Chapter 5: Structure and Shape of Organic Molecules

Chapter 5: Structure and Shape of Organic Molecules

5.1 Functional Groups

Why Study Organic Chemistry?

  • Most compounds in our lives are carbon-based.

  • Importance highlighted by references:

    • DNA structure (https://en.wikipedia.org/wiki/DNA#/media/File:DNA_Structure+Key+Labelled.png)

    • Proteins and hemoglobin (https://www.britannica.com/science/sickle-cell-anemia)

Examples of Organic Molecules

  • Common organic molecules discussed include:

    • Coffee (Caffeine, with its structure shown)

    • Testosterone

    • Ascorbic acid (Vitamin C)

    • Sucrose

    • Ibuprofen (e.g., Advil)

5.2 Line Diagram Review

Structural Representations

  • Structural Formula: A diagram that conveys the structure rather than merely the molecular formula.

    • Lewis Dot Structure: Shows all valence electrons.

    • Example: H:HH:H depicts covalent bonds as lines.

    • Nonbonding electrons implied if omitted.

    • Line Diagram: Each bond represented by a line; hydrogen atoms bonded to carbon are implied but not shown. Example structure for ethanol: CH<em>2CH</em>2OHCH<em>2CH</em>2OH.

Hybridization & Molecular Shape Review

  • Lone pairs exert greater repulsive force.

  • Different types of bonds (single, double, triple) count as regions of electron density.

  • Example Structures:

    • Tetrahedral: 4 regions of electron density, uses 1s and 3p orbitals, forms 4 sp³ hybrid orbitals (Geometry: 109.5°).

Functional Groups

  • Definition: An atom or group of atoms that convey specific physical and chemical properties.

Hydrocarbons and Functional Groups

  • Types of Hydrocarbons:

    • Alkanes (C-C single bonds, saturated): General formula C<em>nH</em>2n+2C<em>nH</em>{2n+2}.

    • Alkenes (C=C double bonds, unsaturated): General formula C<em>nH</em>2nC<em>nH</em>{2n}.

    • Alkynes (C≡C triple bonds): General formula C<em>nH</em>2n−2C<em>nH</em>{2n-2}.

    • Aromatic compounds (cyclic structures with alternating double bonds).

C-Z Single Bond Functional Groups

  • Alkyl Halides (R-X): Csp3C sp^3/Csp2C sp^2, exhibiting a halo group (F, Cl, Br, I).

  • Alcohols: R−OHR-OH.

  • Ethers: R−O−RR-O-R.

  • Amines: R−NH<em>2R-NH<em>2, R</em>2NHR</em>2NH which represent amino groups.

Functional Groups: C=O Group

  • Aldehydes (C=O at the end): R−C(=O)HR-C(=O)H.

  • Ketones (C=O within chains): R2C=OR_2C=O.

  • Carboxylic Acids: R−COOHR-COOH (Contains both carbonyl and hydroxyl).

  • Esters: R−COORR-COOR (Derived from carboxylic acids).

  • Amides: R−NR2C=OR-NR_2C=O.

Environmental Implications

  • Discussion on sunscreen ingredients (e.g., oxybenzone) harming coral reefs, highlighting the balance between human use of products and chemical effects on marine ecosystems.

5.3 Infrared Spectroscopy

Spectroscopy Overview

  • UV/Visible Spectroscopy: Detects electronic transitions.

  • Infrared (IR) Spectroscopy: Detects molecular vibrations.

  • Microwave Spectroscopy: Detects molecular rotations.

Energy Absorption in IR Spectroscopy

  • Molecules absorb specific wavelengths of light corresponding to vibrational frequencies, making certain bonds vibrate at particular energies.

Analyzing IR Spectra

  • Peaks correspond to specific functional groups and bond types:

    • Alkanes: C-H stretch within 2853−2962cm−12853-2962 cm^{-1} (medium-strong).

    • Alcohols: O-H stretch 3200−3550cm−13200-3550 cm^{-1} (broad, strong).

    • Carbonyls: C=O stretches vary based on functional groups (e.g., esters 1735−1750cm−11735-1750 cm^{-1}).

5.4 Alkanes, Cycloalkanes, and Alkenes

Alkanes

  • Acyclic compounds with formula C<em>nH</em>2n+2C<em>nH</em>{2n+2}.

  • Only single bonds present.

  • Exhibit a homologous series differing by one CH2CH_2 unit.

Boiling Point Trends

  • Explanation: Lighter alkanes are gases at room temperature while heavier ones are liquids due to increasing intermolecular forces. Example data supports this:

    • Methane (CH₄): b.p. −162°C-162°C

    • Butane (C₄H₁₀): b.p. −0.5°C-0.5°C.

Constitutional Isomerism

  • Same molecular formula but different structural connectivity can significantly change chemical properties.

  • Increasing numbers of carbon atoms lead to higher diversity of possible isomers.

Conformational Analysis

  • Conformations result from rotation around C-C single bonds, leading to different spatial arrangements without actual isomerism.

  • Stability dictated by steric hindrance; staggered configurations are more stable than eclipsed.

5.5 Chirality

Chirality Definition

  • Chiral objects lack symmetry; their mirror images cannot be superimposed.

Enantiomers

  • Enantiomers: Molecules that are mirror images of each other, having identical properties except for optical activity.

  • Chiral centers must contain four different substituents.

R/S Nomenclature System

  • Used to describe the stereochemistry of chiral carbons by assigning priorities among substituents.

Stereoisomers and Optical Activity

  • Stereoisomers can exhibit optical activity, differentiating by interaction with polarized light, leading to different rotations (e.g., R and S configurations).