What do plants and hair dyes have in common? (organic compounds)

From the verdant green of ferns and the eye-catching yellow of lemons, to the rich purple of eggplant and the mouth-watering red of tomatoes, plants and their fruits are flush with color.

The world of plants is rich with color, extending from green foliage to multicolored flowers and fruits. Wherever we see color, there has to be a molecule absorbing part of the visible spectrum to create that color.

In order to understand which molecules can absorb visible light and hence cause color in nature, it’s crucial to look at the structure of organic molecules. Most molecules in plants consist of a backbone of carbon atoms, generally also bonded to oxygen and hydrogen atoms, with atoms of nitrogen and other elements in smaller numbers. Most of these molecules are not colored. For example, sugars and starches contain only carbon, hydrogen, and oxygen, they do not absorb any visible light and they are colorless.

What distinguishes colorless molecules, such as starch, from colored molecules like chlorophyll?

Colored molecules have a distinguishing feature: their backbones consist of sequences of carbon atoms linked to each other by alternating single and double bonds. These alternating sequences are an essential structural feature for an organic, carbon-based molecule to absorb light and appear colored.

Organic compound	Chemical Structure	Color of pigment
Chlorophyll		Green
β-carotene		Orange
Indigo		Blue
Tyrian purple		Purple
Lycopene		Red
Canthaxanthin
Astaxanthin		Pink

Colors in plants and animals

Chlorophyll is green and responsible for the green color of foliage and leaves. More importantly, by enabling plants to produce oxygen during photosynthesis, it is critical to sustaining our life on earth.

Carotene is a pigment that absorbs blue and indigo light, and that provide rich yellows and oranges. The distinctive colors of mango, carrots, fall leaves, and yams are due to various forms of carotene, as is the yellow of butter and other animal fats. This pigment is important to our diet, as the human body breaks down each carotene molecule to produce two vitamin A molecules.

Lycopene, canthaxanthin, and astaxanthin share a similar structure to carotene. The red tones of tomatoes, guava, red grapefruit, papaya, rosehips, and watermelon indicate the presence of lycopene. In a similar process to the color change of fall leaves, lycopene is present in green fruit, but is only revealed upon ripening, when the dominant green chlorophyll breaks down. Canthaxanthin produces the pink colors of flamingos, some crustaceans, salmon, and trout. In its synthetic form, it is used to ensure captive flamingos retain their coloring, as a red food colorant, and even as a tanning aid. Astaxanthin provides the red colors of cooked salmon, red bream, trout, lobster, and shellfish. In a live animal, astaxanthin is combined with a protein and is blackish in color. When boiled, the protein breaks down to unmask the true "lobster red" of astaxanthin.

As any fashionista knows, pigment is much more than a dietary necessity. For millennia, plants have been used to make dyes. Indigo is a natural dye with a lineage that can be traced back to the ancient Egyptian city of Thebes in 3000 BC. Egyptian mummies dating back to around 2400 BC were wrapped in cloth including traces of indigo, and by 2000 BC, its use was widespread in India. The Picts who tried to halt Julius Caesar in Britain in 58 BC wore blue paint. The dye was obtained either from the indigo plant, or from other European plants, such as woad. Indigo is still ubiquitous in blue jeans, although today it can be produced synthetically, as well as through fermentation of the indigo plant (which is not itself blue).

With the addition of two bromine atoms, indigo becomes Tyrian purple, a substance laboriously extracted from certain seashells and worn by Roman emperors as a symbol of their status.

First requirement for color - the role of double bonds

The backbones of all of these colored molecules consist of sequences of carbon atoms linked to each other by alternating single and double bonds.

Adjacent carbon atoms are bonded to each other by single, localized, electron-pair bonds. Additionally, each carbon donates one electron to a molecular orbital that extends over the whole carbon skeleton. These electrons, no longer localized in a double bond between two adjacent atoms, are now free to range over the whole molecule and hence are "delocalized." This electron delocalization stabilizes the molecule. This stabilization or lowering of the energy is equivalent to an additional half bond between adjacent carbon atoms.

Delocalized electrons, held in molecular orbitals, can absorb visible light and so become a source of color. Therefore, an alternating sequence of single and double bonds is a necessary structural requirement for color in organic molecules, because it produces electrons delocalized in molecular orbitals.

Second requirement for color - the role of molecular size

The existence of electrons in molecular orbitals is one requirement for color. The size of the molecule (which determines the size of the molecular orbital) is another.

For light (radiation) to be absorbed, an electron in a molecular orbital must be kicked up into an empty orbital of higher energy. This excitation energy, the energy difference between the two levels, ?E, varies with the size of the molecule. When the molecule is very large, the electrons are highly delocalized, and the molecule is very stable. The energies of the molecular orbitals will be lowered and the energy difference between those orbitals (?E) will be reduced. Only low energy photons in the infrared part of the spectrum can be absorbed. Because visible light cannot be absorbed, the molecule will appear colorless. At the other extreme, very small molecules (for example, with only two single/double bond sequences) will achieve little delocalization and stabilization, and ?E, the spacing between levels, will be correspondingly large. The molecule will then absorb energy only in the ultraviolet part of the spectrum and will be colorless. It will behave similarly to normal, unstabilized molecules like alcohol, which are colorless, absorbing in the invisible ultraviolet part of the spectrum.

A molecule will only appear colored if it is an intermediate size, where the energy spacing ?E matches the photon energy of visible light.

Conjugated systems

A "conjugated" system in an organic compound consists of alternating single and double bonds in a chain of atoms, usually carbons; a result of such an arrangement is that the "pi-bonding" electrons involved in the second bond of the double bonds are no longer localized, but can be considered to belong to the whole conjugated chain. The excited states of such electrons occur at much lower energies than those of the usual paired electrons, resulting in energy-level schemes that can absorb and emit light. The absorptions of the conjugated cyclic benzene C6H6 or the linear 2,4 hexadiene CH3-CH=CH–CH=CH-CH3 are still in the ultraviolet. The conjugated linear ten carbon chain 2,4,6,8 decatetraene C10H14, however, has the absorption moved into the blue end of the spectrum and a pale yellow color results.

Bathochromic shift

In addition to extending the length of the conjugated chain, there are a variety of other means of obtaining the desired "bathochromic" shift of the absorptions to lower energies. Such shifts are produced by the presence of electron-donor groups that pump electrons into the conjugated system, such as the -NH2 group in the dye methyl violet C’ (C6H4NH2)3, or electron acceptor groups that pump electrons out of the conjugated system, such as the -NO2 group.

In general, systems that have many resonance structures tend to provide large bathochromic shifts.