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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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Computational ChemistryAlumniBacteriochlorophyllChemistryComputational And Theoretical ChemistryChemical Sciences
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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;

ChemistryComputational ChemistryMathematicsModelsPhilosophyChemical Sciences
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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?

AIArticlesArtificial IntelligenceBloggingCodingChemical Sciences
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ChatGPT is a powerful language model developed by OpenAI that has the ability to generate human-like text. This model is trained on a vast amount of data and can be fine-tuned to perform a wide range of tasks, including computational chemistry. In this blog post, we will discuss the benefits and possibilities of using ChatGPT in computational chemistry.

Computational ChemistryChemical Sciences
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The 20 th Mexican Meeting on Theoretical Physical Chemistry (RMFQT) just occurred last week and it was a special edition for various reasons: The fact this meeting has been organized for two decades speaks volumes about a thriving national scientific community; being the 20th anniversary, the comitee saw fit to hold it at the very same place where it first began, Cuernavaca, an idyllic warm town just an hour south of Mexico City.

ChemistryComputational ChemistryDFTExcited StateFukuiChemical Sciences
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To calculate what the bonding properties of a molecule are in a particular excited state we can run any population analysis following the root of interest. This straightforward procedure takes two consecutive calculations since you don’t necessarily know before hand which excited state is the one of interest.

Computational ChemistryJCTCMolecular DynamicsPaperPhotochemistryChemical Sciences
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Photosynthetic organisms are so widespread around the globe they have adapted to various solar lighting conditions to thrive. The bacteria Blastochloris viridis absorbs light in the near infrared region of the electromagnetic spectrum, in fact, it holds the record for the longest wavelength (~1015 nm) absorbing organism whose Light Harvesting complex 1 (LHC1) has been elucidated.

Computational ChemistryGaussianModelsTheoretical ChemistryWhite PapersChemical Sciences
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Canonical Molecular Orbitals are–by construction–delocalized over the various atoms making up a molecule. In some contexts it is important to know how much of any given orbital is made up by a particular atom or group of atoms, and while you could calculate it by hand given the coefficients of each MO in terms of every AO (or basis set function) centered on each atom there is a straightforward way to do it in Gaussian.

ChemistryComputational ChemistryGoldInorganic ChemistryPaperChemical Sciences
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Stabilizing Gold in low oxidation states is a longstanding challenge of organometallic chemistry. To do so, a fine tuning of the electron density provided to an Au atom by a ligand via the formation of a σ bond. The group of Professor Rong Shang at the University of Nagasaki has accomplished the stabilization of an aurate complex through the use of a boron, nitrogen-containing heterocyclic carbene;

ChemistryRandom ThoughtsMoleculesChemical Sciences
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Molecules. Atoms glued by bonds; nuclei incarcerated by electrons; electrons forming an inhomogeneous gas contained not by outer walls but by an electrostatic potential in its interior ironically named ‘external potential’ . Molecules. The study object of chemists. The fundamental construct on which the chemical understanding of the universe relies.

ChemistryCodingComputational ChemistryDFTPatentsChemical Sciences
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Density Functional Theory is by far the most successful way of gaining access to molecular properties starting from their composition. Calculating the electronic structure of molecules or solid phases has become a widespread activity in computational as well as in experimental labs not only for shedding light on the properties of a system under study but also as a tool to design those systems with taylor-made properties.

Computational ChemistryComputational And Theoretical ChemistryExcitonExciton Energy TransferExcitonsChemical Sciences
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I’m very honored to have been invited to this edition of this long standing event, the Virtual Winter School of Computational Chemistry. In this talk I walk through the basics of what are excitons and how do they move or transfer across matter; and of course, a primer on how to calculate the energy transfer with Gaussian. This is a very basic introduction but I hope someone finds it useful.