Contributor Post Created with Sketch. Recommended by Ricochet Members Created with Sketch. 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. RightAngles Member

    Now see, if I’d had you as a teacher I might not have been such a science bonehead. Okay maybe I would have.

    • #1
    • July 21, 2018, at 6:57 PM PDT
    • 3 likes
  2. Hank Rhody, Badgeless Bandito Contributor

    RightAngles (View Comment):

    Now see, if I’d had you as a teacher I might not have been such a science bonehead. Okay maybe I would have.

    “If at first you don’t succeed”, as the saying goes, well, mix yourself another bloody Mary and try try again.

    • #2
    • July 21, 2018, at 7:12 PM PDT
    • 5 likes
  3. Gary McVey Contributor
    Gary McVey Joined in the first year of Ricochet Ricochet Charter Member

    I’m glad you called out 3M on that theft of intellectual property thing. Also, since we’ve got that RBBBF audible radio program coming up, it’s about time we alerted people to the benefits of recreational alcohol. I think extensive exposure to the laws of organic chemistry might interest more curious young people into taking the plunge. 

    • #3
    • July 21, 2018, at 7:32 PM PDT
    • 4 likes
  4. Sam Rhody The Insane Member

    Hank Rhody, Possibly Mad (View Comment):

    RightAngles (View Comment):

    Now see, if I’d had you as a teacher I might not have been such a science bonehead. Okay maybe I would have.

    “If at first you don’t succeed”, as the saying goes, well, mix yourself another bloody Mary and try try again.

    I thought that if at first you don’t succeed, skydiving wasn’t for you. 

    • #4
    • July 21, 2018, at 8:53 PM PDT
    • 9 likes
  5. Arahant Member

    Quite a series, I must say. Now, I’m hungry. I wonder why.

    • #5
    • July 22, 2018, at 1:43 AM PDT
    • 4 likes
  6. Gary McVey Contributor
    Gary McVey Joined in the first year of Ricochet Ricochet Charter Member

    And if there’s anyone on this site besides Hank who knows about combining mind-bending complex ideas with mouth-watering new and appetizing food combinations, it’s Arahant. It’s only 1:47 am here. Maybe there’s some kind of underground delivery service that would bring me bockwurst, sauerkraut, a selection of quality cheeses, some Polish sausage, a hot tureen of Berliner potato and sausage soup, and…

    …A Viennese iced cake baked in the shape of a benzine ring. 

    • #6
    • July 22, 2018, at 1:51 AM PDT
    • 3 likes
  7. Arahant Member

    Gary McVey (View Comment):
    some Polish sausage, a hot tureen of Berliner potato and sausage soup,

    I do have the potato and Polish sausage soup here for dinner tonight.

    • #7
    • July 22, 2018, at 1:57 AM PDT
    • 2 likes
  8. Gary McVey Contributor
    Gary McVey Joined in the first year of Ricochet Ricochet Charter Member

    I still don’t get it. How is it that hydrogen and flourine create one of the most corrosive, explosive, energy-laden of rocket fuels, and yet somehow combined another way, can be major family members of safe, stable products like Teflon? I guess I should admit the obvious: he sorta did explain it well enough for everyone but me. 

    But he’ll never manage to explain table salt to me. Shake some salt into a pan of water. Now, by contrast, toss a block of solid sodium over a protective wall into a tank of water. Hah? No wonder that Morton’s Salt girl keeps skipping along in the rain. She knows something the rest of us don’t. 

    The rest of us–except Hank Rhody. 

    • #8
    • July 22, 2018, at 2:19 AM PDT
    • 3 likes
  9. Gary McVey Contributor
    Gary McVey Joined in the first year of Ricochet Ricochet Charter Member

    Arahant (View Comment):

    Gary McVey (View Comment):
    some Polish sausage, a hot tureen of Berliner potato and sausage soup,

    I do have the potato and Polish sausage soup here for dinner tonight.

    Damn you, Arahant. Your comment practically amounts to midwestern hate speech, taunting the hungriest among the most sausage-deprived in the middle of the night when the stores are closed. The sausage-deprived community…

    Uh, wait…there’s something a little off about the phrasing…

    • #9
    • July 22, 2018, at 2:24 AM PDT
    • 5 likes
  10. Arahant Member

    Gary McVey (View Comment):
    The sausage-deprived community…

    Yeah, we don’t want to know about those midnight desires, Gary.

    • #10
    • July 22, 2018, at 2:35 AM PDT
    • 3 likes
  11. Henry Racette Contributor

    Terrific series, Hank, if a bit quixotic: if you’re going to dip into the chemistry of photoresist etching as part of how to make a computer, I can only assume you’ll be talking about fab stepper technology and Czochralski wafer forming next. 

    The idea of using appetizers to model hydrocarbons was brilliant. Do you cater?

    • #11
    • July 22, 2018, at 12:18 PM PDT
    • 7 likes
  12. Arahant Member

    Henry Racette (View Comment):
    Do you cater?

    Yeah, send over the octane platter with a side of oxygen slices.

    • #12
    • July 22, 2018, at 12:30 PM PDT
    • 5 likes
  13. Hank Rhody, Badgeless Bandito Contributor

    Henry Racette (View Comment):
    and Czochralski wafer forming next. 

    Covered in part one.

    No, I don’t cater. I have been gorging myself on science all day.

    • #13
    • July 22, 2018, at 1:19 PM PDT
    • 4 likes
  14. Hank Rhody, Badgeless Bandito Contributor

    Gary McVey (View Comment):
    I still don’t get it. How is it that hydrogen and flourine create one of the most corrosive, explosive, energy-laden of rocket fuels, and yet somehow combined another way, can be major family members of safe, stable products like Teflon?

    Hmm… let me try another analogy.

    Young Frankenstein, okay? At the start Doctor Frankenstein is engaged to that New York socialite. He’s Hydrogen, she’s Fluorine. HF; it’s one of the more corrosive acids. Makes ’em easy to separate, to react with other things. He reacts to the lab assistant (Inga? I think her name was Inga) who represents, I don’t know, oxygen. You get water. Meanwhile, the fiancee comes to visit, and meets the monster, who is Carbon. There’s some difficulty in forming the bond to begin with, but they’re essentially inseparable afterwards. The one bond is extremely easy to split apart, but once you’ve configured the elements with partners more to their liking then it’s much harder to reconfigure them again. The materials are much less reactive now.

    Sodium in water is like an Aircraft Carrier putting in to port in Orlando while there’s also a national convention of the Pretty Young Single Nurse’s Association (one of my favorite charities). You’d better believe there’s an explosion. Now imagine that each and every young sailor on that aircraft carrier is married to a drop-dead gorgeous prom queen back home. Sure; they like the nurses, sure they’re glad to mingle with them, but if things get anywhere beyond that “Sorry ladies, I’m taken.” The men are still Sodium, but their wives are the Chlorine, and that’s enough to get the sailors to dissolve harmlessly into the water.

    • #14
    • July 22, 2018, at 1:56 PM PDT
    • 7 likes
  15. Gary McVey Contributor
    Gary McVey Joined in the first year of Ricochet Ricochet Charter Member

    the Pretty Young Single Nurse’s Association (one of my favorite charities)

    Isn’t that being merged next weekend with the Rhody Balzer Booze Fund?

    • #15
    • July 22, 2018, at 2:21 PM PDT
    • 3 likes
  16. Hank Rhody, Badgeless Bandito Contributor

    Gary McVey (View Comment):

    the Pretty Young Single Nurse’s Association (one of my favorite charities)

    Isn’t that being merged next weekend with the Rhody Balzer Booze Fund?

    One certainly hopes.

    • #16
    • July 22, 2018, at 2:23 PM PDT
    • 5 likes
  17. Henry Racette Contributor

    Hank Rhody, Possibly Mad (View Comment):

    Henry Racette (View Comment):
    and Czochralski wafer forming next.

    Covered in part one.

    No, I don’t cater. I have been gorging myself on science all day.

    Ha! And so you did. What I get for spending three months buried in a project and not giving social media the attention it deserves. ;)

    • #17
    • July 22, 2018, at 4:33 PM PDT
    • 2 likes
  18. Hank Rhody, Badgeless Bandito Contributor

    Henry Racette (View Comment):
    not giving social media the attention it deserves.

    So you gave it more than zero attention? Sounds like a mistake.

    • #18
    • July 22, 2018, at 4:36 PM PDT
    • 1 like
  19. Henry Racette Contributor

    Hank Rhody, Possibly Mad (View Comment):

    Henry Racette (View Comment):
    not giving social media the attention it deserves.

    So you gave it more than zero attention? Sounds like a mistake.

    It’s a relative thing. The rest of my life sets the parameters for “worthy use of my time” pretty low. 

    • #19
    • July 22, 2018, at 4:38 PM PDT
    • 3 likes
  20. RossC Inactive

    Hank you may have missed an opportunity to show the link between organic chemistry and the LGBTQ community. No, it is not lube. Molecules with the same atomic makeup that can be twisted around carbon double bonds are called isomers and have different properties depending on the orientation of the atomic groups. The normal shape is called a “Cis Isomer” and the twisted shape is called “Trans Isomer”. Here is a picture.

    The butenes are different, the one on the right for one thing has seen the musical Grease over 25 times. Anyway I wonder if this is where the Cis/Trans thing comes from? It’s gotta be right?

    But seriously if I can Isomerize hydrocarbon molecules I can make a bloody fortune. Normal Butane is valuable enough and goes into cigarette lighters and camping fuel, but Iso-Butane can be blended with gasoline which sells at a substantial premium to Normal Butane. Trans can be awesome.

    • #20
    • July 24, 2018, at 10:40 AM PDT
    • 10 likes
  21. Gary McVey Contributor
    Gary McVey Joined in the first year of Ricochet Ricochet Charter Member

    The readers of this series have minds that are insanely great, when they aren’t greatly insane. Often, both. 

    • #21
    • July 24, 2018, at 10:53 AM PDT
    • 2 likes
  22. Arahant Member

    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.

    • #22
    • July 24, 2018, at 10:55 AM PDT
    • 6 likes
  23. Judge Mental, Secret Chimp Member

    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.

    It is a prefix that is almost entirely unused in American English, except for this example and maybe one or two others. Whereas trans is used ubiquitously. Cis seems like an odd choice in the gender wars. (BTW, the dictionary recognizes trans but not cis. Evidence of my point.)

    • #23
    • July 24, 2018, at 11:00 AM PDT
    • 1 like
  24. Matt Balzer, Imperialist Claw Member

    Judge Mental (View Comment):

    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.

    It is a prefix that is almost entirely unused in American English, except for this example and maybe one or two others. Whereas trans is used ubiquitously. Cis seems like an odd choice in the gender wars. (BTW, the dictionary recognizes trans but not cis. Evidence of my point.)

    Maybe so, but if you’ve got a trans on the other side I dunno what your other options are.

     

    • #24
    • July 24, 2018, at 11:03 AM PDT
    • Like
  25. Arahant Member

    Judge Mental (View Comment):
    (BTW, the dictionary recognizes trans but not cis. Evidence of my point.)

    You need a better dictionary. Mine from 1980 has it.

    • #25
    • July 24, 2018, at 11:03 AM PDT
    • Like
  26. Judge Mental, Secret Chimp Member

    Arahant (View Comment):

    Judge Mental (View Comment):
    (BTW, the dictionary recognizes trans but not cis. Evidence of my point.)

    You need a better dictionary. Mine from 1980 has it.

    Ricochet dictionary.

    • #26
    • July 24, 2018, at 11:06 AM PDT
    • Like
  27. Arahant Member

    Judge Mental (View Comment):
    Ricochet dictionary.

    Ricochet has a dictionary?

    • #27
    • July 24, 2018, at 11:08 AM PDT
    • Like
  28. Judge Mental, Secret Chimp Member

    Matt Balzer (View Comment):

    Judge Mental (View Comment):

    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.

    It is a prefix that is almost entirely unused in American English, except for this example and maybe one or two others. Whereas trans is used ubiquitously. Cis seems like an odd choice in the gender wars. (BTW, the dictionary recognizes trans but not cis. Evidence of my point.)

    Maybe so, but if you’ve got a trans on the other side I dunno what your other options are.

     

    Only if you are defining the majority in terms of their relation to the minority. Wouldn’t it make more sense to go in the other direction? But better choices would include ortho, meaning straight, and matching the popular term, or the more correct, normal.

    • #28
    • July 24, 2018, at 11:09 AM PDT
    • 3 likes
  29. Judge Mental, Secret Chimp Member

    Arahant (View Comment):

    Judge Mental (View Comment):
    Ricochet dictionary.

    Ricochet has a dictionary?

    You’re right… the spell checker just knows.

    • #29
    • July 24, 2018, at 11:11 AM PDT
    • Like
  30. Arahant Member

    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.

    • #30
    • July 24, 2018, at 11:18 AM PDT
    • 1 like

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