Chapter 2: Aqueous Soln’Properties of water (H2O)very few inorganic compounds are liquids at earth’s temperature. The physical and chemical characteristics of water unique to earth (70% of the earth’s surface) which makes the existence of life possible.

H2O Structure• O-H bond length: 0.958 Å

(1 Å=10-8 cm = 0.1 nm)• Bond angle: 104.5• Dipole moment: asymmetric of

charge across the molecule. • Solvent : very polar• Effective VDW radius: 1.4-1.6 Å• Dipole moment: 1.85 Debye unit

H-bondings in H2OThe hydrogen bonds generated by electrostatic nature of the molecule hold molecules together

Unique properties of water because of the H-bondings:Density- 1.0Latent heat of melting: 79.72 cal/gLaten heat of evaporation: 540 cal/gSpecific heat: 1

most other substances-near 0.2liquid NH3-1.23liquid H2-3.4

Surface tension: highest except for mercury

H-bond : ~20 KJ /mole10% .

H-bond : 1.4 Åvan der Waals

0.5 Å.

:D-H…A D-H “donor group”

N-H O-HA “acceptor atom” lone pair electrons N O

�-D-H��… ��A

H-bondings in Ice

every oxygen at the center of a tetrahedron formed by 4 oxygen atoms; as ice melts open lattice is disrupted.Ice is much less dense than water. At 0

C, bonds rupture and lattice disorganization increase densityFrom 4 C on, increased energy leads to increasing inter-atomic distances.

( ) open structure, 0.92 g/ml (1.0 g/ml)

H-bondings also persist in the liquid stateThe heat of sublimation of ice at 0 ºC is 46.9 KJ/molekinetic energy of gaseous water: ~ 6 KJ/mole41 KJ/mole required to disrupt the H-bonding force in ice.Heat of fusion of ice: 6 KJ/moleLiquid water is ~15% less hydrogen bonded than ice at 0 ºC .

Ice: H-bond lifetime - about 10 microsecWater: H-bond lifetime - about 10 psec

3-6 20 psecLiquid water is a rapidly fluctuating space-filling network of hydrogen bonded, over a short distances, resembles that of ice.

Ice: 4 H-bonds per water molecule, water at 0 ºC: 4.4 H-bonds, Water at 10 ºC: 2.3 H-bonds per water moleculeThis indicates tetrahedral like H-bonding environment but becomes less ordered in liquid water.

Solvent Property of water: like dissolves like

Hydrophilic compound: ionic or polar in natureHydrophobic compound: nonpolar (eg: oil, CH4 etc)

Dielectric constant D:The force to separate two opposite charged to infinite distance. Thus, the dielectric constant of a solvent is a measure of the ability to dissolve ionic compounds. The D value of H2O is 78.5.

1 22

9 2Dr

8.99 10

kq qF

k x J m C�

�

� � �

The ions are solvated or hydrated in solvent.

Solvent properties of waterFor ionic compound dissolved in water, the Ions are always hydrated in water and carry around a "hydration shell“Water forms H-bonds with polar solutes

A nonpolar solute "organizes" waterThe H-bond network of water reorganizes to accommodate the nonpolar soluteThis is an increase in "order" of water. ”a decrease in ENTROPY”

Amphiphilic molecules

Also called "amphipathic"Refers to molecules that contain both polar andnonpolar groups. : fatty acidsEquivalently refer to molecules that are attracted to both polar (hydrophilic) and nonpolar (hydrophobic) environments

Micelle and bilayerWater tends to hydrate the hydrophilic portion of the amphiphile, but it tends to exclude its hydrophobic portion. Therefore,Micelle are globular structure with thousand amphiphiles aggregate in ordered fashion as shown in the figure.The interactions stabilized a micelle or bilayer are collectively described hydrophobic forces orhydrophobic interactions.

suprastructure membrane

Basics about Acids, Bases, and BufferDefinition of acid or baseArrhenius: substance donates protons and hydroxides ions

Bronsted & Lowry: Acid: substance donates protonsBase: substance accepts protonsCH3COOH + H2O � CH3COO- + H3O+

NH3 + H2O � NH4+ + OH-

Lewis: (aqueous & non-aqueous soln’)Acid: substance accept electron pairBase: substance donate electron pairThe Lewis definition encompasses the Bronsted-Lowry definition: In the reaction of H+ and OH-,H+ is a Lewis acid because it accepts an electron pair from the OH-. Since the OH- donates an electron pair we call it a Lewis base. As an example not described by the Bronsted-Lowry definition, Al3+ in water is a Lewis acid. It reacts with water to form an aqua complex: the Al3+ accepts the electron-pair from water molecules. In this example the water acts as a Lewis base.

Ka (dissociation constant)In biologically relevant compounds various weak acids and bases are encountered, e.g. the acidic and basic amino acids, nucleotides, phospholipids etc.

Weak acids and bases in solution do not fully dissociate and,therefore, there is an equilibrium between the acid and its conjugate base. This equilibrium can be calculated and is termed the equilibrium constant = Ka. This is also sometimes referred to as the dissociation constant as it pertains to the dissociation of protons from acids and bases.

For weak acid dissociates in water HA + H2O �� A- + H+

the equlibrium constant can be calculated

[HA]]][A[H -�

�Ka

pKa = -logKa

)[HA]

]][A[Hlog(log-�

���� pKaKa

Ka (dissociation constant)

)[HA]

][A-][Hlog(log ����� pKaKa

)[HA][A-]log(-][Hlog ���

pH = -log[H+]

)[HA][A-]log(�� pHpKa

The smaller the pKa value the stronger is the acid. This is due to the fact that the stronger an acid the more readily it will give up H+ and,therefore, the value of [HA] in the above equation will be relatively small.

The Henderson-Hasselbalch Equation

)[HA][A-]log(�� pHpKa

the dissociation constant of weak acid or base can be determined experimentally.

)[HA][A-]log(�� pKapH��

At the point of the dissociation where the concentration of the conjugate base [A-] = to that of the acid [HA]

pH = pKa + log[1] = pKa

solute Ka

At pH below the pK, [HA] > [A-]

When [HA] = [A-]At pH = pK, In other words, the term pKa is that pH at which an equivalent distribution of acid and conjugate base (or base and conjugate acid) exists in solution.

At pH above the pK, [HA] < [A-]

)[HA][A-]log(�� pKapH

Buffer Solution (buffer solution)?

Consider a reaction HA + H2O �� A- + H3O+

HA A- conjugate acid base ( )( : )

• Resist to change in pH of the solution. This phenomenon is known as buffering.

• Solution must contain conjugated weak acid-base pair.• Buffer Capacity: amount of acid or base added in order to

change pH of the solution by 1.

Titration* curve of buffer solution

The effective pH buffering zone of weak acid or base can be calculated from the dissociation constant

pH = pKa 1

CH3COOH + H2O � CH3COO- + H3O+

)[HA][A-]log(�� pKapH

When [A-]/[HA]>10, pH changes rapidly.

Importance of biological pH buffering

• In most biochemical studies it is important to perform experiments, that will consume H+ or OH- equivalents, in a solution of a buffering agent that has a pKa near the pH optimum for the experiment.

The pH of blood is maintained in a narrow range around 7.4 (diagram). The primary buffers in blood are hemoglobin in erythrocytes and bicarbonate ion (HCO3

-) in the plasma. The role played by the bicarbonate is as the followings

CO2 + H2O �� H2CO3

H2CO3 �� H+ + HCO3-

Henderson-Hasselbalch equation

pH = 6.1 + log [HCO3-/(0.03)(PCO2)]

Since CO2 is a dissolved gas.This factor has been shown to be approximately 0.03 times the partial pressure of CO2 (PCO2).

Transport of CO2 and the Bohr effect

Representation of the transport of CO2 from the tissues to the blood with delivery of O2 to the tissues. The opposite process occurs when O2 is taken up from the alveoli of the lungs and the CO2 is expelled. All of the processes of the transport of CO2 and O2 are not shown such as the formation and ionization of carbonic acid in the plasma. The latter is a major mechanism for the transport of CO2 to the lungs, i.e. in the plasma as HCO3

-. The H+ produced in the plasma by the ionization of carbonic acid is buffered by phosphate (HPO4

2-) and by proteins. Additionally, some 15% of the CO2 istransported from the tissues to the lungs as hemoglobin carbamate.

buffers mimic biological environment

C NH2HOH2C

CH2OH

CH2OH

C

(CH 2)2OH

(CH 2)2OH

N

CH 2OH

CH 2OH

CH 2OH

3HSON

SO H3N

Tris

Bis-Tris

PIPES

N3HSOOH

N

HEPES

Titration of polyprotic substance

• Polyprotic:Substances contain more than one acid-base group. eg. H3PO4 or H2CO3are called polyprotic acid.H3PO4 �� H2PO4

- + H+

K1=7.08 X 10-3 pK1=2.15

H2PO4- �� HPO42- + H+

K2=1.51 X 10-7 pK2=6.82

HPO42- �� PO4

3- + H+

K3=4.17 X 10-13 pK3=12.38

Dissociation of more H+ becomes difficult as pK values go up.The difference between successive pK value is > 4.0, it can be assumed that, at a given pH, the members of the conjugate acid-base pair with nearest pK value predominate.

Polyprotic acids with closely spaced pK’s

For substance where the pK’s of a polyprotic acid differ by less than ~2 pH, the resulting ionization is the average ionization constant of the groups involved (molecular ionization constants).

BA KKHAH

HAAHHK ���

����

][])[]]([[1

)(

2

][][]][[2

DC

DCKK

KK

HAAHAHK ���

��

��

�

KA >> KB, then K1~KA

If KD >> KC, then K2~KC

Ampholytes, Polyampholytes, pI and Zwitterion

Ampholytes:substances contain both acidic and basic groups(one acidic and one basic group)Polyampholytes:If substances contain many acidic and basic groups.

Isoelectric point, pI:Proteins contains many different amino acids some of which containionizable side groups, both acidic and basic. Therefore, the pI is described as the pH at which the effective net charge on a molecule is zero.(A molecule with a low pI would contain a predominance of acidic groups, whereas a high pI indicates predominance of basic groups.)

Titration of Simple Amino AcidsAmino acids are more complicated than simple weak acids since amino acids have at least 2 ionizing groups.Glycin, for example, has both a carboxylic acid and an amino group that can ionize

Zwitterion:Substances bear charged groups of opposite polarity.

Gly is still neutral because the + charge is netualized by the -charge.

pI of Glycin amino acid (titration diagram)

Glycine is neutral at pH 6; it has no net charge here.

�� ��

pK1=pH 2.35 pK2=pH 9.78

2)( ji pKpKpI ��

01.62)78.935.2( �� �pI

Complex titration curves of proteins

5 Complex Amino Acids are: glutamicacid, aspartic acid, lysine, arginine and histidine. Each of these 5 amino acids has 3 ionizable groups and therefore, 3pKs.