Speeding up scientific progress by sharing organic chemistry techniques, lab safety resources and computational procedures
Cooperation and shared ideas often provide that spark of inspiration for the next important scientific discovery – and prevent researchers from wasting time on things that others know do not work. But despite the clear advantages, the research community is surprisingly poor at sharing certain elements of scientific information effectively. Whether it’s missing details in the supporting information (SI) of a paper, standard practices not translating to the next generation, or difficulty accessing appropriate instructions for a procedure, these barriers to clear and open communication impede the progress of science.
However, as more science communication has moved online, there’s been a huge rise in privately maintained websites addressing this knowledge gap as experienced researchers look for new ways to share their wisdom with a wider audience.
One of the earliest examples is Not Voodoo, an organic chemistry website that has been operating for more than 20 years. Curated and managed by Alison Frontier, a synthetic organic chemist at the University of Rochester, US, this extensive online resource catalogues hundreds of organic chemistry techniques, providing instructions for standard methods, solutions to common practical problems and tips to get the best and most reproducible results from new reactions. ‘I was acutely aware as a graduate student of how lucky I was to be surrounded by so many postdocs who just knew all these tricks and could help with any experiment,’ she explains. ‘Not everyone has access to that kind of in-lab support and that inspired me to take everything that I had collected during that time and make it available to everyone.’
Initially created for students entering a research lab for the first time, the website features a huge collection of ‘how to’ pages, detailing the individual steps in common organic techniques (such as monitoring a reaction or recrystallising a product) which often aren’t described in experimental procedures. Guided by questions from her students, Frontier has continued developing additional pages ever since, expanding the site to include general advice on work ups, purification techniques and solvents, alongside a vast catalogue of handy organic tricks.
‘The problem with experimental laboratory science is that all the little tips and tricks are not written down in any reference book and often these practices don’t appear in the SI either as experienced researchers will just do them automatically,’ says Frontier. ‘I feel very strongly that organic chemistry should be reproducible so you have to fill in that knowledge gap somehow.’
The troubleshooting section of the site outlines some of the problems that can arise during a typical experiment: struggling to weigh an oily liquid, failing to reproduce an earlier experiment, and cleaning up a dirty NMR spectrum are just a few examples. It offers both solutions and explanations to help avoid these issues in future. The ‘tips and tricks’ tab shares advice on almost every aspect of practical organic chemistry, from choosing a protecting group to handling emulsions, and includes clever strategies to simplify workup and purification procedures.
But one of the most interesting parts of the site is the ‘rookie mistakes’ collection. This list of over 300 common (and avoidable!) experimental errors shows that many daft things can go wrong during an experiment and allows visitors to share their own frustrating lab bloopers by voting for the mistakes they themselves have made. ‘I originally thought people will watch out for these mistakes and maybe save a little bit of time, but actually, students have told me it’s something reassuring after a bad day in the lab,’ says Frontier. ‘You’re made aware of what things can go wrong, but also that everybody makes mistakes, even researchers who are probably quite competent normally, and that you’re not alone or incompetent.’
For Frontier, it’s crucial that there is no judgement here. Voting is anonymous and users can add their own rookie mistakes to the list if a particular lab mishap hasn’t already been mentioned. ‘If you don’t have to say who you are and where you’re from, there’s a freedom to that which allows us to talk about these mistakes without any judgement, accusation or guilt,’ she explains. ‘You have to have a healthy discussion about this side of practical chemistry but I think there’s still a barrier to admitting to these failures openly.’
Breaking down communication barriers and starting conversations is the aim of The Safety Net. Alexander Miller and fellow academic Ian Tonks created this collection of safety resources as they began their independent research careers. ‘We were worried about how to set a culture of safety and how to ensure that, when we were training students for the first time and thinking about students training new students down the road, knowledge was going to transfer. We wanted to ensure that the way we were doing things would be preserved over time,’ explains Miller, a catalysis researcher at the University of North Carolina at Chapel Hill, US. ‘When a lab starts there’s a unique opportunity to set the culture and for us that meant making safety a core priority.’
The Safety Net, which went live in 2017, shares the bank of safety documentation originally developed by Miller and Tonks for internal use within their own groups. The standard operating procedures (SOPs) provide thorough step-by-step instructions for a range of general lab skills such as handling a base bath or using a gas cylinder, and highlight the key hazards and safety requirements at each stage of the process. The shorter safety checklists act as helpful in-lab reminders of specific experimental protocols relating to different pieces of equipment, while the safe operating cards allow researchers to label unattended or particularly hazardous experiments for the benefit of others in the lab. ‘For us, the SOPs and checklists are a great refresher, even if you’ve already been trained. If you haven’t done a certain procedure in six months, it’s really helpful to have those reference points to jog your memory,’ says Miller.
Six years on and the website is still growing. In addition to new documentation produced internally, Miller and Tonks now receive a steady stream of contributions from other groups also looking to share their knowledge and experience. Although the site focuses principally on issues relating to synthetic chemistry, Miller hopes that ultimately The Safety Net could become a support system for researchers across the whole of practical chemistry. ‘We know to go to SciFinder to search for structures, chemical data and literature but there’s not a similar centralised resource to search for safety information, so that’s the longstanding goal or challenge,’ he explains. ‘A lot of the time, a particular lab doesn’t have skills or experience in a particular type of chemistry or procedure. We want to be there for the “How would I start doing this?” or “What do I do in this situation?” and be the starting point for that conversation and learning process.’
For Emmett Leddin, who is currently working towards an MD at Michigan State University in the US, becoming the go-to resource for computational chemistry happened by accident. ‘I never really expected it to be anything more than a local resource. The website grew out of some different PDF guides I modified to train students in my graduate lab,’ they say. ‘I turned them into a website after they got a lot of interest at a summer training activity and now I get hits from all over the world.’
Based on the content of their doctoral research, Comp Chem Website originally focused on setting up Amber (molecular dynamics) simulations of biomolecular systems with protein DNA complexes. It provides clear instructions, supported by pictures and troubleshooting suggestions. Entering the world of computational chemistry can be daunting, particularly for traditionally practical chemists. Vast user guides and confusing terminology and abbreviations can make the field feel impenetrable to outsiders, but Leddin’s friendly and simple tone carefully guides even the most inexperienced user through the fundamentals of the program.
Having information that is available to people when they need it without barriers should be at the heart of science
‘I think that there are absolutely benefits to learning about computational chemistry as a bench chemist,’ says Leddin. ‘You’re always going to miss something if you don’t have people that are cross-trained, or at least have some sort of understanding of the other side of the project.’ Subsequently they expanded the site to provide similar support for a variety of coding languages and computational programs including R, Gaussian and Caver.
But despite its name, Comp Chem Website is not purely focused on the specialist details of computational chemistry software. In a section entitled ‘Other programs and lab skills’, Leddin walks the user through computer-based lab skills relevant to all chemists, regardless of their field. General tasks such as creating posters or managing references can be unexpectedly fiddly, with dedicated software packages often assuming a higher base-level of knowledge than many chemists possess when they begin their research career. ‘Again, I had this knowledge and it was relevant to the students that were in the lab with me so it felt important to share that,’ says Leddin. ‘I’m a fan of open science and open resources – I think having information that is available to people when they need it without barriers should be at the heart of science.’
The support offered by these kinds of online resources is an invaluable training tool to scientists everywhere. The increasing interdisciplinarity of many projects means more researchers than ever are venturing into unfamiliar scientific territory and detailed and accessible online resources will be key to helping them build confidence in new skills outside of their specialties. Whatever the topic, freely sharing knowledge, experiences, and mistakes can only be a benefit to the scientific community.
Helping everyone thrive
Emmett Leddin’s commitment to open communication without barriers also inspired their second online project – Thrive Lifeline. Created during the pandemic, Thrive began as a hotline for individuals in science, technology, engineering, mathematics and medicine (Stemm) facing an unsafe environment or isolation from necessary support during the Covid-19 lockdowns. The dedicated team of crisis responders is available 24/7 to offer mental health support or advice in times of acute stress.
Since then, this group has evolved into an international online community, supporting and championing those with marginalised identities in Stemm fields. ‘If you’re facing barriers because of your identity in science, we want to help you through that,’ says Leddin. ‘There’s the crisis hotline to help you stay safe in the moment, but our extensive resource database also offers coping skills, advice and links to other organisations tailored to specific identities to provide more long-term support for anyone involved in the Stemm community.’
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