Chemistry – The Chemistry of a PhD

March 29, 2019March 25, 2019

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.

January 14, 2019

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.

December 3, 2018December 3, 2018

My Placement Year in Switzerland

Increasingly, universities are offering integrated masters science degrees over bachelor degrees. These normally include an additional year of study and/or a placement year in industry or an academic research group. In this post I’ll tell you about the science I did on my placement in Switzerland and how it is linked to a major drug approval that happened a few months ago.

During my MChem placement year (2014/2015) at University of Strathclyde I worked as a Research and Development (R&D) intern for Corden Pharma Switzerland (CPS). They are a Contract Manufacturing Company of different Active Pharmaceutical Ingredients (APIs), Drug Products and Packaging Services. This means they produce various chemical products for pharmaceutical application for lots of different company clients.

CPSlogo — Picture caption: Corden Pharma logo with slogan “Experts taking care” Source: cordenpharma.com

The APIs produced at the CPS facility fall into a few categories: carbohydrates, lipids, peptides and other small molecules. At the start of my year there I worked on a short carbohydrate project where I produced a sugar-like compound for a big pharma client.

I spent the rest of my time working on a small molecule project for a slightly smaller company client. As part of a team of a few chemists I helped to make a large lipid-like molecule that helps deliver corrective pieces of nucleic acid into cells to treat genetically-linked diseases. This type of treatment is known as RNA interference (RNAi).

You may have heard of DNA, deoxyribose nucleic acid, a long double stranded molecule made up of individual nucleotides that contain the instruction manual for everything in our cells. There is another type of nucleic acid in the body called RNA, ribose nucleic acid. It possesses some structural differences to DNA such as the type of sugars and bases in the molecule and it exists as a single strand instead of a double strand.

DNA RNA — Picture caption: An partially unwound DNA molecule interacting with a single strand of mRNA. Source: Microsoft clipart

When a cell wants to carry out a particular function, the piece of DNA that codes for the protein that carries out that job is unwound by helicase enzymes. A temporary copy of that portion of DNA is made by RNA. This process is known as transcription.

This newly formed “messenger RNA” (mRNA) leaves the cell nucleus – the central region of the cell where DNA is stored – and travels to a ribosome that reads the instructions from the mRNA and builds the desired protein out of amino acids. Translation is the name given to this process.

protein translation — Picture caption: A green large green ribosome protein interacting with the RNA strand and building a new protein molecule. Blue tRNA molecules bring individual amino acids to the ribosome for building the protein. Source: clipart-library.com

But what if the protein being coded for is a harmful protein that leads to a disease symptom? The theory behind RNAi is that you can send foreign copies of RNA into cells to tell a ribosome to stop producing a particular protein.

These RNAs can tell the ribosome to stop making protein because they are complementary (similar in structure) to the original RNAs and so they bind together like a zip. This so-called interference could be used to treat diseases that are known to be caused by certain genes. Alnylam Pharmaceuticals have a great video that explains the science here.

RNAi won the 2006 Nobel Prize in Physiology/Medicine. It was awarded to Andrew Z. Fire and Craig C. Mello for successfully silencing a muscle gene in roundworms by injecting complementary RNA strands.

RNAi roundowrms — Picture caption: comparison of three green roundworms before and after treatment by RNA. Source: nobelprize.org

Their work showed that RNAi exists naturally in the body to regulate production of all proteins and can be done synthetically. The technique is now used by biologists around the world to shut down certain genes in cells and see the effect that it has. Researchers have also been trying to utilise it for medical use by giving patients complementary RNAs for disease-relevant proteins.

However, the body is usually very good at knowing where things should be in the body so it doesn’t expect to find bits of RNA outside of cells, e.g. in the bloodstream where most drugs end up.

The molecule I helped to make on my project allowed the attachment of these corrective RNAs to a big lipid. These big lipids then form nanoparticles (tiny bubbles) around the RNAs that help smuggle the RNAs across the cell membrane and into the cell where they can interact with ribosomes and shut down the production of harmful proteins.

I’m not allowed to tell you specifically how I made the molecule or what it looks like due to the confidentiality agreement I signed at the start of my placement year but it was wonderful to hear in August that the first RNAi therapy using this sort of chemistry was approved by the US Food and Drug Administration (FDA).

The treatment that was approved is called Patisiran (marketed as Onpattro by Alnylam Pharmaceuticals who developed it) and contains RNA strands that halt the formation of a protein called transthyretin. Transthyretin production leads to the symptoms of a genetic disorder called hereditary transthyretin (hATTR) amyloidosis. This is a rare disease where some 50,000 patients a year experience nerve damage due to the clumping of overproduced transthyretin.

Alnylam’s website says 51% of patients treated with Onpattro “experienced improvement in quality of life at 18 months” compared to 10% of patients who were treated with a placebo. This first-in-line treatment means that now one disease can be safely treated this way it might be possible to treat other genetically-linked diseases using RNAi.

It was really cool to see the science my project being approved as a new type of treatment which will hopefully pave the way for future RNAi therapies. While at times I was frustrated with the tricky chemistry I was doing on placement, I’ve been reminded by this approval that sometimes the goal of helping patients is met, which makes it worthwhile.

fiona matterhorn — Picture caption: Fiona in winter clothing standing in front of the famous triangular shaped Matterhorn mountain in snowy Zermatt, Switzerland.

Outside of the lab I enjoyed sampling different Swiss cheese and chocolate and travelling around the country on their first-class public transport system as well as further afield. While the country is very expensive, it’s a beautiful place to live with the Alps and picturesque old towns. I enjoyed being back last weekend and showing my friend Emily around – check out my Instagram for a post about her job as a consultant process engineer.

I learned a lot of chemistry (and Swiss German) on my placement and would thoroughly recommend taking any opportunity to gain industrial experience during your degree to give a taste of what life as a scientist is like.

Have you come across RNAi? Does it seem like a viable way to treat diseases? Have you visited Switzerland? Let me know in the comments below.

I kept a photo-a-day blog on blipfoto during my time in Switzerland and wrote a few blog posts about living en Suisse, one of which was reposted on globalgraduates.com.

November 26, 2018November 26, 2018

Chemistry PhD: A Day in the Life

I find people’s routines really interesting. Everybody’s different. Some people are early birds while others are night owls. Some people work long hours and others manage to fit a lot of work into a short period of time. In this post I chat about what a typical day looks like for me and the various things I get involved with both inside and outside of the lab as a PhD student.

Picture caption: Fiona in a lab coat taking a selfie in the chemistry lab.

Day in the life:

0630: My alarm goes off. More often than not I press the snooze button for a little while.

0630-0700: If I’m sufficiently awake I go for a run then get ready for uni. I’m currently training for the Brighton Half Marathon at the end of February next year.

0815: Get the bus to campus.

0845-0900: Depending on how the buses are, get into the office, check e-mail and RSS feeds.

MORNING: I spend the morning either at my desk doing data analysis or in the lab running experiments.

1200: I eat lunch with colleagues. I usually bring a packed lunch but occasionally I treat myself to lunch at one of the university cafes.

AFTERNOON: I usually have a bit of an energy slump after lunch so I switch to low-brain-power tasks e.g. running TLCs in the lab or writing up analysis.

1600: I usually kick back into gear at this time of the day so I will have a burst of activity in the lab or at my desk.

1800-1830: leave office

Evenings: I don’t tend to do work on my PhD when I’m not on campus. In the evenings I’m either chilling at home, going along to something at my church or going to review something at the theatre.

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This is what a typical day where I have nothing in the calendar looks like. There are other things that pop up throughout the week which mixes things up. I generally prefer days when I have a meeting or two in the calendar. This is because it makes me more productive with my time because in my head I’m thinking “I have to get this done by X because of Y”. Below are some other things that are typical of chemistry PhD life outside of doing experiments:

Cleaning the Lab

Picture caption: a set of super sensitive scales, known as a balance, reading 0.0000 g.

While everyone in my lab has responsibility for their own lab space, we have a rota for cleaning the communal areas of the lab. This involves checking our balances don’t have residual chemicals on them; cleaning up the TLC plate area; and checking our communal rotary evaporator for removing toxic/smelly substances has been cleaned.

Solvent Run

In a lab capable of up to nine chemists working in it at once, we get through a lot of chemicals, especially solvents! Solvents are the liquids we run our reactions in. Sometimes its water but its usually an organic solvent such as dichloromethane, tetrahydrofuan or an alcohol. We take it in turns to check our communal solvent stocks in the lab and top them up from the school’s central store as needed.

Picture caption: multiple plastic bottles with different coloured lids containing different solvents.

Supervisor 1-2-1s

About once a week I sit down with my lab supervisor to review the chemistry and other work I’ve done, troubleshoot any problems I’m having and I propose what I plan to do next. About once a month I give a slightly “bigger picture” version of this project update to my main PhD supervisor. This helps me to build up a record of what I do on a weekly/monthly basis and gain input on my project from people with more experience than me.

Teaching

PhD students can undertake casual work with at my university to earn extra money. So far I have demonstrated in undergraduate labs – walk around and make sure everyone is carrying out their experiments safely and helping with any issues they have; invigilated exams; marked exam papers and taught tutorials and workshops for undergraduate chemistry/life science courses.

Attend lectures/seminars

As I am undertaking a research postgraduate degree instead of a taught one I don’t have any mandatory classes as part of my course. That doesn’t mean I can’t take advantage of the learning that’s happening around me on campus. Last year I attended a module called Fundamental Cancer Biology which helped me to consolidate what I’d learned about the biology side of cancer from my own personal reading which I found very helpful.

The life science school puts on a number of seminars that are mainly geared towards postgraduate students and research staff. While the term “seminar” can mean different things, in Sussex’s School of Life Science this session is usually an hour long where an in-house/invited speaker talks for about 45 minutes about their research followed by questions. It tends to be a very applied talk with only general concepts covered in the first few minutes. I enjoy seminars because you get the chance to learn about all kinds of research outside of your own.

Conferences

A few times a year I go to conferences. These are 1-3 day events where researchers in academia/industry meet in a specific location to hear talks about research around a specific area. I’ve been to conferences about medicinal chemistry, genome stability, the specific class of drug target I’m working on, and more! There’s a conference for everyone.

Picture: Fiona giving a presentation at the RSC Kinase 2018 conference. A single slide summarises my PhD project with diagrams of chemical structures and biological processes.

While I haven’t had the chance to go abroad yet I’ve been to conferences on my own campus and in Glasgow, Cambridge and London so far. I sometimes take a poster summarising my research and am now applying to talk at some conferences now that I’m later on in my PhD. They’re a good opportunity to network and catch-up with people from my field of research.

Public Engagement

It is becoming increasingly common that researchers are required to demonstrate the impact their research has on society by communicating that research to the public. I’ll do a separate post about the various public engagement activities I’ve been involved in another time but very briefly, from time to time I take part in science fairs, schools events at the university and sometimes go into schools to talk about chemistry.

liquidnitrogenPACA — Picture caption: Fiona pouring liquid nitrogen onto the floor, creating a large fog, as part of a public engagement show about chemistry at a school

***

Juggling these things requires a lot of time management which I have varying levels of success at doing. I like that there’s a lot of variety in my work but primarily the goal of my PhD is to spend time in a lab making molecules. The other things give me a change of scene and enable me to develop other skills that will be useful for whatever job I do after my degree.

What does your typical working day look like? Is there an established routine or is every day different? Let me know in the comments below.

November 19, 2018November 19, 2018

How do I know I’ve made the right molecule?

I spend my days in a chemistry lab making drug-like molecules. A lot of these end up being small quantities (less than 0.1 g!) and usually have the appearance of a white/off-white powder. Occasionally I get a colour which is very exciting.

Picture caption: stacked boxes of sample bottles of ca. 40 different chemical products I’ve made in the last few months

The question a non-chemist might ask is “how do you know you’ve made the product”? Lots of different analytical techniques have been developed over decades to help chemists determine the chemical structure of the products they’ve made.

In this post I will give you an introduction to the seven analytical techniques I carry out on my samples to prove I have made the right molecule. These various bits of data go in my experimental write up which will make up a large chunk of my thesis.

1) LCMS

LCMS stands for Liquid Chromatography Mass Spectrometry. This combines two techniques: liquid chromatography allows to you separate a mixture into its components while mass spectrometry will tell you the molecular weight of each of those components.

Picture caption: A large grey boxed machine on a lab bench. This is our LCMS instrument in the lab.

Ideally the read off of a pure sample will just show that there’s one component in your mixture and the molecular weight from the mass spec will match the calculated weight of your product (i.e. the number you get when you add up the molecular weights of the individual nitrogen, carbon, oxygen, hydrogen etc. atoms).

2) 1H NMR

NMR stands for nuclear magnetic resonance. There are many different “flavours” of NMR. Proton NMR (written as “1H”) looks at the different hydrogen atoms present in a molecule and the different environments they’re in.

Picture caption: The blue door that leads to the NMR lab with safety signs warning about strong magnetic fields.

For example, some protons will be attached to carbon atoms, while others will be attached to nitrogen atoms. This means they will have a different “magnetic environment” due to the different number of electrons in different atoms and how they’re distributed between different atoms and chemical bonds.

Below is an NMR spectrum for ethanol, the type of alcohol found in alcoholic beverages. There are three different proton environments in the molecule of ethanol: a hydrogen attached to an oxygen (blue); a hydrogen attached to a carbon that’s attached to a carbon and an oxygen (green); and a hydrogen that’s attached to a carbon that’s attached to another carbon (red).

ethanolnmr — Picture caption: a graph with three sets of peaks/spikes corresponding to different hydrogen atoms found in ethanol (chemical structure of ethanol also shown).

The appearance of the peaks is affected by the number of nearby protons e.g. the CH3 peak is split into a triplet because there are two protons on the adjacent carbon atom. Undergraduate chemistry degrees have entire modules dedicated to interpreting NMR spectra, so I won’t go into too much detail here.

***

LCMS and 1H NMR are usually the minimum pieces of data you need to be sure you’ve made the right compound to move on with other chemistry. The two pieces of data combined give sufficient evidence that you’ve made something that weighs the same as the expected molecular weight; has the expected number of protons in the predicted magnetic environments to be the right products; and gives an indication of the purity of the compound.

For a PhD thesis you usually need to provide “full characterisation” for compounds which involves more analysis than those two techniques. I agreed with my supervisor that I would only get full analysis for final compounds that are to be tested by a biologist or compounds that don’t appear to have been made before by anyone else.

I determine if a compound is new by doing a literature database search and if zero hits come up in the search, I can assume no one has published the synthesis of this molecule before. I need to provide as much information as possible to prove it is the right compound. Below are 5 additional types of analysis I get on samples that fall into the final/unknown category.

***

3) HRMS

High resolution mass spectrometry is just a slightly higher quality version of LCMS. Having two mass spectrometry experiments that match up gives more concrete evidence about what the molecular weight of my chemical product is.

Picture caption: blue lab door leading to the mass spectrometry lab, covered in warning signs about high voltage and magnetic fields.

4) 13C NMR

13C NMR is like 1H NMR but it instead looks at the different environments of carbon atoms in a molecule. There are lots of different types of NMR experiment that are used depending on atoms are in your compounds e.g. fluorine, phosphorus. Going back to the ethanol example, I would expect to see two peaks in a 13C NMR spectrum of ethanol because there are two types of carbon atom present in the molecule.

Picture caption: a grey space ship like instrument in the centre of a room. This is one of the university’s NMR instruments that I run 1H and 13C NMR experiments on.

There are also different types of NMR experiment that combine different types of NMR e.g. COSY, NOESY, HSQC, HMBC etc. which I may talk about in another post some time.

5) IR spectroscopy

IR spectroscopy involves firing infrared radiation (IR) at your sample to determine what types of chemical bonds are present. Different chemical bonds have different energies and absorb and emit different levels of IR. An IR spectrum (see below) will tell me if I have C-H/C=O/C-N bonds present in my product, but not how many there are.

6) Melting Point

We know that ice melts at 0 °C. Similarly, different products will have characteristic temperature at which they change phase. Recording the melting point of a sample will allow a chemist making the same compound in the future to compare their melting point with yours. The melting point also gives an idea of how volatile a compound is i.e. how easily might it boil off into the atmosphere.

7) Rf value

The final type of analysis I get is an Rf value, which stands for retention factor. You may have carried out chromatography at school or a science fair, whereby you separate a mixture into its components by running a liquid through a medium such as filter paper.

I use a slightly more sophisticated version of this technique called thin layer chromatography (TLC) where I run a spot of my product up a silica plate. The Rf value is a ratio of the distance travelled by the spot of product divided by the distance travelled by the liquid.

Picture caption: small white silica plates with run TLC experiments on them. Lines and spots have been drawn on in pencil for samples that are not visible under normal light.

This gives an indication of how clean the product is (I’ll see multiple spots if there are any impurities). It also tells you how well the product dissolves in that particular liquid – it will travel further up the plate if it dissolves really well in the e.g. water that I run my TLC plate in.

There are other types of analysis beyond this set that I could also use but they are either excessive, time consuming or unnecessary for the type of molecules I make. I think of full characterisation as compiling as much evidence as possible to be sure I’ve made the right molecule, fitting various jigsaw puzzle pieces together to build up a concrete picture of what my product is.

Some of the techniques are qualitative rather than quantitative and aren’t necessarily as sophisticated as others e.g. IR just tells me I have a C-N bond present while NMR will tell me if there are protons attached to that nitrogen, how many, and what other protons/carbons they are close to.

Picture caption: a big pile of printed data to analyse on my desk, and an IR spectrum on the computer screen.

These seven types of data I get are the standard ones expected in most theses and journals, but it wasn’t always that way: in the 1960s chemists only had IR and MP techniques available whereas now ¹H NMR and mass spectrometry are the standard minimal analytical techniques, with MP and IR as added extras.

Last month a new analytical technique, called micro-electron diffraction, was published and generated a lot of excitement amongst chemists – on my Twitter feed at least! MicroED might save chemists a lot of time analysing compounds in the future by rapidly generating a 3D “X-ray skeleton” of the molecule using electron beams. This would save having to do all these other analyses.

For more information about different types of spectroscopy and analytical techniques used in chemistry, check out the resources below:

Does it surprise you how much analysis is done on one sample? What types of analyses do you use in your work to make sure a job has been done properly? Let me know in the comments below.