Module 1A
Review Chapter: Structure and Bonding
-Do not distribute without permission-
Organic chemistry is study of carbon compounds. Ninety percent of more than 30 million
chemical compounds contain carbon. Carbon is group 4A element, it can share 4 valence
electrons and form 4 covalent bonds.
Figure 1: The periodic table of elements. Illustration from Brooks/Cole Cengage Learning.
Learning Objectives
This module will consider:
• what kinds of atoms that make up organic molecules.
• the principles that determine how the atoms in organic molecules are bound together.
• how to best depict organic molecules.
1 The Atom
1.1 Atomic Structure
• An atom has a small diameter - 2×10−10 m or 200 pm.
• It consists of a nucleus (with a diameter of ∼10−15 m), which is surrounded by a cloud
of electrons. The nucleus consists of a proton and a neutron.
– Proton - positively charged
– Electron - negatively charged
– Neutron - uncharged or neutral
GPMAYLEM 1 Organic Chemistry ∥ 2022
Figure 2: The volume around the nucleus (protons + neutrons) is occupied by orbiting electrons.
Illustration from Brooks/Cole Cengage Learning.
1.2 Atomic Number and Atomic Mass
• Atomic number (Z) - number of protons in nucleus
• Mass number (A): number of protons plus neutrons
• All atoms of same element have the same Z value.
• Isotopes - atoms of the same element with different numbers of neutrons and thus different
A (Figure 8)
• The atomic mass (atomic weight) of an element is weighted average mass in atomic mass
units (amu) of an element’s naturally occurring isotopes.
Figure 3: Isotopes of carbon. Illustration from Brooks/Cole Cengage Learning.
1.3 Atomic Orbitals
• Four different kinds of orbitals for electrons based on those derived for a hydrogen atom
• Denoted s, p, d, and f
• s and p orbitals most important in organic and biological chemistry
• s orbitals: spherical, nucleus at center
• p orbitals: dumbbell-shaped, nucleus at middle
• d orbitals: elongated dumbbell-shaped, nucleus at center
For the following items, refer to Figure 5.
• Orbitals are grouped in shells of increasing size and energy
• Different shells contain different numbers and kinds of orbitals
GPMAYLEM 2 Organic Chemistry ∥ 2022
Figure 4: Shapes of s, p, and d orbitals. Illustration from Brooks/Cole Cengage Learning.
• Each orbital can be occupied by two electrons
• First shell contains one s orbital, denoted 1s, holds only two electrons
• Second shell contains one s orbital (2s) and three p orbitals (2p), eight electrons
• Third shell contains an s orbital (3s), three p orbitals (3p), and five d orbitals (3d ), 18
electrons
Figure 5: Orbitals are grouped in shells of increasing size and energy. Illustration from
Brooks/Cole Cengage Learning.
2 Chemical Bonding Theory
• Atoms form bonds because the resulting compound is more stable than the separate
atoms.
• Ionic bonds in salts form by electron transfers.
• Organic compounds have covalent bonds from sharing electrons.
• Lewis structures (electron dot) show valence electrons of an atom as dots. For example,
hydrogen has one dot, representing its 1s electron, while carbon has four dots (2s2 2p2 )
due to 4 e- in valence shell.
• Kekulé structures (line-bond structures) have a line drawn between two atoms indi-
cating a 2 e- covalent bond.
GPMAYLEM 3 Organic Chemistry ∥ 2022
• Carbon has four valence electrons (2s2 2p2 ), forming four bonds (CH4 ).
• Nitrogen has five valence electrons (2s2 2p3 ) but forms only three bonds (NH3 ).
• Oxygen has six valence electrons (2s2 2p4 ) but forms two bonds (H2 O).
• Valence electrons not used in bonding are called nonbonding electrons, or lone-pair
electrons. Nitrogen atom in ammonia (NH3 ) shares six valence electrons in three covalent
bonds and remaining two valence electrons are nonbonding lone pair.
• Covalent bond forms when two atoms approach each other closely so that a singly
occupied orbital on one atom overlaps a singly occupied orbital on the other atom.
• Two models to describe covalent bonding: valence bond theory and molecular orbital
theory.
• Valence bond theory - electron sharing occurs by overlap of two atomic orbitals
• Molecular orbital (MO) theory - bonds result from combination of atomic orbitals
to give molecular orbitals, which belong to the entire molecule
• Sigma (σ) bonds - circular cross-section and are formed by head- on interaction
• Pi (π) bonds - “dumbbell” shape from sideways interaction of p orbitals
Figure 6: Lewis structures of methane (CH4 ), ammonia (NH3 ), water (H2 O), and methanol
(CH3 OH). Illustration from Brooks/Cole Cengage Learning.
Figure 7: Kekulé structures of methane (CH4 ), ammonia (NH3 ), water (H2 O), and methanol
(CH3 OH). Illustration from Brooks/Cole Cengage Learning.
GPMAYLEM 4 Organic Chemistry ∥ 2022
Figure 8: Number of bonds formed by H, C, N, and O. Illustration from Brooks/Cole Cengage
Learning.
References
1. McMurry, J. (1984). Organic chemistry. Monterey, CA: Brooks/Cole Pub. Co.
GPMAYLEM 5 Organic Chemistry ∥ 2022