chemistry hacks

572 Articles

A Beginner’s Guide To X-Ray Crystallography

January 21, 2020 by 6 Comments

In graduate school, I had a seminar course where one of the sections was about X-ray crystallography. I was excited, because being able to discern the three-dimensional structure of macromolecules just by shining X-rays on them seemed like magic to me. And thanks to a lackluster professor, after the section it remained just as much of a mystery.

If only I’d had [Steve Mould] as a teacher back then. His latest video does an outstanding job explaining X-ray crystallography by scaling up the problem considerably, using the longer wavelength of light and a macroscopic target. He begins with a review of diffraction patterns, those alternating light and dark bands of constructive and destructive interference that result when light shines on two closely spaced slits — the famous “Double-Slit Experiment” that showed light behaves both as a particle and as a wave and provided our first glimpse of quantum mechanics. [Steve] then doubled down on the double-slit, placing another pair of slits in the path of the first. This revealed a grid of spots rather than alternating bands, with the angle between axes dependent on the angle of the slit pairs to each other.

Photograph 51, an X-ray crystallogram of the B-form of DNA, by Gosling and Franklin, 1952. Source: Wikipedia

 

To complete the demonstration, [Steve] then used diffraction to image the helical tungsten filament of an incandescent light bulb. Shining a laser through the helix resulted in a pattern bearing a striking resemblance to what’s probably the most famous X-ray crystallogram ever: [Rosalind Franklin]’s portrait of DNA. It all makes perfect sense, and it’s easy to see how the process works when scaled down both in terms of the target size and the wavelength of light used to probe it.

Hats off to [Steve] for making something that’s ordinarily complex so easily understandable, and for filling in a long-standing gap in my knowledge.

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A Safer, Self-Healing Polymer Battery

January 15, 2020 by 4 Comments

Lithium-ion batteries are notorious for spontaneously combusting, with seemingly so many ways that it can be triggered. While they are a compact and relatively affordable rechargeable battery for hobbyists, damage to the batteries can be dangerous and lead to fires.

Several engineers from the University of Illinois have developed a solid polymer-based electrolyte that is able to self-heal after damage, preventing explosions.The material can also be recycled without the use of high temperatures or harsh chemical catalysts. The results of the study were published in the Journal of the American Chemical Society.

As the batteries go through cycles of charge and discharge, they develop branch-like structures known as dendrites. These dendrites, composed of solid lithium, can cause electrical shorts and hotspots, growing large enough to puncture internal parts of the battery and causing explosive chemical reactions between the electrodes and electrolyte liquids. While engineers have been looking to replace liquid electrolytes in lithium-ion batteries with solid materials, many have been brittle and not highly conductive.

The high temperatures inside a battery melt most solid ion-conducting polymers, making them a less attractive option for non-liquid electrolytes. Further studies producing solid electrolytes from networks of cross-linked polymer strands delays the growth of dendrites but produces structures that are too complex to be recovered after damage. In response, the researchers at University of Illinois developed a similar network polymer electrolyte where the cross-link point undergoes exchange reactions and swaps out polymer strands. The polymers stiffen upon heating, minimizing the dendrite problem and more easily breaking down and resolidifying the electrolyte after damage.

Unlike conventional polymer electrolytes, the new polymer also shows properties of conductivity and stiffness increasing with heating. The material dissolves in water at room temperature, making it both energy-efficient and environmentally friendly as well.

Tetraethyl Lead: The Solution To One, And Cause Of Many New Problems

January 15, 2020 by 101 Comments

From the 1920s until the 1970s, most gasoline cars in the USA were using fuel that had lead mixed into it. The reason for this was to reduce the engine knocking effect from abnormal combustion in internal combustion engines of the time. While lead — in the form of tetraethyllead — was effective at this, even the 1920s saw both the existence of alternative antiknock agents and an uncomfortable awareness of the health implications of lead exposure.

We’ll look at what drove the adoption of tetraethyllead, and why it was phased out once the environmental and health-related issues came into focus. But what about its antiknock effects? We’ll also be looking at the alternative antiknock agents that took its place and how this engine knocking issue is handled these days.

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A DNA-Based Computer Calculates Square Roots Up To 900

January 12, 2020 by 20 Comments

While DNA-based computing may not be taking over silicon quite so soon, there is progress in the works. In a paper published by Small, researchers from the University of Rochester demonstrate a molecular computing system capable of calculating square roots of integers up to 900. The computer is built from synthetic biochemical logic gates using hybridization, a process where two strands of DNA join to form double-stranded DNA, and strand displacement reactions.

DNA-based circuits have already been shown to implement complex logic functions, but most existing circuits prior to the recent paper were unable to calculate square root operations. This required 4-bit binary numbers – the new prototype implements a 10-bit square root logic circuit, operating up to the decimal integer 900.

The computer uses 32 strands of DNA for storing and processing information. The process uses three modules, starting off with encoding a number on the DNA. Each combination is attached to a florescent marker, which changes signal during hybridization in the second module. The process for calculating the square root controls the signals, with the results deducted from the final color according to a threshold set in the third module.

We’re beginning to see the end of Moore’s Law approaching, with companies like Intel and AMD struggling to shrink transistors 10 nm wide. Nevertheless, with DNA molecules still about 10 time smaller than the best transistors today and DNA computing systems continuing to gain in sophistication, biochemical circuits could potentially be holding solutions to increasing the speed of computing beyond silicon computing.

Engineering Your Way To Better Sourdough (and Other Fermented Goods)

January 8, 2020 by 23 Comments

Trent Fehl is an engineer who has worked for such illustrious outfits as SpaceX and Waymo. When he got into baking, he brought those engineering skills home to solve a classic problem in the kitchen: keeping a sourdough starter within the ideal, somewhat oppressive range of acceptable temperatures needed for successful fermentation.

A sourdough starter is a wad of wild yeasts that you make yourself using flour, water, and patience. It’s good for a lot more than just sourdough bread — you can scoop some out of the jar and use it to make pancakes, waffles, pretzels, and a host of other bread-y delights. A starter is a living thing, a container full of fermentation that eats flour and has specific temperature needs. Opinions differ a bit, but the acceptable temperature range for active growth is about 60 F to 82 F. Too cold, and the starter will go dormant, though it can be revived with a little love. But if the starter gets too hot, all the yeasts and bacteria will die.

While there are of course commercial products out there that attempt to solve this problem of temperature control, most of them seem to be aimed at people who live in some wonderland that never gets warmer than 80F. Most of these devices can’t cool, they only provide heat. But what if you live in a place with seasons where the climate ranges from hot and humid to cold and dry?

The answer lies within Chamber, a temperature-regulated haven Trent created that lets these wild yeasts grow and thrive. It uses a Peltier unit to heat and cool the box as needed to keep the mixture fermenting at 26°C /78.8°F.

Thanks to the Peltier unit, Trent can change the temperature inside the chamber simply by alternating the direction of current flow through the Peltier. He’s doing this with an H-bridge module driven by a Raspberry Pi Zero. When it starts to get too warm in the chamber, the fan on the outside wall vents the heat away. A second fan inside the chamber pulls warm air in when it gets too cold.

Trent says that Chamber performs really well, and he’s recorded temperatures as low as 60F and as high as 82F. He mostly uses it for sourdough, but it could work for other temperature-sensitive food sciences like pickling, growing mushrooms, or making yogurt. We think it could be ideal for fermenting kombucha, too.

Chamber works well enough that Trent has put further development on the back burner while he makes use of it. He does have several ideas for improvements, so if you want to help, check out his website and Github repo.

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A Car That Runs On Homemade Chemical Reactions

December 25, 2019 by 11 Comments

The race for chemical engineering is quite literally on. Every year, the American Institute of Chemical Engineers (AlChE) brings together hundreds of university students to face-off to design the fastest car using techniques they’ve learned from chemical engineering courses.

The Chem-E-Car competition races cars which are only powered by chemical reactions. The goal is to come up with an elegant solution – you can’t simply jettison matter out the back as the method of locomotion. In particular, the rules don’t allow the use of liquid or obnoxious odor discharge, commercial batteries, brakes, or electrical/mechanical timing devices. However, this doesn’t mean that electronics are absent from these designs. Many teams must gather data in order to design a control system to improve the performance of their car.

Students have to build a power system, stopping mechanism, circuitry, and mechanical assembly for the body of the car, all to fit in a size constraint not much bigger than a shoebox. The competition primarily judges the accuracy of the chemical reaction for stopping the car more so than speed or power. Given that the load the car must carry is typically unknown until the day of the competition, this is a significant challenge, allowing teams to find a way to design a flexible reaction that can accommodate a range of loads and distances.

For example, this 2015 entry from the Rice University team (PDF) uses a fuel cell for locomotion and an iodine clock reaction as a timer for braking. The fuel cell powers an Arduino which monitors a light-dependent resistor. In between the LED and that LDR, the clock reaction turns opaque at a predictable time and triggers the motors to stop turning.

While many schools choose not to disclose their designs in order to gain a competitive edge, we applaud the teams who have shared the story of their builds. Kudos to the Rice team mentioned above, to the 2014 Rutger’s team whose white paper outlines the construction of aluminum air batteries worthy of Walter White, to the car from the Universitas Negeri Semarang, Indonesia powered by a thermoelectric generator (PDF), the UC Berkeley team for outlining numerous approaches to developing their power system, and the two Ohio State team’s entries seen winning the regional competition in the video below.

If you were on a team that compete the the Chem-E-Car, we want to hear about it!

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The Story Of The Quickening: Mercurial Metal

December 11, 2019 by 49 Comments

Of all known metals, mercury is probably one of the most famous, if only for its lustrous, liquid form at room temperature. Over the centuries, it has been commonly used in a wide variety of applications, including industrial chemical processes, in cosmetics, for telescope mirrors, thermometers, fluorescent lamps, dental fillings, bearings, batteries, switches and most recently in atomic clocks.

Though hardly free from the controversy often surrounding a toxic heavy metal, it’s hard to argue the myriad ways in which mercury has played a positive role in humanity’s technological progress and scientific discoveries. This article will focus both on its historical, current, and possible future uses, as well as the darker side of this fascinating metal.

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