Or is it that you have two spots in close proximity in your thin layer chromatography and this is the reason you are not able to separate the two compounds?

If this is the case you could try to crystallize it and if you are lucky you might get crystals of your starting material and the product crystallizes seperatly. However you could get a variety of other crystals e.g. co-crystallization of both compounds.

Best thing - make the experiment! Try to crystallize it and put a crystal onto the diffractometer and check what you've got!

Thank you sir for your kind reply, but in TLC both the spots are very close to each other and I am not able to isolate my product.I tried the crystalization but both the compounds(starting material as well as product) are getting crystalize so can i submitt this mix crystal for single crystal XRD. If I do so then can the structure of product be elucidated in presence of known starting material?

It's all about the "how do the two molecules crystallize together"!

If they form some sort of co-crystal you will get a structure with your starting material AND your product in the same unit cell. So yes you can get the MOLECULE structure of your product. Still you won't have the crystal structure of the product but that might be just a 'problem' from a crystallographic point of view.

And again - as long as you haven't given a crystal to single crystal diffraction it is hard to tell what happend upon crystallizing the mixture.

Check if you have different colored crystals or different shaped crystals. If so make sure you tell the crystallographer that this might be the reason since you haven't been able to clean your product properly.

Regardless of what happens in TLC - you might still be able to crystallize the compounds separately!

Good luck!

Thank you very much sir for your valuable suggestion. I will follow your suggestion

In my opinion, there is no harm in mounting your crystal in XRD if you are getting a single crystal. Submit your crystal without any heistation and get your crystal structure solved. I am sure it will work. I also have a crystal in which the complex and the ligand crystalized out together as a single crystal, still the structured was well solved.

Thank you sir for you valuable suggestion

I think two other high probable cases.

1) The crystal is a twin crystal.

There are so many kinds of twin crystals. Usually, twin crystal is distinguished from the external shape but sometimes it is not. Even if the crystal is beautiful at a glance, the crystal becomes twin when one or two hundred unit cells become twin( see my paper, Simple method for preparing monoclinic single crystals of zeolite ZSM-5 and analysis of their structure, Zeitschrift für Kristallographie 01/2010; 225(4):139-145). You can check if this crystal is twin or not when you take X-ray photograph ( Weissenberg or precession).

2) Space group is wrong.

The selected space group is wrong in almost all cases when single crystal analysis is unsuccessful. I do not know how you determine the space group of the crystal. In some case, the space group is not correct even from literatures. Especially when R value is over 0.1, you must remember this. When the computer determine the space group, please doubt the space group. Generally speaking, computer is good at determining the space group from normal crystal parameters. However, when a axis is twice longer than other two axes, computer can not determine correct space group.

You can also check this, if you take X-ray photograph ( Weissenberg or precession).

Please do not ignore the strange spots. They are not comfortable for you but they are so important for you. After you succeed in the structure analysis, you will feel the spots are precious and the guide to the truth.

I think that it is a little difficult to accept your work unless you determine the structure of another compounds or twin structure.