I have synthesized NCQDs using citric acid and urea as precursors. The powder-color of the quantum dot after the freeze-dried is green; however, the color will change to black as stored at room temperature?
I do not know your chemistry, so do not know if this is relevant.
pH shift during freezing is a well known phenomenon. During freezing the molecules are taken out of solution due to freezing, the water is then removed. If colour is affected by pH shift then this may be a causal factor in the colour change.
Other causes of colour change in freeze dried samples have been due to secondary chemical change, e.g. oxidation, or residual mositure causing a gum formation which they may support biological life.
Another point to account, when you freeze dry your samples, you have changes in the surface area, pore volumes and interaction with adsorbents and molecules in the environment. What you could try is to degas your sample (Applying vacuum with temperature), to remove all adsorbents inside de NCQD, and if you see some color change, that could be the phenomenon occurring. These type of color change was observed by me before in nanocomposites of Oxide Metals and nanocarbon structures.