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Structures of molecules can be difficult to piece together at first when you are just starting in an organic chemistry class. One of the tricks that can greatly help with this is to know the uncharged or “normal” state for atoms that are commonly found in organic molecules. Here is a table of the most common of those:
– C has four bonds and no lone pairs
– N has three bonds and one lone pair
– Halogens (F, Cl, Br, I) have one bond and three lone pairs.
– O has two bonds and two lone pairs
– H has one bond and no lone pairs
Three more rules:
- C, N, O are central atoms, meaning that they will always be in the middle of your molecule.
- H and halogens are terminal atoms, meaning that they will only have one bond and be at the ends of molecules.
- With the exception of H, atoms in group I & group II are only counterions (+1 or +2 and not involved in resonance).
Remember, these rules are for when the atom is uncharged; this does not apply to charged atoms. For example, a carbocation (a positively charged carbon atom) will have only three bonds with no lone pairs while a carbanion (a negatively charged carbon atom) wlll have three bonds with one lone pair.
Notice that all of these atoms still follow the octet rule. However, beware of atoms that do not follow the octet rule, as phosphorus is an example of an atom that can have more than an octet of electrons. Shown below is triphenylphosphine oxide, a byproduct of the Wittig reaction.
Elements with open d-subshells, like phosphorous and sulfur, do not always follow the octet rule. More examples of this are SF6 and PCl5. However, carbon, nitrogen and oxygen will follow the octet rule.
A problem we see students constantly running into is that they do not readily recognize strong acids. This is a terrible mistake and should never happen. You will need to quickly recognize strong acids and which atom they will be protonating. As far as strong acids go, you should immediately recognize the Magnificent Seven:
STRONG ACIDS: HI, HCl, HBr, HNO3, H2SO4, HClO3, H3PO4
Just think that that it’s the three hydrogen halides and the four acids that have N, S, Cl, and P as central atoms. Many students remember the other four acids with the mnemonic, something you would never say to a girlfriend: “Never Say ‘Please Clean’ ”.
Once you have recognized that you have a strong acid present in your reaction, it is necessary to determine what it is protonating. Remember that H+ is electron-deficient (Lewis acidic) and will look for an electron-rich (Lewis basic) atom to protonate. This could be a nitrogen atom, such as an amine, or an oxygen atom in a carbonyl or an alcohol. Most often, the atom being protonated will have a lone pair somewhere.
Take Home Message: Know the strong acids, the mnemonic Never Say ‘Please Clean’ might help
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Learning organic chemistry is like trying to work in a foreign country where if you don’t know the language, it is going to be very difficult to learn how to do your job. You have just been transported to the mythical country of “ochemia”, a small island nation in the south Pacific, where your job is to write chemistry reactions.
Frequently, in a chemistry lecture, professors start tossing out organic chemistry terms far too quickly. Because students aren’t fluent in “ochemia” yet, they need to translate each word in their head to understand what the instructor has just said. By the time this mentally translation is done, the student has just missed the next sentence and has lost half of the lecture. Our goal is to get as fluent as we can in the language of chemistry as quickly as we can. Here are some terms it will be helpful to memorize so that you don’t have to do a mental translation when you hear them:
Meth = 1
Eth= 2
Prop = 3
But = 4
Pent = 5
Hex = 6
Hept = 7
Oct = 8
Non = 9
Dec = 10
Electrophile = wants electrons, has a positive or partial positive charge
Nucleophile = has electrons, has a negative or partial negative charge
Halogen = F, Cl, Br, I
Aprotic solvents = do not contain OH or NH bonds
Protic solvents = contain OH or NH bonds
Lewis Acid = electron acceptor
Lewis Base = electron donor
Carbonyl group = (C=O)
Cis = same side of a double bond or ring
Trans = opposite sides of a double bond or ring
A comprehensive organic chemistry glossary can be found at: http://www.chemhelper.com/glossary.html
As always, for more help in organic chemistry, please go to Organic Chemistry
