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Scientific exploration, made practical

Molecule Explorer

Explore drug molecules, inspect public physicochemical data, and calculate pH-dependent ionization for learning and analytical method planning.

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Molecule Explorer artwork by Practical Pharma Science
Explore. Understand. Apply.
Compound data · Ionization concepts · Analytical insights

Compound explorer

Search PubChem by compound name. Data shown below are public database descriptors, not experimental measurements.

Try:
Enter a compound name or choose a popular example.
2D compound structure

Compound

Structure image and descriptors supplied by PubChem. Confirm identity, salt form, stereochemistry, and data suitability before professional use.

Interpretation note: XLogP is a computed estimate of octanol/water partitioning for the represented structure; it is not logD at a specified pH. PubChem does not provide a universal, verified pKa for every compound in this lookup, so pKa must be sourced or entered separately.
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Compound identity & data-quality check

Cross-check the selected record before using descriptors in a scientific workflow.

Waiting for compound searchNo record checked yet
Database recordSearch a compound to inspect its source record.
Structure identifierCID and InChIKey will be checked when available.
Descriptor provenanceDatabase-derived values will be labelled separately from estimates.

A matching name is not proof of material identity. Confirm salt form, stereochemistry, hydrate/solvate state, purity and the supplier’s documentation before laboratory use.

Interactive 3D molecular structure

Rotate, zoom, and inspect the selected compound’s available 3D conformer.

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Your 3D molecule will appear here

Search for a compound, then select “Load 3D structure”. A 3D conformer must be available from PubChem.

Mouse/touch rotationScroll/pinch zoomElement-colored atoms
3D coordinates represent a conformer, which may be computed rather than experimentally determined. A single conformer does not capture all molecular flexibility, protonation states, solvent effects, or the biologically bound conformation. Viewer requires an internet connection and the external 3Dmol.js library.
No 3D structure loaded.

Compound-specific pKa references

Reference values are linked to public sources and shown with provenance. Values can vary with experimental conditions, solvent, temperature, and the reported method.

Choose a compound to view its sourced reference value. Use the “Apply to calculator” button only after confirming that the source matches the compound form and conditions relevant to your work.

Sources: PubChem compound records, including experimental dissociation-constant entries with references to ChEMBL and published literature.
These are reference entries for demonstration, not a complete pKa database. The ibuprofen record reports more than one literature value; the displayed value is tied to a specific source entry. Do not treat a single value as universally correct for all conditions.

pKa & ionization calculator

Explore the Henderson–Hasselbalch relationship for a single monoprotic acid or base.

Estimated ionized fraction for a weak acid
3.1%
Neutral fraction: 96.9%

Acid: fraction ionized = 1 / (1 + 10^(pKa − pH)).

How to interpret the result

For a weak acid, the deprotonated form A⁻ is counted as ionized. For a weak base, the protonated form BH⁺ is counted as ionized. At pH = pKa, the model predicts 50% ionization.

This is an idealized, single-site equilibrium calculation. Polyprotic compounds, multiple ionizable sites, activity effects, solvent composition, temperature, and matrix effects may require more advanced treatment. Ionization alone does not predict retention time or solubility.
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pH–speciation curve

Follows the calculator above. The gold line marks your solution pH.

Neutral fractionIonized fractionSolution pH

Idealized Henderson–Hasselbalch model. Assumes one independent ionization site, equilibrium and a defined pKa; it does not account for activity coefficients, solvent effects, aggregation or coupled ionization sites.

Working from a structure, not a known pKa? pH Assist Pro estimates pKa for every ionizable centre from the structure, classifies zwitterions, finds the isoelectric point and plots per-site titration curves.
See pH Assist Pro →

Multiple ionizable-site estimator

Approximate the fully neutral fraction for up to three independent ionizable sites. This is a simplified microspecies model, not a full polyprotic equilibrium solver.

Estimated fraction fully neutral (independent-site assumption)
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Enter site pKa values to calculate.

This multiplies independent-site neutral fractions. Real polyprotic compounds can have coupled equilibria, tautomerism, zwitterionic states, and microstate-specific pKa values. Do not use this estimate as a validated logD, solubility, or retention prediction.

Molecular property interpretation engine

Connect compound descriptors and ionization concepts to practical analytical questions—with explicit assumptions and uncertainty.

Evidence-aware interpretation

Analytical behavior assessment

Search for a compound above, then enter a verified pKa and select the appropriate ionizable-group model to generate a qualitative interpretation.

Current XLogP
Not loaded
Computed descriptor from PubChem
Estimated logD at selected pH
Not calculated
Idealized neutral-only partition model

What the model suggests

  • Load a compound and provide a verified pKa to generate an interpretation.
This tool does not predict retention time. Interpretations are qualitative and depend on structure, stationary phase, mobile-phase composition, temperature, ionic strength, and other method conditions.

Model inputs & assumptions

The engine uses the pKa, pH, and acid/base selection in the calculator to estimate the ionized and neutral fractions. It uses the compound's PubChem XLogP only when available.

For an idealized monoprotic compound where the ionized form is assumed to partition negligibly into the organic phase, approximate logD = logP + log₁₀(fraction neutral). This is a simplified estimate—not a measured logD and not reliable for every compound, especially zwitterions, polyprotic molecules, or systems where ion pairing matters.

Before using this output in method development, verify pKa, compound identity/salt form, and lipophilicity values from appropriate primary sources or experimental data. The model does not account for multiple ionizable sites or solvent-dependent pKa shifts.

Method design studio

Turn the selected molecule and your analytical goal into a documented starting method to screen.

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Molecule-to-HPLC method design studio

Generate a documented starting method proposal from the selected molecule and analytical objective.

Search a compound first, then generate a method hypothesis. This is a screening starting point, not a validated method.

Rule-based guidance only. Verify analyte stability, buffer compatibility, column pH limits, system pressure, solubility and critical-pair selectivity.

Calibration-based RP-HPLC retention model

Fit a simple linear log k versus organic modifier model using your own experimental calibration data. This is not a universal retention predictor; it only applies within a justified calibration domain.

Enter at least three valid experimental calibration points.
R²
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Predicted k
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Predicted tR
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when t₀ supplied

No fitted model yet.

A high R² does not establish predictive validity. Validate with independent compounds or conditions, inspect residuals and prediction error (e.g., RMSE/MAE), and define the model’s applicability domain. This simple linear model is not suitable for extrapolation or every gradient method. For regulated use, follow appropriate analytical development and validation principles, including ICH Q14 and Q2(R2).
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Retention-model validation

Compare predictions with independent observed retention factors or retention times.

n—
MAE—
RMSE—
Bias—

Metrics require numeric observed/predicted pairs. Keep calibration and independent validation data separate; metrics on training data are not independent validation.

Chromatogram simulator

Draw a synthetic chromatogram from retention times you supply and check approximate resolution between neighbouring peaks.

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Multi-analyte chromatogram simulator

Generate a synthetic chromatogram from peak parameters or experimental/calibrated inputs.

Illustrative synthetic example. Peak parameters are not inferred from molecular properties.

This simulator does not model instrument-specific dispersion, adsorption, overload, gradient migration or detector response. Do not treat it as a compound-specific prediction unless peak parameters come from an appropriate calibrated model.

Scientific report

Export everything you have done on this page as a timestamped HTML or PDF summary.

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Scientific report export

Create a timestamped, printable report with the current compound details and any advanced-module results entered below.

The downloadable HTML report is self-contained and can be opened in a browser. “Print / Save as PDF” opens the browser print dialog; choose “Save as PDF”. This report is a tool-generated summary, not a regulated or validated record.

Practical analytical tools

Use molecular properties as a starting point for scientific reasoning—not as a substitute for method development or experimental verification.

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Molecular structure

Review a database-sourced 2D structure and key identifiers for the selected compound.

pH

Ionization concepts

Explore how pH relative to pKa affects the idealized ionized fraction.

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Physicochemical descriptors

Inspect formula, molecular weight, XLogP, hydrogen-bond counts, and topological polar surface area when available.

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Chromatography thinking

Use charge state, hydrophobicity, and method conditions as discussion points—not as a retention-time prediction.

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LC–MS preparation

Consider molecular mass and structure while planning confirmatory analytical work.

pKa

pH Assist Pro

Structure-based pKa for every ionizable centre, zwitterion and isoelectric-point classification, per-site titration curves and CSV export.

See pH Assist Pro →