CM1501-Week 1A & 1B-Struc Bonding

CM1501 Week 1A & 1B Structure & Bonding
For lab matters, visit IVLE module

CM1501_LAB/CM1501
Textbook
Organic Chemistry, Second Edition

Janice Gorzynski Smith
University of Hawaii
Monday Lecture: 45 mins
Thursday Lecture: 90 mins
(no break)
Teaching Staff
DR Zeng Huaqiang:
chmzh@nus.edu.sg
MS Ong Yue Ying:
chmoyy@nus.edu.sg
2
CM1501 Course Schedule

Week 1
Week 2
Chapter 1: Structure and Bonding

Chapter 2: Acids and Bases
Chapter 3: Introduction to Organic Molecules & Functional Groups
Week 3
Chapter 4: Alkanes
Week 4
Chapter 5: Stereochemistry
Chapter 6: Understanding Organic Reactions
Weeks 5-6
Chapter 7: Alkyl Halides and Nucleophilic Substitution

Chapter 8: Alkyl Halides and Elimination Substitution
Week 7
Week 8
Chapter 9: Alcohols, Ethers and Epoxides
Weeks 9-11
Chapter 11: Alkynes
Chapter 10: Alkenes

Chapter 16: Conjugation, Resonance and Dienes
Chapter 17: Benzene and Aromatic Compounds
Chapter 22: Carboxylic acids and Their Derivatives
Week 12
Chapter 19: Carboxylic Acids and the Acidity of the O-H Bond
Chapter 21: Aldehydes and Ketones
Week 13
Chapter 25: Amines and whole class tutorial
CM1501 Assessments
Mid-Term Exam
30 %
Final Exam
50 %
Practical Section
20 %
Total
100 %
Mid Exam: 04-10-2012, 4:10-5:50pm at MPSH1, section A+B

Final Exam: Monday, 03-12-2012 (1:00-3:00 pm)
CLOSED BOOK EXAMINATION

4
What is Organic Chemistry?

Volume of atom depends on the size
of the electron cloud.
Organic chemistry is the study of carbon compounds.

Why is it so special?
-
90% of more than 30 million chemical compounds contain

carbon.
Examination of carbon in periodic chart answers some of

these questions.
Carbon is group 4A element, it can share 4 valence

electrons and form 4 covalent bonds.
5
Silicon As An Alternative Element for Life?
12
6
28
14 Silicon
Carbon
Smaller in size and lighter in
mass.
mass.
Can
Larger in size and heavier in
form
double
or
triple
bonds.
Can form alkane hydrocarbons
or long carbon chains
CO2 is gas & soluble in water
Difficult to form double or triple

bonds.
Silanes, the analogs of alkane
hydrocarbons, are highly reactive
and may decompose easily
SiO2 is non-soluble solid.
The Periodic Table

The nucleus (very dense; very small: 10-15 m; Neutral atom
protons = electrons
1 fm) contains positively charged protons
Cations
and uncharged neutrons.

The
electron
cloud
(10-10m;
protons > electrons

~
2)
is Anions
composed of negatively charged electrons.
protons < electrons
Atomic number
Isotope
The Periodic Table

Atomic weight: the weighted average of the mass of all isotopes
reported in atomic mass units (amu)
Carbon as the example: 12.011 = 12 x 98.9% + 13 x 1.1%
A comparison of two isotopes of the element carbon

8
The Periodic Table

1A
2A
3B
4B
5B
6B
7B
8B
8B
8B
1B
2B
3A
4A
5A
6A
7A
8A
2
8
8
18
18
32
32
http://www.dayah.com/periodic/
The Periodic Table

Periodic Trends
Elements in the same row are similar in size.
Elements in the same column have similar electronic and
chemical properties.
From left to right
From top to bottom
- +
Atomic radius
Atomic radius
Electronegativity
Electronegativity
Ionization energy
Ionization energy
10
The Periodic Table

Atomic Orbital:
A region of space that is
high in electron density
1s (1)
2s (1)
2p (3)
3s (1)
3p (3)
4f
3d (5)
Four types: s, p, d, and f
s and p orbitals most

important in organic and
biological chemistry.
There are ONE s orbital,

THREE p orbitals, FIVE
d orbitals and SEVEN f
orbitals.
Each orbital can hold

two electrons.
Energy gradient
Electron filling
priority
11
The Periodic Table

Orbitals and Shells
Orbitals are grouped in shells of increasing size and energy
Different shells contain different numbers and kinds of orbitals
Each orbital can be occupied by two electrons with opposite spins

3d
3p
3s
2p
Hund's rule
2s
1s
Pauli exclusion principle

12
The Periodic Table

Orbitals and Shells
Orbitals are grouped in shells of increasing size and energy
Different shells contain different numbers and kinds of orbitals
Each orbital can be occupied by two electrons with opposite spins
13
The Periodic Table
8A
Noble Gas
Configuration
2
2+8
2+8+8
2
8
8
18
18
32
6s24f145d106p6
1s2
2s22p6
3s23p6
2+8+8+18
2+8+8+18+18
4s23d104p6
5s24d105p6
2+8+8+18+18+32
14
The Periodic Table

Columns
1A
1s1
Vary the inner shell while

keeping outer shell constant
1s2 2s1
2
1s2 2s22p6 3s1

2
1s2 2s22p6 3s23p6 4s1

2
1s2 2s22p6 3s23p6 4s23d104p6 5s1

2
18
1s2 2s22p6 3s23p6 4s23d104p6 5s24d105p6 6s1

2
18
18
15
The Periodic Table

Rows
Second row
Vary the outer shell while

keeping inner shell constant
First row
2
2
1s2 2s22p6
1s2
1s1 1s2
2s1
2s2
2s22p2
2s22p1
2s22p4
2s22p3
2s22p6
2s22p5
16
The Periodic Table

Shapes of Atomic Orbitals
s orbitals: spherical, nucleus at center

p orbitals: dumbbell-shaped, nucleus at middle
d orbitals: cloverleaf-shaped, nucleus at center
1s orbital
2p orbital
3d orbital
No electron density at the planar nodes

http://winter.group.shef.ac.uk/orbitron/AOs/6s/index.html
17
The Periodic Table

Shapes of Atomic Orbitals
s orbitals: spherical, nucleus at center

p orbitals: dumbbell-shaped, nucleus at middle
d orbitals: cloverleaf-shaped, nucleus at center
Y
X
Z
http://winter.group.shef.ac.uk/orbitron/AOs/6s/index.html
18
Bonding
Review
Through bonding,
1) two atoms are joined in a stable arrangement.
2) atoms attain a complete outer shell of valence
electrons, a stable noble gas configuration.
2+8
2+8+8
2+8+8+18
Ionic bonds: transfer of electrons from one element

to another.
2+8+8+18+18
Covalent bonds: sharing of electrons between two

nuclei.
2+8+8+18+18+32
19
Bonding Forces
Ionic Bond
Generally occurs when elements (e.g., Na) on the far left side of the
periodic table combine with elements (e.g., Cl) on the far right side,
ignoring noble gases.
Cl
1s22s22p63s23p5
Na 1s22s22p63s1
Change in electronic configuration
2+8+8 (2+8+7)
2+8 (2+8+1)
2+8
2+8+8
20
Bonding Forces
Covalent bond
First row elements such as hydrogen can accommodate two
electrons around it, making it like the noble gas helium.
Bonding in Molecular Hydrogen (H2)
Hydrogen forms one covalent bond. Each has a filled valence shell
of two electrons
Lewis structure representation
21
Bonding Structure
Noble gas configuration & Octet Rule
Second row elements can have no more than eight electrons
around them. Atoms such as C, N, O, F with four or more valence
electrons form enough bonds to give an octet.
Examples:
1) Carbon has four valence electrons (2s22p2), forming four
bonds.
2) Nitrogen has five valence electrons (2s22p3) but forms
only three bonds.
3) Oxygen has six valence electrons (2s22p4) but forms two
bonds.
22
The Periodic Table
23
Exceptions to the Octet Rule

Elements in Groups 2A and 3A in the Second Row
Elements in the Third Row
24
Bonding Structure
Lewis structures
Lewis structures are electron dot representations for molecules.
Three general rules for drawing Lewis structures:
1.
2.
3.
Draw only the valence electrons.

Give each hydrogen two electrons
Give second-row elements (C, N, O, & F) an octet of electrons, if possible.
In a Lewis structure, a solid

line indicates a two-electron
covalent bond.
25
Bonding Structure
Lewis structures
Lewis structures are electron dot representations for molecules.
Three general rules for drawing Lewis structures:
1.
2.
3.
Draw only the valence electrons.

Give each hydrogen two electrons
Give second-row elements (C, N, O, & F) an octet of electrons, if possible.
26
Formal Charge
Formal charge is the charge assigned to individual atoms in a
Lewis structure.
Formal charge is used to determine how the number of
electrons around a particular atom compares to its number of
valence electrons.
The number of electrons owned by an atom is determined by

its number of bonds and lone pairs.
An atom owns all of its unshared electrons and half of its
shared electrons.
27
Formal Charge
The number of electrons owned by different atoms is indicated
in the following examples:
Example 1: neutral
Example 3: anion
Example 2: neutral
28
Formal Charge
Formal charge observed with common bonding patters

29
Structural (constituitional) isomers

1. Chain isomerism
2. Positional isomerism
3. Functional group isomerism
Isomers
Stereoisomer (spatial isomer)

1. Cis-trans isomer/geometric isomer
2. Chiral carbon/optical isomer
More than one arrangement of atoms is possible for a given

molecular formula.
The above two are valid Lewis structures and both exist. These two
compounds are called isomers.
Ethanol and dimethyl ether are constitutional isomers.
30
Resonance Structures
Some molecules cannot be adequately represented by a single Lewis structure.
Resonance structures are two Lewis structures having the same placement of
atoms but a different arrangement of electrons
Neither resonance structure is an accurate representation for the true
structure, which is a composite of both resonance forms and is called a
resonance hybrid.
Electron delocalization adds stability.
The hybrid is a weighted average of the contributing resonance structures.
31
Basic Principles
1. Resonance structures are not real. An individual resonance
structure does not accurately represent the structure of a
molecule or ion. Only the hybrid does.
2. Resonance structures are not in equilibrium with each other.
There is no movement of electrons from one form to
another.
3. Resonance structures are not isomers. Two isomers differ in
the arrangement of both atoms and electrons, whereas
resonance structures differ only in the arrangement of
electrons.
32
Resonance Hybrids
A better resonance structure is one that has 1) more bonds,

2) fewer charges, and 3) negative charges preferentially
localized on more electronnegative elements.
Major resonance
structure
33
Drawing Resonance Structures
Rule [1]: Two resonance structures differ in the position of multiple bonds and
nonbonded electrons. The placement of atoms and other single bonds always
stays the same.
Rule [2]: Two resonance structures must have the same number of unpaired
electrons.
34
Rule [3]: Resonance structures must be valid Lewis structures: hydrogen
must have two electrons and no second-row element can have more than
eight electrons.
35
Curved Arrow Notation
Shows the movement of an electron pair: the tail of the arrow always
begins at the electron pair, either in a bond or lone pair. The head points to
where the electron pair moves.
Example 1:
Example 2:
36
A lone pair is located on an atom directly bonded to a double bond
37
In the above examples,
An atom bearing a (+) charge is bonded either to a double bond
or an atom with a lone pair.
38
Molecular Dimensionality
Two variables define a molecules structure: bond length and
bond angle.
Bond length decreases across a row of the periodic table as the

size of the atom decreases.
Bond length increases down a column of the periodic table as the

size of an atom increases.
39
Bond length
40
Bond angle
Bond angle determines the shape around any atom bonded to two other
atoms.
The number of groups surrounding a particular atom determines its
geometry. A group is either an atom or a lone pair of electrons.
The most stable arrangement keeps these groups as far away from each
other as possible.
Predicting Geometry Based on Counting Groups Around the Central Atom
41
Bond angle
Two groups around an atom
42
Bond angle
Three groups around an atom
43
Bond angle
Four groups around an atom
44
Drawing Three Dimensional Structures
A solid line is used for a bond in the plane.

A wedge is used for a bond in front of the plane.
A dashed line is used for a bond behind the plane.
45
The molecule can be turned/rotated in many different ways,
generating many equivalent representations. All of the following
are acceptable drawings for CH4.
46
Note that wedges and dashes are used for groups that are
really aligned one behind another. It does not matter in the
following two drawings whether the wedge or dash is skewed to the
left or right, because the two H atoms are really aligned.
47
A Nonbonded Pair of Electrons is Counted as a Group
In water (H2O), two of the four groups attached to the central O atom
are lone pairs. The two H atoms and two lone pairs around O point
to the corners of a tetrahedron. The H-O-H bond angle of 105 is
close to the theoretical tetrahedral bond angle of 109.5. Water has a
bent shape, because the two groups around oxygen are lone pairs of
electrons.
48
A Nonbonded Pair of Electrons is Counted as a Group
In ammonia (NH3), one of the four groups attached to the central N
atom is a lone pair. The three H atoms and the lone pair point to the
corners of a tetrahedron. The H-N-H bond angle of 107 is close to
the theoretical tetrahedral bond angle of 109.5. This shape is
referred to as a trigonal pyramid.
49
109o
Methane (CH4)
In both NH3 and H2O, the

bond angle is smaller than
the theoretical tetrahedral
Ammonia (NH3)
bond
angle
because
of
repulsion of the lone pairs

of electrons. The bonded
atoms are compressed into
a smaller space with a
Water (H2O)
smaller bond angle.
50
Drawing Organic MoleculesCondensed Structures
Drawing every bond in organic molecule can become tedious.
Several shorthand methods have been developed to write

structures.
Condensed structures typically dont have C-H or C-C single

bonds shown.
51
Drawing Organic MoleculesCondensed Structures
All atoms are drawn in with two-electron bond lines omitted.
Atoms are usually drawn next to the atoms to which they are
bonded.
Parentheses are used around identical groups bonded to the same
atom.
Lone pairs are omitted.
52
Condensed Structures
53
54
Skeletal structures
Assume there is a carbon atom at the junction of any two lines or at
the end of any line.
Assume there are enough hydrogens around each carbon to make
it tetravalent.
Draw in all heteroatoms and hydrogens directly bonded to them.
55
Skeletal structures
56
Skeletal structures
A charge on a carbon atom takes the place of one hydrogen
atom.
Negatively charged carbon atoms have one lone pair and
positively charged carbon atoms have none.
Cannot be bonded to 3 H
atoms, otherwise octet
will be lost
57
Orbitals and Bonding

Hydrogen
When the 1s orbital of one H atom overlaps with the 1s orbital of
another H atom, a sigma () bond that concentrates electron
density between the two nuclei is formed.
This bond is cylindrically symmetrical because the electrons
forming the bond are distributed symmetrically about an
imaginary line connecting the two nuclei.
58

Methane
Carbon has four valence electrons; two in the 2s orbital and
one each in 2p orbitals.
Carbon forms four identical bonds in methane
Ground
state
Methane (CH4)
Excited
state
59

sp3 Hybrid Orbitals
The mixing of a spherical 2s orbital and three dumbbell shaped 2p orbitals
together produces four hybrid orbitals, each having one large lobe and one
small lobe.
The four hybrid orbitals are oriented towards the corners of a tetrahedron, and
form four equivalent bonds.
60

sp3 Hybrid Orbitals
Each bond in CH4 is formed by overlap of an sp3 hybrid orbital of
carbon with a 1s orbital of hydrogen. These four bonds point to the
corners of a tetrahedron.
+
C (sp3)
Bonding Using sp3 Hybrid Orbitals
4
H (1s)
61

sp2 & sp Hybrid Orbitals
One 2s orbital and two 2p orbitals form three sp2 hybrid orbitals.
One 2s orbital and one 2p orbital form two sp hybrid orbitals.
sp3
62

Determining Hybridization Patterns
To determine the hybridization of an atom in a molecule, we
count the number of groups around the atom. The number of
groups (atoms and nonbonded electron pairs) corresponds to the
number of atomic orbitals that must be hybridized to form the hybrid
orbitals.
63
2s22p5
Hybrid orbitals of
NH3 and H2O
64
Total must have 1s

and 3p orbitals
altogether.

Hybridization in BF3
B: sp2 + one empty 2p orbital

F: sp2 + one filled 2p orbital
Dotted lines refers to

extra electron density
The bonds between B and F are the result of sp2 hybrid orbital overlap
This leaves the B atom and each of the F atoms with a p orbital not used in the bond
formation. The filled F orbital and unfilled B orbital give rise to localized interactions
65

B: sp2 + one empty 2p orbital
sp2
+
filled 2p
empty 2p
66
CM1501 Week
Lecture
1A1& 1B
Structure
Structure
& Bonding
& Bonding

Resonance Structures for BF3
The presence of the resonance contributors in the bottom
line account for the partial double bond character in BF3
B:
sp2
+ one empty 2p orbital
67
CM1501 Week
Lecture
Structure
& Bonding
1A1& 1B
Structure
& Bonding
Although F is more
electronegative than B,
there is still a positive
charge on F because fluorine
has to share some of its
electron density with boron
so that the whole molecule
BF3 will be stable.

Resonance Structures for
68

Each carbon is tetrahedral.
Each carbon is sp3 hybridized
69

Each carbon is trigonal and planar.
70

Each carbon is trigonal and planar.
Unlike the CC bond in ethane, rotation about the CC double bond in

ethylene is restricted as it involves the breaking of bond .
71

Each carbon is
diagonal and linear.
Each carbon is sp
hybridized
Two bonds and
two bonds
72

Each carbon is
diagonal and linear.
Each carbon is sp
hybridized
Two bonds and
two bonds
73
74

Bond Length and Bond Strength
As the number of electrons between two nuclei increases, bonds become
shorter and stronger.
Stronger bond does not

mean better stablility
75

The length and strength of CH bonds vary depending on the
hybridization of the carbon atom.
76
s is smaller than p. Degree

of overlapping with s is
larger compared to p, hence
larger percent of scharacter, the stronger the
bond.
Although sp3, sp2 and sp hybrid orbitals are

similar in shape, they are different in size
77
Electronegativity and Bond Polarity

Electronegativity is a measure of an atoms attraction for electrons in a
bond.
Electronegativity values for some common elements
78

Calculated values, not
determined by
experiments
Periodic Electronegativity Values
79

Electronegativity values are used as a guideline to indicate whether the
electrons in a bond are equally shared or unequally shared between two
atoms. When electrons are equally shared, the bond is nonpolar. When
differences in electronegativity result in unequal sharing of electrons, the
bond is polar, and is said to have a separation of charge or a dipole.
80

Bonding between atoms of different electronegativity values results in unequal
sharing of electrons.
Example: In the C-O bond, the electrons are pulled away from C (2.5) toward O
(3.4), the element of higher electronegativity. The bond is polar, or polar covalent.
The bond is said to have dipole; that is, separation of charge.
+ means the indicated

atom is electron
deficient.
E = 2.5
E = 3.4
- means the indicated

atom is electron rich.
The direction of polarity in a bond is indicated by an arrow with the head of the
arrow pointing towards the more electronegative element. The tail of the arrow,
with a perpendicular line drawn through it, is drawn at the less electronegative
element.
81
Polarity of Molecules
Use the following two-step procedure to determine if a molecule
has a net dipole:
1.
Use electronegativity differences to identify all of the polar bonds and

the directions of the bond dipoles.
2.
Determine the geometry around individual atoms by counting groups,

and decide if individual dipoles cancel or reinforce each other in space.
Electrostatic potential plot of CH3Cl
82
Polarity of Molecules
A polar molecule has either one polar bond, or two or more bond dipoles
that reinforce each other. An example is water:
A nonpolar molecule has either no polar bonds, or two or more bond

dipoles that cancel. An example is carbon dioxide:
83
The Periodic Table

Column
(2+8+8+1) 1s22s22p63s23p64s1
2s1
(2+8+1) 1s22s22p63s1
(2+1) 1s22s1
(1) 1s1
2
8
8
18
18
32
1s2
1s1
3s1
4s1
2s1 2s2
2s22p2
2s22p4
2s22p6
2s22p6
3s23p6
Rows
3d104s24p6
4d105s25p6
4f145d106s26p6
84

CM1501-Week 1A &amp; 1B-Struc Bonding

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CM1501 Week 1A & 1B Structure & Bonding

For lab matters, visit IVLE module

CM1501 Week 1A & 1B Structure & Bonding

Organic Chemistry, Second Edition

MS Ong Yue Ying:

CM1501 Week 1A & 1B Structure & Bonding

CM1501 Course Schedule

Chapter 1: Structure and Bonding

Chapter 7: Alkyl Halides and Nucleophilic Substitution

Chapter 9: Alcohols, Ethers and Epoxides

Chapter 11: Alkynes

Chapter 10: Alkenes

Chapter 25: Amines and whole class tutorial

CM1501 Week 1A & 1B Structure & Bonding

Mid Exam: 04-10-2012, 4:10-5:50pm at MPSH1, section A+B

CLOSED BOOK EXAMINATION

CM1501 Week 1A & 1B Structure & Bonding

What is Organic Chemistry?

Organic chemistry is the study of carbon compounds.

90% of more than 30 million chemical compounds contain

Examination of carbon in periodic chart answers some of

Carbon is group 4A element, it can share 4 valence

CM1501 Week 1A & 1B Structure & Bonding

Silicon As An Alternative Element for Life?

Smaller in size and lighter in

Larger in size and heavier in

Difficult to form double or triple

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

and uncharged neutrons.

protons > electrons

composed of negatively charged electrons.

protons < electrons

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

A comparison of two isotopes of the element carbon

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

From top to bottom

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

Four types: s, p, d, and f

s and p orbitals most

There are ONE s orbital,

Each orbital can hold

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

Orbitals are grouped in shells of increasing size and energy

Different shells contain different numbers and kinds of orbitals

Each orbital can be occupied by two electrons with opposite spins

Pauli exclusion principle

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

Orbitals are grouped in shells of increasing size and energy

Different shells contain different numbers and kinds of orbitals

Each orbital can be occupied by two electrons with opposite spins

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

CM1501 Week 1A & 1B Structure & Bonding

The Periodic Table

Vary the inner shell while

CM1501-Week 1A & 1B-Struc Bonding

CM1501-Week 1A & 1B-Struc Bonding