Books in Scientia – Periodic Kingdom


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Title and author

The Periodic Kingdom by Peter Atkins

What’s it about?

Good question… it’s about the periodic table. The book is written as though the periodic table is a continent, a new land to be discovered and explored. Atkins plays the role of the anthropologist, describing its trends and intricacies as a scholar who has lived amongst the native tribes, learned their way of life, their history and their governance, and is sharing this knowledge with the reader.

What are the good bits?

Atkins has a unique writing style (that simply infuriated me when battling through his enormous eponymous physical chemistry textbook) which is quite well suited to this interesting premise.

What are the not-so-good bits?

A couple of parts of the book are out of date, in particular mention of the elements joliotium and hahnium. Although the uncertainty surrounding the names of these elements is acknowledged in the text, other names ended up being chosen after the book was published. From what I could find on the all-knowing internets, there were no further editions after the 1995 original to update these details.

Atkins also referred to carbon as the ‘King of Mediocrity’ to which I raise a hearty objection. Or maybe he was being facetious…

What does it say on p147 line 8?

For this part of my reviews I usually choose a page at random, but for this book there was a particular quote from the epilog [sic… WTF is this by the way, isn’t Atkins British? He should know better] I wanted to use.

The real world is a jumble of awesome complexity and immeasurable charm. Even the inanimate, inorganic world of rocks and stone, rivers and ocean, air and wind is a boundless wonder. Add to that the ingredient of life and the wonder is multiplied almost beyond imagination. Yet all this wonder springs from about one hundred components that are strung together, mixed, compacted, and linked, as letters are linked to form a literature

FUCK. YEAH. Chemists, this is our “mote of dust suspended in a sunbeam”. Why isn’t this quote famous? The whole freaking world is made of elements. Just elements. That is it. And those elements are OURS. Why are people scared of them? They are amazing. The world is made of elements and they are amazing and it is amazing. The end.

Who should read it?

Despite its clear and easy to understand explanations of the trends of the periodic table, I doubt this would interest those without a chemistry background or a significant interest in the technicalities of the periodic table. I’d be interested to know who Atkins imagined the audience for this book would be.

How good is it?

It’s good, but slightly dated, and the style is something of an acquired taste I presume.

3 squeezy solvent wash bottles out of 5

kingdom stars


Flavour Tripping with Miraculin – Renée Reports

Earlier today I hosted a quite interesting afternoon tea with some friends at work. I’d purchased some miraculin tablets, and a few assorted foodthings to try ‘flavour tripping’. Miraculin is a protein found in the fruit of the Synsepalum dulcificum plant, native to West Africa. When a miraculin tablet is dissolved in the mouth, the protein binds to your taste buds and changes your perception of flavours. The remarkable effect of this is that sour or bitter tastes are changed to taste sweet.

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The tablets themselves are pretty nothing, with a flavour I would describe as ‘cardboard fruit tingles’. You have to be sure to roll the tablet very well around your tongue, and coat it all over or you’ll find there are parts where your tastebuds can still detect sour flavours. The foods we tried this afternoon included;

  • Lemons and limes: in a word, delicious. Especially the limes. It’s a delight to sink your teeth into a wedge of lime and have the taste of sweet citrus fill your mouth, no puckering or squinting required!
  • Salt and vinegar chips: unusual, the acidity of the vinegar is completely muted and there is a dull sweetness present, but the chips still tasted overall like a savoury snack. Ordinarily I find salt and vinegar chips revolting, but I could’ve easily eaten the packet on miraculin.
  • Natural yoghurt: as expected, the sour flavour of natural yoghurt was modified so it tastes just like a sweetened yoghurt. Very pleasant.
  • Sharp cheddar: the sharpness of the vintage cheddar was muted, so that the cheese tasted like a colby or other mild firm cheese.
  • Goats cheese: very close in flavour to cream cheese icing commonly found on carrot cake. Easily could’ve eaten the whole lot.
  • Vegemite: pretty gross, vegemitey but somehow sickly as well. Do not recommend.
  • Tabasco: the hottest sweet chilli sauce I’ve ever tried.
  • Vinegar: I read somewhere that on miraculin vinegar would taste like apple juice… HELL NO. Look, it’s drinkable but it’s still vinegar really. Drinkable vinegar. Yum…
  • Guinness: I also read that Guinness was going to taste like chocolate. It did not. It’s interesting that the bitterness of the beer is completely gone, but the chocolate I was hoping for was sorely lacking and it was not really very nice at all.

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After trying these, a few other items I’d be interested in sampling;

  • Balsamic vinegar
  • Wasabi
  • Mustard
  • Rocket, endive or other bitter leaf vegetable

If you are curious about trying Miraculin I’d definitely recommend giving it a go. At $2-3 bucks a pop, the tablets aren’t cheap, but it’s worth it because it’s a lot of fun and really messes with your perception of some foods. We found the effects of the Miraculin tablets lasted about 30-40 minutes. I still have a couple of tablets left, so if you have any suggestions for other things that could be fun to try, hit me up.


Long Hair Lab Hack

At the end of my recent glove post I mentioned that I wear my hair down in the lab, and was admonished for doing this (and rightly so). My reason for wearing my hair down to work is pure vanity, I prefer the way I look with my hair down and I’ve also found that wearing my hair in a ponytail all the time leads to a lot of breakages where the elastic goes which makes my hair look quite yuk.

But, what I didn’t mention earlier is that when I am doing ‘wet chemistry’ type activities in the lab I usually do have my hair secured away from my face. I want to share the way that I do this in case there are any other long-haired lab lubbers out there who have the same problems as me, like:

  •          Not carrying hair ties
  •          Not wanting to use rubber bands
  •          Generic laziness
  •          Extreme vanity

OK so here goes. How to secure your hair away from your face with a pen (or pipette):

  1.        Using both hands, sweep your hair into a ponytail
  2.        Keeping the ponytail straight, twist the entire ponytail very tightly (but not so tight that it kinks back on itself) in a clockwise direction
  3.        Coil the twisted ponytail around itself, starting at the base, to form a bun and hold the end with your left hand
  4.        With your right hand, grab a pen and with the pointy end skewer the bun. Start by incorporating some of the non-bun hair (see pic) and push/weave through so you skewer both ‘sides’ of the bun ring. Using some non-bun hair is important as this will help it be weighted correctly and stay secure for longer.

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I have used the (clean and disposable!) pipette here mainly to illustrate this point. It’s too long to actually be practical. I find a pen is the perfect length and it’s pretty much hidden when done correctly – see pic at the bottom.

 

Extra tips

  •          Instructions are for a rightie, if you’re a leftie do it in reverse I guess
  •          Your hair needs to be past shoulder length for this to work
  •          Make sure if you use a pen, that the tip is pointing upwards. If it’s pointing downwards you may end up drawing all over the back of your shirt (yes, I learned this the hard way).
  •          I suspect this might not work with super straight or fine hair.

 

penhair

Flawless execution of pen hair using this pen.

 

Let me know if you have any lab hair hacks!


A Boundless Dorkery of Chemistry Songs

Reading back my tweets in shame
Whoa oh oh ahhh oh
And the world’s gonna know I’m lame
Whoa oh oh ahhh oh.

 

.

My twitter followers might have caught one or two of my tweets where I take a pop song and change the words to make it it chemistry themed. If this is not definitive proof of my boundless dorkery, I don’t know what is. I’m going to start collecting them together in blog posts before twitter eats them into oblivion (because some have already been lost and the world is certainly poorer for it). I find inspiration for these songs all around me, in fact it’s quite possible that I might be a creative genius. Now if only I could be this brilliant when it came to my science…

.

Monsters Ghost Peaks by Something for Kate: March 21, 2014

I was sitting in the lab of chromatography
Waiting to discover something about some fuel
I couldn’t find my compounds
And I couldn’t separate them
It was like trying to think in reverse
And I don’t want to rinse a non-crosslinked phase
And I don’t want to inject acid or base
But these ghost peaks follow me around
Hunting me down
And I can’t bake them out
Bake them out

 

Scenes from an Italian Restaurant Chemistry Laboratory by Billy Joel: March 18, 2014

Alkyl nitrite, chlorophenol red
Perhaps a solvent wash bottle instead
We’ll get a fumehood near the sink
In our old familiar place
You and I face to face
Ruthenium red, sodium sulphite
It all depends on your reaction tonight
I’ll meet you any time you please
In our chem laboratory

 

Blame Myself by Sky Ferrera: March 14, 2014

How could you know what it feels like
For analytes to coelute
You think I’d learn to dilute
How could you know what it feels like
When your analysis is moot
Chromatographic pursuit
I just want you to realise
I blame I blame I blame myself
For this separation

 

Elevation Separation by U2: March 12, 2014

A mix
What I can see is nix
Very complex matrix
Maybe you can separate my kind
Explain these controls
Can’t isolate the whole
The goal
Separation

 

The (Tungsten) Wire by Haim: March 6, 2014

You know I’m bad at mass spec detection
It’s the hardest thing for me to do
And it’s said it’s the most important part
The analytes go through
And I’d give it all away
Just so I could say that
I know I know I know I know
That you can detect them another way

.
You know there’s no rhyme or reason
To the way you fragment for me
I didn’t change the ionisation source
Not intentionally
I know it’s hard for me to say it
But I can’t bear to stay and
I just know I know I know I know
That I can’t detect them another way

 

Royals Chemists by Lorde: March 1, 2014

I’ve never seen an atom in the flesh
I cut my teeth on retort rings in laboratories
And I’m not proud of synthesis
In the round bottom flask
No percent yield envy

But everybody’s like solvents, test tubes, shimming in the spec room
Chromate stains, lab coats, spills in the weighing room
We don’t care, we’re winning Nobel Prizes in our dreams

But everybody’s like crystals, rotavaps, diamonds on IR machines
Ring strain, science, analysis of gold beads
We don’t care, we aren’t caught up in a boat or chair

And we’ll never be chemists (chemists)
It don’t run in our blood
Those electrons ain’t for us
We crave a different kind of buzz

 

Riptide by Vance Joy: February 18, 2014

I was scared of Schlenk lines and the Shark
I was scared of arrow curls and starting new reactions
Oh all my friends do synthesis

 

Buy Me a Pony by Spiderbait: February 12, 2014

Don’t you wanna be
Doing chromatography
Or mass spectrometry
But you’ll never make it if you can’t separate it

 

One More Time by Britney Spears: January 15, 2014

Radiation is killing me (and I)
I must confess I still believe (still believe)
When I found radium I lost my mind
Give me a prize
Nobel me baby one more time

 

Roar Pour by Katy Perry:  January 4, 2014

I’ve got the eye of a chemist, menace,
Dancing through the premise
Cos I am a scientist
And you’re gonna watch me pour

 

Any sciencey singers out there who want to join me in some kind of Bernie Taupin/Elton John-esque type relationship? We could be amaze.


Flavours of Gloves in my Chemistry Lab

 Earlier this week, a flippant twitpic of my gloves sparked a bit of a conversation on twitter about glove use in the chemistry laboratory. I was directed to these two posts from Professor Andrea Sella’s blog, and reminded of this one from ChemBark.

In my summer breaks as an undergrad I worked in the ‘inorganics’ section of an environmental lab (this meant working mainly with water), and I remember looking across the corridor to the ‘organics’ section and noting that their gloves were different to the ones I was using. I didn’t really understand at this point the difference between different glove materials until one of the chemists I worked with explained this to me. I think this was my first proper introduction to glove use in the lab.

I’ve worked in over half a dozen different labs over my career now, but I’ve found the glove culture to be reasonably consistent between them. People tend to wear gloves in the lab the majority of the time, with not much consideration for whether the task actually requires them. It’s common to see people using lab computers, door handles, pens and other items while wearing gloves. This means that EVERY SURFACE in the lab is potentially contaminated. Think about that.

My colleague recently reviewed the gloves we use in our laboratory, and their compatibility with the solvents and samples we typically work with. The bulk of our chemistry is done with hydrocarbon fuels and organic solvents. If this type of work was done as an undergrad lab class, I’d probably agree with Prof Sella and say gloves are not necessary for a one-off potential exposure and any spills could be easily dealt with using soap and water. However, I work with this stuff every day and I am concerned about the effects of repeated, long term exposure to organics which is why I use gloves most of the time. The result of the review was the acquisition of some new glove types which I’ve started using for different situations;

  • Our staple nitrile glove has been replaced with a black version (because black is the most badass), which has the benefit of being slightly thicker than the blue ones we had been using before. I use this glove 95% of the time, either for working on GC-MS instruments (where I am gloved to protect the instrument from dust and fingerprint oils) or when I am transferring or pipetting small amounts of sample or solvent. Although nitrile is permeable to most of the liquids I’m working with, the glove provides a temporary barrier and a few seconds grace where I can remove the glove before my skin comes into contact with the liquid.

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  • Also made of nitrile, these gloves are considerably thicker than above with a textured outside surface for better grip. These gloves are marketed as disposable, so I’m a little uncomfortable using these very frequently because their stiffness means they would take up a lot of space in landfill – probably the space of at least half a box of regular nitriles. Also, they’re permeable to most of our common lab solvents, although the grace time is longer given the thickness. On the plus side, the extra grip is fantastic and dexterity in this glove is very good.

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  • These gloves are new to me and the best glove we could find for working with hydrocarbon fuels. They’re impermeable to kerosene and gasoline type fuels, so they are my new go-to glove for working with larger volumes. They have a weird, flat shape and are very smooth which is not great so if I need extra dexterity I use a nitrile glove one size up from my usual over the top.

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  • I’ve started doing washing up of glassware using these elbow-length beauties. Before I was using either nitriles or supermarket washing up gloves, both of which are practically useless because I would always dunk my arms too far into the washing up and just get all the water and fuel and detergent and any other junk filling up all the space between the glove and my hand anyway. These are much better because it’s almost physically impossible for me now to dunk my arms in above the glove line – I’d have to fall into the sink (which may be possible, our sink is enormous).

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  • These PVA gloves are used only for handling dichloromethane. DCM will instantly plough through all gloves except these. They’re a total pain to use, very stiff and dexterity is extremely poor but the only choice when handling DCM. I also had an accident with dichloromethane early on in my career so I am quite wary of any extra exposure to this solvent.

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So while I do think about glove use more than some, there are a few of my own glove-related behaviours that I may need to think about more;

  • I tend to wear my hair down and loose most days so occasionally in the lab I find myself needing to get hair out of my face while my hands are gloved. If blowing it away with a large exhale doesn’t work (ie if my hair is stuck in my lipstick), I generally use the back of my hand to push it away.
  • Similarly, if I happen to have an itch on my face or other part of my body, I will use a gloved hand to scratch it, but use some part of my hand other than my fingers, which are most likely to be ‘contaminated’.
  • I often re-use disposable nitriles if I think they’re not contaminated.
  • I often use gloves simply to work in a dirty/dusty environment ie around our GC gas lines.

Holy moly, who’d have thought I would write >1000 words about gloves? GLOVES.

 


Books in Scientia – Molecules of Murder

molecules of murder

Title and author

Molecules of Murder: Criminal Molecules and Classic Cases by John Emsley

What’s it about?

A number of case studies of murders carried out with natural and synthetic poisons. Major cases covered range from recent (Alexander Litvinenko, 2006), to well over a century old (Thomas Bartlett, 1886).

What are the good bits?

Many of the cases in this book will be familiar to readers, poisoning murders are quite rare so they often receive a lot of media coverage. However, Emsley covers the cases in a surprising level of detail, and I certainly learned new things even about the cases I’d read about before.

There is also a nice glossary with chemical terms and structures which I suspect would be very helpful for the non-chemist reader, though I confess I did not need to use this more than once or twice. Apart from the technical terms, the book is written in very clear language.

What are the not-so-good bits?

There’s nothing that’s not good about this book. It was interesting and informative, but it didn’t get me all fired up and passionate about chemistry like some other pop-chem books have.

What does it say on p193 line 19?

the consultant instructed that the blood and urine samples should be urgent sent for analysis…this was not carried out…and when the mistake was realised, they covered it up by saying that…the results had come back negative

Emsley recounts an error made by hospital staff in one of the murder cases. It brought to mind the case of Annie Dookhan, the chemist who was recently jailed for altering and falsifying forensic drug analyses. I wonder if any murders were missed or falsely confirmed due to her tampering?

Who should read it?

Those interested poisonings, toxicology or even crime fiction fans who might want a little foray into real crime.

How good is it?

Reasonably. Not the most exciting book you’ll ever read, despite the number of murders, but interesting and a worthwhile read nonetheless.

3.5 funnels out of 5

murder stars


Papes for the Peeps – Analysis of Antioxidants in Fuels

This is the latest in a series of posts where I attempt to translate my published research into a format suitable for a non-specialist audience.

My paper “Synthetic Phenolic Antioxidants in Conventional and Alternatively-Derived Middle Distillate Fuels Analysed by Gas Chromatography with Triple Quadrupole and Quadrupole Time of Flight Mass Spectrometry” was recently published in the ACS journal Energy and Fuels (paywalled).

This piece of work describes two new methods for determining antioxidant compounds in jet and diesel fuels. Antioxidants are added to some fuels to stop the fuel reacting with oxygen while in storage. When fuels react with oxygen, they can become unsuitable for use and cause engine problems. Although these antioxidants serve an important purpose, they are only permitted to exist in the fuel up to a certain concentration. Sometimes, if a fuel is suspected to be reacting with oxygen, the users might want to add antioxidant to stop the fuel from going bad – but if they don’t know how much antioxidant is in there (if any), how will they know how much to add without going over the limit?

The antioxidants are present in the fuel at very low concentrations, which makes it difficult to measure them without the bulk of the fuel interfering in the analysis. It’s possible to extract the antioxidants from the fuel, which then makes the measurement easier, but the extraction process is often long, resource intensive (uses lots of solvent) and frequently doesn’t work well enough. My laboratory recently acquired two new GC-MS (gas chromatography – mass spectrometry) instruments with advanced detection systems so I decided to see how these instruments would go at detecting antioxidants in fuels at low levels, and without any sample treatment.

SPA1

Left: generic structure of these antioxidants, where ‘R’ can represent a methyl or tertiary butyl group in 1-3 of these R positions. Right: BHT, a common antioxidant used in fuels, foods and other products, where the R group opposite the OH is a methyl and the two R groups adjacent to the OH are tertiary butyl.

 

I have posted before about how gas chromatography and mass spectrometry work, and in this study it is the mass spectrometers that play a key role in the detection of the antioxidant compounds. The two different instruments I used are able to exploit different characteristics of the target molecules, in order to detect them at low levels, without interference.

Triple Quadrupole (QQQ) MS

The QQQ achieves excellent sensitivity by fragmenting molecules in the mass spectrometer more than once. For example, using the antioxidant shown in the picture above, the spectrum for this compound is

 qqq1

Which means that ordinarily, I would use the strong signal from the ion with a mass of 205 to look for this compound. But fuels have so many other moelcules in them, that there are loads of other compounds that also generate a signal at 205 and these swamp the signal from the target compound. So I can program the QQQMS to collect the strong ions, and perform another fragmentation on it. This generates a new mass spectrum with a new set of fragment ions. In this case, the fragmentation of 205 produces a signal at 145. So I can get the QQQMS to monitor these specific fragmentations, and keep track of the transition of each ion into another ion as it is broken apart in the spectrometer. So while there may be many compounds that have a signal at 205, there is only one molecule which has a signal of 205 fragmenting to 145. By using this approach, I can be very specific in my identification and measurement of my target compounds and this specificity brings with it excellent sensitivity and low detection limits.

Quadrupole Time of Flight (QTOF) MS

The QTOF is able to detect very specific compounds because it can measure their mass very accurately. The other mass spectrometers in our lab are able to measure the weight of ions to one atomic mass unit (amu). Using the example above, the most accurate mass of the main ion we can obtain with these instruments is 205 amu. And again, there will be many other compounds with fragment ions of the same molecular weight. However, if we calculate the mass of this fragment (C14H21O) accurately, it comes out as 205.1587. Another possible ion with the same molecular weight is C13H19NO, but the accurate mass of this ion is 205.1461. This difference of 0.0127 amu is enough for the QTOF to distinguish between these two molecules, so I can program the instrument to look only for the accurate mass ion I’m interested in and discard the other closely matching, but interfering compounds.

Exploiting the strengths of these two mass spectrometers has allowed me to detect and measure low levels of antioxidant compounds in very complex  fuel mixtures.


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