PHYSICAL ORGANIC CHEMISTRY

Yu-Tai Tao (陶雨台）

Tel: (02)27898580
E-mail: ytt@chem.sinica.edu.tw
Website:http://www.sinica.edu.tw/~ytt

Textbook:
“Perspective on Structure and Mechanism in Organic
Chemistry” by F. A. Corroll, 1998, Brooks/Cole
Publishing Company

References:
1. “Modern Physical Organic Chemistry” by E. V. Anslyn
and D. A. Dougherty, 2005, University Science Books.

Grading: One midterm (45%) one final exam (45%) and

4 quizzes (10%) homeworks
 Chap.1
Review of Concepts in Organic Chemistry
§ Quantum number and atomic orbitals
Atomic orbital wavefunctions are associated with four
quantum numbers: principle q. n. (n=1,2,3), azimuthal q.n. (m=
0,1,2,3 or s,p,d,f,..magnetic q. n. (for p, -1, 0, 1; for d, -2, -1, 0, 1, 2.
electron spin q. n. =1/2, -1/2.
§ Molecular dimensions
Atomic radius
ionic radius, ri：size of electron cloud around an ion.
covalent radius, rc：half of the distance between two atoms
of same element bond to each other.
van der Waal radius, rvdw：the effective size of atomic cloud
around a covalently bonded atoms.

Cl- Cl2 CH3Cl

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

Molecular volume and surface area can be the sum of

atomic volume (or group volume) and surface area.
Principle of additivity (group increment)

Physical basis of additivity law: the forces between atoms in the same molecule or
different molecules are very “short range”.
Theoretical determination of molecular size：depending on
the boundary condition.

Boundary is a certain minimum value of electron density.

Molecular volume (1 au = 6.748e/Å3 ),

0.001au 0.02au expt’l

CH4 25.53 19.58 17.12

C2H6 39.54 31.10 27.34

C3H8 53.64 42.76 37.57

C4H10 67.64 44.13 47.80

§ Heats of formation and reaction
Heat of formation：Difference in enthalpy between the
compound and starting elements in their standard states
obtained indirectly from other components of known
ΔHf°
correct for necessary phase change (such as vaporization,
sublimation)
correct for ΔH at different T by heat capacity
experimental measurement by calorimeter
　　m C(gr) ＋ n/2 H2 (g) 　　　CmHn 　　　　ΔH O f°

To calculate the heat of formation of (g)

O
O

6 C(gr) ＋ 4 H2(g) ＋ O2(g) ΔHf°

O
(g)
O

＋ 7 O2(g) 6 CO2(g) ＋ 4 H2O(g)

(s)
O ΔHcomb= -735.9 Kcal/mol
6 C(gr) ＋ 6 O2(g) 6 CO2(g)
ΔHcomb= -94.05 (Kcal/mol C) × 6
4 H2(g) ＋ O2(g) 4 H2O(g)
ΔHcomb= -68.32 (Kcal/mol H2)
O O

ΔHsubl= 21.46 Kcal/mol

(s) (g)
O O

ΔHf°= 6 × (-94.05) ＋ 4 × (-68.32) ＋735.9 ＋21.46

= -80.22 (Kcal/mol)
Relative difference in heat of formation
O
OCCF3
+ CF3COOH　　　　　　　　　∆H= -10.93 Kcal/mol
O
OCCF3
+ CF3COOH　　　　　　　　　∆H= -9.11 Kcal/mol

∆H= -1.82 Kcal/mol

H2
CH3CH＝CHCH3 CH3CH2CH2CH3 ΔH=-28.6Kcal/mol
cis H2
CH3CH＝CHCH3 CH3CH2CH2CH3 ΔH=-27.6Kcal/mol
trans
The heat of hydrogenation is much smaller than the heat of
combustion. Both will give the difference of the stability of
the two isomers.
§ Bond increment calculation of heat of formation
Principle of additivity：The property of a large molecule
can be approximated by adding the contribution
of its component.
 H H H
H H
For butane H H
H H H
(-3.83) × 10 ＋ 3× (2.73) ＝ -30.11 Kcal/mol
§ Group increment calculation of heat of formation

3 × (-10.08) ＋ 2 × (-4.95) ＋ 1 × (-1.90) ＝ -42.04 Kcal/mol (obs. -41.66)

CH3 CH3

CH3 CH3 4 × (-10.08) ＋ 2 × (-1.90) ＝ -44.12 Kcal/mol (obs. -42.49)

Further refinements correct for van der Waal strain, angle strain….

The electrostatic model for the stability of branched alkane

+1
Charge on H：0.278× 10-10 esu
+1 +1
+1 +1 +1 +1 H
H H H H H H
-3
-2
-2
-2
-2 -2 -1 -2 Charge on C：neutralizing charge
H H H
+1 +1 +1
H
+1
H H
H H +1 H Branched more stable
+1 +1 +1 +1
JACS 1975, 97, 704.
Homolytic & Heterolytic Dissociation Energies

homolysis ΔH°hom ：standard homolytic

A－B(g) A． (g) ＋B． (g) bond dissociation
energy
heterolysis electron transfer
A+ (g)＋B- (g)

ΔH°het：standard heterolytic bond

dissociation energy

In gas phase：ΔH°het >ΔH°hom

In solution： solvation of ions can lower ΔH°het, so that
heterolysis becomes favorable.
Use bond dissociation energy to calculate reaction ΔH°r
e.g. CH3－H CH3． ＋ H． ΔH°r＝ +104 Kcal/mol
Cl－Cl Cl． ＋ Cl． ΔH°r＝ +58 Kcal/mol
Cl． ＋ CH3． CH3Cl ΔH°r＝ -84 Kcal/mol
＋） Cl． ＋ H． H－Cl ΔH°r＝ -103 Kcal/mol
CH3－H ＋ Cl－Cl CH3Cl ＋ HCl ΔH°r＝ -25 Kcal
Hess Law：The difference in enthalpy between products
and reactants is independent of the path of the
reaction.
by heat of formation
ΔH°r＝ΣΔH°f(prd) －ΣΔH°f(pre)
= -23.7 Kcal/mol at 300℃
§ Bond length and bond energy
Bond length is nearly a constant property between
molecules.
 § Polarizability
The ability of electron cloud to distort in response to
external field, defined as the magnitude of dipole induced
by one unit of field gradient.

¾Polarizability decreases across a row of the periodic table,

. (C>N>O>F, CH4>NH3>H2O)
¾ Polarizability increases along a column,(S>O, P>M, H2S>H2O)
C-I bond is more polarizable than C-Cl
¾alkanes are more polarizable than alkenes, may due to
Electronegativity. sp2 carbons are more electronegative than
sp3 carbons.
§ Bonding Model
Valence Bond Theory (VB) G.N. Lewis 1916
Chemical bonds result from the sharing of electron pairs
between two approaching atoms.
The bond is localized.
means two
+ bonding
electrons in
H H H－H the region
H：H
between two
atom
The region is orbital.

Cl + Cl Cl Cl each achieve
a filled shell

H + Cl H Cl

σ bond from S and P σ bond by P and P

σ ：cylindrical symmetry

For complex molecules, hybridization and resonance are

used to describe molecules in terms of orbitals which are
mainly localized between two atoms.
Hybridization Theory：
For carbon 1s22s22p2
the 2s, 2px, 2py, 2pz hybridize to form four equivalent sp3
4 bonds can be formed on carbon
highly directional sp3 orbital provide for more efficient
overlap.
methane CH4 + 3 4
s p sp3
H
H
H
109.5° C C
H H

H H H

ethene π bond, plane sym.

H H H H s + 2p → 3sp2
1 2 0° or
H H H H one p remaining
acetylene

H H or H H
s + p → 2sp
two p remaining
H-C-C linear

No. of Hybri Geometry

ligand d
4 sp3 Tetrahedr CH4, CCl4, CH3OH,
al
3 sp2 Trigonal CH2=CH2, H2C=O, C6H6,
CO3=, CH3．
2 sp linear HC≡CH, CO2, HCN,
H2C=C=CH2
 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 and
reactive 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 of
these 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.
H 2C H 2C H 2C H 2C
C CH 2 C CH 2 C O C O
H 3C H 3C H 3C H 3C
more stable
two equivalent structure
H H H H
C C C C
charge located equally on two C’s
H C H H C H
H H the allyl cation is planar for
maximum p interaction
H H
H H restricted rotation around
single bond
H H H
H C O H C O H C O
C C C C C C
H H H H H H
major significant minor
§ Dipole moment：the vector quantity that measures the
0.1 e 0.1e
separation of charges. +q -q 1 electron charge = 4.8x10-10 esu
-8
d = 1.5x10 cm
bond dipole = q × d = 0.1× (4.8× 10-10esu)
× 1.5× 10-8 cm
= 0.72× 10-18esu．cm
= 0.72 D (1 Debye = 10-18esu．Cm)
Molecular dipole is the vector sum of various “bond dipoles”.
It provides information about molecular structure and bonding.
e.g. CH3F μ= 1.81 D
H
H C F q= 1.81× 10 -18
= 0.27 e-
H 1.385× 4.8× 10-10
1.385Å
For dichlorobenzene
Cl μ= 2.30, 1.55, 0
Cl Cl Cl
μ= 1.61 D Cl

Cl
Cl
From trigonometry, the calculated angles between two bond
“dipole moment” are 89° , 122° , 180°.
support the concept that benzene is planar.
The dipole moment results from unequal sharing of the
electron. due to different attraction for electron
electronegativity
Polar bond = [covalent bond] +λ [ionic bond]
λ= weighing factor
% ionic character = λ2 × 100 %
(1 +λ2)
HCl +0.17 electron charge on H．
- 0.17 electron charge on Cl． λ = 0.45
 § Electronegativity & Bond Polarity
Electronegativity：The power of an atom in a molecule
to attract electrons to itself. Pauline 1932
χp：based on the difference in bond energy of AB
and A-A + B-B other scale of electronegativity,
2
more related to atomic properties.
Mulliken χ = I + A I：ionization potential of atom
M
1934 2
A：e- affinity of atom
Allen χspec：based on the average I.P.of all of the valence P
1989 and S electrons.
Nagle
1990 χα：based on atomic polarizability
Benson VX：no. of valence electron /covalent radii
1988
Third Dimension of Periodic Table J. Am. Chem. Soc. 1989, 111, 9004.
 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.

red ----negative potential

blue --- positive potential
green---neutral

-0.24 -0.17
δ δ
δ F
δ δ
0.09 0.36
 Molecular Orbital Method
Electrons are distributed among a set of molecular
orbitals of discrete energies. The orbitals extend over the
entire molecule.
First Approximation：
the MO is a linear combination of contributing atomic orb.
Ψ = c1ψ1 + c2 ψ2 + ‥‥‥ + cn ψn
ψ’S are basis set
c’S coefficient, reflect contribution
The no. of MO’s (bonding + non-bonding +antibonding)
= total no. of a.o.’s
For H2, 2e- For HHe+, 2e-
σ*

1s
1s 1s
He 1s

σ’*
For CO, 10e-
π x*, π
y*
2Px,2Py,2Pz
σ’ 2Px,2Py,2Pz
π x, π y

σ’*
2s
2s
σ
C O
MO for methane
First approach
ψsp31 ＝ 1 (C2s ＋ C2px ＋ C2py ＋ C2pz )
2
ψsp32 ＝ 1 (C2s ＋ C2p － C2p － C2p )
2 x y z

ψsp3 ＝ 1 (C2s － C2p ＋ C2p － C2p )

3 x y z
2
ψsp34 ＝ 1 (C2s － C2p － C2p ＋ C2p )
2 x y z

each sp3 overlap with a 1s of each of these has a shape

H to form CH4 of , pointing to the
bond angle 109.5°
corner of a tetrahedron

This implies identical bonds for the bonding electrons.

But ESCA data of methane shows

1s

290eV 23.0eV 12.7eV

The M.O. formed above is symmetry incorrect.

 The symmetry of the M.O. must conform to the symmetry
of the molecule in such a way that the M.O.’s are either
symmetric or antisymmetric to all the symmetry elements of
the molecule.
Solution：form the delocalized methane M.O. directly form
unhybridized orbitals：1C2s, 3C2p’s, 4H1s

ψ1 ＝ 0.545 C2s ＋ 0.272 (H1 ＋ H2 ＋ H3 ＋ H4)

ψ 2 ＝ 0.545 C2px＋ 0.272 (H1 ＋ H2 － H3 － H4)
ψ3 ＝ 0.545 C2p ＋ 0.272 (H1 － H2 ＋ H3 － H4)
y
ψ4 ＝ 0.545 C2pz＋ 0.272 (H1 － H2 － H3 ＋ H4)

ψ2 ψ3 ψ4

ψ1

The energy of on M.O. increase with the no. of nodes in the M.O.

+ -
+ +
+ +
+ +
+ -
ψ1
- +
+ +
+
+
- -
+ -
Group orbitals from qualitative molecular orbital theory(QMOT)
planar methyl

pyramidal methyl Walsh diagram

Building larger molecule from group orbitals
 Valence Shell Electron Pair Repulsion Theory
(VSEPR)

In predicting the shape of molecules, bonds are treated as

repulsive points and the repulsive points made as far apart as
possible.
－ counting the number of electron groups：unshared pair
is a group, each bond is a group, whether single or multiple.
－ 2 groups linear
3 groups trigonal
4 groups tetrahedral
－ non-bonding electron pair more repulsive
－ bonding pair to electronegative groups less repulsive

H H H
H N O
H C H H C C H H
109.5° H H
H H H H
∠H-C-H =109.5° ∠H-C-H = 109.3° ∠H-N-H = 107° ∠H-O-H = 104.5°
Bonding electron
polarized toward
Cl Cl
1.76Å 1.781Å
Cl,
H C 1.09Å H C 1.096Å
H H
H H
predicted ∠H-C-H = 109.5° ∠H-C-H = 110°52'
　　　　 ∠H-C-Cl = 109.5° ∠H-C-Cl = 108°0'
 Effect of lone pair on bond angle
Repulsion：lone pair occupies larger domain
lone pair：lone pair＞lone pair：bond pair＞bond pair：bond
pair
120.2° > 109.5°
P
F F
F 96.9° < 109.5°

Effect of lone pair on bond length

The closer and larger domain of lone pair prevents a
bonding pair getting closer. The adjacent bond longer
F 1.68Å
1.79Å
F F
Br
F F
Effect of electronegativity on bond angle
PX3 ∠XPX(° ) OSX2 ∠XSX(° )
PF3 97.8 OSF2 92.3
PCl3 100.3 OSCl2 96.2
PBr3 101.0 OSBr2 98.2

Increasing electronegativity, the bonding pair shifts further

away from the central atom. angle decreases
Multiple bond domain ≣ > ＝ > －
122°
O
S
O
＞ O
S
O ＞O S
O
O O
S 109° H
H
H Multi-center bond
H3CO 98° OCH3 122° B 97° B occupies less domain
H
H H than a single bond
Multi-center bond 122°
Trigonal bipyramidal molecules
5 points are non-equivalent
(1) the axial bond is longer than
eq. bond rax/req = 1~1.4
√3 r (2) larger domain electron pair
90°
(lone pair, multiple bond)
120°
occupies equatorial position
√2 r (3) more electronegative atom
occupies axial position
eg. PF3Cl2, PF2Cl3
PCl5
Cl 1.01 F 0.96 F
1.2
Cl F F
Cl P S O S
Cl F F
Cl F F
1.05
0.91 0.9
F F
O
Kr O Xe
O
F F

F F F F
F F Cl Cl
Cl P Cl P Cl P Cl P
F Cl Cl Cl
F F F Cl
Limitations：
－ not applicable to ionic comp’d
－ for localized bonding/non-bonding pair, not for
delocalized
－ for sufficiently large ligands, steric interaction prevails
 § Variable Hybridization and Molecular Geometry
For carbon bonded to different atom, different
hybridizations are proposed.
For CH4, CCl4：sp3 hybridization % S = 25
% P = 75
hybridization index

For spn, define λ 2 = n ,

λ：hybridization parameter
1 λ 2
%S= ,%P=
(1 +λ2) (1 +λ2)
2
sum of P-fraction Σ λi 2 = n,
i (1 +λi )
sum of S-fraction Σ 1 =1
i (1 +λi2)

Interorbital angle θab , 1+ λa λb cosθab = 0

if a = b,
-1
1+ λa2 cosθaa = 0, cosθaa =
C

a b λa2
θab

sp3 → θaa = 109.5 ° the S character↑ , λ↓

For CA3B
sp2 → θaa = 120 °
sp3.5 sp → θaa = 180 °
more P Cl b
108° 3sin2 θab = 2 (1- cosθaa )
sp2.86
H
C
H from θab = 108° , θaa = 110.5 °
a
a from θaa = 110.5° , λa2 = 2.86
more S-character H 110.5°
a
∴sp2.86 for C－H
1 1
from 3 ( 1 + 2.86 ) + 1 +λb2
= 1, λb2 = 3.5
 For CH2Cl2
-1
λCl2 = = 2.69
1.082Å 1.772Å cos111°47
H Cl ′ ∴sp2.69 for C－Cl
1 1
112° C 111.47°
from 2 ( )+2( )=1
1 + 2.69 1 +λH2
H Cl
λH2 = 3.37, sp3.37 for C－H

-1
from cosθHH = , θHH = 107° ≠ 112 ° (expt’l)
λH2
λHH2 = 2.67,

Cl λCl2 = 3.39,
H
C
θClCl = 107°

H Cl

the inter-orbital bond angle smaller than the inter

nuclear bond angle
Cl F F
108.9° 106.7°
108.0°
C C C
H H H H
109.54° H H
110.52°
H H (by inter nuclear) H
bent bond

Experimental support of variable hybridization:

NMR coupling constants J13C-1H::
cyclopropane 161, cyclobutane 134, cyclopentane 128,
cyclohexane 124, cycloheptane 123, cyclooctane 122
 H
Cyclopropane
H H H

115 ° 1
H H

bent bond from sp3 hybridization (or variable hybridization)

Sp3.94
θcc=105°

sp2.36 H

Walsh orbital：
from sp2 hybridization
 Prediction of Physical Properties with diff.
Bonding model
1. Alkene Geometry
C－C ethane ethene ethyne
bond length 1.54Å 1.34Å 1.20Å
by σ,πformulation：
sp3 hybrid. % S = 25
in ethene sp2 hybrid. % S = 33.3 S↑bond legth dec.
addition π bond, shorter bond
in ethyne sp hybrid. % S = 50, no quantitative prediction
by bent bond formulation：
H 1.54Å H
onlysp3 C C
C－C distance 1.32Å
hybridization H 1.54Å H

H C C H C－C distance 1.18Å

1.54Å

2. Acidity
ethane 10-42 sp3 S character increase
greater e--pulling
ethene 10-36.5 sp2 power for the orbital
ethyne 10-25 sp better stabilization
of the anion
bent bond formulation
H H
H H
H
H C C C C H C C
H
H
further decrease in
decreased repulsion repulsion
conformation of propene
H
CH2 H
H
H3C C H CH2 I H
H
CH2 II
H
H I H

more stable by 2Kcal/mole

σ,π-formation predicts Ⅱ to be more stable, because more
repulsion between double bond and the C－H bond in I
Bent bond formulation：
H
H
H CH2 H CH2
H

H H
more stable
The bent bond (Ω bond ) is agreed in cyclopropane
proposed or shown to more suitable than σ,π description
in CF2＝CF2, CO2, CO, benzene

Conclusion