The Todd Group

This page contains information for current members of the Todd group. Click a section to expand.

Getting Started

The following is a checklist of key things to do and documents for new members of the group:

Get a LabArchives account for experimental write-ups (invite from Mat Todd)
Get a ChemInventory account for chemical inventory management (invite from postdoc)
Join the G25 MS Team (invite from postdoc), read through carefully Risk assessments and Standard Operating Procedures.
Get authorisation to use myFinance to order chemicals/etc. (ask Mat Todd and Fiona Marquet) The guide on ordering is here.
Organise and complete NMR training (see NMR facility manager, Nikita Harvey)
Organise and complete LCMS training (see senior group member/postdoc) – see below for guides on LCMS usage
Organise and complete the lab safety induction (see Eve Carter)
Familiarise yourself with Risk Assessment forms for conducting reactions (on MS Teams)
Complete the Out of Hours form (ask Justine Newson) and get it signed by Mat Todd
Complete safety training with Cory Beckwith
Complete online training (list of courses here for PhD students and here for staff, plus liquid nitrogen and gas cylinders if you will be in the lab)

Research Mentoring and Advice

Meetings and Reviews

All students have weekly meetings with Mat in the lab. We have weekly group meetings during semester. Everyone should play an active role in any online open meetings relevant to their projects. Your lab co-workers are all fantastic sources of inspiration and ideas. All of these help with reviewing your progress, thinking about your objectives and devising experiments.

It’s also important to have periodic strategy meetings where we examine the last few months’ work and set targets for the coming few months. The timings of these meetings are set, approximately, by UCL Research Log. For these meetings you should come prepared with a maximum of three Powerpoint slides covering:

1) Key achievements in the review period 2) Challenges/Roadblocks you’ve faced 3) Aims for the next period (these can include big new things, not just the logical, incremental things).

We’ll discuss these together and set aims you’re happy with. We’ll cover other things, such as

1) How to best structure your working day 2) Reading wider than your project 3) Writing up your data and thesis accurately 4) Preparing now for your career aims 5) How to make your project open source 6) Any other help or inputs you need to make your project fun, fascinating and productive.

Ways of Working

Everyone has different ways of working. There are few rules.

Some people like the early morning, some people are night owls. Some people enjoy long hours, some people don’t. I’ve seen people put in long hours and get little done, and I’ve seen people do short, regimented hours (for example because of caring responsibilities) and be extraordinarily focussed and productive. I will never check on your hours, but it’s my job to check on what you’ve achieved and what you’ve thought about in a given timeframe. There are some general things that can be said about working hours:

1) Lots of people have found that it can be productive to come in to lab and get an experiment going first thing, so that it can be doing its magic while you’re doing everything else you need to do, and so that the experiment can be monitored during the day and action taken (like a workup/column) the same day. If you find you’re coming in to lab and immediately starting to think about lunch, you might want to change something.

2) You should keep re-examining whether your working day is working for you. Are you in a good place with your schedule, or might you need to re-examine? It can be easy to get stuck in a rut if you’re not careful. Mix things up.

3) You have access to a real-life science lab! Of the kind that maybe you dreamed about when you were little. It’s really amazing. You can do novel science any day of the week. You can run experiments of your own design. You, with your own hands, can make molecules that have never existed in the universe before. You can answer fundamental scientific questions all on your own. Don’t take this for granted. Before you know it, your project will be over and you may never again have such freedom. Use the time you have as fully as you can before it’s over.

4) The lab is a communal place. It works best by people sharing expertise, papers and ideas. This happens best in person, not on WhatsApp. This means that it helps to be around lab when other people are around. If you notice that lots of people are in between 8 and 6, and you come in at 7pm, you might be missing out. If you don’t keep similar hours to others, it also makes lab maintenance harder, since it helps if you’re around to fix the piece of kit you’re responsible for when it’s broken, not hours after it’s broken. That said, the lab is available 24/7. With the right training, and if you’re following all the right safety protocols, you can work whenever you like. If you’re excited by your cool science, don’t fear that working weekends is weird. It’s really not. (Remember, Mat will never check to make sure you’re doing this).

5) You live in a competitive world. If you want to get a job in science, or research, you need clear evidence of your awesome abilities, and that almost always means authorship on some good papers. You can increase your chances of getting those good papers by devising and carrying out lots of good, thoughtful experiments. Putting in lots of hours in lab does not guarantee success, but it helps to make it more likely. Often you will find that work goes in bursts - there can be periods of intense activity when you need to finish a set of key experiments and the momentum you generate in those times can be very satisfying. And then there are quieter periods where you can reflect, read, plan and write. You should mix the graft with the thought to make sure that your PhD is fun, fascinating and productive.

Thin Layer Chromatography

This is the most useful assay for reaction completion you will ever use. There are lots of guides online about how best to do a TLC. Remember that the chamber the plate is in needs to be saturated with solvent vapour (so put a filter paper in there), and the baseline needs to be above the level of solvent. Always do TLCs with multiple lanes (starting materials, reaction mixture and co-spots). Your spots should be small, and ideally applied with glass spotters, not plastic ones (in case plasticisers leak out). The ideal Rf values for distinguishing spots from each other and for accuracy are between values of 0.1 and 0.5. Rf values above 0.7 are useless, since spots run into each other and the Rfs just aren’t accurate (because of solvent evaporation from the top of the plate). To translate a TLC into a chromatographic separation, you want your desired spot to have an Rf of 0.3-0.4. If you can separate spots on a TLC by 0.1 you should be able to isolate those spots 100% pure by either a manual column or the Biotage, with no mixed fractions. With experience you’ll get this number down from 0.1 to 0.05. Use TLC before LCMS.

Mass Balance

Let’s say you install a sensor on either side of the Sydney Harbour Bridge. Over the course of an hour it counts 1000 cars entering the bridge. The sensor the other side counts 750 cars coming off. You’d worry, right? So if have a gram of reagents in a chemical reaction, and you’re expecting a 100% yield of product of 800 mg, and you isolate, from your crude reaction mixture, 350 mg you should similarly worry. You should be wondering where the mass has gone. This is the mass balance. If you’re asked how a chemical reaction went, the first thing to describe is the approximate mass balance. Until you have some sense of where the mass has all gone, you don’t have a good sense of the reaction outcome. You should certainly not be throwing anything away until this is sorted out. Naturally there will be some loss (reactant byproducts into the aqueous etc) but you should not routinely be losing lots of mass.

What Else Did You Get?

Related to the crucial concept of mass balance is having a clear sense of what else has been formed in a reaction besides the product you want. If your product yield is below about 60% you will be asked (by me, by others, by your thesis examiners etc) “what else did you get?” You need to be able to say something about where the rest of the mass went, e.g. “two other products were also formed that accounted for the remaining mass balance, but I’m not sure what they are yet” or “45% of the starting material was also reclaimed.” To not know this is to miss a crucial aspect of doing the experiment beyond making a molecule: Finding Out What Happened. If you don’t know what else happened, it’s quite hard to improve the reaction next time: it makes a big difference to what you do next time if there’s starting material left vs. if all the starting material was converted to something else.

General Experimental Write-up Guidelines

Reaction Numbering

Reactions need to be given a unique identifier. The number takes the following form: YourInitialsX-Y where X is the reaction type and Y is the attempt number.

Reaction Type

A reaction type means ‘starting material-arrow-product.’ If you are attempting a certain transformation of a particular starting material to a particular product, then any attempt at that reaction has the same reaction number, regardless of reagents/conditions. The reaction has this number regardless of the outcome. It is the intention that counts. Stereochemistry of products is important – if the intended stereochemical outcome is different, the reaction has a different number. The numbering of reactions is unique to you; you do not use the same numbers as previous people in the group even if you are repeating their work.

Attempt Number

Attempt number just increases by 1 each time you do the reaction. Screening several different reaction conditions on small scale on the same page of your lab book can be named with ‘A’ ‘B’ ‘C’ after the full name if so desired, rather than exhaustively giving each reaction a different Y, so e.g. MHT1-2-3A, MHT1-2-3B etc. For reactions that produce multiple products, and where those products are isolated e.g. by column chromatography, additional numbers may be needed, MHT1-1-1, MHT1-1-2 etc, and the relevant spectra and vials should be labelled as such.

Example

The first three reactions in MHT’s lab book are shown below. The first reaction here is the first in the lab book. This transformation is given the number ‘1.’ It is the first attempt at this reaction, so it is called ‘MHT1-1.’ (ignore the third number - scheme needs fixing) The second reaction is the same transformation (remember, regardless of reagents), so also has X = 1. It is the second attempt so has the identifier MHT1-2. The third reaction is a different transformation, so has a different X, and this is the first time it has been done, so Y = 1, giving MHT2-1. Notice that there is no space between “MHT” and the first “1” - this helps with searching.

It is very useful to be able to find each example of each transformation, along with the yields. We used to have to keep tallies of this, but if you keep your ELN ordered and tidy, you should easily be able to find all the relevant attempts of a particular reaction.

ELN Write-Up

Accuracy

As a scientist, it is very important that you have a strong sense of when accuracy in measurement is needed and when it is meaningful. Consider three things in particular:

The Sanity Check. Is what you’re saying meaningful? Is the level of accuracy you are reporting really justified? Reporting concentrations of solutions used in work-up to three significant figures is clearly unnecessary, since nobody cares, e.g 0.5 N HCl is fine for a work-up, 0.507 N HCl is silly unless the solution is being used as a reagent. Never trust anyone who reports journal impact factors to three decimal places.
Mismatch. Ensure measured and calculated accuracies match. If you weigh something to an accuracy of 3 significant figures, report the number of moles to the same level of accuracy (e.g. 1.30 mmol - not 1.304658 mol) since otherwise you’re inventing precision - here the calculated value is more precise than you have measured, which is impossible. If Mat ever writes “accuracy mismatch” on your writing, he’s talking about this, and you should check for other examples of this sin in your work.
Consistency: Be consistent with accuracy. Thus within one preparation (but not necessarily within one report/thesis/paper) amounts should usually be reported with consistent accuracy. Typically this means reporting masses to three significant figures (e.g. 354 mg). Not doing this is a form of mismatch, since highly accurate measurements of one thing are made irrelevant by less accurate measurements of another thing. There are rare exceptions (like the concentration of work-up reagents, mentioned above, which do not impact the accuracy of your yield).

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Sample Characterisation

If you want to make a molecule, the first thing to do is check whether it’s been made before. Use SciFinder frequently (often you’ll need to use it daily). You can access previously-used methods, characterisation data etc. It’s the most important resource we have. Besides being able to search for literature examples of reactions you may be attempting, it’s also a very rapid way to find characterisation data for compounds you’re making (from the “experimental properties” link).

If you want to know how to handle a reagent, check e-EROS online.

When you use a starting material for the first time, acquire a 1H NMR spectrum of it to check its purity and to compare with your reaction product.

In general there are two kinds of characterisation required for molecules before we can publish the work:

For Known Compounds

These are compounds previously synthesised either in the group or by others in the chemical community. For these compounds we require three pieces of characterisation that match the literature (usually a 1H NMR, IR and low resolution mass spectrum). For crystalline solids we need a melting point and a comparison with the literature value, which can count as one of the three pieces of data. For enantiopure or scalemic compounds we require an optical rotation and a comparison with the literature value.

For Novel Compounds

For novel compounds, we require the full level of characterisation. This includes 1H and 13C NMR and IR spectra. We also need a low-resolution mass spectrum. For crystalline solids we require a melting point. If you have distilled a liquid, we require the boiling point. The ‘killer’ bit of characterisation that finishes off the data is either a high-resolution mass spectrum or (better) an elemental (CHN) analysis (not both). For enantiopure or scalemic compounds we require an optical rotation and some indication of the level of enantiopurity - this must come from chiral HPLC or NMR shift reagent analysis.

For any compounds that undergo some form of further evaluation (e.g. biological evaluation) we need some assessment of purity, which is usually gained from comparison of melting points (for known compounds) or analytical HPLC analysis (for novel compounds).

RF values are important for internal purposes, but have questionable reproducibility between labs. Thus while we need these values in lab books and internal reports, we do not generally report them in publications.

Spectra should be kept in order of their unique identifier in folders. The identifier and structure should be written clearly so that someone browsing the file can locate the appropriate spectrum quickly. Think about the people who will come after you. Generally if you’re asked to produce a spectrum, you should be able to find it in a few seconds.

For NMR spectra, expand regions of interest - typically maybe 3-4 expansions for a 1H, one aromatic and one alkyl for a 13C. For writing up the data you will need the exact J values for each well-defined peak, and an accurate J needs ppm values for the relevant peaks to an accuracy greater than 2 decimal places. You must make sure the integrals for peaks have horizontal start and end lines, so that the values are real. Draw the structure of the molecule on the front page of the spectrum. Assign the peaks. If the spectrum shows a byproduct, draw this structure also. If the spectrum shows an unidentified product, draw the intended reaction and product on the front page, and indicate that the spectrum does not show this product. (It’s all about putting yourself in somebody else’s shoes and asking yourself whether your spectra would be clear to them – no mental notes)

For publication purposes, we almost always require scanned copies of 1H and 13C NMR spectra for the supporting information. Thus you must examine and assign spectra very carefully to ensure that there are no ‘rogue’ peaks and no large solvent peaks. Obtaining clean NMR spectra and assigning them is the most important skill of the synthetic chemist. Once you’ve done all the above with your spectrum, you can show it to Mat.

Experimental Write-Up (for papers/reports/theses/etc.)

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Checklist of Common Little Errors

Weird Hidden Formatting

Sometimes there is formatting in Word that you can’t see. You can reveal formatting if you click the little backwards “P” that looks like this in Word Home Bar:

This can show that you’ve double spaces and other things. In particular it can reveal a spacing SNAFU that arises often when you copy from a non-Word source into Word, where the spaces appear as little blue circles, like this:

These can mess up spacing of your text and you should replace them with regular spaces. Usually if you paste into a simple text editor and then copy from that to Word, these odd spaces aren’t carried over.

General Writing Advice

Writing Accurately vs Writing Well

When you join a lab, you will have been through a lot of education. You may feel that you can write. Most lab scientists are quickly disabused of this idea. Writing science is hard. You will find that your writing goes through a very large number of edits. Don’t freak out. Don’t lose confidence. We’re always students of writing.

When you write something, the first thing to ensure is that it’s error free. You can’t be making little tiny errors that will distract your reader, like speling mistakes or annoying spaces where there shouldn’t be any or repetition of words where words are not needed because words have appeared where edits should have been made. Generally speaking, don’t submit anything for anyone to read (particularly Mat) if there are any simple errors in the document (i.e. things that Word can find and highlight). You may ask yourself “why do little tiny errors matter? Surely it’s the substance of the writing, not the little things?” No. Errors are distracting and their presence suggests to the reader that the work has not been well thought through. It will appear cobbled together. The reader starts to doubt the quality of what they are reading.

The second thing to do when you’re writing something is to make sure that the content is meaningful and correct. Sentences should appear in a logical order. Paragraphs should have a coherent theme, with new paragraphs being used for new thoughts. References should be used correctly (see elsewhere for more on this). Statements should be made that can be backed up with data. Words should be used precisely.

The third thing to do is to make sure it’s interesting. There is no law that says that science should be dull to read. To convey the excitement of what you are doing you should make it interesting to read. To achieve this requires a lot of practice, training and editing. It is an aim for a PhD student to construct an interesting thesis.

Consider Your Audience

When you write, think about who is going to read it. How you write changes depending on your audience. For most student reports and theses your audience is someone of your level of education (e.g. another undergrad, or grad student) who is trained in your broad scientific discipline (chemistry) but who is totally unfamiliar with your project. We can call this a “same-level stranger.”

Once you have a clear idea of your reader, you will be able to pitch the complexity and jargon suitably. There’s no need to explain what a molecule is to a same-level stranger. But you might need to explain what a Minisci reaction is, or an alanine scan or a gametocyte.

Don’t try to be too clever. Don’t feel the need to include complicated terms in order to sound impressive. If your same-level stranger would not understand it, explain it. There is nothing more likely to switch your reader off than feeling confused by jargon.

There may be times you need to alter your writing because you’re doing something for a different audience. When writing grant proposals, you can often assume a higher level of knowledge by your audience (at least for the technical bits). When writing for a general audience (e.g. a general science magazine) you may need to simplify things further.

An Important Point about Correctly Referencing the Literature

You reference (or “cite”) a paper so that your reader can get more details about the statement you’ve just made. You don’t cite a paper so that your reader is taken to the paper where you got that statement from.

So for example, let’s say that at the beginning of your report or thesis, you want to say “Acetyl CoA is a molecule that plays an important role in many biological processes.” A statement like this really needs a reference. There are three options for you. The first is to reference a review which is on the subject of acetyl CoA and its role in biological processes. The second is to reference some major research paper, or series of papers, which have demonstrated that acetyl CoA is involved in biological processes, and which have been cited by others many times. The third is to reference a research paper which has in it the sentence “Acetyl CoA is a molecule that plays an important role in many biological processes” because that covers your ass. What’s the best thing to do? 1 is better than 2, and you should NEVER do 3. The purpose is to direct the reader to a bigger source of information. If you did 3, and just reference some other paper that says something similar to what you’re saying, then the reader has not been directed to a more comprehensive source, and has to go one step back, and look at the references in the paper you’ve cited in order to find more information.

If this is surprising or confusing to you, go and read the first few paragraphs of any research paper. Look at the references that are included there. They will be richer, bigger sources of information. They will not be references to other small research papers that just say the same thing.

Writing Living Papers (As You Go Along)

This section is about a way of writing up your work as you go along, to improve your ability to plan your research and accelerate the submission of your papers. The upshot is: you need to be leading the writing of at least one so-called “living paper” at any one time.

During the course of a research project it can become easy to drown in experiments and data. You get caught up in finishing short-term goals and sometimes it’s easy to neglect thinking about the big picture - the “Why am I doing this research?” or “What is my big aim?”.

On the other hand, when you write up papers or write your thesis, the story of your project - why you did it and what’s the impact - needs to be very clear. It’s often the case that when you write up your work you realise that there are additional questions that need answering, or additional controls that were needed (which is why people writing up often need to come back into lab!).

So on the one hand you are busy in lab with the minutiae but on the other hand you need to keep clear in your mind the bigger picture. The need for these two ways of thinking is sometimes called “the rat’s head and the ox’s neck”.

Now, we try to mitigate against this. You write interim reports. You present your work at group meetings, or at conferences. You chat about your work with others. All of these things help you to re-evaluate what you’re doing and why, essentially checking that the whole project is going in the right direction, that you’ve not overlooked something obvious, that you’re asking the most meaningful questions. There’s no better way to learn than to teach.

But frequently it’s the act of writing your research down that helps your brain engage with the project the best. When you write what you’ve done, you really need to present it in the very best light, in a way that is maximally robust and defensible. When you write an introduction, you’re forced to ensure you’re up to date with the literature. When you write the experimental, you’re forced to ensure your data can support your conclusions. When you write the R&D, you have to engage with your research project’s story, and to make sure the whole thing makes complete sense.

At the same time, to progress in your career, and to demonstrate your productivity and scientific abilities, you need to publish papers.

So to combine these things, you need to create a written description of your project’s current status and have it on the boil at all times. In other words, you need to be writing “living papers” - a description of where you’re up to in the form of a paper that is, when you’ve completed a piece of work, ready to submit to a journal. Rather than waiting for the end of a phase of experimental work before writing it up, you maintain a paper as you go along.

In the group’s open projects, each Github repository has a place to do this - the “Story So Far” on the wiki. This is an excellent (low-tech) place to write up where the project is up to. It’s the most valuable thing we write for project outsiders - people who want to know where we’re up to. We’re constantly being asked for this by potential contributors.

Alternatively, we can use Google Docs, which are perhaps better for defined pieces or work. Ultimately it doesn’t matter which we use, since we can of course cross-reference them. But we want to minimise work, so we should pick one rather than the other.

A living paper contains the features of any paper:

A working title.
Your name and address, and the names of any other contributors to the research.
An abstract (though this is often easier to write at the end)
A couple of paragraphs of intro, setting the scene for the work and its justification, and ending with a clear research question
R&D
A conclusion
References
Experimental (this can be a separate document if it’s v bulky)

Obviously the thing about living papers is that all the above changes over time. Data are added in, diagrams change, conclusions change. There are new subsections needed as a result of new data.

Each lab member needs something like this. You might find you need more than one - projects are often written up as multiple papers, each with a separate theme and research question.

For the early stages of paper writing, you could do a lot worse than consult George Whitesides’ very nice discussion of what a paper is. You’ll notice he says “A paper is not just an archival device for storing a completed research program; it is also a structure for planning your research in progress”.

So, practical steps. Start a Google Doc or start contributing to a relevant Github wiki page. Share that with Mat so that you’re on the same page. Start setting aside some time for writing regularly - if a week goes by and you’ve not looked at the paper, then you’re neglecting it. Keep your diagrams/figures somewhere convenient with a sensible naming convention, so that you can easily update them as you need to. Importantly, you can link to pages in your ELN if you wish to, as a way to maintain a link between data you mention in the paper and where the data came from, or are kept. Make the Google Doc public (“anyone with the link can view”) and put (between authors and abstract) this: “The licence for this living paper is CC-BY-4,0, meaning you can use anything contained in this paper for any purpose, provided you cite this paper”.

Does this take time? Yes, particularly to do it well. Is it worth it? Yes. Not in the short term, but in the medium term (because it will help you plan) and the long term (because it will accelerate your being able to submit peer-reviewed publications).

General Lab Guidance

Working Safely

Everyone in the group (PDRAs and PhD students) will have certain responsibilities to maintain the lab to ensure that we all work as efficiently and safely as possible. A list of lab jobs can be found here along with some general lab rules and guidance on the use of communal equipment.

The lab jobs will be reviewed periodically and updated. Any issues, contact Eve.

Current waste rota

Current consumables rota

Housekeeping

It is imperative that communal areas and the apparatus stored within them are left clean for the next person to avoid contamination and risk of injury.

Glassware is limited so promptly clear up after yourself, particularly with more specialist equipment such as columns and don’t hoard items you’re not using on a daily basis.

Cleaning – Glassware should be cleaned thoroughly on BOTH the inside and outside. First, rinse with detergent/water and then with acetone. You may need to do this multiple times to remove stubborn stains. If it is not possible to get an item clean, it must be subjected to harsher cleaning agents (e.g. acid/base bath) or suitably disposed of. Rinse with acetone before drying.

Solvent Winchesters must be returned to the solvent cabinets when they are not in use (particularly overnight). We have a safety obligation to do this, and in addition, it makes it easier for others to locate solvents they need. Please don’t open several bottles of the same solvent and keep the flammables cabinet tidy. This allows us to quickly check stock levels.

Good gloving practice – Gloves when used properly can help protect your skin from contamination from chemicals and other hazards. It’s essential that you wash your hands once gloves have been removed. Disposable gloves must be discarded once removed and not saved for future use. Remove gloves before touching personal items, such as phones, computers and one’s skin. If for any reason a glove fails, and chemicals come into contact with skin, consider it an exposure and seek medical attention.

Balances – The balances are a glove-free area to prevent cross contamination. If you’re weighing out something particularly toxic, use clean gloves and dispose of them after use. The balance spirit level should be checked before every use and the balance adjusted accordingly. If you are unsure how to do this, ask someone to show you. The balance should always be spotless. Any spills should be dealt with immediately, to prevent permanent damage, using either ethanol or IPA.

Rotavaps – Ensure that the dry ice/IPA is topped up in the trap before applying vacuum. Do not use the ‘continuous’ function or apply full vacuum with solvent remaining in the collection flask as this will pull solvent through the pumps. Additionally, empty the collection flask to remove low boiling solvents, before attempting to remove higher boiling ones. Clean the adaptors and empty the collection flask after use, ready for the next user and set the bath temperature back down to 25 ºC. If you are removing higher boiling solvents such as water and DMF, clean the rotavap thoroughly to prevent contamination for the next user. Do not use the rotavaps on the benches to remove anything potentially toxic or smelly. The rotavap in the fumehood can be used for this purpose. Fill in the log book and clean the rotavap thoroughly after use.

Cutting TLC plates– Cut whole plates using the guillotine and do not leave odd shapes. When finished, wipe down the area and DO NOT leave loose silica lying around.

TLC station – Keep the TLC dips area tidy. Either dip TLC plates directly into the stain bottles or use the pipettes provided. Don’t leave dirty/broken glass pipettes lying around and clear up after yourself. If you get stains on the bench, give it a wipe.

Hi-Vac line – The vacuum should only be used to remove trace amounts of solvents. Excess solvent should be first removed on the rotavap. The trap gets blocked very easily if too much solvent is pulled in. Ensure that you top up the Dewar with liquid nitrogen when using the line. Some solvents take longer to remove than others, but don’t leave compounds on there for longer than required as space is limited. After switching off the line, ensure that you check the trap for any condensed solvent. This needs to be removed to ensure that the best possible vacuum is maintained.

Floor/bench space – The floor space should be kept completely clear. Everything (including solvent Winchesters when in use) should be placed on the bench and not stored on the floor or on stools.

Sharps – Needles must never be left around unprotected. Do not resheath needles. Dispose of them directly or store in a small vial for reuse if necessary.

Waste Disposal

In general, small amounts of waste (acetone washings, used silica, sharps etc.) can be contained and stored in individual fumehoods and then transferred to the dedicated storage area. However, for particularly hazardous waste, you may need to quench these if appropriate and move them to the final storage area and arrange for their disposal.

Solvent waste– Waste should be separated into chlorinated or hydrocarbon (non-chlorinated) and transferred to 10 L plastic drums which are stored in the waste fumehood. Drums can be collected from stores, and it is our responsibility to clearly label these with the type of waste (non-chlorinated or chlorinated) and the lab number (i.e. G25). Once full, these will need to be taken outside to the storage facility, ready for collection. DO NOT TOTALLY FILL waste containers as the contents can potentially expand when warmed. This presents a danger to us and those collecting the waste. It is not one individual’s responsibility to collect waste drums from stores. Take initiative and collect more if needed.
Bins – Gloves and other waste should be placed in yellow tiger stripe hazardous waste bags. Once full, these should be tied off with cable ties that can found in the consumables draw. Yellow bags will be taken outside for disposal by the cleaners if left by the door in the evening with a Safe to Clean card placed on the door. Waste paper towels generated from handwashing can be disposed off in the small bin (clear bag) near the handwash sink. No laboratory waste should be placed in this bin.
Aqueous waste – In general, aqueous acidic and basic waste should be neutralised and transferred to the appropriate 10 L waste drum in the waste fumehood.
Hazardous waste – Filled containers of silica waste need to be appropriately labelled and disposal arranged. This is done through stores and is the responsibility of the person allocated to hazardous waste disposal. Very toxic waste and heavy metals (e.g. Pd, Cu, Ni) need to be transferred to clearly marked containers and their disposal arranged via stores. For commonly used heavy metals (i.e. Pd), waste containers can be stored in the waste fumehood rather than individual areas.
Glass bins– Glass waste is put into one of the designated bins. Once full these need to be closed, sealed with tape and taken outside.

Lab Shutdown

At the end of the day, everyone needs to ensure that their area is shut down before leaving. The last person to leave should double check that the UV lamps, Biotage, rotavaps, pumps and hi-vacs are turned off. Fume hood sashes should be closed when leaving the lab - at any time of day.

Ordering from Stores and MyFinance

The SoP stores stock list (sheet 1) and the MyFinance codes for MHT consumables, chemicals and solvents can be found (sheet 2) here.

The MHT consumables and chemicals are everyone’s responsibility. If something is about to run out please order some more from stores or from MyFinance.

If we get a new SoP stores stock list please update the one we have.

The MyFinance codes for the consumables, chemicals and solvents are on sheet 2. These codes can be updated if you find a better or cheaper product.

Chemical Inventory (Reagent Management)

It is essential to manage reagents correctly to not adversely affect your chemistry or that of others.

All new compounds should be added onto ChemInventory immediately and assigned a suitable sub-location. If you don’t have access to ChemInventory please contact Ed or Jamie. All empty reagent bottles should be removed from the inventory before disposal. Empty bottles, or reagents that have been deemed unusable should be labelled as such, removed from the database and disposed of. – This is the responsibility of everyone in the lab.

As a lab we will carry out an annual stock take (likely in December) to ensure that the inventory is up to date. It’s the responsibility of those assigned to managing the inventory to coordinate this and advise group members on appropriate locations for chemicals. This needs to be in line with what’s expected by UCL and the UK in general.

General guidelines for using the inventory system can be found here.

How-To’s and Manuals

Using the LCMS

Using the Analytical LCMS

A general guide on using the Analytical LCMS in G25 can be found here. The guide was prepared by Edwin G. Tse and Paul T. A. King and can be updated by anyone in the group. It serves as a walk-through for how to properly use the Analytical LCMS. This is not a substitute for proper training. Please check the lab job table to find the proper person to train you.

here is the LCMS sample preparation guide.

Using the Preparative LCMS

The operation of the preparative LCMS is identical to the analytical LCMS, with the addition of a fraction collector. A general guide on using the preparative instrument can be found here and was prepared by Edwin G. Tse. This is not a substitute for proper training.

LCMS Shutdown and Reboot

The LCMS should only be shut down in the case of extended time away from lab. When rebooting, it is imporant that things are done in the proper order. A quick guide to rebooting can be found here.

General Troubleshooting

A list of common issues encountered while using the analytical and preparative LCMS instruments can be found here. Where the fix is known, the solution is provided. If new issues are encountered while operating the LCMS instruments, it and its solution can be added to this list as a point of reference for the future.

Using the Biotage

Biotage Selekt

A general guide on using the Biotage Selekt in G25 can be found here. The guide was prepared by Yuhang Wang and can be updated by anyone in the group.

Biotage user manual can be found here.

Information on Biotage columns can be found here.

Write down your name and type of purification (i.e. normal or reversed phase) on the table affixed to the fumehood sash. Only write down your name if you are ready to run your purification, otherwise wait until you are closer to being ready.

There is no booking system and you can use the purification system as required, when it is not in use. There are currently 12 racks available.

Please don’t keep racks and tubes in your fumehood for prolonged periods of time. Combine your fractions as soon as possible after doing a column and clean the tubes thoroughly, finishing with several acetone rinses. Alternatively, transfer your tubes to a normal test tube rack (return later) and return the empty Biotage rack. Make sure there is no permanent marker on the tubes or on the rack. To ensure that the tubes dry quickly for the next user, place them upside down onto tissue on the bench or place them in the large drying cabinet at the back of the lab, before returning them to the Biotage or the designated cupboard.

We have bought many Sfär cartridges of varying sizes. You can reuse these several times by simply flushing with MeOH at the end of a run (to remove any impurities remaining on the column), followed by a less polar solvent. The column should then be dried by doing an air flush. As the Sfär columns contain spherical silica with a high surface area, they have a higher loading capacity. This means that you can use a smaller column than you usually would to achieve the same separation. Be aware that your compounds may behave differently on spherical silica in comparison to the standard Merck silica TLC plates we use. You may need to alter your gradient accordingly.

There are many methods of loading (i.e. liquid and dry) and you would have been sent a guide on this (speak to Fahima if you haven’t). Once the silica has reached its lifetime (i.e. you start to see gaps between the silica and the frit) you can remove the frit and dispose of the silica. The empty cartridge can then be refilled as required.

If you need training on the instrument - contact the person in charge.

Group Meetings

How We Do It

Where: M1 (etc), in person. When: Fridays 1pm (mostly). Usually 60 to 90 mins. Fiona will send Outlook invites.

Health and Safety/Lab Operations. These meetings provide an excellent chance for us to talk about lab or admin issues that affect us all. We’ll start each meeting with this.

Research Updates: A description of where your project is up to. Minimise background and previous work (one slide maximum). Be clear on your long- and short-term aims. Describe key challenges you’re facing in more detail. Work hard on making clear, attractive slides. Include necessary references on each relevant slide, not at the end. Send your deck to Mat after the meeting, or upload directly to Github. 20 minutes, with 10 mins for any extra discussion. People should ask questions during the presentation. At the end, the Devil’s Advocate (DA – the person doing next week’s update) should lead any remaining questions.

Lit Club: A description of three recent papers published within a year. Two slides maximum (no animations) per paper. Include the citation and author names. Get across the key idea and key result of the paper – don’t get lost in the details or just paste in all the tables and diagrams. Pick any papers from any Nature of Science journal (i.e., including Nature Chem, Chem Bio, Science Translational Medicine etc), JACS, Angewandte, Chemical Science, ACS Central Science or PNAS. The papers do not have to be relevant to your work, or relevant to anything in the group. Pick papers because you find them interesting. 10 minutes, including questions. The Devil’s Advocate (DA – the person doing next week’s lit club) should lead the questions.

MiniProblem: If it’s your turn, distribute (by email, immediately after the previous meeting) a short problem or two or three on synthetic or medicinal chemistry. People should come prepared to discuss the solutions on a whiteboard. 10 minutes.

Grant Codes and Admin

Please ask current postdocs for more information when:

encountering issues with instruments that you are unable to fix (i.e. Biotage and LCMS)
looking for quotes on lab equipment, etc.
you need help with NMR or mass spectrometry instruments in SoP
you need to replace the argon cylinder in the lab
you need to have hazardous chemical waste (including silica) removed
you need a 19F NMR spectra for a sample

Project Codes

Core: Project 549163, Award 156780 <– don’t use this from now on for consumables.
Discretionary: Project 549163, Award 156782.
Dmitrij: Project 552026, Award 156780, Task 100.
Yuhang: Project 564082, Award 177365, Task 100.
Tom: Project: 566966, Award 180330. Now use 531853.100.156535 and quote “T.Knight (566966)”
Daniel: Project 570934, Award 184398, Task 100
Antibiotics UK: Project 568406, Award 183633
EPSRC/IAA/KEIF Generative (Ed): Project 571160, Award 174591
Yinuo: Project 571228, Award 177365, Task 100
Gates/SGC Contraceptives grant: Project 572553, Award 184940
Chemistry MRes Student Spending: Project 574868, Award 177365
READDI-AViDD: Project 575169 (SoP) or 575170 (LMCB), Award 185702
Kangping: Project 575864, Award 177365, Task 100
Mohsen: Project 575863, Award 177365, Task 100
Shared G25 Consumables: Project 577764, Award 156780, Task 100 (except for ISD projects (Tasks 2001, 2002C and 2002R) and buildings projects which are linked to Task 1000)
Evans Mainsah AREF Fellowship: Project 579579, Award 187158
PBC Dept (only for Mat, who keeps forgetting what this is): 502704.100.156780
Faculty Fund Protein Science Initiative: Project 581304, Award 156780, Task 100

Chemistry Resources

Useful Web Resources

Fun site for exploring chemistry mechanisms via animations: Chemtube3d

A useful online resource for general guidance on laboratory techniques Not Voodoo

An illustrative guide to using a Schlenk Line by Dr. Andryj Borys Schlenk Line Survival Guide

Organic chemistry lecture notes developed for the SBM CDT by academics from Oxford Chemistry and their industrial partners which are free to download.

Lab Tips and Tricks by ChemistryViews

Organic Chemistry Portal - Named Reactions

Preparation of Cooling Baths

Evans’ pKa Table

Common NMR Solvent Impurities

Spectral Database for Organic Compounds SDBS

TLC Stain Recipes