Molecules, and normally not atoms, are the smallest parts of chemical substances and of almost all matter occurring on Earth [1] . Molecules define chemistry, inorganic, organic, and biochemistry. Chemical reactions transform matter through the creation of new molecular structures [2] based on interaction of 'electron clouds' of constituent atoms and molecules [3] . The size of most molecules generally reaches only few nanometers, with important exceptions in biochemistry [4] .
More on the water molecule
Under normal conditions (ambient temperature and pressure), only noble gases occur in monatomic form. Other elemental gases, like nitrogen and oxygen, form diatomic molecules (the rare native element minerals also consist of only one type of atoms that, however, are bound in crystal structures and not in molecules). Most matter occurring on Earth (e.g., rocks, minerals, biomass) consists of aggregates and mixtures of chemical compounds whose smallest units are molecules, i.e., bonded atoms. At the scale of the universe, however, matter consists predominantly of ionized atoms in the stars' plasma.
The molecular structure, i.e. the bond-determined spatial arrangement of constituent atoms, controls the properties of a molecule. Isomeric molecules of different structure have dissimilar properties despite same number of atoms for each composing element. Even if a molecule's structure is a mirror image of another molecule, some properties can be quite different (see chirality). Biosynthesis of highly complex compounds works only with molecules of proper chirality.
Quantum mechanics explain chemical reactions with release and absorption of photons that match changes of the orbitals of participating atoms. The atomic orbitals combine to form molecular orbitals. Valence bond theory and molecular orbital theory, assisted by computational chemistry, try to explain how molecular orbitals are formed.
Living organisms build some exceedingly large molecules. For instance, the largest known protein molecule (Titin), has a diameter larger than 1000 nm. The tightly coiled human chromosomal DNA-molecule is still several times larger.