1. Chapter 3
Introduction to
Organic Molecules
and
Functional Groups

2. Introduction to Organic Molecules and Functional Groups
A functional group is an atom or a group of atoms with characteristic chemical and physical properties. It is the reactive part of the molecule.
Most organic compounds have C—C and C—H bonds. However, many organic molecules possess other structural features:
Heteroatoms—atoms other than carbon or hydrogen.
 Bonds—the most common  bonds occur in C—C and C—O double bonds.
These structural features distinguish one organic molecule from another. They determine a molecule’s geometry, physical properties, and reactivity, and comprise what is called a functional group.

3. Introduction to Organic Molecules and Functional Groups
Heteroatoms and  bonds confer reactivity on a particular molecule.
Heteroatoms have lone pairs and create electron-deficient sites on carbon.
 Bonds are easily broken in chemical reactions. A  bond makes a molecule a base and a nucleophile.
R : usually saturated hydrocarbon unit (alkyl)
Don’t think that the C—C and C—H bonds are unimportant. They form the carbon backbone or skeleton to which the functional group is attached.

4. Introduction to Organic Molecules and Functional Groups
The hydroxy group makes the properties of ethanol very different from the properties of ethane.

5. An Overview of Functional Groups
Hydrocarbons
Hydrocarbons are compounds made up of only the elements carbon and hydrogen. They may be aliphatic or aromatic.

6. An Overview of Functional Groups
Hydrocarbons
Aromatic hydrocarbons are so named because many of the earliest known aromatic compounds had strong characteristic odors.
The simplest aromatic hydrocarbon is benzene. The six-membered ring and three  bonds of benzene comprise a single functional group.
When a benzene ring is bonded to another group, it is called a phenyl group.

7. There must be smarter way to use these hydrocarbons !!
An Overview of Functional Groups
Hydrocarbons
Alkanes have no functional groups and very unreactive.
They combust (“burn” in air) and the C-C bonds can be broken in the absence of air at very high temperatures (~700 oC) (pyrolysis reactions).
There must be smarter way to use these hydrocarbons !!
Polyethylene (-[CH2-CH2]n-), a common packaging material, is so resistant to environmental degradation (both chemical and biological) that it persists for years in landfill disposal sites.

8. An Overview of Functional Groups
Compounds containing C-Z s Bonds

9. An Overview of Functional Groups
Compounds containing C-Z s Bonds
The electronegativity difference between C and Z causes the C-Z bond to be polar:
Alcohol : meant “spirit”. anything that was distilled. “spirit of wine” – distilled wine
i.e. ethanol (ethylalcohol)
Ether : originally named for diethylether due to its volatility and anesthetic effect.
cf. petroleum ether: low boiling fraction for petroleum

10. An Overview of Functional Groups
Compounds containing C-Z s Bonds
Examples

11. Compounds Containing a C=O Group

12. An Overview of Functional Groups
Compounds Containing a C=O Group
This group is called a “carbonyl group”.
The polar C—O bond makes the carbonyl carbon an electrophile, while the lone pairs on O allow it to react as a nucleophile and base.
The carbonyl group also contains a  bond that is more easily broken than a C—O  bond.

13. An Overview of Functional Groups
Compounds Containing a C=O Group
Examples

14. Introduction to Organic Molecules and Functional Groups
A functional group determines all of the following properties of a molecule:
Bonding and shape
Type and strength of intermolecular forces
Physical properties
Nomenclature
Chemical reactivity

15. Intermolecular forces (attractive)
Ions, ionic molecules
Ions, ionic molecules
with polar compound
polar compound
Ions, ionic molecules
with nonpolar compound
Figure 13.1
nonpolar compound
Induced dipole :
Ion induces polarization to generate dipole.
dispersion :
Instantaneous dipole generated by short time fluctuations in the charge clouds
induces polarization to generate dipole.

16. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces
Intermolecular forces are interactions that exist between molecules. Functional groups determine the type and strength of these interactions.
Ionic compounds contain oppositely charged particles held together by extremely strong electrostatic inter-actions. These ionic inter-actions are much stronger than the intermolecular forces present between covalent molecules.

17. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces
The nature of the forces between molecules depends on the functional group present. There are three different types of interactions, shown below in order of increasing strength:
van der Waals forces
dipole-dipole interactions
hydrogen bonding

18. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces—van der Waals Forces
van der Waals forces are also known as London forces + repulsive interaction.
They are weak interactions caused by momentary changes in electron density in a molecule.
They are the only attractive forces present in nonpolar compounds.
even for methane, CH4
Even though CH4 has no net dipole, at any one instant its electron density may not be completely symmetrical, resulting in a temporary dipole. This can induce a temporary dipole in another molecule. The weak interaction of these temporary dipoles constitutes van der Waals forces.

19. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces—van der Waals Forces
All compounds exhibit van der Waals forces.
The surface area of a molecule determines the strength of the van der Waals interactions between molecules. The larger the surface area, the larger the attractive force between two molecules, and the stronger the intermolecular forces.

20. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces—van der Waals Forces
van der Waals forces are also affected by polarizability.
Polarizability is a measure of how the electron cloud around an atom responds to changes in its electronic environment.

21. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces—Dipole-Dipole Interactions
Dipole—dipole interactions are the attractive forces between the permanent dipoles of two polar molecules.
These attractive forces caused by permanent dipoles are much stronger than weak van der Waals forces.

22. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces—Hydrogen Bonding
Hydrogen bonding typically occurs when a hydrogen atom bonded to O, N, or F, is electrostatically attracted to a lone pair of electrons on an O, N, or F atom in another molecule.
can be extended to p-electrons of a benzene ring.

23. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces—Hydrogen Bonding
Intramolecular Hydrogen bonding :
reduces intermolecular interactions.
Hydrogen bonding in nylon

24. Introduction to Organic Molecules and Functional Groups
Intermolecular Forces
Note: as the polarity of an organic molecule increases, so does the strength of its intermolecular forces.

25. Introduction to Organic Molecules and Functional Groups
Physical Properties—Boiling Point
The boiling point of a compound is the temperature at which liquid molecules are converted into gas.
In boiling, energy is needed to overcome the attractive forces in the more ordered liquid state.
The stronger the intermolecular forces, the higher the boiling point.
For compounds with approximately the same molecular weight:

26. Introduction to Organic Molecules and Functional Groups
Physical Properties—Boiling Point
For two compounds with similar functional groups:
The larger the surface area, the higher the boiling point.
The more polarizable the atoms, the higher the boiling point.

27. Introduction to Organic Molecules and Functional Groups
Separation of a mixture : distillation
Liquids having different boiling points can be separated in the laboratory using a distillation apparatus.

28. Introduction to Organic Molecules and Functional Groups
Physical Properties—Melting Point
The melting point is the temperature at which a solid is converted to its liquid phase.
In melting, energy is needed to overcome the attractive forces in the more ordered crystalline solid.
The stronger the intermolecular forces, the higher the melting point.
Given the same functional group, the more symmetrical the compound, the higher the melting point. --- packing effect

29. Introduction to Organic Molecules and Functional Groups
Physical Properties—Melting Point
Symmetry also plays a role in determining the melting points of compounds having the same functional group and similar molecular weights, but very different shapes.
A compact symmetrical molecule like neopentane packs well into a crystalline lattice whereas isopentane, which has a CH3 group dangling from a four-carbon chain, does not. Thus, neopentane has a much higher melting point.

30. Introduction to Organic Molecules and Functional Groups
Physical Properties—Solubility
Solubility is the extent to which a compound, called a solute, dissolves in a liquid, called a solvent.

31. Introduction to Organic Molecules and Functional Groups
Physical Properties—Solubility
Compounds dissolve in solvents having similar kinds of intermolecular forces.
“Like dissolves like.”
Polar compounds dissolve in polar solvents. Nonpolar or weakly polar compounds dissolve in nonpolar or weakly polar solvents.
Water and organic solvents are two different kinds of solvents. Water is very polar and is capable of hydrogen bonding with a solute. Many organic solvents are either nonpolar, like carbon tetrachloride (CCl4) and hexane [CH3(CH2)4CH3], or weakly polar, like diethyl ether (CH3CH2OCH2CH3).
Most ionic compounds are soluble in water, but insoluble in organic solvents.

32. Physical Properties—Solubility
An organic compound is water soluble only if it contains one polar functional group capable of hydrogen bonding with the solvent for every five C atoms it contains. For example, compare the solubility of butane and acetone in H2O and CCl4.

33. Introduction to Organic Molecules and Functional Groups
Physical Properties—Solubility
To dissolve an ionic compound, the strong ion-ion interactions must be replaced by many weaker ion-dipole interactions.

34. Introduction to Organic Molecules and Functional Groups
Physical Properties—Solubility
ethanol is water soluble since it has a small carbon skeleton of  five C atoms, compared to the size of its polar OH group.
Cholesterol has 27 carbon atoms and only one OH group. Its carbon skeleton is too large for the OH group to solubilize by hydrogen bonding, so cholesterol is insoluble in water.
The nonpolar part of a molecule that is not attracted to H2O is said to be hydrophobic. (“water hating”)
The polar part of a molecule that can hydrogen bond to H2O is said to be hydrophilic. (“water loving”)

35. Introduction to Organic Molecules and Functional Groups
Application—Vitamins
Fat soluble vitamins : vitamin A, D, E, K
Water soluble vitamins : vitamin B complex, C

36. Fat soluble vitamins : vitamin A, D, E, K
vitamin D
vitamin E (tocopherol)
vitamin K

37. Water soluble vitamins : vitamin B complex, C
Vitamin B2(riboflavin)
Vitamin B12
Vitamin C (ascorbic acid)

38. Introduction to Organic Molecules and Functional Groups
Application—Soap

39. Introduction to Organic Molecules and Functional Groups
Application—The Cell Membrane

40. Introduction to Organic Molecules and Functional Groups
Application—The Cell Membrane
Transport Across a Cell Membrane:
Polar molecules and ions are transported across cell membranes encapsulated within molecules called ionophores.
Ionophores are organic molecules that complex cations. They have a hydrophobic exterior that makes them soluble in the nonpolar interior of the cell membrane, and a central cavity with several oxygens whose lone pairs complex with a given ion.

41. Introduction to Organic Molecules and Functional Groups
Application—The Cell Membrane
Transport Across a Cell Membrane:

42. Introduction to Organic Molecules and Functional Groups
Synthetic ionophores
Crown ethers are cyclic ethers containing several oxygen atoms that bind specific cations depending on the size of their cavity.
They are named using the general format x-crown-y, where x is the total number of atoms in the ring and y is the number of oxygen atoms.
Charles Pedersen at DuPont

43. Introduction to Organic Molecules and Functional Groups
Influence of Functional Groups on Reactivity
Recall that:
Functional groups create reactive sites in molecules.
Electron-rich sites react with electron poor sites.
All functional groups contain a heteroatom, a  bond or both, and these features create electron-deficient (or electrophilic) sites and electron-rich (or nucleophilic) sites in a molecule. Molecules react at these sites.

44. Introduction to Organic Molecules and Functional Groups
Influence of Functional Groups on Reactivity

45. Introduction to Organic Molecules and Functional Groups
Influence of Functional Groups on Reactivity
An electron-deficient carbon reacts with a nucleophile, symbolized as :Nu¯.
An electron-rich carbon reacts with an electrophile, symbolized as E+.
For example, alkenes contain an electron rich double bond, and so they react with electrophiles E+.

46. Introduction to Organic Molecules and Functional Groups
Influence of Functional Groups on Reactivity
On the other hand, alkyl halides possess an electrophilic carbon atom, so they react with electron-rich nucleophiles.

47. Introduction to Organic Molecules and Functional Groups
Biomolecules
Biomolecules are organic compounds found in biological systems.
Many are relatively small with molecular weights of less than 1000 g/mol.
There are four main families of small molecule biomolecules:
Simple sugars—combine to form complex carbohydrates like starch
Nucleotides—are the building blocks of DNA
Amino acids—join together to form proteins
Fatty acids—are the building blocks of triacylglycerols, lipids that are stored as fat droplets in adipose tissue.
Biomolecules often have several functional groups.

48. Figure 3.9 Simple and complex biomolecules

49. Figure 3.9 continued Simple and complex biomolecules

50. Homework
3.3, 3.4, 3.6, 3.9, 3.10, 3.19, 3.21, 3.27, 3.32, 3.35, 3.38, 3.39, 3.41, 3.42

51. Preview of Chapter 4 Alkanes
What are alkanes?
Systematic naming of Alkanes.
Conformations of Alkanes.
how flexible or rigid are various alkanes
- Reactions of Alkanes.

52. Assignment for March 4th Class.
What is the general molecular formula for an acyclic alkane?
What is the general molecular formular for a cyclic alkane with one ring?
What is the meaning of conformation?
What are eclipsed conformation and staggered conformation?
What are angle strain and torsional strain in cycloalkanes?