3D Molecule Viewer

Visualize molecules in 3D. Load predefined molecules or input your own molecular data.

Format: Element symbols followed by numbers (e.g., H2O, C6H6). Use parentheses for groups (e.g., (CH3)2CO).
Common Molecular Formulas
Water: H2O Methane: CH4 Ethanol: C2H5OH Benzene: C6H6 Aspirin: C9H8O4 Caffeine: C8H10N4O2 Glucose: C6H12O6
XYZ Format: First line: atom count, Second line: comment (optional), Then lines with: Element X Y Z coordinates
Example: Water Molecule
3 Water molecule O 0.0000 0.0000 0.0000 H 0.7570 0.5860 0.0000 H -0.7570 0.5860 0.0000
SMILES Examples: Water: O, Methane: C, Ethanol: CCO, Benzene: c1ccccc1
Common SMILES Examples
Water: O Methane: C Ethanol: CCO Benzene: c1ccccc1 Aspirin: CC(=O)Oc1ccccc1C(=O)O Caffeine: CN1C=NC2=C1C(=O)N(C(=O)N2C)C

Molecule Information

Select a molecule or input your data to view information here.

Molecule Information

Select a molecule to view its information here.

Interactive Controls: Rotate the molecule by dragging with your mouse. Zoom with the scroll wheel. Pan by holding Shift while dragging.

Visualization Modes

1

Ball and Stick: Atoms are represented as spheres (balls) and bonds as cylinders (sticks). This model shows both the atomic positions and the bonds between them.

2

Space Filling: Atoms are represented as spheres with sizes proportional to their van der Waals radii. This model shows the space occupied by the molecule.

3

Wireframe: Bonds are represented as lines connecting atomic centers. This model provides a simplified view of the molecular structure.

4

Cartoon: Used for proteins and nucleic acids. Shows secondary structures like alpha-helices and beta-sheets in a simplified representation.

Common Molecular Structures

Molecule Formula Structure Type Uses/Properties
Water H₂O Bent Universal solvent, essential for life
Methane CH₄ Tetrahedral Natural gas, greenhouse gas
Ethanol C₂H₅OH Alcohol Fuel, solvent, alcoholic beverages
Benzene C₆H₆ Aromatic ring Industrial solvent, precursor to many chemicals
Glucose C₆H₁₂O₆ Monosaccharide Primary energy source for cells
Caffeine C₈H₁₀N₄O₂ Purine alkaloid Stimulant found in coffee and tea

Understanding Molecular Geometry

  • Linear: Atoms in a straight line (180° bond angles)
  • Trigonal Planar: Atoms in a flat triangle (120° bond angles)
  • Tetrahedral: Four atoms arranged in a pyramid (109.5° bond angles)
  • Trigonal Bipyramidal: Five atoms with two distinct positions
  • Octahedral: Six atoms at the corners of an octahedron
  • Bent/Angular: Three atoms with a bond angle less than 180°

VSEPR Theory: The Valence Shell Electron Pair Repulsion theory explains molecular shapes based on the repulsion between electron pairs in the valence shell of atoms. Electron pairs arrange themselves to be as far apart as possible, determining the molecular geometry.

Frequently Asked Questions

Atoms are color-coded according to the CPK coloring convention, which is a standard in chemistry for representing different elements:
  • Hydrogen (H): White
  • Carbon (C): Black or Gray
  • Nitrogen (N): Blue
  • Oxygen (O): Red
  • Chlorine (Cl): Green
  • Fluorine (F): Light Blue
This color scheme helps quickly identify different elements in complex molecular structures.

Bond lengths are determined by several factors:
  • Atom sizes: Larger atoms form longer bonds
  • Bond order: Double and triple bonds are shorter than single bonds
  • Electronegativity: Bonds between atoms with large electronegativity differences may be shorter
  • Hybridization: sp-hybridized orbitals form shorter bonds than sp² or sp³
Typical bond lengths: C-C single bond ~1.54 Å, C=C double bond ~1.34 Å, C≡C triple bond ~1.20 Å.

These models provide reasonably accurate representations of molecular structures. Bond lengths and angles are based on experimental data or computational chemistry calculations. However, they are simplified in several ways:
  • Atoms are represented as perfect spheres
  • Bonds are represented as straight lines or cylinders
  • Electron clouds and orbital shapes are not shown
  • Molecular vibrations and flexibility are not represented
For most educational purposes, these simplifications are acceptable and help in understanding molecular geometry.

Molecular formula shows the types and numbers of atoms in a molecule (e.g., C₆H₁₂O₆ for glucose). Structural formula shows how the atoms are connected (the molecular structure). 3D molecular models provide the most complete representation of structure, showing the spatial arrangement of atoms. Different molecules can have the same molecular formula but different structures (isomers), which is why structural information is crucial in chemistry.

Molecular geometry is crucial because it determines:
  • Chemical reactivity: How molecules interact with each other
  • Physical properties: Melting point, boiling point, solubility
  • Biological activity: How drugs interact with receptors in the body
  • Spectroscopic properties: How molecules interact with light
  • Polarity: Whether a molecule has a dipole moment
Understanding molecular geometry helps predict and explain the behavior of substances in chemical reactions and biological systems.