CDB 1013 – ORGANIC CHEMISTRY

LECTURE 1.1:
THE BASICS

PROF. DR. MASAHARU KOMIYAMA

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LEARNING OUTCOME
By end of this lecture, student should be able to

1. Write electron configuration for any given atom.

2. Draw chemical structures of organic compounds using
several methods.
3. Calculate formal charges of each atom in the chemical
compounds, particularly organic compounds.
4. Discuss the difference in methods to draw chemical
structures.
5. Explain stability of organic compounds through their
resonance structures.

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PERIODIC TABLE - RECALL

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ATOMIC STRUCTURE
 Elements are made of atoms.
 An atom consists of a dense, positively charged nucleus containing protons and
neutrons and a surrounding cloud of electrons.

Atomic
number
Atomic
symbol

Atomic mass

Each element have unique atomic

Did you
know?

number (Z), a number equal to the

number of protons in its nucleus.

Atomic number (z) = number of protons (unique to each elements)

Mass number = number of protons + neutrons (may vary from isotope to isotope)

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ELECTRON CONFIGURATION
How the electron configures themselves in electron cloud?

K shell
(1s orbital, 2 e)

L shell
(2s, 2p orbitals, 8 e)

M shell
(3s, 3p, 3d orbitals,
18 e)

Bohr diagrams indicate how many electrons fill each principal shell

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ELECTRON CONFIGURATION (CONT.)
How the electron configures themselves in electron cloud?

Z=6 → 6e

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VALENCE ELECTRONS (VE)
 The outermost electrons (in the outermost shell).
 The presence of valence electrons can determine the element's chemical
properties and whether it may bond with other elements.

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 CLASS ACTIVITY 1.1
Write the electron configuration and determine how many valence electrons does
each of the following atoms have?

http://kcd-elements.tumblr.com/ 8
CLASS ACTIVITY 1.1 - ANSWER

Period

Group

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ISOTOPES
 Each of two or more forms of the same element that contain equal numbers of
protons but different numbers of neutrons in their nuclei, and hence differ in
relative atomic mass but not in chemical properties; in particular, a radioactive
form of an element.

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ISOTOPES – CARBON-14 DATING
 We have some radioactive materials in our bodies.
 One of the isotope is carbon-14.

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CHEMICAL BONDS

What does the electron configuration

have to do with chemical bonds?

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CHEMICAL BONDS – THE OCTET RULE
 This rule states that the elements lose or gain electrons in order to achieve
noble gas configurations (outermost shell is full).
 Atoms tend to combine in such a way that they have eight electrons in their
valence shells, giving them the same electron configuration as (the nearest)
Noble gas.

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CHEMICAL BONDS – THE OCTET RULE
“The Giver”

 To reach noble gas configuration, sodium has to either gain 7 electrons OR lose
one electron.
 It is easier for sodium to release one electron than to add 7 electrons to its
orbital.

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CHEMICAL BONDS – THE OCTET RULE
“The Receiver”

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CHEMICAL BONDS – THE OCTET RULE

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IONIC BONDS – GIVER & RECEIVER
 Sodium and fluorine undergoing ionic bonds to form sodium fluoride.
 Sodium loses its outer electron to give it a stable electron configuration, and
this electron enters the fluorine atom exothermically.

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ELECTRONEGATIVITY
 Electronegativity is a measure of the ability of an atom to attract electrons – the
higher the electronegativity, the higher its ability to attract electrons.

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ELECTRONEGATIVITY (CONT.)
 Electronegativity is a measure of the ability of an atom to attract electrons.

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DOES CARBON GIVE OR RECEIVE ELECTRONS?
How the electron configures themselves in electron cloud?

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DOES CARBON GIVE OR RECEIVE ELECTRONS?

 Carbon like to “share” electrons – known as covalent bond.

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DOES CARBON GIVE OR RECEIVE ELECTRONS?

Carbon atoms have the ability to form huge network…

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COVALENT BONDS
 Covalent bonds form by sharing of electrons between atoms of similar
electronegativities to achieve the configuration of noble gas.

1. Duplet rule, only for covalent bond involving hydrogen (H K-shell will be full).

2. Octet rule, for (almost) other atoms (each atom fulfil octet rule).

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CLASS ACTIVITY 1.2
Using octet rule, draw the chemical structure of the following compounds
Number of electrons-dot = ve atom 1+ ve atom 2 + … + ve atom n

1. O2 6. PCl5 11. C4H10

2. N2 7. SF6 12. C4H8
3. Cl2 8. H2SO4 13. C4H6
4. CH3OH 9. SO3 14. C4H9Cl
5. HNO2 10. C2H6O 15. C6H6

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EXCEPTION TO OCTET RULE
 Molecules containing atoms of Group 3A elements, particularly boron and
aluminum

6 electrons in the

:
: F: valence shells of boron : Cl :
and aluminum
: :

: :
:F B : Cl Al
:F: : Cl :
:

:
Boron trifluoride Aluminum chloride

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EXCEPTION TO OCTET RULE
 Molecules Atoms of third-period elements have 3d orbitals and may expand their
valence shells to contain more than 8 electrons
 Phosphorus may have up to 10

:
: Cl : :O:

: : : :

: : : :
: Cl Cl :

: :

:
CH3 -P- CH3 P H- O-P- O-H

:
CH3 : Cl Cl : O-H

:
Trimethyl- Phosphorus Phosphoric
phosphine pentachloride acid

 sulfur, another third-period element, forms compounds in which its valence shell
contains 8, 10, or 12 electrons

: O: : O:
:

H-S- H CH 3 -S-CH 3 H-O- S-O-H

:

:
:

:O : Compounds that do NOT follow

Did you
know?
octet rule are very reactive. It will
Hydrogen Dimethyl Sulfuric
react to form more stable
sulfide sulfoxide acid
compound that follow octet rule.

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NEXT CLASS

Alkane Formal Charge

LEWIS Resonance
STRUCTURE Isomer

Reading Material: Main Reference Chapter 1

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LEWIS STRUCTURE - ATOM
Lewis dot structure: The symbol of an element represents the nucleus and all inner
shell electrons while dots represent valence electrons

K-shell

L-shell

M-shell

N-shell

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LEWIS STRUCTURE - BOND
Atoms bond together so that each atom acquires an electron configuration the
same as that of the noble gas nearest it in atomic number

Lone pair electrons

Hydrogen do NOT follow octet rule

Did you
know?
due to its small size (and its orbital).
Instead of octet, it goes duplet.

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LEWIS STRUCTURE - BOND
The number of shared pairs
 one shared pair forms a single bond
 two shared pairs form a double bond
 three shared pairs form a triple bond

Did you know?

In neutral molecules
 hydrogen has one bond
 carbon has 4 bonds and no lone pairs
 nitrogen has 3 bonds and 1 lone pair
 oxygen has 2 bonds and 2 lone pairs
 halogens have 1 bond and 3 lone pairs

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LEWIS STRUCTURE - BOND
For more complicated molecules and molecular ions, it is helpful to
follow the step-by-step procedure outlined here:
1. Determine the total number of valence (outer shell) electrons. For
cations, subtract one electron for each positive charge. For anions,
add one electron for each negative charge.
2. Draw a skeleton structure of the molecule or ion, arranging the atoms
around a central atom. (Generally, the least electronegative element
should be placed in the center.) Connect each atom to the central
atom with a single bond (one electron pair).
3. Distribute the remaining electrons as lone pairs on the terminal
atoms (except hydrogen), completing an octet around each atom.
4. Place all remaining electrons on the central atom.
5. Rearrange the electrons of the outer atoms to make multiple bonds
with the central atom in order to obtain octets wherever possible.

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FORMAL CHARGES
 Formal charge: the charge on an atom in a molecule or a polyatomic ion
 To derive formal charge
1. Write a correct Lewis structure for the molecule or ion
2. Assign each atom all its unshared (nonbonding) electrons and one-
half its shared (bonding) electrons
3. Compare this number with the number of valence electrons in the
neutral, unbonded atom

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FORMAL CHARGES (CONT.)
 Formal Charge Observed with Common Bonding Patterns for C, N, and O

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STRUCTURAL FORMULA OF ORGANIC COMPOUNDS

Condensed
VS

Skeletal
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CONDENSED STRUCTURES
 Condensed structures are most often used for compounds having a chain
of atoms bonded together, rather than a ring.
 The following conventions are used:
1. All of the atoms are drawn in, but the two-electron bond lines are
generally omitted.
2. Atoms are usually drawn next to the atoms to which they are bonded.
3. Parentheses are used around similar groups bonded to the same
atom.
4. Lone pairs are omitted.

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CONDENSED STRUCTURES (CONT.)

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CONDENSED STRUCTURES (CONT.)
 Condensed structures containing heteroatom

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SKELETAL STRUCTURES
 Skeletal structures are used for organic compounds containing both
rings and chains of atoms.
 Three important rules are used to draw them:
1. Assume there is a carbon atom at the junction of any two lines or at
the end of any line.
2. Assume there are enough hydrogens around each carbon to make it
tetravalent.
3. Draw in all heteroatoms and the hydrogens directly bonded to them.

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SKELETAL STRUCTURES (CONT.)

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SKELETAL STRUCTURES (CONT.)
Take care in interpreting skeletal structures for positively and
negatively charged carbon atoms, because both the hydrogen atoms
and the lone pairs are omitted. Keep in mind the following
 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.

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SKELETAL STRUCTURES (CONT.)
Skeletal structures often leave out lone pairs on heteroatoms,
but don't forget about them.

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CLASS ACTIVITY 1.3
1. Convert each skeletal structure to a Lewis structure.

e. f. g.

h. i. j. k.

2. Write the condensed structures for compounds 1a to 1k.

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CLASS ACTIVITY 1.3
2. Convert each molecule into a skeletal structure

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RESONANCE
For many molecules and ions, no single Lewis structure provides a truly
accurate representation

carbonate ion

You have to show the electron movement (using arrow) and the formal
charges for every atoms.
 Curved arrow: a symbol used to show the redistribution of valence
electrons
 In using curved arrows, there are only two allowed types of electron
redistribution: from a bond to an adjacent atom AND from an atom to
an adjacent bond
 Electron pushing is a survival skill in organic chemistry!!! learn it well!
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STABILITY OF RESONANCE
Rule 1: filled valence shells
 Structures in which all atoms have filled valence shells contribute more
than those with one or more unfilled valence shells

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STABILITY OF RESONANCE
Rule 2: Maximum number of covalent bonds
 Structures with a greater number of covalent bonds contribute more than
those with fewer covalent bonds

+ •• +
CH3 O
••
C H CH3 •O
•
C H

H H
Greater contribution Lesser contribution
(8 covalent bonds) (7 covalent bonds)

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STABILITY OF RESONANCE
Rule 3: Least separation of unlike charge
 Structures with separation of unlike charges contribute less than
those with no charge separation

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STABILITY OF RESONANCE
Rule 4: Negative charge on the more electronegative atom
 Structures that carry a negative charge on the more electronegative
atom contribute more than those with the negative charge on the
less electronegative atom

O O O
(1) C (2)
C C
H3 C CH3 H3 C CH3 H3 C CH3
(a) (b) (c)
Lesser Greater Should not
contribution contribution be drawn

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STABILITY OF RESONANCE

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ISOMER
 Isomers are different molecules having the same molecular formula.

 Ethanol and dimethyl ether are constitutional isomers because they

have the same molecular formula, but the connectivity of their atoms
is different.
 For example, ethanol has one C – C bond and one O – H bond,
whereas dimethyl ether has two C – O bonds.

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ISOMER (CONT.)
 Nitromethane and methyl nitrite, both of which have the molecular
formula CH3NO2.

 Nitromethane used to power race cars, is a liquid with a boiling

point of 101°C.
 Methyl nitrite is a gas boiling at 12°C, which when inhaled causes
dilation of blood vessels.

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ISOMER (CONT.)

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ISOMER (CONT.)
 Constitutional isomers: compounds with the same molecular
formula but a different connectivity of their atoms

Molecular Constitutional
Formula Isomers
CH4 1
C5 H1 2 3
C1 0 H2 2 75
C1 5 H3 2 4,347
C2 5 H5 2 36,797,588 World population is about
C3 0 H6 2 4,111,846,763 6,000,000,000

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ISOMER (CONT.)
 Stereoisomer: Isomers with the same connectivity but a different
orientation of their atoms in space.

 The cis isomer has two groups on the same side of the double bond.
 The trans isomer has two groups on opposite sides of the double bond.

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CLASS ACTIVITY 1.4
1. Draw all reasonable resonance structures for each species.

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CLASS ACTIVITY 1.4
2. Keeping the same atomic connections and moving only electrons, write a more
stable Lewis structure for each of the following. Be sure to specify formal
charges, if any, in the new structure.

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CLASS ACTIVITY 1.4
3. With reference to compound A and B drawn below, label each compound as an
isomer, a resonance structure, or neither.

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CLASS ACTIVITY 1.4
4. Classify each pair of compounds as constitutional isomers, stereoisomers,
identical molecules, or not isomers of each other.

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NEXT CLASS

Bond Strength Sigma- and Pi- bond

H YBRIDIZATION
Molecular Orbital Bond Length
Dipole Moment

Reading Material: Main Reference Chapter 1

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