Dye Structure and Colour

The components involved in histological staining are dyes and proteins. The fundamental process involved is the chemical bonding between the carboxyl groups of one and the amino groups of the other. The commonest bonds involved are ionic bonds, although there are exceptions especially in the case of nuclear staining of DNA.

The use of colour to identify individual components of tissue sections is accomplished mainly with chemical dyes, although other means are occasionally used. Dyes, however, are the largest group that we can manipulate.


What dyes are
In short, dyes are coloured, ionising, aromatic organic compounds.

It must be appreciated that they are individual chemicals, and like all chemicals, they are similar in their reactions to some other chemicals, and distinctly different from others. It may seem that this is a statement of the obvious, but we sometimes appear to view dyes as something other than ordinary chemicals, and I want to stress that the same rules that apply to sodium chloride, acetic acid, benzidine and a host of others also apply to dyes. This includes the possibility that they are toxic. They may be carcinogenic or mutagenic, or harmful to your health in some other way.

Just because we call something by an appealing name and because it has an appealing colour, does not make it any the less harmful. Handle dyes with care! Put your own safety first!


What colour is
Dyes are aromatic organic compounds, and as such are based fundamentally on the structure of benzene. To us, benzene appears to be a colourless fluid. In fact it absorbs electromagnetic radiation just as dyes do, but it does so at about 200 nm so that we do not see it.

The perception of colour is an ability of some animals, including humans, to detect some wavelengths of electromagnetic radiation (light) differently from other wavelengths. Normal daylight, or white light, is a mixture of all the wavelengths to which we can respond and some to which we cannot, in particular the infra-red and ultra-violet rays. We respond to wavelengths between about 400-700 nm. When an object absorbs some of the radiation from within that range we see the waves that are left over, and the object appears coloured. In reality this range we see makes up only a very small fraction of the electromagnetic spectrum.


In scientific terms there is nothing special about the wavelengths in the visible range, other than being the major components of sunlight which are not removed by the earth's atmosphere. Their special importance is based exclusively on the ability of human retinas to respond to them, and to discriminate between them to a significant degree. These discriminations are what we call colour.

Wavelengths just outside the visible range are considered colourless, even though there is no substantive difference between them and the limiting wavelengths inside the range. Some animals (bees, for example) can see these other wavelengths but, because humans do not, we consider them colourless. The point is that colour is a subjective phenomenon, and thinking of colour as something objective is misleading. For that reason, we should refer to the wavelengths involved rather than describe the human response to them.

When some of the wavelengths found in white light are absorbed, then we see what is left over as coloured light. The colour that we see is referred to as the complementary colour of the colour that was removed. For instance, if the red rays are removed from white light, the colour we detect is blue-green. Blue-green is complementary to red, and red is complementary to blue-green.


Complementary Colours
Removed Observed   Removed Observed
Violet Yellow-green Yellow-green Violet
Blue Yellow Yellow Blue
Cyan Orange Orange Cyan
Blue-green Red Red Blue-green
Green Purple Purple Green


Absorption of light leaving the complementary colour


The perception of colour is merely a human evolutionary adaptation to the absence of some wavelengths in white light. Suppose however, that the same thing happens outside the range to which our eyes respond. Suppose a chemical removes radiation which has a wavelength about 200 nm, as benzene does. Is this coloured?

Well, obviously it is not. There has been no impact on the wavelengths of white light, so it is not coloured. However, what has happened to the ultra-violet radiation that was absorbed by the benzene is no different to what happens to the blue radiation that is removed when we look through a solution of acid fuchsin. The difference is solely whether we can detect it visually. Colour is not an objective phenomenon, it is the human detection and perception of electromagnetic radiation.


Why dyes are coloured
Colour in dyes is invariably explained as a consequence of the presence of a Chromophore. Since, by definition, dyes are aromatic compounds their structure includes aryl rings which have delocalised electron systems. These are responsible for the absorption of electromagnetic radiation of varying wavelengths, depending on the energy of the electron clouds. For this reason, chromophores do not make dyes coloured in the sense that they confer on them the ability to absorb radiation. Rather, chromophores function by altering the energy in the delocalised electron cloud of the dye, and this alteration results in the compound absorbing radiation from within the visible range instead of outside it. Our eyes detect that absorption, and respond to the lack of a complete range of wavelengths by seeing colour.

Chromophores are atomic configurations which can alter the energy in delocalised systems. They are composed of atoms joined in a sequence composed of alternating single and double bonds. Double bonds in organic compounds can be of two types. If the atoms with double bonds are not adjacent, they are termed isolated double bonds, and exist independently of other double bonds in the same molecule. If adjacent atoms have double bonds they are termed conjugated double bonds and the bonds interact with each other. Chromophore configurations often exist as multiple units, having conjugated double bonds, and are more effective when they do so. This is due to the interaction between the double bonds, which causes partial delocalisation of the electrons involved in the bonds. In this case, although specific atoms are involved in the bonds, the electrons are distributed over a larger area than the specific atoms and also involve adjacent atoms that have double bonds.

The point of this is that conjugated systems have partially delocalised electrons, and the energy in these delocalised electrons can impact on the energy of the delocalised electrons of the parent aromatic compound by extending the number of electrons involved in the system and the energy needed to keep the whole system in place.


Conjugated double bonds (red)


Another common chromophore is the nitro group. This chromophore is a nitrogen with two oxygen atoms attached. One oxygen is shown attached with a single bond, the other with a double bond. In fact, like the carbon atoms in benzene, these two oxygen atoms are attached to the nitrogen with bonds of equal strength. The extra electrons are delocalised between the three atoms.


Nitro group


The quinoid ring is found in many dyes. It is a ring structure with two points at which chromophores can attach. It should be thought of as a closed system of conjugated double bonds. The attachment of configurations which add delocalised electrons to the system at one point, and the attachment of configurations which extend the atoms involved in the delocalisation at the other, causes very dramatic shifts in the wavelengths which these compounds absorb. For this reason, quinoid ring configurations are considered to be extremely powerful chromophores, producing very intensely coloured compounds.


Ortho- and para- quinoid ring chromophores


To sum this up, chromophores are atomic configurations that contain delocalised electrons. Usually they are represented as nitrogen, carbon, oxygen and sulphur that have alternate single and double bonds. By incorporating the delocalised electrons in these configurations into the delocalised electrons in the aryl rings of aromatic compounds, the energy contained in the electron cloud can be modified. If the energy incorporated into the electron cloud is changed, then the wavelength of the radiation it absorbs will also change. If this change in the wavelength to be absorbed is sufficient to cause any absorption at all within the visible range, then the compound will be coloured.

Below are the usual chromophores seen in histological dyes:–

–C=C– –C=N– –C=O–
–N=N– –NO2 Quinoid rings


Other effects
There is more than one effect when chemical groups are attached to aryl rings. Any delocalised electrons and their energy can simply be added to that already present, thus increasing it. Also, the delocalised electrons may be shared by more atoms than those in the original structure, by adding in to the delocalised system the atoms in the chromophore and any modifiers that may be present. Whether these effects occur jointly or separately, the final impact is an alteration in the overall energy of the electron cloud with a subsequent effect on the wavelength of radiation to which the whole molecular system reacts.

Another possibility is that electrons may be removed from the electron cloud, and this may result in loss of colour. Removal of electrons may cause the remaining electrons to revert to local orbits. A good example would be Schiff's reagent. When sulphurous acid reacts with pararosanilin, a sulphonic group attaches to the central carbon atom of the compound. This disrupts the conjugated double bond system of the quinoid ring, causing the electrons to become localised and the ring to cease being a chromophore. Consequently, the dye becomes colourless.


Below are the usual auxochromes found in histological dyes:–



Auxochromes are groups which attach to non ionising compounds yet retain their ability to ionise. While this definition is largely correct, it is also inadequate. This is because it restricts the definition of the auxochrome to ionisation, and does not comment on the effect of auxochromes on the absorbance of the resulting compound.

The word auxochrome is derived from two roots. The prefix auxo is from auxein, and means increased. The second part, chrome means colour, so the basic meaning of the word auxochrome is colour increaser. This word was coined because it was noted originally that the addition of ionising groups resulted in a deepening and intensifying of the colour of compounds.


Colour enhancing by an auxochrome
To the left is naphthalene, a colourless compound.
The addition of a single hydroxyl group to naphthalene produces 1-naphthol which is also a colourless compound, but one which can ionise.
If instead of a hydroxyl group we add the nitro group, which is a chromophore, we get the compound 2,4-dinitronaphthalene. The addition of this chromophore has caused it to become pale yellow.
If instead of a hydroxyl or nitro groups, both a hydroxyl and nitro groups are added, we get the deep yellow dye, martius yellow.
The addition of both an auxochrome and a chromophore results in a much stronger alteration of the absorption maximum of the compound. The hydroxyl group must have deepened the colour, showing that auxochromes are also chromophores.


Sometimes the term auxochromophoric is used to denote the action of an auxochrome that modifies the colour as well as permitting ionisation. This term infers that the colour modifying effects of auxochromes are rare, but this is not the case. The effect on absorption should not be considered an incidental aspect of the auxochrome's action, but an integral and fundamental part of it. The word auxochromophoric is redundant.

Edward Gurr proposed the terms colligator and non-colligator to distinguish between ionising auxochromes and colour modifying effects.

Auxochromes are of two types. They may have a positive charge as the amino group and its substituted variants. Or they may be negatively charged as the carboxyl and hydroxyl groups, and the sulphonic group. This last is commonly used to convert basic dyes to acid dyes. Both negatively charged and positively charged auxochromes may be present on a single molecule.


The process by which electrons are stimulated by radiation is resonance. It should be made clear at the outset that resonance is not the same as vibration.

Resonance is the induction of a response in one energy system from another energy system in close proximity, which is operating at the same energy level (frequency). In aromatic organic compounds, including dyes, the two energy systems are electromagnetic radiation, and the delocalised electron cloud. Do not confuse resonance with the imaginary resonance hybrids used in an older explanation for the structure of benzene.


Absorption of benzene compared to some dyes


Colour modifiers such as methyl or ethyl groups alter the colour of dyes by altering the energy in the delocalised electrons. By themselves they cannot do this enough to cause absorption in the visible range, but they can affect the shade significantly when absorption is already in that range. Adding more of a particular modifier results in a progressive alteration of colour. Compounds that differ from each other in this kind of regular fashion are called homologues. A very good example is seen with the Methyl violet series.


Alteration of colour by modifiers
      Without any methyl groups the parent dye is called pararosanilin and is red.
When four methyl groups are added we get the reddish purple dye methyl violet.
As more methyl groups are added we get the purple blue dye crystal violet which has six such groups.
If a seventh methyl group is added, the resulting dye is methyl green.


The Colour
The colour of the dye is caused by the absorbance of electromagnetic radiation. We have constantly referred to the wavelength that is absorbed in the singular, but a simple scan of a dye solution with a spectrophotometer shows that dyes do not remove a single wavelength. Rather they absorb radiation on either side of the wavelength most completely removed (the absorption maximum). Plotting the wavelength absorbed against the degree of absorbance usually results in a display resembling a bell curve. If any part of this curve is in the visible range, the dye will appear coloured.

White light is a mixture of wavelengths. Some of these have a relationship to the energy in the delocalised electron cloud of the dye molecule. By the process of resonance, previously described, the electron cloud will respond to the energy contained in that radiation by absorbing it, and removing it from the spectrum. As a consequence the white light will cease to be white and will display the colours of the wavelengths left over. The transmitted light will have the complementary colour to the wavelengths removed.


The Effect
When light illuminates a dye, some of it is absorbed as energy. Since energy is not destroyed, something must then happen. We could use an analogy of heating water - the water's temperature rises, molecular vibration increases. However, we do not see anything else, as the water just sits there being water.

The same can happen with dyes, we may not observe anything particular as the effect may be at the atomic level. There are several possibilities, however.

  1. The energy level in the electrons in an unaffected dye is called the ground state. When electromagnetic radiation, as light energy, is absorbed the electrons become more energised.
  2. With most dyes, there is then a gradual decay and the electrons return to the ground state. We do not see anything. Nevertheless, something may happen that we do not see. Possibly there is an increase in temperature, or some chemical changes occur which disrupt the dye's structure and cause it to lose colour - fading.
  3. Another possibility is that the return to the ground state is not gradual, but sudden. If this is accompanied by emission of any residual energy in the form of light, we observe the dye glowing - fluorescence. Since the emitted light must always contain less energy than the absorbed light, as some was used to energise the electrons, the emitted radiation is always at longer wavelengths than the absorbed radiation. By manipulating the light available, we can cause ultra-violet light to be absorbed and visible light to be emitted.
  4. A third possibility is that the electrons stabilise in their newly energised state. After a passage of time they then return to the ground state. If this happens gradually, we may observe nothing, with the same possibilities regarding fading and temperature increase as before.
  5. If return to the ground state happens suddenly, and the residual energy is emitted as light, we once again see the dye glowing - phosphorescence. As with fluorescence, the light emitted is always a longer wavelength than the light absorbed, but the disparity is greater with phosphorescence due to the greater energy consumed in keeping the electrons in the excited state.

Note that the difference between fluorescence and phosphorescence is in whether the electrons stabilise in the excited state before returning to the ground state. With any stability, no matter how long (or short), it is considered phosphorescence.


The explanation of the relationship between structure and colour depends on the basic atomic structure of the aryl ring, and the shared or delocalised electrons that this atomic arrangement has. The ability to absorb radiation is inherent in this structure. The effect of other atomic configurations is to modify the energy contained in the delocalised electron cloud so that the compound absorbs electromagnetic radiation at a wavelength in the visible range. Some also ionise, enabling the compound to chemically react with ionising tissue groups.

Colour, fading, fluorescence and phosphorescence are all seen to be different effects of the same fundamental process.


Fessenden R J, and Fessenden J S, (1990)
Organic Chemistry, 4th ed.,
Brooks/Cole Publishing Company, Pacific Grove, California
Almost any modern organic chemistry reference text used for 1st or 2nd year university organic chemistry courses would contain much the same information.

Burstone, M.S.
Enzyme Histochemistry and its application to the study of neoplasms
Academic Press, New York, NY, USA



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