Organic Chemistry

Muh. Yanis Musdja The Study of the Compounds of Carbon

Carbons Place on the Periodic Table

Why does Carbon form so many interesting compounds?

Easily forms bonds with other C atoms. Forms double and triple bonds with other C atoms. Can form long chains (and rings) of C-C bonds. Ubiquitous/Found everywhere. Depending on bonding (presence of single, double, or triple bonds) carbon compounds can exhibit tetrahedral, trigonal planar or linear geometries Though carbon and hydrogen form the backbone structure, carbon can also bond to other elements, like O and N, which are called heteroatoms

Carbon Skeletons
Since carbon bonds four times, it can assume a very complex set of bonding arrangements. Single bonded carbons can rotate relative to one another, so arrangements can be represented in different ways, as shown below:

Consider the Diversity of Carbon Compounds

Single Bonds
C C C C C C C C C C C C C

Double Bonds
C
C C C C C

Rings
C
C C C C C C

C
C

C C

C
C C C C

C
C

C
C

C
C C C

C
C C

Hydrogen Skins
H
C C
H

H
C C C

H
C C C C

H A C atom single-bonded to one other atom gets three H atoms.

C C C C C

H
A C atom single-bonded to two other atoms gets two H atoms. A C atom single-bonded to three other atoms gets one H atom. H
C C
C C
H

A C atom single-bonded to four other atom is already fully bonded (no H atoms).

H A double-bonded C atom is treated as if it were bonded to two other atoms.

A double- and singlebonded C atom or a triple-bonded C atom is treated as if it were bonded to three other atoms.

Hydrocarbon Representations
H H H H H H H C C C C C C H H H H H H H

Expanded Structure

CH3CH2CH2CH2CH2CH3

Condensed Structure Bond-line Representation

C6H14

Molecular Formula

Isomers
Note that for the formula C6H14, several possible structures exist. These alternate forms are called structural isomers. Note that each of these isomers is a different compound with different properties - and a different name. CH3 CH3CH2CH2CH2CH2CH3 CH3 CH3CHCH2CH2CH3 CH3CH2CHCH2CH3 CH3 CH3CHCHCH3

CH3
One more isomer exists. Can you suggest what it is?

Functional Groups

Groups of atoms bonded in a particular way. They tend to act as a unit and react in a similar way despite the rest of the compound. Many functional groups contain electronegative elements (N,O) and contain polar bonds.
Incomplete list of Functional groups:

1. -C=C2. -CC3. -C-OH

alkene
alkyne alcohol

4. -C-O-C5. -C-NH2

ether
amine

Most basic organic compounds: hydrocarbons

Hydrocarbons contain only the elements C and H. They are all non-polar. They are classified by the types of C/C bonds they contain:

1. C-C single bonds only

2. C=C double bonds 3. CC triple bonds

alkanes
alkenes alkynes

4. Alternating double and single aromatic

Examples
Alkane: CH3CH2CH2CH2CH3

Alkene: CH2=CHCH2CH2CH3 or
Alkyne: CHC-CH2CH2CH3 or Aromatic:

Hydrocarbon Nomenclature
PREFIX + ROOT + SUFFIX

Roots
methethpropbutpenthexheptoct-

Number of C atoms
1 2 3 4 5 6 7

Note that beginning with 5 Cs, the roots are numerical

8
9 10

nondec-

Rules for Naming Alkanes

Note that alkanes contain only single bonds and have the generalized formula CnH2n+2

Rules for Naming Organic Compounds

Alkane Nomenclature Examples

Suggest appropriate names for the following:

CH3
CH3CHCH2CH2CH3

Br
CH3CHCHCH2CH3 CH3

CH3

Cl

CH2CH3 CH3

CH3

CH3CHCH2CHCHCH3

CH3CH2CHCHCH2CHCH3 Br

Alkane Nomenclature Examples (II)

Suggest appropriate names for the following:

CH3
CH3CHCH2CH2CH3 2-methylpentane CH3 Cl

Br
CH3CHCHCH2CH3 CH3 2-bromo-3-methylpentane CH2CH3 CH3

CH3CHCH2CHCHCH3
CH3 4-chloro-2,5-dimethylhexane

CH3CH2CHCHCH2CHCH3
Br 4-bromo-5-ethyl-2-methylheptane

Alkane Nomenclature (III)

Suggest reasonable structures for the following names:

5-bromo-2,2-dimethyloctane

3-ethyl-2,3,4-trimethylhexane

Alkane Nomenclature (IV)

Suggest reasonable structures for the following names:

5-bromo-2,2-dimethyloctane

4-ethyl-2,3,5-trimethylheptane

CH3

Br

CH3

CH2H3

CH3CCH2CH2CHCH2CH2CH3 CH3

CH3 CH CH CH CH CH2 CH3 CH3 CH3

Cycloalkane Representations
cyclopropane
H C H C H C H H H

cyclobutane
H H C H C H H C H C H H

Cycloalkanes
Cycloalkanes contain rings, and have the generalized formula: CnH2n Cycloalkanes are usually represented by polygons, as shown below:

Cyclopropane

Cyclobutane

Cyclopentane

Cyclohexane

Cycloalkane Nomenclature
When only one substituent is on the ring, numbering is not necessary. Cl

Chlorocyclohexane

When two or more substituents are present, the substituent that is first alphabetically is assumed to be on carbon one, and the others are numbered, clockwise or counter-clockwise to give the smallest number arrangement.

CH3

1-chloro-3-methylcyclopentane
Cl Cl

Alkenes
Alkenes contain at least one double bond. Their molecular formula is CnH2n

The double-bonded carbons have trigonal planar geometries.

An expanded structure for ethene, the simplest alkene, is shown below:

C
H

C
H
121.7o

116.6o

Alkenes (II)
Note that there is no rotation around a double bond, in contrast to single bonds. This factor leads to the possibility of cis-trans, or geometric, isomerism. When atoms are bonded to double-bonded carbons, they are constrained to remain in the same position. For example, two kinds of 2-butene exist as is shown below:

CH3
C H
cis-2-butene

CH3
C H

CH3
C H C

H
CH3
trans-2-butene

CH3 groups are cis, or same side of double bond

CH3 groups are trans, or opposite one another

Alkene Nomenclature
The double bond plays a prominent role in alkene nomenclature. Despite whatever else is present, the carbon chain is numbered from whichever end is closest to the double bond. When a double bond is present, the name ending is changed from -ane to -ene.

Alkene Nomenclature (II)

Example 1:

CH3
C H C

CH2CH3
H

This compound is called 2-pentene, or more correctly, cis-2-pentene, since the continuing carbon chains are situated on the same side of the double bond. Generally, if sufficient structure information is provided, you should assign a cis or trans designation to the name

Alkene Nomenclature (III)

Other rules we have learned also apply to alkenes, except that the double bond dictates the direction of chain numbering. For example:

CH3CH2

C
H

Br

CH2CHCH3
trans-6-bromo-3-heptene

Note that the double bond determines chain numbering, not the bromo group.

Alkene Nomenclature (IV)

Provide a complete, correct name for the following:

Br CH3 C H C H CH2CCH3 CH3

Alkene Nomenclature (IV)

Provide a complete, correct name for the following:

Br CH3 C H C H CH2CCH3 CH3

cis-5-bromo-5-methyl-2-hexene

Cycloalkenes
Cycloalkenes, which have a molecular formula of CnH2n-2, share many characteristics of alkenes, however, in order to form rings, the double bond generally must be in the cis form. When naming a cycloalkene, it is understood that the doublebonded carbons are numbered 1 and 2. Examples:

Cyclohexene

3methylcyclohexene
CH33 CH

Alkynes
Hydrocarbons containing a triple bond are called alkynes, and have molecular formulas of CnH2n-2. The triple bonded carbons exhibit linear geometries, with bond angles of 180o. This geometry prevents them from forming rings. Nomenclature for alkynes is completely analogous to the method for alkenes.

Aromatic Hydrocarbons
Aromatic hydrocarbons are ring structures with multiple double bonds. The double bonds are conjugated, alternating double and single bonds. Aromatic hydrocarbons have molecular formulas approaching CnHn. These structures are planar, with all ring carbons exhibiting a trigonal planar geometry, and a high degree of resonance. A number of aromatics are notorious carcinogens

Aromatic Nomenclature
CH CH 33 OH OH COOH OH

OH

NH2 NH 2

Benzene

Aniline

Toluene

Phenol

Benzoic Acid

Aromatic Nomenclature (II)

Nomenclature for aromatics is performed much like other cyclic compounds.

If only one substituent is present, numbering is unnecessary

If one of the common names, such as phenol, is used, it is understood that the substituent is on carbon 1. Other substituents present are numbered or given a special designation used in aromatic chemistry. In general, substituents are numbered by counting clockwise or counterclockwise to produce the lowest numbering pattern.

Aromatic Nomenclature (II)

Nomenclature for aromatics is performed much like other cyclic compounds. If only one substituent is present, numbering is unnecessary If one of the common names, such as phenol, is used, it is understood that the substituent is on carbon 1. Other substituents present are either numbered or given a special designation used in aromatic chemistry. 1-2 substitution is called ortho 1-3 substitution is called meta 1-4 substitution is called para

Aromatic Nomenclature (III)

Examples:
NH2 CH33 CH OH OH
CH CH 33

Cl

Br Br

CH33 CH 2,4-dimethylphenol

3-chloroaniline or meta-chloroaniline

4-bromotoluene or para-bromotoluene

Hydrocarbon Chemistry
Hydrocarbons are generally derived from natural sources, particularly petroleum. The most plentiful compounds in petroleum are alkanes. A number of reactions can be used to convert one type of hydrocarbon into another. Organic compounds are much more reactive when heteroatoms, N and O, are present.

Alkanes
Alkanes are generally considered to be unreactive. They are commonly combusted as gasoline, diesel, kerosene, etc. They can also be reacted with the halogens, e.g. Cl2 and Br2, to form halogenated forms. The halogenated forms can be used to produce other compounds.

Alkenes
The double bond in alkenes makes them much more reactive than alkanes. The pi electrons in the double bond are relatively loosely held, and the double bond is subject to attack by substances attracted to negative charge (electrophiles). Generally, substances are added to the doubly bonded carbons, and the double bond is lost. Ethylene and propylene are heavily used to produce polymers polyethylene and polypropylene.

Alkynes
Alkynes have two pi bonds, and react much like alkenes, except that stoichiometrically they tend to react twice as much. The most common alkyne, acetylene, is capable of participating in unusual reactions with strong bases, and it combusts at very high temperature, which makes it ideal for welding torches.

Aromatic Compounds
Although aromatic compounds contain double bonds, they do not react like alkenes, because the loss of double bonds would eliminate their stabilizing resonance. Instead, aromatic compounds tend to undergo substitution reactions, where other substances replace hydrogen atoms on the ring carbons. A number of aromatic hydrocarbons are produced as pollutants when other hydrocarbons are burned.

Functional Groups
When organic compounds contain elements other than carbon, called heteroatoms, such as oxygen and nitrogen, the structural units containing the heteroatoms are called functional groups. These functional groups add unique chemical characteristics to the compound, which makes them very important in biological applications.

Alcohols
When a carbon atom is bonded to an -O-H group, often designated as R-O-H, where R is used as a general designation for a carbon group, the molecule is called an alcohol. The -OH group is very polar, and most small alcohols have high boiling points and good water solubility. Besides simple alcohols, alcohols are found biologically in carbohydrates and various metabolites.

Alcohol Nomenclature
Alcohols often have common trivial names, but IUPAC nomenclature rules suggest that the alcohol name contain the -ol suffix. The alcohol group is considered higher priority than any carbon-containing group, and the chain should be numbered from whichever end is closest to the alcohol group. Other groups are named and numbered as shown previously

Alcohol Nomenclature (II)

Examples:
CH3CH2-OH
Cl OH 4-chloro-2-pentanol Ethyl alcohol (trivial name) Ethanol (IUPAC name)

CH3CHCH2CHCH3 Br CH3 OH CH2CH2CHCH2CHCH3 OH

6-bromo-4-methyl-2-hexanol

3-methylcyclohexanol CH3

Ethers
Another oxygen-containing functional group is the ether. The ether group, sometimes designated as R1-O-R2, contains an oxygen bridge between two carbon atoms. Ethers, unlike alcohols, do not participate in hydrogen bonds, and are not considered polar. Ethers, which are important medical and industrial chemicals, are not commonly found naturally in biological systems.

Ether Nomenclature
Although IUPAC recommends a method for naming ethers, we will only focus on a trivial method that is in common use. With this method, the two carboncontaining groups connected by the oxygen are listed alphabetically, followed by the name ether.

Ether Nomenclature (II)

Examples:
CH3-O-CH2CH3 O CH3 Ethyl methyl ether

Cyclohexyl methyl ether

CH3CH2-O-CH2CH3

Diethyl ether

Diethyl ether was used for years as an anesthetic until it was replaced due to safety considerations.

Carbonyl Groups
The carbonyl group contains a carbonoxygen double bond. This functional group can be found in the interior of a carbon chain, where it is called a ketone, or on a terminal carbon, where it called an aldehyde. A commonly used representations of ketones and aldehydes look as follows:
O || R1-C-R2 Ketone O || R-C-H or Aldehyde RCHO

Carbonyl Groups (II)

Carbonyl groups, particularly aldehydes, are very reactive, and appear in many biological compounds. Like alcohols, carbonyl groups are found in carbohydrates, and they are observed during many metabolic processes These compounds are moderately polar, and the smaller ketones and aldehydes are water soluble. A number of ketones have common names, such as acetone and methyl ethyl ketone (MEK), and are widely used industrial solvents.

Ketone Nomenclature
When a ketone is present in a compound, it is considered higher priority than anything discussed thus far, and the chain is numbered from whichever end is closest to the ketone. If an alcohol is also present, it is given a number and is called a hydroxy group. When a ketone is present, the suffix for the name is changed to -one.

Ketone Nomenclature (II)

Examples:
O || CH3CCH3 O || CH3CCH2CH3

Acetone (trivial name)

2-propanone (IUPAC name)

Methyl ethyl ketone (trivial name)

2-butanone (IUPAC name)

O OH || | CH3CHCCH2CHCH3 | CH3

5-hydroxy-2-methyl-3-hexanone

Aldehyde Nomenclature
When an aldehyde is present in a compound, it is considered higher priority than anything discussed thus far, and the chain is numbered from aldehyde end. The aldhyde group is understood to be on the terminal carbon, so it needs no number. If ketones are also present, they are called oxo groups and are given a number. When an aldehyde is present, the suffix of the name is changed to -al. Remember, aldehydes can be represented as:
O || R-C-H or RCHO

Aldehyde Nomenclature (II)

Examples:
O || CH3C-H O || CH3CCH2CHO Formaldehyde (trivial name)

Methanal (IUPAC name)

3-oxobutanal

O OH || | CH3CHCCH2CHCHO | Cl

5-chloro-2-hydroxy-4-oxohexanal

Carboxylic Acids
Carboxylic acids have the generalized formula:
O || R-C-OH

or RCOOH

The carboxyl name is a contraction of carbonyl and hydroxyl group names, which are both present. The hydrogen on the hydroxyl group is acidic, and carboxylic acids are notable for their acidic behavior. Carboxylic acids are found in many biological compounds, most notably amino acids.

Carboxylic Acid Nomenclature

The carboxylic acid structure requires that this functional group be on a terminal carbon. The carboxyl group has higher priority than any other functional group, and if it is present, it is understood to be on carbon number 1, and the chain is numbered away from it. Other groups present are numbered appropriately, and the names suffix is changed to -oic, followed by the word acid. There are many trivial names, such as acetic acid that are commonly used.

Carboxylic Acid Nomenclature (II)

Examples:
O || CH3C-OH OH | CH2CH2CH2COOH Acetic acid (trivial name)

Ethanoic acid (IUPAC name)

Gamma-hydroxybutyric acid or GHB (trivial name) 4-hydroxybutanoic acid

Cl CH3 | | CH3CHCCH2CHCOOH | Cl

4,5-dichloro-2-methylhexanoic acid

Amines
Amines act as bases in organic chemistry. They contain the amino functional group: R-NH2 These compounds are notable for their basic nature and strong odors. Nitrogen-containing compounds, or amines, are found in a variety of biological compounds including amino acids and nucleic acids.

Amine Nomenclature
Amines are commonly named by referring to the alkyl group attached to them, followed by the word amine.

In IUPAC, or systematic, nomenclature, the amine is numbered from which ever end of the chain is closest.
The final e of the name is replaced by the suffix -amine.

If a higher priority group is present, the amine is called an amino group and given a number. All of the oxygencontaining functional groups are considered higher priority.
Finally, though we wont cover them, amines exist where more than one carbon group is attached to the nitrogen atom.

Amine Nomenclature (II)

Examples:
NH2 | CH3CHCH3 NH2 | CH3CHCH2CH2-OH Isopropyl amine (trivial name) 2-propanamine (IUPAC name)

3-amino-1-butanol

NH2 | CH3CHCOOH

Alanine (amino acid) 2-aminopropanoic acid