Xin@QuantumChem

Good alignment

Final Effect

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

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

I almost said protein folding was CompChem's holy grail, finally solved by AI. But I held back, just said: "It's AI predictions, double-check if they make sense."

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

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

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

Sorry this post is incorrect. I accidentally copied the TS3 structure into TS1. The corrected results should be:

THIS POST is wrong: I wrongly copied the TS3 structure into TS1 in this post. The corrected results profile should be

Oh, sorry, I made a mistake. I copied the TS3 structure into TS1. The corrected figure should be. As for wB97M-V/def2-TZVPD, its relative energy of TS1 is very close to M06-2X/def2-TZVPP (within <0.1 kcal/mol). I will share the notebook, IRC and data very soon.

This is stricter than just comparing their own barrier height. Evaluating MLIP energies on the same DFT geometries, probe how similar the PES is. Answer the question: Given a decent DFT energy profile, can the MLIPs reproduce the relative energy along that path? It's crucial for the reactive MD.

DFT was used to locate transition states and minima; UMA and Orb-v3 single-point energies were computed on the same structures with DFT.

TS1 is located by DFT (black line). Red and green lines are from Orb-v3 and UMA.

TS1

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

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

I'd like to name it as "QM/MM".

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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.🪜

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.

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

Kvass and Khinkali

This is a transition state structure (red is oxygen, blue is Nitrogen, Green is Nicle) of C-N splitting reaction. Create a deamon around the structure breaking the C-N bond.

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

It should be the warm start. AIMNet2's model downloading and loading are also fast.

t0 = perf_counter()
E=mol.get_total_energy()
t1 = perf_counter()

Correctness: AIMnet2 should be AIMNet2. Single-point energy calculation.

Just run the following command in Colab. Works fine!
!uv pip install --system git+https://github.com/aligfellow/vib_analysis.git

Google Colab

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...

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