Organic Chemistry Introduction (CHE140)

CHE140 Unit Logistics and Final Week Checklist

• Superpass Session: Happening next week. Requests for specific topics can still be emailed to Roc. Scheduled for Wednesday, June 3.

• Final Exam: Monday, June 8, at $09:00$ in the morning. Students are advised to leave ample time for public transport delays.

• Practice Material: A second practice exam and answers for all materials will be uploaded next week.

• Mastering Chemistry: Due on June 5. Students can still earn the full $10\%$ of this grade component by completing as much as possible by the end of week fifteen.

• Lab Reports: Maximizing lab report submissions is critical for the final grade. Reports for missed labs will not be marked.

• Missed Workshops: If a student has a valid reason for missing a workshop, they must contact the CHE140 mailbox to discuss a potential makeup quiz.

• Unit Responses: There is currently a $20\%$ response rate (approximately 100 out of 500 students). Higher response rates are needed to facilitate proper changes to the unit. Responses can be submitted after the final exam.

History and Overview of Organic Chemistry

• Definition: Organic chemistry involves the study of carbon-based molecules, primarily used in the creation of medicines and materials.

• Ancient Evidence:

  • Ancient Egypt/Byzantium: Archaeologists discovered tablets containing a recipe for soap involving water, burnt charred wood (potassium hydroxide, $KOH$), and vegetable oil or animal fat. This is the oldest record of an organic reaction.

  • Indigenous Australians: Used chemical processing to remove toxic bases from nuts and seeds to make them edible.

  • Middle East: Practiced organic chemistry under the guise of mysticism.

  • China: Herbal medicine utilized chemistry for heart and liver disease treatments and chemotherapy agents, which have since been adapted into Western medicine.

• Evolution of Alchemical Thought:

  • Alchemists: Sought to turn lead into gold; developed a pre-periodic table using symbols for lead, tin, copper, and water.

  • Renaissance: Science grew as wealthy individuals invested in expensive glassware and experimentation.

• Vitalism and the Wöhler Synthesis:

  • Vitalism: The philosophical belief that organic compounds possessed a "vital spark" of life and could not be created from inorganic matter.

  • Friedrich Wöhler: A German chemist who synthesized Urea ($NH_2CONH_2$), a biological byproduct, from the inorganic ionic solid lead cyanate mixed with ammonia and water. This effectively disproved vitalism by showing the crossover from inorganic to organic matter.

• Real-World Applications: Organic chemistry created anesthetics, antibiotics, plastics, petroleum-based fuels, and water treatment processes (preventing diseases like dysentery).

The Centrality of Carbon in Life

• Key Elements: Organic chemists focus primarily on Carbon ($C$) and Hydrogen ($H$), followed by Nitrogen ($N$), Oxygen ($O$), Sulfur ($S$), and Phosphorus ($P$) (critical in biological areas).

• Halides: Fluorine, Chlorine, Bromine, and Iodine are used in medicines to prevent them from breaking down too quickly in the human body.

• Why Carbon?

  • Forms extremely stable Carbon-Carbon ($C-C$) bonds.

  • Capable of forming backbones for complex molecules like DNA.

  • Capable of single, double, and triple bonds, providing structural rigidity or the ability to rotate.

  • Bond strength spectrum: Some bonds are strong and permanent, while others are weak enough to allow parts of a molecule (like an active drug component) to fly off.

• Molecule Representations:

  • Written representation/Structural formula: Shows all atoms and bonds.

  • Space-filling model: Demonstrates that electrons occupy physical space.

  • Ball-and-stick model: Easier for viewing geometry.

  • Line structures (Zigzags): Each point/vertex is a Carbon. Hydrogens attached to Carbon are hidden, but four bonds per Carbon must always be accounted for.

• Visualization: Atomic Force Microscopy (AFM) developed in the early 2000s allowed scientists to actually "see" molecules at the scale of an angstrom (the size of a bond). It uses an electrically charged point to tap around the molecule on a gold plate to create a picture.

Hydrocarbons: Alkanes, Alkenes, and Aromatics

• Saturated Hydrocarbons (Alkanes): Contain only single bonds. The general formula is typically $C_nH_{2n+2}$. Examples include Methane ($CH_4$), Ethane ($C_2H_6$), Propane ($C_3H_8$), and Butane ($C_4H_{10}$).

• Unsaturated Hydrocarbons: Contain double bonds (Alkenes) or triple bonds (Alkynes).

• Cyclic Alkanes: Closed ring structures requiring three or more carbons (e.g., Cyclopropane, Cyclohexane).

• Isomerism: Compounds with the same molecular formula but different connectivity (structural isomers).

  • Example: Linear Butane vs. Branched Butane.

  • Impact on Properties: Linear molecules have higher surface areas and stronger dispersion forces, leading to higher boiling points. Bulkier, spherical branched molecules have smaller surface areas and lower boiling points.

• Bond Rotation:

  • Single Bonds: Allow for "free rotation" where groups can flip-flop.

  • Double Bonds: Rigid and cannot rotate. This leads to cis-trans isomerism.

    • Trans: Groups are on opposite sides (transverse).

    • Cis: Groups are on the same side.

  • Biological Example: Retinal in the eye is an alkene that changes position when hit by light, allowing for low-light vision.

• Aromatic Compounds: Contain alternating double and single bonds in a ring (e.g., Benzene). Important for the structural stability of the DNA double helix.

  • Warning: $4$-aminophenol is an aromatic compound used in Lab $5$; it is toxic and must not be inhaled.

Functional Groups

Functional groups are specific groupings of atoms that determine the chemical behavior of a molecule.

• Alcohols: Contain an $-OH$ group. They are polar and undergo hydrogen bonding.

• Ethers: Oxygen atom between two Carbon atoms ($R-O-R$). Historically used as anesthetics (e.g., Diethyl ether used by Queen Victoria), but difficult to dose safely.

• Aldehydes: Carbon double-bonded to Oxygen ($C=O$) with at least one Hydrogen attached ($R-CHO$). Always found at the end of a chain.

• Ketones: Carbon double-bonded to Oxygen ($C=O$) attached to two other Carbons ($R-CO-R$). Found in the middle of a chain.

  • Metabolism Example: Ethanol is converted by enzymes into Acetaldehyde (causes hangovers) and then into Acetate (vinegar).

  • Toxicity: Methanol converts into Formaldehyde, which is used to preserve ("pickle") organs; this makes methanol consumption lethal.

• Carboxylic Acids: Contain the $-COOH$ group (carbonyl + alcohol). These are weak acids (e.g., Acetic acid/vinegar).

• Esters: Contain the $-COOR$ group. They are often fragrant. Ethyl formate, which smells like rum and tastes like raspberries, is found in the center of the Milky Way galaxy.

• Amines: Contain Nitrogen ($N$). Derived from Ammonia ($NH_3$). They act as bases and are essential in amino acids.

• Amides: Contain a Carbon double-bonded to Oxygen attached to a Nitrogen ($CON$). These form the peptide bonds that link amino acids into proteins.

IUPAC Naming Conventions (Systematic Nomenclature)

Names are structured as Prefix-Parent-Suffix to provide a universal language for chemistry.

• Parent Chain: The longest continuous carbon chain.

  • $1 = \text{meth-}$

  • $2 = \text{eth-}$

  • $3 = \text{prop-}$

  • $4 = \text{but-}$

  • $5 = \text{pent-}$

  • $6 = \text{hex-}$

  • $7 = \text{hept-}$

  • $8 = \text{oct-}$

• Numbering: The chain is numbered to give the principal functional group or first substituent the lowest possible number.

• Substituents (Alkyl Groups): Branched chains are named as methyl ($CH_3$), ethyl ($C_2H_5$), etc. If multiple identical groups exist, use prefixes like di-, tri-, or tetra-.

• Alphabetical Order: Substituents are listed alphabetically (e.g., ethyl before methyl) regardless of their numerical position.

• Suffixes: Alkanes ($-ane$), Alkenes ($-ene$), Alcohols ($-ol$), Aldehydes ($-al$).

Proteins and Biological Molecules

• Amino Acids: Molecules containing both an amine ($NH_2$) and a carboxylic acid ($COOH$). There are $20$ common amino acids.

• Zwitterion: In neutral solutions, amino acids exist with a positive charge on the Nitrogen and a negative charge on the Oxygen.

• Protein Structure:

  • Primary: The sequence of amino acids linked by amide (peptide) bonds.

  • Secondary: Alpha helices and beta sheets formed via hydrogen bonding.

  • Tertiary: The overall three-dimensional folding of a single protein chain.

  • Quaternary: Multiple tertiary structures coming together (e.g., Hemoglobin, which carries oxygen).

• Functions: Proteins serve as skin, hair, muscles, enzymes (catalysts), and components of the immune system.

Questions & Discussion

• Question: Will we get the functional group table in the exam?

  • Answer: No. You will get the VSEPR table and data sheets provided in the practice exam, but you must memorize the functional groups, including alkyl halides.

• Question: Will spelling be penalized in naming?

  • Answer: No, spelling will not be strictly judged as long as the intent is clear.

• Question: Why is the naming in an example $2,2,5$-trimethyl-octane instead of $4,7,7$?

  • Answer: You must number the chain from the end that gives the substituents the lowest possible numbers. $2$ is lower than $4$, so the numbering starts from the end closest to the double methyl group.

• Question: Will we be asked to name compounds from scratch in the exam?

  • Answer: No. You will be given names and asked to identify or draw the structure, or given a structure and asked to identify the correct name from options. You will not have to generate the IUPAC name entirely on your own.