WATER

 Water
o Essential for life and its properties are central to
the function of all biological molecules.

Uneven distribution of e-
Even distribution of e- = temporary attraction

2) Dipole interactions
o Result when two dipolar molecules interact
with each other through space.
H2O has two O-H bonds (0.95 Å) and has two pairs of non- o When this occurs, the partially negative
bonded electrons that play a key role in forming weak, non- portion of one of the polar molecules is
covalent H (hydrogen) bonds. attracted to the partially positive portion of
the second polar molecule.
A. Structure of Water o This type of interaction between molecules
1. Oxygen’s electronic configuration: 1s22s22p4. accounts for many physically and
2. In water, the 2s and the three 2p orbitals form: four biologically significant phenomena such as
sp3 hybrid orbitals. the elevated boiling point of water.
3. These orbitals are tetrahedral in their orientation,
however, the ideal bond angle of 109° is distorted to Types Dipole interactions
104.5°. a) Dipole-dipole
4. The orbitals are populated such that two orbitals are - Electrostatic interactions between
filled and two contain one electron each. molecules which have permanent
5. The filled orbitals cannot form bonds and are called dipoles.
lone pairs of electrons.
6. The half-filled orbitals participate in the formation of a
sigma bond between oxygen and hydrogen.
7. "Bent" water molecule generates a permanent dipole
moment making water a polar solvent.

b) Ion-Dipole
B. Four Unique Physical Properties of Water - Consists of an ion and a polar
1. Can form H bonds with itself and with many biological molecule interacting.
molecules. - They align so that the positive
- Without H bonds biomolecules will be and negative groups are next to
denatured. one another, allowing maximum
2. Has dipolar character and plays an important role in attraction.
the solvation of many molecules. - Attraction happens due to the
- Solvation – association to solvent molecules. difference in electronegativity
3. Minimizes interactions with non-polar species. between the involved particles
- Non-polar species – fats, lipids, etc. (water usually has higher).
4. A neutral molecule with the ability to ionize.

C. Review on Interactions
1. All Weak Interactions in Aqueous Environment
1) London Dispersion Forces
o Sometimes called an induced dipole-
induced dipole attraction.
o A temporary attractive force that results
when the electrons in two adjacent atoms
occupy positions that make the atoms form
temporary dipoles.
 c) Ion-Induced Dipole
- Consists of an ion and a non-
polar molecule interacting.
- An ion disturbs the electron cloud
by attracting charged atoms.
- Interaction happens due to
thermodynamics.
- Like a dipole–induced dipole
force, the charge of the ion
causes distortion of the electron
cloud on the non-polar molecule.
3) Electrostatic interactions
D.
o Also known as Van der Waals Interaction.
o Attractive or repulsive interaction between
objects having electric charges.
4) H-bonding
o Partial intermolecular bonding interaction
between a lone pair on an electron rich donor
atom, particularly the second-row elements
nitrogen, oxygen, or fluorine, and the
antibonding molecular orbital of a bond
between hydrogen and a more
electronegative atom or group.
Molecules where
Bonding Arrangement
the bond occurs
H bond formed in
H2O.
Bonding of water to
other molecules.
Important in protein
and nucleic acids.
5) Hydrophobic Interaction
o The observed tendency of nonpolar
substances to aggregate in an aqueous
solution and exclude water molecules
Solvent Properties of Water
 Hydrophilic
o Water-loving, tend to dissolve in water.
Consequently, they can form hydrogen bonds with
water.
The formation of hydrogen bonds is energetically
favorable, thus hydrophilic compounds readily
dissolve in water.
 Hydrophobic
o Water-fearing, tend not to dissolve in water.
Consequently, solvated hydrophobic compounds
cause the formation of an ordered shell of
hydrogen bonded water molecules
Removal of the solvated hydrophobic compound
will release these water molecules, increasing the
entropy of the solvent.
This favorable increase in the entropy of the
solvent drives the hydrophobic molecules from
the aqueous phase.
o The hydrophobic effect is responsible for the
spontaneous formation of a number of
important biological structures, such as:
a. Proteins
b. Cell membranes
c. Interaction of small molecules with
larger proteins, such as substrates
with enzymes
  Amphiphilic
o Has characteristics of both properties,
molecules that contain one or more
hydrophobic and one or more hydrophilic
regions (e.g., sodium palmitate).
o These can form micelles if the nonpolar part is
sufficiently large.
- Micelles are aggregates of amphipathic
molecules that sequester the nonpolar
part on the inside, much like the inside
of an orange. Micelles will form
spontaneous driven by the hydrophobic
effect.
o The pH of a neutral compound, such as pure
water at room temperature is 7.
o The concentration of hydronium ions is related
to the concentration of hydroxide ions by the
dissociation of water.
Self-ionization of water
(The process in which water ionizes to hydronium ions and
hydroxide ions.)

F. Mathematics of pH

Acids Bases
 Proton
E. Review on pH  Proton donor acceptor
 pH Bronsted-  Sour  Bitter &
o Parameter most often measured in chemistry Lowry  Turns blue slippery
because it influences the position of chemical litmus into red  Turns red
equilibrium of the majority of chemical litmus into blue
reactions in aqueous solutions, and this can  Potential
 Potential
also be extended to other media. electron pair
electron pair
- In several instances pH also influences Lewis acceptor to form
donor to form a
the reaction kinetics, changing the rate a covalent
covalent bond.
and acting as a catalyst. bond.
 Compound
 pH of a solution  Compound that that
o The negative logarithm of its Hydrogen ion Arrhenius dissociates in dissociates in
concentration. water to form H+ water to form
o pH = -log(H+) OH-

Example: A pH increase of 1 is indicative of a ten-fold

a. The concentration of H+ is 10-7 decrease of H+ concentration. This negative
pH = -log(10-7) = 7 logarithmic relationship between the hydrogen ion
concentration and pH means that:
o A measure of the hydronium ion (H3O+) a. a lower pH indicates a higher
concentration on a logarithmic scale. concentration.
o Biologically important because it affects the b. a higher pH indicates a lower
structure and activity of macromolecules. concentration of hydrogen ions.
o Important in homeostatic processes.
- Most animals breathe not because they 1. Dissociation Constant of Water (Kd of Keq)
lack oxygen but balance the CO2 build-  Relationship between:
up in the blood which increases blood a. H+ ion concentration
acidity. b. OH- ion concentration
o Enzyme function is especially sensitive to pH: c. Concentration of water at equilibrium
each has an optimum pH at which they have  Molarity of pure water: 55.5M
maximum catalytic ability. Extreme pH levels
 Water at room temperature: 25°C
can denature enzymes, completely disrupting
 p = −𝒍𝒐𝒈𝟏𝟎
their function. Other proteins are also
destabilized by extreme pH levels.
[𝐻 + ][𝑂𝐻 − ]
𝐾𝑒𝑞 =
[𝐻2 𝑂]
o pH scale range
o 0-14 from acidic to basic, respectively. [𝐻 + ][𝑂𝐻 − ]
𝐾𝑒𝑞 =
[55.5𝑀]
 𝐾𝑒𝑞 × 55.5𝑀 = [𝐻 + ][𝑂𝐻 − ] = 𝐾𝑤
𝐾𝑤 = [𝐻 + ][𝑂𝐻 − ] a. When 𝑝𝐻 < 𝑝𝐾𝑎 = weak acid
𝐾𝑤 = [10−7 ][10−7 ] = 10−14 predominates.
−𝑙𝑜𝑔10 (𝐾𝑤 ) = −𝑙𝑜𝑔10 10−14 = −(−14 )𝑜𝑟 14 b. When 𝑝𝐻 > 𝑝𝐾𝑎 = conjugate
𝒑𝑲𝒘 = 𝟏𝟒 predominates.

Shaded in grey is the ion product of water. 4. Titration Curve

 Titration
o Experiment in which measured amounts of
2. Acid Strength acid (or base) are added to measured
 Strong acids/bases dissociate completely. amounts of base (or acid).
o Example: HCl → H+ + Cl-
 Equivalence point
 Equilibrium Constant for the Dissociation of o Measured in titration.
Weak Acids (𝑲𝒂 ) o At which enough acid has been added to
exactly neutralize the base (or vice versa).
o Tendency of an acid to dissociate and
donate a H+ ion to a solution.
[𝐻 + ][𝐴− ]
Monoprotic 1
o 𝐾𝑎 = 1 H+ per mole
[𝐻𝐴]
Acid curve
2
Diprotic Acid 2 H+ per mole
curves
𝐻𝐴 ⇌ 𝐻+ + 𝐴− 3
(acid) (conjugate base) Tripotric Acid 3 H+ per mole
[𝐻 + ][𝐴− ] 𝑝𝑟𝑜𝑑𝑢𝑐𝑡
curves
𝐾𝑎 =
[𝐻𝐴] 𝑚𝑎𝑡𝑒𝑟𝑖𝑎𝑙𝑠
+
𝐻𝐴(𝑎𝑞) + 𝐻2 𝑂(ℓ) ⇌ 𝐻3 𝑂(𝑎𝑞) + 𝐴−
(𝑎𝑞) G. Buffers
𝒑𝑲𝒂 = −𝒍𝒐𝒈𝟏𝟎 (𝑲𝒂 )
 A solution whose pH resists change upon addition of
𝒑𝑯 = −𝒍𝒐𝒈𝟏𝟎 (𝑯+ )
either more acid/base.
 Consists of a weak acid and its conjugate base.
 A smaller 𝐾𝑎 means a higher
 Sodium – essential in creating buffers.
value of 𝑝𝐾𝑎 .
 A higher value of 𝑝𝐾𝑎 is equivalent Buffer Systems in the body
to a weaker acid due to less
Bicarbonate-Carbonic Major buffer system in
dissociation of the acid into 𝐻 + acid the body.
and its conjugate base.
Hemoglobin RBC
 Similar to 𝑝𝐻, a single integer
Phosphate All cell systems
difference in 𝑝𝐾𝑎 represents a
Proteins Cells and plasma
tenfold difference.

Examples of acid-base buffers are solutions

3. Henderson-Hasselbach Equation containing:
 Equation to connect 𝐾𝑎 to 𝑝𝐻 of solution
a. CH3COOH – acetic acid
containing both acid and base.
b. CH3COONa – sodium acetate
 Calculate the ratio of weak acid to its conjugate c. H2CO3 – carbonic acid
base using: d. NaHCO3 – sodium bicarbonate
o 𝐴− = conjugate base e. NaH2PO4 – monosodium phosphate
o 𝐻𝐴 = acid f. Na2HPO4 – disodium phosphate

[𝐻 + ][𝐴− ]
𝐾𝑎 =
[𝐻𝐴]
[𝐴− ] 1. Buffer Capacity
𝑙𝑜𝑔(𝐾𝑎 ) = log[𝐻 + ] + 𝑙𝑜𝑔
[𝐻𝐴]
[𝐴− ]  Related to the concentration of the weak acid and
− log[𝐻 + ] = −𝑙𝑜𝑔(𝐾𝑎 ) + 𝑙𝑜𝑔 its conjugate base.
[𝐻𝐴]
[𝐴− ]  The greater the concentration of the weak acid and
𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔
[𝐻𝐴] its conjugate base, the greater the buffer capacity.
Henderson-Hasselbach Equation
Naturally Occurring Buffers
H2PO4- / HPO42-
If the conjugate base and weak acid are Principal buffer in
Dihydrogenphosphate
equal: 𝒑𝑯 = 𝒑𝑲𝒂 cells.
1 / hydrogenphosphate
𝑠𝑖𝑛𝑐𝑒, 𝑙𝑜𝑔 = 0
1
 H2CO3 / HCO3-
An important (but not
Carbonic acid /
only) buffer in blood.
bicarbonate

𝐶𝑂2(𝑔) ⇌ 𝐶𝑂2(𝑎𝑞)
𝐶𝑂2(𝑎𝑞) + 𝐻2 𝑂(ℓ) ⇌ 𝐻2 𝐶𝑂3(𝑎𝑞)
+ −
𝐻2 𝐶𝑂3(𝑎𝑞) ⇌ 𝐻(𝑎𝑞) + 𝐻𝐶𝑂3(𝑎𝑞)
+ −
Net eqn: 𝐶𝑂2(𝑔) + 𝐻2 𝑂(ℓ) ⇌ 𝐻(𝑎𝑞) + 𝐻𝐶𝑂3(𝑎𝑞)

1. Hyperventilation– can result in

increased blood pH.

2. Hypoventilation – can result in

decreased blood pH.