JibbyDee - 26-11-2011 at 10:17
I'm not new to organic chemistry but when I'm required to figure out the mechanism for a particular reaction I barely even know where to start. I'm
doing organic chem lectures and lab this semester so I want to get good at organic chem now. What approach should I take? Should I just start learning
the mechanisms of the common classes of reactions? The problem I have with that I can know a mechanism but have no idea why the various steps in the
mechanism take place. I want to gain a good understanding of the underlying principles behind it all so I'll automatically know why the various steps
in a mechanism occur etc.
The simplest class of reactions I know of are nucleophilic additions to carbonyl groups. Even this I don't fully understand. I just learned about
using amines as nucleophiles to convert ketones into imines. I understand why the nucleophile adds to the carbonyl carbon but in this particular
reaction an -OH group gets protonated and the H2O group leaves. I don't understand whats going on there, I can't even figure out what electrons go
where when that happens. I need some underlying theory. I have a good general chemistry grounding and I've read a good few chapters from Organic
Chemistry by McMurray last year so I know a lot about organic structures, their orbital geometry, stereochemistry and various other things but when it
comes to reactivity theres a huge gap in my knowledge. I have Organic Chemistry by Clayden but have only read the introduction. Should I just start
learning about the classes of reactions covered in this book in hopes that an intuitive understanding will eventually form or are there specific
concepts I should learn which will give me the underlying knowledge required to understand whats going on in the mechanism of an organic reaction?
[Edited on 26-11-2011 by JibbyDee]
devongrrl - 26-11-2011 at 12:58
The mechanisms are all linked to the electronic structure.
Curly arrows, cations, pushing electrons etc.
Think about how electrons going into different shells, eg Pauli exclusion principle and when electron degeneracy comes in. 4s fills before 3d.
Look at how valence shell electron pair repulsion dictates the shape of the molecule.
Also don't forget electronegativity increases as the Group number increases but decreases as you progress down the table.
You can scrape by with memorising the different ways different functional groups interact but to get a better understanding I'd try and ask yourself
why they work that way.
Clayden's text on Orgo is excellent with a wealth of info in it, Chapter 5 describes the use of curly arrows to denote movement of electrons.
I hope there are some ideas here for you to think about.
Khan Academy on the web has some interesting videos you could look at.
BromicAcid - 26-11-2011 at 13:27
Sounds like you're on the right track by really trying to understand the mechanisms. My old orgo teacher always said:
"You learn organic chemistry with a pencil in your hand."
JibbyDee - 26-11-2011 at 18:38
devongrrl: Thanks for the info. I have a reasonable understanding of orbitals, VSEPR theory and electronegativity trends, its just the arrow pushing
part that I'm lacking in. I noticed my organic chem teacher going on about leaving groups and pKa like they are the most important things you could
possibly learn in organic chem so I suppose these are two areas well worth gaining a good understanding of.
EDIT: Yep, this is definitely a good area to start. I never saw the correlation between acidity and leaving groups until now.
[Edited on 27-11-2011 by JibbyDee]
francis - 26-11-2011 at 19:25
Hey, its funny you should say this because I am reading Clayden right now for organic chem...it's my course prescribed textbook.
In my first semester of organic chem I used McMurry and found it very helpful, same with second session but when it came to mechanisms I found the
same problem - it was 'automatic', I had some vague ideas, but wasn't thinking, more sketching when doing mechanisms.
The first few chapters of Clayden are quite good for this stuff (the acidity chapter, I think its chapter 8, is quite helpful).
Clayden doesn't have the reaction summaries nor the clarity of McMurry (it feels like there's too much unnecessary stuff in there) but it is a good
book...the problem sets will help immensely.
Also a book that's remarkably helpful for mechanisms is Robert Grossman's "The Art of Writing Reasonable Organic Reaction Mechanisms".
The whole point of the book is to get a student to write mechanisms for reactions they've never seen before. I think if you've read McMurry you could
easily read Grossman (it's a short book with lots of problems in it) and come out with a fine understanding of electrophilicity, nucleophilicity,
acidity, basicity and how mechanisms work.
One thing he says is to identify the type of reaction, then if it's a polar reaction, identify if it's occurring under acid or basic conditions.
In acid conditions, protonation will usually be a first step and by the same token, under basic conditions deprotonation will usually be a first step.
If you have the reaction, list all the bonds broken and all those made. Identify the nucleophile and the electrophile, based on your knowledge of
functional groups and of the conditions.
Again, in Clayden the first few chapters on structures and orbitals is handy - if you learn to look for the HOMO and LUMO in a given reaction you will
be well able to see how it reacts.
turd - 27-11-2011 at 02:05
As with all things in life - you learn it by working with it.
JibbyDee - 27-11-2011 at 20:23
francis: Thanks a lot. I'm gonna get that book by Grossman. If its small it should be cheap enough. Thanks a lot for the summarised info. Whats the
alternative to a polar reaction? Free radical reactions? I'm reading chapter 5 in Clayden at the moment which seems to be what I'm looking for.
francis - 27-11-2011 at 22:18
Yep, polar reactions usually involve bond breaking to form charged species or charged species bonding to form neutral species, etc (ie the bonds break
heterolytically).
Substitutions, eliminations, additions are the classes of polar reactions he lists, both in acid and base conditions.
The other classes he lists are free radical reactions, pericyclic reactions and transition-metal catalysed reactions like olefin metathesis, Pd
coupling etc (despite the latter being polar, their mechanisms are a bit different).
Also I believe he puts in rearrangements under the Pericyclics section.
Yep, the Clayden early chapters are good. If you read through them and do the problems you'll find it very helpful.
Like I said before, the only problem I have with Clayden is, that for an undergraduate student it is a very hefty book, at least a thousand pages, and
it's a bit less ordered I think than say Ege or McMurry.
It would be good to have the session off and read through it for interest's sakes, but if you're doing three other subjects, and you're writing lab
reports, assignments, etc, its hard to find that kind of time, even if you read it before bed, in the shower, on the toilet, breakfast, lunch, dinner,
on the train home etc.
Re: the imine formation
If you can understand acidity/basicity (pkas), electrophilicity/nucleophilicity, and some basic molecular orbital theory (just HOMOs and LUMOs),
you'll be able to examine the reaction of an amine with a ketone and see why it reacts that way....
Its a bit more difficult than automatically writing mechanisms, which I do quite often (and get wrong answers) 
But its absolutely necessary to be able to predict the mechanism of a reaction you've never seen before, based on those factors I mentioned, plus
reaction conditions.
Knowing those will help, as well, with predicting products.
If you learn various properties of reagents, then you can "reason by analogy", using knowledge of one reaction, predict how others will go.
Nonetheless some memorising can help. I found that making charts of reactions helped: eg start with some alkene, then form the saturated alcohol, then
oxidise it to the carbonyl, then form the imine, etc etc.
Some good examples are here (actually this site is very good, lots of good problems):
http://www.chem.wisc.edu/areas/reich/chem345/phenylacetic-ac...
The site is
http://www.chem.wisc.edu/areas/reich/group/index.htm
(the CHEM343 and CHEM345 are helpful for first session organic chemistry).
Second lastly, see if you can find a copy of Daniel Weeks' Pushing Electrons....its a really helpful little book, which trains you to start drawing
and thinking about resonance structures
(in Clayden they explicitly don't say resonance structures, because the structures don't resonate between each other but rather represent electrons
delocalised over molecular orbitals....I think they call them 'delocalisation structures').
That book helped me a great deal when I started with Organic chemistry. I think spending as much time on problems, perhaps more, as you do on study,
will see you cruise through.
Lastly:
there are some tremendous online video and audio lectures. Check out the Khan Academy's organic chemistry playlist, its great for first-session
organic chemistry. Also, search 'COOL McGill' on Google, McGill has a lot of organic chemistry lectures from a number of years. I think
'freevideolectures.net' aggregates this sort of thing.
And even YouTube: there's a user called 'lamechivanes' who has a series of quite short (5-10 min a piece) videos, from very beginning to second/third
year org chem (I think it's a University of Illinois thing but I'm not sure).