Molecular Visualization
Enter a molecule name or SMILES notation
About the Molecule Viewer
Our molecule viewer generates 2D structural diagrams and calculates key molecular properties including molecular formula, molecular weight, SMILES notation, LogP (partition coefficient), and counts of atoms, bonds, and rings.
Search by common name (e.g., Caffeine, Aspirin, Glucose) or enter SMILES notation directly for any organic or inorganic molecule.
Molecular Properties Explained
- Molecular Formula: Shows the types and numbers of atoms present in the molecule (e.g., C8H10N4O2 for caffeine).
- Molecular Weight: The sum of all atomic masses in the molecule, measured in g/mol. Essential for concentration and dosage calculations.
- SMILES Notation: A text-based representation of molecular structure. SMILES (Simplified Molecular Input Line Entry System) is widely used in cheminformatics databases and software.
- LogP: The partition coefficient measures how a molecule distributes between water and octanol. Higher LogP values indicate greater lipophilicity (fat solubility), which is important for predicting drug absorption and bioavailability.
- Atom, Bond, and Ring Counts: Structural descriptors that help characterize molecular complexity and are used in drug-likeness assessments.
Using SMILES Notation
SMILES is a compact way to describe molecular structures as text strings. Atoms are represented by their chemical symbols, bonds by special characters (= for double, # for triple), and ring closures by matching digits. For example, benzene is written as c1ccccc1 and ethanol as CCO.
You can paste SMILES strings from databases like PubChem, ChEMBL, or DrugBank directly into the search field to visualize any molecule and calculate its properties.
Common mistakes
These are the errors that come up most often, and each one changes the answer rather than merely looking untidy.
Getting SMILES capitalisation wrong
In SMILES notation, case carries meaning. An upper case C is an aliphatic carbon while a lower case c is an aromatic one. Writing benzene as CCCCCC gives hexane rather than c1ccccc1, and the structure returned will be entirely different from the one intended.
Expecting every common name to resolve
Name lookup covers a large set of well known compounds, but trade names, laboratory shorthand, and newly published structures may not resolve. When a name fails, a SMILES string always works and removes any ambiguity about which isomer you meant.
Reading a two dimensional diagram as real geometry
A flat structural diagram shows connectivity, not shape. Bond angles and the arrangement in space are not conveyed by it, so a molecule drawn as a flat ring may be substantially puckered in reality.
Overlooking stereochemistry
Two molecules can share a formula and a connectivity map and still be different substances with different biological activity. If stereochemistry matters for your purpose, it has to be specified explicitly in the SMILES string rather than assumed.
Frequently asked questions
What is SMILES notation?
Simplified Molecular Input Line Entry System is a way of writing a molecular structure as a single line of text. Atoms are written as their element symbols, branches are enclosed in parentheses, and ring closures are marked with matching digits. Ethanol is CCO and benzene is c1ccccc1. It is compact, unambiguous, and readable by essentially every cheminformatics tool.
What does LogP tell me?
LogP is the logarithm of a compound's partition coefficient between octanol and water, and it measures lipophilicity. A positive value means the compound prefers fat to water, and a negative value means the reverse. It is widely used in drug design because it predicts how readily a molecule crosses cell membranes.
Why does the viewer show a flat structure?
A two dimensional depiction shows which atoms are bonded to which, which is what most structural questions are about, and it renders quickly and legibly in a browser. Three dimensional conformation is a separate and computationally heavier problem, since most molecules have many accessible conformations rather than one shape.
Where do the molecular properties come from?
They are computed by RDKit, an open source cheminformatics toolkit used widely in pharmaceutical research, rather than read from a fixed database. That means an unusual or newly drawn structure is handled the same way a familiar one is.