1. Introduction to Organic Chemistry
Yes!!
I can’t wait!!!
I hear everyone fails this in college!!!

2. Intro - Organic Molecules
Living things are composed of organic molecules, which means that they contain carbon
carbon has four electrons in outer shell which can bond with other atoms
carbon can be linked to other carbons or atoms such as hydrogen (H), oxygen (O) and nitrogen(N)
long links of these carbons can form into chains or rings
Some organic molecules ONLY contain linked carbons and hydrogen ---->hydrocarbons (ex: methane)
living organisms tend to be composed of very long and unreactive carbon chains (unlike methane, which is very reactive!)

3. Intro – Functional Groups
In organic chemistry, molecules with similar properties are grouped together
These all have similar groups of atoms, and these groups of atoms are called functional groups
Functional groups can provide physical and chemical properties such as polarity and acidity (ex; carboxyl, -COOH, is a weak acid)
Most reactions in living organisms involves the transfer of a functional group from one molecule to another
The following is a list of common functional groups
OH Hydroxyl
CO Carbonyl
COOH Carboxyl
NH2 Amino
SH Sulfhydryl
PO4 Phosphate
CH3 Methyl
YOU MUST MEMORIZE THIS LIST!!!

4. Intro – Functional Groups

5. Intro – Functional Groups

6. Intro - Macromolecules
Construction of Macromolecules
many macromolecules are polymers, which means that they are constructed of many linked identical or similar subunits
How are macromolecules made? Remove an OH from one molecule, and an H from another molecule
this requires energy
it is called dehydration synthesis (do you see the water above?!)
in living organisms, enzymes assist in these reactions
Macromolecules are disassembled in the opposite way, by adding a water molecule (OH added to one, H to another subunit)
this releases energy
a reaction of this type is called a hydrolysis

7. Intro - Dehydration Synthesis

8. Hydrocarbons - Naming
Compounds containing just carbons and hydrogens are the most basic compounds encountered in organic chemistry.
hydrocarbons.
can be divided into three groups:
those containing just single bonds
those containing one or more double bonds
those containing one or more triple bonds.
Before discussing how to name these compounds, it is instructive to examine how they are represented by chemists.

9. Drawing Hydrocarbons
Recall - carbon makes four bonds and had the tetrahedral geometry
only two bonds can occupy a plane simultaneously.
The other two bonds point in back or in front of the plane.
In order to represent the tetrahedral geometry in two dimensions
solid wedges are used to represent bonds pointing out of the plane of the drawing toward the viewer
dashed wedges are used to represent bonds pointing out of the plane of the drawing away from the viewer
Consider the following representation of the molecule methane:
Two dimensional representation of methane

10. Drawing Hydrocarbons
it can be time-consuming to write out each atom and bond individually.
hydrocarbons can be represented in a shorthand notation called a skeletal structure.
only the bonds between carbon atoms are represented.
Individual carbon and hydrogen atoms are not drawn
bonds to hydrogen are not drawn.
If the molecule contains just single bonds; drawn in a "zig-zag" fashion.
This is because in the tetrahedral geometry all bonds point as far away from each other as possible, and the structure is not linear.
representations of the molecule propane:
Full structure of propane Skeletal structure of propane

11. Drawing Hydrocarbons
Only the bonds between carbons have been drawn, and these have been drawn in a "zig-zag" manner.
no evidence of hydrogens in a skeletal structure.
in the absence of double or triple bonds, carbon makes four bonds total, the presence of hydrogens is implicit.
Whenever an insufficient number of bonds to a carbon atom are specified in the structure, it is assumed that the rest of the bonds are made to hydrogens.
For example:
if the carbon atom makes only one explicit bond, there are three hydrogens implicitly attached to it.
If it makes two explicit bonds, there are two hydrogens implicitly attached, etc.
Two lines are sufficient to represent three carbon atoms.
It is the bonds only that are being drawn out & it is understood that there are carbon atoms (with three hydrogens attached!) at the terminal ends of the structure.

12. Alkane nomenclature
When hydrocarbons contain only single bonds, they are called alkanes.
Alkanes are named using a prefix for the number of carbon atoms they contain, followed by the suffix -ane.
Number root example Structure
1 meth- methane (see board)
2 eth- ethane
3 prop- propane
4 but- butane
5 pent- pentane
6 hex- hexane
7 hept- heptane
8 ox- oxane
9 non- nonane

13. Alkane nomenclature Alkane nomenclature is straightforward;
difficulties come if one of the hydrogen or carbon atoms on the molecule is replaced by another atom or group.
When this takes place, the group which replaces the hydrogen or carbon is called a substituent.
Let's consider the situation in which one of the hydrogen atoms on an alkane has been replaced by another alkane.
Consider the following molecule, 3-methypentane:

14. Alkane nomenclature Consider the following molecule, 3-methypentane
Long chain of five carbon atoms at the top of the image.
If this were all that composed the molecule, it would simply be called pentane.
However, one of the hydrogens on the carbon third from the end has been replaced with an alkane, specifically methane.
How are we to name this molecule?

15. Alkane nomenclature - Rules
First, we identify the longest chain of carbon atoms. We name this alkane. It will serve as the root name for the molecule.
In the example above, the root name is pentane.
Next, we number the carbon atoms, starting at the end that gives the substituent the lowest number.
In the example above, we can count from either end and arrive at 3 for the substituent.
Next, we name the substituent as if it were an independent alkane. However, we replace suffix -ane with -yl. This name will serve as the prefix.
In the example above, methane is the substituent, so we call it methyl.
The compound is named "number-prefixrootname".
In the example above, the name is 3-methylpentane

16. Alkane nomenclature - Rules
What happens if the alkane has more than one substituent?
In this case, the rules above are followed, and the carbons on the longest chain are numbered to give the lowest number possible to one of the substituent.
The substituents are then all named in the prefix (e.g. 2-ethyl,3-methyl).
If more than one substituent is attached to the same carbon atom, the number of that carbon atom is repeated to indicate the number of substituents and the prefixes di- (2) or tri- (3) are used.
If there are more than one substituent on different carbon atoms, the prefixes are ordered alphabetically (e.g. ethene before methane).
The prefixes di- and tri- are ignored when considering alphabetical order. Consider the following compound:

17. Alkane nomenclature
The longest carbon chain has seven carbon atoms, so the root name is heptane.
Numbering from the right gives the lowest number to the first substituent.
There are two methyl substituents at the second carbon atom, so we use the prefix 2,2-dimethyl.
There is another substituent on the fourth carbon atom, so we use the prefix ethyl.
Ethyl comes before methyl alphabetically, so we name the compound 4-ethyl-2,2-dimethylheptane.

18. Alkene Nomenclature
Alkenes are hydorcarbons containing one or more double bonds.
Alkenes are named using the same general naming rules for alkanes, except that the suffix is now -ene. There are a few other small differences:
The main chain of carbon atoms must contain both carbons in the double bond.
The main chain is numbered so that the double bond gets the smallest number.
Before the root name, the number of the carbon atom at which the double bond starts (the smaller number) is written.
If more than one double bond is present, the prefixes di-, tri-, tetra-, etc. are used before the -ene, and (strangely) the letter "a" is added after the prefix for the number of carbon atoms.

19. Alkyne Nomeclature
Hydorcarbons containing one or more triple bonds are called Alkynes.
Alkynes are named using the same general procedure used for alkenes, replacing the suffix with -yne.
If a molecule contains both a double and a triple bond, the carbon chain is numbered so that the first multiple bond gets a lower number.
If both bonds can be assigned the same number, the double bond takes precedence.
The molecule is then named "n-ene-n-yne", with the double bond root name preceding the triple bond root name
(e.g. 2-hepten-4-yne).

20. Functional Group Nomenclature
Alkanes are extremely unreactive.
Carbon-carbon and carbon-hydrogen bonds are among the most stable bonds in chemistry
alkanes serve as a backbone or template on which unreactive carbon or hydrogen atoms can be replaced by substituents consisting of more reactive atoms or groups of atoms.
A substitient consisting of an atom or group of atoms other than carbons and hydrogens is called a functional group.
Functional groups are significant because they are the part of the molecule that undergoes reactions.
One functional group may change into another one, or a functional group might react with a separate molecule to build up a larger structure.
Functional groups are the essential "reacting units" in organic chemistry.

21. Functional Group Nomenclature
We have already encountered two functional groups. The double bonds in alkenes and the triple bonds in alkynes are able to undergo reactions that the single bonds in alkanes cannot.
There are several other significant functional groups, summarized in the table below. Note that in organic chemistry, the letter "R" represents any alkane, and the letter "X" represents any halogen.
Functional group Structure
Alkyl halide R-X
Alcohol R-OH
Ether R-O-R
Amine NR3

22. Naming Alkyl Halides
One of the simplest functional groups is the alkyl halide.
In an alkyl halide, one of the hydrogen atoms in an alkane has been replaced by a halogen.
What are halogens again?
Alkyl halides are easy to name;
name of the alkane is preceded by the number of the carbon on which the halogen is substituted and the name of the halogen,
modified so that -ine is replaced by -o (e.g. 2-bromopropane).
If a molecule also contains a multiple bond, numbers are assigned to give the lowest number to the first functional group. In the event of a tie, the lowest number goes to the multiple bond.

23. Naming Alcohols
The alcohol is a very common functional group and a very easy one to name.
The molecule is named as if it were an alkane (or alkene or alkyne)
except that the suffix -ane is replaced by -ol
and the number of the carbon atom on which the -OH group is located is placed before the name of the compound (e.g. 2-butanol).
The alcohol functional group takes precedence over alkyl substituents, multiple bonds, and halides and always gets the lowest number.

24. Naming Ethers
An ether is a molecule consisting of two alkyl groups connected to an oxygen atom.
Ethers are named by considering one alkyl group (the shorter one) plus the oxygen atom to be a substituent and the other alkyl group (the longer one) to be an alkane.
The alkyl group plus oxygen atom is called an "alkoxy" substituent and is named by replacing -ane suffix from the alkane with -oxy (e.g. methane becomes methoxy).
The allkoxy substituent gets priority over alky and halide substituents, but not over alcohols, which will get the lower number.

25. Naming Amines
An amine is a derivatives of the molecule ammonia, NH3, in which one or more of the hydrogens has been replaced by an alkyl substitutent (R group).
Amines are named by treating the amino group as a substituent and giving it the name "amino" (e.g. 2-aminobutane).
If multiple hydrogens have been replaced by alkyl substituents, then these alkyl substituents are stated before the word "amino" (e.g. 2-dimethylaminobutane).

26. Cycloalkanes
The alkanes we have studied so far have been of two types: linear and branched. There is a third type of alkane in which the molecule does not have ends but instead forms a ring.
These molecules are called cycloalkanes
Figure 1: Skeletal structure of cyclohexane, a cycloalkane

27. Cycloalkanes
Stable cycloalkanes cannot be formed with carbon chains of just any length.
Recall that in alkanes, carbon adopts the tetrahedral geometry in which the angles between bonds are 109.5°.
For some cylcoalkanes to form, the angle between bonds must deviate from this ideal angle, an effect known as angle strain.
Additionally, some hydrogen atoms may come into cloeser proximity with each other than is desirable (become eclipsed), an effect called torsional strain.
These destabilizing effects, angle strain and torsional strain are known together as ring strain.

28. Cycloalkanes
The smaller cycloalkanes, cyclopropane and cyclobutane, have particularly high ring strains because their bond angles deviate substantially from 109.5° and their hydrogens eclipse each other.
Cyclopentane is a more stable molecule with a small amount of ring strain, while cyclohexane is able to adopt th perfect geometry of a cycloalkane in which all angles are the ideal 109.5° and no hydrogens are eclipsed; it has no ring strain at all.
Cycloalkanes larger than cyclohexane have ring strain and are not commonly encountered in organic chemistry.

29. Cyclohexane
Most of the time, cyclohexane adopts the fully staggered, ideal angle chair conformation (Figure 2).
In the chair conformation, if any carbon-carbon bond were examined, it would be found to exist with its substituents in the staggered conformation and all bonds would be found to possess an angle of 109.5°.

30. Methylcyclohexane
Methylcyclohexane is cyclohexane in which one hydrogen atom is replaced with a methyl group substituent.
Methylcyclohexane can adopt two basic chair conformations: one in which the methyl group is axial, and one in which it is equatorial.
Methylcyclohexane strongly prefers the equatorial conformation.
In the axial conformation, the methly group comes in close proximity to the axial hydrogens, an energetically unfavorable effect known as a 1,3-diaxial interaction
Thus, the equatorial conformation is preferred for the methyl group. In most cases, if the cyclohexane ring contains a subsituent, the substituent will prefer the equatorial conformation.

31. OUCH!!!
Stop please stop my head is hurting and I am pretty sure my brain is bleeding?
Do we really have to know all of this for the test?
Will I really have to know all of this for the future in organic chemistry?
Can I quit now and just become a Kindergarten teacher?