Unit 2 – Biological

molecules
Functional groups
• The structural features that make it possible to classify compounds
into families are called functional groups.

• A functional group is a group of atoms within a molecule that has a

characteristic chemical behaviour.

• Chemically, a given functional group behaves in nearly the same way

in every molecule it’s a part of

The chemistry of every organic molecule, regardless of size and

complexity, is determined by the functional groups it contains
Functional Groups with Carbon–Carbon Multiple Bonds
• Alkenes, alkynes, and arenes

• Alkenes have a double bond, alkynes have a triple bond, and arenes
have alternating double and single bonds in a six-membered ring of
carbon atoms
Functional groups with carbon singly bonded to an electronegative atom

Alkyl halides (haloalkanes), alcohols, ethers, alkyl phosphates, amines, thiols, sulfides, and
disulfides

• Haloalkanes: C bonded to halogen (-X)

• Alcohols: C bonded to the oxygen of a hydroxyl group (-OH)
• Ethers: 2C bonded to the same oxygen
• Organophosphates: C bonded to the oxygen of a phosphate group (-OPO 32-)
• Amines:C bonded to a N
• Thiols: C bonded to the S of an -SH group
• Sulfides: 2C bonded to the same S
• Disulfides: C bonded to 2 S that are joined together
In all cases, the bonds are polar, with the carbon atom bearing a partial positive
charge (𝛿+) and the electronegative atom bearing a partial negative charge ( 𝛿-).
Functional groups with a carbon–oxygen double bond (carbonyl groups)

Carbonyl groups (C=O) are present in a large majority of organic compounds and in practically
all biological molecules
These compounds behave similarly in many respects but differ depending on the identity of
the atoms bonded to the carbonyl-group carbon

• Aldehydes: have at least one H bonded to the C=O

• Ketones: have two C bonded to the C=O
• Carboxylic acids: have an -OH group bonded to the C=O
• Esters: have an ether-like O bonded to the C=O
• Thioesters: have a sulfide-like S bonded to the C=O
• Amides: have an amine-like N bonded to the C=O
• Acid chlorides: have a Cl bonded to the C=O
The carbonyl carbon atom bears a partial positive charge (𝛿+),
and the oxygen bears a partial negative charge (𝛿-).
Alkanes
• Saturated hydrocarbons:
• hydrocarbons because they contain only carbon and hydrogen
• saturated because they have only C-C and C-H single bonds and thus contain
the maximum possible number of hydrogens per carbon.
• They have the general formula CnH2n+2, where n is an integer.
Alkanes
• When larger numbers of
carbons and hydrogens
combine, more than one
structure is possible

C4H10: the four carbons can

all be in a row (butane), or
they can branch (isobutane)
 Alkanes

Isomers: two compounds with the

same formula but different
structure
• Constitutionl isomers: atoms are
the same, formula is the same but
arranged differently
Straight-chain alkane Branched-chain alkane
Alkanes - isomers
 Alkanes - names

Straight-chain alkanes are named according to the number of carbon atoms

they contain, with the exception of the first four compounds—methane,
ethane, propane, and butane

The suffix -ane is added to the end of each name to indicate that the molecule
identified is an alkane.
Alkanes - names
Alkanes
Alkanes
Alkanes
 Alkyl groups
Alkyl groups are partial structures, not stable alone. They are part of a more
complex structure
Example: methane (-CH4) minus one –H, gives a methyl group (-CH3)
 Alkyl groups

Just as straight-chain alkyl groups are generated by removing a hydrogen from an end
carbon, branched alkyl groups are generated by removing a hydrogen atom from an internal
carbon.
Primary, secondary..
 Primary, secondary..
• The prefixes sec- (for secondary) and tert- (for tertiary) used for the C4 alkyl
groups refer to the number of other carbon atoms attached to the branching
carbon atom.
• There are four possibilities: primary (1º), secondary (2º), tertiary (3º), and
quaternary (4º).
 Primary, secondary..

• “Citric acid is a tertiary alcohol”: it has an alcohol functional group (-OH)

bonded to a carbon atom that is itself bonded to three other carbons.
 Primary, secondary..
• We also speak about hydrogen atoms as being primary, secondary, or
tertiary.
• Primary hydrogen atoms are attached to primary carbons (RCH3)
• Secondary hydrogens are attached to secondary carbons (R2CH2)
• Tertiary hydrogens are attached to tertiary carbons (R3CH)
There is, of course no such thing as a quaternary hydrogen. Why not?
Primary, secondary..
 Properties of alkanes

Alkanes are sometimes referred to as paraffins, a word derived from the

Latin parum affinis, meaning “little affinity.”

Show little chemical affinity for other substances, are chemically inert to
most laboratory reagents and do not engage in chemical reactions.
 Properties of alkanes
Alkanes show regular increases in both boiling point and melting point as
molecular weight increases, an effect due to the presence of weak
dispersion forces between molecules.
 Conformations of Ethane
Stereochemistry is the branch of chemistry concerned with the three-dimensional
aspects of molecules.

The intersection of a plane cutting through a carbon–carbon single-bond orbital

looks like a circle. Because of this cylindrical symmetry, rotation is possible around
carbon–carbon bonds in open-chain molecules.
 Conformations of Ethane
In ethane, for instance, rotation around the C-C bond occurs freely, constantly
changing the spatial relationships between the hydrogens on one carbon and
those on the other.

The different arrangements of atoms that result from bond rotation are called
conformations, and molecules that have different arrangements are called
conformational isomers
H H
 Conformations of Ethane
Conformational isomers are represented in two ways
1. A sawhorse representation: views the C-C bond from an oblique angle and
indicates spatial orientation by showing all C-H bonds.
2. A Newman projection views the C-C bond directly end-on and represents the
two carbon atoms by a circle. Bonds attached to the front carbon are represented
by lines to the center of the circle, and bonds attached to the rear carbon
are represented by lines to the edge of the circle.
 Conformations of Ethane
HOWEVER: experiments show that there is a small (12 kJ/mol; 2.9 kcal/mol)
barrier to rotation (torsion strain) and that some conformations are more stable
than others.
The lowest energy, most stable conformation is the one in which all six C-H bonds
are as far away from one another as possible—staggered when viewed end-on in
a Newman projection.
 Conformations of Ethane
The highest-energy, least stable conformation is the one in which the six C-H
bonds are as close as possible—eclipsed in a Newman projection.

At any given instant, about 99% of ethane molecules have an approximately

staggered conformation and only about 1% are near the eclipsed conformation.
Conformations of Ethane
 Conformations of Ethane

A graph of potential energy

versus bond rotation in
ethane. The staggered
conformations are 12 kJ/mol
lower in energy than the
eclipsed conformations.
 Conformations of Propane
Propane also has a torsional barrier that results in hindered rotation around the C–C bonds.
The barrier is slightly higher in propane than in ethane—a total of 14 kJ/mol (3.4 kcal/mol)
versus 12 kJ/mol.

The eclipsed conformation of propane has three interactions—two ethane type H–H
interactions and one additional H–CH3 interaction. Since each eclipsing H ←→ H interaction is
the same as that in ethane and thus has an energy “cost” of 4.0 kJ/mol, we can assign a value
of 14-(2x4.0)=6.0 kJ/mol (1.4 kcal/mol) to the eclipsing H ←→ CH3 interaction
 Conformations of Butane
In butane the lowest-energy arrangement, called the anti conformation, is the one in which
the two CH3 groups are as far apart as possible—180° away from each other.

As rotation around the C2-C3 bond occurs, an eclipsed conformation is reached in which there
are two CH3 ←→ H interactions and one H ←→ H interaction. Using the energy values derived
previously from ethane and propane, this eclipsed conformation is more strained than the anti
conformation by 2x6.0 kJ/mol+4.0 kJ/mol (two CH3 ←→ H interactions plus one H ←→ H
interaction), for a total of 16 kJ/mol (3.8 kcal/mol).
 Conformations of Butane
As bond rotation continues, an energy minimum is reached at the staggered conformation
where the CH3 groups are 60°.

The gauche conformation lies 3.8 kJ/mol (0.9 kcal/mol) higher in energy than the anti
conformation even though it has no eclipsing interactions. This energy difference occurs
because the H atoms of the CH3 groups are near one another in the gauche conformation,
resulting in what is called steric strain.
 Steric strain
Steric strain is the repulsive interaction that occurs when atoms are forced
closer together than their atomic radii allow. It’s the result of trying to force
two atoms to occupy the same space.
 Steric strain
As the dihedral angle between the CH3 groups approaches 0°, an energy
maximum is reached at a second eclipsed conformation. Because the CH3
groups are forced even closer together than in the gauche conformation, both
torsional strain and steric strain are present.

A total strain energy of 19 kJ/mol (4.5 kcal/mol) has been estimated for this
conformation, making it possible to calculate a value of 11 kJ/mol (2.6
kcal/mol) for the CH3 ←→ CH3 eclipsing interaction:

total strain of 19 kJ/mol - the strain of two H ←→ H eclipsing interactions

(2x4.0 kcal/mol) equals 11 kJ/mol.
 Steric strain

After 0°, the rotation becomes a mirror image: another gauche conformation is
reached, another eclipsed conformation, and finally a return to the anti
conformation.
 Steric strain

A plot of potential energy

versus rotation for the C2-C3
bond in butane.

The energy maximum occurs

when the two methyl groups
eclipse each other, and the
energy minimum occurs
when the two methyl groups
are 180° apart (anti).
Steric strain
 Steric strain
The most favorable conformation for any alkane has the C–C bonds in
staggered arrangements, with large substituents arranged anti to one another.
Steric strain
 Steric strain
HOWEVER: saying that one particular conformer is “more stable” than another
doesn’t mean the molecule adopts and maintains only the more stable
conformation.

At room temperature, rotations around s bonds occur so rapidly that all

conformers are in equilibrium. At any given instant, however, a larger
percentage of molecules will be found in a more stable conformation than in a
less stable one.
Steric strain
 Summary
A functional group is a group of atoms within a larger molecule that has a
characteristic chemical reactivity. Because functional groups behave in
approximately the same way in all molecules where they occur, the chemical
reactions of an organic molecule are largely determined by its functional groups.

Alkanes are a class of saturated hydrocarbons with the general formula CnH2n+2.
They contain no functional groups, are relatively inert, and can be either straight-
chain (normal) or branched.

Alkanes are named by a series of IUPAC rules of nomenclature (not shown).

 Summary
Compounds that have the same chemical formula but different structures are called isomers.
Compounds such as butane and isobutane, which differ in their connections between atoms,
are called constitutional isomers.

Rotation is possible around C–C single bonds in alkanes because of their cylindrical symmetry,
and alkanes therefore exist in a large number of rapidly interconverting conformations.

Newman projections make it possible to visualize the spatial consequences of bond rotation by
sighting directly along a C–C bond axis. Not all alkane conformations are equally stable.

The staggered conformation of ethane is 12 kJ/mol (2.9 kcal/mol) more stable than the
eclipsed conformation because of torsional strain. In general, any alkane is most stable when
all its bonds are staggered.
Exercises

Work in pairs and solve the following exercises. Each student

should have its own copy of the work and hand it in.

This work will have a numerical score that will be included in the
final mark of the term.
Exercises
Exercises
Exercises
Exercises
Exercises