Physical Organic Chemistry

Prepared By

Dr. Khalid Ahmad Shadid

Islamic University in MadinahDepartment of Chemistry

Topics: What is Physical Organic Chemistry?

What is Mechanism?

Structure and Bonding

Quantum Mechanics & Atomic Structure

Molecular dimensions

Resonance Theory

Electronegativity & Bond Polarity

Intermolecular Forces

Lewis Structures of Common Functional Groups

Carbocations

The Carbanion Chemistry1/31/2015

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Introduction

What is Physical Organic Chemistry?

- Physical organic chemistry is the “ Study of the interrelationships between structure and reactivity of the organic molecules”.

- Understanding mechanisms, explaining observed phenomenon (or predicting it)

What is Mechanism?

- Lowry and Richardson: “ Theory deduced from available experimental data. The experimental results are the facts; the mechanism is conjecture based upon these facts”.

- A mechanism the simplest rationalization that is consistent with all of the available data.

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Scientific method The hypothesis (assumption)

• Doing experiments:

– confirmation– refutation

•“Proof” of a mechanism- a mechanism can never really be ‘proven’- one can propose a hypothetical mechanism- one can conduct experiments designed to refute certain hypotheses- one can retain mechanisms that are not refuted- a mechanism can thus become “generally accepted”

distinguishes a good scientific

Mechanistic studies• allow a better comprehension of a reaction, its scope and its utility• require kinetic experiments– rate of disappearance of reactants– rate of appearance of products• kinetic studies are therefore one of the most important disciplinesin experimental chemistry• allow a better comprehension of a reaction, its scope and its utility

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Why Chemical Reactions Happen?

Understanding Chemical reactions lies in:

The structure and bonding of stable compounds.

Reactivity of compounds.

Reactive intermediates and transition states.

Mechanisms through which compounds transform into other compounds.

Kinetics, thermodynamics and the relationship between the two

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Quantum Mechanics & Atomic Structure Wave mechanics & quantum mechanics

● Each wave function () corresponds to a different energy state for an electron● Each energy state is a sublevel where one or two electrons can reside

Wave functions are tools for calculating two important properties● The energy associated with the state of the electron can be calculated● The relative probability of an electron residing at particular places in the

sublevel can be determined The phase sign of a wave equation indicates whether the solution is positive or

negative when calculated for a given point in space relative to the nucleus Wave functions , whether they are for sound waves, lake waves, or the energy of

an electron, have the possibility of constructive interference and destructive interference

● Constructive interference occurs when wave functions with the same phase sign interact. There is a reinforcing effect and the amplitude of the wave function increases

● Destructive interference occurs when wave functions with opposite phase signs interact. There is a subtractive effect and the amplitude of the wave function goes to zero or changes sign

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Electrons in simple molecules The Energy Carve of Diatomic

In an atom, we know the negatively charged electrons are attracted to positively charged nuclei. As two hydrogen atoms approach each other from an infinite distance, the electrons on one atom become attracted to the nucleus of the other atom. This mutual attraction increases as the distance between atoms decreases. As the atoms get closer and closer, the positively charged nuclei and negatively charged clouds began to repel each other.

http://ch301.cm.utexas.edu/simulations/bond-strength/BondStrength.swf

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Electrons in simple molecules

There is an optimum distance between two bonded atoms at which the energy is at a minimum. This distance is called the bond length = 74 pm (picometers (pm) which is equal to 10-12 meters ) for the hydrogen molecule H2 or (H-H).

 

The energy required to break the bond is called the bond strength or (bond dissociation energy). This energy value is 435 kJ/mol (104 kcal/mol) for a hydrogen-hydrogen bond.

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Electrons in simple molecules

The two separate hydrogen atoms (H) are higher in energy (less stable) than is the hydrogen molecule (H2).

Atoms and molecules like to be in the lowest energy (most stable) state. Thus when a bond is formed, energy is given off and the resulting molecule has a lower potential energy (is more stable) than the starting individual species has. So a hydrogen molecule H2 is more stable than two separate hydrogen atoms. Which mean that: energy must be added to the hydrogen molecule to break the bond, giving the original separate hydrogen atoms”.

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Molecular Orbitals We cannot simultaneously know the position and momentum of an

electron An atomic orbital represents the region of space where one or two

electrons of an isolated atom are likely to be found A molecular orbital (MO) represents the region of space where one or

two electrons of a molecule are likely to be found An orbital (atomic or molecular) can contain a maximum of two spin-

paired electrons (Pauli exclusion principle)

When atomic orbitals combine to form molecular orbitals, the number of molecular orbitals that result always equals the number of atomic orbitals that combine

A bonding molecular orbital (molec) results when two orbitals of the same phase overlap

An antibonding molecular orbital (*molec) results when two orbitals of opposite phase overlap

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Electrons in simple molecules

Molecular Orbital for H2

1. The LCAO-MO Model simply states That:

The shape of a molecular orbital is derived from the shape of the atomic orbitals that overlap to form that molecular orbital.

when two waves are traveling in opposite directions, and they meet, as in the wakes of two boats, their amplitudes cancel each other. During bonding, atoms do the atomic equivalent—wave functions with the same sign overlap in an in-phase overlap, and wave functions of opposite signs overlap in an out-of-phase overlap”.

In-phase overlap is a constructive, or bonding, overlap of atomic orbitals.

Out-of-phase is a destructive, or antibonding, overlap of atomic orbitals.

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To differentiate the antibonding from the bonding orbital, add an asterisk to the σ, giving σ* (sigma star).

Bonding molecular orbitals: lower in energy than the atomic orbitals of which it is composed. Electrons in this type of orbital increase the stability of molecule and favor the molecule bonding.

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Prediction from the MO diagram

Antibonding molecular orbitals: higher in energy than the atomic orbitals of which it is composed. Electrons in this type of orbital decrease the stability and will favor the separated atoms. (Unstable but can exist!)

What if two atoms of Helium combine? Does He2 form?

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Heteronuclear Diatomic Molecules

In the Molecular Orbital diagram for NO: The 2s and 2p atomic orbitals of oxygen are slightly lower than those of nitrogen because oxygen is more electronegative than nitrogen.

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Two AOs in hydrogen atoms

combine to form …

… a bonding molecular orbital,

lower in energy than the AOs, and …

… an antibonding molecular orbital, higher in energy

than the AOs.

Electron density between the nuclei

is increased.

Electron density between the nuclei

is decreased.

A sigma () bond (a type of single bond) is one in which the electron density has circular symmetry when viewed along the bond axis

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What about combination of more than Two p orbital…? conjugated system

The two px orbitals combine to form

sigma bonding and antibonding MOs.

The two pz orbitals and also the two py

orbitals give pi bonding and

antibonding MOs.

A pi () bond, part of double and triple carbon–carbon bonds, is one in which the electron densities of two adjacent parallel p orbitals overlap sideways to form a bonding pi molecular orbital

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Electrons in 1s orbitals have the lowest energy because they are closest to the positive nucleus

Electrons in 2s orbitals are next lowest in energy

Electrons of the three 2p orbitals have equal but higher energy than the 2s orbital

Orbitals of equal energy (such as the three 2p orbitals) are called degenerate orbitals

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Allyl three π molecular Orbital

+

-

Allyl Cataion

Allyl Radical

Allyl Anion

Allyl systems result from the combination of 3 conjugated p-orbitals.Therefore, this will result in 3 π molecular orbitals

2e

3e

4e

HOMO

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π – Molecular orbitals for 1,3-butadiene

π – molecular orbitals for 1,3-butadiene?CH2=CH—CH=CH2

How many AO’s in the π system? fourHow many MO’s result? fourHow many electrons in the π system? four

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The Structure of Methane and Ethane: The Structure of Methane and Ethane: spsp33 Hybridization Hybridization

H

C

H

HH

(line bond structure)

covalentbond

sp3

hybridizedcarbon

H

C

H

HH

(Lewis structure)

H

CH H

H

(3-D stucture)

109o Tetrahedralstructure

Carbon with 4 bonds

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The Structure of MethaneThe Structure of Methane

sp3 orbital● 25% s

character, ● 75% p character

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The Structure of EthaneThe Structure of Ethane

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The Structure of Ethene (Ethylene): The Structure of Ethene (Ethylene): sp2 Hybridizationsp2 Hybridization

sp2 hybridized carbonC C

H

H

H

H

~120o

~120o

~120o1 bond + 1 bond

C C

H

H

H

H

-bond

(-orbitals overlap)

3-Dimensional View

Planar structure

Carbon with (3 + 1) bonds

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An sp2-hybridized carbon atomAn sp2-hybridized carbon atom

A model for the bonding molecular orbitals of etheneformed from two sp2-hybridized carbon atomsand four hydrogen atoms

sp2 orbital● 33% s character, 66% p character

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Restricted Rotation and the Double BondRestricted Rotation and the Double Bond There is a large energy barrier to rotation associated with groups

joined by a double bond● ~264 kJ/mol (strength of the bond)● To compare: rotation of groups joined by C-C single bonds

~13-26 kJ/mol

CH3H3C different from

CH3

CH3

(trans) (cis)

● Restricted rotation of C=C

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The Structure of Ethyne (Acetylene): sp Hybridization

sp2 hybridized carbon180o

1 bond + 2 bond

C C HH

Linear structure

Carbon with (2 + 2 ) bonds

sp orbital● 50% s character● 50% p character

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Bond Lengths of Ethyne, Ethene, & Ethane The carbon–carbon triple bond of ethyne is shorter than the carbon–carbon

double bond of ethene, which in turn is shorter than the carbon–carbon single bond of ethane

Reasons:• The greater the s orbital character in one or both atoms, the shorter is

the bond. This is because s orbitals are spherical and have more electron density closer to the nucleus than do p orbitals

• The greater the p orbital character in one or both atoms, the longer is the bond. This is because p orbitals are lobe-shaped with electron density extending away from the nucleus

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How to Predict Molecular Geometry: The Valence Shell Electron Pair Repulsion Model

Valence shell electron pair repulsion (VSEPR) model:1) We consider molecules (or ions) in which the central atom is covalently bonded to two or

more atoms or groups2) We consider all of the valence electron pairs of the central atom—both those that are

shared in covalent bonds, called bonding pairs, and those that are unshared, called nonbonding pairs or unshared pairs or lone pairs

3) Because electron pairs repel each other, the electron pairs of the valence shell tend to stay as far apart as possible. The repulsion between nonbonding pairs is generally greater than that between bonding pairs

4) We arrive at the geometry of the molecule by considering all of the electron pairs, bonding and nonbonding, but we describe the shape of the molecule or ion by referring to the positions of the nuclei (or atoms) and not by the positions of the electron pairs

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Ammonia

A tetrahedral arrangement of the electron pairs explains the trigonal pyramidal arrangement of the four atoms. The bond angles are 107° (not 109.5°) because the nonbonding pair occupies more space than the bonding pairs

A tetrahedral arrangement of the electron pairs explains the trigonal pyramidal arrangement of the four atoms. The bond angles are 107° (not 109.5°) because the nonbonding pair occupies more space than the bonding pairs

Water

AngularTrigonal pyramidal

Tetrahedral

Methane

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Boron Trifluoride Beryllium Hydride

Carbon Dioxide

LinearTrigonal planar

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Molecular dimensions Atomic radius

ionic radius, ri ： size of electron cloud around an ion.covalent radius, rc ： half of the distance between two atomsof same element bond to each other.van der Waal radius, rvdw ： the effective size of atomic cloud around a covalently bonded atoms.

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Bond length measures the distance between nucleus (or the local centers of electron density).

Bond angle measures the angle between lines connecting different nucleus.

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Resonance Theory：

An extension of valence bond theory for molecules that more than one Lewis structure can be written. Useful in describing electron delocalization, in conjugate system andreactive intermediates.(a)If more than one Lewis structure can be written, which has nuclear positions constant, but differ in assignment of electrons, the molecule is described by a combination ofthese structure (a hybrid of all).(b)The most favorable (lowest energy) resonance structure makes the greatest contribution to the true structure.determining energy ： maximum number of covalent bond, minimum separation of unlike charge, placement of negative charge on most electronegative atom (vice versa).(c)Those with delocalized electrons are usually more stable than single localized structure.

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two equivalent structure charge located equally on two C’s the allyl cation is planar for maximum p interaction restricted rotation around single bond

Resonance Theory：

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Electronegativity & Bond Polarity Electronegativity ： The power of an atom in a molecule to attract electrons to itself. Pauline

1932

In complex molecules with many polar bonds involved, electrostatic potential surfaces (from quantum mechanic calculation) are used to view the charge distribution in the whole molecule.

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red ----negative potentialblue --- positive potentialgreen---neutral

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when there is a difference in the electronegativities of the bonded atoms the electron pairs will spend more time with one atom than the other, they are not equally shared. This also called the Inductive Effect. The "arrow" indicates the direction of the electron shift. This is a polar bond.

As the more electronegative atom exerts a greater pulling power on the shared electrons and so gains more ‘possession’ of the electron pair

The bond is now unsymmetrical with respect to electron distribution and is said to be polar.

Electronegativity & Bond Polarity

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The term dipole is often used to indicate presence of two opposite electric charges on bond separated by a distance.

The more electronegative atom, with the greater share of the electrons, has become partially negative or δ–

and the less electronegative atom has become partially positive or δ+

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Intermolecular Forces

Covalent bonds - Typically the strongest type of bonds - 150-1100 kJ/mol

Intermolecular forces are forces that hold covalent molecules together

electrostatic interactions-dispersion forces-dipole-dipole interactions-hydrogen bonds (H-bonds)

Strength of IM forces depends on: Q - charge on ion µ - dipole moment α - polarizability

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polarizability ( α): ease of electronic distortion; α increases as number of e– ↑; α increases as size (MW) ↑; highly polarizable molecules: more subject to dispersion forces

London dispersion forces: dipole moment forms when there are more electrons on one side of the molecule; when this happens, a dipole in a neighboring molecule is induced.

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pi-stacking‣ Benzene dimer is bound by ~2-3 kcal/mol

Here is an example of arene/perfluoroarene stacking in an inhibitor of carbonic anhydrase II (PDB code: 1G54):

The interactions can be exploited when designing drugs, which are generally inhibitors of proteins.This is called structure-based drug design.

Parallel Displace Edge to FaceFace to Face

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Lewis Structures of Common Functional Groups

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Carbocations (Carbonium ion) The carbonium ions are positively charged highly reactive intermediates

and have six electrons in the outer shell of central carbon. They may be represented as:

they are very reactive toward any nucleophilic reagent

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STRUCTURE AND STABILITY

The carbocations being reactive intermediates have short life and so they are unstable

the greater the resonance and hyper-conjugation the greater is the stability ofcarbocation.

1. Stability depending on the number of canonical forms

Carbocations (Carbonium ion)

Thus a tertiary carbocation like the above will give nine resonating structures while a primary will give only two hyperconjugative forms. This explains why tertiary carbocations are more stable than secondary which in turn is more stable than primary. This also explains why ethyl carbocation (CH3CH2

+) is more stable than methyl carbocation (CH3

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In general the more the number of alkyl groups attached to the C, the greater is the stability.During hyperconjugation some charge delocalization occurs between the p-orbital of the positively charged carbon and the σ bond of the β C-H.

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Now lest us study the stability of triphenyl and phenylalkyl cations.The triphenylmethyl carbocation shows its stability because the positive charge on the carbon is distributed uniformly over a number of structures.

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2. The stability increases when the positive charge is in conjugation with a double bond

This is due to increased delocalization of the positive charge over two atoms instead of being concentrated at one

3. The presence of a heteroatom adjacent to the cationic center and bearing anunshared pair of electrons, like nitrogen, oxygen or halogen increases stability

Such ions are stabilized by resonance

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GENERATION OF CARBOCATIONS By direct ionisation: The direct ionisation of alkyl halides gives

carbocations.

The process is accelerated due to the presence of metal ions like Ag⊕.

Form alkenes: A proton or other positive species adds to one atom of an unsaturated system leaving a positive charge on the adjacent carbon.

Decomposition of an alkyl diazonium ions:

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By protonation of alcohols: The protonated alcohols give carbocations on decomposition.

By reaction of acyl halides in presence of anhydrous aluminium chloride:The FrielelCrafts acylation reactions came under this heading.

GENERATION OF CARBOCATIONS

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The Carbanion Chemistry

The carbanions are formed during heterolytic fission of a C—X bond in which the carbon atom is more electronegative than X.

The shared pair of electron goes to the carbon atom which acquires an octet with a negative charge and X goes out as a positive ion. The above species containing the carbon with the octet anda negative charge is called a carbanion.

So, it is a tricovalent carbon with a pair of electrons and the geometry has been found to be pyramidal resembling ammonia and amines in which the unshared pair occupies one apex of the tetrahedron.Therefore, the central carbon atom is in a state of sp3 hybridisation, but when it is stabilized by declocatization, the hybridization becomes, sp2 for effective resonance. 1/31/2015

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STABILITYSTABILITY Being electron-rich it is a very reactive intermediate and forms the basis of many important

organic synthesis. It can combine with a great variety of electrophiles e.g., alkyl halides and ketonesand can form compounds having carbon-carbon bonds in high yields.

Because of the unshared electron pairs, it can also function as a base and can abstract a protonto form a conjugate acid.

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The benzyl carbanion has been found to be most stable because of the extensive delocalization of the negative charge over the various resonating structures.

The stability becomes greater due to the presence of electron attracting groups like NO2, – C≡Nor carbonyl group in the molecule and it decreases due to electron releasing groups

STABILITYSTABILITY

The stability of the carbanions has been found to be in the order benzyl > vinyl > phenyl > –C2H5 > n-propyl > isobutyl > neopentyl.The effect of groups on the stability of carbanions when present in α position is in the order.1/31/2015

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GENERATION OF CARBANIONS

The carbanions have been generated as intermediates in a large number of reactions.

A new types of carbanions have been prepared which are paired with different metals and this has found the basis for the preparation of many novel organometallic compounds.Some of these metals include group IA, IIA metals besides aluminium, zinc and cadmium.

(a) Abstraction of hydrogen by a base

organic compounds having C—H bonds, the carbon atom being more electronegative will pull the bonding electron towards itself and so hydrogen can go out as a proton. Therefore, in presence of a base this H will be attracted by the base and a carbanion will be obtained.

This acidic hydrogen will be abstracted by bases like NaOH, t-BuO – or alkyl lithium where the alkyl radical will behave like a base.

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In the Grignard reagent, the alkyl radical acts like a carbanion as shown by its reactions with CO2 leading to the formation of carboxylic acids

(b) From Unsaturated CompoundsBy addition: The addition of a nucleophile to an unsaturated C = C bond generates a carbanion

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GOOD GOOD LUCKLUCK

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