A molecule is an electrically neutral entity consisting of two or more atoms bound together. In the rigorous definition used by the International Union of Pure and Applied Chemistry, its bound state must support at least one vibrational state. Molecules may contain atoms of the same chemical element, as in oxygen (O₂), or different elements, as in water (H₂O). Their identity depends not only on which atoms they contain but also on how those atoms are connected and arranged. (goldbook.iupac.org)
Definition and boundaries
A molecule differs from a single atom and from an ion, which has a net electric charge. Charged groups of bonded atoms, such as ammonium (NH₄⁺), are polyatomic ions rather than molecules under the strict neutral definition. Nevertheless, expressions such as “molecular ion” are established terminology for charged species with molecular structures. (goldbook.iupac.org)
Not all substances consist of discrete molecules. Solid sodium chloride contains an extended arrangement of sodium and chloride ions; its formula specifies their ratio, not an isolated molecule. Likewise, covalent network solids have bonding that extends through their structures rather than terminating at the boundaries of small molecular units. The distinction between molecular and nonmolecular substances is therefore structural, not simply a distinction between compounds and elements. (openstax.org)
Composition and representation
A molecular formula records the elements present and the number of atoms of each element. H₂O denotes two hydrogen atoms and one oxygen atom; C₆H₁₂O₆ denotes six carbon, twelve hydrogen, and six oxygen atoms. An empirical formula instead gives the simplest whole-number ratio, so the empirical formula corresponding to C₆H₁₂O₆ is CH₂O. A structural formula adds information about connections between atoms. (openstax.org)
Two substances can have the same molecular formula yet different structures, a phenomenon called isomerism. Acetic acid and methyl formate both have the formula C₂H₄O₂ but differ in atomic connectivity and chemical properties. Other isomers share connectivity but differ in spatial arrangement. Molecular formulas alone therefore cannot uniquely identify many substances. (openstax.org)
Ball-and-stick representations emphasize bonds and angles, while space-filling representations emphasize the volume occupied by atoms. Both are models: their spheres and connecting rods are not literal depictions of atomic surfaces or bonds. Such representations communicate selected aspects of molecular structure rather than its complete electronic description. (openstax.org)
Bonding and electronic structure
The chemical bonds within ordinary molecules are predominantly covalent. Their description involves the distribution of electrons and their interactions with atomic nuclei. Quantum mechanics provides the framework for explaining molecular electronic states, bonding, and stability. (openstax.org)
Valence bond theory describes bonding through overlapping atomic orbitals, often treating bonds as localized between particular atoms. Molecular orbital theory instead uses orbitals that can extend across the molecule. Occupation of bonding orbitals generally stabilizes a molecular system, while occupation of antibonding orbitals counteracts bonding. These approaches offer complementary descriptions rather than literal pictures of electrons following fixed paths. (openstax.org)
Electronic structure also explains properties that simple structural drawings may miss. Oxygen has unpaired electrons and is attracted to a magnetic field, a behavior called paramagnetism. Molecular orbital theory accounts for this behavior, whereas a conventional Lewis structure does not display it adequately. (openstax.org)
Geometry and polarity
Molecular geometry describes the three-dimensional arrangement of atomic nuclei, including bond lengths and bond angles. Lengths are commonly expressed in picometers or ångströms. Electron-pair repulsion models predict many simple geometries by considering the arrangement of bonding regions and lone electron pairs around a central atom. (openstax.org)
Geometry influences molecular polarity. Differences in electronegativity can produce polar bonds, but the combined effect depends on their directions. Carbon dioxide is linear, so its two bond dipoles cancel. Water is bent, so its bond dipoles do not cancel and the molecule has a permanent dipole. Thus, possessing polar bonds does not necessarily make a molecule polar overall. (openstax.org)
Intermolecular interactions
Forces between molecules are distinct from the bonds that hold each molecule together. Van der Waals forces include attractions associated with permanent or induced dipoles. Dispersion forces operate even between nonpolar molecules and depend on polarizability and molecular shape. Hydrogen bonding is another important interaction, particularly in water and many biological substances. (openstax.org)
These interactions help determine boiling points, melting behavior, and physical state. Changing from liquid water to water vapor principally separates molecules rather than breaking their internal oxygen–hydrogen bonds. Molecular size alone does not determine boiling point: molecules with the same formula can have different boiling points because their shapes permit different intermolecular contacts. (openstax.org)
Large and biological molecules
Molecules range from small diatomic species to large macromolecules. Many macromolecules are polymers, built from linked smaller units. Biological examples include proteins and DNA. DNA stores hereditary information in the sequence of its nucleotide units, while molecular diversity also arises from differences in the composition and arrangement of polymer building blocks. (openstax.org)
Experimental identification
Molecular composition and structure are investigated through complementary techniques. Mass spectrometry provides information about molecular mass, possible formulas, and fragmentation patterns. Nuclear magnetic resonance distinguishes nuclei in different chemical environments and helps establish molecular frameworks. Neither a formula nor a single measurement necessarily establishes a unique structure; interpreting molecular identity commonly requires combining several kinds of evidence. (openstax.org)