organic chemistry sh. javanshir faculty of chemistry iran university of science & technology

Organic ChemistrySh. Javanshir

Faculty of Chemistry

Iran University of Science & Technology

4

References:

مک • آلی شیمی مبانیعیسی موری دکتر ترجمه ، یاوری

اشکال رفع : ساعت10-12شنبه – دو شنبه

2

ارزشیابی

% %۳۰۳۰ نمره نمره 44 امتحان میان ترم امتحان میان ترم % %۶۰۶۰ نمره نمره 1414 امتحان پایان ترمامتحان پایان ترم %% ۱۰۱۰ نمره نمره22 کار کالسی و تمرین کار کالسی و تمرین

:فهرستوساختار- 1 شیمیایی پیوند

ها- 2 آلکان

ها- 3 آلکن

ها- 4 آلکین

5) ( استریوشیمی- فضایی شیمی

آروماتیسیته- 6 و بنزن

آروماتیکی- 7 دوست الکترون های واکنش

ها- 8 هالید آلکیل های واکنش و ها هالید آلکیل

ها- 9 الکل

مقدمهو

تاریخچه

دار : کربن ترکیبات به مربوط شیمی آلی شیمی

و یکدیگر با پیوند برای کربن توانائی و تمایلها حلقه یا طویل زنجیرهای تشکیل

دار کربن :ترکیبات

طبیعی طبیعی ترکیبات ترکیبات

نوکلئیک ها، پروتئین ، چرب های اسید، اسیدها

کربن های سنتزی هیدرات ترکیبات

ها کش حشره ها، پالستیک پلیمرها، ها، رنگ ، داروها

Some organic chemicals

DNA

Essential oils

Medicines•Active Pharmaceutical Ingredients•Excipients

Materials

Fuels

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 manufacturedOrganic chemicals in manufacturedproductsproducts

Materials

Fibres & clothings

Plastics

Coatings & lacquers

Packaging

Paper

Films

Medical implants

Wound dressings

12

HistoryHistory

• 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 Wöhler in 1828 showed that urea, an organic compound, could be made from a non-living compound, could be made from a non-living source:source:

7

NH4+ -OCN

HeatC

O

NH2H2NAmmonium cyanate

Urea

Who Said It…?Who Said It…?

““Organic Chemistry nowadays almost drives me mad. To me it Organic Chemistry nowadays almost drives me mad. To me it appears like a primeval tropical forest full of the most appears like a primeval tropical forest full of the most remarkable things; a dreadful endless jungle into which one remarkable things; a dreadful endless jungle into which one does not dare to enter for there seems to be no way out”does not dare to enter for there seems to be no way out”

You You or or

9

AND YOUAND YOU!!

– YOU: YOU:

• DNA, DNA,

• Proteins (enzymes, cell membrane Proteins (enzymes, cell membrane receptors, receptors,

• Carbohydrates (Polysaccharides,…Carbohydrates (Polysaccharides,…

• Lipids (fatty acids,…Lipids (fatty acids,…

– And what you eatAnd what you eat

• ProteinProtein

• CarbohydrateCarbohydrate

• LipidsLipids

– The plants: from COThe plants: from CO22 to complex organic to complex organic

moleculesmolecules

• … … with no complex, noisy, polluting, with no complex, noisy, polluting, smelly factory! smelly factory!

14

What forWhat for??

• Answering questions and solving problemsAnswering questions and solving problems

• Does eating turkey make you sleepy? Does eating turkey make you sleepy?

– Turkey contains L-tryptophan, (amino acid with known Turkey contains L-tryptophan, (amino acid with known sleep inducing effect)sleep inducing effect)

– L-tryptophan is used in the body to produce B-vitamin,L-tryptophan is used in the body to produce B-vitamin,

– B-vitamin is used to produce serotonin, a B-vitamin is used to produce serotonin, a neurotransmitter with known calming effects neurotransmitter with known calming effects

– L-tryptophan needs to be taken without any other amino L-tryptophan needs to be taken without any other amino acids or protein in order to make you drowsy. acids or protein in order to make you drowsy.

– Alcohol is a central nervous system depressant. Alcohol is a central nervous system depressant.

– ……..

15

O

HAcrolein (2-propenal)

S

HThiopropionaldehyde (propanethiol)

- lachrymator from chopped onion- lachrymator and pleasant "odour" from barbacuing meat

Formalin, 35-40% formadehyde in waterPreservative 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.

18

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.

What for?What for?• Why did he leave?Why did he leave?

• Initially:Initially:

• First, there's attraction. First, there's attraction.

• Part of the nonverbal communication may Part of the nonverbal communication may involve pheromones, a form of chemical involve pheromones, a form of chemical communication.communication.

• raw lust is characterized by high levels of raw lust is characterized by high levels of testosteronetestosterone

• The pounding heart is caused by higher The pounding heart is caused by higher levels of levels of norepinepherinenorepinepherine

• The love is due to a rush of The love is due to a rush of phenylethylamine and dopamine. phenylethylamine and dopamine.

– ThenThen……

• Lasting love confers chemical benefits in Lasting love confers chemical benefits in the form of stabilized production of the form of stabilized production of serotonin and oxytocin. serotonin and oxytocin.

• Suppression of vasopressin can cause Suppression of vasopressin can cause males to abandon their love nest and seek males to abandon their love nest and seek new mates. new mates.

The Brain controls the Body The Brain controls the Body through chemistrythrough chemistry

O

OH

O

O

testosterone

development of male reproductive system

progesterone

prepares the uterus for reproduction

20

TAXOLIsolated from the bark of the yew tree, Taxus brevifolia, used for treatment of ovarian cancer.

O

OOH

O

O

H5C6

O

O

O

O

ON

H5C6

H

O

OH5C6

OH

21

Chapter 1.Chapter 1.Structure and BondingStructure and Bonding

.Chapter 1.Chapter 1Structure and BondingStructure and Bonding

22

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.

Structure Makes the Structure Makes the DifferenceDifference

• Benzene causes Leukemia, Toluene Doesn’tBenzene causes Leukemia, Toluene Doesn’t

CH3H

Benzene Toluene

23

Simple Organic Compounds

Nutrasweet

Teflon

CHCl3

Chloroform

O

OH

O

O

Aspirin

HO2CHN CO2Me

OPh

NH2

HO2CHN CO2Me

OPh

NH2

160 times sweeter than

sucrose

Bitter

OOH

OHOHHO

OH

Sugars

Why is it the element of life on earth?Why is it the element of life on earth?

Carbon and hydrogen have very similar Carbon and hydrogen have very similar electronegativities: electronegativities: CarbonCarbon ~2.5 and Hydrogen ~2.5 and Hydrogen ~2.1 ~2.1Therefore, the C-H bond is essentially non-polar.Therefore, the C-H bond is essentially non-polar.

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 BondsStrong Single, Double and Triple Bonds

• 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

Why is it the element of life on earth?Why is it the element of life on earth?

•AverageAverage Bond Energies (KJ mol Bond Energies (KJ mol-1-1))

C-CC-C 607 607 Si-SiSi-Si 230230 C-HC-H 416416 Si-HSi-H 323323

C-NC-N 754754 Si-NSi-N 470470 C-OC-O 336336 Si-OSi-O 368368

Background Review

27

Atomic Structure: Orbitals

s

pn = 2

s

dp n = 3

f

s

dp

n = 4

s n = 1

En

erg

yElectrons 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

1. Principle, shell (n), - orbital energy, size2. Azimuthal, subshell (l), - orbital shape (s, p, d, f)3. Magnetic (ml)- orbital direction (px, py, pz)4. Spin (ms) - +1/2, -1/2

Atomic orbitals are described by four quantum numbers

28

y

x

z

+

-

y

x

z

+-

2pz2py2px

y

x

z

+-

p orbitals - two lobes with opposite signs, e- further from the nucleus, has node

Atomic Orbitalsy

x

z

+

1s

s orbitals - spherical, e- held close to nucleus, one sign

node

Does not represent charge, but the sign of the wavefunction2s

+

-

node

node - region of space with zero electron density 29

S-states probability

Electron Configuration

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

Pauli exclusion principle - only two electrons can occupy each orbital, and they must be of opposite spin

Aufbau principle - the lowest energy orbitals fill up first (1s, 2s, 2p, 3s, 3p, 4s, 3d, etc.)

1s1 1s22s22p2 30

Formal ChargeFormal Charge

Example: NitromethaneNitromethane CH3 NO2 (24 valence e-)

Trial structure26 valence e-

Some of these atoms bear extra e-

Others are e- deficient

Formal charge - expresses surplus and shortage of e- localized on individual atoms

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 = 0N: 5 - 0 - 4 = +1O: 6 - 4 - 2 = 0O: 6 - 6 - 1 = -1

C N O HRemember:

Net charge = 0

C

H

H

H

N

O

O

40

remove 2 e-

and shareC

H

H

H

NO

OC

H

H

H

NO

O

Nitromethane:

• Examine how the electrostatic forces change Examine how the electrostatic forces change as two hydrogen atoms are brought together.as two hydrogen atoms are brought together.

• These electrostatic forces are:These electrostatic forces are:attractions between the electrons and attractions between the electrons and the nucleithe nuclei

repulsions between the two nucleirepulsions between the two nuclei repulsions between the two electronsrepulsions between the two electrons

++ ee–– ++ ee––

Formation of HFormation of H22 from Two from Two Hydrogen AtomsHydrogen Atoms

• Valence Bond TheoryValence Bond Theoryconstructive interference between electronconstructive interference between electronwaves of two half-filled atomic orbitals is waves of two half-filled atomic orbitals is basis basis of shared-electron bondof shared-electron bond

• Molecular Orbital TheoryMolecular Orbital Theoryderive wave functions of moleculesderive wave functions of moleculesby combining wave functions of atomsby combining wave functions of atoms

Models for Chemical Models for Chemical BondingBonding

The 1The 1ss orbitals of two separated hydrogen atoms are far orbitals of two separated hydrogen atoms are far

apart. Essentially no interaction. Each electron is apart. Essentially no interaction. Each electron is

associated with a single proton.associated with a single proton.

Valence Bond Model of HValence Bond Model of H22

As the hydrogen atoms approach each other, their 1As the hydrogen atoms approach each other, their 1ss

orbitals begin to overlap and each electron begins to feel the orbitals begin to overlap and each electron begins to feel the

attractive force of both protons.attractive force of both protons.

Valence Bond Model of HValence Bond Model of H22

The hydrogen atoms are close enough so that appreciable The hydrogen atoms are close enough so that appreciable

overlap of the the two 1overlap of the the two 1ss orbitals occurs. The concentration orbitals occurs. The concentration

of electron density in the region between the two protons is of electron density in the region between the two protons is

more readily apparent.more readily apparent.

Valence Bond Model of HValence Bond Model of H22

A molecule of HA molecule of H22. The two hydrogen 1. The two hydrogen 1ss orbitals have been orbitals have been

replaced by a new orbital that encompasses both hydrogens replaced by a new orbital that encompasses both hydrogens

and contains both electrons.and contains both electrons.

Valence Bond Model of HValence Bond Model of H22

H-H bond is cylindrically symmetrical, H-H bond is cylindrically symmetrical, sigma (sigma (ss) ) bondbond

Valence Bond Theory (VBT)Valence Bond Theory (VBT)

Atomic orbitals overlap to form a chemical

bond.

The electrons are localized in the bond

region.

Orbitals must have the correct symmetry (+/+) or

(-/-) to overlap

Good Overlap

+

+

+pxpx

pxs

s s

sigma bonds ()end to end overlap

+

+

pz pz

py py

pi bonds ()sideways overlap

Valence Bond Theory (VBT)Valence Bond Theory (VBT)Orthogonal: No Overlap

+

+

+

+

+

pzpx

pz

px

py

px

pzs

py

s

Out of Phase (+/-): No Overlap

+

+

+

+

pxs

pxpx

py py

pz pz

Atomic Orbitals and Bond AnglesAtomic Orbitals and Bond Angles

How is this geometric mismatch explained?How is this geometric mismatch explained?

VSEPR Theory - # of e- domains surrounding an atom dictates its geometry

But the e- density in atomic orbitals is orthogonally distributedAll angles in all molecules would be 90o!

y

x

z

y

x

z

y

x

z

Single, double, triple bond or lone pair

2 e- domains

X

180o

linear

120o

3 e- domians

trigonal planar

109.5o

4 e- domains

tetrahedral

The Bonding in MethaneThe Bonding in MethaneH

CH H

HC

H

H

H

H

C:2s 2p

1s

4 x H:

+

C forms 4 bonds to H

Electron configuration of C shows only 2 places to bond

but . . .

1) How does carbon form 4 bonds?2) At 109.5o angles?

Linus Carl Pauling)1901-1994(

Nobel prizes: 1954, 1962

50

120o

109.5o

90o

180o

Bond Angles

C

51

Px

Py

Pz

Px

Py

Pz

52

Methane building blocks

53

2s 2px 2pz2py1s sp3 sp3 sp3 sp3

109.5o

Promote Hybridize

x

z

y

Methane: Carbon

54

CH2O

120o

55

2s 2px 2pz2py1s sp2 sp2 sp2

120o

Hybridized

Formaldehyde: Carbon

Promoted

120o

TrigonalPlanar

2s + 2px + 2pz

56

2s 2px 2pz2py1s sp2 sp2 sp2

120o

Hybridized

Formaldehyde: Oxygen

120o

TrigonalPlanar

Lone PairsLone Pairs

2s + 2px + 2pz

57

Formaldehyde

Sigma bond2 Lone Pairs2 Lone Pairs bondbond

58

59

2s 2px 2pz2py1s sp spPromoted Hybridized

Hydrogen Cyanide: Carbon

2s + 2px

Linear

60

2s 2px 2pz2py1s sp spHybridized

Hydrogen Cyanide: Nitrogen

2s + 2px

Linear

61

bondbond

bondbond

Bonding with Bonding with spsp33 Hybridization Hybridization

single bondssingle bondsare are bondsbonds

H

CH H

HC

H

H

H

H

Methane

C C

H

H

H

H

H

H

C

H

HH H

C

HH

Ethane

s-sp3 bond sp3-sp3 bond

C

F

FH

H

108o

112o

Effect of Electronegative atoms Effect of Electronegative atoms

C

CH3

HCH3

H

:....

Steric RepulsionsSteric Repulsions

..

“Steric Repulsion”

HC

CH3H

CH3112o

106o

The CH3 groups areso large that they pushagainst each other inspace, opening the angle.

C ........

larger repulsionone pair : two pairs

smaller repulsionone pair : one pair

> 120o

< 120o

In alkenes the C=C H angle is typically larger-than the H C H angle. - -

Double bondDouble bond

C

H

H

Double bond and ElectronegativityDouble bond and Electronegativity

more repulsion

less repulsion

Electrons in C-H bondsare shared nearly equally.

Electrons in a C-Cl bond are closer to chlorine and furtherfrom each other.

POLAR BOND

The electronegative Cldraws electrons closerto that end of the bond.

NONPOLAR BOND

Electrons in C-H bondsare closer to carbon(near center of bond) than in the case below.

C ........

H

H

r

.

.C ....

.

.Cl

Cl

polar

R

Fluorines cause even smaller angles.

C CH2

H

H

121.5o

117o

C CH2

Cl

Cl

123o

114o

C CH2

F

F

125o

110o

Hybridization with Non-Carbon Atoms

C O

H

H

H H

C NH3C

H N

H

H

C O

H

H

sp3sp3

sp3sp

sp

sp2sp2

sp3

COMPARISON OF SPCOMPARISON OF SPxx HYBRID ORBITALS HYBRID ORBITALS

more “p” character

more “s” character

sp3 sp2 sp

bigger“tail”

more electrondensity in thebonding lobe

“cusp”

Orbital plots courtesy ofProfessor George Gerhold

25% s-character

33% s-character 50% s-character

• Electrons in a molecule occupy molecular Electrons in a molecule occupy molecular orbitals (MOs) just as electrons in an atom orbitals (MOs) just as electrons in an atom occupy atomic orbitals (AOs). occupy atomic orbitals (AOs).

• Two electrons per MO, just as two Two electrons per MO, just as two electrons electrons per AO.per AO.

• Express MOs as combinations of AOs.Express MOs as combinations of AOs.

Molecular Orbital TheoryMain IdeasMain Ideas

VB Theory - overlap of atomic orbitals, e- density localized in bondMO Theory - combination of atomic orbitals to form molecular orbitals, e-

density spread throughout entire molecule

• Two AOs yield two MOsTwo AOs yield two MOs

• Bonding combinationBonding combination Antibonding combinationAntibonding combination

MO MO = = (H)(H)1s1s + + (H')(H')1s 1s ''MO MO = = (H)(H)1s1s - - (H')(H')1s1s

Linear combination of atomic orbitals methodLinear combination of atomic orbitals methodexpresses wave functions of molecular orbitalsexpresses wave functions of molecular orbitalsas sums and differences of wave functionsas sums and differences of wave functionsof atomic orbitalsof atomic orbitals..

MO Picture of Bonding in HMO Picture of Bonding in H22

LCAO-MO’sLCAO-MO’s

─

2─

anti-bonding

+

2+

Bonding

H 1s orbital H 1s orbital

*

Simple Molecular Orbital Diagram: HSimple Molecular Orbital Diagram: H22

H-H Bonding MO(filled)

H-H Antibonding MO(unfilled)

node

Constructive (+/+) or (-/-) combination of

atomic orbitals; lower energy

En

erg

yDestructive (+/-)

combination of atomic orbitals; higher energy

In stable bonding situations, usually only the bonding orbitals (, ) are filled

s + s sigma () bond

MO Diagrams: More Sigma Bonding (MO Diagrams: More Sigma Bonding ())E

ner

gy

*

s

px

s + px

Sigma-bonding orbitals are cylindrically symmetrical, “egg-shaped”Electron density is centered along the axis of the bond

Single bonds are sigma bonds

*

px px

px + px

Molecular Orbital TheoryMolecular Orbital Theory

• TerminologyTerminology– ground state = lowest energy stateground state = lowest energy state

– excited state = NOT lowest energy stateexcited state = NOT lowest energy state

– = sigma bonding MO= sigma bonding MO

– * = sigma antibonding MO* = sigma antibonding MO

– = pi bonding MO= pi bonding MO

– * = pi antibonding MO* = pi antibonding MO

– HOMO = highest occupied MOHOMO = highest occupied MO

– LUMO = lowest unoccupied MOLUMO = lowest unoccupied MO

MO Diagrams: Pi Bonding (MO Diagrams: Pi Bonding ())

En

erg

y

*

py py

py + py

Electron density is located above and below the axis of the bondDouble and triple bonds have pi-bonds

Comparison of C-H bondsComparison of C-H bonds::

MoleculeMolecule BondBond Energy (kcal)Energy (kcal) Length (pm)Length (pm)

EthaneEthane CC(sp(sp33))-H-H 100100 110110

EthyleneEthylene CC(sp(sp22))-H-H 106106 108108

AcetyleneAcetylene CC(sp)(sp)-H-H 132132 106106

Comparison of C-C bondsComparison of C-C bonds::

MoleculeMolecule BondBond Energy (kcal)Energy (kcal) Length (pm)Length (pm)

EthaneEthane CC(sp(sp33))-C-C(sp(sp33)) 9090 154154

EthyleneEthylene CC(sp(sp22))-C-C(sp(sp22)) 146146 133133

AcetyleneAcetylene CC(sp)(sp)-C-C(sp)(sp) 200200 120120

• You may be surprised to know that the molecule CH2, with divalent carbon, 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 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 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 angle of 120°. Suggest structures for these species and say which orbitals will be occupied by all bonding and nonbonding electrons. Which structure is be occupied by all bonding and nonbonding electrons. Which structure is likely to be more stable?likely to be more stable?