Latest posts tagged with #compchem on Bluesky
Glad to share our new work: RitS (Right into the Saddle): a generative model for direct transition state (TS) prediction.
📄 Paper: chemrxiv.org/doi/full/10.26…
🤠 Code: github.com/isayevlab/RitS
• Flow-matching model with explicit stereochemistry control
• Direct TS generation from SMILEs #compchem
We warmly invite you to join us for engaging scientific discussions in this exceptional setting 💻+🥘=😃
#ComputationalChemistry #CompChem #Science #ScientificWorkshop
Hello everyone!
We’re excited to announce that the OpenMolcas Annual Meeting will take place in Valencia 🇪🇸 from October 5th to 7th!
#ComputationalChemistry #CompChem #Science #ScientificWorkshop
Very happy to share our latest paper in #ChemEurJ 🥳
We've analyzed the electronic structure of small inorganic singlet #biradicaloids and propose to describe the chemical bonding using single π-bonds and single π-antibonds.
#Chemistry #ChemSky #CompChem #OpenAccess #S2N2 #ozone #Science 🧪
Check out the article by Kataev and co-workers, in which ORCA’s #GOAT algorithm is used to sample conformers of macrocycles.
onlinelibrary.wiley.com/doi/full/10....
Try GOAT yourself and check out our tutorial:
www.faccts.de/docs/orca/6....
#ORCA #CompChem #QuantumChem #Conformers #Macrocycles
One week of Avogadro 2.0 highlights - and we're just getting started…
Download: avogadro.cc/install/
Join the community: discuss.avogadro.cc
Thanks to everyone who helped make this release happen. Open science is a team effort! Got ideas on where to go next? 🧪 ⚗️
#opensource #openscience #compchem
Tomorrow morning, 09.30h, #CompChem session at @iqccudg.bsky.social with an interesting second half:
Cu-riosities
#ShamelessSelfPromotion
#BThereOrBSquare
I am happy to share that I am back to my home country, Brazil, to be a lead researcher at the Brazilian Center for Research in Energy and Materials (CNPEM)!
My research group will keep working on binding kinetics, and on the development of methods to simulate the cell cytoplasm.
#compchem
Screenshot of "Manage Plugins" window in Avogadro2, including over 20 plugins. A table shows several plugins including generators, RDKit, cclib, build-ase, xtb, aimnet2, genice2, TurtleMol, multicharge, antechamber, chiraltube, etc. with a README on the right hand side and buttons to search, install from a local directory, remove selected, and install / update selected
Screenshot of an example plugin for Chiraltube, indicating n, m values, number of repeats, and material, with MoS2 selected and the generated nanotube in the background with yellow spheres for sulfur atoms and turquoise spheres for Mo atoms
Screenshot of ORCA input generator, showing Basic, SCF, Basis, and Electronic Property tabs, and input file text.
Avogadro 2.0 isn't just a viewer and editor — it's an extensible platform for chemistry
A plugin system lets you add ML & electrostatic models, new builders and tools. Already over 20 available…
Build the tools you need: avogadro.cc/develop/plug...
#avogadro #openscience #compchem #opensource
Using apple silicon, I was able to speed up clustering molecules using Butina and KMeans. Of course, BitBIRCH continued to be the fastest (which is done entirely on CPUs). These are all great for plugging into current workflows. #Cheminformatics #compchem #RDKit #mlx
Analytics from my YouTube channel showing 2996 subscribers
Almost there! Should definitely make more videos but it's been incredibly busy these last months. #chemsky #compchem
Sometimes you just want to see a molecule move.
Run a quick MD simulation without leaving Avogadro — no scripts, no setup. The new auto-optimize tool includes a dynamics mode. Watch it move in real time. Great for teaching. Great for intuition. Just fun to watch.
#openscience #compchem #opensource
Volumetric rendering of the highest occupied molecular orbital (HOMO) of pentacene. Yellow and blue indicate opposite phases of the wavefunction, with color intensity indicating the magnitude of the wavefunction
Van der Waals molecular surface of coronene, with overlaid electrostatic potential map: red = more negative charge, blue = more positive charge
Rendering of the highest occupied molecular orbital (HOMO) of pyrazine
Rendering of a graphene supercell with solvent-accessible surface (green) indicating a defect site with a hydrogen molecule and overlay of electrostatic potential (blue = more positive, red = more negative)
Visualize molecular orbitals and electron density easily with Avogadro 2.0.
Volumetric rendering of orbitals, plus van der Waals, solvent-accessible and solvent-excluded surfaces for biomolecular work. See the chemistry, not just the atoms.
#compchem #openscience #opensource
Rendering of Ziegler–Natta zirconium catalyst with blue-green translucent sphere representing the Zr atom, and ball-and-stick rendering of cyclopentadienyl (Cp) rings and methyl group
Screenshot of Avogadro 2 template tool, indicating a tab for Element: Formal Charge: and the options for Coordination selected, with options 1: Linear, 2: Linear, 3: Trigonal Planar, 4: Tetrahedral, 4: Square Planar, 5: Trigonal Bipyramidal, 5: Square Pyramidal, 6: Octahedral, 6: Trigonal Prism, 7: Pentagonal Bipyramidal, 8: Square Antiprism
Ball and stick rendering of chlorophyll c2 molecule with larger green sphere representing the Mg(II) ion
Screenshot of symmetric (D5d) ferrocene with rotation axes illustrated as red cylinders. Orange sphere is an iron atom, and grey-white cylinders indicate the cyclopentadienyl ligands. Dialog text indicates D5d symmetry, tabs for "Molecule", "Operations", "Subgroups" with operations active, indicating a table of symmetry elements, classes, and element. At the bottom of the dialog is Tolerance: Normal and a button "Detect Symmetry"
Inorganic and organometallic chemists — Avogadro 2.0 is for you...
A new template tool lets you build octahedral, tetrahedral, and other complexes in seconds. Click to add functional groups. Avogadro also detects symmetry and displays symmetry elements
#compchem #openscience #opensource
Visualization of the COVID spike protein 6vxx with real-time shadows in Avogadro2 to give depth effects. All hydrogen atoms are hidden. Grey spheres are carbon atoms, red spheres are oxygen, blue spheres are nitrogen, and yellow spheres are sulfur atoms.
Screenshot from Avogadro showing a C₆₀ buckminsterfullerene cage with a translucent purple sodium atom inside
Screen rendering of a zeolite supercell showing shadows and depth blurring. Brown spheres are silicon atoms and red spheres are oxygen atoms
Rendering of a protein surrounded by a solvation sphere of water in wireframe view (using red-white lines to indicate the water molecules)
Avogadro 2.0's rendering was rebuilt for modern GPUs. Smooth even with tens of thousands of atoms.
Real-time shadows and ambient occlusion give depth and clarity — and a new layer system lets you hide solvent, toggle styles, and focus on what matters.
#opensource #openscience #compchem
#VISTAtalks on #CompChem 🧪
Wed 8 Apr, 10:00 Buffalo / 16:00 Paris / 22:00 Beijing
* Muehler, Penn State Univ: Strong correlations & topological transitions in reactions
* Le Dé, UC Merced: Photoinduced excited-state proton transfer
quantum-dynamics-hub.github.io/VISTA/
Picture of Aurora Cruz-Cabeza, Kreso Bucar, Sally Price, Will and me post viva
Congratulations to William Wood from the Price group, Sally's last PhD student, on passing his PhD viva yesterday afternoon!
Many thanks to Aurora Cruz-Cabeza for doing most of the heavy lifting in examining Will's thesis as external examiner.
#compchem #chemsky
Do you want quick insight on the crystal packing preferences of a new molecule, and can't wait for complete crystal structure prediction results? Check out @jennieemartin.bsky.social 's template CSP method.
Template CSP makes use of existing CSP landscapes to accelerate new predictions.
#compchem
No fooling, Avogadro 2.0.0 is finally here!
Rebuilt from the ground up: fast modern rendering, improved stability, designed for the next generation of molecular, biomolecule, and materials research & education. 🧪 ⚗️
avogadro.cc/install/
discuss.avogadro.cc
#opensource #openscience #compchem
1/3 Machine learning force fields can predict biomolecular dynamics with quantum accuracy across millions of atoms. Unke et al. trained models on diverse chemical fragments to capture long-range interactions missed by classical approaches. #academicsky #compchem
Opportunity for application scientist at AQEMIA (Paris France | London UK) closing 14-April-2026 #CompChem #cheminformatics #EUChemJobs #UKChemJobs #ChemJobs #chemsky 🧪
jobs.lever.co/aqemia.com/6...
Happy to share the review that @apoorvam.bsky.social, Vanessa and I wrote about recent trends in modeling and simulation of biological phenomena in crowded and cell-like environments! I really like this topic, for me this is the future of #compchem.
arxiv.org/abs/2603.26974
Happy to participate to the "𝐐𝐮𝐚𝐧𝐭𝐮𝐦 𝐂𝐨𝐦𝐩𝐮𝐭𝐢𝐧𝐠 𝐟𝐨𝐫 𝐐𝐮𝐚𝐧𝐭𝐮𝐦 𝐂𝐡𝐞𝐦𝐢𝐬𝐭𝐫𝐲, 𝐌𝐨𝐥𝐞𝐜𝐮𝐥𝐚𝐫 𝐃𝐲𝐧𝐚𝐦𝐢𝐜𝐬, 𝐚𝐧𝐝 𝐁𝐞𝐲𝐨𝐧𝐝" workshop, a great meeting organized by A. Izmaylov (U. Toronto) & Y. Zhang (Los Alamos ) at TSRC Telluride, CO.
#quantumcomputing #compchem quantum-computing-for-quantum-chemistry.raiselysite.com
Text reads: "On the road to Q-Chem 7. Key Feature of the Week: Density Functional Theory. Use our vast library of functionals to model ground and excited states; Get faster results with optimized integral algorithms, RI, and great parallel performance; Improve convergence with new features like “Robust SCF”"
Density functional theory is an essential method in any #compchem toolkit. Popular and general-purpose, it allows researchers to study electronic structure, predict geometries, model spectra, and much more. Follow along this week as we talk about #DFT in Q-Chem!
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...
Something big is coming on 1 April – and no, it's not a joke. 🧪 ⚗️
#opensource #openscience #compchem
🚀 New Webinar - April 15th
In this 30min session, we will show how computational chemistry workflows can significantly reduce lab iterations and accelerate R&D timelines.
Register here: 8079289.hs-sites.com/sophorolipid...
#surfactants #detergents #compchem
