Notation of Molecular Structure

I'm skipping some stuff in this textbook that's about molecule shape, bond angle and other important stuff. I'll get back to it later. Remind me to do that. Right now, I get to go over drawing organic molecules. Awesome. No really, this will be good to do because once this is out of the way, I can assume that you understand how these structures work and move on to whatever I want to. So it's very important that you understand this material. It will let you understand the notation I'll be using from now on. Fortunately, it's easier than you might think: I'm only introducing two structures here.

Condensed Structures:

Condensed structures are what they sound like. They take molecules like the ones I've been showing in previous posts and convey all of the structural information in a short line of text. They're not really practical in certain cases, but for most small molecules, they're easy to write and understand. I'll be using them when I can because I won't need MS Paint or anything like that. Let's start with some rules...

• All of the atoms are drawn in, but single bonds usually aren't.
• Atoms are drawn in next to atoms they are bonded to.
• Parentheses enclose groups of atoms that are all bonded to the same atom.
• Pairs of electrons are omitted.
• Read the structure from left to right and remember that every carbon must be tetravalent.

Don't get it? Don't worry. Here are some examples.

First example: n-butane
Molecular formula: C₄H₁₀
Lewis structure:









Condensed structure: CH₃CH₂CH₂CH₃

Notice the molecular formula, while telling us what atoms are in the molecule, doesn't tell us where they are. The Lewis structure does that. So does the condensed structure. We don't actually get the bonds drawn for us, though. Starting from the left, we have a carbon and three hydrogens. The assumption is that the hydrogens are bonded to the nearest atom, and since each hydrogen can only bond to one thing, that means that the first carbon is bonded to all three of them, leaving one bond open. Next there's another carbon, which must then be attached to that first one, meaning that the first carbon is tetravalent and the second one must still have three more bonds. Two hydrogens are written in after it, so they're both attached to that second carbon, leaving it with one more bond, and so on. With practice, it becomes quite easy to convert between regular Lewis structures and condensed structures, but you probably won't practice, so I'm not sure how easily this will come.

One note on this condensed structure is that it could be further condensed. When the same sequence is repeated, it's acceptable to enclose it in parentheses and use a subscript to note the number of repetitions. So an alternate condensed structure for this molecule would be CH₃(CH₂)₂CH_3. I don't want to be confusing here, but it's the first example the textbook used. Oh well, it does provide the lesson that there isn't necessarily just one condensed structure for a molecule.

Second example: isobutane
Molecular formula: C₄H₁₀
Lewis structure:
The hydrogen atoms are crowding into each other here, which is why I had to cut off two of the bond lengths. In reality all of the hydrogen-carbon bonds would be identical except for the one on the hydrogen attached to the middle carbon. But that's a topic for a more advanced post. I should have just made the carbon-carbon bonds dashes and the hydrogen-carbon bonds hyphens in order to avoid the crowding, but I already made this stupid picture and I'm not recreating it now, so you're stuck with it.

Condensed structure: CH(CH₃)₃

The molecular formula is the same as the previous example. But the condensed structure is completely different. It shows that the first carbon has a hydrogen attached to it, which takes up only one bond, so it has three left. Then there are three CH₃ groups (that's what the parentheses are for) all attached to the same atom, which must be that first carbon. So in our two examples so far, we've used parentheses in two different ways. In the first example, they enclosed a chain of the same repeated group and in the second example, they enclosed identical groups all attached to the same single atom.

Third example: 2-butene Molecular formula: C₄H₈
Lewis structure:









Condensed structure: CH₃CH=CHCH₃

We still depict multiple bonds, which is why I was overjoyed when I realized that I could use the "≡" symbol, already having "=" to represent double bonds. Everything else in this example should be familiar from the two previous examples. The hydrogens are listed directly after the carbons they're bonded to and each carbon is listed after the carbon it's bonded to.

Fourth example: methyl acetate
Molecular formula: C₃H₆O₂
Lewis structure:
Don't worry about the name here. Nomenclature of molecules will come later. Now, if you stayed awake for the post on Lewis structures, you should understand the structure of this molecule.






Condensed structure: CH₃CO₂CH₃

Are you getting the hang of this yet, or will you be a failure forever? We start on the left with a carbon that has three hydrogens attached, then attach the next carbon to it, which apparently has two oxygens attached to it. But how do we know if they're attached by single or double bonds? Well, like I already said, each carbon must be tetravalent. The second carbon is already attached to the first carbon, so that's one. It can't have two double-bonded oxygens attached to it, because that would be five bonds to a carbon atom. It could have a single bond to each oxygen and a bond to the next carbon, but that would leave both oxygen atoms with only one bond and oxygen forms two bonds (uh, unless it's a free radical or an ion or something, but this isn't, so shut up). The only possiblity left is that the second carbon is double-bonded to one oxygen and single bonded to the other, leaving that oxygen with one more bond left, which goes to the next carbon. And finally that last carbon is attached to three hydrogens. Easy.

That's how the textbook does it, but it's not how my professor did it. He would draw the condensed structure like this: CH₃COOCH_3. This is fine, but I had to be careful, because I kept thinking that this version of a condensed structure was depicting a peroxide, in which the oxgygen atoms actually are attached to each other. So don't make that same mistake. And remember to make sure that the atoms have the right amounts of bonds. If that structure really were depicting a peroxide, it would mean that the second carbon is only forming three bonds.

Skeletal Structures:

I like skeletal structures. They're a lot easier to draw than condensed structures, but they're pretty much impossible to type, as far as I know, so I'll have to use MS Paint or something. Many compounds have rings. Using skeletal structures makes depicting rings easy. They're also good for large, branching compounds and the like. They can also be used for smaller compounds down to ones with only two carbon atoms. Again, we'll go over some rules...

• Any time there is a corner where two line segments meet or a point where a line segment just ends, that represents a carbon atom.
• Hydrogens attached to carbons are not depicted. You're supposed to be able to figure out how many hydrogens are attached to each carbon all by yourself. You can do that right? I mean, what are you, a child?
• Atoms that are not carbon or hydrogen (also known as heteroatoms) are drawn in and any hydrogens attached to them are drawn in too.
• Triple bonds mess with the first rule a little bit because they force the atoms involved to form a straight line, so there won't be any corners, but know that if no heteroatoms are shown there, the things forming the triple bond must be carbons.
• Skeletal structures are awesome.
  

Since you've already mastered condensed structures, I'm not going to waste my precious time drawing the Lewis structure for this first example. Figure it out yourself.

First example: n-hexane
Molecular formula: C₆H₁₄
Condensed structure: CH₃CH₂CH₂CH₂CH₂CH₃
Skeletal structure:
Yeah, I was too lazy to try to make it on MS Paint, so I spent more time than it would take me to just draw that damn thing looking around the web for an image I could use and trying to get it the right size. I still managed to make it pretty small and puny, but you get the idea. In the future, I'll either get this figured out or just go all sloppy and draw my skeletal structures in MS Paint.


Both ends are carbons and each corner is a carbon atom. If you can count, you'll realize that's six carbon atoms all in a straight chain. And if you're not stupid, by now you realize that the carbons in the middle of the chain still need two bonds each, so they'll all be bonded to a pair of hydrogens, while the carbons on the ends of the chain will need three hydrogens. And look, that perfectly matches the condensed structure. And it has the same numbers of both types of atoms as the molecular formula. It's almost as though this is science or something.

Second example: cyclohexane
Molecular formula: C₆H₁₂
Condensed structure: Fool, you cannot draw a condensed structure for cyclohexane (it has a ring).
Fine then, Lewis structure:
Yeah, I know. It looks like crap. My awful drawing skills are preserved for all the world to see. Moving on...







That sure is ugly, so let's see the skeletal structure:









Yeah, that's right. It's a hexagon. I'm pretty sure even you are smart enough to know that a hexagon has six corners. Each one represents a carbon. And since each carbon is bonded to two other carbons, that means there must be two hydrogens on each carbon.

That's enough about skeletal structures for now. They can get a lot more complicated, but I'll try to ease you into it, rather than saying, "Look, it's capsaicin."