What’s on my lab bench?

Most people have a desk as a place of work. I’m lucky enough to have three workspaces as a chemist: my desk, my lab bench, and my fume hood, all for different aspects of chemistry research. Today I’m going to give you a tour around my lab bench!

labelled lab bench.png
Picture caption: Fiona’s busy lab bench with different items labeled, from the sink to the sample vials!

My lab bench is used to carry out low-risk tasks involving my chemical samples. Most of the work I do when handling and manipulating my reactions is carried out in a fume hood to reduce my exposure to them but small analytical tests and sample preparation can b carried out on a bench – unless my sample is particularly smelly which thankfully not many of my compounds are!

I share a sink with another chemist in my lab where we wash up our glassware. We’re a bit like a student flat in that neither of us like putting the glassware away in the cupboards so take stuff directly from the drying rack which can turn into a mountain of conical flasks and beakers sometimes!

While I use an electronic lab book for my final write-ups, I keep a rough note of what I’m doing for each experiment in these blue and while notebooks and transfer it to the ELN at the end of the experiment. If I had to grab one thing in the event of a fire, it would be these notebooks as everything else I do is digitally backed up!

I keep final products in these sample vials before transferring them to smaller ones for archive storage about once a quarter. I draw the chemical structure on the yellow circular labels to help me find samples quickly. I try to keep my samples in chronological order but it doesn’t always happen so you’ll often find me hovering over these boxes trying to find vial such and such.

Although the picture doesn’t show it too well, I have to boxes of glass pipettes on my side of the bench, individual disposable glass droppers. I have a rubber atomiser that I attach to them when I need to transfer small quantities of liquid between flasks etc. and then the glass pipette gets recycled. We have two lengths of pipette and I seem to get through the shorter ones a lot quicker than the longer ones.

The tip-ex isn’t actually for correcting written mistakes in my notebooks – I tend to just scribble. I actually use it to mark sample lids so I can differentiate them as my own from my colleagues when using shared equipment. Our group has to use black lids for our NMR tubes so I found it a simple way to identify my samples from the dozens than go on the NMR instrument carousel.

I use a ruler for drawing straight lines on my TLC plates and for measuring the distance between spots once I’ve run TLC experiments (see my How do I know I’ve made the right molecule post).

The small tubes in the little beaker are how we store samples long term. They’re obviously a lot smaller than the glass vials and we typically have less than 0.1 g of a sample left after using what we need for future chemistry. We also use these tubes for transporting samples because they have individual bar codes on them. These are six compounds that I’ve taken out of archive storage for my colleague in biology to come to get whenever she needs them.

The conical flask on my desk contains empty NMR tubes, long skinny glass tubes used to prepare a sample for a particular type of analysis that investigates the magnetic character of the compounds – again see my previous post for more detail. The tubes are capped with the black lids I cover in Tipex.

I don’t keep many chemicals on my desk but these two are for a public engagement activity I’m doing with schools soon and so because they weren’t bought using the group’s research budget, need to be stored separately from the other chemicals I use, which are typically stored under my fume hood or in one of our several filing cabinets.

A calculator is a chemist’s best friend for double checking sample dilution factors and scaling reactions up to bigger quantities (like doubling a recipe). My electronic lab book does a lot of calculations for me but there are always some that need to be done manually like converting concentrations units from % to molar etc.

I hold on to my NMR samples until I’ve definitely got everything I need to write-up an experiment. Cleaning these tubes out isn’t the most fun job in the world so I tend to wait until I have a lot of tubes to clean before the repetitive task of rinsing them out.

My colleague and I share a number of things on our bench like sample vials and empty plastic columns for purification. We try to keep them topped up for each other.

Every chemist needs gloves for handling chemicals. I try to not get through more than a couple of pairs of gloves a day having mastered the technique of removing them in such a way that they can be worn again if I know I’ve been particularly careful and not got much on them.

My green tray has samples ready for being archived. I got this from a colleague who was leaving and it’s the perfect size for storing out mini sample vials. Scientists are a bit like vultures when they know there’s a free for all during a lab clearout or someone moves job, we become quite territorial about our pieces of lab kit.

My cardboard box has random bits and pieces in it like pencils and stickers for my lab vials.

I also have a mountain of plastic rings for storing round-bottomed flasks – spherical pieces of glassware that as you can tell by the name don’t stand up very well on their own.

Sometimes I get deliveries in the post in boxes that I bring into the lab. This tiny box was the perfect size for storing my TLC plates.

The laminated sheets are for writing the reaction schemes for what’s going on in my hood if I’m leaving a reaction on overnight. It allows colleagues and security to check a reaction is running at the temperature it is supposed to and hasn’t randomly heated up or cooled down overnight.

Lastly comes my vacuum pump which is attached to my rotary evaporator. My rotary evaporator, or “Buchi” as they’re named after one particular brand that makes them, is a bit like a kettle.  Attach round-bottomed flasks to it and boil off liquid solvents that I’ve dispersed my reaction in. The vacuum pump allows me to boil te solvents off at much lower temperatures than usual.

You may know about the phenomenon where water boils at a lower temperature at the top of Everest due to the reduced air pressure. My Buchi takes this to the nth degree by creating a vacuum and can actually boil water off at 40 °C! The samples sit in the water bath which is warmed to my desired temperature and rotates to maximise even distribution and mixing of my reaction mixture while also creating a thin film of solvent which then evaporates more easily.

The shelf above my bench contains frequently used chemicals for reaction work-ups/purifications. It includes various acids, bases, substances for removing water, stuff for preparing columns and my NMR solvents. We also have parafilm, a bit like clingfilm, used to seal vials and chemical bottles to stop samples or reagents from going off.

I hope you’ve enjoyed my lab bench tour. Stay tuned for future posts about my desk and fume hood.

What’s your working space like? Let me know in the comment below.

#postitperiodictable Group 2

The second column elements of the periodic table are known as the alkali earth metals. They are like group 1 in that they are relatively soft metals that react with water to produce hydrogen gas however they don’t react as vigorously.

Picture caption: post-it note showing beryllium, element number 4, is used to make springs in electronics

This is due to the group 2 elements having 2 outer electrons instead of one. This is a slightly more energetically favourable electron configuration, meaning the atoms in group 2 are happier with two electrons whizzing around the nucleus than group 1 metals are with their single electron, who just want to give it away as quickly as possible to form their preferred state as a positive metal ion (M+, where M stands for a metal).

Picture caption: post-it note showing magnesium, element number 12, plays an important role in photosynthesis, the process by which plants use light energy to convert carbon dioxide and water into glucose and oxygen gas – the reverse of what our bodies do.

Group 2 metals aren’t precious about their two electrons though. They are also happy to exist as positive metal ions that have lost their negatively charged electrons, but they tend to form M2+. If they formed M+ they would then have a similar electron configuration to a group 1 element which we know isn’t very stable and would get rid of that second electron as quickly as they can.

Picture caption: post-it note showing calcium, element number 20, which makes up a significant component of our bones

This relatively lower reactivity means that group 2 elements are often used in portable hydrogen generators because they release hydrogen slowly enough that there isn’t sufficient heat energy given out over the course of the reaction to ignite the flammable hydrogen gas – which is what we see when group 1 metals react with water.

Group two metals are shiny and usually silvery-white in colour. Some occur naturally as free elements but are often found as ores (typically metal oxides) in the ground and the metal needs to be extracted from those compound mixtures.

Picture caption: post-it note showing strontium, element number 38, which is used to make fireworks appear red in colour

Much like Group 1 the reactivity of the metals increases going down the group because the outer electrons become further away from the nucleus with the increasing number of electrons moving around the nucleus, making them easier to remove – much like how a paperclip becomes easier to manipulate the further away it is from a magnet.

The metals react with water to form metal oxides but because of their 2-electron valency, they form hydroxides with the general formula M(OH)2 as hydroxide (OH) ions have a single negative charge so two are needed to balance the double positive metal ion (M2+). Beryllium is the exception which has a sufficiently protective oxide layer.

Picture caption: post-it note showing barium, element number 56, rarely used but can be found in some paints

They also react with oxygen to form metal oxides and with halogens, such as chlorine, fluorine etc., to form metal halides.

Throughout group 2 we’ve learned about beryllium’s niche role in missiles and rocket parts; the bright light burning magnesium produces which is used in old photography flashes, flares and fireworks; calcium’s key role in forming our bones and teeth and how strontium can be used to mimic calcium to treat osteoporosis; and the lesser used barium and radium which are used for treating digestive disorders and prostate cancer respectively.

Picture caption: post-it note showing radium, element number 88, which used to be used to be painted onto watches to make components glow in the dark

I hope you’ve enjoyed our tour of group 2. Now we move on to the central block of the periodic table, known as the transition elements which spans groups 3 to 10! Keep an eye on the Instagram account for individual posts about each element as well as other content about my life in the chemistry lab.

What’s your favourite element? How are you marking #IYPT2019 ? Let me know in the comments below.

 

What do the numbers on the periodic table mean?

2019 marks the UN’s International Year of the Periodic Table or #IYPT. It’s 150 years since Dmitri Mendeleev presented his organisation of chemical elements to the world. The periodic table is used daily by chemists and other scientists as reference resource for the ingredients of the universe.

dmitri mendeleev statue dmitrimendeleev.com
Picture caption: A statue commemorating Dmitri Mendeleev surrounding by a radial presentation of his periodic table, in source: dmitrimendeleev.com

Ancient Greeks defined “elements” as one of the following four: earth, fire, water and air. They were used to explain how matter worked. Since the elucidation of atomic theory, scientists have broken the universe down into 118 chemical elements.

the four elements learner.org
Picture caption: the four classical elements and the descriptors used to classify them. Source: learner.org

Atoms can be thought of as small particles that make up everything but even they are made up of smaller components, known as sub-atomic particles, and the number of sub-atomic particles in each atoms defines what element the atom is. The three sub-atomic particles we learn about at school are protons, neutrons and electrons. Protons, neutrons and electrons are made up of even smaller components but as I am not a physicist, I’m not so concerned about looking at matter at that scale.

atomic structure explainthatstuff.com
Picture caption: the structure of an atom – a central nucleus made up of protons and neutrons surrounded by fast moving electrons. Source: explainthatstuff.com

Protons are positively charged, electrons are negatively charged and neutrons, as you might guess from its name, are neutral. The number of protons and electrons in a neutral atom are the same in order to balance the charge. An atom’s structure is made up of a central nucleus made up of protons and neutrons with electrons whizzing around the nucleus.

Because the electrons are on the exterior of the atom they are the particles that are actually involved in chemical reactions. Electrons can be completely transferred from one atom to another – in a process known as ionisation which forms ions, charged atoms – or they can be shared between two atoms to form a chemical bond. The degree of sharing between two atoms dictates what type of chemical bond has formed.

bonding weheartit.com
Picture caption: cartoon depicting the different ways atoms share valence electrons to form chemical bonds. In a covalent bond electrons are share fairly equally between atoms; in metallic bonds the electrons are not associated with specific atoms; in an ionic bond one atom loses an electron for another to gain that electron and a coordinate bond occurs when an atom donated two electrons to another atom. Source: pearlsofrawnerdism.com

Most of an atom is made up of empty space: if an atom were the size of a football stadium the nucleus would probably only take up the space of a marble sitting in the centre of the playing ground!

A standard periodic table will usually have 2 elements associated with each element: the atomic number and relative atomic mass number of that element. The atomic number can be defined as the number of protons present in the central nucleus of the element’s atom while the mass number is the total number of protons and neutrons in the nucleus. The mass number is the larger of the two numbers found associated with an element in the table.

The mass number can be quantified by a constant (a number that is shown to stay the same across numerous calculations) called Avogadro’s number. Avogadro’s number is 6.02 x 10^23. Essentially, what Avogadro’s number describes is the number of atoms you need of a particular element for the weight of your sample to match the mass number in grams.

A single unit of 6.02 x 10^23 atoms is described as a “mole”. It’s a bit like saying you have “a dozen” eggs = 12 eggs. A “mole” of atoms is 6.02 x 10^23 atoms which, if your element is carbon, would equal 12 g because 12 is the mass number of carbon.

moles hinkhousescience.com
Picture caption: a happy cartoon mole placing 6.02*10^23 carbon atoms on a scale to make 12 g of carbon (aka one mole!) credit: hinkhousescience.weebly.com

The number of neutrons does not correlate perfectly with the number of protons, its more to do with the number of neutrons required to allow that number of protons to be in close proximity with each other while maintaining stability – imagine trying to force two magnets together. They repel, much like the positively charged protons do if they get too close together.

The presence of protons in the nucleus makes the nucleus overall positively charged and the electrons whizz around within the proximity of the nucleus because they, as negatively charged particles, are attracted to that positively charged nucleus.

As an element gets bigger – with more and more protons, neutrons and electrons packed into its structure – its properties change. The smaller elements at the top of the periodic table are gases like hydrogen (atomic number 1), helium (atomic number 2) and oxygen (atomic number 6) while the heavier elements towards the bottom of the table are metals like gold (atomic number 79), lead (atomic umber 82) and uranium (atomic number 92).

phases pt periodictable.com
Picture caption: periodic table coloured according to the phase (solid, liquid, gas) an element exists in at room temperature. Most elements are solid, coloured red; some gas (blue) and only two are liquid, bromine and mercury. Source: periodictable.com

Mendeleev chose to arrange the elements by atomic number rather than mass number and very cleverly left gaps because at the time there were only 56 known elements. He was successfully able to predict the properties of the yet undiscovered elements, such as germanium, gallium and scandium.

There are other periodic tables that have additional information on them such as the size of atoms, density of elements and melting points. Trends can be seen as you go along the rows and columns of the periodic table, which I may discuss in further detail in a future post. But normally the most basic ones have the atomic and mass numbers of each element on them, as well as the symbol used to abbreviate the element’s name.

desnity pt periodictabloe.com
Picture caption: Graphic showing the increasing density of the elements going down the periodic table and also peaking in the middle of the table going left to right. Source: periodictable.com

On my Instagram and twitter account I will be posting about each element over the course of this year and will summarise each column of the periodic table in a longer blog post here. I hope you enjoy exploring the periodic table with me this year along with everyone else marking #IYPT as we learn about the stuff that makes us and everything around us.

Did you learn about the periodic table at school? Do you have a favourite element? Let me know in the comments below.