Structure-first chemical reasoning

Let the molecule become the catalogue.

Use the SMILES structure as the navigation surface: detect functional groups, highlight the matching substructure, then connect each group to local orbital character and chemically relevant reaction families. The 3D orbital renderer remains a neighboring tool rather than being forced into this page.

Loading catalogue + RDKit.js…

Canonical SMILES—

Detected group types—

Detected group instances—

RendererRDKit.js

Structure map

RDKit.js loads the molecular depiction here.

electron-rich / δ− tendency electron-poor / electrophilic tendency π-delocalized / conjugated region H-bond donor-capable heteroatom −I inductive withdrawal path +M mesomeric donation path Rule-based qualitative map. Colours describe local chemical tendency, not orbital phase and not a DFT electrostatic-potential or electron-density surface. −I/+M paths are substituent-effect annotations, not charge-density streamlines.

Dark-background RDKit depiction.Click a detected group to highlight it.Electronic map is anchored to detected atoms and functional-group rules.

Selected chemistry

structureSMARTS rulechemistry note

Citric acid

Build the molecule, then select a functional-group card to connect the highlighted structure to orbital character and reaction families.

Reaction families are prompts for chemical reasoning, not predictions under unspecified conditions.

Detected in this molecule

Reactive and interaction-relevant groups

SMARTS-based group detection.

Substituent effects

Inductive and mesomeric donor/acceptor language

These effects describe how a substituent perturbs electron distribution. They are separate from the local δ+/δ− polarity colours above.

−I · inductive acceptor

Withdraws through σ bonds. The effect is strongest close to the substituent and decays with bond distance. Halogens are classic −I groups.

+I · inductive donor

Pushes electron density through the σ framework in the simplified substituent-effect picture. Alkyl substitution is the usual reference example.

−M · mesomeric acceptor

Withdraws through a conjugated π system. Carbonyl-derived and nitro substituents are common examples when attached in the appropriate conjugated orientation.

+M · mesomeric donor

Donates a lone pair into an adjacent conjugated π system. O/N lone-pair donors and aryl halogens can show this effect when direct orbital overlap is possible.

Fischer esterification connection

R–C(=O)–OH + R′–OH ⇌ R–C(=O)–OR′ + H₂O (H⁺ catalysis)

Carbonyl protonation increases electrophilicity before alcohol attack. A nearby −I substituent can increase carbonyl polarization; a conjugated +M donor can reduce electrophilicity, while −M withdrawal can increase it. The observed rate and equilibrium still depend on sterics, catalyst, solvent, alcohol activity and removal of water.

Halogens and acidity: a halogen near a carboxyl group often lowers the acid's pK_a by −I stabilization of the conjugate base. It does not, by itself, imply that every solution containing a halogenated molecule has a lower pH.

Knowledge layer

Functional-group catalogue

Data source: /data/functional_groups.json

Move between representations

Catalogue2D groups + reactivity knowledge 3D moleculeconformer + local orbital layer Superposition studiobasis-function mathematics Molecular overlaplocalized bonding pictures

Architecture: the catalogue answers “what chemistry is present?” locally in the browser. The `/api/model` endpoint answers “what 3D local orbital model should we render?” on the server. Both begin from the same SMILES string but do different work.

For deployment, pin and self-host RDKit.js + RDKit_minimal.wasm rather than relying on an unversioned CDN asset.