This entry presents Serotonin (C10H12N2O; CAS 50-67-9; PubChem CID 5202) as a 3D-printable ball-and-stick model in which every atom carries its engraved element symbol (C, H, N, O), so the model can be read without a colour key. Atomic coordinates come from the PubChem-computed 3D conformer (not an experimental crystal structure); coordinates and connectivity are unchanged.

Project scope and purpose

MolGod is an open educational-science project that publishes engraved ball-and-stick models of individual chemical compounds. Models are generated deterministically from public structure data and released under CC BY-SA 4.0 together with their identifiers and provenance.

Standard molecular STL files encode geometry only; atom identity, conventionally conveyed by colour, is lost in single-material additive manufacturing. In these models the element symbol is a recessed engraving on each atomic sphere, so atom identity is part of the mesh and remains readable in any print material, visually and by touch.

The design objective is to shorten the time learners need to identify the atoms of a molecule, so that instruction can concentrate on connectivity, bond order and three-dimensional geometry, and to reduce teacher preparation to scaling and slicing a ready file. This is a design rationale: the effect on learning outcomes has not yet been formally evaluated.

Project rationale, related peer-reviewed research and the validation plan: How MolGod engraved molecular models are made.

Structure at a glance

• 25 atoms: 10 C, 12 H, 2 N, 1 O

• 26 bonds: 16 single, 10 aromatic

• Two rings (one 5-membered and one 6-membered), fused along a shared edge, both aromatic

• Functional groups: one phenolic hydroxyl group (Ar-OH) and one primary amino group (-NH2)

• Three hydrogen-bond donors and two acceptors (computed)

• Fraction of sp3-hybridised (tetrahedral) carbon atoms: 0.2 (computed)

Use in teaching

• Counting task: students tally the engraved symbols (10 C, 12 H, 2 N, 1 O; 25 atoms) and rebuild the formula C10H12N2O from the model alone.

• Aromaticity: identify the two aromatic rings and the 10 bonds recorded as aromatic; the model draws them as one Kekulé structure (alternating single and double bonds), while in the real molecule they are delocalised, intermediate between single and double.

• Functional groups: find the phenolic hydroxyl group (Ar-OH) and the primary amino group (-NH2) on the model and name each one.

File and printing

STL mesh of 311,952 triangles, a closed (watertight) single solid. Coordinates are in ångström and STL stores no unit, so scale the model deliberately in your slicer. Measured bounding box: 7.077 × 7.535 × 6.772 Å; at scale factor 10 (1 Å to 10 mm, file read in millimetres) the print measures about 70.8 × 75.3 × 67.7 mm. SHA-256: 6361ae3ad97ef5483d800a6c623529797de5651fd9e1677798f87c3e17bdf955.

Validation

• InChIKey identical to the PubChem record (PubChem FTP SDF, file dated 2026-10-08): QZAYGJVTTNCVMB-UHFFFAOYSA-N

• Molecular formula and hydrogen-bond donor/acceptor counts identical to PubChem

• Mesh: triangle count in the header equals the actual count; 0 edges not shared by exactly two triangles; 1 connected solid; SHA-256 equal to the published file

Source, licence and identifiers

Full record: Serotonin 3D molecular model and data (CAS 50-67-9) · Licence and provenance record: License and provenance of the Serotonin 3D model · Same file on Wikimedia Commons: File:Serotonin-3D-molecular-model-engraved-CAS-50-67-9.stl

• MolGod ID: MolGod ID MG_646-942-545-67

• Wikidata: Q167934

• EC number: 200-058-9

• ChemSpider ID: 5013

• IUPAC name: 3-(2-aminoethyl)-1H-indol-5-ol

• InChIKey: QZAYGJVTTNCVMB-UHFFFAOYSA-N

• SMILES: C1=CC2=C(C=C1O)C(=CN2)CCN

• Molar mass 176.21 g/mol (exact mass 176.094963011)

Licence: CC BY-SA 4.0 (licence text). Required attribution: "Serotonin 3D model by MolGod.org — https://molgod.org/molecule/50-67-9/ — CC BY-SA 4.0".