Papers › ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using...

ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback

15 Feb 2024arXiv:2402.10980archive 2025-07-28

Henry W. Sprueill, Carl Edwards, Khushbu Agarwal, Mariefel V. Olarte, Udishnu Sanyal, Conrad Johnston, Hongbin Liu, Heng Ji, Sutanay Choudhury

The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided computational screening framework unifying linguistic reasoning with quantum-chemistry based feedback from 3D atomistic representations. Our approach formulates catalyst discovery as an uncertain environment where an agent actively searches for highly effective catalysts via the iterative combination of large language model (LLM)-derived hypotheses and atomistic graph neural network (GNN)-derived feedback. Identified catalysts in intermediate search steps undergo structural evaluation based on spatial orientation, reaction pathways, and stability. Scoring functions based on adsorption energies and reaction energy barriers steer the exploration in the LLM's knowledge space toward energetically favorable, high-efficiency catalysts. We introduce planning methods that automatically guide the exploration without human input, providing competitive performance against expert-enumerated chemical descriptor-based implementations. By integrating language-guided reasoning with computational chemistry feedback, our work pioneers AI-accelerated, trustworthy catalyst discovery.

PaperPDFCodeCode Syntology ran

In Syntology Open this paper in Syntology's Atlas, the map of the papers in Syntology's graph and their citations.

For agents, Syntology's MCP tool lists every function and class Syntology harvested from this paper and whether it ran (how to connect): get_harvested_code_for_paper(arxiv_id="2402.10980")

Code

Syntology Ran 5 of 7 code samples harvested from 1 repository linked to this paper; 2 have no recorded run. Of those that ran: 2 ran · our draft was wrong; 3 ran with no contract checked.

By repository: official repository: 7 samples from 1 repository, 5 ran. The run record, sample by sample. “Ran” means executed on a synthesized input, not that the code is correct or reproduces the paper.

pnnl/chemreasoner officialmentioned in papermentioned on GitHub report

Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.

Code Syntology ran Syntology

7 samples harvested; 5 ran; 0 honoured the contract we drafted; 2 have no recorded run. Read from Syntology's graph 2026-09-24; that is when this build read the record, not when the samples ran.

2ran · our draft was wrong
3ran
2unverified

Licence: 7 of the 7 samples are pointer only, meaning Syntology does not serve that copy's text. This page shows no code text for any sample; each one links to its file in the repository.

Harvested from pnnl/chemreasoner. “Ran” means the sample executed on a synthesized input. It does not mean the output is correct, and nothing here reproduces the paper's results. “Honoured” and “violated” refer to a contract Syntology drafted from the code itself; “our draft was wrong” and “fixture could not drive it” are failures of Syntology's instrument, not of the code.

Each sample ends with its code_sha256, Syntology's identity for that exact code. An agent fetches the stored sample with Syntology's MCP tool get_code(code_sha256="…") (how to connect); click an identity to copy that call.

Repository labels, per sample. official repository: The archive marks this repository official for the paper. named in the paper: The archive records that the paper mentions this repository; it is not marked official. community (archive-listed): In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper. found in paper text by Syntology: Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted. community: Not in the archive's code links for this paper; a community repository Syntology harvested. Samples from a repository marked official are listed first. Licence labels name the repository's licence as recorded at harvest. “Pointer only” means Syntology does not serve that copy's text, for one of four reasons: no licence file was found; the licence was not identified; the licence is recorded as permissive but that copy's record is not marked cleared; or the licence is outside the permissive list Syntology serves text under (MIT, Apache-2.0, BSD and similar). Some licences outside that list permit redistribution, such as WTFPL, and GPL-3.0 under its conditions; they are simply not on the list. Hover a licence label for the reason. File links open the file on GitHub at the default branch, which may have changed since the harvest.

convert_to_string pnnl/chemreasoner/src/search/state/reasoner_state.py official repository ran · our draft was wrong licence not identified · pointer only · 60724ebc4ce5a746 · report
fstr pnnl/chemreasoner/src/search/state/reasoner_state.py official repository ran licence not identified · pointer only · e23f5c50c52a38d0 · report
generate_adsorption_energy_list_prompt pnnl/chemreasoner/src/search/state/reasoner_state.py official repository ran licence not identified · pointer only · 9fa4ecc48250be00 · report
load_sim_trees pnnl/chemreasoner/src/evaluation/chemreasoner_coherence_evaluation.py official repository ran · our draft was wrong licence not identified · pointer only · 2babba9bf041fb33 · report
parse_answer pnnl/chemreasoner/src/search/state/reasoner_state.py official repository ran licence not identified · pointer only · 8ad4e051476a3e90 · report
ReasonerState pnnl/chemreasoner/src/search/state/reasoner_state.py official repository unverified licence not identified · pointer only · 3725e3d4a3318ddd · report
generate_expert_prompt pnnl/chemreasoner/src/search/state/reasoner_state.py official repository unverified licence not identified · pointer only · ebc1c7ad9a578aff · report

Tasks

Computational chemistryGraph Neural NetworkHeuristic SearchLanguage ModelingLanguage ModellingLarge Language Model

Results from the paper archive 2025-07-28

No leaderboard rows for this paper in the archive.

Methods

Graph Neural Network

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections