Organic 2 – to bigger molecules
Expanding ideas towards Biology & Materials Science
Essentials from Organic 1
Organic 2 has been described as Organic 1 with thousands of resonance structures, plus spectroscopy. While the mechanisms do get more complicated as we head towards Biochemistry, they are based on the same ideas studied in the first semester. Most second semester pathways rely on acid-base reactions (proton transfers), nucleophilic attacks, and leaving groups breaking off. Some rearrangements occur but not many. With that in mind, you should come into Organic 2 with a solid understanding of the Substitution, Elimination, and Addition pathways that were covered in the first semester. The following playlists cover each of those key mechanisms.
You must be comfortable with drawing resonance structures, not from memory but as an instinctive skill. This will save you a lot of time as the mechanisms become more and more dense. In fact in some of the more intimidating mechanisms in Organic 2, up to half of the structures you draw will be delocalization patterns that help explain issues such as observed regioselectivity. Practice resonance structures until you are genuinely comfortable with drawing the required patterns.
Organic 2 Themes
While different classes will cover topics in different order, the main themes in Organic 2 are: the development of alcohol chemistry to deliver aldehydes, ketones, and carboxylic acids; the use of those compounds to make important derivatives such as acetals and esters; the study of extended pi systems and the chemistry of benzene; the application of spectroscopic techniques to structure elucidation; the use of functional groups to make C-C bonds and build bigger molecules (e.g. polymers). The material below gathers these ideas together with links to videos and tutorials to help you learn the topics. Mechanism videos for all of the reactions typically taught in Organic 2 are collected on the Reactions page.
Alcohols are one of the most important and versatile classes of Organic molecules available in bulk for synthesis. The ability to manipulate the functional group, by oxidation, alkylation, etc. makes these compounds essential as synthetic intermediates. The playlists below cover some of the alcohol basics with all of the important reactions studied collected on the Reactions page.
Aldehydes, ketones, carboxylic acids, and their derivatives, are important in both chemical synthesis and biosynthesis. They each serve as versatile electrophiles in reactions with nucleophiles, and the electron-withdrawing carbonyl group actives the alpha protons. The ability to react as both electrophiles and electrophiles sets these compounds up to be useful in condensation reactions such as the aldol family. Some of the reactions studied in this section are collected in the playlists below with the rest on the Reactions page.
After studying the consequences of extended pi bond conjugation we move into the reactions of aromatic systems. Chemistry at the benzylic position and then within the cycle itself is discussed in detail. The electron-rich aromatic cycle of benzene (and its relatives) serves as a useful electron sink and is able to help stabilize various intermediates formed at the benzylic position. The first playlist below left summarizes these reactions. Reactions at the aromatic cycle, with both electrophiles and nucleophiles, are summarized in the second playlist with the rest on the Reactions page.
Carbonyl species with alpha protons are weakly acidic, which means they are able to enolize to enols. Those species are weakly nucleophilic and react with good electrophiles like the halogens. The video below left summarizes the enol-based bromination of a ketone. Deprotonation with base produces enolates, which are much stronger nucleophiles and which react with a broad selection of electrophiles. Reactions of enolates are summarized in the below right playlist with the rest on the Reactions page.