Organic Chemistry Lecture Notes

Introduction to Organic Chemistry

Organic chemistry is primarily the study of carbon-containing compounds.
It is fundamental to understanding life, medicine, and the synthesis of various materials.
The lecture aims to teach how to draw molecules and understand their structures.

Poll Everywhere Introduction

Use Poll Everywhere (pollev.com/robertchapman742) for interactive responses.
The initial question is: "What do you think organic chemistry is?"

Spearmint and Caraway Oil Experiment

Participants are given vials containing spearmint and caraway oil.
These oils are chemically almost identical, being different enantiomers.
A poll will be conducted to determine if people perceive a difference in smell.
Safety precaution: Those allergic to peppermint or sensitive to smells should avoid smelling the oils.
The lab next week will focus on chirality and use polarized light to differentiate the oils.

Responses on Organic Chemistry

Common answers include: carbon chemistry, life, carbon-hydrogen bonds, molecules, medicine, organisms, carbon, structures, food, body chemistry.
Organic chemistry is relevant to nutrition for understanding the composition and metabolism of food (carbohydrates, glucose, fats).
It is crucial for biomed students to understand amino acids, their reactions, and molecular structures.

Applications of Organic Chemistry

Organic chemistry extends beyond academic exercises, playing a significant role in various industries.
Examples include the synthesis of complex molecules, such as pharmaceuticals. Top 200 drugs sold in 2023 are mostly organic molecules.
Organic molecules are essential for life, forming the basis of amino acids, DNA, glucose, fats, and cell walls.
Organic chemistry is vital in the synthesis of synthetic materials, including plastics and fibers.
BASF in Ludwigshafen, Germany, is an example of a large-scale chemical facility that converts crude oil into commodity chemicals.
Crude oil is used to manufacture plastics and other essential chemicals.

Drawing Molecules

The lecture will cover methods for drawing molecules accurately to represent their three-dimensional structure.
Molecular drawings closely represent the actual shapes of molecules at the angstrom scale.

Course Outline

Lecture 1: Drawing and naming molecules.
Lecture 2: Three-dimensional structures and tricks to understand them.
Lecture 3: Molecular functionality related to human composition.
Lectures 4-7: Focus on structure and chirality, including the spearmint and caraway oil experiment (Experiment 3A).
Later lectures: Reactivity of molecules. More in depth discussion in ten twenty course.
Experiment 3B: Specific lab skills.

Smelling the Oils - Initial Poll Results

Initial poll results indicate varying perceptions: some find the oils smell the same, while others detect differences.
Differences in smell perception may be due to variations in olfactory receptors.
The varying perceptions are linked to the chirality of the molecules and the chiral nature of the proteins that detect them.

Alkanes: The Simplest Hydrocarbons

Alkanes consist of carbon and hydrogen atoms with each carbon forming four bonds.
Methane ($\text{CH}_4) has a tetrahedral structure.
Ethane ($\text{C}2\text{H}6) is another simple alkane.
The general formula for alkanes is $C<em>n H</em>{2n+2}$ .

Drawing Butane ($\text{C}4\text{H}{10})

Molecular Formula: C4H{10} is the most condensed but least informative way to represent butane.
Lewis Structure: Shows every atom and bond, but is clunky.
Condensed Structure: A simplified representation, e.g., $\text{CH}3\text{CH}2\text{CH}2\text{CH}3.
Skeletal Structures: A zigzag line where each bend and end represents a carbon atom; hydrogens are implied.
Skeletal structures capture the three-dimensional shape of the molecule.

Rules for Skeletal Structures

Each corner or endpoint represents a carbon atom. Hydrogen atoms are not explicitly drawn.
The number of implied hydrogen atoms can be determined by counting the bonds to each carbon atom.
For a carbon with a single bond to its neighbor, there are three implied hydrogens.
For a carbon with a double bond (alkene), the number of implied hydrogens is reduced accordingly.
For a carbon with a triple bond (alkyne), no hydrogen atoms are implied.

Examples of Skeletal Structures and Determining Hydrogen Atoms

Example 1: A four-carbon chain with a chlorine atom. Missing hydrogens are added to complete each carbon's four bonds.
Example 2: A cyclic structure. Hydrogens are added to each carbon in the ring. A carbon outside the ring has three hydrogens.
Example 3: A structure with an oxygen atom. Oxygen typically has two bonds. Missing hydrogens are filled in.
Double bonds reduce the number of hydrogens on adjacent carbon atoms.

Level of Carbon Substitution

A substituent is any atom or group other than hydrogen attached to a carbon atom.
Primary Carbon: Attached to one other carbon atom.
Secondary Carbon: Attached to two other carbon atoms.
Tertiary Carbon: Attached to three other carbon atoms.
Quaternary Carbon: Attached to four other carbon atoms.

Examples of Carbon Substitution Levels

End carbons in a chain are primary.
Carbons bonded to two other carbons are secondary.
A carbon bonded to three other carbons is tertiary.
A carbon bonded to four other carbons is quaternary.

Practice with Condensed Formulas and Skeletal Structures

Converting condensed formulas into skeletal structures.
Identifying and labeling primary, secondary, tertiary, and quaternary carbons in a given molecule.

Identifying Hydrogen Atoms in Organic Molecules

Given an organic molecule, determine the number of hydrogen atoms around specific carbon atoms (A, B, C, D).
Hydrogen count is determined by the number of bonds already present around the carbon atom.

Naming Organic Molecules (IUPAC Nomenclature)

The naming of organic molecules generally consists of a prefix (substituents), a base (number of carbons), and a suffix (family).
It is less critical to memorize all naming rules, but understanding core principles is important.
Prefix: Describes the substituents attached to the main molecule.
Base: Indicates the number of carbon atoms.
Suffix: Specifies the family of the organic molecule (e.g., alkanes).

Naming Alkanes

The suffix for alkanes is "-ane."
Cycloalkanes have the prefix "cyclo-".
The number of carbons is indicated by prefixes: meth (1), eth (2), prop (3), but (4), pent (5), hex (6), hept (7), oct (8), non (9), dec (10).
Substituents are named similarly, with "-yl" added: methyl, ethyl, propyl.

Examples of Naming Alkanes with Substituents

Example: Methyl octane (a methyl group attached to an eight-carbon chain).
Number the chain so that the substituents have the lowest possible numbers.
Find the longest chain in the molecule.
List substituents at the front of the name in alphabetical order.
Use "di-", "tri-", "tetra-" for multiple substituents of the same type.

Naming More Complex Alkanes

Example: 2-methylhexane (a methyl group on the second carbon of a six-carbon chain).
Example: 3-ethyl-2,4,7-trimethylheptane (ethyl group at position 3, three methyl groups at positions 2, 4, and 7 of a seven-carbon chain).

Naming Cycloalkanes

Cyclopentane: A five-carbon ring.
Ethylcyclopentane: An ethyl group attached to a cyclopentane ring.
1-ethyl-3-methylcycloheptane: Ethyl group at position 1, methyl group at position 3 of a seven-carbon ring.
1,1,3-trimethylcyclopentane: Two methyl groups at position 1, one methyl group at position 3 of a five-carbon ring.
1,1-dimethyl-3-chlorocyclohexane: Two methyl groups at position 1, chlorine at position 3 of a six-carbon ring.

Practice Naming Molecules

Further examples of converting skeletal structures to names and vice versa.

Preview of Next Lecture

Recap of Lewis structures.
Predicting molecular shapes and three-dimensional geometry.