This repository contains the input files, output geometries, and agent traces associated with the case-study benchmarks and additional evaluation tests reported in the revised manuscript and Supporting Information.
Unless otherwise noted, each project directory contains five independent runs:
Directory/
├── run1/
├── run2/
├── run3/
├── run4/
└── run5/
Each run directory contains the files associated with that independent run, including the corresponding input file(s), output geometry file(s), and agent trace (.mhtml).
The primary case-study benchmark directories are located under Case_study/. Additional evaluation datasets are organized separately under robustness_test/, configuration_test/, tool_ablation/, and model_comparison/.
Case_study/Case_study7_chem_reasoning_TS/ uses a different directory structure.
The following project directories are located under Case_study/.
| Directory | Corresponding Figure |
|---|---|
Case_study1A_spermidine_protection/ |
Figure 2a |
Case_study1A_spermidine_protection_generic/ |
Figure S14a |
Case_study1B_Co-porphyrin_phenyl/ |
Figure 2b |
Case_study1B_Co-porphyrin_phenyl_generic/ |
Figure S14b |
Case_study2_Co-Pc_ligand_binding/ |
Figure 3 |
Case_study2_Co-Pc_ligand_binding_generic/ |
Figure S18 |
Case_study3A_isomers/ |
Figure 4a |
Case_study3B_zirconocene/ |
Figure 4b |
Case_study3C_CpRusumanene/ |
Figure 5 |
Case_study4A_MoCl3PNP/ |
Figure 6a |
Case_study4B_ligand_exchange/ |
Figure 6b |
Case_study5A_isomers_and_enantiomers/ |
Figure 7a |
Case_study5B_fragment_identification/ |
Figure 7b |
Case_study6_ethylene_insertion/ |
Figure 8 |
Case_study7_chem_reasoning_TS/ |
Figure 9 |
The following project directories are located under robustness_test/.
| Directory | Corresponding Figure |
|---|---|
Case_study1B_Co-porphyrin_phenyl/ |
Figure S15a |
Case_study1B_Co-porphyrin_phenyl_generic/ |
Figure S15b |
Case_study1B_porphyrin_generic/ |
Figure S16 |
The following project directories are located under configuration_test/.
| Directory | Corresponding Figure |
|---|---|
Case_study2_Pb-Pc_ligand_binding/ |
Figure S20 |
Case_study3C_CpRusumanene/ |
Figure S19 |
The following project directories are located under tool_ablation/.
| Directory | Corresponding Figure |
|---|---|
Case_study1B_Co-porphyrin_phenyl/ |
Figure S21a |
Case_study1B_Co-porphyrin_phenyl_generic/ |
Figure S21b |
Case_study2_Co-Pc_ligand_binding/ |
Figure S22 |
Case_study6_ethylene_insertion/ |
Figure S23 |
Case_study6_ethylene_insertion_TS_only/ (a) |
Figure S24 |
Case_study6_ethylene_insertion_TS_only_wotools/ (b) |
Figure S24 |
(a) Generated using the full agent setup.
(b) Generated using the tool-ablation setup.
The following directories are located under model_comparison/. Each directory name corresponds to the underlying LLM used for the test.
| Directory | Corresponding Table |
|---|---|
GPT5.2/ |
Table S25 |
opus4.5/ |
Table S25 |
opus4.8/ |
Table S25 |
Note: The
.mhtmlfiles are unedited local snapshots of the Estructural web-platform GUI. GitHub does not render.mhtmlfiles as webpages, so please download the files and open them locally in a web browser to view the original interactive traces.
The agent traces preserve the layout of the Estructural web-platform GUI, as illustrated below.
In the saved trace, the Thinking and Tool sections can be expanded or collapsed by clicking their headers.
