Chem211E Unit 01

Chem211E Organic Chemistry Unit I.
Structure and Bonding | 1
Unit I
Structure and Bonding
Contents of Unit I.
1.1 Review: Atomic Structure
1.1.1 Nucleus
1.1.2 Orbitals
1.2 Bonding
1.2.1 Chemical Bonding Theory
1.2.2 Bonding
1.2.3 Lewis Structures
1.2.4 Formal Charge
1.2.5 Isomers
1.2.6 Exceptions to Octet Rule
1.3 Resonance
1.3.1 Resonance Thoery
1.3.2 Resonance Structure
1.3.3 Resonance Hybrid
1.4 Molecular Shape
1.4.1 Bond Length
1.4.2 Bond Angle
1.5 Organic Structures
1.5.1 Condensed Structures
1.5.2 Skeletal Structures
1.6 Orbital Hybridization
1.6.1 Hydrogen
1.6.2 𝑠𝑝3 Hybrid Orbitals
1.6.3 𝑠𝑝2 Hybrid Orbitals
1.6.4 𝑠𝑝 Hybrid Orbitals
1.6.5 Hybridization of Atoms other than Carbon
1.7 Bond Length and Bond Strength
1.7.1 Comparison of Carbon-Carbon Bonds
1.7.2 Comparison of Carbon-Hydrogen Bonds
1.8 Electronegativity and Bond Polarity
1.8.1 Electronegativity
1.8.2 Polarity of Molecule
1.9 Molecular Orbital Theory
At the end of the unit, the students shall be able to:

1. Explain the types of bonding involving carbon and other atoms.
2. Draw Lewis and Kekulé molecular structures involving carbon and other atoms.
3. Draw shorthand, skeletal and condensed, structures of organic molecules.
4. Discuss the formation hybrid orbitals and its differences.
5. Determine polarity of molecules based on electronegativity differences between atoms forming a
bond.
Chem211E Organic Chemistry Unit I. Structure and Bonding | 2
1.1 Review: Atomic Structure

The Dalton’s atomic theory on the nature of matter was based from below hypotheses:
• Elements are composed of extremely indivisible small particles called atoms. These atoms can neither be created
nor destroyed.
• All atoms of a given element are identical, having the same size, mass, and chemical properties. The atoms of one
element are different from the atoms of all other elements.
• Compounds are composed of atoms of more than one element. In any compound, the ratio of the numbers of atoms
of any two of the elements present is either an integer or a simple fraction.
• A chemical reaction involves only the separation, combination, or rearrangement of atoms; it does not result in
their creation or destruction.
Below laws govern the formation of compounds:
Law of definite proportions states that different samples of the same

compound always contain its constituent elements in the same proportion
by mass.
Law of multiple proportions states that if two elements can combine to form
more than one compound, the masses of one element that combine with a
fixed mass of the other element are in ratios of small whole numbers.
Law of conservation of mass states that the total mass of substances present
at the end of a chemical process is the same as the mass of substances
present before the process took place.
1.1.1 The Nucleus

Through experimentation, scientists have learned that an atom consists of a dense, positively charged nucleus
surrounded at a relatively large distance by negatively charged electrons. The nucleus consists of subatomic particles
called neutrons, which are electrically neutral, and protons, which are positively charged. Ideally, an atom is neutral
in charge, the number of positive protons in the nucleus and the number of negative electrons surrounding the
nucleus are the same.
Figure 1.1 Schematic view of an atom. Source: McMurry (2018)
Below table shows properties of these elementary particles. Since the mass of an electron is negligible, the
nucleus contains almost all the mass of the atom. Electrons circulate around the nucleus at a distance of
approximately 10−10 m. Thus, the diameter of a typical atom is about 2 × 10−10 m (≈ 2 𝑎𝑛𝑔𝑠𝑡𝑟𝑜𝑚 Å).
Table 1.1 Properties of Elementary Particles

Mass
Particle Charge
Grams Atomic Mass Units
Electron 9.109383 x 10 -28 0.0005485799 -1
Proton 1.672622 x 10 -24 1.007285 +1
Neutron 1.674927 x 10 -24 1.008665 0
A specific atom is described by its atomic number (Z), which gives the number of protons
in the nucleus of each atom of an element, and its mass number (A), which gives the total of
protons and neutrons present in the nucleus of an atom in the element. All the atoms of a given
element have the same atomic number but they can have different mass numbers, depending 𝑋 : element
on how many neutrons they contain. Isotopes are atoms of the same element having the same 𝐴 : mass number
atomic number but different mass numbers. The weighted average mass in atomic mass units 𝑍 : atomic number
(amu) of an element’s naturally occurring isotopes is called the element’s atomic mass (or
atomic weight).
Example
23 𝐴𝑡𝑜𝑚𝑖𝑐 𝑛𝑢𝑚𝑏𝑒𝑟 = 11 𝑁𝑜. 𝑜𝑓 𝑝𝑟𝑜𝑡𝑜𝑛𝑠 = 11

11𝑁𝑎 𝑀𝑎𝑠𝑠 𝑛𝑢𝑚𝑏𝑒𝑟 = 23 𝑁𝑜. 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 = 11
𝑁𝑜. 𝑜𝑓 𝑛𝑒𝑢𝑡𝑟𝑜𝑛 = 23 − 11 = 12
Example
1 𝑀𝑎𝑠𝑠 𝑛𝑢𝑚𝑏𝑒𝑟 = 1 𝑁𝑜. 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 = 1

1𝐻 𝐴𝑡𝑜𝑚𝑖𝑐 𝑛𝑢𝑚𝑏𝑒𝑟 = 1 𝑁𝑜. 𝑜𝑓 𝑝𝑟𝑜𝑡𝑜𝑛𝑠 = 1
𝑁𝑜. 𝑜𝑓 𝑛𝑒𝑢𝑡𝑟𝑜𝑛 = 1 − 1 = 0


In addition to neutral atoms, charged ions can also be observed in organic chemistry. A cation is positively
charged ion and has fewer electrons than its neutral form. While an anion is negatively charged ion and has more
electrons than its neutral form.
1.1.2 Orbitals
According to the quantum mechanical model, the behavior of a specific electron in an atom can be described by
a mathematical expression called a wave equation. The solution to a wave equation is called a wave function, or
orbital (𝜓). The square of the wave function (𝜓 2 ) occupies a three-dimensional space in a plot describing a volume
around a nucleus that an electron can occupy. The orbital would appear as a blurry cloud indicating the region of
space around the nucleus where the electron has been.
The orbitals in an atom are organized into different layers, or electron shells, of successively larger size and
energy. Each shell contains a certain number of subshells, or orbitals. It is a region of space that is high in electron
density. Each type of orbital occupies a certain space and has a particular shape.
A. Four Kinds of Orbitals

There are four different kinds of orbitals, s, p, d, and f.
Figure 1.2 Representations of s, p, and d orbitals. Source: McMurry (2018)

A.1 𝒔 Orbital
The s orbitals are spherical electron density, with the nucleus at their center. It is lower in energy than
other orbitals of the same shell, because electrons are kept close to the positively charged nucleus. An s orbital
is fi lled with electrons before a p orbital in the same shell.
A.2 𝒑 Orbital
The p orbitals are dumbbell-shaped. A p orbital is higher in energy than an s orbital (in the same shell)
because its electron density is farther away from the nucleus. A p orbital is filled with electrons only after an s
orbital of the same shell is full
The three different p orbitals within a given shell are oriented in space along mutually perpendicular
directions, denoted 𝑝𝑥 , 𝑝𝑦 , and 𝑝𝑧. As shown in below figue, the two lobes of each p orbital are separated by a
node, it is a region with no electron density. Furthermore, the two orbital regions separated by the node have
different algebraic signs, + and – indicated as different color in below figrue, in the wave function that is
responsible to chemical bonding and chemical reactivity.
Figure 1.3 Shapes of 2p orbitals. Source: Smith (2010)
A.3 𝒅 Orbital
The four of the five of d orbitals are cloverleaf-shaped. The fifth d orbital is shaped like an elongated
dumbbell with a doughnut around its middle.
Figure 1.4 Distribution of electrons in each orbital contained in an electron shell. Source: McMurry (2018)
Across each row of the periodic table, electrons are added to a particular shell around the nucleus. It is added
first to the shells closest to the nucleus. These electrons in the inner shell of orbitals are called core electrons while
the outermost electrons are called valence electrons. The core electrons usually does not participate in the chemical
reaction since it has highest-energy of arrangement. The valence electrons has lowest-energy of arrangement thus,
the electrons are held loosely, they participate in chemical reactions. Each orbital contains a maximum capacity of
two electrons.
1.2 Bonding
1.2.1 Chemical Bonding Theory
In 1858, August Kekulé and Archibald Couper proposed that carbon is tetravalent—it always forms four bonds
when it joins other elements to form stable compounds. Furthermore, carbon atoms can bond to one another to form
extended chains of linked atoms.
Then an extension to the Kekulé–Couper theory was proposed due to the possibility of multiple bonding between
atoms. Emil Erlenmeyer proposed a carbon–carbon triple bond for acetylene, and Alexander Crum Brown proposed
a carbon–carbon double bond for ethylene.
In 1865, Kekulé suggested that carbon chains can double back on themselves to form rings of atoms.
In 1874, Jacobus van’t Hoff and Joseph Le Bel proposed that the four bonds of carbon are not oriented randomly
but have specific spatial directions. Van’t Hoff suggested that the four atoms to which carbon is bonded sit at the
corners of a regular tetrahedron, with carbon in the center.s
Figure 1.5 Van’t Hoff’s tetrahedral carbon atom. Source: Smith (2010)
1.2.2 Bonding
The link between two atoms in a stable arrangement is called bonding and denotes stability. Atoms can either
attain a complete outer shell of valence electons or a stable nobles gas configurations of electrons.
A. Types of Bonding
A compound may have either ionic or covalent bonds. A molecule has only covalent bonds.
A.1 Ionic Bond

It is a bond that involves the transfer of electrons from one element to another. The resulting ions are held
together by extremely strong electrostatic interactions. Ionic compounds form extended crystal lattices that
maximize the positive and negative electrostatic interactions. Thre transfer of electrons forms stable salts
composed of cations and anions.
A.2 Covalent Bond.

It is a bond that allows sharing of electrons between two nuclei. The number of covalent bonds an atom
forms depends on how many additional valence electrons it needs to reach a noble-gas configuration. An atom
with one, two, three, or four valence electrons form one, two, three, or four bonds, respectively, in neutral
molecules. While atoms with five or more valence electrons form enough bonds to give an octet.
𝑝𝑟𝑒𝑑𝑖𝑐𝑡𝑒𝑑 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑏𝑜𝑛𝑑𝑠 = 8 − 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑣𝑎𝑙𝑒𝑛𝑐𝑒 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠
When elements form fewer than the four bonds their octet consist of both bonding (shared) electrons,
represented as lines in below figure, and nonbonding (unshared) electrons, also called lone pairs represented as
dots in below figure.
Figure 1.6 Bonding and nonbonding electrons of elements. Source: McMurry (2018)
1.2.3 Lewis Structures

Lewis structure, or electron-dot structure, is a way of indicating the covalent bonds in molecules in which the
valence electrons of an atom are represented as dots (e.g. hydrogen has 1 dot, carbon has 4 dots, oxygen has six dots).
A stable molecule results whenever a noble-gas configuration is achieved for all the atoms—eight dots (an octet) for
main-group atoms or two dots for hydrogen. In Lewis structure, a solid line indicates a two-electron covalent bond.
Kekulé structure, or line-bond structures, is a way of representing bonds in molecules in which a two-electron
covalent bond is indicated as a line drawn between atoms.
Figure 1.7 Lewis- and Kekulé-structures. Source: McMurry (2018)
There are three general rules for drawing Lewis structures:

1. Draw only the valence electrons.
2. Give every second-row element, in the periodic table, no more than eight electrons.
3. Give each hydrogen two electrons.
Figure 1.8 Lewis structure in formation of covalent bond. Source: Smith (2010)
Figure 1.9 Bonding and nonbonding electrons. Source: Smith (2010)
Below are steps in drawing a Lewis structure:

1. Arrange atoms next to each other.
2. Count the electrons in each element.
3. Arrang the electrons around the atoms.
4. Assign formal charges to all atoms.
Example
Draw a Lewis structure for methane, a compound with molecular formula 𝐶𝐻4.
Solution
Source: Smith (2010)
Example
Draw a Lewis structure for methanol, a compound with molecular formula 𝐶𝐻4 𝑂.
Solution
Example
Draw a Lewis structure for ethylene, a compound with molecular formula 𝐶2 𝐻4. Assume the atoms are arranged
as shown on below structure.
Solution
Step [4] Move lone pair
Example
Draw a Lewis structure for acethylene, a compound with molecular formula 𝐶2𝐻2 . Assume the atoms are
arranged as shown on below structure.
Solution
Step [4] Move lone pair
To check the validity of the Lewis structure drawn, the answer in the following three questions must be Yes.
1. Have all the electrons been used?
2. Is each 𝐻 surrounded by two electrons?
3. Is each second-row element surrounded by no more than eight electrons?
One lone pair is transformed into one new bond for each two electrons needed to complete an octet. A lone pair
is used consecutively to form multiple bond if the carbon atom was not able to satisfy the octet rule after placing all
electrons in bonds and lone pairs. e.g. acetylene. four electrons were needed to complete an octet, so two lone pairs
were used to form two new bonds, forming a triple bond.
1.2.4 Formal Charge
A formal charge is the change assigned to individual atoms in a Lewis structure. It can be calculated as using
below equation. The sum of the formal charges on the individual atoms is equivalent to the net charge on the
molecule or ion.
𝐹𝑜𝑟𝑚𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠
= −
𝑐ℎ𝑎𝑟𝑔𝑒 𝑣𝑎𝑙𝑒𝑛𝑐𝑒 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 𝑎𝑛 𝑎𝑡𝑜𝑚 "𝑜𝑤𝑛𝑠"
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 1 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓

= − [ ]
𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 𝑜𝑤𝑛𝑒𝑑 𝑢𝑛𝑠ℎ𝑎𝑟𝑒𝑑 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 2 𝑠ℎ𝑎𝑟𝑒𝑑 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠
Example
Example
Determine the formal charge on each atom in the ion 𝐻3𝑂+ .
Solution
Step 1. Determine the atom present in the ion
Oxygen, 𝑂 and Hydrogen, 𝐻
Step 2. Determine the number of valence electrons

For oxygen, 𝑂 : 6 For hydrogen, 𝐻 : 1
Step 3. Calculate the number of electrons an atom “owns”

𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 1 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓
= − [ ]
𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 𝑜𝑤𝑛𝑒𝑑 𝑢𝑛𝑠ℎ𝑎𝑟𝑒𝑑 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 2 𝑠ℎ𝑎𝑟𝑒𝑑 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠
For oxygen, 𝑂 For hydrogen, 𝐻
− 1 1
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑒 𝑜𝑤𝑛𝑒𝑑 = 2 + (6) = 5 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑒 − 𝑜𝑤𝑛𝑒𝑑 = 0 + (2) = 1
2 2
Step 4. Calculate for the formal charge

𝐹𝑜𝑟𝑚𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠
= −
𝑐ℎ𝑎𝑟𝑔𝑒 𝑣𝑎𝑙𝑒𝑛𝑐𝑒 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 𝑎𝑛 𝑎𝑡𝑜𝑚 "𝑜𝑤𝑛𝑠"
For oxygen, 𝑂 = 6 − 5 = +1 For hydrogen, 𝐻 = 1−1= 0
Below table shows formal charge observed with common bonding patterns of carbon, nitrogen, and oxygen
atoms.
Table 1. 1 Formal Charge with Common Bonding Patterns
Source: McMurry (2018)

1.2.5 Isomers
Isomers are molecules with several atoms having the same molecular formula but arranged in different
molecular structure or connectivity of atoms, e.g. ethanol and dimethyl ether, both have the same molecular formula
𝐶2𝐻6 𝑂. These type of isomers are called constitutional isomers.
1.2.6 Exceptions to the Octet Rule

A. Hydrogen
The hydrogen atom accommodate two electrons only in bonding.
B. Elements in Groups 2A and 3A

Elements in group 2A and 3A do not have enough valence electrons to form an octet in a neutral molecule.
This explains the reactivity og these molecules.
C. Elements in the Periodic Table’s Third Row

Elements in third row have more than eight electrons due to empty d orbitals available to accept electrons.
1.3 Resonance
Resonance structures or resonance forms are representation of two Lewis structures having the same arrangement
of atoms but differ on the arrangement of electrons. A resonance hybrid represents a structure of the composite of both
resonance forms. It shows characteristics of both resonance structures.
Each resonance structure implies that electron pairs are localized in bonds or on atoms. In reality, resonance
allows certain electron pairs to be delocalized over two or more atoms, and this delocalization of electron density
adds stability. A molecule with two or more resonance structures is said to be resonance stabilized.
Example
Draw resonance structure of an anion (𝐻𝐶𝑂𝑁𝐻)−
Solution
1.3.1 Resonance Theory

Below are basic principles of resonance theory:
✓ Resonance structures are imaginary, not real. An individual resonance structure does not accurately represent
the structure of a molecule or ion. The real real structure, resonance hybrid, is a composite of the different
forms.
✓ Resonance structures are not in equilibrium with each other. There is no movement of electrons from one form
to another. They have single, unchanging structures, and they do not switch back and forth between resonance
forms. When two resonance forms are nonequivalent, the actual structure of the resonance hybrid is closer to
the more stable form than to the less stable form.
✓ 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. The curved arrow indicates
movement of these electrons, not the movement of atoms.
✓ Resonance structures obey normal rules of valency. The resonance forms follow the octet rule to main-group
atoms.
✓ Resonance hybrid is more stable than any individual resonance structure. Resonance leads to stability. The
larger the number of resonance forms, the more stable a substance is because electrons are distributed over a
larger part of the molecule and are closer to more nuclei.
Below structure shows difference between resonance structure and isomers:
The atom position is the same in both

The atom placement is different where C has
compounds but the location of an electron pair is
an 𝑂 − 𝐻 bond and D has additional 𝐶 − 𝐻 bond.
different.
1.3.2 Resonance Structure

Below shows three rules to follow in drawing resonance structures:
Rule 1. Two resonance structures differ in the position of multiple bonds and nonbonded electrons. The
placement of atoms and single bonds always stays the same.
Rule 2. Two resonance strucutes must have the same number of unpaired electrons.
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.
The curve arrow notation shows the movement, or reposition, of an electron pair in the resonance structure. The
tail of the arrow denotes the initial location of an electron pair, either in a bond or lone pair. While the head points
where the electron pair will be transferred. A curved arrow always begins at an electron pair and ends at an atom
or a bond.
Example
Follow the curved arrows to draw a second resonance structure for the ion shown below
Solution
Example
Follow the curved arrows to draw a second resonance structure for the ion shown below
Solution
Example
Follow the curved arrows to draw a structure for the two different resonance structure shown below
and
Solution
Example
Follow the curved arrows to draw a structure for the two different resonance structure shown below
and
Solution
1.3.3 Resonance Hybrid

The resonance hybrid is the composite of all possible resonance structures. It is more stable than any resonance
structure because it delocalizes electron density over a larger volume.
Each resonance structure contributes equally to the resonance hybrid. When two resonance structure are
different, the “better” resonance form will be the major contributor and other forms are minor contributors. The
“better” resonance structure contains more bond and fewer charges. Below are two resonance structure showing the
major and minor contributor. The X structure is identified to be the major contributor thus, the resultant resonance
hybrid is similar to this “better” resonance structure.
Example
Determine the resonance hybrid of the two resonance structure as shown below
Solution
• Double bond position. Structure A and B has a 𝐶 − 𝑂 and 𝐶 − 𝑁 double bond, respectively. A dashed line in
the hybrid indicates partial double bond character between these atoms.
• Location of the charge. A negative charge resides on different atoms in A and B. The 𝛿 −, partial negative
charge, indicates that the charge is delocalized on the 𝑁 and 𝑂 atoms in the hybrid.
1.4 Molecular Shape

The bond length and bond angle are varibales that define a molecule’s structure.
1.4.1 Bond Length

Bond length is the average distance, reported in picometer or angstrom, between the center of two bonded nuclei.
✓ 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.
Table 1.2 Average Bond Lengths
1.4.2 Bond Angle

Bond angle determines the shape around any atom bonded to two other atoms. The bond angle and shape around
a given atom can be determine considering the groups, atoms or lone pair of electrons, surrounding it. Then, we
consider the valence shell electron pair repulsion (VSEPR) theory in determing the shape.
The bond angle involving atoms in the second-row, of the periodic table, has only three possible arrangements
that are dependent on the number of groups surrounding it.
Table 1.3 Molecular Geometry and its Corresponding Bond Angle
• Any atom surrounded by only two groups is linear and has a bond angle of 180°.
and
• Any atom surrounded by three groups is trigonal planar and has bond angles of 120°.
and
• Any atom surrounded by four groups is tetrahedral and has bond angles of approximately 109.5°.
and
In drawing a three-dimensional geometry of a tetrahedron on two-dimension, 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 (refer
to 1.10). Molecules in three-dimensional geometry can also be drawn in different equivalent representations as
shown in Fig. 1.11. The wedges and dashes are used for groups that are aligned one behind another as shown in Fig.
1.12.
Figure 1.10 Drawing three-dimensional geometry of a tetrahedron on two-dimension. Source: Smith (2010)
Figure 1.11 Acceptable and equivalent drawings of a three-dimensional geometry. Source: Smith (2010)
Figure 1.12 Equivalent positions of a wedge and dash lines in three-dimensional geometry. Source: Smith (2010)
Ammonia (𝑁𝐻3) is another example of an atom that is represented in three-dimensional geometry. The 𝑁 atom
is surrounded with three 𝐻 atoms and one lone pair. The 𝐻 − 𝑁 − 𝐻 bond has 107° as shown on below figure. Its
molecular shape is referred as trigonal pyramid, where one group surrounding the 𝑁 atom is not another atom
(nonbonded electron pair).
Water is also represented in three-dimensional geometry. The 𝑂 atom is surrounded by two 𝐻 atoms and two
lone pairs. The 𝐻 − 𝑂 − 𝐻 bond has 105° as shown on below figure. It has a bent molecular shape, because there are
two lone pairs of electrons surrounding oxygen.
The lone pairs of electrons in 𝑁𝐻3 and 𝐻2 𝑂 cause repulsion making bond angles smaller than the theoretical
tetrahedral bond angle (109.5°). Below table shows a summary of determining molecular geometry based on the
number of groups around an atom.
Table 1.4 Molecular Geometry of Specific Compounds

No. of groups
Geometry Bond angle Examples
around an atom
2 Linear 180° 𝐵𝑒𝐻2 , 𝐻𝐶 ≡ 𝐶𝐻
3 Trigonal planar 120° 𝐵𝐹3 , 𝐶𝐻2 = 𝐶𝐻2
4 Tetrahedral 109.5° 𝐶𝐻4 , 𝑁𝐻3 , 𝐻2𝑂

Example
Determine the geometry around the indicated atom in below specie.
Solution
Step 1. Set an atom as basis
The given shows carbon, 𝐶 as basis
Step 2. Determine the number groups around the atom

2 groups Two atoms
No lone pairs
Step 3. Determine molecular geometry based on the number of groups surrounding the atom
⟹ Linear
Example
Determine the geometry around the indicated atom in below specie.
Solution
Step 1. Set an atom as basis
The given shows nitrogen, 𝑁 as basis
Step 2. Determine the number groups around the atom

4 groups Four atoms
No lone pairs
Step 3. Determine molecular geometry based on the number of groups surrounding the atom
⟹ Tetrahedral
1.5 Organic Structures

1.5.1 Condensed Structures
This type of structure is often used to compounds with atoms bonded in chain. It is interpreted from left side of
the molecule and considers carbon atoms represented in tetravalent geometry. Below are conventions in writing the
condensed structures:
✓ All the atoms are drawn. The two-electron bond lines are omitted.
✓ Atoms are drawn next to the atom to which it is bonded.
✓ Parenthesis are used around similar groups bonded to the same atom.
✓ Lone pairs are omitted.
Below are condensed structures containing 𝐶 − 𝑂 double bond. It represents the only way for all atoms to have
an octet.
𝐶𝐻3𝐶𝐻𝑂 𝐶𝐻3𝐶𝑂𝐶𝐻3 𝐶𝐻3 𝐶𝑂2𝐻 𝐶𝐻3𝐶𝑂2 𝐶𝐻3
Example
Convert the given Lewis structure to a condensed formula
⟹ or
Example
Example
⟹ or
Example
Example
Example
⟹ or
Example
Convert the given condensed formula to a Lewis structure
Example
Convert the given condensed formula to a Lewis structure
⟹
1.5.2 Skeletal Structures

This type of structure can be used to compounds with atoms bonded in chain and ring. Carbon chains are drawn
as zigzag while rings are drawn as polygons. Below are conventions in writing the 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 all heteroatoms and the hydrogens directly bonded to them.
Example
Draw the skeletal structure of hexane. Also, determine the condensed structure.
⟹ ⟹
Skeletal structure Condensed structure
Example
Draw the skeletal structure of cyclohexane. Also, determine the condensed structure.
⟹ ⟹ No condensed structure
Skeletal structure
Example
Draw the Lewis structure of the given skeletal structure.
Example
Example
Example
Example
Draw a complete structure for vanillin showing all 𝐻 atoms and lone pairs. Vanillin is the principal component
of the extract of the vanilla bean.
Vanillin 𝐶8𝐻8 𝑂3
When heteroatoms are bonded to a carbon skeleton, the heteroatom is joined directly to the carbon to which is
it bonded, with no 𝐻 atoms in between. In contrast, when carbon attachments are bonded to a carbon skeleton, the
𝐻 atoms will be drawn to the right of the carbon to which they are bonded regardless of the location.
1.5.3 Skeletal Structures with Charged Atoms

The skeletal structure omits hydrogen atoms and lone pairs. Below are conventions in writing the skeletal
structures with charged carbon atoms:
✓ A charge on a carbon atom takes the place of one hydrogen atom.
✓ The charge determines the number of lone pairs. Negatively charged carbon atoms have one lone pair and
positively charged carbon atoms have none.
Example
Example
⟹ ⟹
Skeletal structures of heteroatoms use formal charge on an atom to determine the number of lone pairs.
Example
Neutral 𝑂 atom owns six electrons:
⟹ • Two bonds (four bonding electrons)
• Two lone pairs (four unshared electrons)
Example
Positively charged 𝑂 atom owns five electrons:

⟹ • Three bonds (six bonding electrons)
• One lone pair (two unshared electrons)
1.6 Orbital Hybridization

According to valence bond theory, a covalent bond forms when two atoms approach each other closely and a singly
occupied orbital on one atom overlaps a singly occupied orbital on the other atom. The electrons are now paired in the
overlapping orbitals and are attracted to the nuclei of both atoms, thus bonding the atoms together.
Atoms using new orbitals, called hybrid orbitals, do not use pure s and pure p orbitals in forming bonds.
Hybridization is the combination of two or more atomic orbitals to form the same number of hybrid orbitals, each
having the same shape and energy. A given number of atomic orbitals hybridize to form an equivalent number of
hybrid orbitals. The superscripts for hybrid orbitals correspond to the number of atomic orbitals used to form them.
• One 2𝑠 orbital and three 2𝑝 orbitals form four 𝑠𝑝3 hybrid orbitals
• One 2𝑠 orbital and two 2𝑝 orbitals form three 𝑠𝑝2 hybrid orbitals
• One 2𝑠 orbital and one 2𝑝 orbitals form two 𝑠𝑝 hybrid orbitals
The number of groups, atoms and nonbonded electron pairs, around an atom corresponds to the number of atomic
orbitals that must be hybridized to form the hybrid orbitals.
Table 1.5 Hybrid Orbitals Corresponding to the Number of Groups Around an Atom
Molecular Shape Linear Trigonal planar Tetrahedral
No. of groups around an atom 2 3 4
No. of orbitals used 2 3 4
One 𝑠 One 𝑠 One 𝑠
Atomic orbitals
One 𝑝 Two 𝑝 Three 𝑝
Hybrid orbitals formed Two 𝑠𝑝 Three 𝑠𝑝2 Four 𝑠𝑝3
Unhybridized orbitals Two 𝑝 One 𝑝 None
Orientation
1.6.1 Hydrogen
In the 𝐻2 molecule, the 𝐻 − 𝐻 bond results from the overlap of two singly occupied hydrogen 1𝑠 orbitals forming
a sigma (𝜎) bond that results to a concentrated electron density between the two nuclei.
The 𝜎 bond is cylindrically symmetrical, as shown on the left figure,

because the electrons forming the bond are distributed symmetrically about
an imaginary line connecting the two nuclei. All single bonds are 𝜎 bonds.
1.6.2 𝒔𝒑𝟑 Hybrid Orbitals

Carbon atom contains a total of six electrons, two core electrons and four valence electrons, that are distributed
and placed in atomic orbitals of lowest energy for stable arrangement. This lowest energy electron configuration of
an atom is called its ground state and shown in below figure.
Based from the initial electron distribution, there are only two unpaired valence electron thus, forming two
bonds in order to achieve molecular stability. However, this non-octet carbon molecule is highly reactive. In order to
achieve stability, an electron from 2𝑠 orbital shall be moved to higher energy orbital. This higher energy electron
configuration of an atom is called excited state.
Figure 1.13 Carbon atom valence eletron distribution in orbitals. Source: Smith (2010)
Hybridization of one 2s orbital and three 2p orbitals for carbon forms four hybrid orbitals, called 𝑠𝑝3 hybrids,
each with one electron. These new hybrid orbitals are intermediate in energy between the 2s and 2p orbitals. The
four hybrid orbitals form four equivalent bonds (Fig. 1.14).
Figure 1.14 Formation of 𝑠𝑝3 hybrid orbital. Source: Smith (2010)

Figure 1.15 Molecular shape and orientation of single and multiple 𝑠𝑝3 hybrid orbital. Source: Smith (2010)
Each bond in 𝐶𝐻4 is formed by overlap of an 𝑠𝑝3 hybrid orbitals of carbon. The asymmetry of 𝑠𝑝3 orbitals arises
because the two lobes of a 𝑝 orbital have different algebraic signs, + and −. When 𝑝 orbital hybridizes with an 𝑠
orbital, the positive 𝑝 lobe adds to the 𝑠 orbital but the negative 𝑝 lobe subtracts from the 𝑠 orbital. The resultant
hybrid orbital is therefore unsymmetrical about the nucleaus and is strongly oriented in one direction.
When each of the four identical 𝑠𝑝3 hybrid orbitals of a carbon atom overlaps with the 1𝑠 orbital of a hydrogen
atom, four identical 𝐶 − 𝐻 bonds are formed. These four bonds point to the corners of a tetrahedron. All four 𝐶 − 𝐻
bonds in methane are 𝜎 bonds, because the electron density in concentrated on the axis joining 𝐶 and 𝐻 (Fig. 1.16).
Figure 1.16 Molecular structure of 𝐶𝐻4 using 𝑠𝑝3 hybrid orbital. Source: Smith (2010)
The same kind of orbital hybridization that accounts for the methane structure also accounts for the bonding of
carbon atoms into chains and rings. Consider ethane as an example represented by below structure. The two carbon
atoms bond to each other by 𝜎 overlap of an 𝑠𝑝3 hybrid orbital from each (𝐶 − 𝐶 𝑏𝑜𝑛𝑑). The remaining three 𝑠𝑝3
hybrid orbitalds of each carbon overlap with the 1𝑠 orbitals of three hydrogens to form the six 𝐶 − 𝐻 binds.
Figure 1.17 Carbon-carbon bond formed by 𝜎 overlap. Source: McMurry (2018)
Example
Illustrate the molecular structure and determine the hybrid orbitals of ethane, 𝐶𝐻3𝐶𝐻3 .
Solution
Step 1. Draw a valid Lewis structure
Step 2. Determine hybridization

4 groups around 𝐶 𝑠𝑝3 hybridized
Step 3. Determine hybrid orbitals in each bond

• The 𝐶 − 𝐶 bond are formed from 𝐶𝑠𝑝3 − 𝐶𝑠𝑝3
• All 𝐶 − 𝐻 bond are formed from 𝐶𝑠𝑝3 − 𝐻1𝑠
1.6.3 𝒔𝒑𝟐 Hybrid Orbitals

Formation of 𝑠𝑝2 hybrid orbitals follow the same process as 𝑠𝑝3 hybrid orbital formation. The 𝑠𝑝2 hybrid orbitals
are formed from one 2𝑠 and two 2𝑝 orbitals, leaving one 2𝑝 orbital unhybridized (Fig. 1.18). Considering carbon has
four valence electrons, each of these orbitals has one electron that can be used to form a bond (Fig. 1.19).
Figure 1.18 Formation of three 𝑠𝑝2 hybrid orbitals using one 2𝑠 and two 2𝑝 orbitals,
leaving one 2𝑝 orbital unhybridized. Source: Smith (2010)
Figure 1.19 Formation of 𝑠𝑝2 hybridized carbon atom. Source: Smith (2010)
Example
Illustrate the molecular structure and determine the hybrid orbitals of ethylene, 𝐶𝐻2𝐶𝐻2 .
Solution


• The 𝐶 = 𝐶 bond is formed from 𝐶𝑠𝑝2 − 𝐶𝑠𝑝2
In 𝑝𝑖 (𝜋) bond, the electron density is not concentrated on the axis joining the two nuclei. This bond is usually
weaker, thus more easily broken than 𝜎 bonds since, since it is farther from the two nuclei.
Each 𝐶 − 𝐻 bond results from the end-on ovelap of an 𝑠𝑝2 hybrid orbital on carbon and the 1𝑠 orbital on hydrogen
forming 𝜎 bonds. Similarly, one of the 𝐶 − 𝐶 bonds results from the end-on overlap of an 𝑠𝑝2 hybrid orbital on each
carbon atom forming 𝜎 bonds. The second 𝐶 − 𝐶 bond results from the side-by-side overlap of the 2𝑝 orbitals on each
carbon. This overlap creates an area of electron density above and below the plane containing the 𝑠𝑝2 hybrid orbitals.
Each carbon in ethylene (𝐶𝐻2 = 𝐶𝐻2) is 𝑠𝑝2 hybridized and form trigonal planar atomic arrangement with 120°. In
a carbon-carbon double bond has two components:
• a 𝜎 bond, formed by end-on overlap of two 𝑠𝑝2 hybrid orbitals
• a 𝜋 bond, formed by side-by-side overlap of two 2𝑝 orbitals
Figure 1.20 Formation of 𝜎 and 𝜋 bond in 𝐶 = 𝐶. Source: Smith (2010)
Example
Illustrate the molecular structure and determine the hybrid orbitals of boron trifluoride, 𝐵𝐹3 .
Solution

3 groups around 𝐵 𝑠𝑝2 hybridized

• The 𝐵 − 𝐹 bond are formed from 𝐵𝑠𝑝2 − 𝐹2𝑝
The three 𝑠𝑝2 hybrid orbitals

(𝐵 − 𝐹 𝑏𝑜𝑛𝑑𝑠) lie in a plane and
are 120° apart. While the 𝐵 atom
has a vacant unhybridized 2𝑝
orbital located above and below
the plane of the 𝐵𝐹3 molecule.
1.6.4 𝒔𝒑 Hybrid Orbitals

Formation of 𝑠𝑝 hybrid orbitals follow the same process as 𝑠𝑝3 hybrid orbital formation. The 𝑠𝑝 hybrid orbitals
are formed from one 2𝑠 and one 2𝑝 orbital, leaving two 2𝑝 orbital unhybridized (Fig. 1.21). Considering carbon has
four valence electrons, each of these orbitals has one electron that can be used to form a bond (Fig. 1.22).
Figure 1.21 Formation of two 𝑠𝑝 hybrid orbitals using one 2𝑠 and one 2𝑝 orbital,
leaving two 2𝑝 orbitals unhybridized. Source: Smith (2010)
Figure 1.22 Formation of 𝑠𝑝 hybridized carbon atom. Source: Smith (2010)
Example
Illustrate the molecular structure and determine the hybrid orbitals of acetylene, 𝐶2 𝐻2.
Solution

2 groups around 𝐶 𝑠𝑝 hybridized

• The 𝐶 ≡ 𝐶 bond is formed from 𝐶𝑠𝑝 − 𝐶𝑠𝑝
• All 𝐶 − 𝐻 bond are formed from 𝐶𝑠𝑝 − 𝐻1𝑠
Each 𝐶 − 𝐻 bond results from the end-on overlap of an 𝑠𝑝 hybrid orbitals on carbon and the 1𝑠 orbital on
hydrogen forming 𝜎 bond. Similarly, one of the 𝐶 − 𝐶 bonds result from the end-on overlap of an 𝑠𝑝 hybrid orbital on
each carbon atom forming 𝜎 bond.
Each cabon atom also has two unhybridized 2𝑝 orbitals that are perpendicular to each other and to the 𝑠𝑝 hybrid
orbitals. Side-by-side overlap between the two 2𝑝 orbitals on one carbon with the two 2𝑝 orbitals on the other carbon
creates the second and third bonds of the 𝐶 − 𝐶 triple bond forming both 𝜋 bonds. The electron density from one of
these bonds is joining the two nuclei above and below the axis while the other bond is joining the nuclei in front and
behind the axis. Each carbon in acetylene (𝐶𝐻 ≡ 𝐶𝐻 ) is 𝑠𝑝 hybridized and form linear atomic arrangement with 180°.
In a carbon-carbon triple bond has three components:
• a 𝜎 bond, formed by end-on overlap of two 𝑠𝑝 hybrid orbitals
• two 𝜋 bonds, formed by side-by-side overlap of two sets of 2𝑝 orbitals
Figure 1.23 Formation of 𝜎 and 𝜋 bond in 𝐶 ≡ 𝐶. Source: Smith (2010)
Example
Illustrate the molecular structure and determine the hybrid orbitals of beryllium hydride, 𝐵𝑒𝐻2 .
Solution

2 groups around 𝐵𝑒 𝑠𝑝 hybridized

• Both 𝐵𝑒 − 𝐻 bond are formed from 𝐵𝑠𝑝 − 𝐻1𝑠
Table 1.6 Summary of Covalent Bonding Seen in Carbon Compounds

No, of groups
Hybridization Bond angle Example Observed bonding
bonded to 𝐶
4 𝑠𝑝3 109.5° 𝐻3𝐶 − 𝐶𝐻3
3 𝑠𝑝2 120° 𝐶𝐻2 = 𝐶𝐻2
2 𝑠𝑝 180° 𝐻𝐶 ≡ 𝐶𝐻
1.6.5 Hybridization of Atoms other than Carbon
Covalent bonds fromed by other elements can also be described using hybrid orbitals.
Example
Illustrate the molecular structure and determine the hybrid orbitals of ammonia, 𝑁𝐻3.
Solution
• Consider octet rule in each atom

• Show unbonded lone pairs

4 groups around 𝑁 𝑠𝑝3 hybridized

• All 𝑁 − 𝐻 bond are formed from 𝑁𝑠𝑝3 − 𝐻1𝑠
Step 4. Determine hybrid orbitals in lone pair

• The 𝑁 atom has four 𝑠𝑝3 hybrid orbitals
The three 𝑠𝑝3 hybrid orbitals are used for the bond
One 𝑠𝑝3 hybrid orbital is occupied by the lone pair
Example
Consider the molecular structure of methylamine, 𝐶𝐻3 𝑁𝐻2, as
shown on the figure and determine the hybridization of the atoms in
the molecule.
Solution


4 groups around 𝑁 𝑠𝑝3 hybridized

• All 𝐶 − 𝐻 bonds are formed from 𝐶𝑠𝑝3 − 𝐻1𝑠
• The two 𝑁 − 𝐻 bonds are formed from 𝑁𝑠𝑝3 − 𝐻1𝑠
• The 𝐶 − 𝑁 bond are formed from 𝐶𝑠𝑝3 − 𝑁𝑠𝑝3
• The 𝑁 atom has four 𝑠𝑝3 hybrid orbitals

The three 𝑠𝑝3 hybrid orbitals are used for the bond
One 𝑠𝑝3 hybrid orbital is occupied by the lone pair
Example
Consider the molecular structure of water, 𝐻2 𝑂, as shown on the
figure and determine:
a. Hybridization of the atoms
b. Orbitals used to form each bond
c. Type of orbital does each lone pair reside
Solution


4 groups around 𝑂 𝑠𝑝3 hybridized

• All 𝑂 − 𝐻 bond are formed from 𝑂𝑠𝑝3 − 𝐻1𝑠

• The 𝑂 atom has four 𝑠𝑝3 hybrid orbitals
Two 𝑠𝑝3 hybrid orbitals are used for the bond
Two 𝑠𝑝3 hybrid orbital is occupied by the lone pairs
Example
Illustrate the molecular structure and determine the hybrid orbitals of methanol, 𝐶𝐻3𝑂𝐻.
Solution


Rule of hybridization:
4 groups around 𝐶 𝑠𝑝3 hybridized 𝑠𝑝 : two groups around an atom
𝑠𝑝2 : three groups around an atom
4 groups around 𝑂 𝑠𝑝3 hybridized 𝑠𝑝3 : four groups around an atom

• The 𝐶 − 𝑂 bond is formed from 𝐶𝑠𝑝3 − 𝑂𝑠𝑝3
• The 𝑂 − 𝐻 bond is formed from 𝑂𝑠𝑝3 − 𝐻1𝑠

• The 𝑂 atom has four 𝑠𝑝3 hybrid orbitals
Two 𝑠𝑝3 hybrid orbitals are used for the bond
Two 𝑠𝑝3 hybrid orbital is occupied by the lone pairs
Example
Consider the molecular structure of acetone, (𝐶𝐻3 )2 𝐶𝑂, as shown on
the figure and determine:
Solution

Step 2. Determine unknown

a. Determine hybridization
3 groups around 𝑂 𝑠𝑝2 hybridized
b. Determine hybrid orbitals in each bond

• The two 𝐶 − 𝐶 bond are formed from 𝐶𝑠𝑝3 − 𝐶𝑠𝑝2
• The 𝐶 = 𝑂 contains 𝜎 and 𝜋 bonds:
The 𝜎 bond is formed from the end-on overlap of 𝐶𝑠𝑝3 − 𝑂𝑠𝑝2
The 𝜋 bond is formed from the side-by-side overlap of 𝐶2𝑝 − 𝑂2𝑝
c. Determine hybrid orbitals in lone pair

• The 𝑂 atom has three 𝑠𝑝2 hybrid orbitals
One 𝑠𝑝2 hybrid orbital is used for the 𝜎 bond of the double bond
The two 𝑠𝑝2 hybrid orbitals are occupied by the lone pairs
Example
Consider the molecular structure of methanethiol, 𝐶𝐻3 𝑆𝐻, as shown
on the figure and determine:
Solution

Step 2. Determine unknown

a. Determine hybridization
4 groups around 𝑆 𝑠𝑝3 hybridized
b. Determine hybrid orbitals in each bond

• The 𝑆 − 𝐻 bond are formed from 𝑆𝑠𝑝3 − 𝐻1𝑠
• The 𝐶 − 𝑆 bond are formed from 𝐶𝑠𝑝3 − 𝑆𝑠𝑝3
c. Determine hybrid orbitals in lone pair

• The 𝑆 atom has four 𝑠𝑝3 hybrid orbitals
The two 𝑠𝑝2 hybrid orbital is used for the bond
The two 𝑠𝑝2 hybrid orbitals are occupied by the lone pairs
1.7 Bond Length and Bond Strength

1.7.1 Comparison of Carbon-Carbon Bonds
When the number of electrons between two nuclei increases, the bonds become shorter and stronger. Thus,
triple bonds are shorted and stronger than double bonds, which are shorter and stronger than single bonds (Fig.
1.24). Moreover, the 𝜎 component of a bond is stronger than the 𝑝𝑖 component.
Figure 1.24 Relationship of bond length and bond strength of 𝐶 − 𝐶 bonds. Source: Smith (2010)
Table 1.7 Bond length and bond strength between 𝐶 − 𝐶 and 𝐶 − 𝐻
1.7.2 Comparison of Carbon-Hydrogen Bonds

The length and strength of a 𝐶 − 𝐻 bond vary depending on the hybridization of the carbon atom (Fig. 1.25).
This variation can be checked based on the atomic orbitals used to form each type of hybrid orbital. A percent s-
character indicates the fraction of a hybrid orbital due to the 2𝑠 orbital used to form it (Table 1.8). The 2𝑠 orbital
keeps electron density closer to a nucleus compared to a 2𝑝 orbital. As the percent 𝑠-character increases, a hybrid
orbital holds its electrons closer to the nucleus, and the bond becomes shorter and stronger (Fig. 1.26).
Figure 1.25 Relationship of bond length and bond strength of 𝐶 − 𝐻 bonds. Source: Smith (2010)
Table 1.8 Calculation of % 𝑠-character for each hybridization

Hybridization Percent 𝒔-character
𝑠𝑝 hybrid 𝑜𝑛𝑒 2𝑠 𝑜𝑟𝑏𝑖𝑡𝑎𝑙
= 50% 𝑠 − 𝑐ℎ𝑎𝑟𝑎𝑐𝑡𝑒𝑟
𝑡𝑤𝑜 ℎ𝑦𝑏𝑟𝑖𝑑 𝑜𝑟𝑏𝑖𝑡𝑎𝑙𝑠
𝑠𝑝2 hybrid 𝑜𝑛𝑒 2𝑠 𝑜𝑟𝑏𝑖𝑡𝑎𝑙
𝑡ℎ𝑟𝑒𝑒 ℎ𝑦𝑏𝑟𝑖𝑑 𝑜𝑟𝑏𝑖𝑡𝑎𝑙𝑠
𝑠𝑝3 hybrid 𝑜𝑛𝑒 2𝑠 𝑜𝑟𝑏𝑖𝑡𝑎𝑙
𝑓𝑜𝑢𝑟 ℎ𝑦𝑏𝑟𝑖𝑑 𝑜𝑟𝑏𝑖𝑡𝑎𝑙𝑠
Figure 1.26 Relationship between 𝑠-character and bond strength and length. Source: Smith (2010)
1.8 Electronegativity and Bond Polarity

1.8.1 Electronegativity
Electronegativity is a measure of an atom’s attraction for electrons in a bond. Below describe trends of
electronegativity in the periodic table (Fig. 1.27).
• Electronegativity increases across a row of periodic table as the nuclear charge increases (excluding the
noble gases).
• Electronegativity decreases down a column of the periodic table as the aromic radius increases, pushing the
valence electrons farther from the nucleus.
Figure 1.27 Electronegativity trend in periodic table. Source: Smith (2010)
When comparing two different elements, the more electronegative element attracts electron density toward itself
while the more electropositive gives up electron density to the other element. Electronegativity values are used to
indicate if the electrons bond are equally shared (forming nonpolar bond) or unequally shared (forming polar bond
or polar covalent bond) between two atoms. The 𝐶 − 𝐶 bond is nonpolar and 𝐶 − 𝐻 bond is also considered nonpolar
because the electronegativity difference between 𝐶(2.5) snd 𝐻(2.2) is small (Fig. 1.x). While 𝐶 − 𝑂 bond is polar and
formed from unequal sharing of electrons. The electrons are pulled away from 𝐶(2.5) toward a more electronegative
𝑂(3.4). The polar bond have dipole or separation of charges (Fig. 1.29) and the electronegative difference between
two atoms is usually ≥ 0.5 units.
Figure 1.28 Atoms in nonpolar bond. Source: Smith (2010)
Figure 1.29 Atoms in polar bond and forming dipole. Source: Smith (2010)
The direction of polarity in a bond is ofted indicated by an arrow, with the head of the arrow pointing toward
the more electronegative element. The tail of the arrow, with a perpendicular line drawn through it, is positioned at
the less electronegative element (Fig. 1.29). Below symbol indicates unequal sharing of electron density.
s
• 𝛿 + : an atom is electron deficient (has partial positive charge)

• 𝛿 − : an atom is electron rich (has partial negative charge)
The distribution of electron density in a molecule can be shown using an electrostatic potential map. The colors
in these map indicates the areas of electron density. Electron-rich regions are indicated in red while electron-
deficient are in blue region. The intermediate electron density are shown in orange, yellow, and green. Figure 1.30
indicates the more electronegative atom 𝐶𝑙 pulls electron density, making it electron rich and in red region. While
carbon is electron deficient and in blue region.
Figure 1.30 Electrostatic potential map of 𝐶𝐻3𝐶𝑙. Source: Smith (2010)

1.8.2 Polarity of Molecule

A polar molecule has either one polar bond, or two or more bond dipoles that reinforce. While a nonpolar molecule
has either no polar bonds, or two or more bond dipoles that cancel. Below two-step procedure determines if a molecule
has a net dipole:
Step 1. Use electronegativity differences to identify all the polar bonds and the directions of the bond dipoles.
Step 2. Determine the geometry around individual atoms by counting groups, and decide if individual dipoles
cancel or reinforce each other in space.
Example
Below shows determination of net dipole in the given molecules.
Molecule Water, 𝐻2𝑂 Carbon dioxide, 𝐶𝑂2

Molecular
structure
Molecular
Bent Linear
shape
Electronegativity
𝑂(3.4) − 𝐻(2.2) = 1.2 𝑂(3.4) − 𝐶(2.5) = 0.9
difference
Net dipole
The two individual dipoles reinforce. The two dipoles cancel.

Polarity of
Polar Nonpolar
Molecule
Electrostatic
Potential plots
The electron-rich (red) region is
Both electronegative 𝑂 atoms are
concentrated on the electronegative 𝑂
electron-rich (red) and the central 𝐶 atom
atom. Both 𝐻 atoms are electron-deficient
is electron-deficient (blue).
(blue-green).
Example
Determine if the molecule is polar or not.
Molecule Formaldehyde, 𝐶𝐻2 𝑂 Boron trifluoride, 𝐵𝐹3
Molecular
structure
Electronegativity 𝐶(2.5) − 𝐻(2.2) = 0.3

𝐹(4.0) − 𝐵(2.0) = 2.0
difference 𝑂(3.4) − 𝐶(2.5) = 0.9
Net dipole
Three polar bond

Polarity of One polar bond
All dipoles cancel, no net dipole
Molecule
Polar molecule Nonpolar molecule
Example
Molecule Ammonia, 𝑁𝐻3 Dichloromethane, 𝐶𝐻2 𝐶𝑙2
Molecular
structure
Electronegativity 𝐶(2.5) − 𝐻(2.2) = 0.3

𝑁(3.0) − 𝐻(2.2) = 0.8
difference 𝐶𝑙(3.2) − 𝐶(2.5) = 0.7
Net dipole
Three polar bonds Two polar bonds

Polarity of All dipoles reinforce Both dipoles reinforce
Molecule
Polar molecule Polar molecule
Example
Molecule Carbon tetrachloride, 𝐶𝐶𝑙4 trans-1,2-Dichloroethylene, 𝐶2𝐻2 𝐶𝑙2
Molecular
structure
Electronegativity 𝐶𝑙(3.2) − 𝐶(2.5) = 0.7

𝐶𝑙(3.2) − 𝐶(2.5) = 0.7
difference 𝐶(2.5) − 𝐻(2.2) = 0.3
Net dipole
Four polar bonds Two polar bonds

Polarity of All dipoles cancel, no net dipole Two dipoles cancel, no net dipole
Molecule
Nonpolar molecule Nonpolar molecule
The bond is polar whenever 𝐶 or 𝐻 is bonded to 𝑁, 𝑂, and all halogens even if the electronegativity differences
between atoms are small.
1.9 Molecular Orbital Theory

Molecular orbital theory describes covalent bond formation from mathematical combination of atomic orbitals
(wave functions) on different atoms to form molecular orbitals. A molecular orbital describes a region of space in a
molecule where electrons are most likely found.
A molecular orbital has a specific size, shape, and energy. There are two ways for the orbital combination to occur,
an additive way and a subtractive way. The additive combination leads to formation of a molecular orbital that is lower
in energy and roughly egg-shaped, while the subtractive combination leads to formation of a molecular orbital that is
higher in energy and has a node between nuclei. Note that the additive combination is a single, egg-shaped, molecular
orbital; it is not the same as the two overlapping 1s atomic orbitals of the valence bond description. Similarly, the
subtractive combination is a single molecular orbital with the shape of an elongated dumbbell.
Figure 1.31 show molecular orbital of hydrogen gas (𝐻2) where two singly occupied 1𝑠 atomic orbitals combine to
form two molecular orbitals. The filled orbital forms a bonding MO at lower-energy while the unfilled orbital shows
antibonding MO at higher-energy.
Figure 1.31 Molecular orbitals of 𝐻2 . Source: McMurry (2018)
The bonding MO indicates that electrons spend most of their time in the region between the two nuclei, thus
bonding the atoms together. The additive combination is lower in energy than the two hydrogen 1𝑠 atomic orbitals.
While the antibonding MO indicates that any electrons it contains cannot occupy the central region between the
nuclei, where there is a node, and cannot contribute to bonding. Thus, the two nuclei repel each other. The
subtractive combination is higher in energy than the two hydrogen 1𝑠 orbitals.
Figure 1.32 show molecular orbital of ethylene (𝐶2𝐻4 ) where two 𝑝 atomic orbitals combine to form two molecular
orbitals. The lower-energy, 𝜋 bonding MO has no node between nuclei and results from combination of p orbital lobes
with the same algebraic sign. The higher-energy, 𝜋 antibonding MO has a node between nuclei and results from
combination of lobes with opposite algebraic signs. Only the bonding MO is occupied; the higher-energy, antibonding
MO is vacant.
Figure 1.32 Molecular orbitals of 𝐶2 𝐻4. Source: McMurry (2018)
References:
[1] Smith, J.G. (2008). Organic Chemistry (3rd Ed.). McGraw Hill
[2] McMurry, J. (2008). Organic Chemistry (7th Ed.). Brooks/Cole Thomson Learning, Inc. USA
[3] McMurry, J. (2003). Organic Chemistry (5th Ed.). Thomson Learning, Inc. SG ISBN 981-243-587-5
[4] Zumdhal, SS & Zumdhal, SA (2012). Chemisrty: An Atoms First Approach. Brooks/Cole Cengage Learning
[5] Chang, R (2010). Chemistry (10th Ed). McGraw-Hill
Unit I. Structure and Bonding

Summary and Key Concepts
General Information:
The general rule of bonding: Atoms “strive” to attain a complete outer shell of valence electrons
𝐻 “wants” two electrons. Second-row elements “want” eight electrons.
Formal charge is the difference between the number of valence electrons of an atom and the number of electrons it
“owns”.
Curved arrow notation shows the movement of an electron pair. The tail of the arrow always begins at an electron
pair, either in a bond or a lone pair. The head points to where the electron pair “moves”.
Electrostatic potential plots are color-coded maps of electron density, indicating electron-rich and electron-defi
cient regions.
Lewis Structures:
A properly drawn Lewis structure shows the number of bonds and lone pairs present around each atom in a
molecule. In a valid Lewis structure, each 𝐻 has two electrons, and each second-row element has no more than eight.
This is the first step needed to determine many properties of a molecule.
Resonance:
The basic principles:

✓ Resonance exists when a compound cannot be represented by a single Lewis structure.
✓ Resonance structures differ in the position of only nonbonded electrons and π bonds, not atoms.
✓ The resonance hybrid is the only accurate representation for a resonance-stabilized compound. A hybrid
represents the compound better than any single resonance structure because electron density is delocalized
The difference between resonance strucutes and isomers:

✓ Two isomers differ in the arrangement of both atoms and electrons.
✓ Resonance structures differ only in the arrangement of electrons.
Geometry and Hybridization:

The number of groups around an atom determines both its geometry nd hybridization.
Molecular Shape Linear Trigonal planar Tetrahedral

No. of groups around an
2 3 4
atom
No. of orbitals used 2 3 4
One 𝑠 One 𝑠 One 𝑠
Atomic orbitals
One 𝑝 Two 𝑝 Three 𝑝
Hybrid orbitals formed Two 𝑠𝑝 Three 𝑠𝑝2 Four 𝑠𝑝3
Unhybridized orbitals Two 𝑝 One 𝑝 None
Hybridization 𝑠𝑝 𝑠𝑝2 𝑠𝑝3

Bond angle 180° 120° 109.5°
Orientation
Example
Drawing Organic Molecules:

✓ Shorthand methods are used to abbreviate the structure of organic molecules.
✓ A carbon bonded to four atoms is tetrahedral. The best way to represent a tetrahedron is to draw two bonds
in the plane, one bond in front, and one bond behind.
Bond Length:
✓ Bond length decreases across a row and increases down a column of the periodic table.
✓ Bond length decreases as the number of electrons between two nuclei increases.
✓ Bond length decreases as the percent s-character increases.
✓ Bond length and bond strength are inversely related. In general, shorter bonds are stronger bonds.
✓ Sigma (σ) bonds are generally stronger than π bonds.
Electronegativity and Polarity:

✓ Electronegativity increases across a row and decreases down a column of the periodic table.
✓ A polar bond results when two atoms of different electronegativity values are bonded together. Whenever C
or H is bonded to N, O, or any halogen, the bond is polar.
✓ A polar molecule has either one polar bond, or two or more bond dipoles that reinforce.

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Chem211E Organic Chemistry Unit I.

Structure and Bonding | 1

Structure and Bonding

At the end of the unit, the students shall be able to:

1.1 Review: Atomic Structure

Below laws govern the formation of compounds:

Law of definite proportions states that different samples of the same

1.1.1 The Nucleus

Figure 1.1 Schematic view of an atom. Source: McMurry (2018)

Table 1.1 Properties of Elementary Particles

23 𝐴𝑡𝑜𝑚𝑖𝑐 𝑛𝑢𝑚𝑏𝑒𝑟 = 11 𝑁𝑜. 𝑜𝑓 𝑝𝑟𝑜𝑡𝑜𝑛𝑠 = 11

1 𝑀𝑎𝑠𝑠 𝑛𝑢𝑚𝑏𝑒𝑟 = 1 𝑁𝑜. 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 = 1

2 𝑀𝑎𝑠𝑠 𝑛𝑢𝑚𝑏𝑒𝑟 = 2 𝑁𝑜. 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 = 1

3 𝑀𝑎𝑠𝑠 𝑛𝑢𝑚𝑏𝑒𝑟 = 3 𝑁𝑜. 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 = 1

A. Four Kinds of Orbitals

Figure 1.2 Representations of s, p, and d orbitals. Source: McMurry (2018)

Figure 1.3 Shapes of 2p orbitals. Source: Smith (2010)

A.1 Ionic Bond

A.2 Covalent Bond.

𝑝𝑟𝑒𝑑𝑖𝑐𝑡𝑒𝑑 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑏𝑜𝑛𝑑𝑠 = 8 − 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑣𝑎𝑙𝑒𝑛𝑐𝑒 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠

1.2.3 Lewis Structures

Figure 1.7 Lewis- and Kekulé-structures. Source: McMurry (2018)

There are three general rules for drawing Lewis structures:

Figure 1.9 Bonding and nonbonding electrons. Source: Smith (2010)

Below are steps in drawing a Lewis structure:

Source: Smith (2010)

Source: Smith (2010)

Step [4] Move lone pair

Step [4] Move lone pair

1.2.4 Formal Charge

𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 1 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓

Step 2. Determine the number of valence electrons

Step 3. Calculate the number of electrons an atom “owns”

Step 4. Calculate for the formal charge

Table 1. 1 Formal Charge with Common Bonding Patterns

Source: McMurry (2018)

1.2.6 Exceptions to the Octet Rule

B. Elements in Groups 2A and 3A

C. Elements in the Periodic Table’s Third Row

1.3.1 Resonance Theory

Below structure shows difference between resonance structure and isomers:

The atom position is the same in both

1.3.2 Resonance Structure

1.3.3 Resonance Hybrid

1.4 Molecular Shape

1.4.1 Bond Length

Table 1.2 Average Bond Lengths

Source: Smith (2010)

1.4.2 Bond Angle

Table 1.3 Molecular Geometry and its Corresponding Bond Angle

Source: Smith (2010)

Table 1.4 Molecular Geometry of Specific Compounds

2 Linear 180° 𝐵𝑒𝐻2 , 𝐻𝐶 ≡ 𝐶𝐻

3 Trigonal planar 120° 𝐵𝐹3 , 𝐶𝐻2 = 𝐶𝐻2

4 Tetrahedral 109.5° 𝐶𝐻4 , 𝑁𝐻3 , 𝐻2𝑂

Step 2. Determine the number groups around the atom

Step 2. Determine the number groups around the atom

1.5 Organic Structures

𝐶𝐻3𝐶𝐻𝑂 𝐶𝐻3𝐶𝑂𝐶𝐻3 𝐶𝐻3 𝐶𝑂2𝐻 𝐶𝐻3𝐶𝑂2 𝐶𝐻3

1.5.2 Skeletal Structures

Skeletal structure Condensed structure

1.5.3 Skeletal Structures with Charged Atoms

Positively charged 𝑂 atom owns five electrons: