Lab Clutter and Cleanliness

It’s the time of the year that our laboratory inspections have rolled around again, and once again, as it is every year, one of the key pieces of advice is to keep our spaces “free of clutter”. And once again, as we do every year, I expect we will be judged as failing to meet this criterion.

The response from the lab manager is always something like “This is a real laboratory.” “We’re doing work, of course there’s stuff all over the place”, or my favourite “I’m actually working on that right now” (where ‘right now’ means ‘anytime within the last 4 weeks’).

The lab I work in has a very poor culture of tidiness, which is suspect is due to a several cultural and historical factors. One contributor may be the constant quiet tousle for work space in the organisation, and if labs are seen to be underutilised the murmurs will start… “Look at that big bench with nothing on it. When’s the last time you saw someone working there? What do they use that fumehood for if there’s nothing in it?”. There’s also a reluctance common amongst older chemists to throw anything away, which inevitably increases clutter. However, it’s my opinion that the main cause of lab clutter in my workplace is simply laziness.

Over the last few years, as my feelings of ownership over the workplace have increased, I’ve began to rearrange, replace, and rehome items I felt were cluttering the laboratory. The one recent change which has made me exceedingly happy, is allocating personal bench and hood space to every person in the team. It took over 4 years working here to get everyone to agree to it but it’s made a massive positive improvement on the way I conduct lab work. We now have 1 full bench and hood for our sole personal use, and a few remaining spaces that will continue to be communal areas. Leading up to this was a period where I couldn’t even find a spare 30 cm2 to decant something into a beaker; people would work wherever they could find a skerrick of bench, and leave glassware, containers and all manner of laboratory miscellany about the place with reckless abandon. When I did manage to clear a space for myself I sometimes felt it necessary to leave it looking like this.

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As a small team of only 4 people, we have a large lab space of approximately 150 square metres over 3 laboratories. Granted, we do have quite a lot of stationary equipment and instruments with large footprints which take up a fair bit of room. But even so, as the newest employee (at almost 5 years), I feel as though my colleagues have forgotten (or never realised) exactly how good we’ve got it and don’t appreciate the space we have. All of my previous workplaces had shared benches and hoods which were always kept tidy and uncluttered. I don’t remember any fights or meetings had over messiness. The first lab I worked in didn’t even have offices and we hot-desked in the lab without any issues.

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This is what my hood looks like right now. Given that I don’t do any synthesis, I’ve no need for a permanent Schlenk setup or anything like that. My bench is much the same, housing only a box of kimwipes, a box of pasteur pipettes and a sharps disposal container. My colleagues have commented to me things like “you haven’t done any lab work for two weeks”, an assumption they’ve made simply because they haven’t seen any glassware or equipment on my bench/hood in that time. What they’ve failed to realise is that of course I’ve been working in the lab, it’s just that I’ve just done this really weird thing called cleaning up after yourself.

Of course I’m not a complete lab cleanliness saint, and sometimes I leave stuff lying around too. Out of laziness, forgetfulness, or spite (the spite thing never works BTW, a messy person does not care or even notice that you have made things more messy).
 

Safety issues aside, I feel like a messy lab displays a real lack of pride in the work that you do. We often have visitors to our lab, students, visiting scientists, sales reps, other professionals and frankly it’s embarrassing to me thinking about the state our labs have been in at times. It doesn’t look like we’re working hard, it looks like we are shameful filthy pigs.

 

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Postscipt. One piece of clutter I was rather fond of was this HPLC energy bar which used to sit on top of our instrument, in what I saw as a particularly knee-slappingly hilarious (and harmless) joke. Health and Safety Inspectors did not agree and now it is gone.


A Discussion of #chemophobia on Twitter: in Blogversation with @chemtacular

Over the last few months, there has been an ongoing conversation between some chemists on twitter discussing the use of the word, and hashtag, (#)chemophobia, kicked off (I think) by this post from @mustlovescience. One of the main drivers behind this dialogue is @chemtacular, who led a charge to replace the use of #chemophobia, which is described in this post from her blog Tales from the Critical State. Feeling a little stifled by twitter’s 140 character limit, @chemtacular and I (@reneewebs) have decided to go long-form and discuss this over a few posts on our respective blogs, a ‘blogversation’ if you will (I love terrible portmanteaux, go ahead and judge me I don’t care!).

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To break down and expand upon some points that @chemtacular raised in her post:

My issue is that this term [chemophobia] is used by chemists to describe a negative portrayal of chemistry.

This I agree with, and I can provide a couple of examples here where chemistry has been misused or misunderstood, but there is not necessarily a fear element involved.

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Left image source: Reddit Chemistry .Right image source: also Reddit Chemistry I think but I couldn’t find the original thread, if anyone has the link please let me know so I can add it

Cases like these is where the hashtag #boguschem is perfect.

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I also have a hard time with this word [chemophobia] because it is used in such a way that it strengthens the rift between the public and chemistry when there doesn’t have to be one

This I believe it the strongest argument against using the word chemophobia, especially on twitter. Consider this Totally 100% Real* twitter interaction I captured earlier:

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*not actually any % real

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When the chemtwitosphere jump on some dodgy chemistry in the media (which we often do), what do we hope to achieve by tweeting about it, whether we include the hashtag #chemophobia in the discussion or not? I suggest there would usually be two reasons;

  1. We want to point out that the individual or organisation in question has made a scientific error, ideally in a polite and civil way that would educate them and encourage them to think about making a change their marketing or labelling. Climb On Products is an example of one company who did make such a change, although I’m not sure of the circumstances in which this came about.
  2. We want to have a joke or commiserate amongst our community, to laugh and cry together about crimes against ‘our’ chemistry. We’re a passionate bunch of chemists, and to bond (pun intended) over these shared frustrations is something that helps to connect us.

What do you think @chemtacular, are there other situations you can think of where we might need to frame things differently again?

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I spent an afternoon tweeting with chemists … and the best we could do to come up with a term that wasn’t dismissive, punching down, or dissing chemistry was #BogusChem

@chemtacular, I would love if you could expand upon this – why is the choice of wording in the phrase so important? On twitter you’ve talked about being wary of using certain words like ‘abuse’ and ‘exploitation’, or derivations of these. And finally, is it possible that maybe there just isn’t an English word or short phrase that exists to perfectly convey what we’re trying to say?

I look forward to your response.


I am the Blogroll, Cu Cu Ca CHoO

Here’s a reproduction of my recent Blogroll article which appears in this month’s issue of Nature Chemistry.

Bloggers combine chemistry and the arts for striking results.

‘Creative’ may not be the first adjective that comes to mind when describing chemists. Despite comparisons one might make between chemical synthesis and the ‘dark arts’, the stereotype of a chemist is that of a methodical, analytical thinker rather than a creative and artistic one. Several chemistry bloggers are helping to dispel this myth, however, by sharing their science in the form of photographs, digital art or poetry.

Kristof Hegedüs blogs at Pictures from an Organic Chemistry Laboratory, where each day he shares a photograph of something from his lab. Subjects range from crystals, to experimental set-ups and interesting reagents. Each post is accompanied by a short description to explain what is shown in the picture. Nevertheless, the focus is primarily on the photography, with the simple aesthetics of laboratory glassware a recurring theme.

A recent post from the Picture it… Chemistry blog featured the opium poppy Papaver somniferum, popularly known for its psychoactive alkaloids. The blog post begins on a surreal note, with a picture of a poppy growing out of an Allihn condenser used to demonstrate a laboratory extraction of opioids. The post concludes with discussion of total syntheses of morphine and codeine, incorporating some classics of synthetic chemistry such as the Diels–Alder reaction and reductive amination.

Finally, to transition from pictures back to words, Mark Lorch at Chemistry Blog recently hosted a number of limerick poems written by Nicholas Dawson. With topics ranging from Viagra to the vulcanization of rubber to phlogiston theory, it was a refreshing and whimsical way to rediscover some of the milestones of chemical history.

As an addendum to this post, I’d like to mention two more blogs with great creative representations of chemistry. I was frustrated that I discover both of these blogs LITERALLY in the one or two days after the submission deadline for the Nature Chemistry article. The first is Compound Interest which has featured a series of infographics on the elements, and is now expanding into molecules. The second is James Kennedy, whose infographics on the chemicals in food, have been an absolute hit on the internet, and even made it to the mainstream media. The chemistry blogosphere is a wonderful place to be!


Aroma analysis of vegemite 3. Data analysis and interpretation

This is Part 3 of my vegemite aroma analysis series. If you haven’t read Parts 1 and 2, you can do so here and here. In a wonderful complement to my vegemite posts, Vittorio Saggiomo of Labsolutely has also done NMR and a microscopy video of marmite.

As a reminder, here is the output from the GC of the vegemite aroma analysis. There are many detection systems that can be coupled to the end of a GC which provide different kinds of information about the compounds which are analysed. In this case, the detector I used was a mass spectrometer (MS, or mass spec for short).

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Mass spec is the most useful type of detector because it provides information about the structure of each molecule exiting the GC column, and often this information is good enough to deduce the identity of the chemicals in the separated mixture. At each point along the chromatogram (many times per second) the spectrometer collects a mass spectrum of the compounds present, which look something like this.

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The mass spectrum is generated when the compound is ionised by electrons created within the mass spectrometer. Ionisation causes the molecules to fragment, and the mass and abundances of the fragments are measured by the spectrometer and provide key pieces of information about the chemical’s structure. In the spectrum above, each vertical line represents a molecular fragment and its relative abundance, with the number above it representing the molecular weight. Modern mass specs come with software that automatically searches huge libraries of compounds and finds likely matches to the spectrum collected. However, it is possible (and -[NERD ALERT]– fun!) to work it out by hand.

The matches collected by the software to the mass spectra of the vegemite aroma compounds, and their relative abundances are tabulated below.

% total compound Associated odour
1.7 limonene citrus, fruity, mint
0.2 benzaldehyde almond, burnt sugar
0.8 benzeneacetaldehyde cocoa, honey, spice, rose, lilac
0.1 phenylethyl alcohol floral, rose
0.7 octanoic acid fatty, pineapple, banana, sweat, cheese
12.5 octanoic acid, ethyl ester fruity, fatty, floral, green, menthol, anise
0.1 2-phenylethyl acetate floral, honey
0.2 2-phenyl-2-butenal cocoa, floral, musty
0.5 sulfurol sulfur, meaty, chicken broth
0.1 nonanoic acid, ethyl ester fruity, rose, wax, rum, wine
0.1 p-isopropenylphenol phenol, antiseptic
2.1 1-decanol fatty
1.6 n-decanoic acid fatty, rancid
16.6 ethyl trans-4-decenoate wax, leather, pear
2 n-decanoic acid fatty rancid
43.8 ethyl decanoate fruit, oil, sweet, wax
0.2 niacinamide odourless
0.2 decyl acetate floral, orange, rose
1.2 caryophyllene spice, wood, cloves
0.2 3-methylbutyl octanoate apple, coconut, grass, pineapple
0.2 farnesene apple
0.8 beta selinene woody, herbaceous, peppery
0.2 5-methyl-2-phenyl-2-hexenal cocoa, mocha
0.7 alpha selinene amber, orange, pepper
2.5 2,3-dihydrofarnesol floral, green
1 dodecanoic acid fatty, soapy
4.3 ethyl laurate floral, soapy, wax, peanut
0.3 isopentyl pentadecanoate floral, wine
0.1 1-(2,4-dimethylphenyl)-propanone no info
0.9 tetradecanoic acid flowery, woody
0.2 trans-nerolidyl formate wax, floral
0.1 farnesol acetate flowery, green rose
0.5 cis-9-hexadecenoic acid wax, old-person smell
0.5 n-hexadecanoic acid wax
0.8 ethyl 9-hexadecenoate wax
0.4 hexadecanoic acid ethyl ester rancid
0.1 octyl 2-phenylethyl ester oxalic acid citrus, fruity mint

Based solely on the aroma descriptors I was able to find in online odour chemical databases, I think that the chemical ‘sulfurol’ probably contributes significantly to the odour of vegemite.

sulfurol

Chemical structure of sulfurol (2-(4-Methyl-1,3-thiazol-5-yl)ethanol).

Other compounds of interest that were detected in the aroma analysis are;

  • Niacinamide: a derivative of one of the B-vitamins that vegemite is loaded with.
  • Caryophyllene: a compound common which contributes a peppery spiciness.
  • Hexadecenoic acid: notable for the fact that ‘old person smell’ is attributed to this compound!

The compounds revealed in the analysis are not an exhaustive list of all of the chemicals contributing to the aroma of vegemite. There were many more small peaks in the chromatogram that I did not search the mass spectrum of. It’s also likely that some of the chemicals that contribute to the aroma of vegemite, do not give a visible signal in the chromatogram, or were not picked up by the SPME fibre.

It’s interesting to note that many of the aromas in the table above are described as sweet, fruity or flowery, which are certainly not words you would use to describe the aroma of vegemite. There could be several explanations for this;

  • The odour thresholds for these chemicals may be quite high. That is, they may have to be present in large amounts in order for the odour to be detected.
  • When odours from different chemicals are mixed together, the whole may not be equal to the sum of the parts.
  • Some compounds smell different depending on their concentration, or may even vary from person to person.
  • The mass spec library searching program may not have been able to correctly identify some of the chemicals.

More specialised aroma analysis by GC can include the use of an olfactory detection port (ODP). Here, once the mixture is separated by the GC, the effluent is split in two with half going to a conventional detector (such as an MS) and the other half to the ODP or ‘sniffing port’ where an aroma analyst can smell what is exiting the column and assign odours to specific compounds.

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Olfactory detection port from gerstel.com

I hope you’ve enjoyed this 3-part series on the chemical analysis of vegemite aroma. Thanks once again to Chris Slape for the inspiration, and if you have any questions, comments or ideas for future analyses 🙂 please leave them below.


Aroma analysis of vegemite 2. Separation of vegemite aroma chemicals by gas chromatography

This is Part 2 of my vegemite aroma analysis series. If you haven’t read Part 1, you can do so here.

Now that the vegemite aroma compounds have been extracted from the sample, and onto the SPME fibre, they will be separated using gas chromatography (GC). GC is a versatile analytical technique with many applications in areas like environmental science, forensics and petrochemicals. Separation of mixtures is a really useful way of finding out what is in them by splitting them up into their component parts. Lots of different kinds of samples of varying complexity can be analysed with GC, the main limitation being that they must have a boiling point below about 400°C. GC enables the analysis of many complex mixtures by separating them out into their individual component chemicals. The separation happens in a very long (usually 15 – 100 metres) and thin tube called a column. The column is housed in an oven which increases temperature over time and this facilitates one mode of separation. The temperature ramping up over time causes chemicals to travel through the column faster if they have a lower boiling point and slower if they have a higher boiling point. The other influencer of separation is a polymer coating applied to the inside of the column walls (very similar to the coatings on SPME fibres mentioned in Part 1). Different chemicals will interact differently with particular coatings and this also affects the separation. These two interactions give the analyst very useful information with respect to the chemical properties of the mixture components.

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A gas chromatograph, with the oven door open. Green arrow = injection port, blue arrow = column, red arrow = outlet to detector.

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Now, back to the vegemite! In order to get the aroma chemicals trapped on the SPME fibre into the GC, the fibre is inserted into the heated injection port. 

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The high temperature of the injector causes the aroma compounds to become gaseous and desorb from the SPME fibre. A flow of helium gas sweeps the molecules out of the injector and onto the GC column for separation. The output of the GC following separation of the vegemite aroma is below.

chrom_zoom out

There are maybe four main peaks in the chromatogram, representing the compounds which were most concentrated on the SPME fibre. But a zoomed in view of the chromatogram reveals many, many more peaks. Each peak represents at least one different chemical comprising the aroma of vegemite.

chrom_zoom in

In the next post, I will discuss how we go about discovering which chemicals these peaks in the chromatogram are, and what contribution they might have to the distinctive aroma of Australia’s favourite spread.


Aroma analysis of vegemite 1. Sample preparation and aroma sampling

Vegemite: that salty, yeasty, vitamin B-rich, Australian sandwich spread. Its taste and odour are distinctive, iconic and entrenched in the Australian cultural identity. But what are the chemical compounds that make up the unique smell of vegemite? This is a topic close to my heart (or nose), as I drive past the Kraft factory where vegemite is manufactured on my way to work, so the aroma often fills my nostrils and makes me crave a thick slice of sourdough toast slathered with butter and vegemite. I was shocked to find that this area of research into sensory analysis of vegemite is sorely lacking in the scientific literature, so I decided to do my own experiment* which I will take you through in a series of three blog posts.

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VEGEMITE. IS GOOD.

The aromas we smell from foods, fragrances or anything with an odour, comes from chemicals that are released from the object into the surrounding atmosphere and then into our noses. In order to escape from the object into the air (and noses), these aroma chemicals must be ‘volatile’, where volatile means the compounds do not require much energy to enter the gas phase and may do so spontaneously, or with a little heat or pressure.

In order to do the analysis of the aroma of vegemite I will be using two popular analytical chemistry techniques: solid phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). These will be discussed later on.

  1. Sample preparation

A sample of vegemite was taken directly from a refrigerated** 600 gram jar purchased from a supermarket and manufactured in Melbourne, Victoria. The sample was transferred by means of an ordinary household knife to a 20 mL glass headspace sampling vial with rubber septum. The weight of the vegemite sample transferred to the sampling vial was approximately 2 g. At the same time, a sample of vegemite from the same jar was applied to buttered toast in order to ensure the sample was of the acceptable quality.***

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Headspace sampling vials will generally be of a much larger volume than the sample. The sample only takes up a small part of the vial, with the remaining volume available for the formation of an atmosphere concentrated with volatile compounds emitted from the sample. The vial lid has a rubber septum which permits a sampling needle to pierce the top while the vial remains sealed, with no gases escaping.

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Headspace sampling vial showing rubber-lined cap and tool to crimp cap and seal the atmosphere inside.

  1. Aroma sampling by solid phase microextraction (SPME)

The SPME sampler looks like this…

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… and here it is taken apart…

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The parts of a SPME sampler (left to right): body, needle/fibre assembly, retaining screw, depth gauge.

The needle-like part of the SPME sampler houses what we call a ‘fibre’. The fibre is made from fused silica or stainless steel and coated with a thin layer of polymer. The fibres can be made with different polymer coatings which can help you analyse different types of volatile compounds. The type of polymer coating is indicated by the colour of the needle hub (in this case red is polydimethylsiloxane). When the SPME sampler is assembled, pressure applied to the spring allows the delicate fibre to be either exposed or protected by the needle.

To encourage maximum release of volatile chemicals from the vegemite sample, the vial was placed in a laboratory oven set to 65 °C for about half an hour and allowed to come to thermal equilibrium.  In order to sample the aroma, the SPME sampler needle housing the fibre is used to puncture the vial septum. Once the needle is pushed through into the vial, the delicate fibre can be exposed. When the fibre is exposed to an atmosphere of volatile chemicals, they become temporarily trapped on the polymer coating. The extraction of volatile compounds from the vial onto the fibre only needs a few minutes, in this case I did the extraction of the vegemite aroma for 15 minutes.

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The SPME sampler inserted into the vial containing vegemite in a laboratory oven.

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Close up of SPME sampler inserted into the vegemite-containing vial. You can just see the thin fibre circled in red.

Once the extraction of the aroma chemicals is complete, the next stage of the experiment can begin. This will be the gas chromatography-mass spectrometry and will be discussed in the next post.

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*Although all of the work and analysis was done by me, full credit for the idea to do this goes to fellow practitioner of Teh Scients Dr Chris Slape (@is_chris).

**I am of the opinion (and so is Kraft) that it is entirely unnecessary to keep one’s vegemite in the fridge. However, storing vegemite in the fridge provides me with the benefits of accessibility and domestic harmony, so there it lives.

***It was.


The Up-Goer Five Challenge for Chemists

Once again, SeeArrOh has started a chemblogo/twittersphere storm with the Up-goer Five Challenge for chemists. Using the online text editor,  I had a couple of goes at this, one for twitter on the hashtag #upgoer140, which is my attempt at explaining chromatography in less than 140 characters;

I use a box which takes stuff that was close together and makes them not be near to each other any more #chromatography #upgoer140

 

And then another longer version in which I try to explain my work looking at the thermal degradation of fuels;

I use a box which takes stuff that was close together and makes them not be near to each other any more. Then I can see what each of the things are, when before it was hidden from me.

Usually I use the box for looking at stuff that makes cars and other things like flying and water cars go. When the flying cars are flying, this stuff can get too hot and then new stuff is formed, which can be bad and make the flying cars stop flying.

I use the box to look at the new stuff that is formed when it gets hot to try and find out things about the new stuff. I want to know what it is, where it came from and how to make it stop happening.

 

It’s actually pretty hard, but quite fun too. I recommend giving it a go.