1. Chapter 2. Fundamental Concepts in Understanding Bioenergy and Biobased Products Organic Chemistry

2. 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.

3. 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 + H 2 O  A-H + B-OH

4. Condensation: A-H + B-OH  A-B + H 2 O A-H + B-H  A-B + H 2 (dehydrogenation) Rearrangement: (e.g.) Isomerization. A Variety of Reactions Among Organic Compounds (continues) No Changes in Molecular Formula, but Just Rearrangement of Carbon Atoms

5. Structural Formulas

6. 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

7. Sometimes it will be important to distinguish the 3-D structure of a molecule Bond Below Plane Bond Above Plane

9. Different Organic Compound Classes IUPAC Nomenclature Prefix / Parent / Suffix

10. Alkanes are also called paraffins

11. 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

12. Alkanes with Side Chains Branched alkanes result when carbon atoms in the chain bond to other carbon atoms, forming side chains. CH 3 -CH 2 _ CH 2 -CH 2 -CH 3 + H 2 CH 3 -CH 2 -CH 2 -CH 3 + CH 4 CH 3 -CH-CH 2 -CH 3 + H 2 CH 3 Same Chemical Formula of C 5 H 12, but different carbon structures: Isomers

13. 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 Alkanes with Side Chains

15. C-H bonds are non-polar => Alkanes are non- polar Alkanes are not soluble in water, a highly polar compound The absence of polarity means that alkane molecules do not strongly interact

17. Common Name is Ethylene

18. The location of each double bond is indicated in the prefix and the subfix becomes -dienes

19. - 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.

20. Three isoprene units => Isolated from roses Two isoprene units => A distinctive lemon odor They are responsible for the fragrant odors of pine trees and the bright colors of tomatoes and carrots.

27. Phenylalanine benzyl heptanoate