Ideal Gas Law Simulation

Merlot chemistry - 31 March, 2015 - 00:17
An effective tool to help students learn about all aspects of the ideal gas law. One of the best web gas law simulations.
Categories: Education

Assessing Blood Pressure

Merlot chemistry - 31 March, 2015 - 00:17
This learning module presents the proper technique and common errors associated with assessment of blood pressure. The information is targeted at new learners in the clinical and health sciences and can serve as a review for current practitioners. The program includes audio of blood pressure sounds, interactive simulations, and self-assessment tools.
Categories: Education

DNA from the Beginning

Merlot chemistry - 31 March, 2015 - 00:17
DNA from the Beginning is an animated tutorial on DNA, genes and heredity. The science behind each concept is explained using animations related to DNA topics, an image gallery, video interviews, problems, biographies, and links related to DNA. There are three sections, Classical Genetics, Molecules of Genetics and Organization of Genetic Material. Key features are the clear explanations of classical experiments and the excellent photographs of researchers and their labs.For information and credits on the development of DNA from the Beginning, go to
Categories: Education

VR Molecules

Merlot chemistry - 31 March, 2015 - 00:17
VR Molecules presents dynamically and interactively the vibration and rotation modes for 24 molecules (out of a more extensive list) containing up to twelve atoms. It allows the user to create and save on his or her hard disk documents containing, much in the same way as Power Point presentations, up to 10 "pages״, each featuring one or two molecules with specific parameters (viewpoint, active modes, etc.). These presentations can be made available through the Internet, with optional sound and text explanations associated with each page.The latest, augmented version of VR Molecules, called VR Molecules Pro 1.1, is available online as well as in a stand-alone version (Mac and Windows). To view a video of the award winning author, go to View VR Molecules - Chemistry Award Winner 2007 video VR Molécules est un logiciel de simulation (en ligne et en mode local) permettant de visualiser et d'explorer les modes de vibration et de rotation des molécules (24 molécules sont disponibles). Il peut tout aussi bien être utilisé par le professeur pour préparer des démonstrations en classe, intégrer des animations (interactives ou non) dans ses documents HTML, que par les étudiants pour revoir les démonstrations présentées en classe et explorer par eux-mêmes la vibration et la rotation des molécules.La plus récente version (1.12) de VR Molécules, est accessible en deux versions : en ligne et en mode local (à télécharger, pour Mac et Windows).
Categories: Education

Neuroscience for Kids

Merlot chemistry - 31 March, 2015 - 00:17
The entry point to an extensive site concerning the nervous system and neuroscience. The site includes descriptive materials, experiments, activities, links to articles, resources for teaching neuroscience, and a listing of Internet resources related to the neurosciences.
Categories: Education

Virtual Chemistry Laboratory

Merlot chemistry - 31 March, 2015 - 00:17
Here's your chance to mix chemicals without wearing safety goggles. You won't spill any acid on the spectrometer in this lab. Choose solutions from the vast database and mix 'em together till the cloned cows come home. Marvel as the chemical solutions react in real time.
Categories: Education

PhET - Physics Education Technology at the University of Colorado

Merlot chemistry - 31 March, 2015 - 00:17
A collection of simulations and virtual labs focusing on first-year college physics. An interview with the award winning author can be found in About us at Phet VideoPhET provides fun, interactive, research-based simulations of physical phenomena for free. We believe that our research-based approach- incorporating findings from prior research and our own testing- enables students to make connections between real-life phenomena and the underlying science, deepening their understanding and appreciation of the physical world. To help students visually comprehend concepts, PhET simulations animate what is invisible to the eye through the use of graphics and intuitive controls such as click-and-drag manipulation, sliders and radio buttons. In order to further encourage quantitative exploration, the simulations also offer measurement instruments including rulers, stop-watches, voltmeters and thermometers. As the user manipulates these interactive tools, responses are immediately animated thus effectively illustrating cause-and-effect relationships as well as multiple linked representations (motion of the objects, graphs, number readouts, etc.) PhET Interactive Simulations, University of Colorado,
Categories: Education


Merlot chemistry - 31 March, 2015 - 00:17
Educational physics applets designed to be scripted in JavaScript for use in quizzes, homework problems, and Just in Time Teaching activities. Includes applets that can be used in a wide range of classes and at different levels.
Categories: Education

Music Acoustics

Merlot chemistry - 31 March, 2015 - 00:17
The acoustics of musical instruments and the voice. The "Basics" directory introduces and explains general concepts. There are "Introduction to the Acoustics of [instrument name]״, data bases, technical material, web services (including a hearing test) and a FAQ.
Categories: Education


Merlot chemistry - 31 March, 2015 - 00:17
MecMovies is an extensive collection of examples, theory, and games designed to complement the entire Mechanics of Materials course. The software features impressive graphics and animation that are highly effective in visually communicating course concepts to students. Special emphasis is placed on developing the learner?s understanding and proficiency in basic concepts and skills through interactive exercises and games. Classroom implementation of the software has produced improved student performance and more positive student attitudes regarding the Mechanics of Materials course. To see a video with the award winning author, go to View MecMovies video
Categories: Education

Question time

Chemistry World blog (RSC) - 26 March, 2015 - 16:44

Guest post by Heather Cassell

Throughout my time in the lab I have greatly appreciated having post docs, PhD students and technicians looking after me. So I try to be as supportive as I can to the students in the lab, especially the undergraduates. This mainly involves answering lab based questions, such as: ‘Do you know where this reagent is?’ ‘How do I get rid of this waste?’  Or ‘this is broken, what should I do?’ The questions are usually straightforward, and I’ll do my utmost best to help (unless I’m in the middle of setting up a big experiment – some people just don’t understand that setting up 64 well plates takes concentration!)


But sometimes the questions are more philosophical, asking if I enjoy working in science, or what the value of postgraduate studies such as a masters or PhD can be. The answer to the first question can vary from ‘yes, science is amazing’ to ‘no, run away whilst you can, science is awful, it has no future or jobs’, depending on how things are going in my project, how much paperwork I have to do, and how many meetings I have to attend.

I try to suppress my first reaction to the question (especially when it’s the latter) and give them an honest view of life as a PhD student and what it is like working on short term contracts as a post doc; many students don’t realise that post docs are short term contracts and that when the money is gone so is the job. I’m happy to talk about the different options open to students once they have finished their undergraduate degree, especially as lab based science doesn’t suit everyone.

It’s not just the undergraduates that have questions. I also enjoy talking to the PhD students, especially discussing their results and helping them decide what they should do next. But here again, timing is everything. As nice as it is to be able to lean on my own experience to help people at an earlier stage in their careers, I sometimes use these ‘agony aunt’ sessions to help my own projects out: if I’m filling tip boxes, making buffers or other lab prep, I’d love to talk about your work, especially if you help me fill boxes as we talk! I think that’s a fair arrangement, don’t you?

So if you’re an undergraduate considering a career in scientific research, why not find a post-doc in your lab, help them prep their buffers and learn what that career has in store for you?

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Categories: Education

Volunteers for Viagra

Chemistry World blog (RSC) - 19 March, 2015 - 13:21

Guest post by Rowena Fletcher-Wood

It was the 1990s, and drug giant Pfizer was on the trail of an elusive angina medication to relieve constricted blood vessels and lower blood pressure. Pharmaceutical chemists in Sandwich, UK, were focusing their efforts on drugs that release NO (nitric oxide), a highly reactive radical that expands blood vessels and releases physical tension. One promising candidate was sildenafil, which was trialled in Morriston Hospital, Swansea.

It’s always difficult to recruit volunteers for a drug trial: even the best trials in animals, computer simulations and in vitro can’t take into account the full complexity of the human body, it’s strikingly unobvious differences from the rat and the complex interconnectedness of its mechanisms. Unexpected things happen, some of them bad, and some of them beneficial.

Sildenafil, later renamed Viagra for marketing, seemed to be a no-go for angina relief, and the trials were unsuccessful. Pfizer recalled the drug, and an unexpected thing happened: the volunteers resisted. ‘[P]eople didn’t want to give the medication back’, said Pfizer’s Brian Klee, ‘because of the side effect of having erections that were harder, firmer and lasted longer.’

At once, Pfizer started to investigate these reports. Using penile tissue from impotent men, senior scientist Chris Wayman introduced pulses of electricity both before and after introducing Viagra to their surrounding solution. The effect was immediate and pronounced: Viagra-treated tissue relaxed its blood vessels where untreated tissues did not, just as phallic vessels would relax to welcome the heavy flow of blood to the region. This revealed another significant property of Viagra: limiting erections to when the patient was sexually stimulated – and so foregoing the social inconvenience and dangerous blood restriction of constant arousal.

Catalytic domain of human phosphodiesterase 5 with bound Sildenafil. Image by A2-33 (Own work) CC BY-SA 3.0, via Wikimedia Commons

Pfizer was as impressed as the volunteers. One thing led to another, and very soon Viagra was on the market, and selling at an unprecedented rate as the first oral treatment for erectile dysfunction. Although other treatments did precede Viagra, they were not comfortable options: regular injection or an unpleasant prosthetic implant.

Viagra works in a very clever way, by mimicking a compound in the body and so blocking one of the enzymes that it binds to: the enzyme binds Viagra instead, and its function is blocked. This enzyme is PDE-5, a phosphodiesterase, and it works by mopping up cGMP, or cyclic guanosine monophosphate, which is the stuff that provides the erection. How? It all comes back to NO. Naturally produced by the stimulated brain, NO basically sets up a small factory making cGMP, only to have it swallowed up and broken back down by PDE-5, unless Viagra comes along. It’s striking chemical similarity to cGMP is enough to confuse PDE-5, inhibiting its action and leading to increased cGMP levels. Viagra is naturally decomposed and cleaned out by the body, with no further effects than a prolonged reaction to stimulation and a surprising effectiveness in relieving altitude sickness.

Worth volunteering for?

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Categories: Education

Academic family: Adolf Butenandt and Richard Kuhn

Chemistry World blog (RSC) - 12 March, 2015 - 12:11

Guest post by JessTheChemist

‘In order to avert such shameful occurrences for all future time, I decree with this day the foundation of a German national prize for art and science. Acceptance of the Nobel prize is herewith forbidden to all Germans for all future time. Executive orders will be issued by the Reich minister for popular enlightenment and propaganda.’ – Adolf Hitler, 1937

Portrait of Richard Kuhn
By ETH Zürich (ETH-Bibliothek Zürich, Bildarchiv) CC BY-SA 3.0, via Wikimedia Commons

Since my February blog post on Carl Djerassi, I have been wondering more and more about all the chemists out there who may have deserved a Nobel prize in chemistry but perhaps died before they could be awarded one or who were prevented from winning a medal for reasons out of their control.

It is well known that the second world war led to huge advancements in chemistry, with, for example, the first organophosphate compounds developed. These were initially used as deadly chemical weapons but have since changed the world through their use as pesticides. While many German scientists were advancing their field, two were forced to decline their Nobel prize in chemistry due to threats of violence and a decree by Adolf Hitler. These talented chemists were Adolf Butenandt from Austria and Richard Kuhn from Germany.

In 1929, Butenandt isolated estrone, a female sex hormone responsible for sexual development and function. He later isolated and identified androsterone, a male sex hormone. Butenandt was awarded the Nobel prize in chemistry in 1939, along with Leopold Ružička, for the identification of the sex hormones including oestrogen, progesterone and androsterone. Kuhn is known for synthesizing vitamins B2 and B6 and discovering carotenoids, the red and yellow coloured biological pigments. He also discovered the nerve agent Soman (o-pinacolyl methylphosphonofluoridate) while carrying out research for the German army. In 1938 Kuhn was awarded the Nobel prize for chemistry for his work into carotenoids and vitamins. Both Butenandt and Kuhn declined their prizes due to political pressures but were both able to accept their medals and diplomas after the war.

Butenandt and Kuhn’s academic family trees are intertwined and contain a number of very well-known names that you may recognise from your lab cupboards (including Bunsen and Schlenk). In 1902 the German chemist, Hermann Fischer, won the Nobel prize in chemistry for his discovery of the Fischer esterification. A few years later, in 1905, Adolf von Baeyer won the prize for his work into organic dyes and hydroaromatic compounds. Richard Willstätter, yet another German chemist, researched the structure of plant pigments, including chlorophyll, and won the prize in 1915. Adolf Windaus won in 1928 for his work on sterols and vitamins. In addition to chemists, Butenandt and Kuhn are both connected to Otto Warburg, a physiologist who investigated the metabolism of tumors and the respiration of cells. In 1931 he was awarded the Nobel prize in physiology for his work into the respiratory enzyme.

What is very obvious from this academic tree is that both of these chemists were destined to excel in chemistry due to the sheer number of Nobel prize winners that they are connected to. Another obvious conclusion is that chemistry was really progressing in Germany before the second world war; at the beginning of the 20th century, Germany won more Nobel prizes than any other country (38 between 1901 and 1931). After the second world war, Germany’s domination in science was reduced significantly and only 16 Nobel prizes were awarded to German scientists between 1950 and 1980.

As ever, if you would like to see your favourite or even least favourite Nobel prize winner’s family tree explored, send a tweet to @Jessthechemist.


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Categories: Education

Creepy crawlies under (and on) the covers

Chemistry World blog (RSC) - 5 March, 2015 - 11:00

It’s a full moon and a cold night. You may be tucked up in bed safely away from the worries of the day, but the night holds its own horrors. On a recent cover of Angewandte Chemie that peaceful night’s sleep was very much in danger of disruption from a rather unpleasant source.

© Shutterstock

Good night, sleep tight

In this disturbing image a resting girl seems to be blissfully unaware of the impending danger she faces. Personally, I would be a little more wary about getting into a bed that had ’bed bug aggregation pheromone’ written on the side of it. But if that wasn’t enough to put you off, then the array of compounds littered across the sheets should surely do the trick. These chemicals are, of course, a mix of volatile components given off by bed bugs.

The cover art accompanies an article from Gerhard Gries, of Simon Fraser University. Gries told me that he wanted to create a creepy image showing a girl ambushed by these bugs that ’come out at night to feed on us humans.’  Delightful. The photo of the bugs was taken in Gries’ lab of their very own bed bug colony. Lead author Regine Gries looks after and feeds the bugs herself, yes literally feeds the bugs herself. Bed bugs favour human blood and there’s no better source than a brave researcher.

The key ingredient in the bugs’ pheromone mix was unearthed in this study: Histamine. Because histamine is not as volatile as the other oxygen- and nitrogen-containing components in bed bug pheromones,  it is harder to detect, and had not yet been found. The bed bugs send out these pheromone signals to let others know when they can find food and safe shelter, and crucially they only settle down when histamine is present. Gries’ lab is now working on using their creepy crawly knowledge to create traps and detectors to monitor if your home is bugged. You can read more about the research on the main Chemistry World site.

Don’t let the bed bugs bite

While the results are of great importance, the journey there was equally interesting. As well as donating blood samples, there was other dirty work to do. To gather enough material for the mass spectrometry samples, the team spent four weeks collecting faeces from 300 bugs!  As it involves both the presence of human parasites and the collection of faeces, it certainly doesn’t sound like the most pleasant experiment ever conducted in the name of science. Another round of applause should also be given to the inhabitants of the ’heavily infested residential apartments’ who so generously donated their living space for experimentation.

I wish you all a good night, sleep tight and don’t forget to set a histamine trap so that the bed bugs don’t bite. 

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Categories: Education

Have your say: vote in the ‘Take 1 minute…’ competition

Chemistry World blog (RSC) - 4 March, 2015 - 12:39

Guest post from Holly Salisbury, Royal Society of Chemistry

We challenged early career researchers to explain the importance of chemistry to human health in just 1 minute. The shortlisted videos are now online and we want YOU to pick your favourite entry.

The chemical sciences will be fundamental in helping us meet the healthcare challenges of the future, and we are committed to ensuring that they contribute to their full potential. As part of our work in this area, we invited undergraduate and PhD students, post-docs and early career researchers to produce an original video that demonstrates the importance of chemistry in health.

We were looking for imaginative ways of showcasing how chemistry helps us address healthcare challenges and entries could be no more than 1 minute long.

The winner will receive a £500 cash prize, with a £250 prize for second place and £150 prize for third place up for grabs too.

We want you to get involved: watch our 6 shortlisted videos and vote for your favourite before 11.59pm (GMT) 17 April 2015!

Which was your favourite? Vote here!


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Categories: Education

February 2015: Science Stories

Royal Society R.Science - 27 February, 2015 - 17:39

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Categories: Education

Prevent problems with proper planning

Chemistry World blog (RSC) - 26 February, 2015 - 17:32

Guest post by Heather Cassell

One of the great joys of being in the lab is being in charge of your own experiments, from designing what you want to study to the interpretation of the results. Having responsibility for your work from conception to completion is challenging and ultimately rewarding.

The first step in designing your experiment is to find out what you want to know. That sounds simple and obvious, but it really is key to providing focus when planning your work. You must consider why you are doing this experiment, what it could show, how it fits with your other work, and, importantly, will you be able to interpret the results in a meaningful way, providing answers you can build on?

Inspiration for your experiments can come from diverse sources, beyond the traditional scientific lectures or academic literature, a conversation with a current or former colleague can be all it takes. But whatever the source of the idea, it is always a good idea to check if anyone else has beaten you to it by consulting the literature. Not that repeating existing work is a bad idea – you can see if existing studies are reproducible and if so, embellish or add to the data. Or you can change the design of your experiment to fit with your own previous studies, and may find something new.

Once you know what you want to do, it’s time to plan the details: what samples do you have, how many repeats do you need to make your results significant, and – more importantly – how are you going to tell if your experiment has worked properly? This is where planning the correct controls can make a big difference: I learned the hard way that it is good to include both positive and negative controls for every experiment. I wasted a lot of time trying to get an experiment to work, changing conditions one-by-one, when it was really a denatured enzyme stopping the reaction. A positive control means you always get a result, which is much better than no result. This is especially true when you are doing PCR; there are few sadder sights for a biochemist then a picture of a gel with just a ladder.

But I’ve also had it the other way – where I happily reported what seemed like a great result, only to find out that it was an artefact of the experimental design and my results became insignificant when I included different controls. Proper planning could have prevented that problem.

But that’s it! Once you have your experiment planned, designed and justified to the powers that be, you can return to your natural home in the lab and try it out. Ideally, things will run smoothly and every experiment will go without a hitch. You may encounter problems – but fear not! Every experimental error is an opportunity to learn, get back to the drawing board, then return, freshly inspired, to the bench.

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Categories: Education

The carbon revolution

Chemistry World blog (RSC) - 19 February, 2015 - 17:12

Guest post by Rowena Fletcher-Wood

A carbon nanotube, animated by Schwarzm, and released here under a CC-BY-SA licence

If necessity is the mother of invention, discovery is more than fuelled by fashion. After the 1985 groundbreaking discovery of the buckminsterfullerene, the ground for stable carbon allotropes with interesting shapes and properties was just that – broken. In 1990, Richard Smalley postulated the existence of carbon nanotubes as long, extended hexagon-based versions of C60, or ’buckytubes’. Carbon dirt had never looked so good before, and the mucking about began.

Graphene flakes were first isolated at Manchester University by Andre Geim and Konstantin Novoselov in 2003, when they noticed the technique surface scientists were using to clean graphite samples – peeling off the contaminated upper layer using pieces of sellotape. The pieces of sellotape went in the bin, but Geim and Novoselov fished them out again – and started painstakingly peeling off thinner and thinner layers until they made 1 atom thick graphene. They were awarded the Nobel prize for physics in 2010.

Sumio Iijima, who is often credited with the discovery of carbon nanotubes,  attributes his discovery to serendipity. He had been studying diamond-like carbon, an amorphous diamond phase, using the new arc discharge method developed by Donald Huffman and Wolfgang Krätschmer in 1990. The rod-like carbon dirt surrounding his diamonds captured his attention: carbon tubes 3-30nm in diameter. Later, attempts to introduce transition metals to these tubes would lead him to create single-walled carbon nanotubes, a finding submitted to Nature for publication on 23 April 1993, one month before the US team headed by Bethume submitted exactly the same accidental result.

But whilst Iijima may claim that ’discovery was not simply coincidence – it was the power of serendipity’, it would be fairer to say that carbon nanotubes were rediscovered. Carbon-based filaments were recorded as long ago as 1889 by Robert Bacon when decomposing methane. But back in 1889, there was no such thing as a transmission electron microscope (TEM), and so no nanoscale imaging to view and characterise these filaments. The first TEM appeared in 1939, and the first TEM images of tubular nanoscale carbon tubes was published in 1952 by L. V. Radushkevich and V. M. Lukyanovich – but in a Russian journal, and in Russian. Published during the cold war, this paper went largely unread in the west. Although single-walled carbon nanotubes were first announced in the 1993 issue of Nature, TEM images from Oberlin et al. in 1976 indicate that successful synthesis had already been achieved.

And the carbon fever has not died down. In 2013, carbon ’sea urchins’ were accidentally prepared by researchers at Queen Mary and Kent Universities, growing on the surface of their carbon nanotube equipment. Intentionally roughening the surface accelerated the synthesis of these spiky iron-filled carbon balls with unusual magnetic properties. Although exciting applications such as permanent magnets, cancer therapy and batteries that charge from waste heat have been proposed, it seems likely that, like other carbon nanomaterials, new discoveries will outpace implementation: cheap and efficient production of carbon nanomaterials of a high enough quality has not yet been achieved.

It is only when nanomaterials are of a very high quality that the awesome properties may be observed, such as very high conductivity, luminescence or the ability of graphene sheets to filter hydrogen from the atmosphere for generating electricity. When we speak of the 1991 discovery of carbon nanotubes, it is perhaps the discovery of their properties and future potential to which we refer, rather than simply the creation of a new carbon allotrope. Carbon nanotubes have the highest pressure resistance of any known material, withstanding pressures of up to 63Gpa. They are ultra absorbant, heat-resistant, and at very high temperatures carbon nanotubes shimmer, loose their shape and become almost invisible, just like their origins.


If you are interested in hearing more about nanomaterials, structures and unusual properties, the Environmental Chemistry Interest Group of the Royal Society of Chemistry are holding an event in London on 24 June.

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Categories: Education

The scent of science: our guest bloggers’ memorable smells

Chemistry World blog (RSC) - 16 February, 2015 - 17:51

Last week, we heard from Derek Lowe about the evocative smells associated with working in the lab. Inspired by Derek’s olfactory adventures, the Chemistry World and Education in Chemistry teams shared their own experiences.

This week, we hear from our regular guest bloggers Tom Branson, Heather Cassell, JessTheChemist and Rowena Fletcher-Wood about their own smelly memories, along with a few more from the #labsmells hashtag.

@ChemistryWorld For some reason memories of the synthesis of 4-allyl-2-methoxyphenol (eugenol) in 1st year lab has stuck with me #labsmells

— Astril Tifs (@firstilast) February 14, 2015

Rowena Fletcher-Wood

Chemistry has ruined me for marzipan.

Not just marzipan, of course, almonds, almond flavouring, even apricots. If you waft a piece of almond cake under my nose unexpectedly, I will automatically give an sudden and violent sniff, and recoil physically. I can’t help it, it’s an instinct, and that smell is the smell of hydrogen cyanide.

Early on in my chemistry career, when I was still in school, we conducted an electrolysis of brine, rapidly evolving chlorine gas into the lap until I felt woozy and had to go outside. It wasn’t the only time I nearly gassed myself. There were more than a few faulty fume hoods, or ones we had simply forgotten to switch on, and the ammonia gas cylinder that popped its collection flask and started dumping poisonous gas into the lab. We used cyanide during my undergraduate in solutions to create colour chemistry. It was terrifying – the only way you knew it was going wrong was if you smelt the cyanide, and the difference between first smelling it and the toxic effects of it is not much. I bent over the solution, sniffing frantically so as not to miss the first signs. I was so paranoid I was imagining smelling it, confused between reality and expectation. But the smell was never as strong as in marzipan – ergo marzipan must be fatally toxic.

I’ve been doing full time chemistry for eight years now. I think like a chemist. The logic circuits in my brain just can’t accept that marzipan is a safe food. It’s toxic. Step AWAY from the marzipan.

@ChemistryWorld I once isolated chamazulene from chamomile. 28 years on, when I smell chamomile, I am back in that lab. #memory #labsmells — La L (@La_L_NL) February 14, 2015

Heather Cassell

Within the lab there are many smells that I enjoy, such as yeast and agar which remind me of growing E. coli, a bacterium I also like the smell of. I like the smell of acetone and isopropanol used in small amounts in reactions and for cleaning glassware. Dilute acetic acid as it reminds me of the vinegar on fish and chips. Another bacterium, actinomycetes, release geosmin as they are growing – that compound gives soil the particularly earthy smell, especially after a heavy summer shower.

But there are also lab smells I really don’t enjoy, for example the beta-mercaptoethanol that I use to set sodium dodecyl sulfate (SDS)-gels for electrophoresis. I now have its use down to a fine art to reduce the exposure time: open the bottle one-handed, pipette the amount needed with the other hand, close the bottle again a quickly as possible whilst adding the liquid to the gel solution. Only once the bottle is closed do I gently mix and pouring the gel mix into the glass plates. Then there’s the smell of chlorine, released from a too concentrated Virkon solution. It’s bad enough when used in solution to clean glassware after growing bacteria, but it is definitely worse if it is in an aspirator trap. As soon as you turn the pump on it fills the room with a chlorine smell that can strip the hairs from your nose, and will linger in your clothes and hair for ages.

@ChemistryWorld nothing can be worse than the 2-bromoskatole I made during my phd! Smelt of it for a week-but got me a seat on the tube! — Adrian Dobbs (@APDobbs) February 15, 2015

Tom Branson

I’m certain that my aversion to the smell of ethanol stems from one overindulgent night. Not one spent sniffing chemicals in the lab but rather one spent drinking chemicals in the pub. Vodka shots used to be my bread and butter, but no longer. My senses are now unable to disassociate the highly alcoholic drink from its active ingredient. Since that fateful night I now grimace every time I have to disinfect a biosafety cabinet. A sharp whiff of ethanol and my mind leaps back to that memory, or at least the after-effects. However, one good thing that has come from my dislike of pure ethanol is a new fondness for gin and tonic.

@ChemistryWorld #labsmells 880 ammonia. The teacher told us all not to inhale near the bottle. Taught me the value of obedience.

— Lee Vousden (@Lee_Vousden) February 13, 2015


As a PhD student, I frequently worked with elemental fluorine, the flammable and highly toxic halogen gas. Fluorine can be smelled at around nine parts per billion, which is a similar odour detection threshold to that of hydrogen sulfide. It is hard to describe the smell of fluorine, but it is unpleasant and vaguely smells like a mixture of ozone and chlorine. Although the smell is remarkably offensive, its pungent odour does mean that the smallest leak in your reaction set-up can be identified very quickly and fixed. So while fluorine was a smelly, unpleasant chemical to work with, its smell was extremely useful from a safety perspective.

I love the #labsmells of Cp* in the morning. Smells like – chemistry.

— John Arnold (@pbn2au) February 13, 2015


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Categories: Education

The scent of science

Chemistry World blog (RSC) - 13 February, 2015 - 15:43

M-H Jeeves

In this month’s Chemistry World, Derek Lowe writes about the memorable smells associated with a career in chemistry, including the fragrantly fruity funk of esters and the suspicious seaside stench of amines.

Inspired by Derek’s olfactory adventures, I asked a few of the Chemistry World and Education in Chemistry team to recount their own experiences of lab smells, and opened it up to the twittersphere under the hashtag #labsmells:

@broadwithp @ChemistryWorld being able to navigate chemistry dept corridors by different #labsmells emanating from certain labs

— Alex Sinclair (@Alex_Sinc) February 11, 2015

Philip Robinson, Deputy Editor, Chemistry World

As a PhD student in the ‘dry’ half of a biochemical NMR group, most lab smells were associated with a sense of relief that I was at last free of the chaotic caprice of real chemistry. But on occasional trips down the corridor to see how the other half lived I’d often encounter the bold odour of the yeast cultures that were busily building our proteins.

That heavy, dense aroma, fusty and overripe evokes equal parts revulsion and pleasure and sends me further back, to boyhood, sat in the back of the family car holding my breath to avoid the scent as we drove past Edinburgh’s reeking breweries. But those many years later, my tastes matured, I’d often stand outside the department when the wind blew just right, looking up at the darkening blue of the evening sky and drawing in deep lungfuls of that delicious air. Opening a jar of vegemite brings it all back these days.

@ChemistryWorld H2S. Smelly and deadly.

— Rams (@ramadam09) February 11, 2015


@broadwithp @ChemistryWorld This week I will be introducing my research students to the swern oxidation. #labsmells

— Sarah Zingales (@SKZingales) February 11, 2015

Phillip Broadwith, Business Editor, Chemistry World

One of my most memorable lab aromas is when Paul (Docherty) was using hexanoic acid in the lab. Also known as caproic acid, from capra, the latin name for goats, because that’s exactly what it smells like. In fact, in the listing for caproic acid in The Merck Index, under ‘properties’, you’ll find the sentence ‘Oily liquid, bp 205ºC. Characteristic goat-like odor’.

It’s one of a family of alkyl acids that all have interesting odours, varying as the chain length increases from smelling of pain (formic) through vinegar (acetic), cheese (propanoic), vomit (butanoic) and animal faeces (pentanoic), before the molecules become less volatile as they get heavier.

Fortunately, I didn’t need to raid the chemical store to find out about these smells, because Dylan Stiles (former CW columnist) wrote a brilliant post about it on his (now defunct) Tenderbutton blog. (the archived blog can be accessed using the username tender, password button)

@ChemistryWorld @Dereklowe i love the smell of the lab in the morning. It’s better than coffee, it’s olfactory inspiration.

— Louis Redux (@LouisRedux) February 11, 2015


@chemistryworld @dereklowe These days we’re working with tons of Py, Me2S and MeSH in the lab. They’re disgusting, indeed. Nice article :)

— Fer (@gomobel) February 11, 2015

Katrina Krämer, Graduate trainee, Chemistry World 

In the last half year of my PhD project I started making phosphine ligands using diphenylphosphine as the nucleophile. I got to know phosphines (tertiary ones that is) as tame, usually colour- and odourless powders. Secondary phosphines, however, are a completely different story.

I agree that there are many nasty smells in the lab, but at least I can place those smells – amines smell like rotten fish, thiols like garlic or old cheese. Describing the smell of HPPh2, however, is difficult: somehow sickly sweet, with some rotten carcass thrown into the mixture, a strong metallic aftertaste and extremely potent – I don’t think I ever smelled anything even remotely resembling this, and I don’t think I want to ever again.

After getting a bunch of looks that could kill from my labmates after rotavapping a flask with residual HPPh2 on the bench (we didn’t have a rotavap in a fumehood), I set up a massive bleach bath next to my fumehood, in which I immediately immersed all glassware that had come into contact with the nasty phosphine. But even through the bleach (since diphenylphosphine is stable enough to survive some days of bleaching) I could still smell the phosphine when I opened the bucket. From then on, I started doing all glassware washing inside my fumehood rather than in the sink.

When my supervisor suggested I should try different phosphines, in particular asymmetric ones like HP(Ph)Me, I vehemently declined – having done my homework, I knew that other secondary phosphines were another step down the ladder of evil odours. After sending him some further reading on the topic, my supervisor agreed, so luckily HPPh2 was the nastiest smell I ever encountered.

1 yr on, toluene still makes me heave – MT @ChemistryWorld Lab aromas conjure memories & emotions @Dereklowe

— lauren tedaldi (@LaurenTedaldi) February 11, 2015


@ChemistryWorld ..the smell of benzaldehide semilar to almond juice always remindes me of summer smell♥★

— salwa (@salwayussef) February 11, 2015

Paul MacLellan, Deputy Editor, Education in Chemistry

I had the pleasure of doing a PhD in organo-sulfur chemistry. By far the most onerous compound I had to make was a small thioester substrate. It wasn’t the worst-smelling compound I dealt with – indeed, the next step in the synthesis involved reducing it to a terrifyingly metallic-smelling thiol. But the reduction could be done on a small scale, whereas I had to make several grams of the thioester at a time.

Over a couple of weeks I built up something of a reputation in the surrounding labs (it didn’t help that this was early on in my lab career and I wasn’t perhaps as rigorous in containing the odours as I came to be soon after). Some people commented on the stench of the thioester being reminiscent (in the worst way) of bacon. Others identified marijuana. But to me, the smell inexplicably conjured memories of camping as a kid.

This remained a mystery to me for a year or so until a friend of mine visited my lab. While I was showing her around she picked up a faint background odour. A long-suffering Londoner, she identified it immediately. ‘Fox piss.’ Perhaps my parents should have pitched our tent more carefully.

.@dftchemist @ChemistryWorld undergrad sweat (due to hard work) is every PI’s favorite lab smell, isn’t it?

— FX Coudert (@fxcoudert) February 11, 2015


.@ChemistryWorld Least favorite #labsmell, disc crash in the morning. Like overheated brakepads – burning plastic+metal & vaporized data.

— Preston MacDougall (@ChemicalEyeGuy) February 11, 2015

Matt Gunther, Science Correspondent, Chemistry World

The smell of cyanoacrylate, commonly known as superglue, is a laboratory smell that will forever haunt me. As part of my research I was tasked with imaging invisible organic matter on a steel surface. Inspired by CSI, I decided to form acrylate vapour in an enclosed chamber – the vapour reacts with the organic to produce a white residue.

One day, I opened the chamber and the smell hit me. Before I had to time to react to the smell, I realised I couldn’t see. Turns out I’d superglued my eyes shut.

.@ChemistryWorld Favorite #labsmells are anethole and its derivatives. Remind me of origami at the nanoscale.

— Preston MacDougall (@ChemicalEyeGuy) February 11, 2015


@ChemistryWorld @RealTimeChem I remember the first and only time I smelled phosgene! I bailed real fast! #labsmells #rottenhay

— Dave Belyea (@ve5rb) February 11, 2015


There are many more examples of memorable lab aromas on the #labsmells tag, or you can join in the conversation on Facebook.

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