Wow! I just got done with my first day of summer quarter where I am taking the Organic Chemistry series, yikes! I was scared at first but it turns out it might not be that bad after. But it was the first day so who knows how thiswill turn out. Anyways this is just a general blog (for me mostly) to help me study, understand and digest concepts I have learned everyday. So I decided to do this not only to helpme out but others who might be going through the same thing as I am this summer. Ok so like this summer class enough of the chit chat and lets get down to business. So here is what we covered today on day 1 of many Organic Chemistry summer days.
What is Organic Chemistry?
Well from what understand historically Organic Chemistry was defined to be a disc
ipline of learning and understanding living system molecules. But, as of today that definition now applies to what we call biochemistry. The reason why this is no longer
the definition of what organic chemistry is because of a simple experiment that proved that molecules that were thought of to only be produced by living system can be synthesized outside of it. And what served to prove this point was a simple experiment that made Urea from Ammonia (NH3) and carbon dioxide(CO2). So this experiment called for a new overall definition of what Organic Chemistry is which leads to our modern definition which is the study of molecules containing Carbon and Hydrogen. Easy right?
A Review of Molecular Information
So assuming that most of us have already taken some sort of General Chemistry course before even starting Organic Chemistry, itwould be important and essential for us
to review on some key concepts that will overall contribute to subjects in Organic Chemistry. So lets start with some common molecular information that will be useful.
- Covalent bonds: share electrons and are fairly stable thus allowing atoms to stay close together
- Lone pairs of electrons: do not participate in bonds and do determine what the charge is
- Geometry (electron pairs and molecular): the three important geometry's that should be determined and known for Organic Chemistry are linear, trigonal planar and tetrahedral
- Formal charge: to determine the charge of an atom on a molecule simply get the number of valence electrons of the atom (usually is that number on top of each column i.e: Carbon is 4, Nitrogen is 5, Oxygen is 6 etc.), subtract the number of bonds from it and then subtract the number of electrons not in bonds with the atom
Formal Charge
Now formal charge is super important so lets just see a simple explain just to get used to this concept. Lets take the molecule ammonium for example (NH4)
As we can see here it nitrogen has a charge of +1. Now why is this? Well if we look at the number of valence electrons in Nitrogen, it has 5. Ok so now how many bonds are there on Nitrogen? There are 4 Hydrogens attached to it so it has 4 bonds. Ok cool, so lets subtract the number of bonds attached to nitrogen from the number of valence electrons in Nitrogen. So 5-1=+1. Is that it? Well yeah pretty much becaus
e there are really no electrons that are not in bonds with Nitrogen to start with there is nothing more to subtract. Thus the formal charge of ammonium is +1. Sweet.
Ok so lets look at one more just so we can get a hang of what is going on here. Let take the functional group Amine (NH2)
Alright lets do this! We already see that Nitrogen has a charge of -1, so lets figure out why. Again lets get the formal charge for Nitrogen in this molecule for this since the Hydrogens are not really interesting, no Hydrogen is interesting. So the number of valence electrons in
Nitrogen is 5 and it is
bonded to 2 Hydrogens. So lets get the the number of valence electrons in Nitrogen and subtract the number of
bonds to it thus 5-2=3. Ok now this picture is not really good at showing this but Nitrogen has 2 lone pairs of electrons on it still. So with that in mind lets count the number of electrons on Nitrogen that are not in bonds and when we do we see we get 4. Ok so lets take are already calculated number, 3, and lets subtract the number of electrons not in bonds to it. So 3-4=-1. Thats it, we subtracted everything we could so we get the formal charge of Nitrogen in this Amine molecule to be -1, awesome! So in a nut shell what we did in this molecule was the following:
- number of valence electrons of the atom - number of bonds from it - number of electrons not in bonds with the atom
- And in practice 5-2-4=-1
There we have it, formal charge in a nut shell. And just as a little helper in the future here is a simple table that shows you a pretty common pattern for three common neutral atoms in Organic Chemistry: Carbon, Oxygen and Nitrogen.
| Netural atoms | Bonds | e- pairs | Sum |
| C | 4 | 0 | 4 |
| O | 2 | 2 | 4 |
| N | 3 | 1 | 4 |
A Review of Acid/Base Chemistry
Alright so lets do some basic review on the two Acid/Base theories we learned way back in General Chemistry shall we?
- Brønsted–Lowry Acid/Base
- Acid: donates H+ (i.e. H3O+, HCl, CH3OH)
- Base: accepts H+ (i.e. OH-, CH3OH, -NH2)
- Lewis Acid/Base
- Acid: accepts electron pair (BH3 and any from above)
- Base: donates electron pair (Cl- and any from above)
Drawing Organic Molecules
So we all know molecules can get large, I mean HUGE at times. Do we really want to draw Lewis Structures when things get large? Of course not, at t
his point we do not have the time nor the patients to deal with something so time consuming. Thus there are two other forms we can use when it comes to drawing and representing an organic molecule. So first there is the condensed form where we basically do not draw the bonds between every atom and we just group them together. This method is quick but it is not good enough for what we want to do especially when it comes determining a molecules geometry. The second way is the skeletal/line-angle representation. How to draw a molecule in this way is fairly simple. We just need to follow these so called rules:
- every line represents a bond
- at the end of every line there is a carbon with the appropriate number of hydrogen unless otherwise
- triple bonds have to be linear (180 degrees) on both sides
- structures can be in rings and small rings do not have triple bonds
- 5/6 member rings with alternating double and single bonds are most likely to occur
In practice it is fairly easy and a very lazy way of drawing a molecule. But it is efficient as it is faster and it helps us determine a molecules shape, pretty cool. Heres a good figure to show you how great this method is in practice:
Saturation/How Many Hydrogens Do I Need?
Alright, the final topic of the day that was covered was saturation and take it from me its pretty simple. Knowing how many Hydrogens we need is essential to help us determine the shape and structure of a molecule. Knowing the units of saturation can help us extremely when it comes to this and how we do is is fairly simple and can be summed up in this little "formula": 2n+2 where n equals the number of carbons in a molecule. So lets take the molecule C5H10 for example. We have 5 carbons thus n=5. Using our little "formula" 2n+2 we get 2(5)+2=12. Ok so now what do we do with this number? Simply put it, we take this new number and compare it to the number of hydrogens, this is where we usually subtract the number of hydrogens from this number we obtained. In this case we have 10 Hydrogens, so 12-10=2. Now to obtain the units of unsaturation we divide it by 2. So here its 2/2 which equals 1. For C5H10 we have 1 unit of unsaturation. Ok we got that now comes the important stuff, you know finally getting to know what the hell this means. Well what a unit of saturation tells us is simply this:
- If a molecule has 1 units of unsaturation the molecules structure can contain a double bond or even a ring. Each unit can have a double bond.
- If a molecule has 2 units of unsaturation the molecules structure can contain a triple bond
So this is good and all when all we have is just a Carbon and Hydrogen in a molecule. But what if there is something different right? How will this help? Well for Organic Chemistry, especially where we are starting now, we will just deal with two common atoms we will deal with: Oxygen and Nitrogen. Well to simply put it Nitrogen is equivalent to a Carbon and Hydrogen in unsaturation count. For example the molecule C6H11N now becomes C7H12. Just quickly the units of unsaturation for C6H11N (or now C7H12) can be solved like this:
n=7
2n+2=2(7)+2=14+2=16
H=12
16-H=16-12=4
4/2= 2 units of unsaturation
And now that we got Nitrogen covered lets do Oxygen. Ok so get this, for Oxygen it is equivalent to... nothing! Zero! Nada! Yeah its that simple believe it or not. So lets take for example C6H12O which now becomes simply C6H12. So lets now do this for fun:
n=6
2n+2=2(6)+2=12+2=14
H=12
14-H=14-12=2
2/2= 1 units of unsaturation
Conclusion
Ok so that was all we covered today in the two hours and thirty minute class. Get ready for day two tomorrow and I hope this helps!
-Chingo
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