Chemistry picture of the week: Buggy research

When I talk about bugs in my research, I wish I was talking about software or something. No, the problem we are currently experiencing in my lab is more literal than that.

A couple of weeks ago, I and coworkers in the same section of the lab noticed these black particulates accumulating on our lab bench. We shrugged it off for a week or so, but it soon became a real annoyance. Having to brush little black things off of your precious clean vials, or, worse, having to pick them out from a product you filtered the day before can be, if not detrimental, then irritating at the very least. We observed that the black things were confined to below the large air conditioning vent above our lab benches. We notified the building manager about it. He expressed concern over the situation, saying that it could mean that there is something wrong with the air conditioning. He would have someone look at it.

I turn up to work on the next day, having missed the air conditioning technician who came by earlier that morning. A coworker accosts me: “Hey, have you looked at those black things? Like… really looked at them?” His tone is mischievous and ominous and I’m really not a fan of it. The air conditioning technician had identified the black stuff as thrips — tiny insects that are killed in the air conditioning system but are too small for the filters. As a consequence, our work benches were being rained on by tiny dead insects. I don’t think I really need to qualify that declaration with a record of my reaction. I think that statement — “rain of dead insects” — is graphic enough on its own.

I have to give it to my university: they were very prompt at identifying the issue. The building manager even followed up with the information that Campus Services has agreed to upgrade the filters to stop it.

We are still dealing with the rain of dead bugs, but hopefully not for long — especially since we have recently spotted a few live ones crawling around. And I swear… They’re getting bigger.

You can reach me in the comments, by e-mail on chemistryintersection@gmail.com or on Twitter, where I tweet about daily science happenings as @Lady_Beaker.

 

Chemistry picture of the week: Fibre hunting

In an unfortunate series of coincidences, my last post appears to have been prophetic, regarding my partner’s cold, which I mentioned in passing. Where the prophecy lied was the nature of the disease — it turned out to be a monster flu that absolutely wiped me out for two weeks. At best, even standing was too much effort for me for the past couple of weeks. But finally, the illness is over and I can return to business as usual. That business, of course, is crystals.

As you may have read in the guest post I wrote for #RealTimeCheminFocus, I recently had a breakthrough in my project — in the sense that I finally found a way to synthesise the material I had been aiming for all year. I have since been experimenting with a number of synthetic variables to see how many different variations of this material I can make, and how its structure and properties can vary. The material is a coordination polymer, which is an “infinitely” repeating assembly of metal ions and organic ligands. My ultimate aim is to take these compounds through postsynthetic modification — simply, chemical reactions of the coordination polymer to give different properties. In order to do this, I have been working on characterising my compounds so that I can tell how they change once I put them through these experiments.

Today, I was preparing samples to send to an analytical laboratory for elemental analysis. Elemental analysis involves breaking down a compound to its elemental components in order to give a percentage composition of the compound, most often in terms of carbon, hydrogen and nitrogen. Other elements can also be analysed for, but often require more sample, and are more expensive than a “basic” CHN analysis. In most cases, especially if other forms of characterisation are possible, analysis for anything other than these three elements is unnecessary. If a compound contains an impurity that does not contain carbon, hydrogen or nitrogen, it can still be seen in the elemental analysis by proxy, since the impurity will affect the overall percentage composition. Elemental analysis is excellent for determining the exact amount of counter-ions and solvent in coordination polymers, where these variables can be unclear.

For elemental analysis results to be usable, it is critical that the samples I send are as pure and clean as possible. Crystalline samples are preferred, since the composition of a crystal is uniform. Coordination polymers are almost always formed through crystallisation from a reaction mixture, so all that remains is to collect the crystals, wash them of possible soluble impurities and then dry them. In my group, there is also a practice of checking the quality of the sample under a microscope prior to packaging it for elemental analysis. Painstakingly sifting through piles and piles of cubic crystals using a small needle, I found a surprising number of fibres of confusing origin, pieces of glass and other assorted debris. Of course, there is no way to tell by eye whether the sample is truly pure or not, which is why we need this analysis in the first place, but removal of this visible debris can only help make the analysis results more helpful for accurate composition determination.

Besides, looking at the piles of shiny, beautiful crystals that I strived so hard for so long to make fills me with great joy. Just being able to pack up enough material for analysis is a great victory in my book. Let’s just hope that victory doesn’t turn into defeat in confusion once I receive the results.

I am available for correspondence through the comments, and via e-mail at chemistryintersection@gmail.com. You can also find me tweeting away as @Lady_Beaker.

What is it made of: Your scarf

Describing things from the natural world is always more challenging than describing man-made things, mostly because of the inherent variability and complexity in nature. After perhaps biting off more than I can chew with carrots, I’m stepping it down a notch. This week, I’m going to talk about what your store-bought winter scarf is probably made out of: acrylic fibre.

Image source: http://www.fibre2fashion.com/

Alongside the natural fibres wool and cotton, acrylic fibre is one of the most common materials for warm winter clothes. Apart from its presence in ready-made clothes (like jumpers and cardigans) and accessories (like hats, gloves and scarves) found in clothes stores everywhere, acrylic is also one of the most popular fibres of yarn found in craft stores. It is a soft, lightweight fibre, which holds dye well and is very resistant to wear as well as washing.

In terms of its chemical composition, acrylic fibre is a fibrous polymer. A polymer is a large molecule made from several repeating units, which are called its monomers. It is common for commercial polymers to be made of more than one kind of monomer, as adding a percentage of different monomers can alter the properties of the entire polymer, such as giving it heat or wear resistance.

The chemical structure of acrylonitrile. Image source: https://commons.wikimedia.org

The primary monomer in acrylic fibre is acrylonitrile. The acrylonitrile content of acrylic fibre must be greater than 85%. Fibres with an acrylonitrile content of 35-85% are referred to as modacrylic fibres. Acrylonitrile, on the right, consists of two functional groups: vinyl (two carbons connected by a double bond) and nitrile (carbon and nitrogen connected by a triple bond). The vinyl group is what undergoes the reaction to polymerise this molecule into polyacrylate — acrylic fibre. The double bond between the carbon atoms is broken in favour of each of the carbon atoms forming a bond each with a different acrylonitrile molecule.

The structure of polyacrylonitrile. Image source: http://pslc.ws/

On the left is the structure of polyacrylonitrile, a polymer which consists entirely of the monomer acrylonitrile. The square brackets represent the repeating unit of the polymer, while the n represents the number of repeating units. This value is usually not a single number, but rather a range, as the length of polymer chains can be difficult to control precisely. As noted above, acrylonitrile is not the only monomer present in acrylic fibre, so the structure on the left is not entirely representative of its chemical structure — but as acrylic fibre should be at least 85% of this monomer, it is a fair approximation. The co-monomers used in the manufacture likely vary from manufacturer to manufacturer.

Acrylic fibre is found in everything from hats and gloves to carpets and upholstery to sweaters and cardigans. This material is testament to how versatile synthetic polymers can be — a far cry from the tough, hard stuff the word “plastic” evokes in our minds.

You can find me on Twitter as @Lady_Beaker, reach me via e-mail at chemistryintersection@gmail.com or by the comments down below.

Chemistry picture of the week: Sticky notes

Managing a chemistry PhD project is chaotic. On a day-to-day scale, in a synthetic project, there are three main tasks: to work up (complete) old reactions, to analyse their products and to set up new reactions. Even without any other considerations, these three tasks alone can spin out of hand when considering the volume of reactions we work with. As a PhD student, however, your job is not only to carry out your project, but to plan and manage it as well. We need to constantly analyse the data that we get and shift our goals and focus accordingly. It is extremely common to attain a result you weren’t even remotely aiming for, but that ends up being much more promising than any other results to date — and just like that, the focus of your project has changed.

There is also a delicate, difficult balancing act that goes to doing science on a deadline. With the strict three year time limit on our scholarships (in Australia), we need to be conscious of the months that go into pursuing an evasive, yet promising result. A thesis cannot solely be filled with a thousand things that were tried and did not work — and as I’ve mentioned before, there is no hope on Earth for publishing that kind of science. Thankfully, our supervisors will usually have had at least a number of PhD students before us, and will know the project and timeline to set in order to yield results for a thesis. To benefit from this knowledge, we must be sure to communicate with our supervisors readily if we feel we are banging our heads against a brick wall instead of doing useful work — not only may they know something new to try, but they are also better versed at saying when it is simply appropriate to abandon a project.

Another project management requirement for science projects are the rigorous experimental details we are expected to record. One of the main characteristics of science is that it is reproducible. In order for chemistry experiments to be reproducible, we need to record a number of details: what chemicals you used, what quantities, how long did the reaction go for, what was its appearance and so forth. We record these details into a handwritten lab book; analyses are usually filed separately. With a constantly shifting project focus, a lab book can quickly become disorganised. My lab book in particular deals in three-page spreads dedicated to the same “topic”, which, in my case, is usually a family of very similar reactions. These topics can then repeat later in the book, but are usually spaced by unrelated spreads. We try to work on a few different things at once, for variety and also for the likelihood that something will actually yield usable results.

All of this boils down to the need for extremely good organisational skills to keep abreast of the requirements, current status and future plans of one’s project. The lab notes are a solid friend to turn to when in doubt, because there one will most easily note the experiments that have worked and that haven’t. It is not particularly helpful for the planning of one’s project, however, since the lab book is reserved for experimental details. For to-do lists, lists of samples that need analysing, ideas for new reactions and helpful advice from group members or supervisors, I use sticky notes. Sticky notes are lovely as reminders and place holders, even catalogues — and they can be stuck to any surface! They are ephemereal, and yet a little more permanent than hastily written notes on the back of your disposable glove. Planning a PhD project somehow feels much more friendly and manageable when you do it one colourful sticky note at a time.

If you have any ideas on project management, feel free to contact me in the comments, at chemistryintersection@gmail.com. Alternatively, tweet me @Lady_Beaker.

Chemistry picture of the week: Vials

Last week’s chemistry picture is a little late due to a short vacation I’ve just returned from. As an apology, I’ve included a little picture from my vacation at the end of this post. Hope you enjoy!

I currently work in the field of metallosupramolecular chemistry. Supramolecular chemistry in general deals with the chemistry beyond (“supra”) the molecule — with interactions between molecules in larger assemblies. “Metallo” simply refers to our preference to direct and design our supramolecular chemistry by use of bonds between metal ions and organic molecules we call ligands. An aim of supramolecular chemistry is to design complex aggregates that are difficult to access by molecule-focused chemistry. Instead of the step-by-step method employed by many synthetic chemists, we rely upon self-assembly. This is pretty much exactly what it sounds like: we, the chemists, provide the starting materials and the right conditions, and the forces of nature do the rest. From relatively simple starting materials, we can then generate (relatively) huge, complex assemblies within days or weeks that would take months by step-by-step synthesis.

The problem with this is the unpredictability of nature. As much as we would love for chemistry to work out the way we want it to every time — just as with life — it often doesn’t. The exact interactions between our metal ions and ligands can be very difficult to predict because of the number of possibilities that exist for self-assembled compounds. There are often at least a handful of different results accessible with very small variation in reaction conditions — and others that we may not know of because of their energetically unfavourable nature. We may know what exactly we are targeting, but we almost always have to do a significant amount of fine-tuning before we ever get there: everything from trying different metals, subtly different ligands, solvents, counter-ions, crystallisation techniques and so forth. Even if there are only two components in the reaction mixture, the ligand and metal, the possibilities for trial are still numerous. The more variables you add, the more difficult your job of fine-tuning your system becomes.

The way we deal with this is to simply run as many attempts of different variations of the conditions as possible. This is where the vials come in. Many people are aware of the classic chemistry glassware: conical flasks, beakers and test tubes, for some. In our lab, though, the star of the show is the simple glass vial. Glass vials are inexpensive, so they are plentiful even in a lab full of glassware-hoarders. We can conduct even tens of experiments at a time and nobody is going to grumble about it. Because of their costlessness, they are also essentially disposable if a crystallisation attempt goes awry and the residue can’t be cleaned off. They are small (the ones pictured only take up to 10 mL of solvent), so milligram scale experiments — which we conduct regularly — are feasible. Their small size also means we can hide them in a cupboard for a year so that those more difficult to access compounds can form while we completely forget about them.

In my opinion, there is no better friend for the metallosupramolecular chemist than the glass vial — except maybe the x-ray diffractometer, but that is a different story altogether.

You can contact me in the comments, via e-mail at chemistryintersection@gmail.com or find me on Twitter as @Lady_Beaker, where I tweet about the daily life of a PhD student in chemistry.

And now, here is the picture from my trip I promised:

Taken from a moving car in Victoria, Australia driving toward Melbourne from Mount Hotham.

What is it made of: Carrot

Image source: http://producemadesimple.ca/

The carrot, in all of its ordinariness, must be my favourite vegetable. I love its fresh crispiness when uncooked, and its sweet juiciness when cooked. Despite its unassuming looks and ubiquitous presence in our supermarkets, the composition of a carrot is anything but simple. Nature has this wonderful way of taking bushels of molecules, stirring them up and then spitting out something so perfect and whole as a carrot. As scientists, we struggle a little to take that apart to identify all the small constituents of this complex aggregate — especially since it isn’t as simple as pulling out one molecule at a time to identify it. This difficulty of analysis is true for almost anything that is found “naturally” in the world — that is, over the formation of which we have no direct control. Further, even if thorough analysis was possible, making sweeping conclusions about all carrots based on the analysis of a single carrot would simply not be possible, since nature loves variation. With this in mind, I will still give a fair run-down of the important components of my beloved, ordinary vegetable, the carrot.

A carrot is composed of — like many fruits, vegetables and living organisms in general — primarily water. This ubiquitous, tiny molecule makes up about 85% of the carrot. Slightly less than 10% is made up of carbohydrates — or, between friends, “carbs.” For the uninitiated, carbohydrates are a class of molecules that consist of carbon, hydrogen and oxygen. In its most basic form, the formula of a carbohydrate is one carbon atom per one water molecule. This is where the term carbohydrate comes from: they are the “hydrates (i.e. water) of carbon.” Carbohydrates come in the “simple” variety of glucose, sucroce and fructose, as well as complex carbohydrates, which are natural macromolecules: large molecules consisting of several repeating units.

Image source: https://www.blendspace.com/lessons/L6U11rZ8mwY0pw/copy-of-carbohydrate

The next 1-2% of a carrot is composed of “dietary fibre.” This rather vague term refers to some carbohydrates that are not easily digestible, unlike the carbohydrates mentioned above. An example of such a carbohydrate is cellulose, which is the primary structural component of many plants. Cellulose is the main dietary fibre present in carrots.

Approximately 1% of a carrot is composed of proteins, another type of natural macromolecule. Proteins are huge, extremely complex molecules made of an array of repeating units called amino acids. Similarly to carbohydrates, they are also made up of carbon, hydrogen and oxygen — where they differ from carbohydrates is the added presence of nitrogen.

A simplified view of a protein. The molecule is so large the chemical structure cannot easily be drawn. Image source: http://www.topsan.org/

0.5% of a carrot is made up of fat, a third kind of natural macromolecule. Alike proteins and carbohydrates, fats are made mostly from carbon, hydrogen and oxygen. The repeating unit in a fat is called a fatty acid.

An additional 1% is accounted for by ash. This term accounts for everything that could not be lumped into any of the other categories analysed for. Ash is residue left over after analysis — random stuff lumped into the carrot by nature.

Although they do not make up an appreciable percentage of the carrot’s composition, metals such as calcium, sodium, potassium and magnesium are present in a carrot in trace amounts. Even small amounts are significant, because these metals are very important for the normal functioning of our bodies. Iron and calcium deficiencies, for example, are or at least lead to known and common medical conditions. Vitamin C and various other small molecules are present in carrots, too, in sub-percentage quantities.

Beta-carotene is one such small molecule. This is arguably one of the most important small molecules to the carrot, since it is what gives the vegetable its distinctive orange colour. This molecule is a hydrocarbon, which means it is composed of only carbon and hydrogen. Its structure (pictured below) contains several double bonds between carbon atoms. This leads to the conjugation of electron density — that is, freedom for the electrons in the bonds to move around the molecule. In hydrocarbons like beta-carotene, this often leads to intense colours like the orange of a carrot.

The structure of beta-carotene. Image source: https://en.wikipedia.org/wiki/Beta-Carotene

What I have accounted for in this post is not even nearly the entire story about what carrots are made of – but it is a fair approximation. Perhaps knowledge of the multitude of complex components that make up a carrot will make the bite into the sweet, juicy vegetable all the more satisfying.

The information in this post was sourced primarily from Chemical composition, functional properties and processing of a carrot – a review by Sharma, K. D. et al., J. Food Sci. Technol. 2012, 49(1) 22-32.

You can contact me in the comments, via e-mail at chemistryintersection@gmail.com. I tweet about the daily life of a chemistry PhD student on Twitter as @Lady_Beaker.

What is it made of: Introduction

I think scientific curiosity boils down to two basic questions: “what is it made of?” and “how does it work?” The difference between them is the difference between a child taking something apart, and then having the ability or willingness to put it back together again. There is certainly intersection between the questions, like “how does what it’s made of influence how it works?” or “how would it work if it were made of different things?”. Their answers are also bound to have interplay. I do not believe focus on one of these fundamental questions over the other — simply as a matter of what one is interested in — is uncommon, though.

My question of choice is certainly “what is it made of?” My project is heavily focused on crystallography, a method of analysing chemicals that arguably comes closest of any analytical technique to directly imaging the structure of a compound. I spend a lot of my time looking at the structures of compounds, looking at how they behave in crystalline (ordered) solids. I also really, really like doing what I do, and get very excited when I get a new structure. I think it naturally follows that I am curious about what other things are made of, and what they look like, on a nanometre scale.

In chemistry, your glass is always full!

To this effect, alongside my “chemistry picture of the week” series, I am planning on starting a series of posts titled “what is it made of?” In this series, I plan to pick an utterly commonplace material thing, find out what it is composed of — by web research and not by physical experiments, unfortunately, since I don’t have the facilities for that kind of thing — and report my findings. This series is a way of sating my own curiosity and that of fellow internet dwellers. It is also a potential way to combat chemophobia by the association of chemical structures and terms with common, harmless things. It also works nicely in tandem with the “picture of the week” series. With the “picture of the week”, I want to delve into the daily life of a young chemist, and expose some of the nitty-gritty that goes into doing science. In other words, I want to bring life into science. The “what is it made of” series will aim to do the opposite: bring science into life.

I repeat a sentiment from my first post: I am infinitely excited by how chemistry makes everything. I am excited by how intricate and beautiful and intelligent it must be to be able to ultimately manifest in all of the things we see around us — and by how cleverly we can manipulate it to make things nature won’t. I hope this series will help me share that enthusiasm a little.

I tweet about everyday chemistry things as @Lady_Beaker. You can also contact me via e-mail at chemistryintersection@gmail.com.

Chemistry picture of the week: Dishes

As chemists, we need to be aware of what sorts of chemicals we are dealing with and how we can dispose of them — and clean up after them — appropriately and safely. We also need to be sure that our glassware is as clean and free of residues and chemicals we did not specifically add so that each reaction or measurement we conduct is as reproducible as possible. After all, one would not bake an apple pie in a dish that was previously used to cook chicken wings without cleaning it. A surprisingly large amount of time doing chemistry is spent doing dishes.

Pictured above is the receptacle I use to store dirty chemistry dishes in. My system is to build up a metal bowl full of dishes before I pause to do them. I find this allows me to accomplish a fair amount before I need to stop, while also not hoarding too much glassware at once. I do have lab mates who will build up entire 20 L buckets (yes, several) full of dishes before they do theirs. For those guilty of doing this, I will only say the following: hoarding glassware is a good way to make your chemistry friends disappear.

The way everybody does their dishes varies from group to group, too. In my old research group, with which I did my Honours, we would first wash most visible residue off with appropriate solvents: often one of the fantastic foursome of water, ethanol, acetone or methanol. For some glassware, this would be good enough, and after drying, the glassware would be ready to go. For glassware full of stubborn precipitates, we would dunk them in the base bath (made from mixing potassium hydroxide and isopropanol; the “recipe” for base baths also varies from group to group) overnight. Rinsing with copious amounts of water and drying would then leave the glassware good as new — except for the fact that base baths work by dissolving a layer of glass. Any glassware should not be left in the base bath for extended periods of time. Additionally, glassware susceptible to fracturing or implosion should be dealt carefully when washed in the base bath repeatedly.

The group I did undergraduate work with dealt with sensitive rare earth chemistry as opposed to the largely aqueous metallosupramolecular chemistry I did in my Honours and do now. As such, our wash-up regimen was a bit more rigorous, too. Before glassware was left in the base bath, it would be dunked in an acid bath overnight. I would tell you what it was composed of, but I realise now I never bothered to find out. I suspect it was a solution of hydrochloric acid of some concentration. The rationale was, I believe, that the acid bath would dissolve any metal residues left on the glassware, while the base bath would resolve any organic residues. The base bath was followed by a rinse with first water and then acetone, followed by drying in an oven for at least 24 h, due to the water-sensitive nature of our chemistry.

My current group has deemed the corrosive, flammable base baths an unnecessary hazard for the work we do. For thorough cleaning, we use a detergent and hot water, followed by ethanol if some residue happens not to be entirely water-soluble. To someone used to using base baths to clean stubborn glassware, I have found this method surprisingly effective and safe, comparatively. We let our glassware drip-dry overnight, and then it will be good to go again. Very occasionally, some glassware will require more rigorous cleaning — such as glass frits used for compounds insoluble in common solvents. But I would not say this is often the case.

The way we clean our dishes definitely depends on the kind of chemistry that we do. For sensitive chemistry, more rigorous regimens are required. For less sensitive chemistry, the risks and hazards of those rigorous regimens may outweigh any gain. All groups have their own tips and tricks — we could certainly learn from each other here. If you are a chemist, weigh in: how do your dishwashing procedures vary from the ones I’ve learnt?

You can reach me in the comments, by my Twitter account @Lady_Beaker or by e-mail, at chemistryintersection@gmail.com.

Choosing chemistry

There are several reasons people choose to do certain things with their lives, I think. Reasons, such as enjoying the company of people who also do this thing. Being naturally talented at that thing, or being gifted at several skills suitable to that particular course in life, are popular reasons to choose one thing over another. Enjoyment, an excellent motivator for choice, often follows naturally from success due to one’s talents, but may follow from any number of human experiences. A more difficult to grasp incentive is the feeling of fulfilment over one’s life choices. For science in particular, some people may be driven by a desire to discover, a profound curiosity in the world around us, or a simple need to understand. A love for problem-solving is certainly a great motivator for the pursuit of science.

For me, choosing chemistry was a mixture of many of the reasons above. Raised by two scientists, my curiosity in the world was encouraged and liberally fed through my childhood. Talented at school, I was spurred on by the praise of teachers and sparkling grades. My chemistry teachers were uniformly excellent throughout my school years — talented at teaching and earnestly enthusiastic about their subject matter. In high school, my delight at solving the puzzle-like problems in chemistry class was what really kept me enjoying the subject. High school was where love for chemistry truly took root in my heart, I think. Those last years were when my teacher first began talking about chemistry in more than abstract terms. I learnt how to draw molecules, paving way to an ability to visualise chemicals. I learnt how to count molecules, mathematically, through a concept known as the “mole.” Through these relatively simple concepts, and many others, chemistry became a tangible thing in the world around me. And I was in love.

Some chemists like to call chemistry the “central science,” with respect to the three well-established scientific fields of biology, chemistry and physics. Physics deals with energy, and biology deals with life. Chemistry deals with matter, which is everything that is physical, tangible — real, if you will. As a science of matter, chemistry bridges physics and biology, and, because matter is ubiquitous, is arguably important to the study of both. I will leave antimatter to the physicists, though.

I take great delight in looking around me, knowing that everything I see is made of atoms and molecules. Everything around me is chemistry. Everything “natural,” like grass and trees and people, and everything synthetic, like my phone, computer, my eyeglasses — they are all a part of chemistry. As I learn more about chemistry, I learn more about the building blocks of everything around me. To me, that is infinitely exciting, fulfilling and beautiful. Learning and doing chemistry makes me feel somehow more deeply connected to the world around me. It is a feeling which keeps me passionate and excited about chemistry — and more than that, it makes me want to share that feeling.

It is heartbreaking to me how negative the current public image of chemistry is. Consider how even the term “chemical” is perceived. It evokes an instant vision of smoking chimneys, car exhausts and bottles of poisonous cleaning agents. While I wish to dispel this misconception of chemicals, at the very core of it, I want to show you, the reader, something beautiful and exciting. I am writing this to spread the joy of chemistry.

Welcome to Chemistry Intersection.

If you wish to contact me, e-mail me at chemistryintersection@gmail.com. Follow my twitter account @Lady_Beaker for tweets in the daily life of a PhD student in chemistry.