The Chemical Context of Life:
Atoms, Bonding, Molecules
Today s Topics:
•  Atomic Structure and
bonding
Matter
Compounds
Elements
Two or more types of atoms
bonded together in a fixed ratio
Made up of only One
type of atom
Now a
NEW SUBSTANCE
–  Periodic Table
•  Ionic Bonds
•  Covalent Bonds
•  Hydrogen Bonds
(if time)
+
Figure 2.2
Sodium
Sep 2, 2015
Chlorine
Sodium Chloride
Electrons are
arranged in
SHELLS
Structure of Atoms
Helium
Potassium:
1 outer shell electron
Fluorine:
7 outer shell
electrons
Atoms differ by the number of
protons and electrons
Electrons are
–
Nucleus
Figure 2.11+ Electron
Shells
arranged in
First shell
(2 electrons
maximum)
shells
Hydrogen (H)
–
–
–
–
–
–
–
–
–
–
–
Second
–
–
6+ – –
7+ – –
8+ –
shell
(8 electrons
–
–
–
maximum) Carbon (C) Nitrogen (N) Oxygen (O)
shell
8 Third
X
(18
electrons
maximum)
–
–
–
– –
––
–
–
–
15+
–
–
–
–
– –
–
–
Various ways to draw molecules
– –
–
–
–
–
16+
–
– –
– –
–
–
–
Phosphorus (P)
Sulfur (S)
H
O
H
O
H
H
H-O
|
H 2O
H
1
•  The periodic table of the elements
shows the electron distribution for all the
elements
Hydrogen
1H
Atomic mass
First
shell
Lithium
3Li
Beryllium
4Be
Boron
3B
Carbon
6C
2
He
4.00
Atomic number Helium
2He
Element symbol
Electron-shell
diagram
Nitrogen
7N
Oxygen Fluorine
8O
9F
Neon
10Ne
Second
shell
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur
13Al
16S
11Na
12Mg
14Si
15P
Chlorine
17Cl
Argon
18Ar
Third
shell
Isotopes differ in the number
of neutrons
Bonding:
Ionic Bonding
12C
99%
1%
tiny bit
13C
Are these isotopes
charged?
14C
Do they have different
chemical bonding
properties?
When atoms have very different
Electronegativities, form an Ionic Bond
Hydrogen
1H
Atomic mass
First
shell
Lithium
3Li
Second
shell
Beryllium
4Be
Weak
ElectroNegativity
Boron
3B
Carbon
6C
2
He
4.00
Nitrogen
7N
Third
shell
Theft
Sharing
Figure 2.6 Ionic Attraction
between Sodium and Chlorine
Atomic number Helium
2He
Element symbol
Electron-shell
diagram
Strong
ElectroNegativity
Oxygen Fluorine
8O
9F
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur
13Al
16S
11Na
12Mg
14Si
15P
Nearly
Empty
Outer
Shells
Covalent Bonding
Chlorine
NearlyCl
Full
Outer
shells
17
Electronically
Stable
Neon
10NeFull
Outer
Shells
Argon
NON18Ar
Sodium atom (Na)
(11 protons, 11 electrons)
Chlorine atom (Cl)
(17 protons, 17 electrons)
Ionic
attraction
+
_
REACTIVE
Sodium ion (Na+)
(11 protons, 10 electrons)
Chloride ion (Cl–)
(17 protons, 18 electrons)
2
What are some other ionic compounds?
Covalent Bonds
Form between atoms of similar electronegativity
Hydrogen
1H
Atomic mass
First
shell
Lithium
3Li
Beryllium
4Be
Boron
3B
Carbon
6C
Atomic number Helium
2He
2
He
4.00
Nitrogen
7N
Element symbol
Hydrogen
1H
Electron-shell
diagram
Oxygen Fluorine
8O
9F
First
shell
Neon
10Ne
Lithium
3Li
Second
shell
Beryllium
4Be
Boron
3B
Carbon
6C
Chlorine
17Cl
Argon
18Ar
Element symbol
Electron-shell
diagram
Nitrogen
Oxygen Fluorine
8
9F
O
N
Intermediate
ElectroNegativity
Second
shell
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur
13Al
16S
11Na
12Mg
14Si
15P
Atomic number Helium
2He
2
He
4.00
Atomic mass
7
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur
13Al
16S
11Na
12Mg
14Si
15P
Third
shell
Chlorine
17Cl
Neon
10Ne
Argon
18Ar
Third
shell
Figure 2.8
Figure 2.8
Covalent Bonding: Sharing
Covalent Bonds have a Specific Geometry
Same electronegativity
H
Name
(molecular
formula)
H
•  Full outer shells
•  Atoms overlap
•  Physically connected
with fixed geometry
H-H
Molecules have
covalent bonds
Structural
formula
Electron-shell
diagram
Water (H2O).
Spacefilling
model
H
O
H
Methane (CH4).
H
H
C
H
H
H2
Fig. 2-12b
Double Bonds
Name and
Molecular
Formula
ElectronLewis Dot
distribution Structure and
Diagram
Structural
Formula
Oxygen (O2)
These oxygen atoms
share two pairs of
electrons.
Spacefilling
Model
Missing
2
3
4
electrons
always
makes
2
3
4
bonds
water
cytosine
3
Fig. 2-18
Molecular Shape determines
Function
Key
Natural endorphin
Molecular
Shape
Determines
Function
Carbon
Hydrogen
Nitrogen
Sulfur
Oxygen
Morphine
Natural
endorphin
Morphine
Endorphin
receptors
Two Types of Covalent Bonds
Polar covalent bonds
Oxygen is more electronegative
than hydrogen
Non-polar
δ–
Polar
δ+
H
Polar
covalent
bonds
δ–
O
Partial negative
charge on the oxygen;
H
δ+
Partial positive charge
on the hydrogen.
Like little magnets:
S
N
S
N
S
+
N
+
+
+
+
+
Hydrogen Bonds
+
Liquid water
+
4