Molecule Properties

Compare related molecules and see what a functional-group change does to calculated properties.

Reference moleculeComparison molecule

Benzene structure: Aromatic hydrocarbon — Benzene and Phenol, neutral two-dimensional structures drawn by RDKit.

Phenol structure: Phenolic hydroxyl · O–H; oxygen site highlighted — Benzene and Phenol, neutral two-dimensional structures drawn by RDKit.

Aromatic hydrocarbonThe ring contains carbon and hydrogen. It has no conventional hydrogen-bond donor or acceptor sites in this descriptor scheme.

Phenolic hydroxyl · O–HThe hydroxyl group contributes one donor site and one acceptor site. The hydrogen attached to oxygen distinguishes it from an ether.

Inspect a property

H-bond donors: 0 → 1 sites

A donor needs an appropriate hydrogen attached to a heteroatom. Phenol has an O–H group; anisole has O–CH₃ and cannot donate that hydrogen. These are conventional descriptor counts, not all possible weak interactions.

Difference: +1 sites

Property	Benzene	Phenol
H-bond donors(sites)	0	1
H-bond acceptors(sites)	0	1
Polar surface area(Å²)	0.00	20.23
Crippen logP	1.69	1.39
Molecular weight(g/mol)	78.11	94.11

Fixed examples calculated with RDKit 2026.03.6. Neutral structures; no pH-dependent ionisation is modelled. Descriptor values and “drug-like” ranges do not establish efficacy or safety.

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Quick reference

Change one chemical feature

Benzene, phenol and anisole share an aromatic ring. Adding a hydroxyl group introduces oxygen and an O–H hydrogen. Replacing that hydrogen with methyl creates an ether. These related structures make the consequences easier to inspect than a comparison of unrelated molecules.

Donors, acceptors and polar surface

A conventional hydrogen-bond donor needs a suitable attached hydrogen; an acceptor needs an appropriate lone pair. Phenol has one of each in RDKit’s site-counting scheme. Anisole keeps an oxygen acceptor but loses the O–H donor. Topological polar surface area assigns different contributions to these oxygen environments.

A descriptor is not an outcome

Crippen logP is an atom-based estimate of neutral octanol/water partitioning. It is not a measured solubility, pH-dependent logD, permeability or potency. Molecular weight and hydrogen-bond counts help describe a compound; satisfying a drug-likeness heuristic does not establish efficacy or safety. The examples here remain neutral.

Check your understanding Optional

Replacing phenol’s O–H hydrogen with methyl gives anisole. What happens to the conventional hydrogen-bond counts?

Both donor and acceptor sites disappear.The donor is lost; one acceptor remains.Both counts stay the same because oxygen is still present.

At the bench

Use the same chemistry engine to calculate descriptors and inspect your own molecules after comparing these fixed examples.

Open Molecule

Sources and model notes

These interactive examples explain selected relationships using the assumptions shown beside their controls. Calculated quantities and illustrative inputs are identified in each tool; use the linked Drybench app to work with your own data.

RDKit · Wildman–Crippen logP

Official descriptor documentation and reference to the atom-contribution method. Values here were calculated using the installed RDKit engine, not copied from a measured-property table.

RDKit · Hydrogen-bond site descriptors

Definitions of hydrogen-bond donors and acceptors; the tool uses NumHBD and NumHBA, not the historical N/O proxy counts.

Lipinski et al. · Solubility and permeability

Original discussion of physicochemical heuristics for absorption and permeability, which do not establish therapeutic efficacy.