Getting ready for Organic Chemistry is key.

Periodic Table: the student needs to have a good understanding of why the periodic table is organized the way it is. Knowing roughly where the main atoms reside in the table will be a huge help.   

Periodic Trends: knowing why the elements are organized in rows and groups based on their electronic structures will allow the student to make predictions on properties when the elements show up in Organic molecules.   

Electronegativity: since Organic Chemistry is full of terms such as “electron-poor” and “electron-greedy” the student needs to have the ability to assess electron density patterns within a molecule quickly. 

Valence: the number of bonds an atom may form, and the number of lone pairs that are (or are not) present, will dictate the reactivity of organic molecules and their ability to act as nucleophiles or electrophiles. 

Atomic Size: related to periodic trends, the size of atoms will play a very important role in their ability to hold a negative charge as conjugate bases and as leaving groups in substitution and elimination reactions. 

Acids & Bases: first studied in General Chemistry, Organic acid-base reactions are the first time students are required to put together all of the concepts studied thus far, including the mechanism of the proton transfer process.

Octet Rule: almost all of the elements used in the undergraduate Organic Chemistry sequence are at the top of the periodic table and thus are in search of the perfect electronic “octet” in their valence shell.

Types of Bonds: are a result of the relative electronegativities of the atoms involved; very different electronegativities (e.g. Na and Cl) means ionic bonds through electron transfer, while close electronegativities means sharing in covalent bonds.

Shapes of Molecules: will be dictated by the number of sigma bonds and lone pairs involved; 4 sigma bonds = tetrahedral (with slight variations if lone pairs replace sigma bonds); 3 sigma bonds = trigonal planar (i.e. flat), and 2 pairs = linear. 

Reactivity: is mostly governed by atoms in molecules being electron-rich or electron-poor; electron-rich atoms (i.e. bases or nucleophiles) attack electron-poor atoms (i.e. Lewis acids or electrophiles).

Kinetics: relates to how fast a reaction occurs and how high activation barriers will be; simple ideas like a crowded environment means slower reactions while accessible environments (i.e. easier to get to) means faster reactions and lower Eact.

Thermodynamics: atoms and molecules want to become more stable and have a variety of pathways (mechanisms) to low energy states; some pathways are reversible, which leads to equilibria and the application of Le Chatelier’s principle.

This video explains the transition into Organic Chemistry 1.

Consider the simple acid-base reaction between HCl and NaOH that is studied extensively in General Chemistry. We know that the products are NaCl (salt) and water, that heat is given off so the reaction is known to be exothermic, meaning the products are more stable than the reactants. Everyone beginning Organic Chemistry has done that reaction at least once in General  Chemistry lab. We can use that reaction (shown in Figure (i) below) as a starting point for Organic reactions and mechanisms.

In Organic Chemistry we need to dig deeper and ask why this reaction occurs, why it is exothermic, and how might it be described in terms of the required bonds being formed and broken. Most of the answers will employ the simple concepts listed above.

We know that NaOH and NaCl contain ionic bonds because of the big differences in electronegativity between Na (0.93) and O (3.5) an Cl (3.0). This means Na metal gave away its single valence electron to become Na+ in each of those salts with O and Cl being able to complete their octet by picking up that electron. We notice that Na+ on the left of Equation (i) is still Na+ on the right so it has not changed chemically and is therefore ignored as a spectator ion in the eventual mechanism.

So why is the right-hand side of this equation favoured so heavily and how might we describe the bond-forming and breaking events that need to occur to turn reactants into products? From first principles we can talk about reactivity and stability of the different species using bond energies and considering where the electron excess (the negative charge) will be more stable. In Figure (ii) the water product has a stronger covalent bond than in HCl and the negative charge prefers to be on the large chloride ion.

The products are more stable than the reactants, which explains why heat is released during this reaction, but what courses the starting materials to react the way they do? Why do O and H bond to give water and Na+ swaps its anion to become NaCl? The why and the how will lead us to a reaction pathway (a mechanism!). Again, electronegativity will explain most of this. The O in hydroxide is negatively charged and electron-rich while the H in HCl has a slight positive charge and is electron-poor as seen in Figure (iv).

We find that the electron-rich part of NaOH (the O) attacks the electron-poor part of HCl (the H) with the O acting as electron-donor (base) and the H acting as electron-acceptor (acid). The extra lone pair from O becomes the new bond pair in water and the covalent bond between H and Cl breaks, to deposit a fourth lone pair in chloride, thus avoiding breaking the octet rule. The mechanism for this process may be described using the Organic Chemistry “curved arrow” notation as described in Figure (iv).

Notice what we did here; we identified the bonds that needed to be formed and broken and then considered which of the involved atoms would be electron-rich and which would be electron-poor. The electron-rich part of the NaOH molecule (O, the basic center, or later, the nucleophile) then attacked the electron-poor part of the HCl molecule (H, the acid, or later, the electrophile). This type of analysis will get you far in Organic Chemistry even when the molecules and mechanisms get to be quite complicated.

Consider the reaction in Figure (v) below. We have to decide which starting material is the acid, which is the base, which bonds need to form and break, which side of the reaction is preferred, and which mechanism arrows need to be applied. That sounds like a lot to remember but it’s a process that becomes easier with more practice. To begin, the molecule with the metal involved is usually the base since the atom next to the metal is negative and thereby electron-rich. Here the alcohol is the acid and sodium amide the base.

Since the Na+ does not change we can ignore it again and focus on the O-H bond that needs to break and the N-H bond that needs to form. Knowing that the O is better with the negative charge, since O it is more electronegative than N, the right side will be favoured. We correlate this idea with pKa values early in the first semester. Now the mechanism may be written as in Figure (vi) with the electron-rich N attacking the electron-poor H on O and giving the observed products.

The discussion of acid-base chemistry from the Organic Chemistry perspective usually comes early in the undergraduate course sequence and provides a platform for the investigation of some 120 reactions and mechanisms over the two semesters of study. Use the GenChemBasics PDF file below to review the main topics before beginning Organic 1.