Reaction of the week

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.

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...

A Note on Complexity and Isomerism

My textbook has a table with information that I did not include in my last post, but that may improve understanding of isomerism. In case it is not obvious, the number of isomers grows with the size of a molecule. In my last post, I showed the two isomers of butane. Larger alkanes have even more, because with more atoms, there are more ways to rearrange them. Small alkanes are easy to understand in this regard. A hydrocarbon with one carbon has no isomerism. The same is true for two or three carbons. When we get to four, as already demonstrated, there are two possibilities: a straight chain and one with a branch. Five carbons means three isomers. With seven carbons, we get nine isomers, which is still manageable, but then add a single carbon and there are eighteen isomers. The table ends with icosane (C₂₀H₄₂), which has 366,319 constitutional isomers.

And that is just acyclic alkanes. There are so many other things to consider, that the complexity is staggering. And that is why we have a systematic method of naming molecules. Anything else would get pretty impractical.

Ribosome Rant

I realize this is a departure from the content I normally post here, but I just started writing a rant on a different site and I think it really belongs here. The Nobel Prizes are being announced this week. The prize in chemistry went to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada Yonath for their work on the the structure of ribosomes. There's a sentiment that I've been seeing somewhat and it got me annoyed enough to actually write this. Here are some examples of the sentiment I am talking about...

I don’t care. For some reason, this year I’m not getting into Wednesday Madness nearly as much as I have in previous years. I’ll be happy if they give it to, uh, a chemist.

≡≡≡

Oh well. Here’s an idea. In lieu of giving out Nobel Prizes in Chemistry to achievements in chemistry (since they only seem to give it to actual chemists every other year anyway, it won’t be much of a stretch), let’s start handing them out to the authors with the best paper titles ever.

≡≡≡

As already announced biologists walked away with this year’s Nobel prize in chemistry once again, this time for work in determining the structure of Ribosomes.

≡≡≡

As chemists we would like to see the Nobel chemistry prize go to a chemist. Our Nobel hopefuls may be a measurable magnitude more chemically interesting, as measured by ChemFeeds, but there is more work for them to do until these topics become world renowned (which seems to be the dominant prerequisite these days).

≡≡≡

And again the Nobel for Chemistry goes to "bio-chemists"....
Congratulations...but as a strictly synthetic organic chemist...I am a bit ticked off.
With all the biology and the nanoscience development in recent years, it'll be eons before an organic chemist wins the prize again.

Alright guys, the applicant to get into school to work on an undergraduate degree (I do already have my A.S. at least) has some news for you: biochemistry is chemistry. I find this reaction deplorable. Chemistry is all about atoms and the bonds between them, what things are made of and how they interact with each other. That is exactly what this prize was awarded for. Perhaps word has not yet reached the innermost confines of your biology-free ivory towers, but ribosomes are made out of atoms and ribosomes have bonds—lots of them. Ribosomes participate in chemical reactions. This really should go without saying.

I could be way off here, but I don't think I would see this in other branches of science. If an annual physics prize went to scientists who did work in astrophysics, would physicists complain that the astronomers are taking physics prizes? I think not, but maybe some of them would. Maybe some of them sequester themselves in ivory towers devoid of any science that is not their own particular specialization, just as apparently some chemists do. My impression is that many, if not most, physicists have a passion for the universe and its fascinating nature. They want to see the physics in everything. I want to see the chemistry in everything. And I'd like to think I'm in good company, but the reactions I've seen to this Nobel Prize have cast some doubts on that.

How arrogant must one be to think, "Only research in the area of chemistry that I focus on should win prizes"? Some might protest that this is an unfair characterization, but if one is willing to dismiss the entirety of biochemistry, I am more than willing to err on the side of assuming that one would go on to dismiss other purportedly unworthy subjects in a similar manner. This exclusive approach is the exact opposite of what I want to stand for. I want chemistry to be inclusive. If we excise some of it because it deals with biological molecules and can therefore be considered biology, we might as well excise the parts that deal with minerals and make that geology and so on until we have divided everything up and there are no more chemists, just former chemists working in other fields of science.

The ribosome people did not win because the biologists are taking over and they did not win because ribosomes are famous and other work was too obscure. They won because they did good chemistry that is of abundant benefit to humanity.

Visualizing Functional Groups

I told you that I would post more functional groups and I meant it. But I also want to make the ones I've already introduced clear. And condensed structures can confuse people. I heard you're easily confused. So we'll spend a bit more time getting acquainted with these. I think I covered the hydrocarbons well enough, so we'll focus on functional groups that contain heteroatoms.

More about alcohols
The nature of the carbon that the hydroxyl group is attached to determines the type of alcohol here. First, there's a primary alcohol...
Note that the carbon attached to oxygen is attached to only one other carbon (in the R group). In a secondary alcohol, this carbon is attached to two other carbon atoms...
And as you might have guessed, in a tertiary alcohol, that carbon is bonded to three other carbons...
If you were thinking that a quaternary alcohol would be one in which that carbon is attached to four other carbons, you sure are dumb. Carbon is tetravalent. You remember that, don't you? It can't form five bonds. There is no such thing as a quaternary alcohol.

If you were wondering, whether an alcohol is primary, secondary, or tertiary has important implications for its chemical properties, hence the distinction. This is also the case with amines, as I already alluded to, but in that case, it's how many carbons the nitrogen is attached to that determine which type of amine the molecule is. So there's some cool new information for you. But now for some clarity on material I already covered in my last post.

Visualizing aldehydes & ketones
Here's the Lewis structure of an aldehyde...



And here, for contrast, is a ketone...
Notice the big difference: with an aldehyde, the oxygen is at the end of a chain and with a ketone, the oxygen is attached to a carbon that is somewhere in the middle of a chain. These structures both have a "carbonyl" group and their chemical properties are often similar, but they can be different in important ways and this distinction is certainly worth remembering.

Carboxylic acids and friends
Carboxylic acids get several other classes of compounds grouped with them as "derivatives of carboxylic acids" quite literally because carboxylic acids can be used to make these other compounds. I won't cover all of them because there's a whole chapter on this stuff and it's way later in my textbook. But because you're slow, I worry about your ability to even deduce the general appearance of these groups from a condensed structure. So here's a carboxylic acid...
Like the aldehydes and ketones, there's a carbon double-bonded to an oxygen and single-bonded to an R-group. But the fourth bond isn't to hydrogen or another carbon. It's to oxygen, which itself is attached to hydrogen. Remember acidity? You know, that thing the last chapter was all about and such. And maybe you even remember that in my "Aspirin" post I said, of the carboxylic acid, "This arrangement of atoms makes it easy for a certain reaction to occur. That reaction is a Brønsted-Lowry acid-base reaction." Really, it's not familiar. Whatever. That proton can totally come off.

Since I like functional groups so much, here are some more in condensed structure...

Acyl halide
R—COX (like a carboxylic acid, but with the second oxygen replaced by a halogen)

Imine (imino group)
R=N—R' (these come in multiple varieties and I haven't really studied them yet)

Peroxide (peroxy group)
R—O—O—R' (the oxygens are actually attached to one another)

Nitrile (cyano group)
R—C≡N

Enough. We will now cover new functional groups as they come up.

Functional Groups

Functional groups are structures within molecules that contribute to the properties of that molecule. In his excellent book, The Same and Not the Same, Roald Hoffmann cites the concept of the functional group as something in chemistry that is not reducible to the physical laws that affect it. Functional groups as concepts seem to be uniquely chemical. I, at least, can't think of anything that's more than superficially analogous. And for organic chemistry, they're hugely important.

C—C bonds and C—H bonds are extremely common in organic molecules. If you remember my post showing how skeletal structures work, you should recall that these bonds are only noted with points and intersections for the former and are left to inference with the latter. Such structures are "skeletal" because they really do show the hydrocarbon skeleton of a molecule. All those C—C and C—H bonds are usually pretty stable. They can contribute to the chemistry of a molecule, but not nearly so prominently as functional groups.

I won't attempt to list every functional group here, because there are lots and lots of them and your puny brain would probably die or something. But I will list some of them. First, I want to introduce a new notation. Actually, I'm not sure if I already introduced it, but I'm too lazy to go back and check and you probably forgot about it anyway. The letter "R" is often used to denote the rest of a molecule apart from a functional group, especially if what remains is a plain old hydrocarbon. This can be convenient for situations when it's only the functional group we care about and drawing the rest of the molecule would be impractical or wouldn't even make sense. If we do this more than once though, and the groups being condensed are not identical, using "R" to denote both would be inappropriate, but "R" for one and "R'" (R prime) for another is fine.

So for an example, I've decided to use 2-butoxyethanol because I've used it to clean graffiti off the walls in the restroom at work.
Of course, while this is the stuff I was using, other molecules that change one or more atoms are easily possible. What if we decided only to focus on part of the molecule? We might do this...
What is "R"? Is it still a chain of four carbons with nine hydrogens? Maybe. Or maybe it's still a straight chain, but one carbon longer than that now. Maybe there's a ring. Maybe it has multiple branches. Maybe there are dragons. No one knows! It's a mystery. Exciting, I'm sure. And that's how "R" works. It's a placeholder. It saves space. "Here be dragons" might work too, but "R" is the standard. I have no idea how it became that way, actually.

Aliphatic hydrocarbons
This term comes from the Greek aleiphas, meaning "fat." Actually, many of the properties fats have come from the long hydrocarbon chains they possess. If an aliphatic hydrocarbon has no π-bonds (that is, no double or triple bonds), it is an alkane. Branches and rings might be present and do affect the properties of alkanes, but they're still called alkanes, although a compound with a ring might be said to be a cycloalkane.

But if π-bonds are present, no matter how few there are or how big the rest of the molecule is, it's not an alkane anymore. A double bond means that the molecule is an alkene. So using what we learned earlier, a molecule that contains this functional group: R₂C=CR₂ (different groups are all "R" here because noting them all with superscripts would be ridiculously clunky) is an alkene. The double bond counts as a functional group. Specifically it is the alkenyl functional group.

Similarly, a triple bond is a functional group. Something with R—C≡C—R' functional group is an alkyne (no matter how many double bonds or single bonds it has). And this is an alkynyl functional group.

Aromatic hydrocarbons
The only hydrocarbons I know of that are not classed as aliphatic are ones containing aromatic rings. You might be anticipating this from the trend with what I've said regarding alkenes and alkynes, but the presence of even a single aromatic ring in an otherwise aliphatic molecule means that the compound is considered aromatic and not aliphatic. Aromaticity is a tricky concept though, and we're not covering it just yet. So for now, the only aromatic ring we'll concern ourselves with is the benzene ring.
It is not a cycloalkene, even thought it might look like one. I mentioned in an earlier post that this type of ring is resonance stabilized. The electrons are evenly distributed around the whole ring. How this happens and whether a particular ring is aromatic or not are subjects for later posts. But this ring, the benzene ring, is aromatic. If it's treated as a functional group, it's the phenyl group. To abbreviate when I'm using condensed structures rather than skeletal structures, I'll probably use "Ph" for "phenyl." So something with this functional group would be R—Ph. Other people sometimes just abbreviate a benzene ring attached to something else as C₆H₅ but I'll try not to do that so as to avoid confusion.

Another well-known aromatic hydrocarbon with its own common name is toluene. It's just like benzene, but where benzene has six hydrogens, one attached to each carbon, toluene replaced on hydrogen with a methyl group, a carbon bonded to three hydrogens. So it's like R—Ph with "R" being "CH₃" except this is a special case and gets its own name. If toluene acts as a functional group itself, with one of the hydrogens on the carbon outside the ring being replaced by a bond to the rest of molecule, and I'll draw a picture just to be sure you're following me...
The functional group is actually not phenyl. It's a benzyl group. If this confuses you, good. I like confusing you. Try to remember that this is a benzyl group and that a benzene ring attached to something is just a pheny group. I know both "benzene" and "benzyl" start with "benz-" and you're really tempted, but don't. Just don't.

Now for some more functional groups...

Alkyl halide (halo group)
R—X (where X is a halogen). It could be an alkyl fluoride, alkyl chloride, alkyl bromide, or alkyl iodide depending on which halogen is attached.

Alcohol (hydroxyl group)
R—OH

Ether (alkoxy group)
R—O—R

Amine (amino group)
R—NH₂ (primary) or R₂NH (secondary) or R₃N (tertiary)

Thiol (mercapto group)
R—SH

Sulfide (alkylthio group)
R—S—R'

Aldehyde (carbonyl group)
R—CHO (for those of you who can't deal with condensed structures very well, the carbon is double-bonded to the oxygen, bonded to the hydrogen, and bonded to the R group, so it could also be R—CH=O)

Ketone (another carbonyl group)
R—CO—R' (or R—C=O—R'). The difference between an aldehyde and a ketone is that in an aldehyde, the carbobyl group is on the end of a chain, but in a ketone, it's in the middle of a chain.

Carboxylic acid (carboxyl group)
R—COOH (like an aldehyde with the hydrogen on the carbonyl carbon replaced by an hydroxyl group, alternatively it's like an alcohol with an oxygen double-bonded to the terminal carbon)

Ester (ester group)
R—COOR' (like a carboxylic acid, but with the hydrogen on the oxygen replaced by a hydrocarbon group).

Amide (carboxamide group)
R—CONH₂ (primary) or R—CONHR (secondary) or R—CONR₂ (tertiary). Not to be confused with amines, which don't have that oxygen double bonded to the carbon that nitrogen is attached to.

What's that? You want more? Fine. Next time, I'll post some more functional groups for you.

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.

Preparation of Salicylic Acid from Methyl Salicylate

I just realized that, although I've skipped a little, I'm done posting material from the first chapter of the textbook. At this rate, it will take me the rest of my damn life to finish the whole book. As much as I'm anxious to move on to the next chapter, right now I'm going to deal with something more important. It's something that I wanted to write about before even starting with material from my textbook, but it occurred to me that you'd need knowledge of notation to follow this. Well, if you actually read the posts about notation of structure, you should now have that knowledge (unless I'm a bad teacher or you're just stupid or something). What I'll be writing about this time is an experiment I did in my first quarter of organic chemistry. I was going to say that it was the very first experiment in the class, but I checked my lab notebook and I was wrong. This was the fourth experiment in the class.

The lab instruction manual has these silly "scenario" sections for each lab. Sometimes they were excessively silly and other times they were actually rather interesting. I'd like to quote this on in its entirety.

The new-age pharmaceutical company Natural Nostrums manufactures drugs from "natural" starting materials. For example, the company manufactures a painkilling drug it advertises as "organic aspirin" starting with methyl salicylate, which occurs naturally in wintergreen oil. Most commercially marketed aspirin is manufactured starting with benzene, a product of petroleum refining. An intermediate in both of these syntheses is salicylic acid.

Natural Nostrums claims that its aspirin, which is supposedly more natural than aspirin made from benzene, has fewer side effects than ordinary aspirin. Critics have accused the company of false and misleading advertising, asserting that salicylic acid made from methyl salicylate is no different than salicylic acid made from benzene, and that the resulting aspirin is no better than any other aspirin.

Les Payne, Director of Operations for the Association for Safe Pharmaceuticals (ASP), is investigating the company. He just shipped your supervisor a sample of salicylic acid manufactured from benzene and a bottle of methyl salicylate that one of his agents obtained from the chemical stockroom at Natural Nostrums. Your assignment is to prepare salicylic acid from methyl salicylate and find out whether or not it differs from salicylic acid made from benzene.

The main purpose of this experiment, in my class, was to introduce laboratory synthesis of one molecule from another (it was our first true synthesis lab—the previous three dealt with identification, extraction, and both purification/identification respectively). But the "scenario" for the experiment touches on what I consider one of the most fundamental concepts in chemistry: the properties of a chemical are caused by the the atoms comprising the chemical and the bonds between them. There's the law of definite proportions, but that's just part of it. Chemistry assumes, because we've tested it countless times, that provided all of the atoms are there in the same proportions and are of the same isotopes, the bonds are in the same places and arranged in the same way, two molecules are not just indiscernible from each other, but identical. Molecules don't "remember" where the atoms making them up used to be. Carbon 12 is carbon 12. Water is water. Salicylic acid is salicylic acid and if I mixed up pure salicylic acid synthesized from benzene with pure salicylic acid synthesized from methyl salicylate, no one could separate the one from the other or tell me which source a randomly chosen molecule came from.

I don't think I've ever seen anyone else articulate just that, even though every chemist knows it to be true. In all my chemistry classes, the closest thing I've seen to anyone pointing out this fundamental fact that really forms the basis for all chemistry is that quote from my lab instruction manual. Maybe people think it's so simple and obvious that it's not worth mentioning. I strongly disagree. Scams like the fictional one described by that scenario really do exist, and people only fall into these traps because they know nothing about chemistry, meanwhile the part of chemistry that makes it clear why these scams are wrong, the same part that's fundamental to all work done in chemistry, isn't considered worth noting.

Then there's homeopathy. Don't get me started on that. Enough ranting though. On with the science! You do want to know how we made salicylic acid from methyl salicylate, right? Of course you do. Well, to begin, here's methyl salicylate.







You might want to just not worry about the ring for now. It's important, but it's not changing into anything else in any reactions I'll be covering for this post. If you are curious, know that the ring has resonance stabilization: the electrons that make up the double bonds in that image are actually evenly distributed across the whole ring. It's called an aromatic ring. That's not because it has a strong aroma. It's for historical reasons. But in this particular case, the molecule actually does have a strong aroma. Methyl salicylate is the chemical that creates the "wintergreen" smell. That's probably a big reason why my professor chose it. When you're doing labs with chemicals that smell bad all the time, ever once in a while it's nice to do a lab with something that smells nice. Anyway, that's methyl salicylate. Here's salicylic acid.








So both of them have that aromatic ring and the hydroxyl group (OH) attached to one carbon with a second group attached to an adjacent carbon. But with methyl salicylate, the group is —COOCH₃ whereas with salicylic acid, the group is COOH. In other words, the difference is that the oxygen the carbon is singly bonded to is attached to a hydrogen or a methyl group, depending on which compound this is. In order to go from one to the other, we need some sort of chemical reaction to change that hydrogen into a methyl group. Chemistry! Oh yeah.

What we do is put melthyl salicylate in a vial, then add an aqueous solution of sodium hydroxide. I wrote a bit about ions a while back, but if you don't remember, ions tend to dissociate from each other in water. The cation (positively charged) is sodium. The anion (negatively charged) is hydroxide, or ⁻OH. At any point, the hydroxide could rip a proton (the nucleus of a hydrogen atom) from a water molecule (this would be an acid-base reaction with water as the acid and hydroxide as the base) and become a water molecule itself, but then the water molecule that it reacted with would be hydroxide, so the total amount of hydroxide ions stays the same.

This mixture is then heated under reflux. What that means in this case is that the mixture is boiling, but there is a glass tube called an air-cooled condenser at the top of the vial. As the vapors from the mixture rise up the tube, the air around them, being cooler than them, absorbs their heat (thermodynamics for the win), and causes them to become liquid again (condensation), at which point they run back down the glass tube into the reaction vial. And all the heat adds kinetic energy to the molecules, which speeds up the rate of reaction. I will now show you the reaction using a mechanism.

Reaction mechanisms show how bonds are formed and broken in reactions using arrows that always start at a pair of electrons and show what those electrons go to. In this case, the electrons from hydroxide form a covalent bond to carbon, breaking the π-bond in the C=O bond, so that the carbon is attached to four things: the ring, the methoxy group (–OCH₃), the hydroxyl group (–OH), and the now negatively charged oxygen that used to be double-bonded, as shown below.But the product of this reaction is an unstable reaction intermediate. It probably exists for only a fraction of a second before the electrons on that oxygen atom form a new bond to the carbon. For reasons that won't be explained right now, the bond that carbon must lose is the one to the methoxy group, so we get this reaction.
Why, look at that. It's almost salicylic acid. Almost. There's just one pesky detail remaining. Being in such basic conditions (lots of hydroxide floating around), the hydroxyl group attached to the ring lost a proton. As long as the conditions are basic, we have no way of putting that proton back on. There's a simple solution to this: douse the whole thing with sulfuric acid. Yes, I'm serious. It's what we did. Well, it wasn't really "dousing." We added more than enough sulfuric acid to neutralize the sodium hydroxide and the disodium salicylate (the name of that last product). At that point, we get salicylic acid. Conveniently for us, salicylic acid is a solid that precipitates out of the solution, so we just filter it out (we use a funnel with filter paper over a vacuum system to pull the liquid through and leave the solid crystals on the filter paper). Finally, we pour cold water onto the filter to wash away any remaining traces of the original solution. Then we just let our crystals dry and we have pure salicylic acid.

We can analyze the purity of our compound by melting point analysis. There are different ways to do this. The method I used was to take three very thin glass tubes (open on one end and rounded at the other) and pressed the open ends of the tubes against crushed powder from crystals, tapping the tubes to shake the samples to the bottoms of them. I put the tubes in a melting point apparatus, basically a heated chamber with a display indicating the temperature and a magnifying glass letting me see the tiny samples in the tubes with ease (I still had to wear my glasses, but shut up). One tube contained my product. One tube (the control) contained salicylic acid from benzene. And one tube contained a mixture of my product and salicylic acid from benzene. For reasons I'll explain in my next post, if my product had not been the same compound as the salicylic acid from benzene, even if the melting points were nearly identical, the tube with the mixture would melt at a lower temperature and over a broad range, as opposed to melting all at once. Since my product was pure, all three samples melted sharply at 160°C.

Vitalism and the Origins of Organic Chemistry

Time flies. I can't believe how long it's been since my last post here. I am slacking a little, but part of the reason that posts here have been infrequent is that I've been spending more time with friends, which is something I had a goal of doing. So I'm not too upset. And I am here, right now, updating this blog. So here we go...

In order to appreciate the distinction between organic chemistry and the rest of chemistry, it take some appreciation for the history of the science. Organic chemistry is frequently defined as being the chemistry of carbon or the chemistry of compounds containing carbon.

My textbook puts it rather simply:

Organic chemistry is the chemistry of compounds that contain the element carbon.

Wikipedia is a bit more specific:

Organic chemistry is a discipline within chemistry which involves the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of chemical compounds that contain carbon.

What neither of these simple definitions tell us is that not all compounds containing carbon are considered organic. My textbook doesn't seem to mention it, but looking up "organic compounds" on Wikipedia reveals this:

For historical reasons discussed below, a few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic.

This is because of the now defunct concept of vitalism. People believed that organic matter and inorganic matter were fundamentally different (as an aside, some attribute this to Aristotle, but I haven't looked into it). Carbonates, oxides of carbon, and cyanides (and carbides, another class of inorganic carbon-containing compounds) are all found naturally outside living systems (in minerals, for example). Other carbon-containing compounds were only known to be associated with life. Then this whole view of things got wrecked in 1828 by Friedrich Wöhler doing this reaction:
Pretty cool, huh? Wöhler combined ammonia with a solution of cyanic acid ammonium chloride (dissolved in water) with silver cyanate and got, as a product, urea, which was previously only known to be produced by the kidneys of animals (mammals and some other animals produce urea as a waste product). Although this didn't immediately strike the deathblow for vitalism (which has, in some form or another, survived to this day, although thankfully not among chemists), it laid the foundation for organic chemistry as a field (these compounds were now something that could potentially be synthesized in laboratories and there wasn't necessarily any essential "life force" that was generating them).

The distinction between organic chemistry and inorganic chemistry is important today because organic compounds have some specific properties of their own that can be studied in detail and because organic chemistry is so important in biological systems. Being biological systems ourselves, we have an interest in organic chemistry as it relates to our health. Pharmacy is one branch of applied organic chemistry.

Addendum:

I forgot to mention this, but before taking organic chemistry, I was under the impression, from general chemistry, that organic compounds had both carbon and hydrogen. My organic chemistry professor pointed out early on that technically, not all organic compounds have hydrogen. For example, carbon tetrachloride (CCl₄) is considered an organic compound, but has no hydrogen. However, most organic compounds do contain hydrogen.