#chem basics

[burnedbyh2so4]

Chem basics

 Atoms consist of 3 subatomic particles.

The nucleus of an atom is significantly small compared to its electron cloud.

London dispersion force< Dipole-dipole Force < H-bonding < Ion-Dipole Force

Isotopes are the same essentially, they jut have different number of neutrons.

Electrons have a negative charge, protons have a positive charge, neutrons have no charge.

Each orbital can hold a maximum of two electrons.

A carbon atom has a total of 4 electrons.

Atoms that in Group 1A (alkali metals) tend to lose electrons. (This is to achieve stability)

The overlap on adjacent atoms has a limit. This limit is the nearest they can get to the other atom. If this distance decreases, the nuclei of both atoms will start to repel each other.

Molecular orbitals are located on two or more atoms.

A hybrid orbital is a combination of s and p orbitals.

In the 3-D structure of a molecule, the bonds to atoms coming out of the plane of the paper are shown as solid wedges.

The angle between sp2 orbitals is 120 degrees.

A curved arrow shows electron pair movement. A curved arrow with only half a head shows one electron’s movement.

A polar bond shares electrons unequally. A portion hogs all the electrons and becomes partially negative while the other is partially positive.

London dispersion forces exist between all molecules.

[science-of-anthropology]

The Dreaded Stereochemistry: Part 1

Stereochemistry, for those who may not have taken ochem yet, is the chemistry of isomers.  Isomers are molecules with the same chemical formula, but different arrangements.  For example, C3H6O can be either 2-propanone (acetone) or 1-propanal.   Which look like this: 

(yeah I drew that on my ipad that is my ipad handwriting, hehe.) 

In ochem, the type of stereochem we tend to talk about most is chirality.  Stereochemistry is actually really complex, and it's also really important, and parts of it really tend to trip people up (I'm looking at you chirality).  I'll try to start basic and work up to the harder stuff.  This first half is going to be terminology and drawing types.  I'll probably be writing part two right after I write part one.  :)  

To start, there are two basic types of isomers: 

Constitutional - Same chemical formula, but the structural connections and possibly the functional groups are completely different.  

Stereoisomers - The same connections and functional groups, but they are arranged in structurally different ways, often differentiated by what they look like in space (IE, a substituate is pointing forward and not backwards.)  

In ochem, we don't really care about constitutional isomers because normally it's not important that they are isomers.  It's not relevant to us that acetone and propanal have the same chemical formula.  We care about stereoisomers, because a lot of the time our reaction product includes both isomers; and because those different isomers have different chemical properties.  There is a lot of chemistry revolving around producing the correct isomer and separating isomers.  For example, in the 50's they had this drug called thalidomide that was used to eliminate morning sickness in pregnant women.  That drug, in the 50's, caused huge deformations in babies.  Later, we find out because one isomer of the drug is safe, and the other causes birth defects.  They were selling it with both isomers, hence the "babies of thalidomide".  Currently they still sell and use the drug containing only the single, safe, isomer.  

Now, before we go any farther there are some terms you need to understand: 

Cis - Latin meaning "on the near (or same) side".  In chemistry, it often means "on the same side of a bond".  

Trans - Latin meaning "on the other side" (or "across).  In chemistry, we mean "on the same side of a bond".  

Rectus - Latin for "right", and in IUPAC and chemical notation it's referred to as "r".  r = right is a perfectly ok way to remember what the difference between R and S is.  

Sinister - Latin for "left"(now go forth, my pretties, and tell your left handed friends that they're sinister.).  In IUPAC and chemical notation it is S.  R/S are opposites of each other.  They are not the same as cis and trans, because they aren't talking about sides of a bond.  I'll get to that later though.  

E/Z - Not used as often as the others, it's important to understand it.  Cis/trans can only be used when there are two substituates because it is describing those things in relation to each other - they are on the same side of the bond or different sides.  But what if you have a molecule that has multiple double bonds? R/S isn't really appropriate, so we use E/Z instead.  E/Z is a way of describing multiple instances of cis/trans isomerism on the same molecule.  E is trans, and Z is cis.  I remember it because Z sounds like C.  I'll go into this, and the naming convention for all of these, a little later.  

Note on the drawing of atoms: Stereo chemistry is confusing to a lot of people in part because of the the drawing.  You are taking something that is 3-D, and transferring it to paper and making it 2-D.  Then you make up notation for how it looks in 3-D.  For example, drawing substituates that are coming out of/going into a flat surface looks like this: 

I think the most important thing to remember, especially if you are a really visual person like me and very good at picturing things, is that the molecules might rotate in space in reality but when you're drawing and notating the do not move. Do not flip them and turn them and look at them in your brain.  Just don't, you'll get confused.  In life, these molecules rotate.  In chemical notation, they do not.  There's two ways of looking at them: face on, and edge on.  Just remember that this: 

Is the same thing as this: 

Notation and Drawing: 

There are three main ways of drawing molecules, and I'll put them here in decreasing use in Ochem.  

Ball-and-stick or line drawings - This is the basic drawings I've been using the whole time on here.  Like the above acetone drawings.  The lines are the bonds, the angles are where the carbons are.  My ochem teacher used to actually write them out like: CH3 - CH2 - CH2 - CH3 and to this day I don't understand how that was possibly faster or easier than drawing 4 lines.  

Newman Projection - This is a more difficult to understand way of looking at it.  It is a way of notating a molecule from edge on.  So this: 

          Looked at from this angle: 

          Has a Newman projection of: 

          The hydrogens can be replaced with any substituate necessary, and the colored bits are for your information and not actually part of how it's notated.  But obviously if you want to show a long molecule this isn't the best way.  

Fischer Projections - Lastly, we have my least favorite of all notations, the Fischer projection is used really heavily in biochem but almost never in ochem (depending on your teacher.  Mine used it a lot, probably because she was trying to get us used to it for biochem.).  It's the molecule arranged as a series of cross hatches and, to be honest, it's just easier for me to show you.  I'm going to use butane as an example: 

           The hydrogen should be looked at as coming out of the page,     and the CH3s at the top and bottom are going into the page.  Or, as my teacher likes to say, the arms on the side give you a hug.  This is often used in biochem because biochem deals with these enormous molecules and this lets them sort of zoom in on the relevant parts.  The just write R, R', etc. at the top and bottom (shorthand for "rest of the molecule goes here, not to be confused with the R of chirality.).  They also use it to show sugars.  

Note: When drawing molecules, the basic zig-zag (as exemplified by butane in the above drawing) is basically never correct.  It's a shorthand for when we don't care about representing the model in 3-d space.  Also, in reality the hydrogens aren't important enough to assign cis/trans/e/z/r/s to.  I've just used this as an example.  Also, when you see the triangle and dashed triangle...it can be either a methyl group like it is, or some people like to actually write the CH3 on there.  If it's a non-methyl substituate, then you write that in there.  

I know this is probably somewhat confusing and not terribly clear because I haven't gone into a ton of detail on how to use these things, but I promise the next entry will fix that.  This entry was just to provide you with the lexicon you'll need to understand part two.  :)  

[science-of-anthropology]

Themochemistry - Part 2

In this bit, I'll cover the other two types of thermo problems you might see (part one is here.).  But first, I'm going to add something that I forgot in the previous entry and meant to have.  

Specific heat - the amount of heat necessary to move one amount of a substance one degree.  So, water's specific heat is 4.18 J/(g*C).  That means that it takes 4.18 Joules to move one gram of water one degree.  Sometimes you will see this with kJ or kG as the unit.  It takes .00418 kilojoules to move one gram of water one degree.  The units here trip me up on a regular basis, so just make sure you read the question very carefully and give the answer in the right form.  

Heat Capacity - The amount of heat required to raise a sample of something one degree.  The official formula for it is q = CΔT.  HehehehEHEHehe....it looks like cat.  C = a given value of specific heat (IE, the 4.18J/(g*C).  This isn't a thing that's used a whole lot, but I figured I'd toss it in.  Specific heat is much more important.  

First, we'll do coffee cup calorimetry.  I hate these problems.  They're boring and needlessly complicated and serve virtually NO purpose except for to help you do your coffee cup calorimetry lab.  You probably won't see them again after this.  

Ok, so the things you'll need to be able to do a CCC problem: mass, the ability to calculate molar weight, and a change in temperature (which is designated as Tfinal - Tinitial, or Δt.  In physics this symbolism gets confusing when you deal with tension, but this isn't physics class, YAY!).  There's no real way for me to explain it except to do it, so here's an example problem: 

When a 5.87-g sample of solid ammonium nitrate dissolves in 90.77 g of water in a coffee-cup calorimeter, the temperature drops from 23.0oC to 18.4oC. Calculate ΔH (in kJ/mol NH4NO3) for the solution process assuming specific heat of the solution is the same as that of pure water*. 

*The reason is because there's not enough of the solute to effect the specific heat of the water.  Highly concentrated solutions don't follow this rule, but this is chem 111 so almost everything you see will.  If they don't, you'll be given a different specific heat.  

Another note about symbols: Because ΔH is already taken by enthalpy, changes in heat are noted by writing q.  Why the thing that starts with an H didn't get to claim ΔH, well, that's beyond me.  Chemists are super weird about names.  

Ok, so on to figuring this out.  Here's what's important: 

q/amount of solute is going to give us the answer.  In this case, we're being asked for the answer in kJ/moles, so we'll need to switch the grams to moles later.  

Find q: Mass of the solution x Specific heat of the solution x Δt

Mass = Ammonium Nitrate + Water, so in our case: 90.77g + 5.87g = 96.64g

Δt = Tf - Ti, so 18.4C-23.0C = -4.6.  Note that negatives are ok, and that this reaction is endothermic, as the temperature of the water was LOWERED 4.6 degrees.  That means the reaction absorbed 4.6 degrees of heat.  

96.64 x 4.184 x -4.6 = -1859.972 J.  We're asked for the answer in the form of kJ/moles, so we change this to -1.9kJ.  

Also, because we're being asked the amount the reaction absorbed and this number signifies how much the water lost, we flip the sign.  Because of the laws of thermodynamics, the amount of heat (energy) in a system is constant.  What the water lost the reaction MUST have gained.  That's why we can simply flip the sign.  

1 mole of NH4NO3 weighs 80g, so the conversion (if you missed how to do that, I wrote it up here.) results in 7.33x10^-2 moles.  

The next step is division.  Divide q by whatever amount you're being asked for.  If you're being asked for one mole/g/kG/whatever obviously you don't need to divide.  For us here:  1.9/7.33x10^-2 = 26kJ/mole

And that's it, basically.  Interesting sidebar: These are called "coffeecup calorimetry" problems because coffee cups are really good insulators.  It's a shorthand for "something that keeps heat from getting out into the general environment".  The calorimetry part is derived from the fact that calories used to be the standardized measure of heat.  This is how they figure out how many calories are in food.  They burn it and measure the change in temp in a closed environment.  The temperature change is then converted into calories.  A calorie is equal to the amount of heat needed to raise one gram of water one degree.  So...calories are a measure of heat, not accurately of energy, and they say absolutely jack all about what your body does with it the food you eat.  

Ok, the third type of problem are Hess's law problems.  

Hess's Law: The enthalpy accompanying a chemical reaction is independent of the pathway between the initial and final states (Stolen from wikipedia: http://en.wikipedia.org/wiki/Hess_law)

That means, essentially, that if you know ΔH for a couple of similar reactions you can rearrange them (and their ΔH) to figure out the enthalpy for a similar reaction.  Now, this isn't a terribly practical thing to know.  Not like actual enthalpy problems, but I kinda like them because they're like a puzzle.  Here's the problem: 

Calculate the standard enthalpy change, ΔHo, for the formation of 2 moles of sulfur trioxide given the following information:

2 S(s)  +  3 O2 (g) --> 2 SO3(g)      ΔH = ?

Given:

S(s)  +  O2 (g) --> SO2 (g)   ΔH = -297 kJ

2 SO2(g)   +  O2 (g) --> 2 SO3 (g)    ΔH = -198 kJ  

So, the goal in manipulating these problems is to have the product be the same as the equation for whom you are trying to find the ΔH. The two given formulas will be added after the manipulation, and anything that is the same on opposite sides of the arrow will cancel.  So our goal is to end up with 2S and 3O2 on the left, and 2SO3 on the right.  The goal is always to manipulate the given formulas in a way so that when they add, and the stuff cancels, they look like the goal formula.  There are two ways of manipulating the given eqs.  They are: 

1. Multiply.  The top one of our two given eq. has Sulfur, and the bottom one doesn't.  Since our source eq. has two sulfer, we multiply the entire eq - INCLUDING THE ΔH - by two, which gives us: 

2S + 2O2 --> 2SO2  ΔH = -594

If you'll notice, our source eq. doesn't actually have any SO2, so that's one of the things we're going to want to cancel.  Luckily, there's now 2SO2 in given 1, and in given 2.  

2. If something you want to be on the left side is on the right side (or visa versa), flip the eq.  If you do this, just make sure you change the sign of the ΔH.  In this particular problem, we don't need to do that.  This isn't math.  You don't need to keep things exactly as they were.  This is chemistry...WE CAN DO WHAT WE WANT!  ;) 

After you've done these things (not necessarily in this order, the order is irrelevant.), then add the results: 

2S + 2O2 --> 2SO2      | ΔH = -594 kJ 2 SO2 +  O2 --> 2 SO3 | ΔH = -198 kJ   -----------------------------|-------------------- 2S + 3O2 --> 2SO3      | ΔH = -792 kJ

Note: These problems DO follow one rule of math: only like terms can be added.  That means you cannot add 3O to 3O2.  You can't add things that are in different states (gas and liquid, for example.  I left them out of the problem, but the state notations are in the question.).  You can't add joules and kilojoules, you need to convert if they're given to you in different units.  

And, that's basically everything.  Hopefully I didn't forget anything, or leave anything super necessary out.  There are probably things I've chosen to leave out that your teacher might want, but I think I've covered the important stuff.  :)  

[science-of-anthropology]

Thermochemistry - Part 1

Alright, here we go.  Thermochemistry.  Thermo is, well, it's a thing.  You will come across this again and again (which is weird, because practically the purpose seems mostly to be to make sure things aren't going to blow up.).  It's in physics, all kinds of chem, and a tiiiiiiny bit in bio.  It's weird, if you're in the sciences long enough you kind of pick up on the competition between them.  There's a saying that Physics is applied math, chem is applied physics, and bio is applied chem.  Which to a certain extent is true, but it's often used to apply hierarchy and that's stupid (math isn't a science anyway, it's a tool to describe how things work.).  Thermo is one of those places where you start to see crossover in the sciences.  I did it in chem and in physics, and I liked the chem version better.  I actually thought chem described what was really happening better than physics did.  

Thermochemistry (or thermodynamics, which is very similar, it's just taught in physics and applies to different types of objects.) is basically the study of how heat moves.  Heat is created when energy enters or leaves a system.  Energy excites (or slows) atoms, which creates heat.  The measurement of that energy is what is covered in thermo.  Both are subject to the laws of thermodynamics (http://en.wikipedia.org/wiki/Laws_of_thermodynamics), but you won't learn about those in chemistry.  In chemistry you'll learn only that the total energy of a system doesn't change.  That's important, and we'll get into it in more detail when we get to Hess' law.  

For now, there are three really important terms that we need to cover: 

Exothermic - A reaction that gives off heat and energy into the environment.  Exo is a greek prefix that means out of.  The energy is going out of the reaction.  Sometimes you'll hear me (or maybe others) say, sarcastically, that something that explodes is slightly exothermic.  For example, putting alkali metals in water is *slightly* exothermic: 

Endothermic - A reaction that removes heat from the environment, taking the energy into itself.  Endo is a greek prefix meaning into.  So, we're humans, we have endoskeletons! Bugs have exoskeletons.  

Enthalpy - Written as H, it indicates the change of energy in a system.  This property can change dependant on the ambient pressure, temperature, or amount of the substance.  Obviously it takes more heat to boil a gallon of water than it does a cup.  

Delta - The greek letter delta, written as Δ, is used to mean "a change in".  ΔH is a change in enthalpy, or heat energy.  

Heat of formation - The heat given off when a specific compound is created.  For elements, it's always 0.  They aren't compounds, they exist in a natural state.  Everything else is a standard based on lots of experimenting and is either given by your teacher in the problem, or you can look it up in the CRC or your textbook sometimes.  It's represented by the symbol Hf, where the f is a subscript.  

For the purposes of chem 111, almost all problems for thermo are done at STP (standard temperature/pressure.).  Meaning you're not going to have to worry about pressure changes until later, and almost always the temperature of your environment will start at 20-odd C, or room temp.  

There are several units of measurement in thermo.  The one you're probably most familiar with is the calorie.  When you see the amount of calories per serving on a food item, what they've done is burned it and measured the amount of heat given off.  You'll probably do something really similar to that in lab, actually, only not with food.  It's imprecise and we don't like it in actual science classes, so we use the Joule instead.  Joules are used in both physics and chem, so learn to love 'em.  Interestingly, volts could also kind of be a unit for thermo too because they measure electron flow and electrons = heat a lot of the time, but it's not a typical thing.  Joules are going to be what you're asked for most of the time.  

In chemistry, there's generally three types of thermo problems that you'll do: Enthalpy, Hess' law, and coffee cup calorimitry problems.  Also, themo is really fiddly about signs.  You need to read the problems carefully and take note of what you're being asked for.  

A negative ΔH is exothermic and a positive ΔH is endothermic because enthalpy is a measurement of the heat of the reaction! Exothermic reactions give off heat, they lose it, they *subtract* the heat from the reaction.  Endothermic reactions gain heat, they take it from the environment to make themselves warmer.  

Enthalpy Problems:

These are the easiest, most practically used, and my personal favorite of the three methods.  They all follow this formula: 

ΔH = H(products) - H(reactants) 

This formula format is actually kind of a standard thing in chem, and you'll see it again when you get to entropy and Gibbs free energy (Gibbs'll blow your mind.).  To be able to do these problems you need to be given the heats of formation for the various compounds.  Because enthalpy is dependent on the amounts present, you will need to multiple by molar values.  Typically, the above formula tends to look more like this: 

ΔH = [moles(Hf prod 1) + moles(Hf prod 2)] - [moles(Hf react 1) + moles(react2)]

Provided that none of those products are elements, you MUST be given the Hf for them to do the problem.  You also must balance the eq. first, or you'll get the wrong answer.  Here's an example problem: 

Calculate the heat given off when one mole of B5H9 reacts with excess oxygen according to the reaction below: 

2B5H9 + 12O2 --> 5B2H3 + 9H2O

Hf:  

B5H9 - 73.2kj

O2 - 0 (It's an element)

B2H3 - -1272.77kj

H2O - -241.82kj

Find ΔH.  

We set the problem up according to what I wrote above, so: 

ΔH = [5(-1272.77) + 9(-241.82)] - [2(73.2) + 0]

ΔH = -8686kj

HOWEVER, because when we did the math there were 2 moles of the stuff, we divide the answer by 2: 

-4343kj of heat is given off.  

You may be asking, "could I have just used one mole in the problem?" NO.  It would give you -8613.4, which is the wrong answer.  Why is it the wrong answer? Well, because we're looking at the heat of formation for the entire problem, right, so it has to be balanced before you can do that.  If you just stuck in a 1 instead of a two, it wouldn't be balanced anymore.  If you wanted to you could divide the entire problem by two (so instead of multiplying by 5 and 9, you'd multiply by 5/2, and 9/2), but that's needlessly complicated.  Just divide the answer by two, it's the same thing.  

Alright, since this is really really long at this point, I'm going to stop now, post, and put the other two methods in their own post.  

[science-of-anthropology]

Limiting Reagents

Ok, so this is closely related to the previous entry.  You have to be able to do stoichiometry to be able to do the math associated with this concept.  Here's the general concept though: 

When you are doing a reaction, the reaction will only last as long as you have reagents.  The reagent you run out of first is called the limiting reagent, because it limits the output of a reaction.  Now, in function (IE, lab) this is going to be pretty easy to spot because you'll have 10g of one thing and 3g of the other and obviously you'll run out of the 3g thing first.  However, mathematically it's different.  

Let's say you have exact same weight amounts of the two reagents.  How do you know which one is the limiting reactant? Or what if you need to know how much of them to react to get the amount of product you want? Well, let's consider the following (balanced) reaction:  

4KO2 + 2H2O --> 4KOH + 3O2

KOH is the main product, and the O2 is a byproduct, but we can use either to test.  Let's say we have 71.10g KO2 and 22.50g H2O, which one is the limiting reagent? You'd THINK the 22.50g H2O, but because of the ratios involved not so much.  Basically you do conversions to see how much of either O2 or KOH you get with each product, and then whichever is less is the limiting reagent.  Let's do the math and see how much O2 is produced: 

71.10 g KO2  x  1 mole KO2 x 3 Mole O2 

         1                  71g KO2     4 mole KO2

Because limiting reagents talk about molar values, it's ok not to convert back to grams.  The answer here is .75 moles O2 are made with 71.10g of KO2.  

22.50 g H2O x 1 mole H2O x 3 mole O2

        1              18 g H2O       2 mole H2O

You come out with 1.875 moles of O2 produced.  That makes the KO2 the limiting reagent, despite having more of it.  

Mostly this is a concept you'll probably deal with in lab.  Chem 111 labs love to ask "which of these was the limiting reagent".  Now you know how to figure it out, instead of half-assing it like I did the whole semester and guessing based on which I used less of.  ;)