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A molecule is the smallest unit of matter which still retains its properties. Molecules made up of the same atom are referred to as elements; those made up of different atoms are called compounds. Examples include water, made up of two hydrogen atoms and one oxygen, and diamonds, made up of carbon atoms.
The most powerful molecule known to Federation science is the Omega molecule. Its power and inherent instability, however, has 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") Dr. Leonard McCoy would mimic this attitude in the latter half of the 23rd century, though he referred to the scattering of his atoms. (TOS: "Space Seed")