I don't understand why we use HPLC as method to determine the purity of NCE/drugs in medicinal chemistry if the HPLC won't show everything that could be a impurity (only compounds with UV absortion).
HPLC doesnt always use UV detector. Sometimes there are mass spec detectors.
You seemed to have used an HPLC-RP with only a UV detector. There are machines with MS detectors included as well.
This is a very good question. Unless you know the nature of the impurity, then you cannot define the purity of the main material. UV depends on the chromaphores of the parent and impurities. These will not be the same although they may be close enough if the impurity is close in structure to the main compound. Using a MS detector doesn't help - you may be able to see a UV-invisible impurity but you cannot quantify it unless you know that it ionizes exactly the same as the main compound.
Unfortunately, there is no universal detector which has the same response for all compounds. So why use HPLC? Well, you can get a good idea of purity, especially if you have orthogonal detectors (like ELS, CAD or MS). If they all give a similar answer then you are probably quite close.
Perhaps the best you can do is to use NMR to quantify the amount of material using an internal standard (or an external reference such as ERETIC II, QUANTAS). This won't tell you about the impurities necessarily but it will give you an overall amount of material in the tube which you can relate back to the weighed material.
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