) approach and three density functional theory (DFT)-based models. The DFT models evaluated include correlations to the maximum surface electrostatic potential (VS,max), atomic charges derived from a solvation model (solvation model based on density), and a scaled solvent-accessible surface method. Results indicate that the scaled solvent-accessible surface approach yielded high mean unsigned errors, rendering it less effective. In contrast, the atomic charge-based method on the conjugated arsonate base provided the most accurate predictions. The ML-based approach demonstrated strong predictive performance, suggesting its potential utility in broader chemical spaces. The obtained values for pKa from VS,max show a weak prediction level, because the way of predicting pKa is related only to the electrostatic character of the molecule. However, pKa is influenced by many factors, including the molecular structure, solvation, resonance, inductive effects, and local atomic environments. VS,max cannot fully capture these different interactions, as it gives a simplistic view of the overall molecular potential field.
https://pubs.acs.org/doi/full/10.1021/acsomega.4c10413
over 1 year ago
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Every chance I get I go and watch the ISS pass by, specially if Iām with my kids. Itās just astounding to think the massive achievement of having an ongoing space lab orbiting Earth. PS I use the Supercluster app to track that and the Tiangong Station šØš³
over 1 year ago
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Sir Fraser Stoddart wasn't only a giant of chemistry, but a kind and charismatic educator who brought his insight on chemistry to many countries of the world, like Mexico, where he had a most bizarre travel to a conference. His passing is sad news to the world chemistry community.
over 1 year ago
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No luck, bot lots of fun!
over 1 year ago
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Iām very excited of being a part of this great team! The new DTK version is out and published! Scalar & vector fields galore with new workflows such as pKa and pKb predictions. Please use it, share it, and cite it! <Ļ|š|Ļ>
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DensToolKit2: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields
In this article, we provide details of the suite DensToolKit-v2, which consists of a set of cross-platform, optionally parallelized programs for analyzing the m
https://pubs.aip.org/aip/jcp/article/161/23/232501/3326229/DensToolKit2-A-comprehensive-open-source-package
over 1 year ago
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Iām exploring sabbatical opportunities starting next summer! Iāll likely be reaching out to many of you, but if you have an opportunity in mind, Iād love to hear about it!
over 1 year ago
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