(13) session 13 molecular representations & nomenclature

3/2/2012

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Session 13

Organic Chemistry, UNAM School of Medicine1

Molecular Representations &

Nomenclature

Dr L.H.A. Prins (Ph.D.)

Dept. of Pharmacy

UNAM

Learning Outcomes

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� By the end of this session, the student should be able to:

�Understand different molecular representations of organic

molecules.

�Draw line-bond structures (Kekulé structures) from Lewis

structures (and vice versa).

�Define functional groups & understand their importance.

�Understand the IUPAC system for naming organic molecules.

Organic Chemistry, UNAM School of Medicine

3/2/2012

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Importance?

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� Line-bond structures are used throughout organic

chemistry to represent different organic molecules. The ability to

draw these is therefore very important!!

� Functional groups are important in determining the chemical

reactivity, physical properties, nomenclature, etc. of organic

molecules.

� IUPAC nomenclature ensures that every compound has only one

name & every name corresponds to only one structure of molecules.

This is to avoid more than one interpretation of a specific

name.Organic Chemistry, UNAM School of Medicine

Molecular representations

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� Organic molecules are represented by different methods.

� Representation methods include:


• Lewis structure

• Condensed structure

Omit bond lines (single bonds) & lone pairs

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5 Organic Chemistry, UNAM School of Medicine

• Empirical formula C2H5

• Molecular formula C4H10

Molecular formula always written in order: CHONX

X = F, Cl, Br, I

• Line-bond structure ??

=

2 bonds2 hydrogens inferred

1 bond3 hydrogens inferred



• Alexander/wedge representation

• Sawhorse representation (for stereochemisty of alkanes)

• Newman projection (for stereochemisty of alkanes)

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NB!!NB!!NB!!NB!! Condensed structures


Use parentheses (brackets) for repeating groups!

NB!!NB!!NB!!NB!! Condensed structures


Heteroatoms = Those atoms that are not C or H.

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Drawing line-bond structures

(Kekulé structures)

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Guidelines:

1. Omit all hydrogen atoms except for functional group H atoms

2.All other atoms must always be shown

3. Show all C-C bonds as solid lines (C=C bonds as 2 solid lines, etc.)

4. Lone pairs do not always have to be shown

5. Formal charges must always be shown

6.Three-dimensional geometry does not always have to be shown

7. End of a line is a terminal carbon

8. Interior carbon atoms are bends in the line




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Examples:

Draw line-bond structure for following Lewis structure:


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Examples:

Draw line-bond structure for following Lewis structure:




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Examples:

Draw Lewis structure for following line-bond structure:


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Functional groups (FG)

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� Functional group:An atom or group of atoms within a molecule that shows a characteristic set of predictable physical and chemical properties

� Functional groups are important for three reasons, they are

� the units by which we divide organic compounds into classes

� the sites of characteristic chemical reactions

� the basis for naming organic compounds




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Highest priority

Lower priority

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Higher priority

Lowest priority

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� Some important notes:� Degree of substitutionCarbon

Alcohol

Primary Secondary Tertiary Quaternary

C OH

H

H

C C OH

C

H

C C OH

C

C

C

Primary Secondary Tertiary

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� Degree of substitution

Nitrogen(Amines)

� R groupR = Alkyl group or carbon chainAlkyl = Hydrocarbon group with one H less than corresponding alkane,

ex. methyl, ethyl, propyl, etc.

Primary Secondary Tertiary

Naming organic molecules

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� IUPAC nomenclature system (abbreviated version):

1. FG provides suffix name (“ane”,“one”, “ol”, “thiol”, etc.)2. Two or more FG’s – FG with highest priority provides suffix

name3. Longest C chain containing FG provides stem name

1 meth- 7 hept-2 eth- 8 oct-3 prop- 9 non-4 but- 10 dec-5 pent- 11 undec-6 hex- 12 dodec-


If C chain is cyclic –“cyclo-” is added as prefix.

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4. Number longest C chain (left to right or right to left) so that

FG/multiple bond/longest side chain (branch) is on the lowest

numbered C possible

5. Name each side group, but change the ending to “-yl”

6. Use a prefix “di-, tri-, tetra-”, etc. to denote how many side

groups of each length are present



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7. Before naming the side group, give the number of the C to

which the side group is attached

8. When identical side groups are on the same C, repeat the

number of this carbon in the name (e.g. 2,2-dimethylhexane)

9. Arrange the side groups in alphabetical order ignoring the

prefixes “di-,tri-, tetra-” etc.


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Examples:


2,4-dimethyldecane

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2

3,3-dimethylhexane3

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Examples:


2,2,4-trimethylpentane4

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4-ethyl-3,3-dimethyl-4-propyl-decane4 10

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Thank you

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END


(13) session 13 molecular representations & nomenclature

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