I've been hesitant to commit to this, but now I suppose that I am, so go cry about it or something. The textbook I was using earlier is in Seattle right now anyway and I (at this point in time) am not. But my vision for this blog was never "Stephen Bahl condenses a textbook for you" or whatever. To be fair, I did post about some of my old labs and such. Alright, so it wasn't much, but surely it broke the monotony somewhat. And the textbook was really only ever a tool for me to introduce concepts from organic chemistry. That was what happened here. You're still confused? Try to keep up. I should explain. Fine. I will. What is wrong with you? Okay, new paragraph: go.
I am now stating it explicitly for you: this blog will change. It will continue to exist and it will continue to be written by me. It will continue to cover topics in chemistry. Those things will remain the same. They are not what is changing. Starting in January, the theme of this blog will be "reaction of the week." And I will keep it up for the duration of the year. This means that next year, I will blog about no less than fifty-two reactions. Fifty-two. 52. LII. Zweiundfünfzig. That's a lot. But it's happening. I've said I'm going to do it, so now it's too late to back down.
Not all of these will necessarily be reactions from organic chemistry. I won't mind throwing in the occasional inorganic reaction or whatever. But I have a stack of index cards in my desk right now with what appears to be upwards of seventy reactions from my organic chemistry class back in 2008. So yeah, it's not like I'm going to run out of reactions for this. 2011 shall be the year of the reaction. Or something. Oh yeah.
Showing posts with label fun. Show all posts
Showing posts with label fun. Show all posts
Monday, December 27, 2010
Saturday, December 18, 2010
Polyketides
I believe my previous post made some claim about marking calendars or some such thing that is now, in retrospect, quite ridiculous. Too bad. I thought it made more sense to extend my hiatus than to come back for another single post and vanish yet again. My vacation has been over for a while, but I've actually had a lot going on. Most importantly, I will be going to a new school in January (the University of Washington) and studying (among other things) inorganic chemistry. It's exciting. But because of this, I've considered shutting down operations here. I've been practically nonexistent on this blog recently, and if I'm too busy with school to ever post again, what's the point of trying to maintain this blog? Well, I'm recommitting myself to this endeavor. I know it seemed like I was doing that in my previous post. Fine. You've got me. I messed up. Just give me one more chance. Maybe. I have plans for this blog and I am almost sure that I know how I want to proceed, but I'll save it for the next post. If my plan works out, next year, despite me going back to school, will be this blog's busiest year so far by, well, a lot. There will be many posts. How many? At least fifty-two. No really, that's my plan.
But we'll save that for my next post, which will not be next year, but sometime soon. I'll try to have at least two more posts this year after the one you're reading now. So bear with me—until my next post, at least. I'm not quite ready for it. But it will be soon. Later this week, even. For now, I'd like to talk about a different subject entirely.
I did get to do some cool, science-related things on my vacation. You know, the one that ended in October that I was supposedly going to come back from and write a bunch of posts here right after that. Yeah, that one. The museums alone gave me a ton of material I could use here (but won't, for now anyway). There was also one, completely unexpected moment that is the inspiration for this post. After a bunch of crap we're not going to talk about right now, I arrived in the city of Bonn on, let's see, the October 3rd. The hostel I had booked was a weird one that didn't have its reception open until 5:00 PM. So I found it from the train station and walked down the street to get some lunch. I had a döner for lunch. I want a döner for lunch every day. They are so good. Almost too good. It's uncanny. Anyway, I was really thirsty, so I hunted down a store where I bought some ice cream and what I thought was orange juice but turned out to be more like orange soda. That sucked, because I hate carbonated beverages, but I was so thirsty that I drank it anyway. When I walked down to the hostel, there were some people talking. One of them was an American who mentioned doing biological research. I asked her about it. We ended up talking for a while, a lot of it about science.
It just so happened that a German biochemist who was there for some reason overheard our conversation. He talked a little about his own research on polyketides. I'd heard of them before, but that was about it. For the past two months, I've occasionally been amused at the realization that I "went all the way to Europe" to learn something. Of course, I knew I would learn things there and actively attempted to do so. But somehow, the realization that I learned some individual thing I could, hypothetically, have learned just as well here, but didn't learn it until I was there is amusing. I was recently made the comment that I had to go all the way to Austria to learn that grated horseradish is awesome. Anyway, I suppose that's how learning things always is. Even when we set out to learn things, we don't know what exactly it is we are going to learn.
From what I recall, he described work on a polyketide produced by bacteria or a series of homologous polyketides produced by bacteria, but the bacteria lived in completely different hosts: one in a beetle, one in a sponge, and one in some other thing I forget. Horizontal gene transfer for the win. Anyway, one thing he emphasized was that polyketides display tremendous variability. I'll spare you pictures because I was recently lambasting my organic chemistry textbook (the one I've been using a lot for this blog) for trying to scare students away with a picture of a big biological molecule. The important thing is that this variability, the incomprehensible number of forms molecules can potentially take is, well, the whole story of biochemistry. Structure determines properties. And those properties, if they're some of the right ones anyway, are what make life possible in the first place. Almost makes me want to switch to majoring in biochemistry...
But we'll save that for my next post, which will not be next year, but sometime soon. I'll try to have at least two more posts this year after the one you're reading now. So bear with me—until my next post, at least. I'm not quite ready for it. But it will be soon. Later this week, even. For now, I'd like to talk about a different subject entirely.
I did get to do some cool, science-related things on my vacation. You know, the one that ended in October that I was supposedly going to come back from and write a bunch of posts here right after that. Yeah, that one. The museums alone gave me a ton of material I could use here (but won't, for now anyway). There was also one, completely unexpected moment that is the inspiration for this post. After a bunch of crap we're not going to talk about right now, I arrived in the city of Bonn on, let's see, the October 3rd. The hostel I had booked was a weird one that didn't have its reception open until 5:00 PM. So I found it from the train station and walked down the street to get some lunch. I had a döner for lunch. I want a döner for lunch every day. They are so good. Almost too good. It's uncanny. Anyway, I was really thirsty, so I hunted down a store where I bought some ice cream and what I thought was orange juice but turned out to be more like orange soda. That sucked, because I hate carbonated beverages, but I was so thirsty that I drank it anyway. When I walked down to the hostel, there were some people talking. One of them was an American who mentioned doing biological research. I asked her about it. We ended up talking for a while, a lot of it about science.
It just so happened that a German biochemist who was there for some reason overheard our conversation. He talked a little about his own research on polyketides. I'd heard of them before, but that was about it. For the past two months, I've occasionally been amused at the realization that I "went all the way to Europe" to learn something. Of course, I knew I would learn things there and actively attempted to do so. But somehow, the realization that I learned some individual thing I could, hypothetically, have learned just as well here, but didn't learn it until I was there is amusing. I was recently made the comment that I had to go all the way to Austria to learn that grated horseradish is awesome. Anyway, I suppose that's how learning things always is. Even when we set out to learn things, we don't know what exactly it is we are going to learn.
From what I recall, he described work on a polyketide produced by bacteria or a series of homologous polyketides produced by bacteria, but the bacteria lived in completely different hosts: one in a beetle, one in a sponge, and one in some other thing I forget. Horizontal gene transfer for the win. Anyway, one thing he emphasized was that polyketides display tremendous variability. I'll spare you pictures because I was recently lambasting my organic chemistry textbook (the one I've been using a lot for this blog) for trying to scare students away with a picture of a big biological molecule. The important thing is that this variability, the incomprehensible number of forms molecules can potentially take is, well, the whole story of biochemistry. Structure determines properties. And those properties, if they're some of the right ones anyway, are what make life possible in the first place. Almost makes me want to switch to majoring in biochemistry...
Saturday, August 29, 2009
The Next Chapter is About Organic Molecules and Functional Groups
I am so excited for this. With the huge hiatus between the "Acid Strength" post and the "Aspirin" post, I hadn't bothered to look at what the next chapter of my text book had in store for this project. Would I skip the chapter? Go over some of it and move on as quickly as possible? Functional groups are one of my favorite things in the whole world and I can hardly wait to write about them. All chemistry is interesting, but functional groups are what truly fascinate me and I hope to study them when I go back to school. But even before then, I'll be doing a little reading up on them while writing posts here. In the meantime, have a little patience for me. I really am back and giving this project my attention, but I want this next post to be my best one so far. I love functional groups.
Friday, August 21, 2009
Aspirin
It's been a while and I need to get a feel for this. I'm also not done with the chapter on acids and bases. So I thought it would be cool to show you aspirin. My book does it, although there's some other stuff before it that I sort of went over, kind of, more or less, already. This will also be an opportunity for me to try to use a program other than MS Paint to render something. We'll see how it works...
Well, that seems to work. I had to make it on this ChemSketch program and then copy the thing into MS Paint in order to upload it here, but whatever. Much easier than drawing everything from scratch.
Now let's make sense of this. There are a few functional groups here, and we'll learn all about functional groups some day. Won't that be exciting? The one we're interested in now is the carboxylic acid group. One of the carbons is attached to an oxygen by a double bond and a second oxygen by a single bond, with that second oxygen itself being attached to hydrogen. This arrangement of atoms makes it easy for a certain reaction to occur. That reaction is a Brønsted-Lowry acid-base reaction. Here's a mechanism...
Okay, those arrows look terrible. I'll have to work on that next time. Anyway, that's the same as the mechanism for the Brønsted-Lowry acid-base reaction I covered in my last post. This reaction can happen in the human body, assuming aspirin gets into the body in the first place. Aspirin is not found in nature. I've sometimes heard it said that aspirin was found in willow bark, but that's incorrect. Willow bark contains salicylic acid. Aspirin is acetylsalicylic acid. The stuff in willow bark would look just like aspirin, but the group attached to that oxygen on top would be replaced with a hydrogen. Aspirin became the analgesic of choice, as opposed to salicylic acid or another derivative of it, because it lacked the irritating side effects of those drugs.
So the reaction can and does occur in the human body. When this happens, the conjugate base, or acetylsalicylate, is formed. The conjugate base is ionic (with a negative charge on the oxygen that gave up hydrogen) and cannot cross cell membranes. Fortunately, this isn't a huge problem because, like other Brønsted-Lowry acid-base reactions, the reaction that turns aspirin into its conjugate base is reversible. My textbook notes that it's the acid that is present in the stomach, and the base that is present in the intestines. This should be pretty intuitive. When conditions are highly acidic, aspirin, which is only a weak acid, even when it does protonate something, will get protonated right away by the acid around it. In basic conditions, there's not much acid around to do the reverse reaction and what is there might be even weaker than aspirin as an acid anyway.
So yeah, aspirin.
Well, that seems to work. I had to make it on this ChemSketch program and then copy the thing into MS Paint in order to upload it here, but whatever. Much easier than drawing everything from scratch.
Now let's make sense of this. There are a few functional groups here, and we'll learn all about functional groups some day. Won't that be exciting? The one we're interested in now is the carboxylic acid group. One of the carbons is attached to an oxygen by a double bond and a second oxygen by a single bond, with that second oxygen itself being attached to hydrogen. This arrangement of atoms makes it easy for a certain reaction to occur. That reaction is a Brønsted-Lowry acid-base reaction. Here's a mechanism...
Okay, those arrows look terrible. I'll have to work on that next time. Anyway, that's the same as the mechanism for the Brønsted-Lowry acid-base reaction I covered in my last post. This reaction can happen in the human body, assuming aspirin gets into the body in the first place. Aspirin is not found in nature. I've sometimes heard it said that aspirin was found in willow bark, but that's incorrect. Willow bark contains salicylic acid. Aspirin is acetylsalicylic acid. The stuff in willow bark would look just like aspirin, but the group attached to that oxygen on top would be replaced with a hydrogen. Aspirin became the analgesic of choice, as opposed to salicylic acid or another derivative of it, because it lacked the irritating side effects of those drugs.So the reaction can and does occur in the human body. When this happens, the conjugate base, or acetylsalicylate, is formed. The conjugate base is ionic (with a negative charge on the oxygen that gave up hydrogen) and cannot cross cell membranes. Fortunately, this isn't a huge problem because, like other Brønsted-Lowry acid-base reactions, the reaction that turns aspirin into its conjugate base is reversible. My textbook notes that it's the acid that is present in the stomach, and the base that is present in the intestines. This should be pretty intuitive. When conditions are highly acidic, aspirin, which is only a weak acid, even when it does protonate something, will get protonated right away by the acid around it. In basic conditions, there's not much acid around to do the reverse reaction and what is there might be even weaker than aspirin as an acid anyway.
So yeah, aspirin.
Monday, February 23, 2009
Stephen Bahl Has Triple Bonds
So I totally realize that I can use a symbol for a triple bond. Yep. It makes things easier. Like here's ethyne, also known as acetylene...
H—C≡C—H
I chose that molecule because I didn't even need MS Paint to do it. Awesome. I'm so excited to have that symbol at my disposal...
≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡
Awesome. The symbol is actually available because of its meaning in logic and mathematics, not because of anything to do with chemistry. But I'll take what I can get.
H—C≡C—H
I chose that molecule because I didn't even need MS Paint to do it. Awesome. I'm so excited to have that symbol at my disposal...
≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡
Awesome. The symbol is actually available because of its meaning in logic and mathematics, not because of anything to do with chemistry. But I'll take what I can get.
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