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What are the colored molecules of Nature? Color in organic molecules.

		Bitter orange oranges growing on a patio in Ronda, Spain. We see an orange as orange because, within the orange, a molecule is absorbing the blue part of visible light.

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.

To understand what molecules can absorb visible light and hence cause color in nature, we must look at the structure of organic molecules. Molecules in plants consist mostly of a backbone of carbon atoms, generally also bonded to oxygen and hydrogen atoms (and, to a lesser degree, to atoms of nitrogen and other elements). Most of these molecules are not colored. For example, sugars and starches contain only carbon, hydrogen and oxygen and they are not colored. But some molecules are colored, such as chlorophyll which is green and responsible for the green color of foliage and leaves. The green color of chlorophyll is critical to our life on earth. Chlorophyll facilitates photosynthesis, converting carbon dioxide in the atmosphere to the oxygen we breathe. Chlorophyll appears green because it absorbs red light from sunlight and it is this absorbed energy which drives photosynthesis. So color in plants is more than decorative: it is essential to life.

What distinguishes colorless molecules, such as starch, from colored molecules like chlorophyll? We can identify a distinguishing feature in their molecular structures. The table below shows the structures of many colored molecules found in plants. These include chlorophyll, carotene (which colors carrots orange), the dyes responsible for the color of flowers, and the natural blue dye indigo (used since antiquity, e.g,. in the form of woad by the "Picts" (painted people) whom Julius Caesar fought in Britain in 58 BC, up to today's all-pervading blue jeans). With two bromine atoms present, the result is Tyrian purple, laboriously extracted from certain sea shells and worn by the Roman emperors as a symbol of their status.

[Figure of formulas]

The backbones of all these molecules 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. These same alternating sequences do not appear in the structures of colorless molecules such as starch and sugar.

		Carbon atoms linked by "one and a half" bonds. The two electrons from the double bond are "delocalized". They are shared by all the carbon atoms in the alternating sequence.

In each of the molecular formulas in the figure, the carbon atoms which make up the skeleton have been omitted for clarity. There is a carbon atom located at every joint or junction in the rings and chains which make up the skeleton. In any sequence, each carbon atom is bonded to two neighboring carbon atoms, one by a single bond (two electrons, shown as a single line) and the other by a double bond (four electrons, a double line). In fact, the two electrons which make up the double bond cannot be assigned to either pair of atoms. They cannot be localized to any one bond. A better representation is "one and a half" bonds, as shown at right.

Adjacent carbon atoms are bonded to each other by single, localized, electron-pair bonds. Additionally, each carbon donates one electron to a molecular orbital (or box) 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 the additional half bond between adjacent carbon stoms, referred to above.

Delocalized electrons, held in molecular orbitals, can absorb visible light, thereby becoming the source of color. An alternating sequence of single and double bonds is therefore the necessary structural requirement for color in organic molecules, because it produces electrons delocalized in molecular orbitals.

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. As can be seen in the figure, organic molecules show color if they contain somewhere between 8 and 15 single/double bond sequences. We can now examine how molecular size regulates the radiation which can be absorbed.

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, DE, varies with the size of the molecule. When the molecule is very large, the electrons are very delocalized, and the molecule is very stabilized. The energies of the molecular orbitals will be lowered and the energy difference between those orbitals DE will be reduced. Only low energy photons in the infrared part of the spectrum can be absorbed. Because visible light cannt be absorbed, the molecule will appear colorless. At the other extreme, very small molecules (say with only 2 single/double bond sequences) will achieve little delocalization and stabilization, and DE, the spacing between levels, will be correspondingly large. The molecule will then absorb only in the ultraviolet part of the spectrum and it will again be colorless. It will behave similarly to normal, unstabilized molecules like alcohol which are colorless, absorbing in the ultraviolet, not visible, part of the spectrum.

Only for a limited intermediate size will the energy spacing DE match the photon energy of visible light and will the molecule appear colored.

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; with the conjugated linear tencarbon chain 2,4,6,8 decatetraene C₁₀H₁₄, however, the absorption has just moved into the blue end of the spectrum and a pale yellow color results.

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. An example of a molecule containing both is shown at the right in Fig. 11; this absorbs at 470 nm in the blue part of the spectrum and is one of the nitrophenylenediamines used in hair dyes, able to penetrate into the hair because of the small size. In general, systems that have many resonance structures tend to provide large bathochromic shifts.

Chlorophyll

Chlorophyll is the green coloration in leaves. In the process of photosynthesis, it absorbs sunlight and uses its energy to synthesise carbohydrates from CO2 and water.

Discovery of photosynthesis

Priestley

In 1780, the famous English chemist Joseph Priestley discovered that plants produce oxygen. He found that plants could "restore air which has been injured by the burning of candles." He put a mint plant into an upturned glass jar in a vessel of water for several days. He then found that "the air would neither extinguish a candle, nor was it all inconvenient to a mouse which I put into it".

Lavoisier

A few years later, in 1794, the French chemist (and Monarchist sympathiser), Antoine Lavoisier discovered the concept of oxidation, and for his efforts was promptly executed during the French Revolution. The judge who pronounced sentence said "The Republic has no need for scientists".

Ingenhousz

So it fell to a Dutchman, Jan Ingenhousz, who was court physician to the Austrian empress, to make the next major contribution to the mechanism of photosynthesis. He had heard of Priestley's experiments, and a few years later spent a summer near London doing over 500 experiments, in which he discovered that light plays a major role in photosynthesis.

Ingenhousz: "I observed that plants not only have the faculty to correct bad air in six to ten days, by growing in it...but that they perform this important office in a complete manner in a few hours; that this wonderful operation is by no means owing to the vegetation of the plant, but to the influence of light of the sun upon the plant".

Mayer

Very soon after, more pieces of the puzzle were found by two chemists working in Geneva. Jean Senebier, a swiss pastor, found that "fixed air" (CO₂) was taken up during photosynthesis, and Theodore de Saussure discovered that the other reactant necessary was water. The final contribution to the story came from a German surgeon, Julius Robert Mayer, who recognised that plants convert solar energy into chemical energy.

Mayer: "Nature has put itself the problem of how to catch in flight light streaming to the Earth and to store the most elusive of all powers in rigid form. The plants take in one form of power, light; and produce another power, chemical difference."

The actual chemical equation which takes place is the reaction between carbon dioxide and water, catalysed by sunlight, to produce glucose and a waste product, oxygen. The glucose sugar is either directly used as an energy source by the plant for metabolism or growth, or is polymerised to form starch, so it can be stored until needed. The waste oxygen is excreted into the atmosphere, where it is made use of by plants and animals for respiration.

Chlorophyll as a Photoreceptor

Chlorophyll is the molecule that traps this 'most elusive of all powers' - and is called a photoreceptor. It is found in the chloroplasts of green plants, and is what makes green plants, green. The basic structure of a chlorophyll molecule is a porphyrin ring, co-ordinated to a central atom. This is very similar in structure to the heme group found in hemoglobin, except that in heme the central atom is iron, whereas in chlorophyll it is magnesium.

There are actually 2 types of chlorophyll, named a and b. They differ only slightly, in the composition of a sidechain (in a it is -CH₃, in b it is CHO). Both of these two chlorophylls are very effective photoreceptors because they contain a network of alternating single and double bonds, and the orbitals can delocalise stabilising the structure. Such delocalised polyenes have very strong absorption bands in the visible regions of the spectrum, allowing the plant to absorb the energy from sunlight.

The different sidegroups in the 2 chlorophylls 'tune' the absorption spectrum to slightly different wavelengths, so that light that is not significantly absorbed by chlorophyll a, at, say, 460nm, will instead be captured by chlorophyll b, which absorbs strongly at that wavelength. Thus these two kinds of chlorophyll complement each other in absorbing sunlight. Plants can obtain all their energy requirements from the blue and red parts of the spectrum, however, there is still a large spectral region, between 500-600nm, where very little light is absorbed. This light is in the green region of the spectrum, and since it is reflected, this is the reason plants appear green. Chlorophyll absorbs so strongly that it can mask other less intense colours. Some of these more delicate colours (from molecules such as carotene and quercetin) are revealed when the chlorophyll molecule decays in the Autumn, and the woodlands turn red, orange, and golden brown. Chlorophyll can also be damaged when vegetation is cooked, since the central Mg atom is replaced by hydrogen ions. This affects the energy levels within the molecule, causing its absorbance spectrum to alter. Thus cooked leaves change colour - often becoming a paler, insipid yellowy green.

As the chlorophyll in leaves decays in the autumn, the green colour fades and is replaced by the oranges and reds of carotenoids.

Chlorophyll in Plants

The chlorophyll molecule is the active part that absorbs the sunlight, but just as with hemoglobin, in order to do its job (synthesising carbohydrates) it needs to be attached to the backbone of a very complicated protein. This protein may look haphazard in design, but it has exactly the correct structure to orient the chlorophyll molecules in the optimal position to enable them to react with nearby CO₂ and H₂O molecules in a very efficient manner. Several chlorophyll molecules are lurking inside this bacterial photoreceptor protein (right).

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