chemiluminescence
I just found a copy of my IB Chemiluminescence project! Feel free to download the .pdf (including all of the data) and have a read but I make no apologies for the mistakes and dubiously explained chemistry within. This was back when I was 17 so it’s a source of nostalgia for me.
I’m at the Aalto FabLab in the DIYLILCNC session as part of the Open Knowledge Festival (#OkFest on twitter).
Basically I, like a lot of people, am pretty interested in 3D printing, CNC and other manufacturing techniques. Mostly I’m interested in these in the sense that I want to be able to use them cheaply and preferably in a local facility or at home. This is why hackerspaces are so cool. People have been talking about using these to make various bits of lab equipment. Not reaction vessels or anything but better clamps and things to make life easier. Even peristaltic pump parts as these can be quite expensive and could be used to make cheaper flow chem set-ups perhaps.
Anyway, I want one and they are making one of the DIYLILCNC machines here at the fablab, so I’m pretty excited.
My friend Oleg prompted me to read this article about analysis of mobile phone data and its implication in treatment of malaria. Nathan Eagle has been using (anonymous) mobile phone user data in developing countries to attempt to identify disease outbreaks through monitoring of the movement of people. The study was reportedly used to try to identify if it was viable to attempt to control malaria by localised elimination of the parasite. The conclusion was that elimination of the parasite would not be effective because the high mobility of people rendered it ineffective.
I wonder how useful this data would be in the prediction of where drug resistance is likely to appear next? If the data can be correlated with known areas of resistance and mass movement of people are observed to new areas, could this information be used to inform drug regimes for treatment of disease? For example switching to alternative medication regimes when resistance is suspected.
Artemisinin (Wikipedia)
Artemisin resistant malaria is scary (one of the reasons that we’re working on things to help combat this) and on its way. It would be great to track the data of people movement from areas such as the Thai/Burma border but I doubt their respective govs will be happy to share the movement of their border populations and crucially of troops operating in the jungle.
I’m always amazed by the price of some bits of lab equipment. Things like aluminium heating blocks are way overpriced and as a result most academic labs make do with oil baths. Obviously these have a number of problems that are highlighted by suppliers but their arguments still don’t justify spending 300 GBP on a heating block for a single round bottom. They argue that they pay for themselves over one or two years due to the price of silicone oil. I don’t know how often they think the oil in baths gets changed but I hadn’t found a single chemist who would agree with this.
Having said that, I’m not a fan of oil baths. They are a real pain when carrying out small scale reactions in parallel. At the beginning of my last year of my DPhil I somehow found time to learn how to turn and mill metal thanks to our in-house workshop and friendly engineers. I made myself a heating block to hold 8 CEM microwave tubes. This thing made life so much easier. No more slippery oil coating and contaminating everything. All for 2 hours of work and a chunk of scrap aluminium worth about £20.
Now our workshop here has made me a heating block to hold 25 mL vials as disposable reaction vessels. I also asked them to turn some B14 to vial adapters so I can attach condensers or any other quickfit glassware to them. Andrew in the workshop designed a beautiful thing made from 2 pieces of PTFE. Connected to the vial it easily hold a vacuum <1 mmHg, so vacuum purging and inert atmospheres are all good (not that I'd recommended using vacuum on parallel sided, non vacuum rated vessels without a proper shield).
Anyway this is the prototype and the heating block is getting anodised. It's going to be beautiful. I would encourage anyone to get to know your lab workshops if you are lucky enough to have them.
Over the years that I’ve been involved with synthesis the solvents I’ve used for reactions and work-ups have changed quite drastically and, unfortunately, I seem to be going backwards according to the solvent selection guide.
Just a scribble graph of solvent use over time.
My “gateway” solvents (heptane, toluene, acetonitrile, ethyl acetate) seem to have led me on a downward spiral towards the environmentally nasty DCM. This is a result of a combination of lazyness and necessity. While at Pfizer, I simply didn’t use any halogenated solvents except for CDCl3 and very very very occasional DCM for sample prep. It just wasn’t hanging around on the bench and the rotavaps were perfectly capable of taking off toluene and ethyl acetate, unlike some found in academic labs. The process solvent choice thing hung around with me through my masters project but I did resort to DCM for some reactions and work-ups. Through the DPhil, my main reactions were carried out in 1,2-DCE but this accounted for a small amount of solvent per reaction. Methodology work with usually only 1-2.5 mL of solvent doesn’t work out to much even when you’re doing hundreds of reactions. Later on we did change this to propylene carbonate which is a solvent that I really enjoyed using. It is probably worth trying out in more reactions and recrystallisations. I did still try to use more benign solvents for most of the starting material synthesis. With no 2-Me-THF, TBME, or MeCN about (this was around the time when acetonitrile production stopped for a while), THF and diethyl ether became the general work horses.
I’ve always been one to avoid columns if I can possibly help it but of course I do need to use chromatography. My column solvents changed from ethyl acetate/heptane at Pfizer to EtOAc/60-80 petrol to ether/40-60 petrol to pentane. Switching to lower bpt solvents mostly to get rid of persistent solvent residues in the annoying oils/gums that I was producing at the time. Column waste is something that is particularly rife in academic labs. People generally use way too much silica for most separations and then use inappropriate solvent systems and then complain that their columns take so long.
Now I’ve somehow slipped into using DCM pretty regularly. MeOH/DCM is being employed too readily but at least my DCM squeezy bottle isn’t around anymore.
Yes yes, DCM is cheap and a great solvent but it’s disposal isn’t. Do any (academic) departments out there charge disposal costs to the individual research groups depending on use?
[I just noticed this topic has recently been discussed over at Org Prep Daily]
I love very old lab chemical containers. I was just making up a new gas drying column and decided to not use indicating calcium sulphate (Drierite) as it’s way more expensive than calcium chloride and torn up bits of cobalt chloride indicator paper. Turns out the indicator paper available from our stores is from the Days of Yore, so was predictably pink when I opened it. No matter, a brief spell in an oven at 115 °C sorted them out.
A lot of enthusiastic users of technology are able to set up their own workshops without much concern to society. These people then have the option to turn this into a start-up and a lot of innovative work has begun this way. Dyson, Apple and a multitude of others all began because they were able to practice their craft independently. This is something that historically seemed to be commonplace among chemists and pyrotechnicians such as Rev. Ron Lancaster, founder of Kimbolton Fireworks who started experimenting on his own (probably) in a shed.
Kimbolton fireworks at their best
Recently, there has been a lot of interest in biohacking or DIY microbiology but not surprisingly, fewer examples exist for proper organic synthesis that isn’t dedicated to the dark side of underground chemistry. @SyntheticRemark recently discussed the potential value of the dark side on his blog. On YouTube plenty of examples of people carrying out benign chemical synthesis can be found (such as the synthesis of luminol from gloves!), but as far as I know there isn’t a lab that is openly carrying out practical chemistry as a “hobby”/micro start-up.
How would one go about setting up a legal synthetic lab independent of an existing institution? I’d love to hear from people who have set-up their own start-up custom synthesis companies as they obviously know what is required. What I mean is a lab that can buy reagents and do reactions without impediment from police or other authorities. After all, surely we should be able to establish a start-up chemical company? The following issues come immediately to mind:
The cost of analytical equipment is one practical limitation that is becoming a lot more manageable these days. The cost of equipment is coming down in price to levels that are almost feasible for private individuals, particularly in the second-hand market with so many larger companies downsizing. Even NMR machines can now purchased for around $25K, apparently.
Bench-top NMR?
Waste disposal is something that people might not think about until they’ve actually made something. This is something that the old-school shed chemists probably didn’t really worry about, but these days is very important ethically and legally. My guess is that small amounts of organic wastes could be disposed of with existing local government measures considering people get rid of old cans of paint cans and pesticides regularly.
I would have thought that you shouldn’t need licences to carry out synthesis, assuming you are not making controlled drugs, explosives or chemical weapons. What do you need in order to get a chemical supplier to deliver to you? What about insurance to allow you to rent some space? How about any necessary approvals from environmental authorities? What is the absolute minimum bureaucracy one must encounter to be able to carry out meaningful organic chemistry?
For the past few weeks I’ve been getting busy in the lab on the resynthesis of a couple of anti-malaria active compounds. It’s a new project but we’re using existing tools that the group has used in the past. Our completely open lab notebooks are in the form of a simple blogging platform, Labtrove. Overall project discussion is handled over at The Synaptic Leap, a site that has been around for a while now. There’s also a project wiki over at OpenWetWare for project updates.
In addition to synthetic work, we’re investigating how to best handle and share our data with the wider world. There’s been quite a bit of discussion about this recently. My boss, Mat Todd, recently wrote about it and this was followed up by ChemConnector, Peter Murray-Rust and others in the comments and their blogs. Jean-Claude Bradley at UsefulChem has a live ELN focusing mainly on the Ugi reaction and melting point data curation. Currently I don’t know many synthetic chemists who are planning on putting all of their NMR and procedural data on the web as they receive it. Most of the people discussing it are involved mostly with the handling of larger chemical databases or data storage. The day-to-day synthetic chemists experience is, from what I’ve seen, largely missing. If you’re doing already doing this please get in touch. Is anyone else doing so or planning to? It would be great to gather a bunch of links together. Egon Willighagen’s Chemical Blogspace is doing a great job of harvesting these but I bet there are more.
In terms of sharing data in a more searchable form, I’ve been experimenting with ChemSpider. There are a number of Mac related issues when it comes to sharing data. Luckily more and more programs are cross-platform, but unfortunately basic issues still exist. Chemspider has a brilliant java spectra viewer, unfortunately this does not run currently run on Macs. Furthermore, my NMR package of choice is iNMR and I just discovered that its support for .jdx files does not include the integration curve nor does it copy all of the metadata across. I’ve contacted iNMR and they are working on the issue.
I think Chemspider have made a fantastic start on their system and it has a vast amount of data already but the ease of deposit still needs to be improved. Right now most organic chemists struggle to make back-ups of their own data and are, for the most part, famously computer illiterate compared to other flavours of scientist. What is very encouraging is that everyone is very eager to help and get things moving. I’ll keep this blog posted with my data experiences as I find my way round the issues that a lot of you have spent years investigating. I’m sure that shortly we’ll have a simple way of getting our data out there where people can use it.