I have synthesized a small organic compound and prepared crystal for x-ray single crystal measurement. They were beautifully transparent, and I remove the remaining DCM from vial.
After ~30 mins, they became completely opaque, looked like some tiny white lego.
Was the lattice containing DCM molecules, and solvent evaporation making them amorphous again?
Taipei RT ~25-30 deg. C.
Many compounds need some solvation to crystallize. Perhaps your compound crystallized because of dichloromethane solvation. When you remove it, crystallinity goes and as a result it turns opaque. If this is a problem while crystallizing in CH2Cl2, use dichloroethane or tetrachloroethane which are high boiling with high vapor pressure; crystals may not crack.
Dear Bryan Po-Wen Chen thank you for asking this very interesting technical question. I can highly recommend the answer given by Balakrishna Maravanji. When an organic compound forms a solvate with dichloromethane, chances are that the crystals easily loose some of the solvent of crystallization and become opaque. If this is the case with your particular compound, then it is just a typical property of this solvate, and there is nothing really to prevent this. What you can do is to quickly transfer a single-crystal to the diffractometer and run the X-ray measurement at low temperature. Alternatively, you can try to use a different solvent for crystallization of your compound. For example, acetonitrile is a very good alternatve solvent for crystallization. Yet another alternative would be sublimation of your compound. Chances are that by sublimation you will directly contain unsolvated single-crystals.
Good luck with your work and best wishes, Frank Edelmann
Thanks for the suggestion, but is it common? I tried to squeeze one brick, and it becoming completely soft and powdery.
Dear Bryan Po-Wen Chen thank you for your kind response and explanation. This behavior is certainly not very common, but occasionally soft crystals are observed. I remember from our early studies the compound N(SiMe3)3 which is a very soft crystalline substance. I assume that in your case the crystals contain a relatively large amount of dichloromethane. It might be interesting to run a thermogravimetric analysis (TGA) of your crystals to see how much dichloromethane is incorporated. For an interesting article about soft crystals please have a look at the following link:
Soft Crystals: Flexible Response Systems with High Structural Order
Article Soft Crystals ‐Flexible Response Systems with High Structural Order
This article has been posted by the authors as public full ext on RG. Thus it can be freely downloaded as pdf file.
Dr. Balakrishna Maravanji, thanks for the suggestions. I already starting preparing crystal with several low/high BP solvents. Let's see what I am gonna get this time.
Dr. Frank T. Edelmann, thanks for the very enlightening guide to "soft crystal", and suggestion on TGA measurement.
First, and it is not my intention to disparage anyone, but this is very common. Depending on the kind of molecule and how the crystal packs, inclusion of solvent is a frequent observation. Since DCM is so volatile, its evaporation from the lattice happens relatively quickly. Sometimes, using chloroform instead still gives a solvate, but one that lasts longer.
As others have mentioned, using other higher boiling solvents works as an alternative method. Some additional strategies:
1. Do you have low temperature capability on your diffractometer? If so, you can transfer your crystal coated in low T oil and the crystal will be stable at temps around 100K.
2. Depending on your molecule, quickly coating your crystal with fast drying epoxy is often enough to give you time to collect X-ray data. The epoxy is amorphous and, while it does contribute to background noise, it does not interfere with the diffraction pattern.
Good luck
Transparent organic crystal became totally opaque after DCM dried, may be due to dehydration i.e. due to water loss or .Crystal lattice might have collapsed after DCM drying.
No need to remove DCM, sometime the solvent is necessary for maintain the lattice construction of crystal by completing the packing structure that matches the space group and unit cell dimensions.
Mouayed A. Hussein, thanks. My operator told me the same thing. Interestingly, I decreased the temperature from 40C to ~28C, also in DCM, the newly prepared crystals were needle-like (previously were polygons). From crystallography, DCM was no longer presented, and the crystals were stable in air too.
I have also experienced this type of situation. One of the alternative solutions is to dip your crystal in silicon oil as soon as you remove them from the crystal tube/beaker. This will slow down the evaporation of the solvent of crystallization and then run X-ray measurements. The other solution is to prepare your crystal in a high boiling solvent such as Acetonitrile, DMSO, etc.
Hope this helps...All the best
Hi Lincoln Dkhar, thanks for ur suggestions.
I tried other solvents as well, seemed that only DCM, CHCl3 lead to solvent incorporated crystals.
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