Session 3

Tutorial I
1. Calculate the vibration modes of the following molecules?
a. I2 Linear 3×2 −5=1
b. H2O Non-linear 3×3 −6=3
c. CO2 Linear 3×3 −5=4
d. NH3 Non-linear 3×4 −6=6
e. CH3OH Non-linear 3 × 6 − 6 = 12

• A molecule with N atoms has 3N degrees of freedom

• 3 degrees of freedom are for translational motion

• Rotation:

• 3 degrees of freedom if molecule is non-linear

• 2 degrees of freedom if molecule is non-linear

• Therefore, the vibrational degrees of freedom or vibrational modes are:

• 3N-5 for linear molecules

• 3N-6 for non-linear molecules
2. What are van der Waals interactions?

• The van der Waals interactions or van der Waals forces are the
intermolecular interactions/forces. They are of two types:

• London Dispersion forces

• Dipole-dipole forces
3. I want you to prepare one litre of a 1M buffer (any buffer) of pH 9. How
will you go about it?

• As you need to prepare a buffer of pH 9, you need to find an acid with pKa between
8-10.

• The closer it is to the required pH, the better it is.

• N-glycyl-glycine pKa2=8.4
• Histidine pKa2 = 9.17
• Boric acid pKa = 9.24
• Ethanolamine pKa=9.44

• You shall weigh 1 mole of the compound and dissolve it in around 950 ml of water.

• Measure the pH.

• Adjust the pH by using NaOH/KOH if the pH is below 9 or using HCl or any other
strong acid if the pH is more than 9. Add water to make the final volume 1 L.

• What if you overshoot it while adjusting?

4. What is the pH of a 10-10 M solution of HCl?

• 𝑝𝐻 = −𝑙𝑜𝑔 𝐻 + = − log 10−10 = 10

• Is this correct?

• An HCl solution cannot be basic.

• Pure water has 10-7 M H+ ions

• We often ignore it while calculating the pH of relatively concentrated acid or base,

as the contribution is small.

• However, if the concentration of the acid becomes comparable or lower than 10-7
M, we need to take this into account while calculating pH.

• The pH of this solution would be

• 𝑝𝐻 = −𝑙𝑜𝑔 𝐻 + = − log 10−7 + 10−10 ≈ − log 10−7 ≈ 7
5. What will be the pH of 10 M HCl solution? Can pH be negative?

𝑝𝐻 = −𝑙𝑜𝑔 𝐻 + = − log 10 = −1
6. What is activity coefficient?

A coefficient introduced by Lewis to explain the deviation of an electrolyte from ideal

behaviour.

A highly dilute solution approaches ideality. The effective concentration of the ions is
equal to the actual concentration.

However, this may not be the case at higher concentrations.

𝐸𝑓𝑓𝑒𝑐𝑡𝑖𝑣𝑒 𝑐𝑜𝑛𝑐𝑒𝑛𝑡𝑟𝑎𝑡𝑖𝑜𝑛 (𝑎)

𝐴𝑐𝑡𝑖𝑣𝑖𝑡𝑦 𝑐𝑜𝑒𝑓𝑓𝑖𝑐𝑖𝑒𝑛𝑡 𝛾 =
𝐴𝑐𝑡𝑢𝑎𝑙 𝑐𝑜𝑛𝑐𝑒𝑛𝑡𝑟𝑎𝑡𝑖𝑜𝑛 (𝐴)

The effective concentration (a) is written as: 𝑎 = 𝛾 × 𝑚𝑜𝑙𝑎𝑙𝑖𝑡𝑦

Ideally, we should consider the effective concentration while calculating pH.

7. The pKa of acetic acid is 4.75. What will be the pH of an aqueous
solution of acetic acid?
a. Is the information sufficient to determine the pH?
b. If yes, calculate.
c. If not, what else do you need?

𝑝𝐾𝑎 = −𝑙𝑜𝑔 𝐾𝑎 = 4.75

𝑙𝑜𝑔 𝐾𝑎 = −4.75

𝐾𝑎 = 10−4.75 = 1.78 × 10−5

𝐶𝐻3 𝐶𝑂𝑂𝐻 ⇌ 𝐶𝐻3 𝐶𝑂𝑂− + 𝐻+

1−𝑥 𝑥 𝑥
𝑥 𝑥
𝐾𝑎 = = 1.78 × 10−5
1−𝑥

2
𝑥 + 1.78 × 10−5 𝑥 − 1.78 × 10−5 = 0

𝑥 = 0.00421𝑀

𝑝𝐻 = −𝑙𝑜𝑔 0.00421 = 2.37

8. What is the buffer capacity?

It is a measure of resistance to pH
change.

It is the amount of acid or base

required for causing a change in 1
pH unit.

𝑑𝑛
𝛽=
𝑑(𝑝𝐻)

Lehninger Principles of Biochemistry

 Example on buffer capacity

Suppose you prepare phosphate buffer of pH 7 using 𝑁𝑎𝐻2 𝑃𝑂4 and 𝑁𝑎2 𝐻𝑃𝑂4

𝐻2 𝑃𝑂4− ⇌ 𝐻𝑃𝑂42−

𝑝𝐾𝑎 = 7.21

𝐴−
𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔
𝐻𝐴

𝐴−
7 = 7.21 + 𝑙𝑜𝑔
𝐻𝐴

𝐴−
𝑙𝑜𝑔 = −0.21
𝐻𝐴

𝐴−
= 10−0.21 = 0.616
𝐻𝐴
Therefore, the two salts 𝑁𝑎𝐻2 𝑃𝑂4 and 𝑁𝑎2 𝐻𝑃𝑂4 need to be added in the 1:0.616 ratio
 Example on buffer capacity (continued….)

For the ease of doing calculations, let’s assume that we prepare 1.616 M and 1.616
mM buffers.

1.616 M 1.616 mM

𝐻2 𝑃𝑂4− ⇌ 𝐻𝑃𝑂42− + 𝐻 + 𝐻2 𝑃𝑂4− ⇌ 𝐻𝑃𝑂42− + 𝐻 +

1M 0.616 M 0.616 M 1 mM 0.616 mM 0.616 mM
Both the buffers will have pH 7

Now, suppose HCl is added to both the buffers such that the final HCl concentration
is 0.5 mM. What will the pH be?

𝐻2 𝑃𝑂4− ⇌ 𝐻𝑃𝑂42− + 𝐻 + 𝐻2 𝑃𝑂4− ⇌ 𝐻𝑃𝑂42− + 𝐻 +

1M 0.616 M 0.616 M 1 mM 0.616 mM 0.616 mM
+ - + -
0.0005 M 0.0005 M 0.5 mM 0.5 mM
Let us calculate the pH now.

𝐻2 𝑃𝑂4− ⇌ 𝐻𝑃𝑂42− + 𝐻 + 𝐻2 𝑃𝑂4− ⇌ 𝐻𝑃𝑂42− + 𝐻 +

1M 0.616 M 0.616 M 1 mM 0.616 mM 0.616 mM
+ - + -
0.0005 M 0.0005 M 0.5 mM 0.5 mM

𝐴− 𝐴−
𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔 𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔
𝐻𝐴 𝐻𝐴
0.6155 0.116
𝑝𝐻 = 7.21 + 𝑙𝑜𝑔 𝑝𝐻 = 7.21 + 𝑙𝑜𝑔
1.0005 1.5
𝑝𝐻 = 7.21 − 0.211 𝑝𝐻 = 7.21 − 1.112

𝑝𝐻 = 6.999 𝑝𝐻 = 6.098

The 1.616 M buffer has higher buffer capacity compared to the 1.616 mM buffer.
9. Shown below are four different Newman projections along the peptide
backbones. Identify the dihedral angle represented and tell the
approximate value.

𝜓 = −90° 𝜙 = −135° 𝜓 = −60° 𝜙 = +60°