Organic Chemistry Notes

Natural vs. Synthetic: The idea that natural is always good and synthetic is always bad is a commercial tactic and not always true. The effect of a molecule depends on the context and the specific molecule.
Some natural compounds can be very toxic.
Toxicity: The degree to which a substance can damage an organism.
LD50 (Median Lethal Dose): The dose required to kill half the members of a tested population, indicating a compound's toxicity.

Certain natural products like botulism, tetanus, and ricin are highly toxic, even in small doses.
Aflatoxin B1, a natural product from fungi, is one of the most carcinogenic substances known.
Knowledge and understanding of chemistry are essential to determine if a compound is safe or harmful, regardless of its origin (natural or synthetic).

Definition: Saturated hydrocarbons containing only carbon-carbon single bonds.
General Formula: $CnH{2n+2}$

Simplest alkane with one carbon atom: $CH_4$ .
Four hydrogens bonded to a central carbon atom.
Carbon requires four bonds.
Tetrahedral carbons are sp3 hybridized.
Each $sp^3$ hybridized orbital on the carbon atom overlaps with the 1s orbitals of the hydrogen atom.
CH bond lengths are the same: 109 picometers.
Angles are the same: 109.5 degrees.
CH bond strength: 412 kJ/mol.
All hydrogen atoms are chemically equivalent in methane.

Formed by replacing one carbon-hydrogen bond with a methyl group ( $CH_3$ ).
Two $sp^3$ hybridized orbitals of each carbon atom overlap to form a sigma bond (carbon-carbon single bond).
Carbon-carbon bond length: 154 picometers.
Bond angle: 109.6 degrees.
Bond strength is slightly lower than that of carbon-hydrogen bond.

Suffix for alkanes: -ane.
Stem names indicate the number of carbons in the chain:
- 1 carbon: Meth-
- 2 carbons: Eth-
- 3 carbons: Prop-
- 4 carbons: But-
- 5 carbons: Pent-
For substituents or branches, replace -ane with -yl. E.g., propyl (3-carbon branch), pentyl (5-carbon branch).
Mnemonic: "Monkeys eat peeled bananas for" (meth, eth, propyl, but).

The properties of simple, linear alkanes are dictated by the length of the carbon chain.
As the number of carbons increases, boiling point and melting point also increase.
- Small-chain alkanes (e.g., methane, ethane) are gaseous at room temperature.
- Medium-sized chains (6-8 carbons) are liquid.
- Long-chain alkanes are solids (e.g., waxes, candles).
These changes are due to increases in intermolecular forces (Van der Waals forces).

A standardized naming system allows clear communication about molecules.
Steps to name a compound:
1. Find the longest carbon chain containing the functional group (stem).
2. Identify substituents (branching points) and number them.
  - Number the longest carbon chain to give substituents the lowest possible numbering.
3. List substituents in alphabetical order with numbers.
4. Use prefixes (di-, tri-, tetra-) for multiple identical substituents.
  - Prefixes (di, tri, tetra) are ignored when determining the alphabetical order of substituents.
Naming like naming people: Prefix (substituents), first and last name (carbon chain/stem), suffix (functional groups).

Example 1:
- Longest chain: 7 carbons (heptane).
- Substituents: methyl at position 2, ethyl at position 4.
- Name: 4-ethyl-2-methylheptane.
Example 2:
- Longest chain: 3 carbons (propane).
- Substituents: two methyl groups at position 2.
- Name: 2,2-dimethylpropane.
Example 3:
- Longest chain: 6 carbons (hexane).
- Substituents: two methyl branches at positions 2 and 5.
- Name: 2,5-dimethylhexane.

Naming can be complex and may require simplification such as using common names (e.g., palitoxin).
Understanding how to identify functional groups is more important than naming complex ones.

Isomers: Molecules that have the same molecular formula but different arrangements of atoms.

Same molecular formula but different bond connectivity.
Also known as structural isomers because they have different structures.
Alkanes form a homologous series that differs by a $CH_2$ group.
As the number of carbons increases, the number of possible isomers also increases.

Different physical properties (melting points, boiling points).
Different signals in spectra.
If we look at $C4H8O$ , these compounds are gonna have vastly different properties, spectra, etcetera.

Alkanes can be extracted from crude oil or petroleum.
Fractional distillation separates alkanes based on boiling points (related to chain length).
Smaller alkanes heat off and evaporate quicker than longer chain hydrocarbons
Uses:
- Natural gas (methane, ethane).
- Crude oil (varying lengths of hydrocarbons).
Cracking (breaking down large alkanes into smaller ones).
Alkanes have strong, nonpolar bonds, making them stable and inert, ideal solvents, and excellent fuels.
Combustion (e.g., octane burning in oxygen to produce carbon dioxide and water).
Kinetically stable (high energy barrier to decompose).
Not thermodynamically stable (release heat when combusted).

Conformational isomers are a type of stereo isomer.
Stereoisomers possess the same bond connectivity but differ in the position of atoms in space.
Rotation around molecule, also referred to as big "R"

Conformational isomers have different energy levels.
Eclipsed conformation: Atoms are directly in line with each other (higher energy).
Staggered conformation: Atoms are offset from each other (lower energy).
Staggered confirmation is more favorable because of less strain as electrons repel each other, and creates torsional strain.
Strain magnitude depends on the proximity and size of neighboring atoms.

The eclipsed conformation is high in energy compared to the staggered conformation.
Dihedral angle: The angle between atoms connected to the carbon-carbon bond.
Bulkier groups (e.g., $CH_3$ ) introduce more significant energy differences. We get a series of eclipse structures and a series of staggered structures.
Confirmation with the two bulky groups as far away from each other is always going to produce the most energetic/lowest energy structures.
Even small hydrogen atoms is still more preferential in energy to offset the substituents from each other.
You can consider the analogy by putting a marble into an egg carton. The marble is easily shaken out of the top of the crest, but stays nestled in the bottom relatively longer.

Zigzag representation puts $CH_3$ groups in a staggered confirmation.
Molecules spend more time in lower energy conformations.
Origami Fold It Game, and protein folding, conformational isomers put onto the protein level.