Chemistry Blog

May 27

There’s something interesting brewing…

There’s something interesting brewing over at the Royal Society of Chemistry.

They’ve been beavering away trying to figure out what the (UK) public thinks for chemistry, chemicals and chemists.

Results are out on Monday 1st June via a live-stream. Be sure to tune in and join in the conversation on twitter with the #Chemperceptions hashtag.

And of course we’ll have all the analysis right here.



May 21

My Extra Credit Assignment: Turn a General Chemistry Topic into a Science Museum Exhibit

When traveling, I always make a point to explore local science museums. I look for engaging exhibits that explain scientific concepts in informative and fun ways. One such exhibit at the Science Museum of Minnesota asks participants to create carbon nanotubes using foam connectors. A few friends and I used our advanced degrees to produce the example shown below (sorry for the potato quality).

The exhibit engaged people of all ages in different ways. Just behind the exhibit you can see the little guy who, moments after the picture was taken, learned all about tearing carbon nanotubes apart while deploying a rather impressive Godzilla impression.


Since becoming a teacher I have a new appreciation for science museum exhibits. They are a literal manifestation of Einstein’s philosophy: “If you can’t explain it to a six year old, you don’t understand it yourself.” The best exhibits make the explanation entertaining too.

So, towards the end of this spring semester when my general chemistry students requested an extra credit assignment, I knew exactly what to assign. I asked them to take one of the concepts they learned in general chemistry and create a science museum exhibit to explain it.

The assignment allowed unlimited space and budget. I was less concerned about reality and much more interested in seeing their knowledge and creativity. In the end I was blown away by their creations and would like to share a few.

Dipole-dipole Board


The above exhibit, created by Taylor Trammell, showcases intermolecular dipole-dipole interactions. Her display contains many magnets–representing molecules–with two opposing sides, one positively charged (north pole) and one negatively charged (south pole). All of the magnets/molecules are free to rotate, except for one. Museum visitors can press a button and control the orientation of that one ‘molecule’. As it’s orientation changes, the other ‘molecules’ will reorientation to maximize dipole-dipole interactions and minimize the energy within the solvent.

A visitor could also walk up to the board with a strong bar magnet and introduce only it’s north or south pole to the magnet-filled board. That would represent the solvation of cations or anions through ion-dipole interactions. Taylor may not know it, but she found a fun way to introduce the solvent reorganization associated with Marcus Electron Transfer Theory.

Collision Theory Booth

According to the Collision Theory of Reactivity, for a chemical reaction to occur the molecules must: 1) collide, 2) have enough energy to make and break bonds, and 3) have the correct orientation when they collide. Emily Nabong demonstrates these rules of engagement through a museum exhibit that repurposes an amusement park throwing booth. Instead of milk jugs or balloons, the target is a Velcro-covered molecule. And instead of baseballs or darts, visitors throw ‘molecules’ with different geometries and Velcro coverage at the target.

If the molecule is thrown with too little momentum or too little accuracy it will not hit the board (collide). Also, if the molecule hits the board with the wrong Velcro alignment it won’t ‘stick’ (correct orientation). The ‘reaction’ will only occur if the molecule is thrown hard enough and with the right orientation.


Amorphous vs Crystalline Solids

Miranda Ave introduced an interactive “build your own solid” exhibit that demonstrates the difference between amorphous and crystalline solids. It’s comprised of two building stations. The first station offers Magnetix (below left), which have curved connectors representing bonds and metal spheres representing atoms. The second station offers Tinker Toys (below right) with only one rod length (bonds) and wood circles that connect at 90° positions (atoms).


Any structure built with the Magnetix will lack long-range order like in an amorphous solid. In contrast, a structure built with the restricted connectivity of the Tinker Toys will have a continuous, repeating pattern like those observed in crystalline solids.

Tearing apart these structures will also help demonstrate differences between amorphous and crystalline solids. Tinker Toys break apart in a ridged manner along cleavage lines while Magnetix structures break in random places.

The building stations will also be accompanied by a display with both crystalline and amorphous solids as well as an atomic picture of their structures.

Viscosity Race

Both Gabby Vega (below left) and Erum Kidwai (below right) proposed races between liquids to demonstrate differences in viscosity. They envisioned racetracks with several lanes, each labeled with a molecular structure. Museum goers would pick their ‘horse’ or lane and then watch as liquids ‘race’ down the track. Afterwards, each solution would be unveiled and the intermolecular forces dictating the viscosity and flow rates of the liquids would be explained.


Boyle, Lussac and Avogadro

Jessica Metzger’s museum exhibit set out to teach people about the relationship between temperature, volume, number of moles of a gas, and pressure. She proposed three different interactive stations. The first (left) contains a cylinder connected to a pressure gauge with a plunger that can be pushed or pulled. When the plunger is pushed (or pulled) and the pressure increases (or decreases), the reading on the pressure gauge will increase (or decrease) just as predicted by Boyle’s law.

The second cylinder (middle) is completely enclosed and placed on top of a heating element. When the visitors press the button a red light will turn on indicating that the chamber is being heated. As the temperature increases, the pressure will increase in accordance with Lussac’s law.

The third cylinder (right) will be taller than the other two with a lid that can move up or down without allowing gas molecules to escape. The station will be equipped with a button that, when pushed, releases compressed air into the cylinder. So, when the button is pressed, the metal lid will move up and increase the cylinder’s volume to accommodate the newly introduced gas molecules (Avogadro’s Law).

PV = nRT

Electronegativity and polarity

Carolin Hoeflich proposed an exhibit to introduce the concept of electronegativity and polarity. The exhibit includes a table with a soft foam cover and blocks representing the elements. The blocks are weighted so that electronegative elements are heavier. Museum-goers can arrange the blocks into molecular structures before dumping marbles–representing electrons–onto the table’s surface. The heavier elements will sink deeper into the foam and therefore ‘attract’ a larger number of marbles. When stepping back and looking at the structure as a whole, museum-goers will see that more marbles = more electronegativity. It’s also a fun way to visualize the dipole moment of a structure.


Osmosis touch screen

Hunter Hamilton introduced a touch screen exhibit to demonstrate the principles of osmosis and osmotic pressure. Visitors will use the screen to create an environment with more or less ions (red spheres) and one of three possible ‘membrane’ options: 1) no membrane, 2) permeable to water but not ions, and 3) permeable to water and ions. Once all selections are made, the visitors presses GO and observes which direction water and ions move in their environment.


Le Châtelier’s Principle

Another touch screen exhibit, by Kelly Wyland, covers Le Châtelier’s Principle. Her screen displays an equilibrium with colors assigned to the reactants and products. It then asks users to predict the color change upon perturbation. After a prediction is made, the screen will show an animation that adds or removes reagents from the reaction mixture’s beaker. The color change of the solution will coincide with the concentration shifts to reach equilibrium.


Reaction Coordinate Slide

I’ve saved the largest and most interactive exhibit for last. Nathan Horvat designed an exhibit with two slides that represent an exothermic and endothermic reaction coordinate diagrams. Children (maybe adults?) would start on the platform in the middle (as reactants) and climb one of two ladders representing the activation energy to the transition state before sliding down to the landing pads (products).

The ladder/slide to the left (or right) is for an endothermic (or exothermic) reaction because the end point is higher (or lower) in energy than the starting point. One thing that I found fun about this exhibit is that, while viewing it in action, you’d likely notice more children choosing the exothermic slide because the endothermic one requires more work for less return. In a statistical fashion, the children would find the product that’s more thermodynamically favorable.

rxn coordIn closing, I want thank my students for a great semester and to share my appreciation for the students who designed these exhibits. It was a pleasure to teach them and to see them come up with such creative ideas. I hope one day, during a random science museum visit, I find one of these exhibits in action.




May 19

A tale of a tired lecture course. Flip it.

It dawned on me that no one cared. The proteins that I found so fascinating just didn’t seem to intrigue them as much as they did me. I thought the video of water molecules flipping as they passed through the channel of aquaporin was marvellous. But it hardly gleaned a reaction from the sea of faces staring blankly out at me. 

Screen Shot 2015-05-19 at 14.42.33

I left the lecture theatre and trudged back to my office. Wondering what was to be done with the course I’d tinkered with for years and never been happy with. Maybe it was time to just stop tinkering, throw it all away and start afresh?

The thought drifted away as I flicked through the, not insignificant, pile of emails that had dropped into my mail box during my brief absence from my desk. Top of the list was request to review a grant proposal.

And then inspiration struck, I could get my students to write grant proposals! That way they could explore the ideas and material that they are interested in without having my predilection for Major Intrinsic Proteins foisted on them.

So I set about a total revamping of the course.

  • The lectures slides went in the bin.

Well actually they got turned into screencasts. But they might as well have gone in the bin, because the students don’t watch them.

  • I gave the students examples of grant proposals that I’d written (ones that had got good reviews, even if they hadn’t been funded 🙁 ).
  • I supplied them with a load of references to papers that contained neat ideas.
  • And I gave a lecture with avenues of research that I thought were intriguing.
  • Then I provided them with a slightly altered version of a research council’s form and told them to complete it i.e they had to write a case for support, lay summary, justification for resources etc.
  • They worked in groups of 6-7 and set about their tasks.
  • The rest of the lectures I turned up to check on how things were going, guide the projects, tell them what I thought might work or not etc.
  • And come the end of the course I marked the proposals based on genuine research council criteria AND each group peer reviewed 3 other proposals using the same criteria. Group members also gave an effort mark to each other (so free loaders didn’t get an easy ride). And the final mark was made up from an amalgamation of my mark, the peer review and the inter-group mark.

The results were great. Some really fabulous ideas sprung up. I’ve had students ask me if they can actually work on their research projects during their final year dissertations, and I bet some of proposals would have made the quality cut off in real funding rounds.

Right, enough from me, I’ve just come across a great idea for a project I need to get into the next funding round. 😉

May 08

Campaign for Clear Code starts here!

I’m concerned about the software that’s installed on my electronic devices.

You should be worried as well.

Have you really considered what you are opening yourself up to every time you download a new app or install an upgrade?

Have you thought about what all those faceless software giants are doing with the code that they are busy sneaking onto your phone?

Do you have any idea what they are slipping directly into your pocket? It certainly isn’t good for you. After all its not you they care about. All that really concerns them is profit, pure and simple. They want you coming back for more, why else would they make those damn games so additive?

Screen Shot 2015-05-08 at 21.26.12

And has that code even been tested properly? They claim it has, but why then does big software continually release patches and updates?

Just stop for a minute and ask yourself this. Do you really know what you are putting on your computer when you downloaded Candy Crush? Have you ever seen the code?

Take a look at this.

if(tic[f][z]==’ ‘)
goto x;

Understand it?

No, me neither.

Want to know where that snippet of code came from? Its just a small part of a computer program for tic-tac-toe. And if a game as simple as that has stuff like that in it then imagine what’s in Candy Crush, Angry Birds or even Powerpoint?

And it gets worse. Because some computer programer, in the pay of cooperate giants, writes this sort of thing before processing it into something that might not even contain recognisable words! The software companies call this ‘compiling’ and afterwards its bears no resemblance what-so-ever to the natural code.

I, for one, won’t stand for this sort of thing being foisted on me by big-software any longer.

Now is the time to take a stand.

I call for a campaign for clear code.

Basically, if a 10 year old child can’t code it then it has no place on my devices.

From this point onwards I’m reverting back to simple code that anyone can understand. I’m using nothing more than Scratch running on a nice wholesome Pi. I urge you to do the same.

And don’t even get me started on anti-virus software. Much better to share infected USB sticks around.

May 05

What has Chemistry got to say?

The XKCD comics have been keeping me entertained and informed for years.

But sadly, in the latest comic, Chemistry seems rather quiet.

So how about some suggestions for the next panel, where Chemistry finds a voice?


Apr 30

Reagent pencils, turning chemistry into child’s play

If you’ve ever sat opposite a doctor and wondered what she was scribbling on her notepad, the answer may soon not only be medical notes on your condition, but real-time chemical preparations for an instant diagnostic test.

Thanks to the work of a team of researchers from California Polytechnic State University, recently published in the journal Lab on a Chip, chemicals formed into pencils can be made to react with one another by simply drawing with them on paper. The team may have taken inspiration from colouring books for their take on a chemical toolkit, but their approach could make carrying out simple but common diagnostic tests based on chemical reactions – for example diabetes, HIV, or tests for environmental pollutants – much easier.

The project started with an established technique called paper-based microfluidics. This uses the capillary effect of paper to carefully mix together what are called reagents – those chemicals mixed to form a reaction, or to measure the presence or absence of a substance. The capillary effect in action is easily seen by dropping two inks of different colours onto a piece of tissue paper. As the liquid is absorbed by the paper the colour drops spread out until they merge with one another and form a colour blend. In the same way two or more reagents can be mixed with water on a strip of paper.

Colouring-in chemistry.
Lab on a Chip/RSC

In this case, the difference is that the reagents aren’t added to the paper via droplets. Instead they’re applied via pencils, meaning that without specialist equipment anyone can set about creating chemical reactions by simply using them on the paper.

The team made the reagent pencils by pulverising a mixture of graphite (just as you’d find in normal pencils), test reagents and polyethylene glycol, which helps to keep the reagent dispersed throughout the mixture, as is used for the same reason in toothpaste. They compressed the mixture into pellets and mounted them into mechanical pencil holders bought from the high street stores.

The reaction paper pad was created by using a waxy ink to print small connected enclosures onto filter paper. The reagent pencils could be used to colour in these areas within the enclosures – when water was added to the paper, the reagents dissolved and, confined by the waxy ink, were forced to diffuse towards one another and react.

Real world uses for real world problems

The team demonstrated a potential use of the reagent pencil technique by using it in place of a common test used by diabetics to check their blood glucose levels, which involves reacting a pinprick blood sample with a chemical solution and examining the result.

One pencil was constructed with a mixture of enzymes, one called horseradish peroxidase (HRP) and the other glucose oxidase (GOx). A second pencil contained a reagent called ABTS. When combined in the presence of glucose these react together to give a blue-coloured product. Comparing the results from their pencils on the pad with the more traditional dropper method used by diabetics the team found the results were identical.

An example of how chemical reactions using pencils can provide instant results.
Lab on a Chip/RSC

The image shows, on the left, the reagents applied via droplets of solution. On the right, the reagent pencils were used. The top row shows the paper at the beginning of the test, the bottom row the result. Applied to the left enclosure, the sample solution carries the two reagents together which react. The coloured product produced is, as shown on the graph, identical between the two methods.

This is of course extremely easy to set up. Traditional diagnostic tests require training, while this pad and pencil system requires no more than skill than required to colour within the lines. The reagents are extremely stable once made into pencils – usually they would degrade in a matter of days as liquids, limiting how and where the tests can be made. However the reagent pencils showed no sign of degrading after two months.

So this pencil tool kit has obvious advantages: a kit of reagent pencils, much like a box of colouring pencils, is easily transported, without the chemicals degrading. Kits could be designed with particular tests in mind – and the reaction mix can be adjusted by applying more or less, without the need or equipment to make-up complex solutions. There’s scope to monitor environmental pollutants, carry out diagnostic tests in remote locations – not to mention teach chemistry in primary schools.

The Conversation

This article was originally published on The Conversation.
Read the original article.

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