In 1893, Werner was the first to propose correct structures for coordination compounds containing complex ions, in which a central transition metal atom is surrounded by neutral or anionic ligands.
For example, it was known that cobalt forms a "complex" hexamine cobalt (III) chloride, with formula CoCl•6NH, but the nature of the association indicated by the dot was mysterious. Werner proposed the structure [[Cobalt(III) hexammine chloride|Co(NH)Cl]], with the Co ion surrounded by six NH at the vertices of an octahedron. The three Cl are dissociated as free ions, which Werner confirmed by measuring the conductivity of the compound in an aqueous solution, and also by chloride anion analysis using precipitation with silver nitrate. Later, magnetic susceptibility analysis was also used to confirm Werner's proposal for the chemical nature of CoCl•6NH.
For complexes with more than one type of ligand, Werner succeeded in explaining the number of isomers observed. For example, he explained the existence of two tetramine isomers, "Co(NH)Cl", one green and one purple. Werner proposed that these are two geometric isomers of formula [Co(NH)Cl]Cl, with one Cl ion dissociated as confirmed by conductivity measurements. The Co atom is surrounded by four NH and two Cl ligands at the vertices of an octahedron. The green isomer is "trans" with the two Cl ligands at opposite vertices, and the purple is "cis" with the two Cl at adjacent vertices.
Werner also prepared complexes with optical isomers, and in 1914 he reported the first synthetic chiral compound lacking carbon, known as hexol with formula [Co(Co(NH)(OH))]Br.