Tincalconite: ‘It’s on the glassware, you boron’

margarita
Margarita Milton

A graduate student in our lab was trying to grow crystals of a large polycyclic aromatic hydrocarbon (PAH) by the slow diffusion method. He set up several dozen batches and put them in a box marked “Crystallizations—DO NOT TOUCH” that he put on a high shelf. This wasn’t the first time he’d set up so many crystallizations, nor would it be the last. It’s very difficult to grow X-ray quality crystals of large PAHs. “Let’s sprinkle some salt in his vials and make him think he has perfect crystals,” I said to another student. “Even you’re not that mean,” she replied.

slow diffusion edit
Slow diffusion

The slow diffusion method is often effective for growing crystals. A small vial is placed inside a larger vial. The compound of interest is dissolved completely in a good solvent within the small vial. A solvent that does not solubilize the compound is placed in the outer vial. The outer vial is capped, and over some amount of time (days to weeks) the bad solvent diffuses into the good solvent and, hopefully, single crystals grow. The graduate student obtained two crystal structures out of more than 100 trials. He insists that certain tricks, such as scratching the bottom of the inner vial to create a site for nucleation, are the keys to success. He also rinses the vials with water and acetone before use—a step that a postdoc in our lab who also wanted to grow crystals chose to skip. Because fresh, new vials are clean, right?

The postdoc was ecstatic when the crystallographer found X-ray quality crystals in some of the vials. For a short time, the postdoc thought he would be the first to obtain a structure of this sort of PAH—something group members had been trying to do for five years. Then the results came back. The X-ray crystal structure was of an inorganic boron hydrate. “But how?,” the postdoc cried. “My material was completely pure!” The crystallographer let the postdoc shake his head in confusion for a bit longer, then quipped, “It’s on the glassware, you boron.”

Indeed, new vials aren’t necessarily clean. If you wash solvent down their sides and rotovap it off, you’ll find a white powder that is a mineral similar to borax called tincalconite (diagramed above). It has a very complicated structure with the formula Na2[B4O5(OH)4]•3H2O. This boron hydrate is innocuous for many purposes, such as screening reactions in vials, since it is unreactive and removed during an aqueous extraction or silica plug. It is harmful, however, if you want to obtain an accurate molar absorptivity because it mixes with your compound and adds to the mass.

The postdoc was dismayed. He had to first clean up his material, then set up the crystallizations all over again, but he didn’t grow any crystals. It’s hard to say exactly how the boron hydrate appears in the manufacturing process, but these vials are made of borosilicate glass (silica doped with boric oxide), which explains the presence of boron. This glass is more thermally resistant than traditional silicate glass, making it the material of choice for laboratories. The postdoc didn’t pursue the matter any further, but he learned a valuable lesson nonetheless: Whether having a glass of wine or trying to grow crystals, always wash your dishes.


Quartzy is the world’s No. 1 lab management platform. We help scientists easily organize orders, manage inventory, and save money. We’re free and always will be. Visit Quartzy.com or reach out at info@quartzy.com.

Interested in writing for The Q? Send us an email!

mmilton

Margarita Milton grew up in New York City. She received her BS in Chemistry from Stony Brook University after working on the synthesis of aromatic belts in the lab of Nancy Goroff. She is currently a graduate student in the Nuckolls Lab at Columbia University, where she creates novel architectures involving perylene diimides. In her spare time, Margarita likes to read and write.

Leave a Reply

Your email address will not be published. Required fields are marked *