Organic Chemistry

Organic Chemistry:

Originally defined as study of compounds from living things /

organisms (compounds from nature ).

Later, chemists made (synthesized) compounds in the laboratory

NOW: Organic chemistry is the study of compounds containing

carbon.

However,
Biochemistry is the study of the chemicals and processes that
sustain life (the life on Earth that is based on carbon compounds).

Biochemistry is based on and overlapped with Organic Chemistry.

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 Organic Chemistry
• Over 10 million organic compounds have been identified
– about 1000 new ones are discovered or synthesized and
identified each day!
– Unlimited number of organic compounds are possible
• Why?
• C is a small atom
– it forms single, double, and triple bonds
– it is intermediate in electronegativity (2.5)
– it forms strong bonds with C, H, O, N, and some
metals.

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 Chapter 1. Bonding and Isomerism

1.1 The Review of Atomic Structure

proton(s) no. of protons = atomic number

nucleus
Atom neutron(s)
electron(s) Atomic weight = no. of proton(s) + no. of neutron(s)

Electrons are located in orbitals

possibility of electrons around the nucleus

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 Quantum Numbers
•n - principal quantum number, n = 1, 2, 3, 4, ……

•  - azimuthal (angular momentum) quantum number,  < n (1, ……, n -

1)

•m - magnetic quantum number, total m values = 2 + 1 (-,…, 0, …, )

•ms – electron spin quantum number, ms values = +½, or -½.

One orbital can only hold up to two electrons (Pauli Exclusion

Principle).

Orbitals are grouped in electron shells (based on n values).

Different orbitals have different shapes (based on values).

e.g. s – sphere, = 0; p – dumbbell, = 1.

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 Table 1.1 Numbers of orbitals and electrons
in the first three shells

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 Shapes of Atomic Orbitals
A p- orbital consists of two lobes arranged in a straight
line with the center at the nucleus.
All s orbitals have the shape of a sphere, with its center
at the nucleus.
Of the s orbitals, 1s is the smallest, 2s is larger, and a
3s is even larger, …etc.

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Aufbau principle for filling electrons on atomic orbitals

Finish
here
7s
6d
6p
6s 5f
5d
Energy 5p
of the 5s 4f
4d
atomic 4p
orbitals 4s
3d
3p
3s
2p
2s

1s Start
here

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Type of Orbitals No. of Orbitals No. of Electrons Shell Number Max. No. of Electrons on the shell Orbitals (No.)

1 2 (2 x 12) 1s (1)
s (=0) 1 =(2 x 0+1) 2
2 8 (2 x 22) 2s 2p (4)
p (=1) 3 =(2 x 1+1) 6
3 18 (2 x 32) 3s 3p 3d (9)
d (=2) 5 =(2 x 2+1) 10
4 32 (2 x 42) 4s 4p 4d 4f (16)
f (=3) 7 =(2 x 3+1) 14

 (2+1) 2(2+1) n 2n2 n2

Electron configuration and Periodic Table

See Table 1.3 on pg. 8 inner electrons valence electrons
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e.g. Carbon 6 electrons: 6C 1s22s22p2
valence shell --- the outermost shell
Kernel of the atom --- nucleus + inner electrons
Valence (shell) electrons: the electrons in the valence shell

chemical symbol with valence electron(s)

to form Lewis symbol a dot for each valence electron
chemical
So the Lewis symbol for carbon element --- C
bonding
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1.2 Review of Chemical Bonding
Only exist in metal elements
Chemical bonding: ionic, covalent, and metallic
(1) Ionic bond --- electrostatic interaction between cations and anions.
Atoms lose the electron(s) --- cations --- positive charge(s)
electropositive atoms, e.g. Na• → Na+ + e
Atoms gain the electron(s) --- anions --- negative charge(s)
electronegative atoms, e.g. Br + e → Br ‾

Na• + Br → Na+ Br ‾ used for transfer of one electron

ionic compound → contains ions

and structure see Figure 1.1 next slide
Normally across the row (period): left → right electronegative↑ electropositive↓
down the column (group): up → down electronegative↓ electropositive ↑
Ion charges: In the periodic table, group1 → 1+, group2 → 2+, group3 → 3+,
group 6→ 2-, group7 → 1-,
Other ions: H+ , Ag+, Zn2+, Cu+ / Cu2+, Fe2+ / Fe3+, etc.
Polyatomic ions: NH4+, OH‾, NO3‾, CO32‾, MnO42‾, SO42‾, CN‾, PO43‾ etc.
The total charge in an ionic compound is zero.
e.g.
9 Ca2+ and OH‾ form ionic compound. Write its empirical formula.
Figure 1.1 Sodium chloride is
an ionic crystal

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 Table 1.4 Electronegativities of some
common elements

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(2) Covalent bond --- shared electron pair(s) between atoms
For atoms like Carbon (in group4), neither strongly electronegative nor
strongly electropositive, they tend to share electron pairs to form a molecule
by covalent bonds. H H
:C: + 4H• → H C H or CH4 molecule H C H
H covalent bond or molecular H
compound
H• + •H → H : H or H2 or H ­H

pure covalent: electron pair equally distributed

between two identical atoms
In general, two atoms have similar electronegativity /electropositivity and
they form covalent bond. Like in CH4 molecule, the electron pair between C
and H are quite evenly shared, so 4 C ­H bonds are covalent bonds.
For atoms with different electronegativity /electropositivity, they form polar
covalent bond. Like in H2O, the electron pairs between O and H are not
-

Dipole using symbol
equallyHshared,Oso 2 O
H­H bonds are polarOcovalent bonds.
arrow toward to more
 +H H +
electronegative atom
12 Polar covalent bonds
 Figure 1.3 The molecular orbital
representation of covalent bond formation

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Figure 1.4 Orbital overlap to form s bonds

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Chapter 1, Page 29 p+p =  bond

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Bond energy (BE) and Bond length are used to evaluate the strength of covalent
Bond. See definitions on pg. 11 in the textbook.
BE ↑ (stronger) → Bond length ↓(shorter)
one electron pair shared between two atoms → single bond “__” e.g. C C
two electron pairs shared between two atoms → double bond “=“ e.g. C C
three electron pairs shared between two atoms → triple bond “≡“ e.g. C C
BE: single bond < double bond < triple bond
Bond length: single bond > double bond > triple bond
Organic Chemistry is the study of compounds containing carbon, so in Organic
Chemistry we mainly study covalent bonding molecules.
Structural formula and Isomerism
Using Lewis structures, we can write the structural formulas of different molecules.
e.g. C2H6O Molecular formula gives information the types and numbers
of atoms in the compound.
Structural formula gives the types and numbers of atoms as well as the
arrangement of these atoms in the compound.
H H H H Isomerism:
O
H C C O and H C C H One molecular formula may have more
H than one structural formulas, which
H H H H correspond to different molecules.
ethanol dimethyl ether
Isomerism
16 is a characteristic of Organic Chemistry
Isomers --- molecules that have the same kinds and numbers of atoms but different
atomic arrangements.
Structural or constitutional isomers --- molecular compounds with same molecular
formula but different structural formulas.
They are different compounds and they differ in physical and chemical properties
because of different structures.

e.g. ethanol, CH3__CH2__OH and dimethyl ether CH3__O__CH3 are structural isomers.
Here we abbreviate the structural formulas by omitting the C __ H single bonds.
Even more abbreviated structures can be written as CH3CH2OH and CH3OCH3
The use of lines to represent carbon backbone or framework is often common in
Organic Chemistry. e.g. CH3CH2CH2CH3

CH3CH=CHCH3

Stereoisomers will be studied in later chapters

Formal Charge (FC) and Resonance (Review)

Using formal charge can help you to write correct structures.
For certain atom in the molecule, VE – valence electrons of the atom
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FC = VE – CB – USE CB – covalent bonds around the atom
Resonance Structures
Resonance is the use of two or more Lewis structures that differ only in the
distribution of the valence electrons in representing the bonding in a species.
The skeleton structure does not change; only the placement of bonds is different.
We indicate resonance structures with a double-headed arrow.
e.g. the Lewis structure of CO32-
2- 2- 2- 2-
O O O O
* C C C C
O O O O O O O O

Calculate the formal charges of C and O atoms in CO32-

FC (C) = 4 – 4 – 0 = 0 FC (O*) = 6 – 2 – 4 = 0 FC(O) = 6 – 1 – 6 = -1

These Lewis structures ------ resonance structures

The real molecule or ion is described by an average of these resonance structures.

Benzene, C6H6

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1.5 Symbols used in Organic Chemistry
(1) Curved arrows
“curved arrow” --- used for transferring a pair of electrons

“fishhook or half-headed curved arrow --- used for transferring

one electron
(2) Straight arrows
“straight arrow” --- used for pointing from reactants to products
in a chemical equation
“double headed straight arrow” --- used for converting
resonance structures
“half headed straight arrow” --- used for a reversible chemical
reaction or an equilibrium
1.6 Hybridization and  /  bonds (Review)
Linus Pauling proposed the theory of orbital hybridization.
(a) Hybrid orbitals can be formed by mixing s, p and / or d orbitals
on an atom in order to form bonds in the molecules.
(b) Hybrid orbitals have an orientation in space that matches the
geometry of a molecule.
(c) The number of hybrid orbitals formed is the same as the number
of atomic orbitals used for the hybridization.
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Hybridization involving s and p atomic orbitals
(a) sp3 CH4 molecule
C atom
C
2p
Energy

sp3 hybridization

2s 4 sp3 hybrid orbitals

Carbon’s four sp3 hybrid orbitals and 4 hydrogens’1s orbitals form
4 C-H bonds. They are equivalent.
H
109.5°
C + 4 H C tetrahedral
H H
H H
¨
NH3 molecule N H2O molecule O
H ¨
H H ¨
H
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(b) sp2
BF3 molecule
B atom
2p 2p
Energy

sp2 hybridization

2s
3 sp2 hybrid orbitals

F
B +3 F
F
B 120°

trigonal

F
planar
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 H H
· ·
C C H2C=CH2 molecule

H H
C=C 1  bond --- overlapping 2 sp2 hybrid orbitals
double bond 1  bond --- overlapping 2 2p orbitals
H
· · ¨ C=O 1  bond --- overlapping 2 sp2 orbitals
C O 1  bond --- overlapping 2 2p orbitals

¨ H2C=O:¨ molecule
H
O atom is also sp2 hybridization, 1 sp2 orbital is used to form  bond
by overlapping with C’s sp2 orbital; two lone pair electrons occupy
the other 2 sp2 orbitals; 1 unhybrid 2p orbital overlaps with 2p orbital
of C’s to form  bond.
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 Benzene molecule --- C6H6 (Delocalized Bonding)

All six carbon atoms are sp2 hybridization. Benzene molecule is a

planar ring structure. Each carbon has one 2p orbital left. Six 2p
orbitals overlap with each other to form a big  bond with 6 electrons.
So the six C-C bonds are equivalent. So are the six C-H bonds
H H H
H C H H C H H C H
C C C C C C
C C C C C C
H C H H C H H C H
H H H

H • • H
H H

• • H H
H H

• •
H H
H H

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 z
(b) sp
Be atom BeCl2 molecule x
y
2p 2p
Energy

sp hybridization
2s
2 sp hybrid orbitals

Be +3 Cl Cl Be Cl
linear

H–CC–H molecule H C C H

1  bond --- overlapping 2 sp hybrid orbitals

CC
1  bond --- overlapping 2 2p orbitals
triple bond
1  bond --- overlapping 2 2p orbitals
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Table 1.6
The main
functional
groups

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1.7 Classifications of Organic Compounds
(1) Classification Based on Molecular Framework
Acyclic Compounds: unbranched chain and branched chain
Carbocyclic Compounds
Heterocyclic Compounds: at least one atom is a heteroatom, (or not carbon)
See examples in the textbook pg. 33-35
(2) Classification Based on Functional group (see Table 1.6 on pg. 36-37)
(a) Hydrocarbons (only contain C and H atoms):
C–C single bond --- alkane
C=C double bond --- alkene
C≡C triple bond --- alkyne
(b) Functional Groups Containing Oxygen
–O–H --- alcohol
–C–O–C– --- ether only C–O single bond
–(C=O)H (–CHO) --- aldehyde
only C=O double bond
>C=O --- ketone
–(CO)OH --- carboxylic acid both C–O single bond and
–(CO)OR --- ester C=O double bond
(c) Functional Groups Containing Nitrogen
–C–NH2 --- amine (primary)
–C≡N --- nitrile
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 (c) Functional Groups Containing both Oxygen and Nitrogen
–(CO)NH2 --- amide (primary)
(d) Functional Groups Containing Sulfur
–S–H --- thiol (also mercaptan)
–C–S–C– ---- thioether (also disulfide)

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Figure 1.11 Examples of natural acyclic
compounds

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 Figure 1.12
Examples of
natural carbocyclic
compunds with
rings of various
sizes and shapes

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Figure 1.13
Examples of
natural
heterocyclic
compounds

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