Wanted: A Virtual Organic Chemistry Set

by James

in Teaching

Second choice: a virtual pet cat

Here’s something I’d really like to have: a virtual organic chemistry set.

What I’d like to do have a simple piece of software that lets me choose a simple molecule from a menu, and then be able to choose a reaction to use with it that one could find in a typical Org 1/ Org 2 course. I’d then like to be able to take this new product and then apply new reactions to it, gradually building up to more complex molecules.

Ideally it would have a very intuitive graphical interface. Furthermore it would be extra great if you could run reactions in reverse, showing how you can break molecules down to simpler components. Finally, it should recognize functional groups: I don’t want to have to choose from the same huge menu of possible reactants every time, I want it to constrict choice based on what I’m dealing with.

In essence, I’d like an electronic chemistry set that would let me build molecules up (and take them apart) like Lego.

Does such a thing exist? If not, it should.

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{ 20 comments… read them below or add one }


Well, let my colleagues the time to finalize it and it will come eventually ;)
One of the projects of my university is called EnCORE, Electronic Organic chemistry Reactions Encyclopedia (in french though) and aims at such kind of applications.


Christine Rogers

The old DOS program called Beaker had some of these features. It also had a nice NMR spectrum simulator that could be used to generate spectra for tests.



I was hoping for an iPad or iPhone app :-)



Well, there’s Jmol’s ‘model kit’ mode:


but that’s really just (‘just’!) an editor. I know some people working on predicting the next steps in biochemical reactions, which is slightly more like it. There was some discussion of showing a molecule in the center of a ‘wheel’ of next steps like this:


(sorry to self-advertise). The image shows completely meaningless relations, and random highlights, but is sortof amybe what you are talking about…


Geoff Hutchison

The hard part about this is the database of reactions, not the visualization or functional group identification.

If you’re aware of a significant database of organic reactions — ideally machine-readable (ChemDraw or MDL Rxn, for example), we can definitely integrate this into Avogadro.

But the only reaction databases I’ve found are either in-progress (e.g., EnCOrE, which I can’t find online) or commercial.

Any ideas?



I’m not aware of such a database. If I had a set of Chemdraw files of a whole set of different reactions for Org 1/ Org 2, how difficult would it be to put something like this into action?


Geoff Hutchison

The reverse-synthesis (retrosynthesis) is pretty unlikely right now, although there are people working on it.

I suspect from a good set of ChemDraw files and some work, it could be done in a few months.

The basic idea is that you’d want to convert the ChemDraw files into a list, each entry with:
1) A reaction name
2) A pattern for the starting functional group
3) The functional group transformation

Given such a list, it’s not hard to see how to code the tool you describe.

The catch is that I’ve got an over-full plate until summer.

But if you’d like to send me a file or two to check out, let me know. geoffh / pitt.edu.



I think that people would pay for this kind of a tool. The first person that puts it together and makes it accessible for the iPhone/iPad would be in a position where they could sell this to undergrads. I think you could learn a lot from a program that lets you play around with different reactions and explore how they work, without necessarily having to do a lot of book learning.


carol gustavson

My daughter is uga and really wants to be vet. However, she feels like organic chemistry is killing her. She studies hard, but says she feels her friends can read and understand so much easier. She says even if she studies first and helps her friends, she later forgets the info.

I am researching because she is so busy. Do you have any insight on this type of situation? She usually does great in biology and math, organic chemistry is a no go.

Thank you,



Some people just have different learning styles. What are the things your daughter does really well? Is she a physically active person? Musical? Writer? These kinds of things could give insight into how she learns and maybe provide a window through which to approach the subject. The more parts of your brain you use while learning or recalling something, the better it should be able to stick in your brain.
Organic chemistry rewards people who learn really well by reading, so I encourage people who aren’t doing well that way to use their other senses. Write things out as much as possible – write and write and write. At the same time, talk to yourself (even if you feel a little crazy). Talk to yourself like you are explaining what is going on.
I think a lot of people who read this blog are chemical educators so maybe they might have some insight as to how to learn the material better.


Peter M

I am an undergrad student, taking a second session Organic Chemistry course.

I have not used the textbook much (it’s the Clayden book, and my puny arms can barely lift it off the ground).

For learning reactions, I read the lecture notes, then rewrite them.

I rewrite the reactions, and the mechanisms, with some notes.

Then I write flashcards, from my notes.

Then I sit and record me reading the flashcards (front and back). I listen to this recording on the way to and from Uni.

Lastly, I write a ‘summary sheet’ of the reactions (similar to what James has here).

I then go and do problems. If I need to, I look at the flashcards to help me.

When I am driving or relaxing, I try and think of a compound, and how to synthesise it using the reactions I know of.

The texts I’ve found helpful are ‘Instant Notes in Organic Chemistry’ by Patrick (which is very condensed – its a small book)….for more extensive info, I’ve tried McMurry’s ‘Organic Chemistry’.

Also – Khan Academy has a section on Organic Chemistry. It’s very helpful.
Use ‘academic earth’ (academicearth.org) to find online organic chemistry lectures.
YouTube has lots of videos of Org 1/2 reactions and mechanisms.

Lots of writing and drawing reactions from these videos can help.

– ACE Organic Chemistry is a program online that proposes questions, and asks you to draw (using their software) the product of a reaction, and/or the reaction mechanism.
What’s great is, if you get the answer wrong, it will give you a hint in the right direction – rather than just revealing the answer.

– ChemSketch: this is free and a good way to find out the names of molecules (you draw them in, and use the ‘name molecule feature’ and it tells you the IUPAC nomenclature.


That’s what I use to study Organic Chem. But my midsession is next week and perhaps I’ll tell you to disregard my advice after I get my marks back :)



Awesome. That’s a great collection of *very specific* study advice. I might have to make this a post in itself! Good call on ChemSketch – I wasn’t aware of that useful tool.



I m very intrest in organic chemistry in machnisam rearrgement



When i need some organic name reaction.



I’m not sure what you’re asking, could you be more specific?


Peter M

Thanks James.

Check out the Org 1/2 (Org 212 and Org 222) lectures that McGill puts up.

Here’s the main online learning site:

Here’s the Org 222 lectures, so far for Winter 2011:

They’ve been really helpful for me. They also have tutorials (where a tutor goes through a bunch of questions). The tutorials are every 5 or 6 lectures.

They teach the Org 212 and 222 courses in WInter, Summer and Autumn each year. So there’s 3 versions of each course – if you don’t like the teacher you can go to 2010 and use those lectures, or 2009, etc.

Also the Khanacademy.org I mentioned, his list of Organic chem lectures is relatively small – but he gives ten minute videos in an informal sort of way, teaching a kernel of the subject in each.

I use Yahoo Answers and chemicalforums.com (the organic section) when I need help with something and can’t ask my lecturer.

Oh and for writing mechanisms, ‘Pushing Electrons’ is a very helpful book (especially for reteaching resonance, and visual depictions of molecules to students who might have forgotten those concepts)….its very simple…short introductions, then lots of problems.


Peter M

The main learning site is http://cool.mcgill.ca/



É mais com química orgânica…


shawki harahshah

Im iteresting to no more about organic chemistry


Joshua Hughes

Well it just so happens that I had an Orgo I professor that wrote an applet to do very nearly what you describe. I loved the “game” he made; you were given a target molecule and then asked to use the few dozen reactions provided to transform your starting material into the product. The only problem is that I can’t get the applet to work on his anymore and keep getting an “Unsupported major.minor version 52.0.” error instead. If you can get it working for you I think It will be just what we all need…and please tell me how you did it if you do. Here’s the site:


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