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Xin@QuantumChem @xinquantum.bsky.social · 03/10/2026

Building catalytic surface using LightCone. Desktop version to be released with Direwolf (a quantum chemistry package). #compchemsky lightcone.quanta-bricks.com

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Xin@QuantumChem @xinquantum.bsky.social · 24/09/2026

So called "molecule-molecule docking", it should be classified into conformer searching. Visualization: lightcone.quanta-bricks.com

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Xin@QuantumChem @xinquantum.bsky.social · 03/05/2026

Testing three LLM models (Opus 4.7, Sonnet 4.6, Gemma 4) on LogP prediction. The pairwise ranking is the most important thing, 76% accuracy is acceptable. Accurate numerical prediction still relies on dedicated models, this test is more about how well LLMs understand chemistry. #compchemsky

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Xin@QuantumChem @xinquantum.bsky.social · 23/04/2026

Catalytic surface editing is pretty easy on LightCone interface. Good for heterogeneous cat. system building. #compchemsky #compchem

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Xin@QuantumChem @xinquantum.bsky.social · 13/02/2026

Two rescued cats. The first is named Isolated Belt (as I found it in an isolated belt bush). The second is Huahua (at least 9 yro). #compchem #biology #chemistry #compchemsky

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Xin@QuantumChem @xinquantum.bsky.social · 20/01/2026

Extreme compression test on C60. Even under very aggressive deformation, xTB stays stable and gives a reasonable energy trend. (Without clear bond breaking). @myzzzz.bsky.social would like to share the detailed files.

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Xin@QuantumChem @xinquantum.bsky.social · 28/11/2025

When it comes to real production level chemistry code, both Gemini 3 Pro and Claude Opus became clumsy. It took them around 40 minutes and multiple rounds of conversation just to finish the project. They’re clearly not great with RDKit or chemistry APIs. #CompChemsky #compchem #Chemistry

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Xin@QuantumChem @xinquantum.bsky.social · 23/11/2025

In one sentence: Orb-v3 is accurate in describing F-Li-Be Molten Salt *without fine-tuning*. AIMD results came from: doi.org/10.1103/PRXE... They also compared with Neutron Diffraction. @myzzzz.bsky.social will benchmark the S(Q) with experimental data. #compchemsky #compchem

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Xin@QuantumChem @xinquantum.bsky.social · 16/11/2025

Wetlab is a different world. A wetlab biologist just told me she uses a visualization website where you input a protein sequence and click, the 3D structures show instantly. The visualization thing is called AlphaFold. #Biology #AlphaFold #compchemsky

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Xin@QuantumChem @xinquantum.bsky.social · 09/11/2025

Centuries of human progress led us to uncover The Double Helix. In the end, we realized that all living things share the same codebook. #science #biology

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Xin@QuantumChem @xinquantum.bsky.social · 02/11/2025

Yesterday I posted an incorrect comparison. I accidentally copied the TS3 structure into TS1 for UMA and Orb-V3, so the MLIP results for TS1 were wrong. Really sorry about that misleading! In the next post I will share IRC of DFT calculation and wB97M-V/def2-TZVPD results. #compchem #compchemsky

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Xin@QuantumChem @xinquantum.bsky.social · 02/11/2025

A failure case for deep-learning potential: the TS1 geometry is so weird that UMA and Orb-v3 underestimate the barrier by ~15 kcal/mol, likely because it far from the training set. Handling chemical reactions is extremely hard for general deep learning models. #compchem #compchemsky

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Xin@QuantumChem @xinquantum.bsky.social · 22/10/2025

UMA (small model) is very close to DFT M06-2X. Maybe I can deploy nanoreactors using UMA model for coarse reaction space sampling. This is a reactive trajectory of a compound with 24 Carbon atoms. #CompChem #ChemChemSky

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Xin@QuantumChem @xinquantum.bsky.social · 06/08/2025

playground.tracto.ai/playground/n... The newly released open-source model from OpenAI can be tried on TractoAI playground for *FREE*.

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Xin@QuantumChem @xinquantum.bsky.social · 01/08/2025

This old theory is revitalized by deep learning. Building accurate kinetic energy functionals (< 0.5 kcal/mol) may be harder than climbing to the top of exchange-correlation Jacob's ladder.🪜

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Xin@QuantumChem @xinquantum.bsky.social · 27/07/2025

Cunning ChatGPT bypassing 3D depth analysis, and calling the rdkit function to generate the coordinate of an Ibuprofen. Grok3 just failed this test and misrecognized it as glucose, as expected.

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Xin@QuantumChem @xinquantum.bsky.social · 23/07/2025

Boltz2 can be run on a $430 RTX5060 Ti (16G) card, although it's much slower than ~$30,000 H100 (RTX 5060 Ti: 1min 47s, H100: 18s), but it doesn't matter, because the cold-start time is about 1 minute for both cards. #CompChemSky #CompChem #GPU

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Xin@QuantumChem @xinquantum.bsky.social · 12/07/2025

This is creepy, but lots of fun. Gemini Veo has a perception of spatial depth and can rotate the molecules. Inspired by www.youtube.com/watch?v=mDyt... #compchem #compchemsky

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Xin@QuantumChem @xinquantum.bsky.social · 09/07/2025

I ran a benchmark on a protein with ~3450 atoms. AIMnet2 takes 4.6 seconds, and UMA(small) takes 7.9 seconds. CUDA 12.4 on a Tesla T4. Additionally, the AIMnet2 checkpoint file is only 11.1 MB. The testing notebook link is shared. #compchemsky #compchem colab.research.google.com/drive/1g1PiW...

colab.research.google.com

Google Colab

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Xin@QuantumChem @xinquantum.bsky.social · 05/07/2025

This is a very interesting package. I will try this on colab notebook.

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Xin@QuantumChem @xinquantum.bsky.social · 04/07/2025

UMA (uma-sm) combined with NEB successfully locates the transition state and path for a Ni-catalyzed reaction. UMA prediction lies between two DFT functional, and the transition state closely matches the result from a literature: www.nature.com/articles/nat... #compchemsky #chemsky #compchem

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Xin@QuantumChem @xinquantum.bsky.social · 27/06/2025

The relationship between Ki and IC₅₀ is described by the Cheng–Prusoff equation. And William L. Jorgensen et al. did an effective calculation for predicting potency in his paper during pandemic. pubs.acs.org/doi/10.1021/...

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Reposted by Xin@QuantumChem

Jan @dermewes.bsky.social · 14/06/2025

2nd virtual lecture in the DFT&Application series starts today at 1500hrs CET (in 15 minutes!). Topics are Hartree Fock, SCF, and their connection to DFT. Join us in Zoom: us06web.zoom.us/j/8607128794... #compchem #dft

us06web.zoom.us

Join our Cloud HD Video Meeting

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Reposted by Xin@QuantumChem

Jo Ma @myzzzz.bsky.social · 11/06/2025

Hey Jan, I just completed UMA benchmark tests on large molecules (biomolecules, macrocycles, and more): quantabricks.substack.com/p/uma-testin... In short, when atoms number below 700, uma is more expensive. Otherwise, GFN2-xTB is more expensive #compchem #CompChemSky

quantabricks.substack.com

UMA testing on large molecules

Meta has just released its deep learning potential model, UMA, which is the most general model that supports different kinds of systems, such as isolated molecules, MOFs, and even surface absorption.

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Xin@QuantumChem @xinquantum.bsky.social · 04/06/2025

Surprisingly, the UMA (by meta) model captures the bond-breaking process in the carbon nanotube stretching test, similar to GFN2-xTB. I hadn't expected deep learning models to extrapolate over bond lengths. #compchemsky #chemsky

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Xin@QuantumChem @xinquantum.bsky.social · 27/05/2025

It's a great time to participate in the horseshoe crab protection activity (helped with counting and tagging). I had only heard stories about the blue blood legend in evolution before, but this time I saw it with my own eyes. #aquatic #science #NYC #drug

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Xin@QuantumChem @xinquantum.bsky.social · 21/03/2025

Interesting results for physical model, average RMSD<5A meaning that the ligands are plugged into the correct docking pocket. Unlike the AI methods, the charge models, protein ionization state or hydrated docking should be considered. This competition is also hosted by @asapdiscovery.bsky.social

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Xin@QuantumChem @xinquantum.bsky.social · 15/03/2025

It's suitable for building AI agents.

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Xin@QuantumChem @xinquantum.bsky.social · 06/03/2025

go.bsky.app/52czHRA #StarterPack for #CADD (computational-aided drug design) enthusiasts, open to researchers, students from both industry and academia. #compchemsky #compchem #chemistry #drugdesign

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Xin@QuantumChem @xinquantum.bsky.social · 17/01/2025

LLM-based ESM3 has just been released. Protein structure predicting is just a starting point of workflows. More functions should be implemented.

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Xin@QuantumChem @xinquantum.bsky.social · 10/01/2025

Seeking Image-to-SMILES conversion for local tiny device deployment. Deep learning offers accuracy but is too heavy. Are there lightweight alternatives without deep learning? Mathpix (SaaS) appears best, but closed-source and need internet.

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Xin@QuantumChem @xinquantum.bsky.social · 21/12/2024

Stretching of a carbon nanotube, a DFTB simulation. Do you know why I placed a nitrogen atom at the center? #CompChem #CompChemSky #Science #Chemistry

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Xin@QuantumChem @xinquantum.bsky.social · 13/12/2024

It looks like a Christmas Wreath

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Xin@QuantumChem @xinquantum.bsky.social · 11/12/2024

Collision Between Two C₆₀ Molecules: A Violent Encounter (An xTB-GFN2 Simulation) #CompChemSky #CompChem #Chemistry #Physics

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Xin@QuantumChem @xinquantum.bsky.social · 29/11/2024

Conchiglie with Kale and ham, The center part of the shell is raw and hard, but tastes good. Is it authentic? #Italian #Italianfood

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Xin@QuantumChem @xinquantum.bsky.social · 22/11/2024

Simulation of a violent collision between two molecules. How many reactions can you find? Simulation using GFN2-xTB. On a preowned desktop computer. It takes about 20 minutes. #compchem #Chemistry #computing

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