TPSA and Crippen cLogP Molecular Property Calculator
Inspect topological polar surface area and Crippen logP for a cited sildenafil parent structure. The existing engine calculates these descriptors from the molecular graph and updates them when the structure changes. The two quantities capture different aspects of a representation and should not be treated as interchangeable permeability measurements.
The existing sildenafil example from the shipped ChEMBL 37 parent library. Its heteroatoms and ring systems provide a practical input for comparing the descriptor definitions. This page reports whole-molecule scalar descriptors, not atom-coloured surface contributions.
Read the descriptor names literally
Topological polar surface area adds contributions assigned to recognised polar fragments. It is fast and reproducible for a specified molecular representation, which makes it useful for exploring a series. It does not require a three-dimensional conformer. That advantage also sets its scope: the same graph receives the same topological estimate even if different solution conformations expose different groups.
The partition coefficient describes equilibrium distribution between two phases, whereas the computed logP is a model estimate of that property. The workspace identifies its algorithm so a comparison can be reproduced. Avoid writing simply lipophilicity when the distinction between measured logP, calculated logP and pH-dependent logD matters to the interpretation.
Make edits that answer a defined question
Use the editor to change one structural feature and inspect how the descriptors respond. Replacing a heteroatom or masking a donor may change several properties simultaneously. The numerical change reflects the new represented graph; it does not isolate a single biological mechanism. Keep the original structure and edited structure distinguishable if you compare them or export their property rows.
For an experimental decision, bring in complementary data such as aqueous solubility under stated conditions, stability, ionisation and permeability in a relevant assay. A low TPSA or high logP can suggest a question but is not a complete permeability argument. Protein binding, efflux, metabolism and formulation can alter exposure independently of these descriptors. Preserve those distinctions when transferring a property comparison into a project report.
Equations and variables
Partition coefficient definition
log P = log10([solute]octanol/[solute]water)
- P
- Partition coefficient of the neutral species under the defined conditions
- [solute]
- Equilibrium concentration in the indicated phase (same concentration unit in both phases)
Topological polar surface area
TPSA = Σ Ai
- Ai
- Polar fragment contribution assigned by the descriptor method (Ų)
- TPSA
- Topological estimate from the represented molecular graph (Ų)
Scope and limitations
- The shipped TPSA method uses the documented RDKit nitrogen/oxygen contribution convention. It is topological, not a solvent-accessible surface calculation on a measured conformation.
- Crippen logP is an atom-contribution estimate. It does not supply logD at a chosen pH, pKa or transport-mediated permeability.
- The represented charge, tautomer and fragments affect interpretation. Do not compare a parent compound with a salt representation without reviewing how the engine describes each.
Sources and provenance
- RDKit descriptor implementation and versioned reference checksBSD-3-Clause
Method implementation; computed molecular properties are estimates.
- ChEMBL 37 parent structures in the shipped compound libraryCC BY-SA 3.0; share-alike
Existing library capture: 28 September 2026. Preserve attribution when redistributing its rows.
- Wildman and Crippen: atomic contributions to molecular propertiesCited method; no reproduced article data
- Ertl, Rohde and Selzer: fast calculation of molecular polar surface areaCited method; no reproduced article data
Technical questions
Is TPSA the same as the exposed polar surface in solution?
No. TPSA is calculated from a molecular graph using a fragment method. Three-dimensional exposure can depend on conformation, solvent and intramolecular interactions. The descriptor is useful for consistent comparisons but does not directly measure the surface presented by a molecule in a particular environment.
Can I use cLogP as logD at physiological pH?
No. LogD depends on the distribution of ionisation states at the stated pH, while logP refers to the neutral species under defined conditions. This workspace does not calculate pKa or pH-dependent distribution coefficients, so those additional quantities must come from a suitable source or measurement.
Why might another calculator give a different value?
Different fragment rules, structure standardisation, ionisation assumptions or software versions can produce different estimates. Compare the method name and represented structure before interpreting the difference as a chemical disagreement. Here the displayed lipophilicity estimate is explicitly Wildman–Crippen.
Connected workflows
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Explore descriptor changes after a declared structural edit.
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Identify the missing inputs needed for CNS MPO.
- DMSO stock reconstitution volume
Distinguish graph-derived mass from the actual material in a vial.
- Fsp3 Calculator: Fraction sp3 Carbons and 3D Saturation
Inspect saturation (Fsp3) and aromatic-ring count alongside TPSA and logP.
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Compare kinase inhibitor scaffolds by their physicochemical descriptors.