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Dictionary
1. (n.) One of the very small invisible particles of which all matter is supposed to consist.

2. (n.) 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.

3. (n.) 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.

Thesaurus
Kekule formula ace acid acidity agent air alkali alkalinity alloisomer anion antacid atom atomic cluster atomic particles base benzene ring biochemical bit branched chain brute matter building block cation chain chemical chemical element chromoisomer closed chain component compound compound radical constituent copolymer cycle dab dimer dole dot dram dribble driblet dwarf earth electron element elementary particle elementary unit farthing fire fleck flyspeck fragment fundamental particle gobbet grain granule groat hair handful heavy chemicals heterocycle high polymer homocycle homopolymer hydracid hyle hypostasis inorganic chemical ion iota isomer jot lattice little little bit lota macromolecule material material world materiality matter meson metamer minim minimum minutiae mite modicum monad monomer mote natural world nature neutralizer nonacid nuclear particle nutshell organic chemical ounce oxyacid particle pebble physical world pinch pittance plenum point polymer proton pseudoisomer quark radical ray reagent ring scruple side chain simple radical smidgen smitch space-lattice speck spoonful spot straight chain stuff substance substratum sulfacid the four elements thimbleful tiny bit tittle trifling amount trimer trivia unit of being water whit
                                                                                                                                                                                                                                       

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