Cycloalkanes

I just found an error in my textbook. Seriously. The book even bolds its own error. The offending sentence reads...

Cycloalkanes have molecular formula C_nH_2n and contain carbon atoms arranged in a ring.

That is only true for cycloalkanes with just one ring. Cycloalkanes can have more than one ring, and each additional ring means two fewer hydrogens. And there are a lot of those. Try to keep up, textbook. Anyway, the examples the book then uses for cycloalkanes are all ones with just one ring. In fact, the examples in this section of the book have all of the carbons in the ring, but this is not necessary or even particularly significant.

The smallest cycloalkane ever is cyclopropane, with a molecular formula of C₃H₈ and a skeletal structure that looks like this...
Yes, it's a triangle. This really should not surprise you if you've been paying attention, which you haven't. I could show it in 3-D, but so far I haven't figured out a way to post my wonderful 3-D images here in this blog thing without them looking like crap (because I am pasting them into MS Paint and saving them there. If you want pretty pictures, go read a pretty pictures blog or something. I hear that they have those. Such things may be more suited to your intellect.

Cyclobutane's skeletal structure looks like a square. This should be easy to visualize. Same with cyclopentane and a pentagon. I have already shown the skeletal structure for cyclohexane here and here.

Also, the book claims that the largest known cycloalkane with a single ring has 288 carbon atoms. But this is in a problem asking for molecular formula (and obviously the molecular formula is C₂₈₈H₅₇₆) and I cannot tell if it is giving me authentic trivia or merely posing a hypothetical for the purposes of asking such a question and reinforcing the concept.

One last thing, which the book apparently omits in this section (although it will probably come up later) is ring strain. The carbon atoms are most stable at a certain bond angles. In the case of alkanes (and lots of other things, really), the ideal bond angle is 109.5° and all four groups attached to the carbon atom are equally far away from each other, forming a tetrahedron with the carbon atom in the center and each attached group in one of the corners. But when carbon atoms form rings, the bond angles become strained. This ring strain causes the molecule to be more reactive. Cyclopropane, with 60° angles between the carbons, has the most ring strain. After that, it becomes important to note that these rings are three-dimensional objects. They can be denoted with two-dimensional skeletal structures on paper, but are under no obligation to lie flat. So cyclobutane does not actually have 90° angles between its carbons, as "puckering" reduces strain and creates larger angles. Later in the chapter, this is explored for cyclohexane in particular, which has the most stable ring among cycloalkanes.

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.

Constitutional Isomers Redux

I suppose that my textbook introduces constitutional isomers in the alkanes chapter because alkanes are pretty straightforward and can ease one into the concept. Constitutional isomers can and do occur in other molecules. Isomerism is when two or more different compounds have the same molecular formulae. In other words, they have the same kinds of atoms and the same numbers of those atoms, but something makes them chemically distinct. Later on, we will explore stereoisomers, and it will be very exciting. But for now, we're looking at constitutional isomers, which differ in the way the atoms are connected to each other. Let's take a look at two molecules that are constitutional isomers of each other...

Name: n-butane (or just butane)
Molecular formula: C₄H₁₀
Condensed structure: CH₃CH₂CH₂CH₃
In stunning 3-D:
Yes, I just figured out that I could render butane three-dimensionally with my nifty software. Anyway...

Name: isobutane (or 2-methylpropane)
Molecular formula: C₄H₁₀
Condensed structure: CH(CH₃)₃
In glorious 3-D:
Both molecules have the same quantities of the same atoms. But the bonds are not identical here. A carbon bonded to two other carbons and two hydrogens is electromagnetically different from one bonded to three other carbons and one hydrogen. Also, the three-dimensional forms are quite different, and when the molecules interact with other bodies (including other molecules just like themselves) the results will be at least slightly different. Although very similar, these two compounds have different chemical and physical properties. They are more like each other than other compounds that have different atoms and other, more striking differences. Because of these facts, we use the term "constitutional isomers" to denote the relationship between these similar molecules.

But when it comes to properties, constitutional isomers are not always so similar to each other as those two. Some constitutional isomers contain different functional groups from each other and, if you remember the importance of functional groups like you should, this means they can have dramatically different chemical and physical properties...

Name: ethanol

Molecular formula: C₂H₆O

Condensed structure: CH₃CH₂OH

In brilliant 3-D:

It's an old friend: ethanol. I don't know how many times I've shown ethanol before, but you had better know that this is what it looks like. And if you managed to actually have some brain capacity, maybe you even remember that this compound is an alcohol, as it has a hydroxyl functional group. Easy, but here's a constitutional isomer of ethanol.

Name: dimethyl ether (or methoxymethane)

Molecular formula: C₂H₆O

Condensed structure: CH₃OCH₃

In spectacular 3-D:
Since the name has "ether" in it, you have deduced, unless you are a total idiot, that this is an ether (the name of the functional group is methoxy in this case). But the molecular formula is the same. The functional groups here are so unlike each other that reactions possible for one would be impossible for the other. Oh, and remember hydrogen bonding? Ethanol has it. Dimethyl ether cannot have hydrogen bonding because there is no hydrogen attached to the oxygen, so these two even have different intermolecular forces. In this way, two constitutional isomers can be quite dissimilar. What kind of atoms a molecule has and how many are very important, but the configuration of the bonds holding the atoms together in a molecule matters a lot too.

Edit: After posting this, I started going back to tag my posts. I noticed that way back in February, I wrote a post about constitutional isomers. I think this new post is better, but here is the old one. If you do not get the concept after reading this post, read the old one. If you still don't get it, tell me, I guess. It seems fairly simple to me and I think I did an adequate job of explaining it both times, but maybe I am wrong...

Cyclic and Acyclic Alkanes

As I mentioned in my Functional Groups post, alkanes are hydrocarbon molecules with no π-bonds. They can be straight chains of carbons with attached hydrogens, or there can be branches or rings or both. All of the fourth chapter in my textbook is dedicated to alkanes. But the first part is just about getting acquainted with them. Alkanes are something of a baseline in organic chemistry. It's when functional groups are added that the chemical properties behind so much of our world come into play. Lacking functional groups, alkanes are not particularly reactive. They can react, though. And I know we'll come to that eventualy. There's a lot to learn from alkanes, though.

Firstly, let's distinguish between acyclic alkanes and cyclic alkanes. If it has a ring, it's cyclic. If it does not have a ring, it is acyclic. Simple, right? It better be. No, two rings is still cyclic. What counts as a ring? Oh, good question. A ring is pretty much what it sounds like. Three or more atoms bonded to each other with a loop that can be formed from the bonds between them. Carbon #1 is attached to Carbon #2 and Carbon #2 is attached to Carbon #3, which is itself attached to Carbon #1. Three atoms is the minimum, but larger rings are more common.

For an acyclic alkane, the number of hydrogens will always be two plus double the number of carbons. H = 2C+2. Actually, a little logic should demonstrate this point. No amount of branching chains changes the formula. But a single ring does. I shall illustrate with some examples. First, here is hexane...

Name: n-hexane
Molecular formula: C₆H₁₄
Skeletal structure:
Well, that's a nice, simple acyclic one. How about an acyclic alkane?

Name: Cyclohexane
Molecular formula: C₆H₁₂
Skeletal structure:
I Know I've shown this one at least once here, once upon a time. Hexagons should hopefully be pretty recognizable. And notice that it has two fewer hydrogens than the last one? That's because of the ring. What? You want to know how the ring makes it so that there are two fewer hydrogens in the molecule? Really? Look, just pretend we sever the bond between two carbons. Any two. Now those two carbons need a new bond to something else because, remember, carbon forms four bonds. So we stick a hydrogen onto each of them, and look at that, it's n-hexane, the same molecule I already showed you just before this one. Amazing. And that is why the ring makes it so that there are two fewer hydrogens than in an acyclic alkane. Simple.

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.

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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.

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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.

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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).

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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.

Strength of Intermolecular Forces

This chapter in the textbook is quite long, but not all of it is well-suited to posts like these. A lot of this reviews concepts from general chemistry and has lots of pretty pictures and I don't want to spend too much time on things like melting point and solubility and soap. The soap thing is something I originally learned in high school and got to see repeated in two general chemistry classes in college and organic chemistry too. I might do a post on it, but for me, it's gotten kind of old. There is some really great material here. I especially like the explanations of biomolecules, but perhaps that's best reserved for later.

In short, I do want to write at least one more post on the odds and ends in the third chapter of my textbook. They will come soon if at all, because I am long overdue on starting the fourth chapter. Before I do either of those things, let's wrap up intermolecular forces.

The strength of intermolecular forces is, in ascending order...

• London Dispersion: caused by fluctuations in charge density across the surfaces of molecules.
• Dipole-Dipole: caused by permanent dipoles.
• Hydrogen Bonding: Caused by extreme loss of electron density on hydrogen when bonded to oxygen or nitrogen (or fluorine, technically).

Note that ion-ion forces, which hold ions together in ionic compounds, could be compared to these forces, although ions are technically not considered molecules. Ion-ion forces are much stronger than any of these intermolecular forces.

Intermolecular forces have the following effects on physical properties...

• Stronger intermolecular forces increase boiling point.
• Stronger intermolecular forces increase melting point.

There's more, but I am skipping it because that's the important stuff and you'd forget the rest anyway. If something I omitted here becomes important later, I'll just blame the problem on you. It's either that or explain the thing when the issue comes up.