#ochem basics

I got partway through writing an entry on electronegativity, ring strain, and molecule shapes when I realized that I've never made an entry about bonding and the periodic table and that I really *should*, because it's pretty much the most basic thing in chemistry.  In fact, it isn't the first thing they teach you in chemistry and I found that when my teacher finally covered it, all of chemistry made sense.  If I'd been writing this blog for viewers instead of for my own benefit, this would have been lesson #1, and I feel that given the amount of followers I have I should put this up for other peoples' benefit.  So here you go.  

To begin, I think I need to explain shells for you to be able to understand anything else.  Electrons, as most people know, are arranged in shells around the nucleus.  Now, those shells take different shapes, and there's a lot of math involved in them that you won't use at ALL unless you're going to be a chemist and take calculus.  The math is used to predict where in the shell an electron will be, because it turns out that shells are more like clouds with layers of no-mans-land between them.  "Jumping" electrons are crossing those no-mans-lands to higher clouds.  Putting energy in (endothermic) makes the electrons jump to the next shell, and when they fall back they release that energy (exothermic).  This is actually the basic principle behind rechargeable batteries and lights (also the reason why batteries and lights are warm.  That, and friction generated by the electrons moving through the various metals involved.).   

Anyway, there are a few things that you need to know when it comes to assigning electrons to shells: 

s, p, d, f carry 2, 6, 10, 14 electrons (e-) respectively.  

E- spin.  In pairs.  Opposite each other.  We represent this with one up arrow and one down arrow in each "slot" (IE, 1s1 has 2 elections, 2s1 has two, etc.).  Fun fact: when all elections are paired, something has no magnetic properties.  When it is missing a spin partner, it has magnetic properties.  

Slots are filled up one electron per slot at a time.  Like this: 

Orbital notation is as follows: 1s1 means 1st orbital, s shell, with one election.  So orbital/shell/number of elections.  

And, lastly, this chart for filling up electron shells in the correct order (start at 1s and follow the arrows): 

(From here.)

How do you know how many electrons you have? Well, that comes from our next topic of discussion: 

The periodic table is magic and you should learn how to use it.  I can't tell you how many times an in-depth knowledge of the periodic table has saved my butt on tests.  It's like taking a test with a cheat sheet.  

Note: Having a table to study with is a must.  I use an ipad for school (I'm an Android devotee, but I couldn't pass up the Apple store's much broader width of educational apps on a device I purchased for the purpose of using it for school.), and I love it.  My whole educational life is on that thing and I *highly* recommend getting one, and a stylus, if you at all can.  That said, I wasn't always of this opinion and didn't get it until about a year ago.  I use an app for my periodic table called EleMints.  There is a paid version, and a free version, and even the free version is great.  If I'd had this at the beginning of my chemical career I definitely would have sprung for the paid version (it's only $5).  There are TONS of periodic tables on the web, and I have yet to discover one that love, but most of them will do.  I would stay away from any of the ones with more than two decimal places for the atomic weight.  It's an unnecessary level of exactness (when will you ever have significant decimals? Never, that's when.), and it can mess up your calculations.  Like it is really not necessary to know that the weight of oxygen is 15.9994.  16 is fine.  If you do use one with lots of decimals (like EleMints, actually) rounding is A-ok.  

I'd also like to take a second and thank the lovely and brilliant wut4, for teaching me - one panicked night during che111 in her apartment - how to really use the periodic table.  If you guys had seen me that night, you'd never have thought I'd possess the depth of knowledge and understand I have now.  I was a hot mess of "HOW I DO DIS THING", and her teaching me what the periodic table meant was really my first moment of grasping all of this.  Good friends are the best <3

So, without further meandering, here is the periodic table of the elements: 

(Yoinked from about.com.  That'll open it, large enough to read, in a new window.  Here's another good one in case you don't like those colors.)  

Isn't it purdy? Hmmm...where should we start? How about the colors.  The colors notate specific groups of elements, and those groups have specific properties.  Now, because I largely deal with organic chemistry on this blog, I do a lot of ignoring of that entire middle section.  Sure, we have organo-metallics, but they're not nearly as common as some of the other things we do.  Also those complexes are a lot more advanced and generally kind of covered in Chem 112.  By and large though genchem (or non-organic chemistry) likes the Alkali metals, the alkali earth metals, and basically all the ones that say "metal" in them.  Mostly ochem just deals with the halogens, carbon, oxygen, nitrogen, and hydrogen.    But remembering the names (and properties) of the various groups can be really handy for all types of chemistry, especially on tests.  

Another thing you can get from the periodic table is the size of the atoms - something that's very important when it comes to electronegativity (which I'll cover next entry).  Size only has a loose correlation to weight.  Here is a periodic table showing size (for things that exist long enough to get that information): 

(ganked from here.)

Now, for me, one of the most important things on the periodic table is atomic number.  This is the number of protons, which conveniently also makes it the number of electrons (for non-ions).  Elections are basically the most important thing in chemistry, so there's that.  

Atomic number is closely related to types of bonds, so I'm going to kind of cover both at the same time.  There are, roughly, two types of bonds that we care about: 

Ionic - Electrons are exchanged by the atoms.  One gives, and one receives.  

Covalent - Electrons are shared by the atoms.  

Now, your teacher will probably make a big deal about how different these two things are.  But, if you're like me, you looked at a Lewis dot structure and couldn't for the life of you figure out what the hell the difference was.  They're both bonded together, right? Here's a really easy way to tell them apart: 

Ionic bonds are electronically charged.  These are the bonds where something positive is attracted to something negative.  

Covalent bonds aren't generally charged in the same way.  These are bonds that we think of as having a certain number of them.  For example, carbon needs 4 bonds to be happy.  It covalently bonds.  

The difference is in that concept I mentioned earlier: shells and valence electrons.  

How do you know how many valence electrons something has? Well, look at the noble gas (far right column) of the row previous.  Subtract that from the atomic number of that gas from the atomic number of the element in question, and you'll have the amount of valence elections.  For example, sodium (Na) has 11 elections.  The noble gas on the row previous is neon (Ne) and it has 10 electrons.  11-10 is one, so Na has 1 valence electron.  

Ionic bonds are normally made up of elements from the first two columns combined with elements from the 16th and 17th column.  Why? Because the elements on the left of the table, in the first and second columns, only ever have one or two valence electrons.  They are actually much more stable when they give up those one or two electrons.  However, giving them up means that there are now two more protons than there are electrons, so now they have a charge: 1+ or 2+.  The loss of these electrons happens easier the farther down in the column you go (because the larger atoms have a harder time holding onto the valence electrons - the farther the e- are from the positively charged center, the less of a hold it has on them.  Which is why things like Cs are *incredibly* reactive.).  There is actually an entire branch of chemistry devoted to this process in a single element: hydrogen, and acid/base chemistry (which I hate with a the fiery passion of a thousand suns.).  

On the other end of the table we have things like Chlorine, which has 7 valence electrons.  Elements on this end of the table adhere to two general guidelines: 

The Octet Rule: On this side of the table, all elements, in general, strive to have 8 valence electrons.  This is why carbon makes 4 bonds - it has 4 valence e-, and it wants 8, so it'll bond 4 more things until it's full.  

Everybody Wants to Be Noble: every element on this side of the table is much happier with a full shell.  They want to have the same number of electrons as the noble gas to the right.  They'll borrow (covalent) or steal (ionic) to get them.  

In an ionic bond, what happens is that during the reaction the thing from the right side of the table steals the valence e- from the thing on the left side of the table.  This gives the thing from the right side a negative charge (more electrons than protons) and the thing from the left side of the table a positive charge (more protons than electrons).  It is those *charges* that hold the compound together.  By and large, things that are ionic are water soluble.  Water also carries a charge (both positive and negative, one of the things that makes water so special...I should do a water entry.), and so it is attracted to other things that have charges, meaning that they are all polar.  Non-polar things don't have charges, only partial charges.  

So I'll toss this out there: like dissolves like.  Non-polar solvents will not dissolve polar things, and visa versa.  So when you are home trying to clean something, think about what it is. Is it water soluble? Obviously not if you can't just rinse it off or have it dissolve.  If it's not, then get something non-polar to try and dissolve it.  This is why rubbing alcohol removes sharpie dye.  This is what soap is based on.  It's a principle that's very useful in a number of practical, real-life ways.  Like cooking: salt won't dissolve in oil.  Butter will.  Almost the entirety of life is based on the idea of polar and non polar things not mixing.  But don't confuse charge for magnetic properties, they aren't the same.  As I mentioned above, magnetic properties come from unpaired electrons.  

Anyway, returning to ionic and covalent.  The formation of ionic bonds is often pretty exothermic, because the loss of the electron is exothermic.  As demonstrated by this making of salt in a lab:

As he demonstrates, it's perfectly edible.  It's exactly the same thing as salt mined out of the earth.  The only difference is that salts obtained out in the natural world have various other minerals embedded in the crystalline structure of the salt, which is what gives them different tastes and colors.  

In a covalent bond, the electrons are shared and not based off of a charge.  Normally these happen with elements in the middle and right side of the table.  Let's take carbon as an example (because it's really the best one.).  It has 4 valence electrons.  Too many to give up, but not enough to be noble.  Carbon will bond to just about anything that'll let it because of the arrangement of its electrons: all of its valence electrons are unpaired.  So it will bond sodium, heck it'll bond 4 sodiums.  Definitely not its favorite arrangement (and probably not very stable), I'll grant, but it'll do it.  Carbon even bonds itself, in a number of different ways: coal, charcoal, diamonds, bucky balls, etc.  All vary only by inclusions, and the shape of the carbon bonds involved.  Carbon really, really doesn't like giving up its electrons.  It can, and often does, form two or three bonds with one single other atom, but not four because the shapes of electron cloud orbits prevent it.  It'll still be looking for friends to play with.  In fact, Ethene - or ethylene - is long strings of: [C=C-C=C-C=C-C=C] and it is polyethylene (many ethylenes).  Or, as you know it, plastic.  

Oxygen is the same way.  It has 6 valence electrons, but it wants 8, so it'll make 2 bonds.  6 electrons is way too many to give up, so oxygen will steal electrons or it will covalently bond.  However, because it only can make 2 bonds it'll happily bond to itself.  This is why oxygen comes in pairs: O2.  It's called a diatom.  It is also why oxygen reactions can often require catalysts.  O2 is a very, very stable molecule.  So you either need to bond it with something that's more attractive to it than its paired oxygen, or you use a catalyst to destabilize the oxygen and split those bonds.  

We all know you can easily pair oxygen and carbon, but since neither of them will give up their electrons they form a covalent bond where they share the electrons.  Neither is positive or negative in a stable form, but they'll easily bond.  Obviously, as our atmosphere is filled with CO2, which looks like: O=C=O and is *extremely* stable.  That's actually part of the problem of removing CO2 from the atmosphere.  It requires a lot of energy to split the CO2 bonds.  Generally more energy than you get out of the process.  So a theoretical "CO2 scrubber" would have to work pretty hard and use a lot of energy to remove a comparatively small amount of CO2.  Energy that has to come from someplace - currently largely fossil fuels - and in doing so would create more CO2 than it removed.  Obviously the exception to this is plants, which is why we look to trees, grass, algae, and the rest to split those bonds for us.  

Covalent bonds are usually very stable, although obviously possible to break because we do it all the time in ochem.  What I mean by stable is not prone to randomly decomposing in your face.  x.x  Also, one last note about ionic/covalent bonds: because of the difference in these two bonds the compounds that result have different properties.  By and large, ionic compounds will disassociate in a solvent, covalent ones one (they will dissolve, but they won't break down into their component parts.).  

Note: when I first learned about disassociation in liquids, I was confused.  Salt in water breaks down in Na+ and Cl-, right, but also salt water still tastes like salt and doesn't so much make with the exploding as you might think.  So think of disassociation like Schrodinger's box.  Schrodinger put a cat in a box with poison and postulated that until you open of the box and see if the cat ate the poison, the cat exists in a quantum state of both alive and dead.  Salt water contains: H+, OH-, Na+, and Cl- ions.  Because the salt *and* the water disassociate (yes water dissolves itself I told you it was magic.).  BUT, because those positive and negative charges are highly attractive to each other you also have: NaOH, HCl, H2O, and NaCl.  However, they move way too fast for them to *really* react the way they should, and maintaining equilibrium keeps them busy.  So until you look at a molecule, it is both an ion and a molecule.  Salt water contains the ions and the fully formed compounds.  Which, by the by, is also why you shouldn't drink it.