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revised 8/ 26/ 2013. Biochemistry 4511. Chapter 2 Water. Colorado River 1999. Colorado River 2013. Water, the Liquid of Life (part 1).

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revised 8/26/2013

Biochemistry 4511

Chapter 2



Colorado River 1999

Colorado River 2013


Water, the Liquid of Life (part 1)

Water is polar. The oxygen atom in a water is partially negative (it carries a partial negative charge). Each hydrogen atom is partially positive. This phenomenon is called polarity. Water is a polar molecule.

Oxygen is electronegative. It does not share electrons equally with hydrogen atoms. The hydrogen atoms, with no inner shell electrons, are stripped of much of their electron density and carry a partial positive charge, the protons are exposed.

In liquid water and especially in solid water, the molecules interact strongly with each other, with preferred orientations.


Water, the Liquid of Life (part 2)

Water has all sort of strange and unusual properties.


  • has a high boiling point and high heat of vaporization.
  • has high surface tension.
  • dissolves many salts (like sodium chloride) and polar molecules (like ethanol).
  • does not dissolve non-polar substances (oil and water don’t mix).
  • has high heat capacity.
  • expands when it freezes, so ice floats. The density of water decreases when it freezes.
  • forms compartments in the presence of amphipaths.
  • is often found on Earth simultaneously as a solid, liquid and gas.

Capillary action is the tendency of a liquid to flow into narrow spaces in opposition to external forces. Water is lifted by surface tension (caused by cohesion between water molecules) and adhesive forces between the water and the surface.


A hydrogen bond is an electrostatic attraction between a hydrogen atom and a Lewis base (an electron lone pair). The hydrogen atom must be covalently bonded to a electronegative atom such as nitrogen, oxygen or sulfur. The name hydrogen bond is a misnomer. A hydrogen bond is not a covalent bond but is a particularly strong dipole-dipole attraction. A hydrogen bond is a molecular interaction, which is an interaction between molecules.


In liquid and solid water there are hydrogen bonds between water molecules. Water is self-complementary in that it can form two hydrogen bonds that donate protons and two hydrogen bonds that accept protons.

(see 3D structure)


We will parse molecular interactions in the following way:

(A) short range repulsive interactions

(B) electrostatics (charge-charge interactions)

(C) dipolar interactions

(D) fluctuating dipole (London Dispersion)

(E) hydrogen bonding interactions

(F) solvent, counter ion, and entropic effects

(G) water and the hydrophobic effect


Interactions between permanent dipoles

From General Chemistry: Principles, Patterns, and Applications (v. 1.0).


NaCl: Melting point 801 °C, 1074 K

  • Boiling point 1413 °C, 1686 K
  • Solubility
  • in water 359 g L−1
    • in ammonia 21.5 g L−1
  • in methanol 14.9 g L−1


Melting point: 146 °C

Solubility in water: 91 g/100 mL


The Hydrophobic


The hydrophobic effect is the tendency of nonpolar substances such as hydrocarbons to aggregate in aqueous solution.

The hydrophobic effect is an entropic phenomenon originating in the tendency of water molecules to form hydrogen bonds with each other.

Water molecules cannot form hydrogen bonds with a hydrocarbon.


Water molecules form a hydrogen bonded "cage" around the hydrocarbon, with restricted mobilities (i.e., with few available rotational and translational microstates).

Water at the interface has lower entropy than bulk water.

When hydrocarbon molecules aggregate, the surface area exposed to water is decreased, releasing low entropy interfacial waters into the bulk solution, increasing the entropy of the system.

The Hydrophobic


You might think that introduction of hydrocarbon into water would disrupt water-water hydrogen bonds at the interface.

But no, that is not what happens.

Instead, water molecules at the interface between bulk water and the hydrocarbon orient in very specific ways that minimize disruption of water-water hydrogen bonds.


When hydrocarbon molecules aggregate in water, the surface area exposed to water is decreased, releasing low entropy interfacial water molecules into bulk solution, increasing the entropy of the system.

The Hydrophobic



The Hydrophobic


Figure 2-8


The Hydrophobic


Table 2-2


Osmosis is the spontaneous net movement of molecules into regions of lower concentration. The net movement of molecules is in directions that tend to equalize concentrations.

Osmotic pressure is the pressure required to halt the next flux of water across the semipermeable membrane.




Water as an Acid and a Base

Autoionization of water:

2 H2O (l) H3O+ (aq) + OH- (aq)

Kw = [H3O+][OH-] = [H+][OH-]

Kw = 1.0 x 10-14(at 25oC)

In pure water [H+] = [OH-]

Kw = [H3O+][OH-]


HA + H2O H3O+ + A –

HA = generic acid

  • There is competition for the proton between two bases, H2O and A–
  • If H2O is a stronger base than A– the equilibrium lies to the right.
  • If A– is a stronger base than H2O the equilibrium lies to the left.

It is easier to remove the first proton in a polyproticacid than the second.That is, Ka1 > Ka2 > Ka3

Polyprotic Acids

Note: Phosphoric acid is a strong acid in its first dissociation, and a weaker acid in its second step and an even weaker acid in its third step.

H3PO4H++ H2PO4– Ka1 = 7.5x10-3pKa1 = 2.2

H2PO4–H+ + HPO42- Ka2 = 6.2 x10-8pKa1 = 7.2

HPO42- H++ PO43- Ka3 = 4.8x10-13pKa1 = 12.4


H3PO4: phosphoric acid

H3PO4H++ H2PO4– Ka1 = 7.5x10-3pKa1 = 2.2

H2PO4–H+ + HPO42- Ka2 = 6.2 x10-8pKa1 = 7.2

HPO42- H++ PO43- Ka3 = 4.8x10-13pKa1 = 12.4