Tag Archives: Science

crystals of potasium phoaphate incorporating the chemical amaranth dye

Amaranth Potassium Phosphate Crystals

Potassium phosphate crystal chemistry

This weekend I grew some potassium phosphate crystals with amaranth dye. I did this back in 2001 in Bart Kahr’s O-Chem class and remembered it recently. It’s a fun demonstration of the chemistry of crystal growth, the different chemistry of the crystal faces, and it’s pretty. I found Prof. Kahr’s paper[1] that gives a “foolproof recipe” and it did not disappoint. Even this fool could make it work.

As the crystals grow, each face of the crystal has a unique topology. The corners are growing with a different spacing of atoms than the faces, and the faces can be different from each other. Sometimes, the faces have the right spacing to allow a dye molecule to stick. In this case, there is a big difference between how well amaranth dye sticks to each face. So as the crystal rows, it only gets dyed in two quadrants.

We can learn about chemistry from crystals

Crystals are super useful to chemists. A good crystal of a chemical can be used to get x-ray diffraction data on the structure of the chemical. The most detailed structures are derived from x-ray diffraction data.

Knowing how molecules assemble into crystals is also really important to materials scientists. If you want to design a material from its atoms, you need to know how they are going to come together. I’ve been working on making an iron battery and reading up on battery chemistry. One of the interesting papers I read talked about designing a cathode material to hold sodium atoms. The chemists designed the “holes” in the structure to hold sodium atoms – and they needed to know how the other atoms would come together to make that shape.

Why chemically dyed crystals are cool

Of course, dyed crystals just look cool. Maybe that’s silly, but if you’re trying to teach organic chemistry, it’s good to have something visual and striking to hold on to. A lot of O-chem is solvents and white powder, so anything that sticks in the memory is a help.

The other reason I think that dyed crystals are so cool is that they dyes can be held still very precisely. One of prof. Kahr’s later papers used a crystal to hold a fluorescent dye in place at a specific orientation. Then they used a fluorescence microscope to look at single dye molecules[2]. I think that’s just really cool. I gather that they are more stable in the crystal than they are in solution.

I also made a time-lapse movie of the crystallization

Instructions (following [1])

  • Dissolve 17 g potassium dihydrogen phosphate (KDP) in 50 ml water with heating. Using a teflon stir bar helps.
  • Dissolve 4 mg amaranth dye in ~1ml of water and add to the mix.
  • Pour into a wide dish and allow to cool and evaporate slowly over ~4-24 hours.


1.Kahr, B. & Vasquez, L. Painting crystals. CrystEngComm 4, 514–516 (2002). http://dx.doi.org/10.1039/B204845K

2.Wustholz, K. L., Kahr, B. & Reid, P. J. Single-Molecule Orientations in Dyed Salt Crystals. J. Phys. Chem. B 109, 16357–16362 (2005).http://dx.doi.org/10.1021/jp053051x

Index of refraction based detection

I had an idea to build an index of refraction-based detector for an electrophoresis set-up. When light passes through a prism, it bends. That’s how prisms cast rainbows. The angle at which the rainbow shows up depends on the material of the prism. If the prism is made of glass, you get a rainbow at one angle. If the prism is made of water, you get a different angle. We can use this phenomenon to detect changes in the material. We need a prism that we can fill with different materials. Then we can see how the angle changes. I built such a prism out of acrylic with my laser cutter. It looks like this:

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I haven’t started flowing things through the prism yet. I’m still figuring out how to detect the angle change. But there definitely is an angle change. I can see the difference in angle between when I have air in the prism and when I have water in the prism. Have a look – that’s air on the left and water on the right:

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So now the question is how tiny a difference can I detect? Adding small amounts of sugar to the water will change the index of refraction a tiny bit. That should change the angle by a small amount as well. If I can measure the angle very precisely, I should be able to detect very small changes in the sugar content of the water.

I’ll try to get my students to build generation 2 of the device. Design, build, test learn. The work will teach them.

More droplet literature reading and a bit of a ramble

There is a neat paper in this issue of the journal Lab on a Chip. The Tuteja lab out of Michigan developed a clever way of making droplets using a laser cut jig and an open platform. I mean literally open (not like open source). They make water in oil droplets that float across the surface of a hydrophobic chip. It reminds me a lot of the beer sphere.

I caught this image of a beer sphere suspended on its surface tension on the surface of a glass of beer. It was so persistent that I was able to get my camera and come back to the table to take a picture.

The Slo-Mo guys got really good footage of surface tension droplets. It’s an interesting phenomenon. Surface tension prevents a water droplet from merging with the water surface. If you have an oil surface, the water will not merge at all. Surface tension isn’t needed. But it looks similar.

I meant to get in the lab this morning and fabricate some devices, but I am not feeling motivated. I ramble a bit about that in the video today. I’m very worried about science funding. That’s dumb. Can’t do anything about it. It’s worrying for nothing. But I am worrying anyway. That’s four hours of my life I will not get back.

Focus on science. Rise above.


Papers on droplet microfluidics I am reading

Monodispersed microfluidic droplet generation by shear focusing microfluidic device,” is from 2006. It’s a study on the design of the flow focusing droplet generator. It explores the role of flow rate and pinched geometry on the droplets. At the time, it wasn’t completely clear what these droplets could be used for. I was looking at them as little storage containers for cells.

In 2016, digital PCR was a clear application of this technology. A PCR reaction was segregated into lots of little droplets. Each droplet either has a DNA molecule or does not. As a consequence, the PCR reaction makes it go green or not. Instead of trying to interpret different levels of green fluorescence (which is relatively hard to quantify), the scientist can just count the bright droplets (much easier to quantify). “Centrifugal micro-channel array droplet generation for highly parallel digital PCR” presents an unconventional droplet generator to make lots of little droplets for that application.

The application I’m working toward is a little different. I want to make particles based on these droplets. The little particles will have a sensor on them so that we can detect what is happening near to the particle. The particle might then respond by glowing green or by releasing a drug. Similar particles have applications in cosmetics and lubricants. I think that we can make them smarter. We can apply them to research (reporting cell environments) diagnostics and maybe therapeutics (some day).

Acrylic microfluidics part 7

One of the reasons I am trying to develop these techniques for acrylic microfluidics is to shorten the design-build-test feedback loop. With the PDMS techniques I worked on and grad school the loop is about a week long. It takes a day to design, a few days to get the photomask, and a day or two to fabricate. If nothing goes wrong, I use to be able to get a design tested on day five.

With acrylic based microfluidics, the loop is much shorter. I can modify a design, cut it with the laser, fabricate the chip, and have it tested all within three hours. Three hours is a significant improvement over five days.

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This morning I came in and cut a new chip with some new parameters. I was hoping to see a narrower width channel which would produce smaller droplets. I didn’t get that, but I can try again (tomorrow not next week). Plus, I learned something. I need to add a viewing area to the chip to see the droplets better.

I made a little video of some of the process. I skipped the bonding step in the video because it’s just 10 minutes of waiting while the hot press does its work.

Here are parts 1 2 3 4, 5 and 6.