Chemistry II - Chapter 11

Organic Compounds

Introduction

• Organic chemistry is the study of carbon compounds.

• Living things are mostly composed of carbon and hydrogen-containing molecules.

• Organic chemicals affect virtually every facet of our lives.

• Products such as clothes, foods, medicines, gasoline, refrigerants, and soaps are composed almost solely of organic compounds.

Characteristics of Organic Compounds

• Each single bond contains two electrons.

• A double bond contains four electrons.

• A triple bond contains six electrons.

• Examples:

  • Ethane: H3C-CH3

  • Ethylene: H2C=CH2

  • Acetylene: $HC C-H$

Bonding Patterns

• Valency of C, H, O, N, and halogens leads to predictable patterns of bonds/lone pairs in neutral compounds.

Shapes of Organic Molecules

• VSEPR theory: The most stable arrangement keeps the groups on a central atom as far away from each other as possible.

• An atom surrounded by two groups is linear and has a bond angle of $180^\circ$.

• An atom surrounded by three groups is trigonal planar and has a bond angle of $120^\circ$.

• An atom surrounded by four groups is tetrahedral and has bond angles of $109.5^\circ$.

• Nitrogen is attached to 3 atoms and has 1 lone pair, making its shape a trigonal pyramid.

• Oxygen is attached to 2 atoms and has 2 lone pairs, making its shape bent.

• Table 11.1 Molecular Shape Around Atoms in Organic Compounds

  • Total Number of Groups: 2

    • Number of Atoms: 2

    • Number of Lone Pairs: 0

    • Shape Around an Atom: linear

    • Approximate Bond Angle: $180^\circ$

  • Total Number of Groups: 3

    • Number of Atoms: 3

    • Number of Lone Pairs: 0

    • Shape Around an Atom: trigonal planar

    • Approximate Bond Angle: $120^\circ$

  • Total Number of Groups: 4

    • Number of Atoms: 4

    • Number of Lone Pairs: 0

    • Shape Around an Atom: tetrahedral

    • Approximate Bond Angle: $109.5^\circ$

  • Total Number of Groups: 4

    • Number of Atoms: 3

    • Number of Lone Pairs: 1

    • Shape Around an Atom: trigonal pyramidal

    • Approximate Bond Angle: ~$109.5^\circ$

  • Total Number of Groups: 4

    • Number of Atoms: 2

    • Number of Lone Pairs: 2

    • Shape Around an Atom: bent

    • Approximate Bond Angle: ~$109.5^\circ$

• A wedge means that the group is coming towards you, while a dash means the group is going away.

Drawing Organic Molecules

• Expanded Structure: Shows all bonds and lone pairs.

• Condensed Structure: All bonds and lone pairs are omitted.

  • Sometimes double or triple bonds are still shown.

  • Each carbon is shown along with the number of hydrogens directly bonded to that carbon.

  • Sometimes, certain bonds are kept in for clarity.

  • When no bonds are shown, parentheses are given to help communicate connectivity.

  • You must use chemical intuition and Lewis structure to determine bonding/shape.

• Skeletal/Line-Angle Structure

  • Involves omitting “C” for carbon atoms, and omitting hydrogens on carbons.

  • Hydrogens on non-carbon atoms are always shown!

  • To interpret, you need to understand Carbon has four bonds when neutral.

  • Skeletal structure is the primary method that organic chemists use to draw molecules. Any organic molecule can be drawn this way.

  • In Skeletal, and sometimes in condensed, we show a chain of tetrahedral atoms in a zig-zag shape, because that reflects the geometry of bonded tetrahedral sites.

  • The zig-zag shape minimizes steric repulsion by giving more space to the hydrogen atoms

Functional Groups

• We organize organic compounds by their functional groups.

• Functional Groups are groups of specific atoms bonded in a specific way.

• Compounds that contain the same functional group have similar physical and chemical properties.

• Functional Groups often have heteroatoms, meaning atoms that are not carbon or hydrogen, such as oxygen, nitrogen, or chlorine.

• Chemists will often abbreviate carbon and hydrogen-containing parts of a molecule with the letter R.

Hydrocarbons

• Molecules that contain only hydrogen and carbon atoms.

  • Alkane: R-H

  • Alkene: $C=C$

  • Alkyne: $-C \equiv C-$

  • Aromatic compound: Benzene ring

Compounds Containing a Carbon-Heteroatom Single Bond

• Alkyl halide: R-X (X = F, Cl, Br, I)

• Alcohol: R-OH

• Ether: R-O-R

• Amine: $R-NH<em>2$, $R</em>2NH$ or $R_3N$

• Thiol: R-SH

Carbonyl Group

• Many important compounds in the body and in nature contain a C=O group, called a carbonyl.

Properties of Organic Compounds

• Organic compounds are composed of covalent bonds.

• Organic compounds have much weaker intermolecular forces than those seen in ionic compounds.

• As a result, organic compounds have lower boiling points and melting points than ionic compounds.

• Organic compounds tend to be liquids or gases at room temperature, while ionic compounds are solids.

• A covalent bond is nonpolar when two atoms of identical or similar electronegativity are bonded.

• Thus, C–C and C–H bonds are nonpolar bonds.

• A covalent bond is polar when atoms of different electronegativity are bonded.

• a covalent bond is nonpolar when the electronegativity difference is between 0-0.4

• a covalent bond is polar when the electronegativity difference is between 0.5-1.7

• a molecule is polar when it has polar covalent bonds and dipoles that do not cancel (e.g. a net dipole)

• a dipole is the change in partial charge in a particular direction.

• There are bond dipoles, which focus only on a bonding area, and there is a net dipole, which describes an entire molecule.

Solubility

• “Like dissolves like”

• Water is very polar, so it will dissolve polar molecules more effectively.

• C–C and C–H bonds are nonpolar, so the more of these there are in the molecule, the less likely that molecule will be soluble in water.

• Organic Solvents always include C–C and C–H bonds, so they typically dissolve nonpolar compounds well.

• When nonpolar compounds are distributed among polar compounds, there is a charge separation that is less favorable (higher energy).

Health and Medicine

• Vitamins are organic compounds needed in small amounts in the diet for normal cell function.

• They are classified into two categories:

  • Water soluble

  • Fat soluble

• Vitamin A—retinol—is an essential component of the vision receptors in the eyes.

  • It also helps to maintain the health of the mucous membranes and the skin.

  • Vitamin A is a very large, mostly nonpolar molecule with only one OH group, making it a fat-soluble vitamin.

• Vitamin C—ascorbic acid—is important in the formation of collagen, the connective tissue of the skin.

  • A deficiency in vitamin C causes scurvy, a condition of sailors in the 1600s who had no access to fresh fruit while at sea.

  • It has many polar bonds and many O atoms, making it a water-soluble vitamin.

• It is important to distinguish water-soluble vitamins from fat-soluble vitamins because of concerns of overdosing

  • Water-soluble vitamins are rapidly cleared from the body in the urine, so there is no concern for taking too much

  • Fat-soluble vitamins are not easily cleared by the body.

  • These molecules are first chemically modified by the body (called “metabolized”) prior to elimination. Therefore, care should be taken to not consume too much of these vitamins.