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Long story short, I'm mostly doing calculations in the past 5 years of my scientific carrier and every year I get less and less confident in my knowledge of organic chemistry which besides was never perfect. Yeah, I still remember pretty well some trivial things like nomenclature, classes of compounds, etc., and I'm pretty comfortable with MO theory, hybridization, etc., but all this are, so to speak, just the foundations of the organic chemistry. What I'm really bad at are the applications, primarily, the reaction mechanisms.

Many times reading a paper on computational studies of a reaction mechanism I caught myself not being able to (relatively quickly) grasp the main idea. I spent a fair amount of time just to recall the very basics of, say, the $S_N2$ reaction. Back many years ago I knew this things. Maybe I knew them not so perfectly and systematically, but even this knowledge of organic chemistry had evaporated almost completely from my head.

So I'm looking for a good resource to refresh and improve my knowledge of organic chemistry primarily (read: almost exclusively) regarding the most common reaction types and their mechanisms. A resource is counted as a good one if:

  • It is goes straight to the point (reaction mechanism) without discussing the basics of organic chemistry I mentioned, rather assuming that the reader knows them.
  • It is (relatively) concise and concentrated on the basics. In other words, I have neither time nor interest to read 2000 pages long Advanced Organic Chemistry book with all the details, exceptions, dirty laundries, etc. Just the basics.
  • On the other hand the basics has to be discussed in sufficient details, i.e. I would not be satisfied with the relevant Wikipedia (or similar) pages.
  • It is trustworthy. I mean, well established authoritative reference.

I admit I might ask for to much, but who knows, maybe there is something I'm looking for out there.

P.S. The type of a resource does not matter: textbook, lecture notes, MOOC video course, whatever.

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  • $\begingroup$ It sounds like you're looking for a sophomore level organic book. It would be a few hundred pages, but you don't have to read the whole thing. $\endgroup$ – jerepierre Sep 23 '15 at 22:01
  • $\begingroup$ Love the question, and wish someone comes up a useful answer. My experience with organic chemistry and calculations is very disappointing: many reaction mechanisms seemed not more than educated guesses at best. $\endgroup$ – Greg Sep 23 '15 at 22:58
  • $\begingroup$ I would be happy to go through my somewhat outdated library and look for the right book for you, but it would help if I had a better understanding of what you wish to do with your calculations. Are you trying to computationally predict rates or outcomes of reactions given the reactants and conditions? If that is the case, you will need experimental data on rates and outcomes to test your methods with. Or someone to collaborate with that can generate such data. $\endgroup$ – iad22agp Sep 24 '15 at 14:48
  • $\begingroup$ @iad22agp, basically, what I wish is the following: given molecules A and B being able to say what types of reactions are expected and know their comventional mechanisms. I know reality is usually different from these simple models, but often not strikingly different. I need a starting direction anyway. $\endgroup$ – Wildcat Sep 24 '15 at 15:29
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    $\begingroup$ Maybe Grossman's book would be helpful: amazon.com/Writing-Reasonable-Organic-Reaction-Mechanisms/dp/…. You can skip the first chapter about basic stuff, the rest is 100% mechanistic oriented. $\endgroup$ – Marko Oct 3 '16 at 19:54
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The book you are looking for is The Art of Writing Reasonable Organic Reaction Mechanisms by Robert Grossman.

One of the book's publishers offers this description of the book:

Intended for students of intermediate organic chemistry, this text shows how to write a reasonable mechanism for an organic chemical transformation. The discussion is organized by types of mechanisms and the conditions under which the reaction is executed, rather than by the overall reaction as is the case in most textbooks. The treatment emphasizes unifying principles, showing how common mechanisms link seemingly disparate reactions. Each chapter discusses common mechanistic pathways and suggests practical tips for drawing them. Worked problems are included in the discussion of each mechanism, and “common error alerts” are scattered throughout the text to warn readers about pitfalls and misconceptions that bedevil students. Each chapter is capped by a large problem set. The author has drawn on his own research and the current literature to ensure that appropriate attention is given to topics across the range of modern organic chemistry. The text is unique in its inclusion of a chapter on reactions mediated or catalyzed by transition metals, an area in which mechanistic understanding is now essential. Relatively new topics such as olefin metathesis and cycloaromatization are covered without giving short shrift to more traditional areas such as carbonyl chemistry. The text assumes a basic knowledge of organic chemistry. It can be used either in a formal course or by students working on their own, and will be particularly useful for graduate students studying for qualifying examinations. It will also be useful to students and researchers in biochemistry, pharmacology, and inorganic chemistry.

Each of the book's chapters are $50 \pm 30$ pages and are packed full of example problems. Each chapter is organized according to the class of mechanism, not around particular reactants or products. The chapters are:

  1. The basics.
  2. Polar reactions under basic conditions
  3. Polar reactions under acidic conditions
  4. Pericyclic reactions
  5. Free-radical reactions
  6. Transition-metal-catalyzed and -mediated reactions
  7. Mixed mechanism problems

The author maintains a good web site with additional problems, additional worked examples, and answers to every problem in the book. You can get a sense of the content of the book by browsing Amazon or by looking some of the answer .pdf files, available for free from Springer.

I found this book very helpful in improving my mechanistic understanding of various types of reactions.

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If I were designing a course from scratch, I'd do something like this:

  • carbonyl addition and conjugate addition
  • nucleophilic substitution
  • elimination
  • reactions of enols and enolates
  • electrophilic aromatic substitution
  • pericyclic reactions
  • radical reactions (?)
  • carbenes (?)
  • organometallic chemistry (?)

The topics with (?) are important, but you can probably get by without them.

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Here I'm in France so the link is in French sorry, but I turned my phone in english and this application is in english so if you have a phone which can have application from google there is this one which is really good :

Organic Reactions

Why this application is good ?

  • First because ten of the most used conpounds in chemistry how to synthesis them, what reactions you can do from them to obtain an alcohol for example and then how to protect them. It gives you the mechanism for most of them.

  • Second it has a name reactions module which have not far from a hundred of reactions for examples Dieckman condensation, Appel's reaction, the mechanism is written full and each molecules involved are in colors so it is really easy to see what is done.

  • Third, because it has a glossary with (not all it is impossible) but a lot of abbreviations such as for example (DHQ)2PHAL and it gives you what it looks like which can always be useful.

  • This application is not all free (in fact I don't remember exaclty) but it is not expensive and you can test it with the free one if it is not.

I hope it can help you, it is easy to carry you can be offline obviously so nothing wrong with this app. It may have but very rarely a typo I may have seen one, one time, but nothing hard to understand.

I hope it can help you.

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