A molecule was a group of two or more atoms, either from the same element or from different elements.

The Omega molecule in a moment of spontaneous stabilization

The most powerful molecule known to 24th century Federation science was the Omega molecule. Its power and inherent instability, however, had caused the Federation to ban all research pertaining to this molecule, and to issue the Omega Directive, requiring the immediate destruction of any such molecules discovered. (VOY: "The Omega Directive")

In 2151, Lieutenant Malcolm Reed stated he was apprehensive of using the transporter and having his molecules compressed. (ENT: "Broken Bow") Ensign Hoshi Sato later said the same when she expressed her discomfort about having her molecules scrambled. (ENT: "The Andorian Incident") Doctor Leonard McCoy would mimic this attitude in the latter half of the 23rd century, when he described the transporter as spreading one's molecules all over the universe. (TOS: "Obsession")

On an NX-class starship almost everything was broken into its molecules and recycled, including waste. This was done by the bio-matter resequencer. (ENT: "Breaking the Ice")

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