First blog of 2023!
Diverging from technology, I’d like to discuss a bit of chemistry today. Having taken Advanced Chem last semester (and not knowing what I can write 750 words about), I figured describing the very convoluted and backward way organic chemists name molecules would be a great thing to do.
Before we start, there are a few prefixes that you need to know:
Here, Meth- means 1, eth- means 2, prop- means 3, so and so forth.
Let’s start with the most basic molecules, Alkanes. These are single bonded Carbon molecules. Not bad!
Here’s an example below:
C’s denote carbons. Now how do we name this molecule?
We simply count up the amount of carbons (here there are 5), find the corresponding prefix from our handy chart (in this case pent-), and simply add the suffix -ane since this is an Alkane molecule (single bonds connecting the carbons, seen above by the single dashes), this molecule is pentane.
That wasn’t bad! But a majority of molecules have branches of either carbon chains (like what we see above), or different elements.
Here is a slightly harder molecule:
I’ll explain the Iodine (I) and bromine (Br) seen here. There are a few molecules that are often attached to these carbon molecules, which we denote with the prefix Iodo- for iodine, bromo- for bromine, fluoro- for fluorine, etc. Since this molecule is more than just a simple chain, we need to order our branches.
We start ordering from the end with the closest branch. Since with this molecule, either end has a Iodo- molecule or a bromo-molecule 1 carbon in, this is a tie and results in us using the very backwards approach organic chemists take to order these molecules: going by the alphabet.
Which letter comes first, I (like iodo-) or B (like bromo)? Bromo, so we start ordering our molecule from that end. So from right to left, we name each carbon with a number, starting with 1, then 2, then 3, then 4, up to 6.
Lastly, we have a carbon branch. Referring to our table, this is a single carbon, so it should start with the prefix Meth-. Since it’s a branch, we end it with -yl, so we call this branch methyl.
Now taking all those parts together, we have our right to left ordered carbon, bromo, iodo, and methyl branches, now it’s time to name! Here’s a picture below, with the carbons ordered and the branches circled.
Again, going by the alphabet, we name the branches before the base molecule, so bromo, iodo, then methyl.
Bromine is attached to the second carbon, so we name this branch as 2-bromo. Iodine is attached to the 5th carbon, so we name it as 5-iodo. (Note here, while the methyl is the next molecule we should name, organic chemists chose to do it alphabetically so we have to name the iodine branch first!). Lastly, we have the methyl branch, attached to the 3rd carbon, so we call it 3-methyl.
Finally, since we have 6 carbons, consulting our handy chart this works out to be hex- as a prefix, so hexane as the base chain of 6 molecules.
Put it all together, and this molecule is 2-bromo 5-iodo 3-methyl hexane.
Nice! We can name linear molecules, but what about circular ones?
Here’s a more complex molecule. Note how the red donut of 5 carbons are connected to each other in a circular fashion. Since they are this way, we add the prefix cyclo- to the ending bit of the molecule. Since this central (red) ring of carbons contains 5 of them, referring to our table this molecule should have pent- in it. Furthermore, we can see the “bonds” or lines around the 4 o’clock region of the molecule are double instead of single, this denotes a double bond, which would mean this molecule is an alkene, slightly different from the Alkanes we named earlier. This means the molecule above would end with the conventions cyclopentene.
Onto ordering the carbons! We found with the previous molecule that we need to order the carbon order so that the branches are in the right places. Since this is a alkene, we must start at a double bond (more organic chemistry backwardness). Yet do we name our carbons clockwise or counterclockwise?
It turns out here that we should follow the red number order, since each way you start naming you name a branch on the 3rd carbon. Since the E in Ethyl comes before the F in fluoro, we name with the red numbers.
All in all, this makes the molecule 3-ethyl 5-flouro 4-iodo cyclopentene.
Here’s Mrs. Brucker’s youtube channel for further information: https://www.youtube.com/watch?v=GJVvOixr–c&list=PLQAytuMyLyMVTdfLoCTSCEsGr6Qb46OMs. She is infinitely better than me at teaching this material!
-Max
5 thoughts on “How to Name Organic Molecules”
Hi, Max, very informative and educative post! You’re just like a really fun teacher who explains things in very easy-to-understand terms and pictures. I especially enjoyed your relaxed tone and little quips of encouragement since they made reading this very entertaining, despite the fact that many people may think chemistry is dull or boring; you’re able to write about the subject in such a way that captures the reader’s attention and keeps them engaged! I remember taking regular chemistry freshman year, and that I had a lot of fun figuring out the names of the molecules and seeing how they fit together. Reading your post took me back to that time. In addition, I think your hand-drawn pictures (love your use of different colors, by the way!) of the molecules add a really neat touch to the explanations, as they offered a visual aid and helped demonstrate your points better. You must be truly passionate about chemistry to take advanced chemistry and even write about it in one of your blog posts, and I respect your enthusiasm for the subject a lot. After all, chemistry isn’t for everyone! Some like it, some don’t. And I’d say that even though I enjoyed it, I wouldn’t want to do it again in the future. Incredible post, Max!
Jiahan Wang
I am still so confused…I was I got a D in chemistry!
hhitzeman
Hi Max! I also took advanced chem last semester and I surprisingly LOVED it. When it comes to school, math and any kind of science class are always at the bottom of my favorites list, but I took advanced chem based on a recommendation from a peer, and it ended up being way more fun than I originally expected. I liked the challenge of it and looking back, I think that if my circumstances were different freshman year (teacher, COVID), I would have liked chemistry a lot more than I did. Obviously the highlight of advanced chem is the crime scene, but even a topic like naming molecules was really interesting to me. It took a while for me to understand it, and I still don’t completely, but since this was such an integral part of the semester and the final exam, I definitely worked on it a lot and found it to be somewhat exciting. I love how you took what you learned in a class and decided to teach it to others in an easy to grasp way. You did such a good job explaining this, and I think that you could give Mrs. Brucker (who has to be one of the best teachers I’ve ever had) a run for her money. Great post!
aknelson
The overwheliming majority of my experience with chemistry has been confined to my honors biology class during sophomore year and my viewings of Breaking Bad- there is not a hint of irony in those statements. It’s safe to say your blog is both engaging and informative on a topic that I hadn’t really devoted any time or attention to studying, and the way you broke the naming process down into a step by step guide reminded me of a good instruction manual or YouTube tutorial- direct, to the point, and helpful. Your inclusion of 5 images and diagrams breaks down a complex subject that would only be multiplied in difficulty if you just gave us a wall of text and more or less left the reader to fend for themself. Our biology class contained a simplified style of molecule and compound naming, and we were mostly taught to identify key compounds with easy names like lactose, fructose, glucose, etc.. We were rarely, if ever, actually taught to identify uncommon compounds and fixated on the ones most crucial to cell function and biology as a whole. Using this article as a reference, I believe I could pick up organic molecule naming really quickly if I dedicated the proper time and effort, and I thank you for sharing your passion for organic chemistry with us all.
dmdelegge
Max, I’m currently taking AP Chemistry and organic chemistry was my first unit. I think I was pretty good at that unit because it was my best test score. But, I did forget quite a bit of it as the year went on. Reading your blog reminded me of a lot of the things that I had learned, so thanks for the review! I always found the prefixes interesting because from the 2nd to 4th prefixes, the lettering broke the usual norm. Eth- as a prefix kind of makes sense, but prop- and but- are unique to me. As a math guy, I would think it would be trit- and tetr-, but I suppose those may be too difficult to say out loud. I only sort of remember the suffixes, but I think the pattern for those are -ane for single bonds on carbon, -ene for double bonds, and -yne for triple bonds. In AP Chemistry, we didn’t get as in-depth as what you showed in your blog, so it was interesting to learn how to name the more complex chains of molecules. Maybe these will show up on the AP exam, who knows, but now I will be prepared to answer those questions!
abmistry