Category Archives: Science

All things scientific

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.

Sources

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

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All Iron Battery: Iron metal/Iron(III)EDTA cell

I have been working on building an all-iron battery. A cheap storage solution needs to happen soon: the pacific northwest has such an abundance of electricity that Bonneville Power needed to shut down wind turbines to deal with the surplus. For stationary batteries, weight and performance are less important than cost.

An iron battery is likely to be cheap. Iron is a very cheap material and iron chemistry doesn’t require special handling for air-sensitivity or toxicity. I ran the numbers. If the world used all of its lead, lithium or iron to build a battery, lead and lithium would be small as a percentage of the grid. Iron looks pretty good. We could make a grid scale iron battery without disrupting the iron market.

So how would an iron battery work? First, we need an anode. That’s easy: we can use the Edison Cell anode made of iron and iron hydroxide. It’s an old technology and is very robust.  We also need a cathode. We need an iron chemical that can be easily reduced. That means some form of Iron(III). Rust, basically. A solid would be great, and a conductive solid would be even better. I tried iron oxide. That didn’t work. It can absorb an electron, and it’s solid, but it’s not conducive and I couldn’t get significant current.

I gave up on having an all-solid chemistry. I decided to try Iron(III)EDTA which is nicely soluble in water. I made the first version of this cell that seemed to work. I tested the design with an iron/copper cell. Half of the Edison Cell and half of the Daniell Cell. I made a salt bridge with 1M KCl and agarose. The result gave 0.9 V.

For all-iron chemistry, I kept steel wool on the anode side. Then I replaced the copper with iron/EDTA. I made a ~0.1 M solution of Iron (III) EDTA in pH 8 buffer (a little Tris/acetate that I had lying around; probably not ideal). I connected up the cathode with a bit of nichrome wire (I would prefer to soak the iron solution into conductive graphite, but I started simple). That gave 0.5 V. So it works, at least a little. Now I need to make it better.

I also just wanted to mention that I “vlog” about this and other things every Monday to Friday. I’m sometimes talking about other projects, but for whatever reason, I’m feeling a bit obsessive with this one. I hope this becomes a somewhat practical battery that folks could make according to a DIY video. Maybe that would be useful to somebody (even if only as a science fair project).

Organ-on-a-chip for safer drugs sooner

We need a new way to test drugs and supplements for safety. The current method is slow and uses animals. Nobody likes animal cruelty. Plus, animal biology is not exactly the same as human biology. There are unpredictable differences. Organ-on-a-chip is a way to culture human cells in a device that mimics the structure of an organ. The device is made of a clear plastic so that scientists can watch the cells under different conditions. If this approach works, it will allow for faster and more accurate safety tests without using animals.

By Timothy.ruban - Own work, CC BY-SA 3.0 - 2017-04-13 06_44_38-Conceptual Schematic of a Human-on-a-Chip - Organ-on-a-chip

Safety is critical. Before a drug enters human safety trials, it is tested on two species of animals. Even so, strange things can happen when moving to a new species. If a compound is not dangerous to rats or dogs, it can still be dangerous to people. BIA 10-2474 is such a compound: it killed a safety trial participant in France.  Conversely, theobromine is safe for humans but dangerous for dogs. If theobromine had been a drug candidate, and it had failed safety tests in dogs, it would have been regarded as too risky to try in people. This despite the fact that it is actually safe. Undoubtedly, there are safe drugs that have been rejected for reasons that are not applicable to people.

With an organ-on-a-chip approach, it may be possible to test drug candidates on human cells in a way that reports whether the compound is actually safe for humans. A 2010 paper in science talks about building a mini-lung that can be used to investigate whole-organ responses like inflammation. That’s not something that shows up in a simple tissue culture model; it requires multiple cell types and structures.

The FDA is now Testing ‘Organs-on-Chips’ Technology according to an FDA blog post:

On April 11, 2017, FDA announced a multi-year research and development agreement with a company called Emulate Inc. to evaluate the company’s “Organs-on-Chips” technology in laboratories at the agency’s Center for Food Safety and Applied Nutrition, one of a number of FDA efforts to help evaluate this chip technology. The flexible polymer organ-chips contain tiny channels lined with living human cells and are capable of reproducing blood and air flow just as in the human body. The chips are translucent, giving researchers a window into the inner workings of the organ being studied.

That’s encouraging. If the FDA determines that organ chips give results that are comparable or better than animal results, we might see lower regulatory hurdles for new drugs. Faster, better approvals are good for patients and investors. Plus, nobody likes animal testing.

Raspberry Pi Computer: standalone “safe” machine

I want a computer that does not rely on a software service agreement to function. Cell phones obviously have to operate as a service since they need a network to operate. The phone is a gateway to the cell service. My kindle is similar for Amazon services. Laptops feel different to me. Computers feel like products. I own my laptop and I want to think of it as a standalone device, not a gateway to a cloud service.

Windows 10 is now a service. The future is clearly going in the direction of software as a service (SaaS as the kids put it). That’s fine, but I like to have at least some device that can’t be remotely bricked by a company.

Raspberry Pi Computer in a Box parts list:

Quick catch-up for other topics this week: I made a video I about sodium-ion batteries and people seemed interested. I think a sodium ion battery would be really cool. But I think the expectations of the youtube viewers may be a little inflated. Sodium is heavier than lithium. It yields less energy per atom, too. So it’s not going to be great for mobile. I made another video talking about that. So why bother with sodium? Lithium is relatively rare and expensive… so sodium might be better for stationary applications. It’s hard to say at this point, but I’m investing my time in an iron battery.

 

Lithium ion batteries are not for DIY

Lithium ion batteries are in all kinds of high performance devices. I made a little video talking about how they work. They store a good amount of energy, release it fast enough for a cell phone, and don’t blow up all that often. Typically, lithium or lithium-ion batteries need to be assembled without the presence of water or oxygen which makes them less than ideal for DIY. The old potato battery with lithium is a bad idea.

What about sodium batteries? Sodium is another alkali metal like lithium. It should work similarly, but it’s way cheaper. You can buy sodium hydroxide for $8 a pound at the hardware store. That’s about half elemental sodium by mass. That’s an order of magnitude less expensive than lithium. The price per watt-hour stored could get considerably lower.  The lowest that prices can go is the price of materials, and sodium is cheap. For now, though, the cost of materials is not the biggest part of the final battery price. The cost of assembly, housing, and associated electronics is a bigger share of the pie, so it makes sense to work on those first.

What is not so good about sodium batteries? Sodium metal stores less energy per atom, so you get a lower voltage. It’s also a lot heavier, so you get less energy per unit mass. Sodium is more explosive in contact with water than lithium. It’s harder to pack into electrodes. Where graphite holds lithium and lets it migrate, the equivalent for sodium doesn’t work so well. As you charge a LiFePO4 battery, you move lithium into a graphite cathode for storage. Lithium slips between the layers of graphite, but sodium doesn’t fit.

If those problems could be overcome, sodium batteries would be great for stationary storage. Sodium batteries would be heavy (no good for mobile) but cheap (good for large scale). Aquion, Faradion, and GE are all working on it. Several articles from academic labs have come out very recently showing off sodium battery technology. So what are the major hold-ups? Two reviews talk about the issues, and they are all challenging.

I’m interested in iron batteries. Iron is cheap, ubiquitous, and I think the sheer volume of iron available may make it a good candidate for grid storage. So I’m playing with it a bit. Check out the vlog: