How to Build a Computer 8: Organic Chemistry


I started with a discussion of the magic of photoresist, however (say it with me!) it got long-winded and I cut it down to the organic chemistry review. Next week photoresist. This week we’re going over some basic organic chemistry. Sounds fun, right? It’s going to be even more fun than that! You wait and see. We’re going to start small though, with methane.

You smell something? No? It’s probably just me.

This is a carbon atom, often found in the presence of ranch dressing. It’s surrounded by four olives, or hydrogen atoms. The pimento is only there for flavor. Carbon though is much like Silicon in that it comes with four electrons in its outer shell. In terms of orbitals that works out to 1s2 2s2 2p2. Carbon is in something of a unique position; you can make long and interesting chains of molecules with it. You can try making chains of other molecules, say, oxygen, but the results get… explosive. Anyway, a single carbon atom makes the simplest possible carbon chain. Let’s make it a more complicated.

In a nod to our RBBBF Sponsors; here’s that ancient friend of mankind; ethanol!

Ethanol is a chain of two carbon atoms (ethane) and a bonus. It comes with an oxygen group off the edge, represented by a chunk of summer sausage. These sort of functional groups make all the difference between a solvent and the active ingredient in vodka.”Organic” chemistry just refers to the fact that you’re playing with carbon atoms. The combination of stringing atoms together like that and adding assorted functional groups means that you can make an astonishingly wide variety of things with these molecules. Here are two more for you. Note that I’m leaving off the hydrogen; they’re needed elsewhere. To garnish martinis.

This is octane, as in the fuel rating of your gasoline. No, I don’t understand how that system works either.

I guess I don’t have anything funny to say about 2,3 dimethylhexane. Nobody does, really.

That’s right, I said it. 2,3 dimethylhexane. Lemme unpack that for ya. “dimethyl” means it’s got two methane groups on it. “2,3” tell you where those groups are located; on the second and the fourth spot from the left. Couldn’t you spin it around and call it 4,5 dimethylhexane then? Sure; it’s a free country, ain’t it? The rules ask you to use the lowest numbers possible, but it describes the molecule just the same.

I’ll run another one by you; what’s in those molecules? If you recall that there’s supposed to be hydrogen making up all the missing spots, Octane is C8H18, in the hexane (whatever you call it) it’s C8H18. Precisely the same atoms, but the slightly different arrangement changes it. Octane boils at 114 degrees Commie (237 degrees Freedom) versus that hexane boiling at 115.6 C (240 F).

Okay, what if you want to make something that’s really long? I’ve only got so many chunks of cheese. But couldn’t you in principle make really long chains of carbon? As long as you want? Sure; it remains a free country. A polymer is a really long chain of repeating small elements. Like what? Polyethylene is just a long chain of carbon atoms; repeating groups of two. It’s plastic. Another? Every other carbon atom, add a Chlorine atom on instead of one of the hydrogens. That’s polyvinylchloride; PVC, as in the pipes. One more; supposing you take your hydrogen and replace them all with fluorine atoms? You get Polytetrafluoroethylene, PTFE. 3M (a cheap Wisconsin Mining & Manufacture rip-off) markets it under the trade name “Teflon”.

That’s all fun, but a bit of a digression. To finish the setup for the photoresist I’ve got to explain two more concepts. One is double bonds. The other is the Benzene ring:

A special Thank you to @MattBalzer for providing the non-localized pi-bond. By which I mean frying up some onion rings.

I put the hydrogen atoms back on to make a point. Carbon atoms make four bonds. There’s one to the hydrogen, one to the carbon clockwise on the ring, one to the carbon counterclockwise and… where is the fourth bond?

The most common bond between carbon atoms is a single bond. You could also make a double bond; share four electrons between two carbon atoms (each bond consists of one electron from each atom at either end). If you’re doing that though you end up with less hydrogen in your molecule. Each double bond means you need two fewer hydrogen atoms to satisfy your requirements. That, incidentally, is the difference between saturated and unsaturated fats. A saturated fat has no double bonds in its hydrocarbon chain; it has all the hydrogen it can handle, thus it’s saturated. Unsaturated fats have one or more double bonds; they could fit some more hydrogen in them. And trans fats? Take an unsaturated fat, add some hydrogen to it to make it partially hydrogenated.

You can have triple bonds too; requires even less hydrogen. C2H6 is ethane; single bond. C2H4 is ethene, double bond, and two less hydrogen. C2H2 is ethyne; you’ve got three bonds between the carbon atoms and only one for a hydrogen atom on either side. Incidentally, that stuff is also called acetylene; or the stuff you burn in your cutting torch.

Benzene is another beast; it’s got a non-local pi bond. A single bond is called a sigma bond, and it’ll allow the molecule to rotate around it. A double bond has pi bonds, which don’t let things rotate. (Nothing to do with circles; there’s only so many greek letters and they tend to get reused.) Benzene has six sigma bonds (again, nothing to do with the black-belt twerps), and maintains the rest of its electrons in a pi bond. This produces a very stable structure and you see it over and over again in organic chemistry. I could give you examples, but there are other Ricochetti who have already written it up. Benzene shows up in aromatic compounds, which make up perfumes. Keep jamming benzene rings together and you get a sheet of graphene.

I hope you can see now why I find organic chemistry to be so much fun. Look at the things that we’ve covered; we’ve talked about plastics and perfumes, about Teflon welding torches, with a dash into dietary science. It gets even better when you start looking at biology; you get DNA and proteins and all kinds of wonderful stuff that we’ll be avoiding because it has nothing to do with making computers. Now that you’ve got an idea of what these molecules are like though you’ve got the basis to understand how photoresist works. Join us next week for photo#resist or even more shamelessly stolen jokes.

We talked about one other everyday application of organic chemistry. Can’t quite remember what though.

This is part eight of my ongoing series on building a computer, the way Frank Sinatra wants it done. You may find previous parts under the tag How to Build a Computer. This week’s post has been brought to you by Muldoon’s Men’s Wear. Since 1950 the dapper gentleman has known that the finest haberdashery comes from Muldoon’s Men’s Wear.

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  1. Hank Rhody, Possibly Mad Contributor
    Hank Rhody, Possibly Mad

    Arahant (View Comment):

    RossC (View Comment):
    Anyway I wonder if this is where the Cis/Trans thing comes from?

    Much older than that. It comes from Latin. In the late Eighteenth or early Nineteenth Century, for instance, there was the Cisalpine Republic in northern Italy. Just old prefixes finding new uses.

    I tend to remember it from “Cisalpine Gaul” and “Transalpine Gaul”. One of which was closer to Rome than the other.

    In the factory there’s a machine called Slot Die. (Used for coating, by the way). There’s an inspection machine called George on either side of it. Never got a straight answer as to why they’re called Georges. No matter.

    No lie, I tended to think of one as “Cis-slot die George” and the other as “Trans-slot die”. I was clever enough to never use those descriptors in conversation because then I’d end up explaining “Cis”. This was before it became a thing in the LG-acronym community, at least to my knowledge.

    • #31
  2. Judge Mental Member
    Judge Mental

    Arahant (View Comment):

    Judge Mental (View Comment):

    Arahant (View Comment):

    Judge Mental (View Comment):
    Ricochet dictionary.

    Ricochet has a dictionary?

    You’re right… the spell checker just knows.

    That is associated with your browser or your operating system, not Ricochet.

    I think you’ve kind of lost track of the point.

    • #32
  3. Gary McVey Contributor
    Gary McVey

    The only real life application I’ve seen for the term is “cislunar”, when an Apollo command module was between Earth and lunar orbit. 

    • #33
  4. RightAngles Member

    In these instances, “trans” means “over” or “through” rather than the implied “across” of sex change.

    • #34
  5. RossC Inactive

    Hank Rhody, Probably Mad (View Comment):
    I tend to remember it from “Cisalpine Gaul” and “Transalpine Gaul”. One of which was closer to Rome than the other.

    OK I looked it up.  Cis-alpine meant Gauls on “this” the Roman side of the Alps who were more or less just like Romans.  Their Trans-alpine brethren were “across” the alps in France who were not like Romans because of the female attire their warriors preferred to don.


    • #35
  6. Jim McConnell Member
    Jim McConnell

    Hank, I wish you wouldn’t post those pictures. Now I’ve gotta head for the deli again for cheese and olives.

    • #36
  7. CurtWilson Lincoln

    Hank Rhody, Probably Mad:

    You get Polytetrafluoroethylene, PTFE. 3M (a cheap Wisconsin Mining & Manufacture rip-off) markets it under the trade name “Teflon”.


    Pedantic nitpick: “Teflon” is the DuPont trade name for PTFE. My father was a DuPont polymer chemist, as was his colleague Bill Gore, who left DuPont to produce actual products with PTFE (e.g. Gore-Tex), when DuPont only wanted to sell bulk PTFE.

    • #37
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