II. Propert ies of Water

1. Ice and Liquid water structure

2. Cohesion / Surface Tension

3. High Heat Capacity

4. Solvent Properties

5. Dissociation: Acids & Bases / pH

II. Organic Chemistry

A. Hydrocar bons--nonpolar

1. alkanes-only single bonds 2. alkenes- C=C double bonds 3. aromatic-cyclic based on benzene

B. Funct ional Groups: alcohol, aldehyde, ketone, carboxyl, amine, organophosphate, sulfhydral

1. polar bonds between C and more electronegative atoms (O and N) 2. Combine two functional groups ester = alcohol + acid 3. amide = amine + acid

C. Isomers

1. Same chemical formula but differ in arrangement of atoms in space 2. Enantiomers (Optical Isomers): C can be bonded to 4 different groups

in 2 ways producing molecules that are mirror images of one another that cannot be superimposed

Water As A Solvent For Life

Water is essential for life on Earth

All living organisms require water more than any other substance

75% of the Earth’s surface is covered

with water

104.5°

Fig. 3.2: Water: Structure and Properties

Water’s molecular structure and capacity to donate and accept hydrogen bonds give it unusual critical

properties that are significant for life

Hydrogen bond acceptors

Hydrogen bond donors

Fig. 3.6: Five Critical Properties of Water 1. Ice and liquid water structure

Temperature ≤ 0°C Temperature > 0°C < 100°C • Ice is less dense than liquid water • Water is liquid at a relatively high temperature > 0°C

(Methane (CH4) is similar in size but liquid only below -161°C)

Hydrogen bond Liquid water

Hydrogen bonds break and re-form Ice

Hydrogen bonds are stable

Hydrogen bonds hold water molecules

together in liquid

High Surface tension

Fig. 3.4

Fig. 3.3/3.4: Five Critical Properties of Water – 2. Cohesion

Water transport in plants

Water has a high specific heat capacity specific heat capacity = amount of energy required to raise

temperature of 1 g of water by 1°C (1 calorie, 1 cal) Large bodies of water stabilize the air temperature.

Heat energy can be absorbed by breaking hydrogen bonds

Five Critical Properties of Water 3. Moderation of temperature

Fig. 2.15 Fig. 3.7

A sphere of water molecules,

called a hydration shell, surrounds each solute ion

Fig. 2.15/3.7: Five Critical Properties of Water 4.Water as a solvent

Fig. 3.8

Review solute concentration in aqueous solutions (Molarity) (page 51 – 52 of text)

Fig. 3.8: Five Critical Properties of Water 4. Water as a solvent (Cont’d)

(a) Lysozyme molecule in a nonaqueous environment

(b) Lysozyme molecule (purple) in an aqueous environment

(c) Ionic and polar regions on the protein’s surface attract water molecules.

Five Critical Properties of Water 4. Water as a solvent (Cont’d)

This reaction is frequently abbreviated as:

H2O H+ OH- +

The KW is the ion product of water,

Kw = [H+][OH-] = 1.0 x 10-14 M2 at 25°C

Thus, in pure water, [H+] = [OH-] = 1.0 x 10-7 M

Page 53

H3O+ (hydronium ion)

OH- (hydroxide ion)

Fig. 3.9: pH SCALE - 1.0 x 10-7 M is a very small number and can change by orders of magnitude (powers of 10x) pH

“Physiological pH” (pH 6.5 – 8.0)

pH = -log[H+] = 7 in pure water at 25°C = neutral pH

CH3-C O

O- CH3-C O

OH + H+

NH3 + H+ NH4+

CH3COOH CH3COO- + H+

NH4+ NH3 + H+

HA A- + H+

Acid ionization constant, Ka = [H+][A-] [HA]

pKa = -log Ka

Ka pKa 1.8 x 10-5 M 4.7

5.8 x 10-10 M 9.2

pKa is a measure of propensity to dissociate: if pH < pKa the HA form predominates if pH > pKa the A- form predominates

Buffers keep pH relatively constant in the range around pKa value by accepting or donating H+ from solution

Response to decrease [H+]

Response to increase [H+] CH3-C

O

O- CH3-C O

OH

[HA] >> [A-]

[A-] >> [HA]

[HA] = [A-]

Organic Chemistry

The chemistry of molecules containing carbon bonded to other elements, principally: H, O, N, P, S …

Hydrocarbons are Nonpolar (electrons are equally distributed) and do not mix freely with water

they are Hydrophobic.

109°

120°

Fig. 4-3 Fig. 4.3: The Shapes of Three Simple Organic Molecules Name and Comment

Molecular Formula

(a) Methane

(b) Ethane

CH4

Ball-and- Stick Model

Space-Filling Model

(c) Ethene (ethylene)

C2H6

C2H4

Structural Formula

Hydrocarbons -- organic compounds containing only carbon and hydrogen. These are the most reduced organic

compounds and react vigorously (i.e. burn) with oxygen.

CH4 + 2O2 CO2 + 2H2O + Heat

Heat

2 2 Methane

(natural gas) Oxygen Carbon Dioxide Water

+ + +

Fig. 4.5: Various Hydrocarbons

Octane C8H18: A major component of gasoline.

(a) Length

Ethane 1-Butene

(c) Double bond position

2-Butene Propane

(b) Branching (d) Presence of rings

Butane 2-Methylpropane (isobutane)

Cyclohexane Benzene

H-C-C-C-C-C-C-C-C-H H H H H H H H H

H H H H H H H H

Aromatic Hydrocarbons -- are a special class of hydrocarbons in which atoms are arranged in a ring structure and are connected by σ-bonds and a system of π-bonds around the ring. The simplest example is benzene, C6H6, and as shown below all atoms lie on a plane with bond angles of 120°

120°

Fig. 4.4: Carbon also forms bonds with a variety of other Elements

O C O

Carbon dioxide (CO2) Urea

CO(NH2)

Hydrogen (valence = 1)

Oxygen (valence = 2)

Nitrogen (valence = 3)

Carbon (valence = 4)

H O N C

Urea

Ethanol Acetone Acetic Acid

Functional Groups Here “R” represents the rest of the molecule

R–OH R–C H

O R–C

R’

O R–C

O

OH R–NH2 R–SH R–O–P–OH

O

OH Alcohol Aldehyde Ketone Carboxylic Acid Amine Sulfhydral Organic Phosphate

Carbonyls

Fig. 5-2a Fig. 5.2a: The Synthesis of Polymers

(a) Dehydration reaction: synthesizing a polymer

Short polymer Unlinked monomer

Dehydration removes a water molecule, forming a new bond.

Longer polymer

1 2 3 4

1 2 3

Organic molecules with certain functional groups can be joined by a covalent bond formed when a molecule of water is removed; this allows the creation of new types of organic molecules.

R-OH + HO-P-OH O

O- R-O-P-OH + H2O

O

O-

Linking Functional Groups Polymers

R–C O

OH + HO–R’ R–C

O

OH N-R’ H

+ H

Ester Amide

R–C O

O-R’ + H2O R–C

O

N-R’ H

+ H2O

Fig. 4.6: Ester bonds link fatty acid carboxyl groups to OH- groups of Glycerol

Nucleus

Fat droplets

(b) A fat molecule a.k.a. Triglyceride

(a) Part of a human adipose cell

10 µm

Isomers: Molecules that have the same chemical formula, i.e. the same number of each of the different kinds of atoms.

Fig. 4.7: There are different classes of Isomers

cis isomer: The two X’s are on the same side.

trans isomer: The two X’s are on opposite sides.

L isomer D isomer

Fig. 4-8 Fig. 4.8: Pharmacological Importance of Enantiomers

Drug

Ibuprofen

Albuterol

Condition Effective Enantiomer

Ineffective Enantiomer

Pain; inflammation

Asthma

S-Ibuprofen R-Ibuprofen

R-Albuterol S-Albuterol

Thalidomide was first used as a sedative and anti-nausea medication, but was found to cause serious birth defects when pregnant women take it during their first trimester.