Chemistry Blog

Dec 06

ACS LiveSlides: Another Step in Multimedia Science Publishing


Last March I introduced the Hanson research group’s five minute GEOSET videos. I’ve since learned that, in July 2013, Prashant V. Kamat (Deputy Editor), George C. Schatz (Editor-in-Chief) and their co-workers at the Journal of Physical Chemistry Letters announced ACS LiveSlides™, a user friendly mechanism for generating and sharing video slideshows for each manuscript. As noted in their editorial piece, they were motivated by the “changing publication landscape and the wide availability of new electronic tools have made it increasingly important to explore new ways to disseminate published research.”

We recently created an ACS LiveSlides™ presentation for our J. Phys. Chem. Lett. manuscript, “Photon Upconversion and Photocurrent Generation via Self-Assembly at Organic–Inorganic Interfaces.” The paper introduces self-assembled bilayers as a means of facilitating molecular photon upconversion and demonstrates photocurrent generation from the upconverted state. It’s arguably the first example of directly extracting charge from a molecular upconverted state if using the first submission date, first public disclosure, or the patent application date as markers. If using the manuscript acceptance date, Simpson et. al’s publication holds that distinction.

An invitation to create an ACS LiveSlides™ presentation immediately followed the message notifying us that our manuscript was accepted. All we needed to do was provide 5-8 Power Point Slides summarizing the manuscript (using a format provided by the ACS) and record an accompanying <10-minute mp3 audio file. The editors took the files (and a list of times for each slide transitions) and published our LiveSlides™ presentation in less than a week. It was an easy process and now anyone can view our presentation. No subscription necessary.

One drawback is that the video cannot be embedded on a webpage. As stated in their terms:

Files available from the ACS website may be downloaded for personal use only. Users are not otherwise permitted to reproduce, republish, redistribute, or sell any Supporting Information from the ACS website…

So we have a backup plan for those preferring an embedded video. Below you’ll find our GEOSET video summary presented by Sean Hill.

Oct 31

Halloween Chemistry: Cinder Toffee!




How about a spot of halloween chemistry? With nice simple explanations for the trick or treaters.

Cinder toffee!!

You’ll need:

  • Sugar
  • Golden syrup
  • A jam/jelly thermometer
  • Bicarbonate of soda
  • Grease proof paper
  • A baking tray
  • A saucepan

Safety:

The toffee mix gets very hot, be careful when handling in and make sure there’s an adult helping.


What to do:

1. Weigh out 100grams (3.5 oz) of sugar into the saucepan.
2. Add 3 tablespoons of syrup
3. Heat the mixture on a stove whilst stirring it.
4. Check the temperature of the mixture.
5. Carry on heating until it reaches 145-150oC (293-302).
6. Quickly stir in 1 teaspoon of bicarb. It will suddenly bubble up.
7. Now pour it into the baking tray, lined with grease proof paper.
8. Leave it to cool.

9. Break it all up (best done with a hammer) and enjoy!

What’s going on?
So that’s a nice simple recipe for a tasty treat but where is the science?

First off there’s the sugar and syrup. There are actually loads of different types of sugars, the stuff you put in your coffee and the granulated sugar used here is sucrose. It looks like this:

Sucrose
Golden syrup is a mixture of water, sucrose and two other sugars called fructose and glucose. They look like this:
Fructose
Glucose
Sucrose is actually made up of a fructose and glucose molecule that have been joined together.
So why do we need these three sugars to make the toffee? Well, when they are mixed all together they interfere with crystal formation. To explain how this works let’s represent each of the sugars with a different shape.
If we have one type of sugar then the molecules can pack together nice and neatly, like in the diagram. And that is exactly what happens in a crystal. But if you mix them all together they can’t form ordered patterns and so you don’t get crystals forming.
So if we tried to make the toffee with just one type of sugar then we’d end up with crystals forming which make for hard dense toffee (more like a boiled sweet). But by using 3 different sugars the crystals don’t form and instead you end up with a brittle, crunchy, glass like toffee.
Then there’s the bicarbonate of soda. You normally put this in cakes to make them rise. That’s because when you heat up the bicarb it turns to carbon dioxide gas (hence the bubbles in your cakes). The same thing happens here. When you spoon the bicarb into the hot sugar it almost instantly gets converted to carbon dioxide and causes the mixture to foam up.

Hope you enjoy the toffee and whilst you do you can find out more about the science of cinder toffer here.

Oct 30

Molecules in Minecraft





Children should be playing more computer games in school. That idea might enrage you if you think kids today already spend too much time staring at screens or if you are already sick of your offspring’s incessant prattling about fighting zombies and the like. But hear me out.

Specifically, I think more children should be playing the online game Minecraft. Minecraft is like a digital version of Lego in which players can construct everything from simple houses to intricate fantasy cathedrals and even complex machines such as mechanical computers. There is no intrinsic aim to the game. Like all good ways of sparking a child’s imagination, it requires them to set their own goals.

But Minecraft is much more than just a game. Used carefully it can also be a powerful educational tool. It allows young people to create and explore places that are completely inaccessible by other means. Within the blocky world, they can roam around historical sites, delve into the geology beneath their feet or fly through the chambers of a heart, and much more besides.

The rich resources of these virtual worlds, coupled with the educational version of the game, allow teachers to immerse young people in a comfortable but exciting learning environment. Minecraft has the ability to bring just about any conceivable structure to the classroom, bedroom or sofa of every player.

Creating complex structures

One of the types of structure I’m particularly passionate is that of proteins. These tiny molecular machines fascinate me. They control just about every biological process in your cells and knit your body together. From replicating your DNA and forming the bases of your skin, hair and connective tissue, to digesting food, fighting infections and transporting oxygen around your blood, proteins do it all.

And just like man-made machines, proteins have to be precisely built if they are to do their jobs. A small part out of place, whether a nut in a car left loose by an errant mechanic, or an atom in a protein mutated by UV light, can cause the whole mechanism to fail. Sometimes this will have disastrous consequences: a failed brake in your vehicle, or cancerous cells in your body.

You don’t have to be interested in biochemistry and its implications to appreciate that proteins are beautiful wonders of nature, just as you can appreciate the elegant design of a car without knowing how it works. The difference is that you can see wonderfully designed cars all the time. But where could you marvel at the structure of a protein? How about Minecraft?

Thanks to the work of my chemistry students and the support of the Royal Society of Chemistry, that is now possible. MolCraft is a world where the majestic helices of myoglobin rise above you. Where you can explore this massive molecule and its iron centre that carries oxygen around your muscles. Or, if you prefer you can fly down a pore through which water molecules normally flow across cell membranes.

Myoglobin in Minecraft.

In MolCraft, anyone can explore the building blocks of these incredible natural nano-machines. You can discover how just 20 chemical building blocks can result in the astonishing diversity of structures and functions that are required to hold living things together.

Histidine as seen in Minecraft.

Histidine as seen by a chemist.

There are plenty of accessible molecular visualisation tools, both physical and virtual. But now we’ve used Minecraft to turn the process of exploring and learning about molecules into a game. MolCraft contains a scavenger hunt, quizzes and clues dotted around the world that can be solved with the help of information found during players’ explorations.

Imagine a science lesson where the class is let lose in Minecraft with instructions to find a set of objects hidden on key parts of molecules. Upon retrieving them the teacher will know which molecules each student has explored and what questions they may have answered to find the objects. All this time, the children think they have just been playing a game.

As well as making MolCraft available to download for free, we’re also working on ways to further integrate the software into education. One idea is to turn it into a complete online learning environment, where students can complete coursework, write assignments, take part in quizzes or help developing other teaching resources, all within the game. Their tutors can then see their work and send them feedback while still immersed in the Minecraft world.

Posing in front of glycine.

Using Minecraft for teaching doesn’t have to stop at proteins. Our other Minecraft-related projects are allowing students to explore and understand deserted medieval villages or reconstruct the architecture of Hull and there’s much more in the pipeline. The only limits are the imagination of teachers and students.

The Conversation

Mark Lorch, Senior Lecturer in Biological Chemistry, Associate Dean for Engagement , University of Hull and Joel Mills, Technology enhanced education, University of Hull

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

Oct 27

Review: Chemistry Sets fit for the 21st Century.




As a kid I loved my chemistry set. Many an afternoon was whiled away in my dad’s shed, totally ignoring the set’s instructions and randomly mixing the contents of the various bottles. To be honest I can’t really remember learning much chemistry, beyond the fact that it was possible to generate some pretty noxious fumes.

I guess its that sort of behaviour that rang the death knell for those sets of old. Today’s high street chemistry offerings seem to have been sanitised to the point of tedium, whilst some even proclaim to be chemical-free (shudder).

But there is hope. MEL science have launched a product that brings the chemistry set smack into the 21st Century. And I was pretty excited to get my hands on one.

IMG_6683

MEL chemistry starter pack and 5 experiment boxes.

MEL chemistry is supplied via a subscription model. The starter pack is £29.95, and includes some glassware, safety specs, a solid fuel burner, a google-cardboard VR clone, a tray, a neat macro lens that clips onto a smartphone and other bits and bobs. On the face of things this looks a little steep, but you should also  take into account a really very good IOS/Android app, which shows various 3D representations (when used with the VR goggles) of all the reagents you are likely to encounter later.

IMG_6689

Tin set unboxed

All the experiments are sold separately, at £9.95 per experiment set, with 3 delivered each month. The idea being that you each month you receive a new kit. This seems really very reasonable to me, and is just the sort of model that maintains the excitement. Fresh chemistry coming through the door each month should keep up the interest.

Each experiment was accompanied by a very good instruction card and a detailed online page. The webpage goes into far more depth that you would expect for the target 12+ age group. But its all clear and well written. A very minor criticism is the commentary to the videos, sometimes the heavy (Russian?) accent makes things a little difficult to follow.

We (a small Lorch and I), cracked open the ‘Tin set’ and fired up the accompanying video. Everything is very well packaged with a lot of thought going into how kids should dispense solutions  safely. My lab assistant, for this experiment, has quite a reputation for knocking fluids flying, but in this case, and despite a couple of up ended bottles, nothing was spilt.

So over to the real action. The ‘Tin set’ contains two experiments. First, the tin hedgehog, which simply involves dropping a zinc pellet into a solution of tin (II) chloride. Tin crystals quickly form on the pellet, these are quite small and would be difficult to see without the help of the clip-on macro lens. So with the expanding crystals captured live on my phone’s screen  my co-experimenter was quite impressed.

Then we moved on to the tin dendrites. Again the method was easy for my pre-teen helper to follow. And this time, as the beautiful branches of tin struck out across the petri dish there was some genuine amazement in the room.

IMG_6694

Tin hedgehog, as seen via the kit’s macro lens.

IMG_6698

Tin dendrites

     

So far so very impressed. By linking all the experiments with excellent online and smart resources they should really engage the budding chemist and ensure they learn a heck of a lot more than just how to gas themselves. In short they are fun, safe and bang up to date.

I’ve got previews of another 4 experiments to try and will let you know what I think. If they are up to the same standard I’ll be signing up for the other 34.

EDIT: Note, a previous version stated that the sets cost £9.95 per month. This should have read £9.95 per experiment set. The text has been altered to correct this.

Sep 22

The chrome plated mystery of the Terracotta army’s swords




QIMG_6487in the 1st Emperor of China prepared well for the after-life. Throughout his reign he commissioned and built an eternal army of some 6000 soldiers, charioteers and cavalry. The  warriors stood in formation, buried at the foot of his tomb, there to guard the Emperor for eternity.

But all did not go as planned. Shortly after Qin was entombed chaos descended on his newly united China. Qin’s heirs, wishing to defeat him (even after his death) attacked his after-life defences. History tells that the underground barracks that housed the vast army of terracotta warriors were set alight. Fires smouldered for 90 days, structures around the ornate statues collapsed smashing the exquisite army. The broken soldiers and their bronze weaponry lay buried in ash and rubble. The great mausoleum was forgotten. Two millennia passed. Until in 1974, a peasant farmer, whilst digging a well, found fragments of a crushed warrior. And excavations began.

The thousands of individual Qin dynasty soldiers, have been painstakingly pieced together and placed back in formation. They are an awe inspiring sight. But I marvelled just as much when I saw no less incredible bronze weapons that armed the officers. Their swords are still sharp and largely unaffected by the 2200 years that have passed since they were forged. Instead of the green corrosion you’d expect on bronze artefacts the blades actually appear gun metal grey. Why this is the case is something of a mystery.
IMG_6489

IMG_6488

There are reports of an analysis of the artefacts conducted by the Chinese Research Institute of Nonferrous Metals and Chinese Academy of Geological Sciences (although I am unable to find the primary data). The suggestions is that a 10-15 micron coating containing chromium oxide (at up to 2% chromium) was found. The conclusion; for millennia this thin layer protected objects from the ravages of time and chemistry.

So where did the chromium oxide layer come from? Did the ancient Chinese metallurgists, as suggested by curators of the Terracotta army, really have chrome plating technologies thousands of years before it was developed in the west? Over the intervening time did the chromium shine lose its lustre as it slowly oxidised, resulting in the grey we see today? Is a 10 micron, dilute layer of chromium oxide really enough to impart anti-corrosion properties?  Or is there another explanation for the immaculate swords?

This isn’t the first time someone’s asked these questions. Its been discussed on a sword forum where suggestions include forgeries and serendipitous impurities in the alloy. The latter seems to be supported by Prof Frank Walsh, an electrochemist now at Southampton University, when he was interviewed for an ABC documentary back in 2003 where:

Professor Walsh notes that the heat from the fires and the presence of carbon would have provided a reducing environment in which chromium atoms could have migrated to the surface of the weapons. There they’d oxidise and form a protective coating … Metals do diffuse over time, so this ‘natural’ explanation is plausible.

For me this isn’t a totally satisfying explanation. Largely since it appears, from the items on display, that only the blade is free of corrosion. The hilt has clearly corroded. If the slow migration of chromium to the surface of the blade is responsible why didn’t this mechanism occur elsewhere on the swords? But the idea that Qin’s weapon smiths knew how to apply anti-corrosion layers to their creations seems rather fanciful.

Which leaves the above questions unanswered. So chemists, time to reopen discussions. What do you think is going on? Can anyone come up with a way that the ancient Chinese might have deliberately or accidentally protected the weapons?  Or what else might have resulted a corrosion free blade, whilst the rest of the weapon is tarnished?

P.S. Any Chinese chemists/metallurgists out there who might be able to track down the analysis of the blades?

Sep 11

Simulating C&EN and JACS


I decided to make a robot that would Tweet fake C&EN headlines and JACS titles. There are many ways one could go about doing this. The way I decided to do it is to use something called Markov chains. This is similar to how your cellphone’s keyboard works: Your cellphone will try to guess which word you want to type next based on your previous history of typing. I’ll give an example below.

Let’s say I have fed these two headlines into my database

  1. “Novel Ruthenium Catalyst”
  2. “Ruthenium Based MOFs”

The Markov chain will think headlines should start with either the word “Novel” or “Ruthenium”. Now let’s tell the bot to roll the dice and start constructing a sentence.

The bot picks: Ruthenium

The bot knows that after the word Ruthenium either “Catalyst” or “Based” are typical. Let’s have the bot roll the dice again.

The bot picks: Catalyst

Now the bot knows that the word “Catalyst” is associated with a full-stop and there is no way for it to generate anything further. So from only two headlines the bot is able to generate something unique, “Ruthenium Catalyst”. Based on these rules and the luck of the dice “Novel Ruthenium Based MOFs” would also be a possible headline for it to make.

I fed a large batch of real C&EN headlines into a database, told my bot to go at it, and Tweet what it comes up with, and also grab the first image on Google Images if someone were to search for that headline. Here is an example

C&EN Simulator

Sometimes I get lucky and the story is funny, usually it just comes out nonsensical, absurd, or worse an actual real headline. You can befriend the bot through this link: @C&EN Simulator

Taking it one step further I also made a JACS bot based on the article titles I have been scrapping at ChemFeeds for the past 7 years.

You can friend the bot here: @JACS Simulator

The bots will update randomly throughout the day. If you have any questions for me leave them in the comments. I can open source the code if there is any interest in such things.

Mitch

Older posts «