CH339K

Lecture 2

Bonding

• Covalent• Ionic• Dipole Interactions• Van der Waals Forces• Hydrogen Bonds

Covalent Bonds

• Electrons form new orbitals around multiple atomic nuclei

• Bond energy results from electrostatic force between redefined electron cloud and nuclei

• Strong – typically 150 – 400 kJ/mol

Ionic Interactions

• Energy from non-directional force between ions• Biomolecules frequently have large numbers of charged groups• Charge-charge interactions stabilize intra- and intermolecular

structures• Coulomb’s Law:

• Energy drops off as function of distance between charges

r

qqk U 21

Dipoles• Fixed dipoles

– Molecules with asymmetric charge distributions form dipoles

• Induced Dipoles– One dipole can induce a charge in an adjacent molecule

NH3+

CH2 C O-

O

NH3+

CH2 C O-

O

van der Waals Interactions• Technically, all induced dipole interactions are van

der Waals interactions• Biochemists usually mean induced dipole-induced

dipole (London Dispersion) forces• Any atom will have an uneven distribution of charge

at any given instant

Van der Waals (cont.)• That temporary dipole will induce a dipole in

adjacent atoms• This results in a net attractive force between

atoms

• Force is weak - .5 to 2 kJ/mol• Net biochemical effect – molecules that FIT

together STICK together.

Van der Waals (cont.)

• If you live in Central Texas, you see van der Waals forces in action every summer night:

Hydrogen Bonds

• Hydrogen Bonds form between– A hydrogen covalently bound to an electronegative

atom

– Another electronegative atom

Hydrogen Bonds (cont.)

• The group to which the hydrogen is covalently bound is the donor.

• The other group is the acceptor.• Donors:

– -OH, -NH2, -SH (lesser donor)

• Acceptors– -N:, =O:, -O:

Hydrogen Bonds (cont.)

• Hydrogen bonds are not just electrostatic – partially covalent

• Therefore, they are directional• Intermdiate strength: 5 – 10 kJ/mol

Water Structure

Water Forms Clusters in Solution

Hydrophobic Effect

Water

• Water– Has a high specific heat– Has a high heat of vaporization– Is an excellent solvent for polar materials– Is a powerful dielectric– Readily forms hydrogen bonds– Has a strong surface tension– Is less dense when it freezes (i.e. ice floats)

Acids and Bases

• Definitions– Arrhenius

– Bronsted-Lowry

– Lewis

Conjugate Pairs• Every acid has its conjugate base• Every base has its conjugate acid

Conjugate Acid Conjugate Base

H3C - COOH H3C-COO-

NH4+ NH3

Acids and bases: pH• Water ionizes

Typical pH Values

Substance pH

Stomach acid 1.5 - 2.5

Coca-cola 2.5

Human saliva 6.5

Human blood 7.5

Human urine 5 - 8

Oven cleaner 14

Acids and Bases• Water thus acts as both a weak acid and a

weak base• (A Strong acid is one that dissociates

completely in water; a weak acid is one that doesn’t.)

• All biochemically significant acids and bases are weak (except for HCl – stomach acid)

Acids and Bases

• Just like water, a weak acid has an ion product, the Ka• For the weak acid HA:

• ThereforeO]HA][H[

]A][[H Keq

2

-

[HA]

]][A[H Ka

-

Acids and Bases• Ka’s for weak acids range over several

orders of magnitude• They are generally small• More convenient to define

pKa = -log Ka

• Just like pH = -log[H+]

Typcal Ka’s and pKa’s

Acid Ka pKa

Acetic 1.8 x 10-5 4.74

Formic 1.7 x 10-4 3.77

Benzoic 6.5 x 10-5 4.19

Carbonic 4.3 x 10-7 6.37

Imidazole 2.8 x 10-7 6.55

Phenol 1.3 x 10-10 9.89

pH for Strong Acids

• Since a strong acid dissociates completely:pH = -log([Acid])

• For a 0.1 M (100 mM) solution of HCl,

pH = -log(0.1) = 1

pH for Weak Acids

• What’s the pH of a 100 mM solution of Acetic Acid?

])[H- (0.1M

][H

CCOOH][H

]CCOO][H[H101.8

2

3

35

0](0.1)[K][HK][H aa2

2

4(0.1)KKK][H a

2aa

[H+] = 0.00134 M

Shortcut

• The quadratic solution is a pain, but we can approxmate:

(0.1)K[HAc]K][H aa

[H+] = 0.00134 M

Titrating a Strong Acid

• 10 ml of an HCL sln• Titrate with 0.5 M NaOH

• OH- + H+ –> H2O

• Takes 8.5 ml NaOH to bring solution to neutrality

Titration of Strong Acid

0

2

4

6

8

10

12

14

0 5 10 15 20

NaOH added (ml)

pH

1

2212211 V

CV Cor CVCV

M 0.425L 0.010

M 0.5 L 0.0085C1

Titrating a Weak Acid• Titrating .1 M Hac• Initial pH is 2.88 instead

of 1• Little change until large

amounts of NaOH have been added

• Buffering effect• Caused by equilibrium

that exists between a weak acid and conjugate base.

Titration of Weak Acid

0

1

2

3

4

5

6

7

8

0 5 10 15 20 25

NaOH added (ml)

pH

Henderson-Hasselbach Equation

[HA]

][AlogpKpH

log[HA]]log[ApKpH

pKlog[HA]]log[A]log[H

pK[HA]

]][A[Hlog

K[HA]

]][A[H

a

a

a

a

a

Predicting pH

• Let’s make 1 liter of a solution that is 0.1 M in acetic acid ( pKa = 4.74 ) and 0.3 M in sodium acetate.

[HA]

][AlogpKpH a

0.1

0.3log4.76pH

5.24pH

Buffering Effect

• Addition of significant amounts of acid or base changes the ratio of conjugate base to conjugate acid

• pH changes as the log of that ratio• Result is resistance to pH change in a

buffered solution