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!

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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.

Reflections on second year

shallow focus photography of yellow star lanterns
Photo by 嘉淇 徐 on Pexels.com

This is my last week in the lab of 2018. It’s only really four days because we’re having our group’s Christmas party on Friday (laser quest and pub lunch) and then I’m at a conference on Monday before taking the rest of the week off before Christmas.

Towards the end of first year I wrote this post about how I thought first year had gone and I listed 5 things I wanted to change. In this post I’m going to see how I did with those goals and create 5 new goals for third year.

  1. Read more papers – I managed this one quite well. In first year I sporadically printed and read papers but this year I got organised and set up an RSS feed and have been pretty good at checking in with it most days – perhaps a little too often with my “inbox zero” tendencies. I use Mendeley to save anything I come across that might be useful for my project. I tried #365papers  and failed miserably though, partly due to me losing the spreadsheet I was keeping track of papers on in an IT nightmare but also me just not getting into a habit.
  2. Make more compounds – I certainly achieved this one. First year involved trying a lot of new chemistry and at the start of this year I optimised a lot of that chemistry making it far easier to get final compounds out. For example, one set of molecules I made last year took 8-9 separate reactions to get there and now with a small change to the chemical structure that I’ve learned doesn’t kill the activity of the drug in most cases, I can get to those compounds in 2-3 steps.
  3. Be more selective in the seminars I attend – In first year I felt I had to go to every single seminar to widen my knowledge but as you specialise you learn what interests you and what a good use of your time is. I still go to the odd seminar outside of my research area so I’m not in too much of a rabbit hole, but I certainly feel like I’ve been using my time a bit better when it comes to seminars.
  4. Attend more conferences – having only been to one conference in first year, I went to a few in 2018 – and still have one to go next week! I started the year by attending the Genome Stability Network Meeting in Cambridge in January, in March I went to the RSC-BMCS Mastering MedChem conference at University of Strathclyde in Glasgow, then RSC/SCI Kinase 2018 in May, again in Cambridge, and still have the RSC Biotechnology Group Chemical Tools in Systems Biology in London a week today.
  5. Use this blog more – this one I’ve technically achieved in the last month or so. Most of the year I found myself “procrasti-blogging” sporadically blogging if I was taking part in a science writing course where an assignment involved writing a blog or the Google Doodle of the day was linked to chemistry. Now I’m making a concerted effort to post regularly on here and also on my dedicated Instagram account.

I think I’ve done quite well in meeting all of those goals. They were fairly realistic goals without quantification. Now here are my goals for third year:

  1. Keep using this blog – weekly blog posts, a couple of Instagram stories/posts a week. Over Christmas I’m going to make a longer term plan for content and schedule as many posts as I can so it doesn’t take up too much of my time during term time. Let me know if there’s anything in particular you’d like to see.
  2. Get the desk/bench balance right – I continue to struggle with staying at my desk more often than being in the lab. Often I choose reading, agonising over lab book/write-up and writing off lab tasks to “tomorrow” that could be done today rather than making stuff in the lab. If anyone has any tips about this please let me know in the comments.
  3. Get something published – I have something to show for my research and I really want to get some of it published in a medicinal journal to show alongside my thesis at the end of the PhD. I’m waiting for some long-promised data from a collaborator which will help supplement my work but I’ve agreed with my supervisor that in February I need to start writing papers for publication without that research.
  4. Speak at a conference – similar to above, I have a sufficient story to tell that I would love to give a talk about just once about my research at a conference rather than just standing beside a research poster at said conferences where people may or may not come over to hear about it. I’d also like to go to a conference outside of the UK because travel is one of the perks of being in research.
  5. Finish the practical side of the project well – I plan to spend another year in the lab before writing up. I have until March 2020 technically but I’m leaving those three months as a “backstop” of sorts – #relevant. I have in my head I’d like to get to 100 final compounds for my thesis (I’m about two thirds of the way there so it seems tangible) and I’d also like to spend some time in the biology labs my group have testing some of those compounds.

Hopefully this time next year I’ll be writing a similar post about how well I did in achieving my third year goals. It’s crazy it’s got to my last year in lab already!

Did you make any goals/resolutions for 2018? Did you achieve them? If not, are you going to reattempt them in 2019? Let me know in the comments below.