Organic & Biological Chemistry
Chemistry
of Life
Alkanes
(Saturated HC’s)
Hydrocarbons
Alkenes
(Unsaturated HC’s)
Alcohols
Ethers
Functional
Groups
Chirality
Biochemistry
Carbohydrates
3/21/2016
Proteins
Nucleic Acids
Some General Characteristics of
Organic Molecules
The Structures of Organic Molecules
• Organic molecules exhibit three different types of
hybridization at the carbon center:
– sp3 hybridized carbons for tetrahedral geometries;
– sp2 hybridized carbons for trigonal planar geometries; and
– sp hybridized carbons for linear geometries.
Drawing Lewis Structures
1.
2.
3.
4.
5.
6.
Follow Step by Step Method (See Ng Web-site)
Total all valence electrons. [Consider Charge]
Write symbols for the atoms and guess skeleton structure
[ define a central atom ].
Place a pair of electrons in each bond.
Complete octets of surrounding atoms. [ H = 2 only ]
Place leftover electrons in pairs on the central atom.
If there are not enough electrons to give the central atom
an octet, look for multiple bonds by transferring
electrons until each atom has eight electrons around it.
CyberChem video
HyperChem
Figure 9.3
HyperChem
Summary of VSEPR Molecular Shapes
e-pairs
Notation
Name of VSEPR shape
Examples
2
AX2
Linear
HgCl2 , ZnI2 , CS2 , CO2
3
AX3
Trigonal planar
BF3 , GaI3
AX2E
Non-linear (Bent)
SO2 , SnCl2
AX4
Tetrahedral
CCl4 , CH4 , BF4-
AX3E
(Trigonal) Pyramidal
NH3 , OH3-
AX2E2
Non-Linear (Bent)
H2O , SeCl2
AX5
Trigonal bipyramidal
PCl5 , PF5
AX4E
Distorted tetrahedral
(see-sawed)
TeCl4 , SF4
AX3E2
T-Shaped
ClF3 , BrF3
AX2E3
Linear
I3- , ICl2-
AX6
Octahedral
SF6 , PF6-
AX5E
Square Pyramidal
IF5 , BrF5
AX4E2
Square Planar
ICl4- , BrF4-
4
5
6
HyperChem
CyberChem video
See Ng Web-site
Methane
Ethene
Ethyne
Figure 9.14: Covalent Bonding and Orbital Overlap
Some General Characteristics of
Organic Molecules
sp3 Hybridzation in Carbon Bonding
Introduction to Hydrocarbons
• Hydrocarbons are compounds with only C and H.
• Four classes:
–
–
–
–
alkanes (all  bonds and no  bonds);
alkenes (a mixture of  and  bonds, but no triple bonds);
alkynes (must contain triple bonds); and
aromatics (have planar, ring structures with alternating single
and double bonds).
• Saturated compounds have only  bonds.
• Unsaturated compounds have both  and  bonds.
Alkanes
HyperChem
Alkanes
Structural Isomers
Alkanes
Nomenclature
Prefix
What Substituent
Base
How many carbons
Suffix
What Family
1. Find longest continuous chain of carbon atoms, and use name of this
chain (see Table 25.1) as the base name of the compound.
2. Number the carbon atoms in the longest chain, beginning with end of
chain that is nearest to a substituent.
3. Name and give the location of each substituent group.
4. When two or more substituents are present, list them in alphabetical
order.
Alkanes
Cycloalkanes
Alkanes
Reactions of Alkanes
• The C-C and C-H bonds are very strong. Therefore,
alkanes are very unreactive.
• At room temperature alkanes do not react with acids,
bases, or strong oxidizing agents.
• Alkanes do combust in air (making them good fuels):
2C2H6(g) + 7O2(g)  4CO2(g) + 6H2O(l) H = -2855 kJ
Unsaturated Hydrocarbons
Alkenes
• Geometrical isomers are possible since there is no
rotation about a C=C  bond.
• Note the overlap between orbitals is above and below the
plane of the  bonds.
– As the C-C bond begins to rotate (moving from cis to trans) the
overlap decreases.
Unsaturated Hydrocarbons
Alkenes
– At 90 the  bond breaks completely.
– Therefore, there is no rotation about a  bond.
– Therefore, cis and trans isomers do not readily interconvert.
Unsaturated Hydrocarbons
•
•
•
•
Alkynes
Alkynes are hydrocarbons with one or more CC bond.
Therefore, alkynes have one  and two  bonds between
two C atoms.
Ethyne (acetylene) is a reactive alkyne: HCCH.
When acetylene is burned in the presence of oxygen
(oxyacetylene torch) the temperature is about 3200 K.
Alkynes are named in the same way as alkenes with the
suffix -yne replacing the -ene for alkenes.
Unsaturated Hydrocarbons
Addition Reactions of Alkenes and
Alkynes
• The most dominant reaction for alkenes and alkynes
involves the addition of something to the two atoms
which form the double bond:
H2C CH2 + Br2
H2C CH2
Br Br
• Note that the C-C  bond has been replaced by two C-Br
 bonds.
Unsaturated Hydrocarbons
Aromatic Hydrocarbons
• Aromatic structures are formally related to benzene.
• Benzene is not reactive because of the stability associated
with the delocalized  electrons.
Functional Groups: Alcohols
and Ethers
Compounds with a Carbonyl
Group
Carboxylic Acids
Chirality in Organic Chemistry
• A molecule that exists as a pair of nonsuperimposable
mirror images is called chiral.
• Organic compounds that contain one carbon atom that is
attached to four different atoms or groups are chiral.
• The carbon atom attached to the four different moieties is
called a stereogenic carbon.
S-ibuprofen:
Introduction to Biochemistry
• Chemistry of living organisms is called biochemistry.
• Biochemical molecules tend to be very large and difficult
to synthesize.
• Living organisms are highly ordered. Therefore, living
organisms have very low entropy.
• Most biologically important molecules are polymers,
called biopolymers.
• Biopolymers fall into three classes: proteins, polysaccharides
(carbohydrates), and nucleic acids.
Proteins
Amino Acids
• Proteins are large
molecules present in all
cells.
• They are made up of amino acids.
Video Summary
Protein Structure
• Pitch is the distance between
coils.
• The pitch and diameter ensure
no bond angles are strained and
the N-H and carbonyl
functional groups are
optimized for H-bonding.
• Tertiary structure is the three
dimensional structure of the
protein.
Carbohydrates
•
•
•
•
•
Carbohydrates have empirical formula Cx(H2O)y.
Carbohydrate means hydrate of carbon.
Most abundant carbohydrate is glucose, C6H12O6.
Carbohydrates are polyhydroxy aldehydes and ketones.
Glucose is a 6 carbon aldehyde sugar and fructose 6
carbon ketone sugar.
• The alcohol side of glucose can react with the aldehyde
side to form a six-membered ring.
Carbohydrates
Disaccharides
• Lactose is formed from galactose and -glucose.
• Sucrose is about six times sweeter than lactose, a little
sweeter than glucose and about half as sweet as fructose.
• Disaccharides can be converted into monosaccharides by
treatment with acid in aqueous solution.
Carbohydrates
Polysaccharides
• Bacteria in the stomach of animals contain cellulases,
which are enzymes that enable animals to use cellulose
for food.
Nucleic Acids
• Nucleic acids carry genetic information.
• DNA (deoxyribonucleic acids) have molecular weights
around 6 - 16  106 amu and are found inside the nucleus
of the cell.
• RNA (ribonucleic acids) have molecular weights around
20,000 to 40,000 amu and are found in the cytoplasm
outside the nucleus of the cell.
• Nucleic acids are made up of nucleotides.
Organic & Biological Chemistry
Chemistry
of Life
Alkanes
(Saturated HC’s)
Hydrocarbons
Alkenes
(Unsaturated HC’s)
Alcohols
Ethers
Functional
Groups
Chirality
Biochemistry
Carbohydrates
Proteins
Nucleic Acids
Saturated compounds
have only  bonds.
Unsaturated compounds
have both  and 
bonds.