Organic Chemistry
Sh. Javanshir
Faculty of Chemistry
Iran University of Science & Technology
‫‪References:‬‬
‫• مبانی شیمی آلی مک موری‪ ،‬ترجمه‬
‫دکتر عیسی یاوری‬
‫‪4‬‬
‫ساعت رفع اشکال ‪:‬‬
‫شنبه – دو شنبه ‪10-12‬‬
‫‪2‬‬
‫ارزشیابی‬
‫امتحان میان ترم‬
‫امتحان پایان ترم‬
‫کار کالس ی و تمرین‬
‫‪% ۳۰‬‬
‫‪ 4‬نمره‬
‫‪% ۶۰‬‬
‫‪ 14‬نمره‬
‫‪ 2‬نمره ‪% ۱۰‬‬
‫فهرست‪:‬‬
‫‪ -1‬پیوند شیمیایی وساختار‬
‫‪ -2‬آلکان ها‬
‫‪ -3‬آلکن ها‬
‫‪ -4‬آلکین ها‬
‫‪ -5‬شیمی فضایی(استریوشیمی)‬
‫‪ -6‬بنزن و آروماتیسیته‬
‫‪ -7‬واکنش های الکترون دوست آروماتیکی‬
‫‪ -8‬آلکیل هالید ها و واکنش های آلکیل هالید ها‬
‫‪ -9‬الکل ها‬
‫مقدمه‬
‫و‬
‫تاریخچه‬
‫شیمی آلی ‪ :‬شیمی مربوط به ترکیبات کربن دار‬
‫تمایل و توانائی کربن برای پیوند با یکدیگر و‬
‫تشکیل زنجیرهای طویل یا حلقه ها‬
‫ترکیبات کربن دار‪:‬‬
‫ترکیبات طبیعی‬
‫اسید های چرب ‪ ،‬پروتئین ها‪ ،‬نوکلئیک اسیدها ‪،‬‬
‫هیدرات های کربن‬
‫ترکیبات سنتزی‬
‫داروها ‪ ،‬رنگ ها‪ ،‬پلیمرها‪ ،‬پالستیک ها‪ ،‬حشره کش ها‬
Some organic chemicals
Medicines
DNA
•Active Pharmaceutical Ingredients
•Excipients
Fuels
Materials
Essential oils
Pigments
The primary use for indigo is as a dye for
cotton yarn, which is mainly for the production
of denim cloth for blue jeans.
Organic chemicals in manufactured
products
Plastics
Coatings & lacquers
Fibres & clothings
Paper
Films
Materials
Packaging
Wound dressings
Medical implants
12
History
• T. Bergman (1770)—difference between substances from
living things and those from minerals
• The term “Organic” was applied to substances, isolated
from living things by Jons Berzelius (Beginning of the 19th
century).
• “Vitalism”—living things imparted a “vital force”, the source
of all organics was living things
• “Vitalism” - belief that “natural compounds” possessed
special
properties, could not be made by man
6
• Wöhler in 1828 showed that urea, an organic
compound, could be made from a non-living
source:
7
Who Said It…?
“Organic Chemistry nowadays almost drives me mad. To me it
appears like a primeval tropical forest full of the most
remarkable things; a dreadful endless jungle into which one
does not dare to enter for there seems to be no way out”
You
or
9
AND YOU!
– YOU:
• DNA,
• Proteins (enzymes, cell membrane
receptors,
• Carbohydrates (Polysaccharides,…
• Lipids (fatty acids,…
– And what you eat
• Protein
• Carbohydrate
• Lipids
– The plants: from CO2 to complex
organic molecules
• … with no complex, noisy, polluting,
smelly factory!
14
What for?
•
Answering questions and solving problems
•
Does eating turkey make you sleepy?
– Turkey contains L-tryptophan, (amino acid with known
sleep inducing effect)
– L-tryptophan is used in the body to produce B-vitamin,
– B-vitamin is used to produce serotonin, a
neurotransmitter with known calming effects
– L-tryptophan needs to be taken without any other amino
acids or protein in order to make you drowsy.
– Alcohol is a central nervous system depressant.
– ….
15
S
O
H
Acrolein (2-propenal)
- lachrymator and pleasant "odour"
from barbacuing meat
H
Thiopropionaldehyde
(propanethiol)
- lachrymator from chopped onion
Formalin, 35-40% formadehyde in water
Preservative that reacts with
proteins causing them to resist decay
Coelacanth, “prehistoric fish”
16
Carbon-14 then goes through radioactive beta decay.
By emitting an electron and an electron antineutrino, carbon-14 (half-life of 5730
years) decays into the stable (non-radioactive) isotope nitrogen-14.
Cosmic ray protons blast nuclei in the upper
atmosphere, producing neutrons which in
turn bombard nitrogen, the major
constituent of the atmosphere .
This neutron bombardment produces the
radioactive isotope carbon-14. The
radioactive carbon-14 combines with
oxygen to form carbon dioxide and is
incorporated into the cycle of living things.
18
What for?
•
Why did he leave?
•
Initially:
• First, there's attraction.
• Part of the nonverbal communication may
involve pheromones, a form of chemical
communication.
• raw lust is characterized by high levels of
testosterone
• The pounding heart is caused by higher
levels of norepinepherine
• The love is due to a rush of
phenylethylamine and dopamine.
– Then…
• Lasting love confers chemical benefits in
the form of stabilized production of
serotonin and oxytocin.
• Suppression of vasopressin can cause
males to abandon their love nest and
seek new mates.
The Brain controls the Body
through chemistry
OH
O
O
O
testosterone
progesterone
development of
male reproductive
system
prepares the
uterus for
reproduction
20
O
O
H5C6
H
H5C6
OH
O
N
O
O
O
O
O O
OH
O
H5C6
O
TAXOL
Isolated from the bark of the yew
tree, Taxus brevifolia, used for
treatment of ovarian cancer.
21
Chapter 1.
Structure and Bonding
Structure is the key to everything in chemistry.
The properties of a substance depend on the atoms it
contains and the way the atoms are connected.
What is less obvious, but very powerful, is the idea
that someone who is trained in chemistry can look at
a structural formula of a substance and tell you a lot
about its properties.
22
Structure Makes the
Difference
• Benzene causes Leukemia, Toluene
Doesn’t
H
Benzene
CH3
Toluene
23
Simple Organic Compounds
OH
O
CHCl3
OH
Chloroform
HO
OH
OH
Sugars
Teflon
O
NH2
OH
O
HO2C
H
N
NH2
CO2Me
O
O
Aspirin
HO2C
H
N
CO2Me
O
Ph
160 times
sweeter than
sucrose
Nutrasweet
Ph
Bitter
Why is it the element of life on earth?
Carbon and hydrogen have very similar electronegativities:
Carbon ~2.5 and
Hydrogen
~2.1
Therefore, the C-H bond is essentially non-polar.
Why is it the element of life on earth?
Carbon has unique properties
• Atomic Number 6 – 1s2 2s2 2p2. Valence of 4.
• Carbon-carbon and carbon-hydrogen bonds are strong, and
quite unreactive - provides solid scaffolds.
• Strong Single, Double and Triple Bonds
•Average Bond Energies (KJ mol-1)
•
•
C-C
607
Si-Si
230
C-H
416
Si-H
323
C-N
754
Si-N
470
C-O
336
Si-O
368
Capable of bonding to itself, metals and heteroatoms. Sits in
middle region of electronegativity.
Geometrically capable of catenation – chains, rings and
multiple bonds.
A Crown Ether
Background Review
27
Atomic Electrons
Structure:
Orbitals
behave as waves
Atomic orbital - mathematical solution to an electron (e-) wave equation,
describes the volume of space where an electron is most likely to be found
f
d
n=4
p
Energy
d
s
p
n=3
s
p
n=2
s
s
n=1
Atomic orbitals are
described by four
quantum numbers
1.
2.
3.
4.
Principle, shell (n), - orbital energy, size
Azimuthal, subshell (l), - orbital shape (s, p, d, f)
Magnetic (ml)- orbital direction (px, py, pz)
Spin (ms) - +1/2, -1/2
28
Atomic Orbitals
y
node
+
+
-
x
1s
z
y
Does not represent
charge, but the sign
of the wavefunction
2s
y
y
node
+
-
+
z
x
z
2px
-
x
-
+
x
z
2p
2pz
y
s orbitals - spherical, e- held close
to nucleus, one sign
p orbitals - two lobes with opposite signs, e- further from the nucleus, has node
node - region of space with zero electron density
29
S-states probability
Electron Configuration
Aufbau principle - the lowest
energy orbitals fill up first (1s,
2s, 2p, 3s, 3p, 4s, 3d, etc.)
Pauli exclusion principle only two electrons can
occupy each orbital, and they
must be of opposite spin
Hund’s rule - if two or more
orbitals of equal energy are
available, one e- occupies
each will their spins parallel
until all orbitals are half-full
1s1
1s22s22p2
30
Formal Charge
Formal charge - expresses surplus and
shortage of e- localized on individual atoms
Example: Nitromethane CH3 NO2 (24 valence e-)
H
O
H C N
H
-
remove 2 e
and share
O
H
O
H C N
H
O
Some of these atoms bear extra eOthers are e- deficient
Remember: C
Trial structure
26 valence e-
N
O
H
Must determine the FORMAL CHARGE of each atom in a valid Lewis structure:
Formal charge = (valence e-) - (nonbonding e-) - 1/2 (shared e-)
Formal charges:
C: 4 - 0 - 4 = 0
N: 5 - 0 - 4 = +1
O: 6 - 4 - 2 = 0
O: 6 - 6 - 1 = -1
H
O
H C N
H
O
Net charge = 0
40
Nitromethane:
Formation of H2 from Two
Hydrogen Atoms
+
•
•
e–
+
e–
Examine how the electrostatic forces change as
two hydrogen atoms are brought together.
These electrostatic forces are:
attractions between the electrons and
the nuclei
repulsions between the two nuclei
repulsions between the two electrons
Models for Chemical
Bonding
•
Valence Bond Theory
constructive interference between electron
waves of two half-filled atomic orbitals is basis
of shared-electron bond
•
Molecular Orbital Theory
derive wave functions of molecules
by combining wave functions of atoms
Valence Bond Model of H2
The 1s orbitals of two separated hydrogen atoms are far
apart. Essentially no interaction. Each electron is
associated with a single proton.
Valence Bond Model of H2
As the hydrogen atoms approach each other, their 1s
orbitals begin to overlap and each electron begins to feel the
attractive force of both protons.
Valence Bond Model of H2
The hydrogen atoms are close enough so that appreciable
overlap of the the two 1s orbitals occurs. The concentration
of electron density in the region between the two protons is
more readily apparent.
Valence Bond Model of H2
A molecule of H2. The two hydrogen 1s orbitals have been
replaced by a new orbital that encompasses both hydrogens
and contains both electrons.
H-H bond is cylindrically symmetrical, sigma (s) bond
Valence Bond Theory (VBT)
Good Overlap
Atomic orbitals overlap
to form a chemical bond.
+
s
s
+
The electrons are
localized in the bond
region.
s
px
px
+
sigma bonds (s)
end to end overlap
px
+
Orbitals must have the
correct symmetry (+/+) or
(-/-) to overlap
py
py
+
pz
pz
pi bonds (p)
sideways overlap
Valence Bond Theory (VBT)
Out of Phase (+/-): No Overlap
+
+
s
Orthogonal: No Overlap
s
px
py
+
+
px
px
pz
s
+
px
+
py
+
py
py
px
+
pz
pz
+
pz
px
pz
Atomic Orbitals and Bond Angles
VSEPR Theory - # of e- domains surrounding an atom dictates its geometry
Single,
double, triple
bond or lone
pair
4 e- domains
3 e- domians
2 e- domains
180o
109.5o
120o
X
trigonal
planar
linear
tetrahedral
But the e- density in atomic orbitals is orthogonally distributed
All angles in all molecules would be 90o!
y
x
z
y
y
x
x
z
z
How is this geometric mismatch
explained?
The Bonding in Methane
H
H
H C H
C H
H
H
H
C forms 4 bonds to H
but . . .
C:
2s
+
2p
Electron configuration of C
shows only 2 places to bond
4 x H:
1s
1) How does carbon form 4 bonds?
2) At 109.5o angles?
Linus Carl Pauling
(1901-1994)
Nobel prizes: 1954, 1962
90o
Bond Angles
109.5o
C
120o
180o
50
Px
Px
Pz
Pz
Py
Py
51
Methane building blocks
52
1s
2s
2px 2py 2pz
Promotey
sp3 sp3 sp3 sp3
Hybridize
x
109.5o
z
Methane: Carbon
53
CH2O
120o
54
1s
2s
2px 2py 2pz
Promoted
sp2 sp2 sp2
Hybridized
120o
120o
Trigonal
Planar
2s + 2px + 2pz
Formaldehyde: Carbon
55
1s
2s
2px 2py 2pz
Lone Pairs
sp2 sp2 sp2
Hybridized
120o
120o
Trigonal
Planar
2s + 2px + 2pz
Formaldehyde: Oxygen
56
Formaldehyde
p bond
Sigma bond
2 Lone
Pairs
57
58
1s
2s
2px 2py 2pz
Promoted
sp sp
Hybridized
Linear
2s + 2px
Hydrogen Cyanide: Carbon
59
1s
2s
2px 2py 2pz
sp sp
Hybridized
Linear
2s + 2px
Hydrogen Cyanide: Nitrogen
60
p bond
p bond
61
Bonding with sp3 Hybridization
Methane
Ethane
H
H
H H
H C H
C H
H
H
H C C H
H
s-sp3 s bond
HH
H
C
HH
H H
sp3-sp3 s bond
single bonds are s
bonds
C
H
Effect of Electronegative atoms
F
o
108
H
oH
112
C
F
Steric Repulsions
CH3
:
.. C .. CH3
..
H
H
“Steric Repulsion”
The CH3 groups are
so large that they push
against each other in
space, opening the angle.
CH3
H
C
106o H
112o
CH3
Double bond
In alkenes the C=C-H angle is typically larger
than the H-C-H angle.
< 120o
smaller repulsion
one pair : one pair
H.
> 120o larger repulsion
one pair : two pairs
. ..
C
.
.
H
C
Double bond and Electronegativity
NONPOLAR BOND
H
117o
H
Cl
114o
Cl
F
110o
F
H.
121.5o
C CH2
more
repulsion
H
123o
C CH2
125o
C CH2
. ..
C
..
r
Cl ..
less
repulsion
.
.
Cl
Electrons in C-H bonds
are shared nearly equally.
Electrons in C-H bonds
are closer to carbon
(near center of bond)
than in the case below.
POLAR BOND
R
C
polar
..
Electrons in a C-Cl
bond are closer to
chlorine and further
from each other.
The electronegative Cl
draws electrons closer
to that end of the bond.
Fluorines cause even smaller angles.
Hybridization with Non-Carbon Atoms
H
H
H C O
H
C O
H
H
sp2
sp3
sp3
sp2
H N H
H
H3C C N
sp3
sp3
sp
sp
COMPARISON OF SPx HYBRID ORBITALS
bigger
“tail”
“cusp”
more “p” character
sp3
25% s-character
sp2
33% s-character
more “s” character
Orbital plots courtesy of
Professor George Gerhold
sp
50% s-character
more electron
density in the
bonding lobe
Molecular Orbital Theory
Main Ideas
• Electrons in a molecule occupy molecular
orbitals (MOs) just as electrons in an atom
occupy atomic orbitals (AOs).
• Two electrons per MO, just as two electrons
per AO.
• Express MOs as combinations of AOs.
VB Theory - overlap of atomic orbitals, e- density localized in bond
MO Theory - combination of atomic orbitals to form molecular orbitals, edensity spread throughout entire molecule
MO Picture of Bonding in H2
Linear combination of atomic orbitals method
expresses wave functions of molecular orbitals
as sums and differences of wave functions
of atomic orbitals.
•
•
Two AOs yield two MOs
Bonding combination Antibonding combination
MO = (H)1s + (H')1s
'MO = (H)1s - (H')1s
LCAO-MO’s
Bonding
anti-bonding
+
─
 2+
 2─
Simple Molecular Orbital Diagram: H2
H-H Antibonding MO
(unfilled)
Energy
node
s*
H 1s orbital
Destructive (+/-)
combination of atomic
orbitals; higher energy
H 1s orbital
s + s sigma (s) bond
s
H-H Bonding MO
(filled)
Constructive (+/+) or (-/-)
combination of atomic
orbitals; lower energy
In stable bonding situations, usually only the bonding orbitals (s, p) are filled
MO Diagrams: More Sigma Bonding (s)
s + px
px + px
Energy
s*
s*
px
px
px
s
s
s
Sigma-bonding orbitals are cylindrically symmetrical, “egg-shaped”
Electron density is centered along the axis of the bond
Single bonds are sigma bonds
Molecular Orbital Theory
• Terminology
–
–
–
–
–
–
–
–
ground state = lowest energy state
excited state = NOT lowest energy state
s = sigma bonding MO
s* = sigma antibonding MO
p = pi bonding MO
p* = pi antibonding MO
HOMO = highest occupied MO
LUMO = lowest unoccupied MO
MO Diagrams: Pi Bonding (p)
py + py
Energy
p*
py
py
p
Electron density is located above and below the axis of the bond
Double and triple bonds have pi-bonds
Comparison of C-H bonds:
Molecule
Bond
Energy (kcal) Length (pm)
Ethane
C(sp3)-H
100
110
Ethylene
C(sp2)-H
106
108
Acetylene
C(sp)-H
132
106
Comparison of C-C bonds:
Molecule
Bond
Energy (kcal)
Length (pm)
Ethane
C(sp3)-C(sp3)
90
154
Ethylene
C(sp2)-C(sp2)
146
133
Acetylene
C(sp)-C(sp)
200
120
•
You may be surprised to know that the molecule CH2, with divalent carbon,
can exist. It is of course very unstable but it is known and it can have two
different structures. One has an H–C–H bond angle of 180° and the other an
angle of 120°. Suggest structures for these species and say which orbitals will
be occupied by all bonding and nonbonding electrons. Which structure is
likely to be more stable?