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Industrial Organic Chemistry 1 (Spring 2024)
Chapter 1
Structure and Bonding
Review of General Chemistry
Assistant Prof. Sang-Ho Lee
Department of Chemical & Biochemical Engineering
Dongguk University
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Outline of the Lecture
1. Course introduction
2. Bonding
3. Lewis Structures
4. Resonance
5. Drawing Organic Molecules
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Course Information
Course
Industrial Organic Chemistry 1 (공업유기화학 1)
Textbook
“Organic Chemistry" 6th Ed.
(By Janice Gorzynski Smith, McGraw Hill)
(By Paula Yurkanis Bruice, Pearson)
Grades (total 100 points)
1. Attendance (10 pts)
2. Assignment (20 pts): Problem sets in each chapter
3. Exam: mid-term (35 pts) and final (35 pts)
Midterm exam on April 19 (3 pm – 4:15 pm)
Final exam on June 14 (3 pm – 4:15 pm)
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Course Information
Instructor
Sang-Ho Lee (이상호)
Assistant Professor
Department of Chemistry
Class: (Thur) 1:30 pm – 2:45 pm
(Fri) 3:00 pm – 4:15 pm
E-mail: slee24@dgu.ac.kr
Homepage: ---------Office: 만해관 102호
Office hour: e-mail for an appointment
TA: Jun Young Park, 박준영 (98juny@naver.com)
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.1
Origin of Organic Chemistry
- Foundations of organic chemistry from mid-1700’s.
- Compounds obtained from plants, animals hard to isolate, and purify.
- Compounds also decomposed more easily.
- Torben Bergman (1770) first to make distinction between organic and
inorganic chemistry.
- It was thought that organic compounds must contain
some “vital force” because they were from living sources.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.1
Organic Compounds
https://portal.re.kr/uat/uia/actionMain.do
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.1
Organic Molecules Around You
simple organic molecules
Ethanol
Aspirin
polymer
Nylon
biomolecule
DNA
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.1
Organic Molecules for Medicine
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.1
Fun Organic Molecules : Nanokid
Nanocar
http://nanokids.rice.edu/cast.cfm
http://nanokids.rice.edu/videos.cfm
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.1
Introduction of Organic Chemistry
Organic Chemistry: The study of carbon compounds
•
Carbon is tetravalent. It has four outer-shell electrons
(1s22s22p2) and forms four bonds.
Out of 50 million compounds presently known >70% contains Carbon !
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.2
Covalent Bond in Organic Compounds
•
•
•
Covalent bonding occurs with elements like carbon
with elements that have similar electronegativity.
Organic molecules have covalent bonds.
In ethane, for instance, all bonds result from the
sharing of two electrons.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.2
Covalent Bond in Organic Compounds
• Electrons are shared between the atoms to complete the
octet.
• When the electrons are shared evenly the bond is said to
be nonpolar or pure covalent.
• When electrons are not shared evenly between the atoms,
the resulting bond will be polar.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.2
Ionic Bond in Inorganic Compounds
• To obtain a noble gas configuration (a full valence shell),
atoms may transfer electrons from one atom to another.
• The atoms, now bearing opposite charges, stay together
by electrostatic attraction.
anion
cation
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
Lewis Structures
Lewis Structures: Electron Dot Representation for Molecules
1. Draw only the valence electrons.
2. Give every second-row element no more than 8 electrons.
3. Give each hydrogen two electrons.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
•
Lone Pair Electrons
Nonbonding electrons (lone pair electrons)
valence-shell electrons that are not shared between two atoms
Non-bonding electrons in heteroatoms are important
in many of useful organic reactions.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
Common Bonding Patterns
Valence
electrons
# Bonds
# Lone Pair
Electrons
C
4
4
0
N
5
3
1
O
6
2
2
F, Cl, Br, I
7
1
3
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
Examples of Lewis Structures
CH4
NH3
H
Carbon: 4 e
4 H@1 e ea: 4 e
8e
H C H
Nitrogen: 5 e
3 H@1 e ea: 3 e
8e
H N H
H
H
H2O
Oxygen: 6 e
2 H@1 e ea: 2 e
8e
Cl2
H O H
2 Cl @7 e ea: 14 e
Cl Cl
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
Multiple Bonds
• If all valence electrons are used and an atom does not
have an octet, they form multiple bonds.
• To give both C’s an octet, change one lone pair into one
bonding pair between the two C’s, forming a double
bond.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
Double and Triple Bonds
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
How do you draw the Lewis Structure of H3O+ ?
Formal charge: a method to keep track of electronic charges state of atoms
Formal charge = number of valence electrons – (e in lone pairs + # bonds)
= group number – (non-bonding e-) – ½ (shared e-)
H3O+
6 – (2 + 3) = +1
+
H O H
H
6 – (2 + 3) = +1
NO+
5 – (2 + 3) = 0
N O+
O
HCO3-
C
O
OH
6 – (6 + 1) = -1
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
Formal Charge
• Formal charge (형식전하) is the charge assigned to individual
atoms in a Lewis structure.
• 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.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
How Electrons are Owned by Atoms?
The number of electrons “owned” by different atoms is
indicated in the following examples:
What is the formal charge on the carbon?
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.3
Common Bonding Patterns
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
PROBLEM
Draw the Lewis structure for each of the following:
a. NO3–
b. NO2+
PROBLEM
Draw the Lewis structure for each of the following:
a. NO3–
b. NO2+
1.5
Exceptions to the Octet Rule
Elements in Groups 2A and 3A (B, Be)
Elements in the Third Row (S, P)
These are exceptions to common octet rule !
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.4
Isomers (이성질체)
• Sometimes more than one arrangement of atoms
(Lewis structure) is possible for a given molecular
formula.
• Isomers are different molecules having the same
molecular formula.
• Ethanol and dimethyl ether are constitutional isomers
(=structural isomers).
n
co
ity
v
i
ct
e
n
isomers
Constitutional
isomers
Stereoisomers
We will learn more about
the isomers in next chapters
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Resonance
Kentaurus
Human?
Horse?
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Resonance
• The structure of some compounds are not adequately
represented by a single Lewis structure.
• Resonance forms are Lewis structures that can be
interconverted by moving electrons only.
• The true structure will be a hybrid between the contributing
resonance forms.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Charge Delocalization
Which bread do you like more?
De (not) + localize (local) = not localized
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Charge Delocalization in Resonance
• Resonance makes a molecule MORE stable
• Delocalization of electrons
– Electrons exist in orbitals that span a greater distance
giving the electrons more freedom minimizing repulsions
– Electrons spend time close to multiple nuclei all at once
maximizing attractions
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Bonds and Arrows in Organic Chemistry
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Basic Principles of Resonance Theory
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.
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.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Drawing Resonance Structures
Rule [1]: Two resonance structures differ in the position of
multiple bonds and non-bonded electrons. The placement
of atoms and single bonds always stays the same.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Drawing Resonance Structures
Rule [2]: Two resonance structures must have the same
number of unpaired electrons.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Drawing Resonance Structures
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.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Curved Arrow Notation
• 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.”
Sample Problem 1.4
Example 1:
Example 2:
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Atoms Without Octets
Resonance structures can have an atom with fewer than 8 electrons.
However, resonance structures can never have a second-row
element with more than 8 electrons.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Important Resonance Pattern
Two different resonance structures can be drawn when a lone pair
is located on an atom directly bonded to a double bond.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Stability of Resonance Hybrids
• In some cases, resonance structures may not represent electron
distributions of equal energy.
• The major contributor is the one in which all the atoms have a
complete octet of electrons (more stable).
The more stable
resonance form
The less stable
resonance form
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Stability of Contributors
•
How do we assess the stability of resonance?
contributors?
Resonance forms can be compared using the following
criteria, beginning with the most important:
1) Has as many octets as possible.
2) Has as many bonds as possible.
3) Has the negative charge on the most electronegative atom.
4) Has as little charge separation as possible.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.6
Stability of Contributors
•
When both resonance forms obey the octet rule, the major contributor
is the one with the negative charge on the most electronegative atom.
N C O
MAJOR
N C O
minor
Oxygen is more electronegative, so it should have the negative charge.
CH3 O N O
MAJOR
CH3 O N O
minor
One with the smallest separation of oppositely charged atoms is more stable
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.7
Determining Molecular Shape
Two variables define molecular shape:
(1) bond length and (2) 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.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.7
Molecular Geometry
• Valence shell electron pair repulsion (VSEPR theory)
– Valence electrons (bonded and lone pairs) repel each other
• To determine molecular geometry…
1. Determine the steric number (SN)
2. Predict the hybridization of the central atom
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.7
Molecular Geometry
A non-bonded pair of electrons is counted as a “Group”
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.7
Drawing 3-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.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.8
Drawing Organic Molecules
• There are many ways to represent molecules
too long to draw
suitable for simple molecules
not enough info
• Which structures above give you the most information about
the structure?
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.8
Drawing Organic Molecules
• All atoms are drawn in, but the two-electron bond lines are
generally omitted.
• Atoms are usually drawn next to the atoms to which they are
bonded.
• Parentheses are used around similar groups bonded to the
same atom.
• Lone pairs are omitted, but sometimes not.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.8
Examples of Condensed Structures
Figure 1.3
Translating some condensed formulas is not obvious, and it will come only with practice.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.8
Condensed Structures with C=O
Figure 1.4
In these examples, the only way for all atoms to have an
octet is by having a carbon-oxygen double bond.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.8
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 the hydrogens directly
bonded to them.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.8
Skeletal Structures
• To draw large molecules quickly, a different type of
representation is needed
Most efficient drawing
• This type of representation is THE main way that
chemists communicate, so it is a language you MUST
master to be successful in organic chemistry
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.8
Skeletal Structures with Charged 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.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Molecular Orbital Theory
• Atomic orbital wavefunctions overlap to form MOs that extend
over the entire molecule.
• Linear combination of atomic orbitals (LCAO)
– between different atoms is bond formation.
– on the same atom is hybridization.
• Conservation of orbitals
the number of new orbitals equals the number of orbitals started with
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Sigma Bonding in Organic Molecules
• All single bonds in organic compounds are sigma (s) bonds.
• Electron density lies between the nuclei.
: cylindrically symmetric bond
• A bond is formed by s-s, p-p, s-p, or hybridized orbital overlaps.
• The bonding molecular orbital (MO) is lower in energy than the
original atomic orbitals.
• The antibonding MO is higher in energy than the atomic orbitals.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Examples of Sigma Bonding
Formation of a s-bond
from two 1s-orbitals
Formation of a s-bond
from one 1s- and a 2pz-orbitals
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Hybridized Atomic Orbitals
• Given the electron configuration for C and H, imagine how their
atomic orbitals might overlap
• Would such orbital overlap
yield methane?
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Hybridization of sp3 Hybrid Orbitals
How can the bonding in CH4 be explained?
4 valence electrons
2 unpaired electrons
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Hybridization of sp3 Hybrid Orbitals
How can the bonding in CH4 be explained?
4 valence electrons
4 unpaired electrons
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Hybridization of sp3 Hybrid Orbitals
How can the bonding in CH4 be explained?
4 non-equivalent orbitals
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Hybridization of sp3 Hybrid Orbitals
How can the bonding in CH4 be explained?
4 equivalent orbitals
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Hybridization of sp3 Hybrid Orbitals
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Hybridization of sp3 Hybrid Orbitals
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Notation for Hybridization
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Figure 1.7
Figure 1.8
Other Hybridization Patterns
sp hybrid orbitals (s + p = two sp)
sp2 hybrid orbitals (s + p + p = three sp2)
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Examples of sp and sp2 Hybridization
BeH2
BF3
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.9
Determining Hybridization
• Count the number of groups (atoms and non-bonded
electron pairs) around the atom.
• The number of groups corresponds to the number of atomic
orbitals that must be hybridized to form the hybrid orbitals.
Hybrid
Orbitals
Hybridization
Geometry
Approximate
Bond Angle
2
s + p = sp
linear
180⁰
3
s + p + p = sp2
trigonal
120⁰
4
s + p + p + p = sp3
tetrahedral
109.5⁰
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.10
Hybridization and Bonding in Ethane
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.10
s and p Bonds in Ethylene
Each carbon is trigonal planar.
Each carbon is sp2 hybridized.
Figure 1.10
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.10
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.11
Bond Length and Bond Strength
• As the number of electrons between two nuclei increases, bonds
become shorter and stronger.
• Triple bonds are shorter and stronger than double bonds, which
are shorter and stronger than single bonds.
• Percent s-character indicates the fraction of a hybrid orbital due
to the 2s orbital used to form it. (for example, sp-hybrid orbital =
50% s-character)
Percent s-character
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.12
Electronegativity and Bond Polarity
Electronegativity is a measure of an atom’s attraction for
electrons in a bond.
Electronegativity values
are used to indicate
whether the electrons in a
bond are equally shared
or
unequally
shared
between two atoms.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.12
Depicting Polarity
• The d+ means the indicated atom is electron deficient.
• The d- 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.
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.12
Molecular Polarity
• The molecular dipole moment is the vector
sum of the bond dipole moments.
• Depend on bond polarity and bond angles.
• Lone pairs of electrons contribute to the
dipole moment.
Peter Joseph William Debye (1884–1966)
Dutch physicist and physical chemist
Nobel Prize in Chemistry (1936)
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
1.13
Electrostatic Potential for Polar and
Nonpolar Molecules
The dipoles of H2O and CO2 can also be visualized using
electrostatic potential plots.
Figure 1.14
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Summary:
Drawing a Lewis Structure for CH3CHO
ills
k
S
y
Ke
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Summary:
Calculating a Formal Charge
ills
k
S
y
Ke
Formal charge: a method to keep track of electronic charges state of atoms
Formal charge = number of valence electrons – (e in lone pairs + # bonds)
= group number – (non-bonding e-) – ½ (shared e-)
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Summary:
Predicting Geometry
ills
k
S
y
Ke
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Summary:
Identifying Isomers and Resonance Structures
ills
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Ke
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Summary:
Using Curved Arrows
ills
k
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Ke
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Summary:
Predicting Hybridization
ills
k
S
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Ke
Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee
Summary:
Determining Net Dipole
ills
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Industrial Organic Chemistry 1 @ Dongguk / Prof. Sang-Ho Lee