Organic Chemistry

Chapter 1 STRUCTURE AND BONDING

Chapter Contents
• 1.1 Atomic Structure: The Nucleus
• 1.2 Atomic Structure: Orbitals
• 1.3 Atomic Structure: Electron Configurations
• 1.4 Development of Chemical Bonding Theory
• 1.5 Describing Chemical Bonds: Valence Bond Theory
• 1.6 sp3 Hybrid Orbitals and the Structure of Methane
• 1.7 sp3 Hybrid Orbitals and the Structure of Ethane
• 1.8 sp2 Hybrid Orbitals and the Structure of Ethylene
• 1.9 sp Hybrid Orbitals and the Structure of Acetylene
• 1.10 Hybridization of Nitrogen, Oxygen, Phosphorus, and Sulfur
• 1.11 Describing Chemical Bonds: Molecular Orbital Theory
• 1.12 Drawing Chemical Structures
Oxycodone, Cholesterol, and Benzylpenicillin
Figure 1.2

Carbon, hydrogen, and other elements commonly found in organic compounds are shown in the colors typically used to
represent them.
Figure 1.3

A schematic view of an atom. The dense, positively charged nucleus contains most of the atom’s mass and is surrounded by
negatively charged electrons. The three-dimensional view on the right shows calculated electron-density surfaces. Electron
density increases steadily toward the nucleus and is 40 times greater at the blue solid surface than at the gray mesh surface.
Figure 1.4

Representations of s, p, and d orbitals. An s orbital is spherical, a p orbital is dumbbell-shaped, and four of the five d orbitals
are cloverleaf-shaped. Different lobes of p orbitals are often drawn for convenience as teardrops, but their actual shape is
more like that of a doorknob, as indicated.
Figure 1.5

Energy levels of electrons in an atom. The first shell holds a maximum of 2 electrons in one 1s orbital; the second shell holds
a maximum of 8 electrons in one 2s and three 2p orbitals; the third shell holds a maximum of 18 electrons in one 3s, three
3p, and 3d orbitals; and so on. The two electrons in each orbital are represented by five up and down arrows, ⇅. Although
not shown, the energy level of the 4s orbital falls between 3p and 3d.
Figure 1.6

Shapes of the 2p orbitals. Each of the three mutually perpendicular, dumbbell-shaped orbitals has two lobes separated by a
node. The two lobes have different algebraic signs in the corresponding wave function, as indicated by the different colors.
Aufbau Principle
Figure 1.7

A representation of van’t Hoff’s tetrahedral carbon atom. The solid lines represent bonds in the plane of the paper, the
heavy wedged line represents a bond coming out of the plane of the page toward the viewer, and the dashed line represents
a bond going back behind the plane of the page away from the viewer.
Electron-Dot and Line-Bond Structures
Valence Electrons and Covalent Bond Formation
Lone-Pair Electrons – Ammonia
Worked Example 1.1
Predicting the Number of Bonds Formed by Atoms in Molecules

How many hydrogen atoms does phosphorus bond to in forming

phosphine, PH??
Worked Example 1.1
Strategy

Identify the periodic group of phosphorus, and find from that how
many electrons (bonds) are needed to make an octet.
Worked Example 1.1
Solution

Phosphorus is in group 5A of the periodic table and has five valence

electrons. It thus needs to share three more electrons to make an octet
and therefore bonds to three hydrogen atoms, giving PH3.
Worked Example 1.2
Drawing Electron-Dot and Line-Bond Structures

Draw both electron-dot and line-bond structures for chloromethane,

CH3Cl.
Worked Example 1.2
Strategy

Remember that a covalent bond—that is, a pair of shared electrons—is

represented as a line between atoms.
Worked Example 1.2
Solution

Hydrogen has one valence electron, carbon has four valence electrons,
and chlorine has seven valence electrons. Thus, chloromethane is
represented as
Valence Bond Theory – H2 Molecule
Figure 1.8
The cylindrical symmetry of the H–H σ bond in an H2
molecule. The intersection of a plane cutting through the σ
bond is a circle.
Figure 1.9

Relative energy levels of two H atoms and the H 2 molecule. The H2 molecule has 436 kJ/mol (104 kcal/mol) less energy than
the two separate H atoms, so 436 kJ/mol of energy is released when the H–H bond forms. Conversely, 436 kJ/mol is
absorbed when the H–H bond breaks.
Figure 1.10

A plot of energy versus internuclear distance for two hydrogen atoms. The distance between nuclei at the minimum energy
point is the bond length.
Figure 1.11

Four sp3 hybrid orbitals, oriented toward the corners of a regular tetrahedron, are formed by the combination of an s
orbital and three p orbitals (red/blue). The sp3 hybrids have two lobes and are unsymmetrical about the nucleus, giving them
a directionality and allowing them to form strong bonds to other atoms.
Figure 1.12

The structure of methane, showing its 109.5° bond angles.

Some Representations of Ethane
Figure 1.13

The structure of ethane. The carbon–carbon bond is formed by σ overlap of two sp3 hybrid orbitals. For clarity, the smaller
lobes of the sp3 hybrid orbitals are not shown.
Figure 1.14

sp2 Hybridization. The three equivalent sp2 hybrid orbitals lie in a plane at angles of 120° to one another, and a single
unhybridized p orbital (red/blue) is perpendicular to the sp2 plane.
Figure 1.15

The structure of ethylene. One part of the double bond in ethylene results from σ (head-on) overlap of sp2 hybrid orbitals,
and the other part results from π (sideways) overlap of unhybridized p orbitals (red/blue). The π bond has regions of electron
density above and below a line drawn between nuclei.
Worked Example 1.3
Drawing Electron-Dot and Line-Bond Structures

Commonly used in biology as a tissue preservative, formaldehyde,

CH2O, contains a carbon–oxygen double bond. Draw electron-dot and
line-bond structures of formaldehyde, and indicate the hybridization of
the carbon orbitals.
Worked Example 1.3
Strategy

We know that hydrogen forms one covalent bond, carbon forms four,
and oxygen forms two. Trial and error, combined with intuition, is
needed to fit the atoms together.
Worked Example 1.3
Solution

There is only one way that two hydrogens, one carbon, and one oxygen
can combine:

Like the carbon atoms in ethylene, the carbon atom in formaldehyde is

in a double bond and its orbitals are therefore sp2-hybridized.
Figure 1.16

sp Hybridization. The two sp hybrid orbitals are oriented 180° away from each other, perpendicular to the two remaining p
orbitals (red/blue).
Figure 1.17

The structure of acetylene. The two carbon atoms are joined by one sp–sp σ bond and two p–p π bonds.
Methylamine
Methanol
Methyl Phosphate
Methanethiol and Dimethyl Sulfide
Figure 1.18

Molecular orbitals of H2. Combination of two hydrogen 1s atomic orbitals leads to two H2 molecular orbitals. The lower-
energy, bonding MO is filled, and the higher-energy, antibonding MO is unfilled.
Figure 1.19

A molecular orbital description of the C–C π bond in ethylene. The lower-energy, π bonding MO results from an additive
combination of p orbital lobes with the same algebraic sign and is filled. The higher-energy, π antibonding MO results from a
subtractive combination of p orbital lobes with opposite algebraic signs and is unfilled.
2-Methylbutane
Worked Example 1.4
Interpreting a Line-Bond Structure

Carvone, a substance responsible for the odor of spearmint, has the

following structure. Tell how many hydrogens are bonded to each
carbon, and give the molecular formula of carvone.
Worked Example 1.4
Strategy

The end of a line represents a carbon atom with 3 hydrogens, CH3; a

two-way intersection is a carbon atom with 2 hydrogens, CH2; a three-
way intersection is a carbon atom with 1 hydrogen, CH; and a four-way
intersection is a carbon atom with no attached hydrogens.
Worked Example 1.4
Solution