Hydrogen and Oxygen bond to make water... but why?
September 24, 2009 9:39 AM   Subscribe

Please help me really grok chemistry.

TMBG's recent song "meet the elements" has got me thinking more about chemistry recently. I never really studied it when I was younger, but I've developed more of an interest now.

I understand certain basic concepts - atoms are made of protons, neutrons, and electrons, atoms combine to make molecules, etc, but I don't really "get" it. When you combine, say, vinegar and baking soda, what's really happening at the atomic level? Why do different combination of 3 basic particles behave so differently? Why do some molecules have more potential energy than others? These things escape me.

If there's anything that's helped you really understand this topic, please recommend it! Books, games, documentaries, websites, youtube movies, anything is fair game. I'm not afraid of college-level math, but I find the "dry" writing style often found in textbooks, scientific papers, and encyclopedias very hard to pay attention to. Something with an amusing writing style, or with a large visual component (videos, diagrams, charts, whatever), or with very down-to-earth language would be most effective, I feel.

Thanks in advance Mefites!
posted by Vorteks to Science & Nature (14 answers total) 29 users marked this as a favorite
What helped me understand some of basic chemistry, as someone who almost failed chemistry in high school and subsequently took over three years so far of chemistry in college, was the Chemistry as a Second Language series written by David Klein. There are three books out (one for gen chem and two for ochem). I don't know how well these books will work as stand-alone books, though, since I used them in conjunction with my textbooks and lectures but they were immensely helpful for understanding many principles in chemistry for me.

I will say that for me that many of the concepts in chemistry didn't really click until I took organic chemistry. So much that I didn't understand in gen chem finally made sense.

Good luck!
posted by rainygrl716 at 10:01 AM on September 24, 2009

Best answer: Pick yourself up a copy of The Cartoon Guide to Chemistry. It's seriously awesome, as are all of Larry Gonick's books.
posted by cerebus19 at 10:16 AM on September 24, 2009 [3 favorites]

As a biochemistry student, I could recommend some first-year general chemistry texts, but they might not be the greatest at using "down to earth" language. I can answer why those three particles behave so differently though (and in the process, give you a basic crash course):

As you're no doubt aware, protons and neutrons form the nucleus of an atom. This is positively charged (protons have a positive charge, neutrons have a neutral charge). Electrons are much smaller than either protons or neutrons and orbit around them in clouds, attracted by magnetism.

Two atoms can connect in a few different ways, best classified as ionic or covalent bonds. Covalent bonds are when two atoms are effectively "stuck together" and tend not to come apart, such as the two hydrogens to the oxygen in water. Ionic bonds are when two atoms are held together essentially by magnetism, such as an atom of sodium and an atom of chloride to make NaCl, table salt. When you put table salt into water, these atoms come apart as "ions", that is, charged atoms.

In this way, ionic bonds are easier to visualize, as we've all played with magnets. The chlorine has a far better ability to attract electrons than the sodium does, so when these two separate, a chlorine atom will take an electron from a sodium atom. All pure atoms on the period table are neutral, so by chlorine taking this electron (negatively charged!), it becomes negative. The sodium becomes positive because it has lost some of its negativity. in actuality, this process has already occurred if they are in their salt form; they are simply held together like the positive and negative poles of two magnets.

When you see baking soda and vinegar react, you're actually seeing sodium bicarbonate and acetic acid undergo a neutralization reaction (when an acid meets a base). Those wikipedia pages do a pretty good job of showing how these molecules are held together. The acetic acid is held together by covalent bonds and in this way, it tends not to be broken up into smaller parts (this is a generalization). The sodium bicarbonate however is drawn in ionic form. You can see the sodium (Na) with the positive charge and the oxygen with a negative. That big reaction you see happen is actually what happens when the negative bicarbonate portion of the baking soda pulls so strongly on the positive hydrogen of acetic acid (the one attached to the oxygen in this case) that it rips it off!

You may have already known all that, in which case, sorry for writing so much for you to read through.

This is related to free energy because in chemistry, things will always become more stable if they can. The more unstable they are, the more free energy they have. They release that energy by becoming stable again. An acid is just a molecule that doesn't have a very good grip on one of its hydrogens (chemists will be mad at me here, but it's simpler to think this way until you pursue the subject further). A base is a molecule that is capable of taking another hydrogen from somewhere and is actually more stable with one. As you can see now, the sodium bicarbonate and the acetic acid are practically made for each other!

That explains your kitchen chemistry, hopefully someone else around here can point you to something a little more fun and illustrated than my little rant here.

Good luck! Remember that if you're starting to get bored, just do a few experiments that blow things up and your interest will come right back. See if you can't buy yourself some sodium metal, look up the reaction between it and water, then try for yourself!
posted by battlebison at 10:22 AM on September 24, 2009 [2 favorites]

Best answer: Seconding Gonick on almost anything (Cartoon Guide to Statistics is mega-boring, though, probably because Gonick has a degree in math).

Also, this is the best thing I've read on MeFi today: TMBG's recent song "meet the elements" has got me thinking more about chemistry
posted by DU at 10:22 AM on September 24, 2009

Response by poster: Thanks for the answers so far! Judging by the Amazon.com reviews, The Cartoon Guide to Chemistry is very much what I'm looking for. I've put it in my cart.

@battlebison - Thanks for taking the time to write all that! I kind of understood some of it, but I'm kinda hazy about the details. For example, you wrote The chlorine has a far better ability to attract electrons than the sodium does. That's one thing I don't understand. Why should that be so? If protons are positive, and electrons are negative, shouldn't there always be one electron in orbit for every proton in the nucleus? Certainly some protons aren't more positive than others, are they?
posted by Vorteks at 10:29 AM on September 24, 2009

thing I don't understand. Why should that be so? If protons are positive, and electrons are negative, shouldn't there always be one electron in orbit for every proton in the nucleus? Certainly some protons aren't more positive than others, are they?

Some configurations of electrons are more stable than other configuration of electrons. This was traditionally understood in terms of "valance", which is a sort of phenomenological description. To understand the "why" of it, however, you really need to dip your toes into quantum mechanics.
posted by mr_roboto at 10:39 AM on September 24, 2009

What really helped me grok chem was when my organic chem textbook started showing electron density maps. Here's a couple neat ones:
Hydrochloric acid reacting with water

Red is where electrons are likely to be; blue is where they're likely not. When molecules hump each other (collide), the blue zones often yoink electrons from the red zones. That would be called a reaction.

At its core, chemistry is about energy and the electrostatic force. You've got positive charges coming from protons and negative charges coming from electrons, and they attract. Boom. Everything is a result of that.

I like analogies, so I'll throw out two. PS these are all ridiculous oversimplifications.

Whenever you have a positive and negative charge that are not right on top of each other, there's potential energy. Why? Because as they close the distance, you can harness the attraction to do useful work. This is your laptop battery: a bunch of positive and negative charges that are separated. When we run off battery, we allow them to meet. But first we use that energy to force electrons through your computer to do useful things like go on mefi. Imagine a weight that is hoisted off the ground. As that weight is lowered, you could lift something else via a lever. In one case, the force is electrostatic and in the other it's gravitic. But the underlying concepts are the same.

Like the weight falling towards the earth, a given system always wants to convert its potential energy to be in the lowest energy state. That lowest state is represented by all the negative and positive charges being as close to each other as possible. In organic chemistry, you'll often have a sequence of steps that take you from the initial reactants to the final products. These middle steps have intermediate states that are actually higher in energy (the charges are even farther apart) than they were when they started. Wtf, right? Well as long as the final state is lower energy the reaction can and does happen (caveat: you need enough energy to create the intermediate states. Catalysts allow intermediate states that are way more chill, thus increasing chances the reaction will run.) Here's a fun little energy graph. Think of sitting on the couch. You're seated, you're mellow, you're not spending too much energy. Suddenly you decide you want to lay down. Well, in order to get there, you have to go through a sequence of moves, each of which is less comfortable than being seated. But when you finally lay down, it's even lower energy. A catalyst would make it easier to get into a prone position, like one of those ez-chairs with a lever that pops out the footrest. You also tend not to want to stand up for a while, feeding my theory that people, like molecules, always want to be in their lowest energy state.

Kinda wordy and unfocused. But there ya go.
posted by dualityofmind at 10:45 AM on September 24, 2009 [5 favorites]

I think the Cartoon Guide will answer that question, but in case you want a more immediate answer:

The chlorine has a far better ability to attract electrons than the sodium does:
You're right, there is one electron in orbit for every proton in the nucleus. Now consider the idea "where is the electron in orbit?"
Atoms (as the book will explain) like to arrange their electrons in groups, so there's a couple of electrons with one type of orbit, and a handful of electrons with another type of orbit, and another handful with a different orbit... These orbits are "energy levels" meaning that once one orbit has its full handful of electrons, starting the next orbit will need electrons with extra energy.
Chlorine has one slot left at lower energy before its handful is complete, and in fact, closing out that group would be a good thing. Chlorine wants an electron.
Sodium has just started a new orbit, with one electron in it, that's "costing it more energy" than all the other electrons. Sure, there's space in that handful to have two electrons instead of just one, but that's effort. (i.e. it's not strongly attacting electrons) What would be awesome, would be if sodium could just ditch that single high-effort electron.
So, sodium and chlorine get together, and sodium lends its extra electron to chlorine's gap, and you have salt.

When you're dealing with tiny things like atoms, you really need to think about electrons in terms of how they're attached to the nucleus, which is energy levels ("orbits") and quantum mechanics. If you wanted to think about it in terms of charge, you kind of have to fudge it, but the following is roughly true:
If you've got N positive charges bunched up right here, and N negative charges running around, there are ways that those electrons can leave a gap and give you a clear sight to the positive nucleus, and ways that those electrons can bunch up so that you don't see the nucleus at all.
posted by aimedwander at 10:56 AM on September 24, 2009

Best answer: Ah! I should have explained. The periodic table is laid in terms of size of the atom. A hydrogen has only one proton, a chlorine has 17. The "atomic number" of an atom is the number of protons in its nucleus. You are absolutely correct, every proton is identical, and their natural states, every atom has one electron for each proton.

Electrons also form in "layers" (more like different clouds, but most people think of them in this way). These are called orbitals and are lettered S, P, D and F. They are named after the appearance of their spectroscopic lines. Damn chemists! But the idea is that electrons in layer S are generally more stable than those in P, P more than D and so on. Because of this and the tendency towards stability in chemistry, electrons will "fill" an orbital before moving onto the next one. The periodic table is also organized to accommodate this! The S orbital can contain only two electrons, so the only atoms in the first layer of the table are hydrogen and helium. The next line starts with lithium, which now has 2 atoms in the S orbital and 1 in the P.

Think of again the tendency towards stability: In some cases, it is more stable to either fill or empty the highest energy orbital on the atom. Noble gases, the last column of the periodic table, do not react with anything because they are already as stable as can be. They have full orbitals! Everything else however, does not. Sodium has one electron too many and chlorine has one electron too few to have a perfect number of electrons to fill an orbital. That is why chlorine takes the electron.

An atom's ability to take an electron can actually be quantified and is called its electronegativity. Sodium has an electronegativity of 0.93, chlorine of 3.16. What these numbers mean is: chlorine is very strongly attracted to electrons, sodium not so much.

Another factor in this is size of the atom. Chlorine is, compared to most organic atoms, huge! It has 17 protons and 17 electrons. It has almost filled its D orbital. Fluorine, another atom that needs only one more electron to fill its outer orbital, has only 9. It is trying to fill its P orbital. The D orbital has a higher energy and is less stable than the P, so given the choice between the two, an electron would be more stable in the P orbital. For this reason, fluorine (3.98) is even more electronegative than chlorine (3.16) in terms of electronegativity.
posted by battlebison at 10:56 AM on September 24, 2009

My suggestion is mostly tongue-in-cheek, but for rote memorization (as opposed to grokking) I find that ditties are helpful. As a biochemist, I have a particular soft spot for The Biochemist's Songbook by Dr Harold Baum from the University of London. The songs are available as mp3 files here.

*wanders off humming Waltz round the cycle, waltz round the cycle, waltz round the TCA cycle today, a decarboxylating complex dehydrogenase turns pyruvate to acetyl coA*
posted by Quietgal at 11:07 AM on September 24, 2009 [1 favorite]

Uncle Tungsten: Memories of a chemical boyhood

It's not a chemistry textbook, it's a book about chemistry and how the love of it shaped the author's life. Surprisingly good reading (check out the Amazon reviews), and in his descriptions of, for example, finding something that fascinated him, and why he was intrigued, etc, I got a lot of "I never thought of it like that before!" moments, even on topics with which I was already very familiar and understood well.

This book is the beauty and wonder counterpart to the dry textbook.
posted by -harlequin- at 12:05 PM on September 24, 2009

The recent "Microscopes zoom in on molecules at last" was an Aha! moment for a lot of us. It's been nice to see all those ball and stick diagrams and models but finally we had visual verification that they aren't approximations... that's what these things really look like!

Also, the tools people suggested to me here were fantastic.
posted by jwells at 12:52 PM on September 24, 2009

battlebison: Ionic bonds are when two atoms are held together essentially by magnetism
What? No. Magnetism is a different creature.

A covalent bond is when an electron spends some time around two nuclei. An ionic bond is when an electron spends all its time around the "wrong" nucleus, making an ion pair. The ions can be held together by electrostatic attraction.

Magnetism is caused by moving electric charges. In magnetic materials like iron the moving electric charges are the electrons orbiting the nucleus. There is also magnetism due to the "spins" of the electron and the nucleus; this is much smaller. In every case the energy due to magnetic interactions between atoms is smaller than the energy due to electric interactions. (It's true that electrostatic attraction follows the same rules as attractions between magnetic poles, that opposite charges attract and like charges repel, but the mechanism is very different.)

Also, chlorine has a nearly-full second P shell; the lightest element with D electrons is scandium. I wrote earlier this month on MeFi about why the periodic table has the shape it does.
posted by fantabulous timewaster at 5:21 AM on September 25, 2009

Check out The Periodic Kingdom - it's a bit of a dry read but only about 100 pages. It explains in layman's terms why the periodic table has the shape it does, which has the side benefit of answering most of your questions. It covers electronegativity as well as why the different orbitals have differing stabilities.
posted by benzenedream at 11:26 PM on November 16, 2009

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