This a guest post by Yamil Hernández, first year PhD student on loan from Puebla, who is working with us in photosynthesis related projects for his thesis. VMD (Visual Molecular Dynamics) is a free widely known visualizer developed by the Theoretical and Computational Biophysics Group from the University of Illinois. It is primarily used to analyze and visualize molecular dynamics (MD) results, as well as to prepare biological systems for further simulations.

I ran a TD-DFT calculation on a platinum complex, fed the log file to ELOTE, and got only half an answer. The molecular orbital composition table printed just fine, every orbital with its atomic percentages. But the excited-state analysis, the whole point of the exercise, came back empty. The CSV had a header and nothing underneath. No transitions, no MLCT/LMCT labels, no summary table.

Some of the most useful reactions in a synthetic chemist’s toolbox — the Wittig, the Appel, the Mitsunobu, the Staudinger, have a common problem: they yield stoichiometric piles of phosphine …

If you have ever run a TD-DFT calculation in Gaussian and stared at the output wondering exactly what each excited state is made of — which orbitals, on which atoms, with what percentage — this pos…

For over a quarter of a century, the Mexican Meeting on Theoretical Physical Chemistry (RMFQT) has served primarily as a national forum, with an increasingly ...

In photosynthesis research, emission spectra—particularly chlorophyll fluorescence—are not merely complementary to absorption measurements but are often more informative. While absorption spectra i…

In photosynthesis research, emission spectra—particularly chlorophyll fluorescence—are 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.

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, …

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 σ 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 σ-bond — 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 σ bond.

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.

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.

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.

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.

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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…

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…

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 ..

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 sca…

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 Grignar…

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...

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 …

Calculating reaction constants, in the correct physical way, requires accurate thermodynamic calculations involving solvation/desolvation energies at high levels of theory, because free energy devi…