Org Prep Daily

October 8, 2006

Call For Authors

Filed under: Uncategorized — milkshake @ 3:36 am


sliva12.jpg Credit: Jirí Slíva

If you are interested in getting your procedures here, please let me know. The kind of procedures I would like to post here is a detailed write-up you would find in Organic Syntheses. Of course, Org Prep Daily does not compare even remotely – Organic Syntheses is a famous source of synthetic procedures and a golden standard of how good procedures should look like. It’s a real journal – and if you publish there you have a new entry in your CV publication list. But you may consider sending your procedures to Org Prep Daily just as well  – you could see it posted the next day. And the bareer to getting your procedure and name into Org Prep Daily page is not that high. Plus, you get puzzling comments from people reading your stuff.

The preparative procedures here don’t have to be new – a good reproduction of original procedures or their slight modification is just as valuable. The criterion is reproducibility and general usefulness. The idea is that you did the procedure with your hands – preferably several times – and you have all experimental details available (NMRs, solvents used for crystallization, volumes, reaction times, etc.) and the procedure is useful to other chemists in medchem labs and academia. It is required that the procedure is robust enough that it will work in hands of an average chemist on the first try unless he does some blatant srew-up. (I hate simple-looking procedures with 81% published yield that later turns out to be 18% in reality). The starting material should be commercially available –  or if not, it should be accessible in just few steps for which there is a good literature procedure. Also, if you submit multiple procedures, they shouldn’t be repetitive (for example, if you send me 10 procedures for 10 very similar aryl-substituted porphyrins differing only by the aryl substituents, I will post only one).

Putting up things here is a disclosure, so one should be careful about the project for which the work was done. If you are unsure about how your company or professor would react to your posting on Org Prep Daily, ask them first. (I would hate getting letters from lawyers asking me to take down some post or to go to court). It is a public domain so the procedures here are for everyone to see and use.

The way this kind of collaboration could begin is that you would e-mail me your procedure with a separate reaction scheme in ChemDraw (with ACS-style drawing setting) and I would put it up for you, with your name or nick of your choice. If things work well and the quality of your submissions is consistent and good, I would give you the site admin access and your could post on this site directly. Please, let me know if you are interested.

Of course, you can just as well start your own blog/chemistry page, for example hosting is free and the software is good and easy to use. But there is a reason why you should consider joining with Org Prep Daily: I would like to maintain a good quality of the procedures that appear here but I will try to make it fast and easy for chemists to post things here. If we convince few professional chemists to send here their good procedures – procedures that otherwise wouldn’t get published – and if Org Prep Daily readership grows, we could gradually improve the quality and make Org Prep Daily into a respectable and perhaps even mainstream chemistry site.


  1. Any suggestions for a good med chem book for chemists?

    Comment by let's get back to work — October 8, 2006 @ 9:01 pm

  2. I don’t know any good book since I did not get into this by reading books. I think J. Med. Chem articles are a pretty good start, especialy the ones that are written by groups from industry (I don’t like to knock academic groups but I have met some self-confident people at universities that don’t have a slightest clue about drug development but they impose the stuff on their students instead of teaching them chemistry).

    In ideal J.Med.Chem article, you would see the whole process from identifying active lead. Next thing is optimizing the lead (to a good potency in cell-based assay) while looking for metabolic liabilities like a weak sites in the molecule or potentialy toxic metabolites. Eventually the efficacy in animal model is tested at and few compounds with best properties like oral absorbtion, MRT, AUC and protein binding would be shortlisted for clinical candidate selection and go into animal tox studies. Each stage usualy means multiple rounds of derivatisation and this is often continued even after the final candidate selection has been made – the idea is to get a strong backup candidate for the project.

    Organic Process Research and Development is another good ACS journal, to give you understanding how the late stage of chemistry process optimisation of clinical candidate looks like. (This journal is dear to me because the procedures there usualy work well – when scaled down by 2 decimal places)

    Also, there is something like a “simple-design appreciation” the feel one develops from looking at structures of marketed drugs. It is a helpful guide, not infallible but quite coinciding with rules for getting good druggable compounds. So get curious about what is on the market, the structures are available from Merck index or from prescription informations. 

    Frankly, there is not much to “learn” about medicinal chemistry – just getting exposed to a project will get you there over few months. It helps to read papers from Lipinski etc but most of it comes by osmosis and practical experience, from thinking about your molecules and talking to people. The really important thing is to be a good chemist with a wide repertoir of reactions that you did with your own hands. The medchem part is just a little add-on which you can start without – but you cannot do medicinal chemistry without training in organic synthesis. The best preparation for medicinal chemistry is actually a short-but-varied total-synthesis project. Reaction methodology development experience is also helpful because it teaches how to patiently vary one parameter at the time, which is very much like the medchem optimisation derivatemania.

    Comment by milkshake — October 8, 2006 @ 10:10 pm

  3. Milkshake, you’re inspiring me to start reading Org Proc Res Dev. I’ve been meaning to hunker down with a couple of issues… seems like a good place to find procedures that work the first time.

    I wish I could contribute to your procedures, but unfortunately I can’t “disclose” the ones I have.

    Comment by Jordan — October 8, 2006 @ 10:18 pm

  4. It’s OK. Best Luck, Jordan.

    Comment by milkshake — October 8, 2006 @ 10:21 pm

  5. hey just an idea milkshake, but if you are going to be collecting a lot of procedures here, have you considered a section just for reagents? it would be a great resource; like a fieser and fieser with peoples experiences and comments tacked on the end

    Comment by kiwi — October 9, 2006 @ 6:08 am

  6. Take it easy. No pressure to update everyday. We have work to do. But please, do not overwhelm yourself and burn out working on this blog, because it’s suppose to be fun, right?

    Comment by Richard — October 9, 2006 @ 10:17 am

  7. You might try “The Organic Chemistry of Drug Design and Drug Action” by Silverman. I think it is one of the best at balancing “med chem” with oranic priciples.

    I don’t like to knock academic groups but I have met some self-confident people at universities that don’t have a slightest clue about drug development but they impose the stuff on their students instead of teaching them chemistry

    cough cough…. like my current group…. cough cough…

    Oh, the stories I could tell… companies formed… VC money burned… oh the tales 🙂

    Comment by milo — October 10, 2006 @ 6:50 pm

  8. I’ve noticed that one procedure I was searching for today and had seen here previously is no longer on this blog. The procedure in question is the “easy iodination of alkynes”, and I managed to find it using an internet archive. Just thought I’d let you know.

    Comment by Dan — February 17, 2012 @ 7:07 am

    • It is back now – thank you! There must be some sort of bug…

      Comment by milkshake — February 17, 2012 @ 10:28 am

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