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Design Your Own Lab Course

Here’s an interesting question from a reader in academia. At his institution, they’re thinking about rewriting the introductory organic lab syllabus. “Rather than put what the faculty would like to see in it”, he writes, “what would your readers like to see in it?”
The questions he raises include these: What organic chemistry lab basics should non-majors be sure to get? And which ones should the chemistry majors have for their advanced courses to build on? What kinds of experiments should be included (and what classics are ready to be dropped?) And which sort of lab curriculum trains people better – the “discovery”-oriented type, or the “cookbook” type?
Add your thoughts in the comments below. I don’t know what specific experiments are common in undergraduate labs these days, so I’ll let those who are comment on the details. My take on the last question is that the course should probably start in more of a cookbook fashion, to get everyone’s fingers wet, but finish up with some sort of parallel-synthesis or method-finding exercise, where everyone gets a chance to do something different and make a small exploration along the way.

40 comments on “Design Your Own Lab Course”

  1. Canageek says:

    Beware how much work this is: McMaster rewrote our lab class from scratch 3 years ago. All new labs, though a lot were based on stuff from J. Chem. Ed. When I was in 2nd year I was in the first group of students to do the new second year labs, and well… there was a lot of ‘Hmmm, that is odd… well, your lab report is now writing up why the experiment didn’t work” and occasionally “Huh, that isn’t supposed to look like that. Go across the hall and take an NMR to see what you made” We also got to see things like a prof sitting in the lab with a laptop, rewriting the lab manual as we went.
    I then went off on a work term, so I’m doing 3rd year labs with the 2nd group of students to go through it. We still find “Huh, that does work a lot better if you use chloroform instead of DCM. You are the first one to successfully do that part of the experiment.”
    On the plus side, we have more experience with NMR and a few other modern techniques than any of the students before us did, as before that the labs were the same ones that one of my profs did as an undergrad.

  2. imatter says:

    Split the labs to three: majors, science non-major, and non-science non-major. But before all that, I’d cut down the math in general chemistry 101 since it’s a focus on exams that doesn’t really equate to chemical knowledge.
    Majors stick to cookbook-type with focus on math (sig. figs., etc) and scientific writing. No group projects. Organic labs for undergrads are now very complicated with synthesis of common OTC drugs.
    Biological science bu not chemistry majors stick to discovery-type, lots of tritrations, working with the chemistry of dyes.
    Complete non-major does discovery-type experiments with lots of group projects.

  3. Donough says:

    What about doing a module on ‘handling and disposal of hazardous substances’ as opposed to the usual 1 hour talk or letter that is usually given (in Ireland anyway; generally disappears after BSc/BEng)? On that tone firefighting or dealing with laboratory incidents could be an option; practical stuff.

  4. Annette says:

    imatter said: “Split the labs to three: majors, science non-major, and non-science non-major.”
    I’m not familiar with a program that has enough teaching lab space or TAs to turn one lab section into three. At my undergrad, there were a maximum of 40 students per class and only one organic lab, which had to split time between Chemistry 201 and Chemistry 202 students. In my graduate program, upwards of 400 undergraduates take organic chemistry each semester, and I can’t imagine the manpower it would take to organize all of these students into three different lab courses. We’d also likely need more than one director of organic labs.

  5. Anonymous says:

    Don’t fall for sales pitches for flashy gadgetry – when I was in grad school, the undergrad teaching labs threw out all of the old but perfectly good Spec-20’s and replaced them with fancy computer-interfaced ones that were constantly failing to work.
    I think it’s important for students to understand the fundamentals behind something before they “let the computer do the work.” It’s bad enough that most of them can’t do math without a graphing calculator. The people running the colleges seem to want to impress prospective students with a lot of flashy high-tech gadgetry, but I think the low-tech way is the best for learning fundamentals. The gadgets can be introduced in upper-level courses once the fundamentals are grasped.

  6. Anonymous says:

    That actually sounds like a really good idea. Start a few controlled fires or something and show the different ways to put them out. At my school everyone just has to go to the lab safety talks at the beginning of every semester if they are in a lab. I am currently at #7 and will lock down my 8th in the Spring.

  7. ProteinChemist says:

    I’ve been teaching non-major organic labs for the last few years. The way my institution has it set up is as mentioned above: 3 distinct classes with non-science, non-major, science non-major (a lot of pre-med here), and chemistry majors. The non-science non-major would be the most difficult to set up I would think, as you need to consider pre-requisites, etc. Even in the science non-major course 6 weeks is spent on basic purification and identification schemes such as recrystallization, melting point, and separations. Little emphasis is placed on the math behind it all. In the majors course there is more emphasis placed on NMR, IR, etc., with math (sig figs and relative recoveries) given only a little more emphasis.
    Ideally, I think that the 3 courses are the way to go, but obviously that is dependent on institution size. Mine is large on the non-majors side – I would estimate ~3-400 per quarter (no semesters, not a typo) with 30-50 majors depending on the year. When I took my initial organic course a decade ago, it was at a small community college, and they offered only one organic section that was between science non-majors and majors coursework in terms of difficulty. At the time it seemed to me that too little attention was paid to the more chemical aspects (MO theory, standard substitution/elimination rxns) in favor of a gross overview of pharmaceuticals. However, it did give me the experience of blowing my own pipets and other small glassware over a bunsen as SUNY was short on lab funding that year.
    This is longer than anticipated, but here is my take. Run 3 sections if possible.
    1) Easy: simple distillation, separations, recystallization, with an emphasis on broad categorization of compounds. This won’t get someone in a research lab, but they at least know not to throw together conflicting molecules.
    2) Moderate: start slow with the basic techniques that tend to be generationally compatible. Look at distillation, recrystallizations, but more quickly than (1) and implement them in basic organic experiments. Since most in this class are thinking about some aspect of medicine or pharmacology, look at very basic natural product synthesis and OTC drugs.
    3) Moderate-Hard: start fast with the basics on easy synthesis reactions and quickly move into those of moderate complexity that can still be performed in a 3-6 hr period depending on scheduling (I’ve seen 3hr, 4hr, and 2x3hr weekly sections at this level). I think the goal in a 1st year organic course for chemistry majors has to be broad understanding so later courses can refine knowledge. With that in mind I think that the final goal should be compound identification that may require adding/modifying functional groups in process. I like the idea of NMR/IR/Spec testing as needed. Maybe even throw in DSC/TGA just for fun?

  8. Anoni says:

    I’ve been teaching 2nd year organic for non-chemists for 2 years now and I’ve noticed a lot of problems with our lab program (despite the fact its been tweaked (read: unchanged) for the last 30 years).
    First we focus heavily on recrystallization which doesn’t suit most of the small bio-organic molecules they are working with, and the scale they are working on.
    Second we’re still using antiquated techniques to characterize compounds, which may be more of a budget limitation. Less emphasis on GC, and IR, more on practical techniques like NMR and TLC. I don’t understand why in all of our lab manuals we give them times (reflux for 30 minutes…etc), we should be getting them to run TLCs of aliquots.
    Lastly, I agree with the general idea of a large parallel or natural product extraction. I’d like to see partners working to synthesize 2 different reagents, which are combined for another final reaction. That way they would be encouraged to help each other and understand the ideas behind both experiments.

  9. p says:

    In the labs I’ve taught, I decided that I wanted first time orgo students to really learn one skill. Not be exposed to lots of things but do one thing a lot of times. So, as Anoni suggests, I have them TLC every experiment. By the end of the semester, they all know how to run a TLC and are pretty good at it.
    I also include a practical bit as half the final exam. They are given a list of 4 or 5 techniques at the beginning of the semester and told that they will have to perform one of these, drawn at random, in front of the prof (me) at the final. They’ll have 5 minutes. TLC, rotovap, set up a distillation, perform an extraction are usually on it.
    That usually runs to 40 or so students. You couldn’t do it with much bigger classes.
    I look forward to seeing what folks in industry think.

  10. Virgil says:

    As a biochemist, it is funny (and scary) to see that the dumbing down of courses for undergraduates is not unique to the life sciences. As a biochemistry undergrad, the organic labs we took in the early ’90s were easily on a par with what is being described here as advanced level for chemistry majors… synthesis of a complex compound every couple of weeks, several purification steps, validation of intermediates at each stage by IR spec, TLC, H-NMR, GC, melting point etc., and a final grade awarded depending on purity/yield of the submitted material. It was not unusual to have maybe 1/3 of the class of 50 succeed at a particular step. Their intermediate material would then be pooled and redistributed to the remainder of the class, for the next synthetic step.

  11. Phil says:

    I worked for 3 years in pharma right out of my B.S. before I came back to grad school. I learned most of the actual wet chemistry I needed by doing undergrad research. The teaching labs were pretty much useless.
    I think the basic skills an undergrad needs to have before moving on to grad school or a job in pharma have all been touched on, but I’ll give a list here.
    1) TLC – they need to understand how to monitor a reaction, even if they move to pharma and transition to an HPLC. It’s the concept of reaction monitoring that counts. Too many times I have seen young graduate students follow a literature procedure without ever taking a TLC or crude NMR. They think that running the reaction for the specified time is sufficient.
    2) Chromatography – especially important for grad school, but an associate in pharma needs to understand the basics before they move onto an automated chromatography machine.
    3) Distillation – This is something that people seem to be intimidated by, when it’s actually much easier than running a column. It just takes patience. Undergrads should at least know how to run a short-path distillation (fractional will take way too long for a lab period).
    4) Recrystallization – This is the only technique that was treated properly in my undergrad labs, and it was useful to have an idea how to do it before I tried to develop conditions to use in process.
    5) NMR – This part is time consuming for teaching labs if you have every student take an NMR. I don’t think learning how to use a specific NMR instrument (like the dinosaur Bruker I used in undergrad) is that important, because a student will need to be trained again on whatever machine they use later. What is important is learning how to interpret the NMR. I think having the TA run NMR on several of the students’ experiments and then having the whole class look at a selection (very clean to kind of dirty to total mess if possible) is the best way. A graduate student TA should be able to take 10 NMRs in half an hour and select 3 to work on in class.
    If a student can do these 5 things in the lab, and they have a good understanding of the concepts they learned in the lecture, they are prepared to be successful associates or graduate students.

  12. Pharma Mike says:

    I am with the cook book approach for the first year, making sure as you go along that the students know why they are adding this or doing that, of course. Then why not have each student use a different starting material so that each makes a different final compound? This would add fun and competition to the exercise and would also more closely mimic the actual work environment of making a string of analogs. For example, if the experiment involves a Grignard reaction on phenyl methyl ketone, have each student start with a different substituted phenyl or with an alkyl group other than methyl, making sure that this change wouldn’t interfere with the basic reaction, of course. The increased teaching value would come from the different yields obtained and the different properties of the final products and the discussion that could evolve from them.
    It’s been a long time since I was in the organic teaching lab so maybe this kind of experiment is done now routinely. But making a new compound is what turned me on back then and still does to this day.

  13. Liz says:

    We had three different labs: for majors, not for majors (that majors or others can take), and baby o-chem which the pre-meds take.
    The unknown lab was probably the most helpful. My prof picked unknowns based on our grade in the course (people that had a higher grade had harder compounds to solve). We used NMR, IR, GC, and some chemical-based approaches. We really had to know how to interpret spectra, which was good. We had a TLC lab too.
    The other helpful lab was a multi-step synthesis, but I think this would be better as Derek said if everyone does something slightly different.

  14. Anonymous says:

    The idea that non-science majors should learn organic lab techniques as a focus does a disservice to the field of organic chemistry. None of them care about extractions, or column chromatography, or even NMR. Instead, what we as chemists should be teaching to these undergraduates, and the public at large, is the relationship between chemical structure and function.
    For example, at my institution, everyone does a dyes and polymer experiment in the organic lab. I think this is a prime opportunity to refresh everyone’s knowledge about intermolecular forces, and how you can relate form to function. What would be even more interesting would be when synthesizing the OTC drugs include a discussion about how it functions biochemically (what functional groups interact with what amino acids on the enzyme). Perhaps have individuals make a small library of compounds, and then reveal which ones would have an effect and which wouldn’t (thus showing everyone the difficulty of rationally designing pharmaceuticals).
    Lay people fear and hate organic chemistry because they view it as entirely academic (as opposed to say biology), and we should all be trying to change that mindset.

  15. Beenawhile says:

    I would start with asking what the goal is, and there are several possible:
    1. Equip someone with working organic lab skills for use in industry
    2. Prepare an org chem major for graduate school
    3. Provide a science major with a useful lab context
    4. Give a future member of the general public an appreciation of chemistry.
    I think the last one is where there is the most opportunity, greatest need, and greatest failure. Here is my take on it: give them a sense that molecules that are all colorless white solids are different in many useful and interesting ways and the flip side also, when compounds display enough of the same properties, they are the same (you know, the whole ‘natural is better’ debate).
    When you look at it that way it is not so important to walk through what an FID is, but more that NMR and IR are useful diagnostics. I would emphasize physical attributes and tie them to chemical structure. For example, different odors of enantiomers, pull in steam distillation of eugenol from cloves to make it concrete.
    From there it can become interesting to know more about structure, and how you get to different ones -a smattering of synthesis.
    This is a bit opposite from the build-it-up-from-atoms approach that has good sense for option 2 above. But, it quickly gets into the sense of observation and deduction.
    If people could leave undergrad with an improved sense of observation and deduction I think society would be a better place.

  16. Phil says:

    I left out extraction accidentally. Undergrads should know how to use a sep funnel and also have an understanding of why you do 3 extractions and then a wash with brine.

  17. dearieme says:

    My own undergraduate organic chem labs were so long ago that they probably teach only two lessons. (1) All lab work must be pursued by individuals – no pair or group work. (2) The end-of-term practical exam should be genuine, and individual – at 2:00 pm you are each told what you are to synthesise and by 5:00 p.m. you should each hand it over for testing, along with your notes and your yield calculations.

  18. ZEKE says:

    11-Phil summed it up quite nicely!
    The TAs should demonstrate these hands-on techniques, TLC especially. This however can be problematic as most TAs are first year grad students with minimal training themselves. The blind leading the blind…
    The undergraduate students, either majors or non-majors, are there to learn Organic Chemistry and lab techniques thereof. Why should it be “watered down” for non-majors?
    Is calculus for non-majors going to be offered too?

  19. anon says:

    In the beginning, cookbook chemistry to teach things like running a tlc plate, chromatography, interpreting an nmr, etc. It is suprising the number of chemists in industry that would rush to put things on a lc-ms, when running a tlc would be faster and give enough information to make the same decision (or who would rather make a fool of themselves in group meeting rather than running an nmr).
    Then, for the chemistry majors, handing them a reasonable procedure out of a patent or journal and having them run it on their own. If there are problems, ask them to determine what went wrong if possible and how they would do things differently the next time (possibly assuming that they could do some basic literature searching).
    Don’t give the undergrad chem majors a polyanna outlook on everything working perfectly all the time, especially if they plan to pursue chemistry as a career. They will go out into industry or grad school, and will get extremely frustrated when things don’t work as expected and they don’t know how to deal with the situation. It will be a long and painful couple of months (for both them and their supervisor) to get them used to reality if they were taught that everything works perfectly all the time when they were undergrads. (I speak from experience on this.)

  20. Doug says:

    PLEASE PLEASE PLEASE include ‘chemicals I won’t touch’. When I learned chem, it was very dry and theoretical. Until I read some of your posts, it never occurred to me that the periodic table meant something. Your posts bring chem to life and that is sadly missing from most instruction.
    I also think it’s very helpful when an instructor/professor says ‘we have no clue why xyz does what it does’. These people are seen by students as infallible and it’s amazing to understand that there is stuff people don’t know.

  21. p says:

    I’m a little confused by the folks talking about “non-science majors” taking organic chemistry. As far as I know there is no one doing such a thing. There are “chem for jocks” type courses but the enrollment in orgo is chemistry majors, pre-meds and chemical engineering students.
    The pre-meds, it could be argued, don’t really need to know how to work in an organic laboratory. They probably don’t need a college education. The other two groups need to learn actual lab skills and I try to design my labs (and my courses) with the idea that I’m teaching future chemists. If some go to med school, so be it.

  22. Thomas McEntee says:

    Back in late 1970s, when a local university (CU Boulder) professor suffered a broken hip several days before the start of the semester, I was asked to leave the process development bench at Syntex Boulder and fill in for the semester in the classroom teaching organic chemistry. What I tried to provide was real-world context; for every class of organic compounds, my students learned about real uses for them. I had little use for MO theory or getting into the nuances of spin-spin splitting. What I wanted them to come away with was an understanding of where and why organic chemistry is so ingrained in what we use in everyday life. Needless to say, some eyebrows were raised among the faculty…but the man who wielded the real power in the chemistry department let me continue down this path. Among all of the faculty, he alone had once worked in the chemical industry.
    Chemistry should be taught as a practical science. Few students in any class will become professors. What students learn should help them navigate in life after they leave school and I am firmly on the side of making chemistry as relevant to society as is possible. To that extent, I support the views above that stress the importance of designing laboratory instruction to prepare students for life beyond academia.

  23. luysii says:

    #22 –“The pre-meds, it could be argued, don’t really need to know how to work in an organic laboratory. They probably don’t need a college education.”
    Agree with the first sentence. Strongly disagree with the second. Here’s why

  24. imatter says:

    @13: I wish pre-med majors don’t have baby-OChem classes. But for everyone’s sanity, it is there.

  25. rhodium says:

    When I had to do a semester of our second semester orgo lab, I had hoped to use more TLC so that students could understand the concept of following a reaction. For our 300 students, I found doing a few TLCs per experiment got to be really expensive, due to plate costs. We do have them look up data, use citations and we expect clear writing. Even if they never take another chem class, our writing requirements make a useful contribution to their education.

  26. Anon the II says:

    I think students should take any regular org lab course and then the next year they should have to teach it to the next years students. I never learned anything in my classes until I had to teach it. Then all that stuff I’d studied before began to make sense.

  27. Moebius says:

    We had a multistep synthesis – of the type protection, transformation, deprotection. We had students divided in three groups, each group was assigned a specific protecting group to put on and remove. At the end, all the students would put the data together, and compare yields, finding out which protecting group was better for the transformation.
    Another lab I did was about extraction, we had a mixture containing an acid, a phenol and an aniline and had to separate the three by extraction (after being explained the theory, we were pretty much left to our own devices to figure out what to use to separate the three).
    It is also nice to try procedures that don’t work extremely well, give side products etc, so students need to scratch their heads a little…

  28. gippgig says:

    I’m a complete outsider here (my interest is theory) but I really like the idea of making a dye (particularly if there is a family of closely related dyes so students could choose a color). The students could then dye a T shirt with their finished product, a good example of a practical application & a great souvenir (“I made this shirt in organic chem lab”).

  29. Donough says:

    @ P
    Engineers could be classed as non-science majors. If you ask me to say calibrate a GC and then run it without instruction I will have problems. While I am technically science, my skill set is very different to the chemists that I work with. Non-science majors could be closer to home than you think.

  30. J3 says:

    The thing I remember most from my undergrad organic lab and something that I was able to include in a lab course that I helped develop was to have the students actually running reactions. The course worked very well (with all experiments having been test run first), and it really gave the students a sense of context. Even a very simple reaction can be a better teaching opportunity for a technique like TLC, distillation or extraction than taking something out of a jar, working with it and throwing it away at the end of the period. Also, it gives a bit of a face to all those transformations that they read about in the text. Combining these into a longer synthetic sequence is, of course, even better.

  31. p says:

    Re 23: I didn’t say they shouldn’t take and know organic chemistry. But that isn’t the same as a college education. You could easily set up medical schools as a six year program. The last four years would be the same as now, the first two years would be all the basic science, with a medical perspective and emphasis, that they need for the four years they currently do. I’m not saying it would make them better people, but their medical training would be just as good. Perhaps better.

  32. rlb says:

    #22 –“The pre-meds, it could be argued, don’t really need to know how to work in an organic laboratory. They probably don’t need a college education.”
    Premed: But professor, why do we have to learn {orgo, physics, integration}?
    Prof: To save lives.
    Premed: ??
    Prof: It keeps stupid people from becoming doctors.

  33. Tim says:

    I’m glad to see some good discussion here… Those of you suggesting cookbook experiments should keep in mind that you can show the students a demonstration and give them a procedure to follow, but in most cases they won’t understand or learn anything. The fundamental procedures should be taught, but providing recipes is often the biggest barrier to understanding (see #27 for a great example of removing the instructions for an extraction experiment).
    Synthetic experiments that I use occasionally are to take procedures from the literature and have students adapt them to generate libraries. Each student prepares a different compound, and the procedure needs to be adapted to their starting materials and reagents (dust off some mole calculations) before proceeding. Different products with different spectra and a fairly high number of failed reactions (which is more realistic).
    These type of experiments work well for smaller classes (I have 40-50 students); I don’t imagine it would be as successful at a large university.

  34. Jordan says:

    In most Canadian universities, not only chemists but biochemistry, biology, microbiology, and physiology students take organic lab (these are generally separate “majors” for undergraduates). The chemical engineers will usually have their own organic chemistry class (often one semester only).

  35. Phil says:

    I lol’d.

  36. Don B says:

    I vote for ProteinChemist & Phil’s approach.
    Don’t bother with teaching organic chemistry to non-science majors. They can find out to make Meth & PCP on the interent.

  37. Anonymous says:

    @34: My experience with US (NorthEast) universities is the same. In particular the burgeoning biotech degree goes a bit further in their chemistry studies.
    @18&21: I think that where facilities exist to have two (or more) levels of organic chemistry, it would be a disservice not to have them available. In my experience, the typical chemistry major is going to take organic in their 2nd year of studies. This will occur after 2-4 ‘intro’ courses and generally in conjunction with other early specialty courses. The non-chemistry major, whatever their ilk, on the other hand, can afford to wait till 3rd or 4th year and still only have taken the intro year-long course that is generally not to the same level as a chemistry major’s intro course. Put all that together, and a single organic offering is going to be (1) too hard for non-majors and (2) too easy for majors. I don’t think that is the best approach for anyone.
    @33: I think that there is a fine line that needs to be drawn in a technical or fundamental approach, but I do think it has its merits. One two-week experiment I have taught is similar to #27, but the 1st week was a set of two easy extractions and the 2nd week was to be designed by the student. In this way they could have that hands-on experience that allowed for a useful 2nd week.
    The problem for the first semester of an orgo lab as I see it is that high school education is extremely variable. My wife and I both have chemistry degrees. I went to a very small private school in an area so rural that even public schools did not have real lab access. My wife went to an inner-city technical school that had majors and had what amounted to a science non-majors organic course in the 11th grade. Needless to say our technical skills upon entering that lab were at two extreme poles. Unfortunately I don’t see this disparity improving, so the burden is on the college/university to ‘waste’ those first few lab periods in bringing the students (the group in which I once numbered) that are behind up to speed.
    @14: I’d like to make the argument that techniques do in fact teach a structure/function (or at least structure/behavior) relationship. TLC, column chromatography, extractions show polarity relationships like nothing else. And on a related note, TLC gives a good appreciation for proper sample load and analytical vs. preparative (i.e. columns) scales.

  38. Industrialist says:

    @31 That’s exactly what happens in the UK. Med school starts at 18. Some put clinical all the way through, but a lot of the more traditional ones have a preclinical section of labs and lecturers followed by clinical training.

  39. Loon E. Toon says:

    My gripe is the cookbook nature of chem labs. Mix xg of compound A in Y mL of solvent B with zg of compound B for 10 min. Any real lab work required working out the conditions; even if we had a protocol, we’d tweak it and try to improve it (and use it for things its maker never intended). When I taught advanced organic, we had a section on lab techniques that were not taught in basic o-chem (TLC, vacuum distillation, etc), a few multistep syntheses, and the final project ‘given compound A, make compound B’, a transformation that could be done in two relatively simple steps. Because of the variability in yield between students, the multistep synthesis could not be entirely cookbook, and the final synthesis the students had to develop the techniques on their own from the literature and their textbooks (the librarians loved me, the TAs came close to revolt).
    I remember one of the students complaining that “this is not how research is done! I’ve done research with Professor xxxxx and we are always told what to do!” But when the class was over, they had an idea of what real o-chem was.

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