The purple from lichens was an important commercial product and came in a variety of forms, for example, orchil and cudbear. By the 1830s the researches of Pierre Jean Robiquet (1780 - 1840), Friedrich Heeren (1803 - 1885), Jean-Baptiste Dumas and Robert John Kane (1809 - 1890) into the constituents of lichens had revealed three color precursors: orcinol, erythrin and pseudoerythrin, but their constitution was not precisely known. Liebig encouraged Schunck to reinvestigate the subject using dye-producing lichens that grow on the basalt rocks of the Vogelsberg in Upper Hessia. In 1842, he discovered a new compound which he called lecanorin. His interpretation of the analyses of lecanorin (now called lecanoric acid) went astray because he used an incorrect formula for orcinol and because his lecanoric acid had partially hydrolysed to give orsellinic acid leading to an incorrect result. The true story was unravelled by Stenhouse some years later. Later he discovered, in addition to lecanoric acid, another new compound, parellic acid from Lecanora Parella.
In 1842 he came back to England and started a career in the chemical industry.
Madder was an important dye and imports into the UK were valued at £1.25 million per year in the 1860s. Schunck started his extensive investigations into the colouring materials in madder in 1846. The main colorant of madder was discovered by Robiquet and Colin in 1827 and called alizarin. Their analysis gave a formula C37H48O10. When purified by Schunck using sublimation and crystallisation, he obtained a result which suggested C14H8O4 , but taking into account the analyses of metal derivatives as well, he chose C14H10O4 as the best result. The modern formula is C14H8O4. He found that oxidation of alizarin with nitric acid gave alizaric acid (phthalic acid) which on heating gave pyroalizaric acid (phthalic anhydride). This led to the suggestion that alizarin was a derivative of naphthalene, a C10 hydrocarbon, although Schunck pointed out that this did not explain the reactions of alizarin. He was vindicated when Graebe and Liebermann (1868) distilled alizarin with zinc dust to give anthracene, a C14 hydrocarbon, and subsequently (1869) synthesised alizarin from anthraquinone.
Schunck showed that alizarin was not the major colour precursor component of fresh madder root, but it was a yellow bitter water soluble component, which he called rubian. Rubian was obtained from the water extract of madder root by adding bone–charcoal and extracting the bone–charcoal with ethanol. Rubian was an uncrystallisable gum, hydrolysable by acids or an enzyme contained in the madder root to give alizarin and a sugar. Rubian was actually a mixture of glycosides of di and trihydroxy anthraquinones of which a major component was ruberythric acid which is an alizarin 2–b–primeveroside. Many other “compounds” derived from the hydrolysis of rubian were described and enthusiastically named by Schunck: rubiretin, verantin, rubiacin, rubiadin, rubiapin, rubiafin and others, but some of these are most likely to be impure alizarin, and best forgotten. Some of Schunck's original samples were examined in 1975 by Wilfrid Farrar. Rubiadine was shown to be 1,3–dihydroxy–2–methyl anthraquinone, which Schunck assigned as the 4–methyl isomer. Rubiacine was identical to nordamnacanthal (1,3–dihydroxyanthraquinone–2–aldehyde) and rubianine was an unusual C–glucoside of unknown constitution.
In 1855, Schunck turned his attention to the subject of indigo, preferring the name indigo-blue to the alternative name, Indigotine.
He grew woad from "good French woad seed", extracted the dye precursor with cold ethanol and after further processing obtained a brown syrup which he called "indican". "Indican" was quite unstable and resisted further purification. Later he also investigated Polygonum tinctorium and believed that it contained the same "indican". Only in the early years of the 20th century was it shown that Schunck's "indican" from woad was not the same as the indican from tropical indigo plants and Polygonum tinctorium, and it was renamed isatan, which was even later shown to be a mixture of isatan A, B and C.
The presence of indigo in urine has long been the subject of much curiosity and Schunck tried in 1857 to show that "indican" was the origin. Believing that the occurrence of indigo was more common than generally supposed at the time, he examined the urine of 40 individuals, all apparently healthy, with ages between 7 and 55 years, mostly of the working class. In all but one case the result was positive. The largest amount of indigo was obtained from a man above the age of 50, a publican by trade. In his own case, the amount "varied most capriciously from a tolerable quantity to a mere trace". He thought this variation might be due to different kinds of diet, but after many experiments, found only one which worked: "I took on the next night, before going to bed, a mixture of treacle and arrowroot boiled with water in as large a quantity as the stomach could bear, and the effect was that the urine of the following night gave a large quantity of indigo-blue". The indigo precursor in urine turns out not to be indican, although it was called medical indican at the time, but indoxyl sulfate or gluconurate.