• Define organic chemistry. • Describe and provide formulas, condensed structures, Lewis dot structures,

and skeletal structures for straight chain alkanes, alkenes, and alkynes up to 10 carbons in length.

• Name organic molecules based on the primary chain and the identity, number, and location of substituents.

• Describe structural differences for aromatic and cyclic hydrocarbons. • Describe structural features of the following functional groups: alkanes,

alkenes, alcohol, aldehydes, carboxylic acids (and fatty acids), amines, esters, and amides. Recognize examples of simple organic molecules that contain these functional groups. Recognize components of larger molecules that represent specific functional groups.

• Be able to draw skeletal or condensed structures for organic compounds. • Be able to draw skeletal or condensed structures for the 18 carbon family of

fatty acids including stearic, oleic, linoleic, and linolenic acid.• Construct reactions illustrating the formation of esters from carboxylic acids

and alcohols and the formation of amides from carboxylic acids and amines.• Define isomers. Distinguish the isomeric relationship between any pair of

molecules and label as constitutional isomers, cis/trans isomers, or optical isomers (conformational isomers in text terminology).

• Explain the importance of optical isomers to biochemistry. Apply this concept to the drug thalidomide.

4. Introduction to Organic Compounds

Organic ChemistryThe chemistry of the compounds of carbon

Pure carbon exists in nature in multiple forms

Buckeyballs C60

Diamond C??

Graphite C??

Hydrocarbons Chemical compounds containing only C and H

Alkanes A class of linear hydrocarbons with no double bonds

Formula: CnH(2n+2)

Alkanes are nonpolar compounds C & H are close in electronegativity (2.5 vs. 2.1)

bonds are nonpolar covalent small or no dipole moment

insoluble in water (like dissolves like)

Naming Alkanes – hydrocarbons with CnH(2n+2)

Methane CH4

Ethane C2H6

Propane C3H8

Butane C4H10

Pentane C5H12

Hexane C6H14

Heptane C7H16

Octane C8H18

Nonane C9H20

Decane C10H22

Cyclic alkanes have ring structuresUse cyclo prefix

CnH2n

Representing hydrocarbon structures – e.g. propaneC3H8

Draw the Lewis Structure for Propane

Is the chain (3 carbons) for propane …. a) straight (180º) b) bent at ~ 109º b) bent at ~ 90º

Naming alkanes that have branched chains and/or substituents

Alkanes as substituents – replace ‘ane’ with yl - CH3 methyl - CH2 - CH3 ethyl - CH2 - CH2 - CH3 proply - CH2 - CH2 - CH2 - CH3 butyl etc. Other substituents halides: - F (fluoro) - Cl (chloro) etc. - OH (hydroxy) etc.

Name of alkane corresponding to longest chain

Naming alkanes that have branched chains and/or substituents

Rules

1. Identify the parent (longest) chain

CH3 – CH2 – CH2 – CH – CH3 | Cl

2. Identify the substituent(s)

3. Assign a number to each substituent based on where it is located on the parent chain. Proceed in the direction that gives the lowest number

2-chloropentane

Naming alkanes that have branched chains and/or substituents

Rules

CH3 – CH2 – CH2 – CH – CH3 | | Cl Cl

2,3-dichloropentane

CH3 – CH2 – CH2 – CH – CH2 | | CH3 CH3

CH3 – CH2 – CH2 – CH – CH2 | CH3

2-methylpentane

a) 2,3 –dimethylpentaneb) 2-metylhexanec) 3-methylhexane

Naming alkanes that have branched chains and/or substituents

Rules

CH3 – CH2 – CH2 – CH – CH3 | CH2 – CH2 - CH3

a) 2-propylpentaneb) 4-methylheptane

CH3 – CH2 – CH2 – CH – CH2 – CH3 | | Cl CH3

a) 2-chloro-4-methylhexaneb) 3-methyl-5-chlorohexane

IsomersSets of molecules with the same molecular formula

…. that are not identical

Constitutional Isomers – Have different atom connectivity (or arrangement)

Cis-trans isomers – Have the same connectivity but differ in 2D orientation typically in molecules with double bonds or rings.

Optical isomers – Have the same connectivity but differ in 3D orientation optical isomers have “chiral” carbon – bonded to 4 distinct groups.

IsomersSets of molecules with the same molecular formula

…. that are not identical

Constitutional isomers Have different atom connectivity (or arrangement)

Butane - C4H10

Hydrocarbons Chemical compounds containing only C and H

Alkenes A class of hydrocarbons with a C=C double bond (unsaturated)

Formula: CnH(2n)

Ethene (or ethylene) CH2 = CH2

Draw the Lewis dot structure for ethyleneDescribe the molecular geometry around each C

Draw the structure with as accurate a geometry as possible.

Propene CH2 = CH – CH3

1-butene CH2 = CH – CH2 – CH3

2-butene CH3 - CH = CH – CH3

Constitutional (Structural) isomers – Have different atom connectivity (or arrangement)Are 1-butene and 2-butene constitutional isomers?

Cis-trans isomers – Have the same connectivity but differ in 2D orientation typically in molecules with double bonds or rings

Draw the Lewis dot structure for 2-buteneDescribe the molecular geometry around the C = C carbons.Draw the structure with as accurate a geometry as possible.

Draw the skeletal structure for the compound.

cis trans

4.5 Isomerism in Organic Compounds

Hydrocarbons Chemical compounds containing only C and H

Alkynes A class of hydrocarbons with a triple bond

Ethyne (or acetylene) CH ≡ CHDraw the Lewis dot structure for acetylene

Describe the molecular geometry around each CDraw the structure with as accurate a geometry as possible.

H - C ≡ C - H

Can you have cis-trans isomerism around a triple bond?a) Yes b) No

ReviewAlkanes can be linear or branched. There can be numerous molecules with the same formula but different bonding arrangements (constitutional isomers)Alkenes are unsaturated hydrocarbons with one or more C=C double bonds.Some alkenes can display cis/trans isomerism based on the nature of the chain extensions and substituents bonded to each C of a double bonded pair. Alkynes are hydrocarbons with C≡C triple bonds. Cyclohexane is not a constitutional isomer of hexane as it has two less H atoms.

Benzene and aromatic hydrocarbons

Toluene or methylbenzene

2,4,6 – trinitrotoluene(TNT)

Aromatic rings have delocalized electrons.These electrons are not confined to a bond between two atoms but are spread out over the entire ring.

Functional Groups

Hydrocarbons Alkanes Alkene contain C=C double bond Alkynes contain C≡C triple bond Aromatic contains ring with multiple double bonds - delocalized

Organic Molecules often contain atoms other than C and H.Most common are bonds to O and N.Specific arrangements of atoms are referred to as Functional groups. This is because they give molecules various functions.Most cellular molecules are organic molecules containing one or more functional groups.

Functional Groups

Alcohols C – OH

O ||

Aldehydes C – C – H

O ||

Ketones C – C – C

Amines C – NH2 (1º)

ethanol CH3 – CH2 - OH

O ||

ethanal CH3 – C – H

O ||

acetone CH3 – C – CH3

ethyl amine CH3 – CH2 – NH2

ethyl ether CH3 – CH2 – O – CH2 – CH3 ether C – O – C

Functional Groups

Carboxylic acids

COOH (carboxyl group)

O || R - C - OH

Acetic acidvinegar is a 5% acetic acid

solution

O ||

CH3 - C - OH

Fatty acids – Carboxylic acids with long chains saturated – no C=C bonds unsaturated – one or more C=C bonds

oleic acid C18 with 1 C=C monounsaturated (9)

Bent structure (cis only) linoleic acid C18 with 2 C=C polyunsaturated (9,12)

Ω – 6 fatty acid

linolenic acid C18 with 3 C=C polyunsaturated (9,12,15)

Ω – 3 fatty acid

stearic acid C18 saturated

O O || ||R - C – OH + HO - R' → R - C – O - R' + H - OH Carboxylic acid + alcohol → ester + water

Functional Group combinations

O H O H || | || |R - C – OH + H - N - R' → R - C – N - R' + H - OH Carboxylic acid + amine → amide + water

Functional Group Combinations with benzene

Benzoic acid Phenolhydroxybenzene Benzaldehyde

Anilineaminobenzene

Fatty acids – Carboxylic acids with long chains saturated – no C=C bonds unsaturated – one or more C=C bonds

oleic acid C18 with 1 C=C monounsaturated (9)

Bent structure (cis only)

linoleic acid C18 with 2 C=C polyunsaturated (9,12)

Ω – 6 fatty acid

linolenic acid C18 with 3 C=C polyunsaturated (9,12,15)

Ω – 3 fatty acid

stearic acid C18 saturated

Animal fats have a higher proportion of saturated fatty acidsThey lack the ability to make polyunsaturated fatty acids↑saturated fats in diet leads to ↑cholesterol biosynthesis & ↑LDL:HDL

Vegetable oils have higher amounts of polyunsaturated fatty acids. This also makes them liquid at RT.

Palm and coconut oil are exceptions to the rule.

• A right-handed and a left-handed baseball glove are nonsuperimposable mirror images.

• Objects such as these are termed chiral (from the Greek cheir, meaning “the hand”).

• Most enantiomers contain a chiral center—a tetrahedral carbon atom bonded to four different atoms or groups of atoms.

4.5 Isomerism in Organic Compounds

• On paper, a chiral carbon is represented with an asterisk.

4.5 Isomerism in Organic Compounds

Identifying Chiral Carbons in a Molecule– Step 1: Locate the tetrahedral carbons (carbons with four

atoms bonded to them). – Step 2: Inspect the tetrahedral carbons. Determine if the

four groups attached to the tetrahedral carbons are different.

– Step 3: Assign the chiral centers. Typically, an asterisk is drawn next to the chiral carbon.

4.5 Isomerism in Organic Compounds

Isomerism in Organic Compounds

Thalidomide Story

1954: synthesized West Germany

1957: approved as sedative/soporific

1960: application to FDA denied

1961: peripheral neuritis & birth defects noted

1962: drug withdrawn in Europe Kelsey awarded medal

Distinguishing Properties of Enantiomers optical isomers that are mirror images of each other

2. They rotate plane polarized light in different directions1. They can’t be superimposed

3. They react differently in a chiral environment!

Protein Surface binding points D

L

Protein Surface correct ligand incorrect ligand

D L

4.5 Isomerism in Organic Compounds

r-thalidomide

sedative & soporific D

s-thalidomide

Lteratogen

Chapter Four Summary (continued)

• 4.3 Families of Compounds—Functional Groups– Organic compounds are grouped into families based on the identity of

the functional group(s) present.– A functional group is a common grouping of atoms bonded in a

particular way. – Functional groups have specific properties and reactivity. Compounds

with the same functional group behave similarly. – Since the functional group is the part of the molecule that is of

interest, we typically represent the hydrocarbon portion as R (the Rest of the molecule).

– The hydrocarbon families the alkenes, alkynes, and aromatics are highlighted in this section.

– Fatty acids are alkane-like biomolecules that are the primary components of dietary fats. Fatty acids with a carbon–carbon double bond in their structure are referred to as unsaturated, while those without a double bond are referred to as saturated.

4.5 Isomerism in Organic Compounds