The Nature of Molecules and
the Properties of Water
Chapter 2
1
2.1 Nature of Atoms: Learning
Objectives
•
•
•
•
Define atoms, elements, and isotopes
Know basic structure of atoms
List elements found in living things
Describe how atomic structure 
chemical properties
• Explain where e- are found in an atom
Nature of Atoms
• Matter
• Has mass
• Occupies space
• All matter is composed of atoms
Scanning Tunneling
Microscopy
Oxygen atoms on rhodium
crystal
3
Atomic Structure
• Atoms are composed of
– Protons
Bohr Atomic Model
• Positively charged particles
• Located in the nucleus
– Neutrons
• Neutral particles
• Located in the nucleus
– Electrons
http://d1jqu7g1y74ds1.cloudfront.net/wpcontent/uploads/2010/02/c-atom_e1.gif
• Negatively charged particles
• Found in orbitals surrounding the nucleus
4
Bohr Atomic Model
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b.
proton
(positive charge)
electron
(negative charge)
neutron
(no charge)
5
Quantum Atomic Model
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Hydrogen
Oxygen
1 Proton
1 Electron
8 Protons
8 Neutrons
8 Electrons
a.
proton
(positive charge)
electron
(negative charge)
neutron
(no charge)
6
Atomic number = Atom’s I.D. #
• Atomic number
• number of protons in an atom
• Determines atom’s identity
• Hydrogen = 1 proton
• Helium = 2 protons
7
Atomic mass
• Mass or weight?
– Mass – refers to amount of substance
– Weight – refers to force gravity exerts on
substance
• Sum of protons and neutrons is the atom’s
atomic mass
• Each proton and neutron has a mass of
approximately 1 Dalton or atomic mass
unit (a.m.u.)
8
Properties of Subatomic Particles
Subatomic Particle Summary
subatomic
particle
Mass
(in Daltons or
a.m.u.)
charge
proton
1
+
neutron
1
neutral
electron
almost 0
-
Elements
• Element
– Any substance that cannot be broken down to
any other substance by ordinary chemical
means
– A given element is made up one type of atom
Iron is an element because it
is made up of only iron atoms
10
http://www.periodictable.com/Samples/026.32/s9s.JPG
Elements
C
• 90 naturally occurring elements
• 12 elements found in living
organisms in substantial
amounts
• 4 elements make up 96.3% of
human body weight
– Carbon, hydrogen, oxygen,
nitrogen
Carbon (C)
O Oxygen (O)
H Hydrogen (H)
N Nitrogen (N)
Na Sodium (Na)
Cl Chlorine (Cl)
Ca Calcium (Ca)
P Phosphorus (P)
K Potassium (K)
S
Sulfur (S)
Fe Iron (Fe)
Mg Magnesium (Mg)
b.
11
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Elements
C
Carbon (C)
O Oxygen (O)
• 4 elements make up 96.3% of
human body weight
H Hydrogen (H)
N Nitrogen (N)
– Carbon, hydrogen, oxygen,
nitrogen
Na Sodium (Na)
• Organic molecules contain
primarily CHON
• Some trace elements are very
important
Ca Calcium (Ca)
Cl Chlorine (Cl)
P Phosphorus (P)
K Potassium (K)
S
Sulfur (S)
Fe Iron (Fe)
Mg Magnesium (Mg)
b.
12
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Periodic Table of the Elements
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1
3
Li
11
8
Key
H
1
H
4
Be
atomic number
chemical symbol
B
13
Al
Na Mg
20
K
Ca
37
38
Rb Sr
55
56
21
22
Sc Ti
25
23
24
V
Cr Mn
41
42
14
Si
28
29
30
31
40
Y
Zr Nb Mo Tc Ru Rh Pd Ag Cd In
57
72
74
75
44
27
76
45
46
77
78
47
79
48
80
49
81
Ta
W
Re Os
Ir
Pt Au Hg Tl
105
106
107
109
110
89
108
32
111
112
113
50
9
7
F
N
10
(Lanthanide series)
Ne
a.
60
61
62
63
64
65
66
91
Th Pa
92
U
93
94
95
96
97
98
Hydrogen (H)
Nitrogen (N)
P
S
Cl
Ar
N
33
34
35
36
Na Sodium (Na)
51
52
83
84
Kr
53
54
I
Xe
85
86
Po At Rn
114
116
99
H
18
Pb Bi
67
Oxygen (O)
17
115
117
118
68
69
70
71
Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
90
(Actinide series)
59
O
16
Fr Ra Ac Rf Ob Sg Bh Hs Mt Ds Rg Cn Uut Fl Uup Lv Uus Uuo
58
Carbon (C)
15
Sn Sb Te
82
C
He
Co Ni Cu Zn Ga Ge As Se Br
39
73
43
Fe
104
88
C
26
Cs Ba La Hf
87
6
5
12
19
2
O
100
101
102
103
Cl Chlorine (Cl)
Ca Calcium (Ca)
P
Phosphorus (P)
K Potassium (K)
S
Sulfur (S)
Fe Iron (Fe)
Mg Magnesium (Mg)
Np Pu Am Cm Bk Cf Es Fm Md No Lr
b.
13
Isotopes
• Atoms of a single element
• Different number of neutrons
• Radioactive isotopes are unstable and
emit radiation as the nucleus breaks up
Carbon-12
Carbon-13
Carbon-14
6 Protons
6 Neutrons
6 Electrons
6 Protons
7 Neutrons
6 Electrons
6 Protons
8 Neutrons
6 Electrons
**
** radioactive
Uses for Radioactive Isotopes
Carbon-Dating
http://www.scientificamerican.com/article.cfm?id=carbon-dating-gets-reset
Nuclear Medicine
http://www.rah.sa.gov.au/nucmed/nucmed/ncmd_info.htm
Electrons and Ions
• e- are negatively charged particles
• located in orbitals
• Neutral atoms
• Equal # of protons and e• Ions
• Atoms with a charge
• Unbalanced # of protons and e16
Electrons and Ions
• Types of ions
– Cation – more protons than electrons
–positive charge
– Anion – fewer protons than electrons
–negative charge
17
Electron arrangement
• Determines chemical behavior of atom
• Bohr model – electrons in discrete orbits
• Quantum model – orbital as area around
a nucleus where an electron is most likely
to be found
18
Electron Orbitals
Electron Shell Diagram
Corresponding Electron Orbital
Energy
Level K
One spherical orbital (1s)
Electron Shell Diagram
Corresponding Electron Orbitals
y
z
Energy
level L
x
One spherical orbital (2s)
Electron Shell Diagram
Three dumbbell-shaped orbitals (2kk)
Electron Orbitals
y
z
Each orbital holds a max
of 2 electrons
x
19
Neon
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Reactivity of Elements
• Valence electrons (e-) –
• e- in outermost energy level
• Inert (nonreactive) elements have all 8 e• Octet rule – atoms with 8 e- (2 e- for small
atoms) in outer energy level are stable
Li
Ne
20
1 valence e-
8 valence e-
Reactivity of Elements
• Octet rule –
• Atoms form chemical bonds to obtain
stable octet (8 paired e- in outer most
energy level)
• Valence e- used in chemical bonding
21
Review Question
Isotopes are atoms of the same element but differ in
the number of
a. Electrons
b. Protons
c. Neutrons
d. Orbitals
e. Bonds
Review Question
Radioactive isotopes –
a. Are unstable
b. Decay over time
c. Emit radiation
d. May occur naturally
e. All of the above
Review Question
An atom with more protons than electrons is –
a. An element
b. An isotope
c. A cation
d. An anion
Review Question
Carbon’s atomic number is 6. How many electrons
are in carbon’s outer shell?
a. 2
b. 4
c. 6
d. 8
Review Question
18
O has an atomic number of 8. How many neutrons
does 18O have?
a. 8
b. 10
c. 12
d. 18
2.3 The Nature of Chemical Bonds:
Learning Objectives
• Describe difference between molecule &
compounds
• Explain ionic bonding vs. covalent
bonding
• Understand how electronegativity plays
a role in bond formation
• Polar bonds
• Non-polar bonds
Chemical Bonds
• Molecules are groups of atoms held
together in a stable association
• Compounds are molecules containing
more than one type of element
• Atoms are held together by chemical
bonds
O2, a diatomic molecule
H2O, a compound
28
http://en.wikipedia.org/wiki/File:Oxygen_molecule.png
https://commons.wikimedia.org/wiki/File:Water_molecule_3D.svg
Ionic bonds
• Formed by the attraction of oppositely
charged ions
• Gain or loss of electrons forms ions
Na
Sodium atom
a.
Na+
Sodium ion (+)
Cl
Cl–
Chlorine atom
Chloride ion (–)
Cl–
Na+
Cl–
Na+
Cl–
Na+
Cl–
Na+
Cl–
b. NaCl crystal
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29
Covalent bonds
• Form when atoms share 2 or more
valence electrons
30
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covalent bond
Single covalent bond
Hydrogen gas
H
H
O
N
O
O
N
N
O2
Triple covalent bond
Nitrogen gas
N
H
H2
Double covalent bond
oxygen gas
O
H
N2
31
Structural vs. Molecular Formulas
• Molecular formulas
• Shows number and types of elements
• Structural formulas
• Shows arrangement of atoms and types of
bonds present
32
http://www.cliffsnotes.com/assets/276058.png
Carbon and Organic Compunds
• Carbon can form up to 4 single covalent
bonds
• Carbon atoms can form linear chains or
rings
• These carbon “backbones” form basis of
organic molecules
Glucose (C6H12O6)
33
http://www.nutritionalhq.com/wp-content/uploads/2011/08/Glucose-molecule-model.jpg
Electronegativity
• Atom’s affinity for electrons
• Differences in electronegativity dictate how
electrons are distributed in covalent bonds
– Nonpolar covalent bonds = equal sharing of
electrons
– Polar covalent bonds = unequal sharing of
electrons
34
http://www.chem.ubc.ca/courseware/pH/section10/eshift1.jpg
35
Chemical reactions
• Chemical reactions involve the formation or
breaking of chemical bonds
• Reactants = original molecules
• Products = molecules resulting from reaction
6H2O + 6CO2
reactants
→
C6H12O6 + 6O2
products
36
Chemical reactions
• Extent of chemical reaction influenced by
1. Temperature
2. Concentration of reactants and products
3. Catalysts
• Many reactions are reversible
37
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Review Question
What property of an atom determines how it forms
bonds?
a. Atomic Mass
b. Atomic number
c. Valance electrons
d. Orbits
e. Neutrons
Review Question
What kind of chemical bond is formed when atoms share
one or more pairs of electrons?
a. Covalent bond
b. Ionic bond
c. Hydrogen bond
d. Polar bond
Review Question
Typically an increase in temperature causes the rate of a
chemical reaction to –
a. Decrease
b. Increase
c. Remain the same
2.4 Water: A Vital Compound: Learning
Objectives
• Describe hydrogen bonding
• Explain how hydrogen bonding gives H2O
very important properties
•
•
•
•
•
Cohesiveness and adhesiveness
High specific heat
High heat of vaporization
Ice floating on liquid water
Universal solvent
Water
• Single most outstanding chemical property
of water is its ability to form hydrogen
bonds
– Weak chemical associations that form
between the partially negative O atoms and
the partially positive H atoms of two water
molecules
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43
a. Solid
b. Liquid
c. Gas
a: © Glen Allison/Getty Images RF; b: © PhotoLink/Getty Images RF; c: © Jeff Vanuga/Corbis
Polarity of water
• Within a water molecule, the bonds
between oxygen and hydrogen are highly
polar
• Partial electrical charges develop
– Oxygen is partially negative δ+
– Hydrogen is partially positive δ–
δ
δ+
δ+
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/image15.gif
44
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Bohr Model
Ball-and-Stick Model
+
+
–
+
104.5
8p
8n
+
+
–
–
–
+
a.
b.
Space-Filling Model
+
–
+
45
c.
Hydrogen bonds
• Each individual H-bond is weak and
transitory
• Cumulative effects are enormous
• Responsible for many of water’s important
physical properties
46
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Water molecule
Hydrogen atom
+
Hydrogen bond
a.
–
Oxygen atom
Hydrogen atom
Hydrogen bond
+
–
An organic compound
b.
Oxygen atom
47
• Cohesion – water
molecules stick to
other water molecules
by hydrogen bonding
• Adhesion – water
molecules stick to
other polar molecules
by hydrogen bonding
48
Properties of water
1. Water has a high specific heat
– A large amount of energy is required to
change the temperature of water
49
http://commons.wikimedia.org/wiki/File:Boiling_water.jpg
Properties of water
2. Water has a high heat of vaporization
- The evaporation of water from a surface
causes cooling of that surface
50
http://www.baltimoresun.com/media/photo/2012-05/70086876.jpg
Properties of water
3. Solid water is less dense than liquid
water
- Bodies of water freeze from the top down
http://www.hdwallpapersplus.com/wp-content/uploads/2012/10/iceberg_2.jpg
51
http://sailboatdiaries.com/wp-content/uploads/iceHbonds.gif
52
4. Water is a good solvent
– Water dissolves polar molecules and ions
–
Water molecules
–
–
Na+
–
–
Hydration shells
Na+
Cl–
+
+
+
Cl–
+
+
Salt crystal
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53
53
4. Water is a good solvent
– When H2O dissolves a polar or ionic
compounds like NaCl
– water is the solvent
–NaCl is the solute
• Both solvent and solute make up a
solution
54
http://bio1151.nicerweb.com/Locked/media/ch03/03_07DissolvingSalt-L.jpg
5. Water organizes nonpolar molecules
– Hydrophilic “water-loving”
– Hydrophobic “water-fearing”
– Water causes hydrophobic molecules to
aggregate or assume specific shapes
Hydrophobic molecule
http://www.uic.edu/classes/bios/bios100/lecturesf04am/hydrophobic.jpg
55
6. Water can form ions
H2O  OH– +
H+
hydroxide ion
hydrogen ion
• H+ ions also known as protons
http://www.kmacgill.com/lecture_notes/lecture_notes_17_files/image003.jpg
56
Review Question
Which of the following types of chemical bonds is the
strongest?
a. Hydrogen bond
b. Ionic bond
c. Covalent bond
d. All are equal strength
2.6: Acids and Bases: Learning
Objectives
• Define mole and molar concentration
• Describe acids, bases, and pH scale
• Relate changes in pH to changes in [H+]
• Understand how buffers work
Molar Concentrations
•The molar concentration of H+ or OH- ions in
a solution is the basis of pH scale
•Molar concentration = 1 mole of solute ÷ 1
Liter of solution (mol/L)
• Amount of substance (in grams) in 1
mole = its molecular weight (mass)
• 1 mole of sodium ion Na+ = 23 g
• 1 mole of sodium chloride (NaCl) =
58.44g
59
Acids and bases
• Pure water
– [H+] of 10–7 mol/L
– Considered to be neutral
– Neither acidic nor basic
– [H+] = [OH-]
• pH is the negative logarithm of hydrogen
ion concentration of solution
pH = -log[H+]
pH= –log 10-7 = -(-7)=7
60
Acids and Bases - pH
• Acid (pH < 7)
– Any substance that dissociates in water to
increase the [H+] (and lower the pH)
– The stronger an acid is, the more hydrogen
ions it produces and the lower its pH
• Base (pH > 7)
– Substance that combines with H+ dissolved in
water, and thus lowers the [H+]
61
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Hydrogen Ion
Concentration [H+]
pH Value
Examples of Solutions
100
10–1
0
1
Hydrochloric acid
10–2
10–3
2
3
Stomach acid, lemon juice
Vinegar, cola, beer
10–4
10–5
4
Tomatoes
5
Black coffee
10–6
6
Urine
Acidic
10–7
10–8
8
Seawater
10–9
9
10–10
10
Baking soda
Great Salt Lake
10–11
10–12
11
Household ammonia
10–13
10–14
Pure water
12
Household bleach
13
14
Basic
Sodium hydroxide
62
Review Question
Which of the following properties of water is not a
consequence of its ability to form H bonds?
a. Cohesion
b. High specific heat
c. Adhesion
d. Ability to function as a solvent
e. Neutral pH
Review Question
Paleontologists distinguish rocks from dinosaur bones by
touching their tongues to the object. If their tongue
sticks, it is considered bone. This occurs because the
water from the tongue moves up the porous spaces of
bone. What property of water is allowing this to occur?
a. Cohesion
b. Capillary action
c. Water ionization
d. Heat of vaporization
Review Question
A water strider is an insect that can walk on water.
How is this possible?
a. Capillary action
b. Hydration shells
c. Hydrophobic exclusion
d. Surface tension
Review Question
Hydrogen bonding between water molecules makes
them tend to stick together. How does this affect the
specific heat (SH) and heat of vaporization (HOV) of
water?
a. The SH and HOV of water are high
b. The SH and HOV of water are low
c. SH is high but HOV is low
d. HOV is high but SH is low
e. None of these answers are correct
Review Question
Which of the following has the lowest concentration of
H+ ions?
a. pH = 2
b. pH = 6
c. pH = 8
d. pH = 12
e. pH = 14
Buffers
• Substance that resists changes in pH
• Act by
– Releasing H+ when a base is added
– Absorbing H+ when acid is added
• Overall effect of keeping [H+] relatively
constant
68
Buffers
• Most biological buffers consist of a pair of
molecules, one an acid and one a base
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–
+
Water
(H2O)
+
+
Carbon
dioxide
(CO2)
Carbonic
acid
(H2CO3)
+
Bicarbonate Hydrogen
ion
ion
+
(H+)
(HCO3–)
69
Buffers Minimize pH Changes
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pH
9
8
7
6
5
4
3
2
1
0
Buffering range
0
1X
2X
3X
4X
Amount of base added
5X
70