You can have inclusions that are barely visible in the nmr. You could also have sovents included in your cell, that might slightly change the crystal color.

It is possible that the crystal is not homogeneous. Some parts of the crystal are trully in the crystalline state, but others may have different orientations or may be amorphous states.

I have learned that the colour of a solid may be imparted by very small amount of highly coloured impurities which could in turn undetectable even under normal NMR analysis trheshold limit (how about a quick treatment of the solution with carbon of the solution before cristalisation? ), also shape and dimension of cristal may change the overall aspect of the solid. Granulometry of cristals may change even for subtle "small" batch to batch variation (even mixing and moreover heat exchange fluxes, thus shape and reactor form..... etc )... I hope thath i will give you some hints ... best regards

As already said, the color is given by ppm quantities of impurities. Of course these quantities are not quantifiable by NMR spectroscopy. Depending on purification procedures and last few step of synthesis you may have used inorganic catalysts (metals?) among your reagents and some may still be there. Crystals trap inclusions. The color variation may depend on concentration of the solution used, type of solvent, speed of growth of crystals and other technical factor. My suggestion is to use a scavenger of metals like the activated carbon charcoal (or something more specific, depending on potential impurities) and then retry the crystallisation on a clean batch.

I agree with the previous fellows. Small impurities can change the color of a solid. Charcoal can remove such impurities and decolorize the solid while in solution.

Also, preparative TLC can give you a very pure solid.

I also agree with previous comments, especially the comment on the size and shape of the crystals. The size of crystals obtained from different crops can vary considerably the colour they present. Small impurities may also be an important factor. Best wishes.

NMR wont be different

Due to impurities present in the MLR after 1st crop isolation. the following crops have colour. but this will depends on the impurity profile of the product. Generally the process of isolation of 2nd crop is different from 1st crop due to this theer is difference in quality of product also. color of crop is also depends on solvent.

The color of a substance is determined by its chemical structure and their physical characteristic (crystalline or amorphous). The shape and the size of its crystalline form, also the possibility of polymorphism, may influence its color.

I am also agree to Giuseppe & rosa's view.

I have also face this problem long back.

I had three lot of same compound and supriseingly all have different in color. all the three of them are having HPLC more then 99%.

so don't bother Just compair TLC very carefully.

you can also go for exact melting point by help of i various instrumental method.