Dye Data Glossary
The chemical names of dyes can be very complicated and unwieldy. As a consequence, the practice of using descriptive names has arisen. Usually we refer to dyes by a relatively simple name that is understood by most people who work with them, that is, we use a common name. Most of us will understand what dye is meant when basic fuchsin is specified. Unfortunately, it is not unusual for a dye to have more than one common name. Examples are magenta, which is an older name for basic fuchsin, or the name light green, which refers to the dye also known as light green SF yellowish (CI 42095).
It is also not uncommon for the same, or a very similar, name to be applied to two different dyes, light green, for instance, has also been used to refer to the dye methyl green (CI 42585). This situation has arisen because dye marketers have, in the past at least, chosen names for their appeal rather than to convey any information. Using a common name by itself can cause confusion, and may result in failure of staining because the incorrect dye was used.
In order to correct the naming confusion, H.J. Conn's Biological Stains recommends that a single common name should refer to a single dye, and that it should never be used to refer to any other dye. This is the recommended name. The book gives a recommended name for each dye listed, and this name should be the one used to identify dyes when a common name is required.
Some dyes are known by many names. Many of these names are historical, but they can also be due to different manufacturers selling the same chemical compound by different names, perhaps to avoid violating another company's copyright or trademark. The dye chromoxane cyanine R (CI 43820), as an example, is also known by the synonyms cyanine R, chrome cyanine R, solochrome cyanine R, eriochrome cyanine R and alizaroyl cyanine RC. Unfortunately, the last two names have also been used to refer to a closely related, but chemically different, dye, chrome violet CG (CI 43810). This is altogether very confusing. In order to avoid confusion, it is advisable not to use these names. Regrettably, however, synonyms are still in use for some dyes.
Due to the confusion in naming dyes, the Colour Index has been produced. This is a compendium of dyes, with large amounts of data, and was prepared by the Society of Dyers and Colourists in the UK and by the American Association of Textile Chemists and Colorists in the US. Originally in book form, it is currently available online. Incorporated into this reference work is a system of identifying individual dyes very specifically. Each individual chemical used as a dye is assigned a specific identifying, five digit number. Individual dyes are identified specifically by reference to their CI number, as has been done in the preceding paragraph on this page. When specifying any dye for use in a staining method the CI number should always be given, so that there is no confusion as to which chemical is meant.
In addition to an identifying number, the colour index also assigns a specific name to each dye. The name is based upon the dye's (textile) mode of action and the base colour, followed by a number. An example is the dye mordant blue 3, the CI name for chromoxane cyanine R (CI 43820). This CI name is therefore a specific identification for the dye. Although it is used less frequently than the CI number, it is as valid an identification and may be usefully included when identifying a dye for a particular staining technique.
Many dyes are chemically similar to each other, and may differ only in minor respects. If the minor differences follow a regular sequence, i.e. 1 methyl group, 2 methyl groups, etc., they are termed homologues. Due to these relationships between dyes, they are grouped into classes based on their structural similarities. In many, but by no means all, cases related dyes can be substituted for each other.
Dyes are generally ionising compounds, and the actual colouring component is located in one or more of the ions. Note that the terms used (acid, basic, neutral) bear no relationship to the pH of a solution of a particular dye.
Many staining methods are carried out with aqueous solutions. Some call for saturated solutions, but this is not very common, and most staining methods specify concentrations below the saturation point. In some cases solubility data is not well authenticated, and should be used with caution. Many dyes contain adulterants, often from the manufacturing process, and these may affect solubility as well as staining performance.
Some methods call for ethanolic solutions of dyes. Solubility data for these also should be used with caution.
Colour is fundamentally dependent on the removal of light of particular wavelengths from the spectrum by the dye concerned. Most dyes absorb at different wavelengths. The absorption pattern often resembles a bell curve, the maximum absorption being called the peak. The peak, sometimes in conjunction with the shape of the absorption curve, can be used to identify dyes with a degree of certainty, but not absolutely. Some dyes have two absorption peaks, sometimes quite far apart in the spectrum. Both should be given, but may not have been. If this data has two numbers, it is likely there are two peaks, except where it is made clear it is due to differences in published data.
This gives the base colour of the dye. It may be found useful when looking for a dye to substitute for another.
The standard formula with elements and numbers of atoms.
The formula weight based on the empirical formula and standard atomic weights. In conjunction with the colour, it may be useful in choosing a substitute dye. This is especially so with trichrome staining, in which it is customary to apply dyes in sequence using them in order of their formula weights, the lowest first. It should be noted, however, that dyes in solution form aggregates, due primarily to van der Waal's forces. These aggregates may affect the way the dyes act.