chemistry 2500 topic #2: isomers and naming organic molecules spring 2011 dr. susan lait

CHEMISTRY 2500

Topic #2: Isomers and Naming Organic MoleculesSpring 2011

Dr. Susan Lait

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Isomers

What happens when an organic molecule is simply described by its molecular formula? In a few cases, the molecular formula gives enough

information. Draw:CH4 C2H6

C3H8 CH4O

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Isomers

Usually, molecular formula is not enough. Draw:C4H10

C5H12

For practice, draw each of the molecules’ structural formula then convert it to line-bond notation.

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Isomers

Molecules which have the same molecular formula but different connectivity are referred to as constitutional isomers. Constitutional isomers often behave differently due to their different shapes. In some cases, they even have different functional groups!

Draw all of the constitutional isomers for C3H8O, and identify the functional group in each molecule.

For practice, draw each of the molecules’ structural formula then convert it to line-bond notation.

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Isomers

Now we will add just one carbon atom… Draw all of the constitutional isomers for C4H8O.

If you Google this question, you’ll find websites telling you there are 1, 5 or 15 structures. They’re wrong. Be very careful asking the Internet for homework help…Please don’t actually do this before class; you’ll spoil the learning experience.

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Isomers

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Nomenclature (Naming Organic Molecules)

When you have to draw a lot of isomers, one way to be sure that no two are the same is to name them all. If the names are different, the isomers are different. If the names are the same, you drew the same thing twice.

Nomenclature also makes it easier for us to talk about organic chemistry in situations where we can’t just draw the molecules.

The rules for organic nomenclature are the same as those you learned in CHEM 2000 (see next page); however, we will now deal with a few more functional groups, a few more different kinds of substituents and molecules which contain more than one kind of functional group.

For those who have not taken (or do not recall) CHEM 2000, nomenclature is described in detail in Sorrell pages 8-18. You are responsible for this information.

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Organic Nomenclature (CHEM 2000 Rules)

To name an organic molecule, work back-to-front: Find the principal functional group. Find the longest chain (or ring) including the principal

functional group and all double/triple bonds. Number the chain starting at whichever end gives the

principal functional group the lower number. (For a ring, start numbering at the principal functional group.)

Name the principal functional group, numbering if necessary.

Name the main chain (or ring), numbering the C=C or CC bonds if necessary. If this gives a name in which the next letter after the ‘e’ of ‘ane’, ‘ene’ or ‘yne’ is a vowel, drop the ‘e’.

Name and number the substituents on the main chain. If a substituent appears more than once, use a prefix to indicate how many there are and include a number for each appearance. List the substituents in alphabetical order (not counting prefixes) followed by the main chain (or ring) name.

Finally, add cis- or trans- (or E- or Z- or R- or S-) to the front of the name if necessary.

OBr

Br

CH3O1

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45

OBr

Br

CH3O

-2-one

-3-penten-2-one

3,4-dibromo-5-methoxy-3-penten-2-one

trans-3,4-dibromo-5-methoxy-3-penten-2-one

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Organic Nomenclature

Essentially, the name of an organic compound consists of up to four fields, each of which gives specific information about the compound: (diagram from Sorrell, p.9; 3rd field re-named)

Saturation index

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The simplest names only involve the second and third fields which indicate the number of carbon atoms in the main chain (second field) and the number and type of multiple bonds (third field). For example: Hexane has six carbon atoms and no multiple bonds (third

field = “ane”).

Hex-1-ene has a single double bond starting with carbon #1. (also called 1-hexene)

Hex-1-yne has a single triple bond starting with carbon #1. (also called 1-hexyne)

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The following prefixes are used to indicate the length of the main chain/ring:

For rings, add cyclo before the compound root:e.g. cyclopentane cyclopentene

# C Compound root

# C Compound root

1 meth 6 hex

2 eth 7 hept

3 prop 8 oct

4 but 9 non

5 pent 10 dec

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In cases of multiple multiple bonds, use the prefixes di, tri or tetra to indicate how many double (or triple) bonds are in the molecule and give a number for the location of each multiple bond.

hexa-1,3-diene is not the same as hexa-1,5-diene(1,3-hexadiene and 1,5-hexadiene are also acceptable names)

hex-1-en-3-yne is not the same as hex-1-en-5-yne(1-hexen-3-yne and 1-hexen-5-yne are also acceptable names)

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Attaching groups to the chain introduces the first and fourth fields. Halogens are not considered “principal functional groups”

so halogens are treated in the same way as carbon chains branching off the main chain. They are described in the “substituents” section at the beginning of the name. Substituents take last priority when numbering the main chain, so substituting Cl for one of the H in hex-1-ene will not change the numbering:e.g. 5-chlorohex-1-ene (or 5-chloro-1-hexene)

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Alcohols, amines and carbonyl-containing functional groups are considered candidates for “principal functional group”. Since there can only be one kind, use the table on p.16 to determine which.

The principal functional group takes priority when numbering the main chain. As such, substituting OH for one of the H in 5-chlorohex-1-ene may result in a re-numbering:5-chlorohex-1-en-3-ol is correct:

5-chlorohex-1-en-6-ol is NOT. It must be 2-chlorohex-5-en-1-ol:

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If there are multiple functional groups, all those which are not the principal functional group are treated as substitutents.

Aldehydes are higher priority than alcohols, so turning the terminal methyl group in 5-chlorohex-1-en-3-ol into an aldehyde relegates the alcohol (hydroxy group) to substituent status, giving us 2-chloro-4-hydroxyhex-5-enal:

No number is necessary for principal functional groups which must be terminal since they, by definition, include carbon #1. These principal functional groups include:

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Principal functional groups (from highest to lowest priority):

*Esters and amides have two ‘halves’ to be named. For details on naming esters and/or amides, consult your CHEM 2000 notes and/or Sorrell p.702.

Functional Group Suffix

Carboxylic acid -oic acid

Sulfonic acid -sulfonic acid

Ester* -oate

Acid Chloride -oyl chloride

Amide* -amide

Nitrile -nitrile

Aldehyde -al

Ketone -one

Alcohol (including phenol)

-ol

Thiol -thiol

Amine -amine

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Substituents (including functional groups which were lower priority than the principal functional group):

Name Name Name

-CH3 methyl -OCH3 methoxy -F fluoro

-CH2CH3 ethyl -OCH2CH3 ethoxy -Cl chloro

-CH2CH2CH3 propyl -OCH2CH2CH3 propoxy -Br bromo

-CH2CH2CH2CH3

butyl -OCH2CH2CH2CH3

butoxy -I iodo

etc. etc.

-NH2 amino

-CH(CH3)2 isopropyl

-OCH(CH3)2 isopropoxy

-NO2 nitro

-CH2CH(CH3)2 isobutyl -OCH2CH(CH3)2 isobutoxy -CN cyano

-CH(CH3)CH2CH

3

s-butyl -OCH(CH3)CH2CH

3

s-butoxy

-C(CH3)3 t-butyl -OC(CH3)3 t-butoxy -OH hydroxy

-C6H5 phenyl -OC6H5 phenoxy =O oxo

-CH2C6H5 benzyl -OCH2C6H5 benzoxy -SH mercapto

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Other names you should know:

benzene toluene* aniline*

phenol benzaldehyde benzoic acid

CH3NH2

OHHO OHO

* = not official IUPAC name but a very common name that you’re likely to encounter

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And now for some practice… Name the following:

If you’re not yet comfortable with line-bond structures, redraw each of these moleculesas the structural formula first.

O

O

O

H

O

H

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OH

O

Cl

H

O

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SH

O

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Classification of Carbon Atoms

Carbon atoms are often classified according to how many other carbon atoms they are bonded to. In the last example on the previous page, there are examples of primary, secondary, tertiary and quaternary carbon atoms:

These classifications only apply to saturated carbons (no multiple bonds). The carbon atoms that form the benzene ring are described as aryl to indicate that they are part of an aromatic ring. Other carbon atoms from double bonds are classified as alkenyl while those from triple bonds are classified as alkynyl. We will use this terminology throughout the course.

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Classification of Carbon Atoms

Occasionally, we also need to refer to carbon atoms (or other groups) in terms of distance from each other. For this purpose, Greek letters are used. refers to the atom attached to a group is the next atom is the one after that is the one after that is the one after that etc.

In one example, the “group” of interest is a carboxylic acid, and the Greek letters refer to the carbon atoms:

In another example, the “group” of interest is a carbocation, and the Greek letters refer to thehydrogen atoms: CH3

CCH2

CH3

H

+

CH2

CH2

CH2

COH

O

CH3

CH2

CH2

CH2

COH

O

CH3

chemistry 2500 topic #2: isomers and naming organic molecules spring 2011 dr. susan lait

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