MolGod/engraved-molecular-models

MolGod engraved molecular models (STL)

Version 1.0 — 63 molecules, 2026-10-22. Molecules are added in later versions; each version is a fixed snapshot.

Ball-and-stick 3D models of small molecules in which every atom sphere carries its recessed element symbol, so the element can be read from the printed object itself rather than from a colour code. Each mesh is generated by MolGod.org from a PubChem-computed 3D conformer; atomic coordinates and connectivity are not modified. These are computed conformers, not experimental crystal structures.

Contents

Molecule	CAS	Formula	File
4-Nitroaniline	100-01-6	C6H6N2O2	stl/4-Nitroaniline-3D-molecular-model-engraved-CAS-100-01-6.stl
Terephthaloyl chloride	100-20-9	C8H4Cl2O2	stl/Terephthaloyl chloride-3D-molecular-model-engraved-CAS-100-20-9.stl
Terephthalic Acid	100-21-0	C8H6O4	stl/Terephthalic Acid-3D-molecular-model-engraved-CAS-100-21-0.stl
Pentamidine	100-33-4	C19H24N4O2	stl/Pentamidine-3D-molecular-model-engraved-CAS-100-33-4.stl
Ethylbenzene	100-41-4	C8H10	stl/Ethylbenzene-3D-molecular-model-engraved-CAS-100-41-4.stl
Styrene	100-42-5	C8H8	stl/Styrene-3D-molecular-model-engraved-CAS-100-42-5.stl
Benzyl Chloride	100-44-7	C7H7Cl	stl/Benzyl Chloride-3D-molecular-model-engraved-CAS-100-44-7.stl
3-Cyclohexene-1-carbonitrile	100-45-8	C7H9N	stl/3-Cyclohexene-1-carbonitrile-3D-molecular-model-engraved-CAS-100-45-8.stl
Benzyl alcohol	100-51-6	C7H8O	stl/Benzyl alcohol-3D-molecular-model-engraved-CAS-100-51-6.stl
Benzaldehyde	100-52-7	C7H6O	stl/Benzaldehyde-3D-molecular-model-engraved-CAS-100-52-7.stl
Acrolein dimer	100-73-2	C6H8O2	stl/Acrolein dimer-3D-molecular-model-engraved-CAS-100-73-2.stl
1-Ethenyl-3-methylbenzene	100-80-1	C9H10	stl/1-Ethenyl-3-methylbenzene-3D-molecular-model-engraved-CAS-100-80-1.stl
3-Hexyn-1-ol	1002-28-4	C6H10O	stl/3-Hexyn-1-ol-3D-molecular-model-engraved-CAS-1002-28-4.stl
1-Ethoxy-2-(2-methoxyethoxy)ethane	1002-67-1	C7H16O3	stl/1-Ethoxy-2-(2-methoxyethoxy)ethane-3D-molecular-model-engraved-CAS-1002-67-1.stl
Cyclopentylamine	1003-03-8	C5H11N	stl/Cyclopentylamine-3D-molecular-model-engraved-CAS-1003-03-8.stl
2-Thiophenecarbonitrile	1003-31-2	C5H3NS	stl/2-Thiophenecarbonitrile-3D-molecular-model-engraved-CAS-1003-31-2.stl
5-Amino-1,2-dihydro-3H-1,2,4-triazol-3-one	1003-35-6	C2H4N4O	stl/5-Amino-1,2-dihydro-3H-1,2,4-triazol-3-one-3D-molecular-model-engraved-CAS-1003-35-6.stl
Hexyl 2-methylbutyrate	10032-15-2	C11H22O2	stl/Hexyl 2-methylbutyrate-3D-molecular-model-engraved-CAS-10032-15-2.stl
Methyl 3-hydroxyisoxazole-5-carboxylate	10068-07-2	C5H5NO4	stl/Methyl 3-hydroxyisoxazole-5-carboxylate-3D-molecular-model-engraved-CAS-10068-07-2.stl
(R)-3-Amino-2-phenylpropionic acid	1008-63-5	C9H11NO2	stl/(R)-3-Amino-2-phenylpropionic acid-3D-molecular-model-engraved-CAS-1008-63-5.stl
Fenadiazole	1008-65-7	C8H6N2O2	stl/Fenadiazole-3D-molecular-model-engraved-CAS-1008-65-7.stl
(R)-(-)-1-CBZ-3-pyrrolidinol	100858-33-1	C12H15NO3	stl/(R)-(-)-1-CBZ-3-pyrrolidinol-3D-molecular-model-engraved-CAS-100858-33-1.stl
Trimethyl(4-vinylphenyl)silane	1009-43-4	C11H16Si	stl/Trimethyl(4-vinylphenyl)silane-3D-molecular-model-engraved-CAS-1009-43-4.stl
Methyl 2-Bromo-4-nitrobenzoate	100959-22-6	C8H6BrNO4	stl/Methyl 2-Bromo-4-nitrobenzoate-3D-molecular-model-engraved-CAS-100959-22-6.stl
3,3'-Dichloro-4,4'-Diaminodiphenylmethane	101-14-4	C13H12Cl2N2	stl/3,3'-Dichloro-4,4'-Diaminodiphenylmethane-3D-molecular-model-engraved-CAS-101-14-4.stl
Cyclohexyl methacrylate	101-43-9	C10H16O2	stl/Cyclohexyl methacrylate-3D-molecular-model-engraved-CAS-101-43-9.stl
1,1'-Oxybis(4-nitrobenzene)	101-63-3	C12H8N2O5	stl/1,1'-Oxybis(4-nitrobenzene)-3D-molecular-model-engraved-CAS-101-63-3.stl
4,4'-Diaminodiphenyl Ether	101-80-4	C12H12N2O	stl/4,4'-Diaminodiphenyl Ether-3D-molecular-model-engraved-CAS-101-80-4.stl
Epichlorohydrin	106-89-8	C3H5ClO	stl/Epichlorohydrin-3D-molecular-model-engraved-CAS-106-89-8.stl
Glycidyl methacrylate	106-91-2	C7H10O3	stl/Glycidyl methacrylate-3D-molecular-model-engraved-CAS-106-91-2.stl
1-Bromopropane	106-94-5	C3H7Br	stl/1-Bromopropane-3D-molecular-model-engraved-CAS-106-94-5.stl
1,2-Dichloroethane	107-06-2	C2H4Cl2	stl/1,2-Dichloroethane-3D-molecular-model-engraved-CAS-107-06-2.stl
Acetic Anhydride	108-24-7	C4H6O3	stl/Acetic Anhydride-3D-molecular-model-engraved-CAS-108-24-7.stl
Toluene	108-88-3	C7H8	stl/Toluene-3D-molecular-model-engraved-CAS-108-88-3.stl
Pentane	109-66-0	C5H12	stl/Pentane-3D-molecular-model-engraved-CAS-109-66-0.stl
Hexane	110-54-3	C6H14	stl/Hexane-3D-molecular-model-engraved-CAS-110-54-3.stl
Cyclohexane	110-82-7	C6H12	stl/Cyclohexane-3D-molecular-model-engraved-CAS-110-82-7.stl
Thiacloprid	111988-49-9	C10H9ClN4S	stl/(3-((6-Chloropyridin-3-yl)methyl)-1,3-thiazolidin-2-ylidene)cyanamide-3D-molecular-model-engraved-CAS-111988-49-9.stl
Vanillin	121-33-5	C8H8O3	stl/Vanillin-3D-molecular-model-engraved-CAS-121-33-5.stl
Phenyl glycidyl ether	122-60-1	C9H10O2	stl/Phenyl glycidyl ether-3D-molecular-model-engraved-CAS-122-60-1.stl
8-Hydroxyquinoline	148-24-3	C9H7NO	stl/8-Hydroxyquinoline-3D-molecular-model-engraved-CAS-148-24-3.stl
Perfluorooctanesulfonic acid	1763-23-1	C8HF17O3S	stl/Perfluorooctanesulfonic acid-3D-molecular-model-engraved-CAS-1763-23-1.stl
Benomyl	17804-35-2	C14H18N4O3	stl/Benomyl-3D-molecular-model-engraved-CAS-17804-35-2.stl
L-menthol	2216-51-5	C10H20O	stl/L-menthol-3D-molecular-model-engraved-CAS-2216-51-5.stl
Triglycidyl isocyanurate	2451-62-9	C12H15N3O6	stl/Triglycidyl isocyanurate-3D-molecular-model-engraved-CAS-2451-62-9.stl
Tridemorph	24602-86-6	C19H39NO	stl/Tridemorph-3D-molecular-model-engraved-CAS-24602-86-6.stl
Bromadiolone	28772-56-7	C30H23BrO4	stl/Bromadiolone-3D-molecular-model-engraved-CAS-28772-56-7.stl
Tris(2,4-di-tert-butylphenyl) phosphite	31570-04-4	C42H63O3P	stl/Tris(2,4-di-tert-butylphenyl) phosphite-3D-molecular-model-engraved-CAS-31570-04-4.stl
Linuron	330-55-2	C9H10Cl2N2O2	stl/Linuron-3D-molecular-model-engraved-CAS-330-55-2.stl
Chlorophacinone	3691-35-8	C23H15ClO3	stl/Chlorophacinone-3D-molecular-model-engraved-CAS-3691-35-8.stl
4-Chlorobenzotrichloride	5216-25-1	C7H4Cl4	stl/4-Chlorobenzotrichloride-3D-molecular-model-engraved-CAS-5216-25-1.stl
Glycidol	556-52-5	C3H6O2	stl/Glycidol-3D-molecular-model-engraved-CAS-556-52-5.stl
Dimorpholinomethane	5625-90-1	C9H18N2O2	stl/Dimorpholinomethane-3D-molecular-model-engraved-CAS-5625-90-1.stl
Theophylline	58-55-9	C7H8N4O2	stl/Theophylline-3D-molecular-model-engraved-CAS-58-55-9.stl
1-Phenethylamine	618-36-0	C8H11N	stl/1-Phenethylamine-3D-molecular-model-engraved-CAS-618-36-0.stl
Methanol	67-56-1	CH4O	stl/Methanol-3D-molecular-model-engraved-CAS-67-56-1.stl
Chloroform	67-66-3	CHCl3	stl/Chloroform-3D-molecular-model-engraved-CAS-67-66-3.stl
Benzene	71-43-2	C6H6	stl/Benzene-3D-molecular-model-engraved-CAS-71-43-2.stl
Ammonia	7664-41-7	H3N	stl/Ammonia-3D-molecular-model-engraved-CAS-7664-41-7.stl
Sulfuric Acid	7664-93-9	H2O4S	stl/Sulfuric Acid-3D-molecular-model-engraved-CAS-7664-93-9.stl
Nitric Acid	7697-37-2	HNO3	stl/Nitric Acid-3D-molecular-model-engraved-CAS-7697-37-2.stl
Warfarin	81-81-2	C19H16O4	stl/Warfarin-3D-molecular-model-engraved-CAS-81-81-2.stl
Naphthalene	91-20-3	C10H8	stl/Naphthalene-3D-molecular-model-engraved-CAS-91-20-3.stl

metadata.csv has one row per molecule: CAS Registry Number, name, molecular formula, molar mass, IUPAC name, InChIKey, SMILES, PubChem CID, atom and bond counts, geometry file, triangle count, file name, file size, SHA-256 of the STL, render file, the MolGod record and the identical file on Wikimedia Commons.

Files

• stl/ — binary STL, closed (watertight) single solid. Coordinates are in ångström; STL stores no unit, so the model must be scaled deliberately in the slicer.
• geometry/ — one JSON per molecule: element and x, y, z (ångström) for every atom, and bonds as zero-based atom index pairs with bond order (aromatic rings in Kekulé form). These are the coordinates the mesh was built from.
• renders/ — a still render of the same mesh, for preview only.

Provenance

Source structures: PubChem (NCBI) computed 3D conformers, identified by the PubChem CID in metadata.csv. Mesh generation and engraving: MolGod.org. The same files are published on Wikimedia Commons (link per row), which serves as the reference copy; the SHA-256 in metadata.csv allows a byte-for-byte comparison.

Scope and purpose

The collection supports a research question in chemistry education: whether labels carried by the model itself help learners interpret atom arrangement, bonding and 3D geometry without a colour key. This effect has not yet been evaluated. Background, references and the planned study: https://molgod.org/engraved-molecular-models/

Loading

from datasets import load_dataset
from huggingface_hub import hf_hub_download

meta = load_dataset("MolGod/engraved-molecular-models", split="train")          # one row per molecule
row = meta[0]
stl_path = hf_hub_download("MolGod/engraved-molecular-models", row["stl_file"], repo_type="dataset")

Possible uses

• Teaching material: printable models whose element labels survive single-colour printing.
• Pairing molecular identifiers (InChIKey, SMILES, CAS) with a closed 3D surface mesh, e.g. for 3D shape or mesh-processing experiments and for grounding structure descriptions in a physical object.

Limitations

• One computed conformer per molecule; no conformational ensemble, no experimental geometry.
• The mesh is a ball-and-stick printing model (spheres and cylinders), not an electron-density or molecular surface.
• Engraved symbols change the sphere surface locally; the mesh is not a clean geometric primitive model.
• Small collection, chosen for chemistry teaching, not a representative sample of chemical space.

Licence and attribution

CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/). Attribution per file: " 3D model by MolGod.org — https://molgod.org/molecule// — CC BY-SA 4.0".

Citation

Each molecule also has its own Zenodo record with a DOI (zenodo_doi in metadata.csv); cite that DOI when you use a single model. To cite the collection:

@misc{koska2026molgod_engraved,
  author       = {Koska, Adrian},
  title        = {{MolGod} engraved molecular models ({STL})},
  year         = {2026},
  publisher    = {Hugging Face},
  howpublished = {\url{https://huggingface.co/datasets/MolGod/engraved-molecular-models}},
  note         = {CC BY-SA 4.0. Project page: \url{https://molgod.org/engraved-molecular-models/}}
}

Source structures (please cite as well when using the geometry):

Kim, S., Chen, J., Cheng, T., et al. (2025). PubChem 2025 update. Nucleic Acids Research, 53(D1), D1516–D1525. https://doi.org/10.1093/nar/gkae1059