Chapter 2. Fundamental Concepts in
Understanding Bioenergy and
Biobased Products
Organic Chemistry
What is Organic Chemistry???
• The original distinction between inorganic and organic
compounds was their source in nature:
• Inorganic Compounds => Mineral Sources
• Organic Compounds => Plants and Animals
• However, the most of organic compounds are now
produced from petroleum.
• The common feature of organic compounds is a
skeleton of carbon that is surrounded by other atoms,
especially hydrogen, oxygen and nitrogen, but also
sulfur, phosphorus, and halides.
A Variety of Reactions Among Organic Compounds
• Addition: (e.g.) A + B  A-B
• Elimination: (e.g.) A-B  A + B
• Substitution: Replacement of one atom or the group of
atoms by a second atom or group of atoms
• (e.g.) A-B + C  A-C + B
• Hydrolysis: Water reacts with organic compounds to split
them into two smaller product molecules
• (e.g.) A-B + H2O  A-H + B-OH
A Variety of Reactions Among Organic Compounds
(continues)
• Condensation: A-H + B-OH  A-B + H2O
A-H + B-H  A-B + H2 (dehydrogenation)
• Rearrangement: (e.g.) Isomerization.
No Changes in Molecular Formula, but Just Rearrangement of Carbon Atoms
Structural Formulas
• Bond-line structures are an extreme shorthand for representing molecules
• C atoms are omitted but C-C bonds are illustrated in a zigzag arrangement
• C-H bonds are omitted while bonds of C atoms to other atoms or molecular groups are
shown explicitly
• Sometimes it will be important to
distinguish the 3-D structure of a molecule
Bond Below Plane
Bond Above Plane
Different Organic Compound Classes
IUPAC Nomenclature
Prefix / Parent / Suffix
• Alkanes are also called
paraffins
Alkanes with Side Chains
• A normal alkane molecule minus one hydrogen atom is known
as an alkyl group: The short hand for an alkyl group is R• The names of the alkyl groups conform to the names of the
corresponding alkanes
Alkanes with Side Chains
• Branched alkanes result when carbon atoms in the
chain bond to other carbon atoms, forming side chains.
CH3-CH2 _CH2-CH2-CH3 + H2
CH3-CH2-CH2-CH3 + CH4
CH3-CH-CH2-CH3 + H2
CH3
Same Chemical Formula of C5H12, but different carbon structures: Isomers
Alkanes with Side Chains
How to name alkanes with side chains?
Step 1) Identify the longest continuous carbon chain (parent part of the IUPAC name)
Step 2) Number carbon atoms along the main carbon chain
- The lowest numbered carbon atom must appear at the end of the chain
closest to the first branch chain
Step 3) Identify side chains and locate them on the main chain
Step 4) Combine “parent part” and “prefix part”
More examples how to name alkanes with side chains
• C-H bonds are non-polar => Alkanes are nonpolar
• Alkanes are not soluble in water, a highly polar
compound
• The absence of polarity means that alkane
molecules do not strongly interact
Common Name is Ethylene
• The location of each double bond is indicated in
the prefix and the subfix becomes -dienes
- Both terminal carbon atoms can bond with terminal carbon atoms
of other isoprenes to form a variety of cyclic and acyclic
compounds with different degrees of saturation and various
functional groups attached.
• They are responsible for the fragrant odors of pine trees and
the bright colors of tomatoes and carrots.
Three isoprene units => Isolated from roses
Two isoprene units => A
distinctive lemon odor
Phenylalanine
benzyl heptanoate