[Acadasol]

I recently put a linker to a cyclic amine. Directly on the nitrogen atom and initially, I got a yellow color but now I got an orange color. Has anyone ever experienced this kind of situation before? Please share your opinion. Is it possible to get different colors for same compounds? Thanks for sharing.

[discodermolide]

I would say that the same compounds must have the same colour. The alteration in colour you have experienced is probably due to the increased presence of impurities. It does not take must of an impurity to produce a colour.
Check to see that the quality of your reagents and starting materials and solvents is the same in both cases. Make sure the reaction conditions are the same in both cases as well as the work-up procedures.

[Acadasol]

I would say that the same compounds must have the same colour. The alteration in colour you have experienced is probably due to the increased presence of impurities. It does not take must of an impurity to produce a colour.
Check to see that the quality of your reagents and starting materials and solvents is the same in both cases. Make sure the reaction conditions are the same in both cases as well as the work-up procedures.

Thanks, I will purify my product today and run HNMR. Hopefully, it's my product because even TLC suggested that it is my product. I will sure get back to you with my findings. Thanks!

[Acadasol]

So, after purification, my product came out pure with the same color as in the first synthesis indicating that the different color observed was due to impurities. Thanks for your contribution.

[Furanone]

One other consideration is that pH can affect the colour. For example, anthocyanins can have a wide range of colours based on changes of pH even though the chemical composition is the same only differing in degree of protonation. This is because colour (light in visible wavelength) is most often determined by conjugated dienes absorbing light at certain wavelengths, and whether it is the acid form or conjugated base form will either decrease or extend the series of conjugated dienes. The red cabbage pH indicator (with abundant anthocyanins) changes colour dramatically with different pHs (see link provided).

http://www.braukaiser.com/wiki/index.php/An_Overview_of_pH

On a side note, when I debranched starch amylopectin using isoamylase/pullulanase and separated on size exclusion chromatography and added iodine to each separated fraction collected in test tubes, they showed the exact same series of colours as the red cabbage at different pHs with a vivid blue for longest chains (amylose) going down to red for shortest chains.

[Acadasol]

One other consideration is that pH can affect the colour. For example, anthocyanins can have a wide range of colours based on changes of pH even though the chemical composition is the same only differing in degree of protonation. This is because colour (light in visible wavelength) is most often determined by conjugated dienes absorbing light at certain wavelengths, and whether it is the acid form or conjugated base form will either decrease or extend the series of conjugated dienes. The red cabbage pH indicator (with abundant anthocyanins) changes colour dramatically with different pHs (see link provided).

http://www.braukaiser.com/wiki/index.php/An_Overview_of_pH

On a side note, when I debranched starch amylopectin using isoamylase/pullulanase and separated on size exclusion chromatography and added iodine to each separated fraction collected in test tubes, they showed the exact same series of colours as the red cabbage at different pHs with a vivid blue for longest chains (amylose) going down to red for shortest chains.

This is interesting. Thanks for sharing...

[Corribus]

Just for future reference, color is a matter of perception; it's not necessarily a molecular property. Concentration can affect perceived color quite dramatically as can extrinsic factors such as the ambient light. 

The definitive way to see if the optical properties have really changed is to take an absorption spectrum, and keep the conditions as identical as possible: concentration, solvent, pH level, and so-forth should be identical. If at that point the spectra are different, then likely your sample has changed: either you have an impurity, or the sample has undergone a reaction (oxidation or polymerization, most likely).