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Definition of molecule : 1. A group of atoms so united and combined by chemical affinity that they form a complete, integrated whole, being the smallest portion of any particular compound that can exist in a free state; as, a molecule of water consists of two atoms of hydrogen and one of oxygen. Cf. Atom.
2. One of the very small invisible particles of which all matter is supposed to consist.
3. The smallest part of any substance which possesses the characteristic properties and qualities of that substance, and which can exist alone in a free state.

Synonyms:

subatomic particle, unit, iota, speck, jot, dot, electron, atom, minim, mote, trifle, mite, drop, bit, fragment, scintilla, smidgen, element, dram, corpuscle, tinge, tittle, spot, ounce, dab, whit, particle, big, crumb, hint, blood cell, ort, pinpoint, touch, pinch, blood corpuscle, dash, scrap, modicum, scruple, shred, ion, soupcon, grain

Usage examples:

• You remember that the molecule of copper sulphate, discussed in our third letter, was formed by a copper atom and a group called sulphate. - "Letters of a Radio-Engineer to His Son", John Mills.
• The tortured molecules of the air in the room were so besieged by the beat of drums, the blare of trumpets, the crackle of lightning, the rumble of heavy machinery, the squawks and shrieks of horns and whistles, the rustle of autumn leaves, the machine- gun snap of popping popcorn, the clink and jingle of falling coins, and the yelps, bellows, howls, roars, snarls, grunts, bleats, moos, purrs, cackles, quacks, chirps, buzzes, and hisses of a myriad of animals, that each molecule would have thought that it was being shoved in a hundred thousand different directions at once if it had had a mind to think with. - "Anything You Can Do", Gordon Randall Garrett.
• And, lastly, every molecule of Man's organism is also, in reality, an individual, and small only by comparison with the human frame. - "The-Light-of-Egypt-or-the-science-of-the-soul-and-the-stars-Volume-2", Burgoyne, Thomas H..