Organic Molecules

~ Structure and Nomenclature ~

•Determining the structure of organic compounds

•Carbon
•Covalent bond (Lewis structure formalism)
•Molecular geometry (bond length, bond angle)

•Electronic structure of atoms and molecules (1st pass)

• σ and π bonds

@ MIT
February 6, 2003 – Organic Optoelectronics - Lecture 2
1
 Charge carrier mobility is dependent
Organic Field Effect Transistors on molecular order within the
semiconducting thin film
pentacene

-VD

source drain
+ + + + semiconductor
insulator gate
substrate

-V
Addition
G IMPROVED MOLECULAR
ORDERING
Current modulation is
achieved by electric Larger grain sizes
field-induced charge Lower defect densities
build-up at the
interface between the Enhanced mobility
organic semiconductor
and the insulator
Dimitrakopoulos, et. al., IBM J. Res. and Devel. 45, 11 (2001). 2
 M.A. Baldo, priv. comm.

PENTACENE

3
 MOLECULE – derived form “molecula” - meaning small mass
(a smallest unit of chemical compound that still exhibits all its properties)

HOMONUCLEAR
diatomic molecules

H2
Cl2

HETERONUCLEAR

HCl

Adapted from Molecular Physics and Elements of Quantum Chemistry by H. Haken and H.C. Wolf 4
Potential Energy as a Function of Internuclear Distance, R

Adapted from Molecular Physics and Elements of Quantum Chemistry by H. Haken and H.C. Wolf 5
 The Size of the System

Photosynthetic Process

The reaction center for bacterial photosynthesis as a

molecular functional unit. The schematic drawing shows
the photoactive molecules, which are embedded in a
larger protein unit. The latter in turn is embedded in a
cell membrane. Light absorption by the central
chlorophyll dimer is the first step in the charge separation
which sets off the chemical process of photosynthesis.
The picture is based on the x-ray structure by
Deisenhofer, Huber, and Michel (Nobel Prize 1988), is
taken from the newspaper “Die Zeit”

Adapted from Figure 1.3 caption of Molecular

Physics and Elements of Quantum Chemistry by
H. Haken and H.C. Wolf

our AREA of INTEREST

water, amonia, chlorophyll DNA
benzene crown ethers log (SIZE) 6
Seeing the shape of molecules
with Transmission Electron Microscope (TEM)

An electron microscope image of hexadecachloro copper

phthalocyanine molecules. The molecules form a thin,
oriented layer which serves as substrate. The image was
made with a high-resolution 500kV transmission electron
microscope and was processed using special image-
enhancement methods. The central copper atoms and the
16 peripheral chlorine atoms may be most clearly
recognized. (This picture was kindly provided by Prof. N.
Uyeda of Kyoto University.)
Figure 1.4 caption from Molecular Physics and
Elements of Quantum Chemistry by H. Haken and
H.C. Wolf

7
 Seeing the shape of molecules
with Scanning Tunneling Microscope (STM)
or Atomic Force Microscope (AFM)

STM scan of
ordered PTCDA monolayer on HOPG

molecular orbital calculation of the

electron density in the highest occupied
molecular orbital of a PTCDA molecule

Agreement between the calculation and

the experiment exemplifies maturity of
detailed understanding of electronic
arrangement on molecules.
However, …
DYNAMIC ELECTRONIC PROCESSES in
MOLECULES and MOLECULAR ASSEMBLIES
are NOT WELL UNDERSTOOD
and present a topic of our research
8
Seeing the shape of molecules
with electron diffraction

Radial distribution functions D

describing the electron density as
a function of the bond length R
between atomic nuclei in the
molecules PH(CH3)2 and PH2CH3,
obtained from electron diffraction
patterns. The maxima in the
distribution functions can be
correlated with the inter-nuclear
distances indicated. [After
Bartell, J. Chem. Physics. 32, 832
(1960)]

Quoted from Figure 2.1 of Molecular

Physics and Elements of Quantum
Chemistry by H. Haken and H.C. Wolf

9
Seeing the shape of molecules
with x-ray diffraction

An simulated electron density diagram of the porphyrine

molecule. The H atoms are not visible, since they are
poorly detected by X-ray diffraction methods compared
to atoms with higher electron densities, such as nitrogen.
The contour lines represent the electron density. Their
interval corresponds to a density difference of one
electron per Å2, and the dashed lines represent an
absolute density of 1 electron per Å2.
Quoted from Figure 2.1 of Molecular
Physics and Elements of Quantum
Chemistry by H. Haken and H.C. Wolf

10
 Mass Spectroscopy

100

Relative
80 m/e = 16 m/e Abundance
1 3.36
Relative abundance

60
12 2.80
13 8.09
14 16.10
40
15 85.90
16 100.00
20 17 1.11

0
0 10 20
m/e Image of a mass spectrometer
methane showing its internal organs.

Adapted from Organic Chemistry by G.M. Loudon

11
 TETRAHEDRAL

methane

TRIGONAL

LINEAR
acetylene

Adaped from Organic Chemistry by G.M. Loudon 12

 3d ___ ___ ___ ___ ___
3p ___ ___ ___

3s ___

2p ___ ___ ___

Schematic representation of
ENERGY

the relative energies of

2s ___
different orbitals in a many-
electron atom. The exact
scale varies from atom to
atom, but the energy levels
tend to be closer together as
the principle quantum number
1s ___
increases.

Quoted from Figure 2.6 in Organic

Chemistry by G.M. Loudon

13
 z

Atomic Orbitals
y
x

s Pz Py Px

dz2 d x 2 −y 2
d xy d zx d yz

Atoms that constitute typical organic compounds such as

H, C, N, O, F, P, S, Cl
have outermost (valence) electrons in s and p orbitals. When molecules are formed
the s and p atomic orbitals form σ and π
14
From NASA website In 0 A.D. 9 elements were known (C, S, Fe, Cu, Ag, Sn, Au, Hg, and Pb) 15
 subtract Antibonding
1s orbitals
node Molecular Orbital
ENERGY (1s-1s)

energy of isolated hydrogen atoms

isolated
hydrogen
atoms

add
1s orbitals Bonding
(1s+1s) Molecular Orbital

Addition Subtraction

Adapted from Organic Chemistry by G.M. Loudon 16

 Hybrid Orbitals
bonding in METHANE

2p ___ ___ ___

}
Mix 2s and 2p
orbitals 2(sp3) ___ ___ ___ ___
2s ___
ENERGY

1s ___
1s ___
carbon in methane
carbon itself

Organic Chemistry by G.M. Loudon 17

 Hybrid Orbitals
bonding in AMMONIA

2p ___ ___ ___

}
Mix 2s and 2p
orbitals 2(sp3) ___ ___ ___ ___
2s ___
ENERGY

1s ___
1s ___
Nitrogen itself Nitrogen in ammonia

Lewis Structure Orbital Picture

N
H
H
H
Adapted from Organic Chemistry by G.M. Loudon 18
 H H H H

H CC H H C C H

H H H H C
C

Bonding molecular orbitals

in ETHANE

sp3-sp3 σ-bond

sp3-1s σ-bond

Adapted from Organic Chemistry by G.M. Loudon

19
 Alkenes, or olefins, are hydrocarbons that contain carbon-carbon double bonds.
Ethylene and propylene are the two simplest alkenes.

3
C C

ethylene

Structures of ethylene,
ethane, propylene, and
propane 3

3
A DOUBLE BOND
2

Adapted from Organic Chemistry by G.M. Loudon 20

 Orbitals of a sp3-hybridized carbon

2p ___ ___ ___

}
Mix 2s and 2p
orbitals 2(sp3) ___ ___ ___ ___
2s ___
ENERGY

1s ___ 1s ___

(a) The general shape of an sp2

hybrid orbital is very similar to that
sp2 orbital
of an sp3 hybrid orbital, with a large
and small lobe of electrons density
separated by a node. (b) Spatial sp2 orbitals
distribution of orbital son an sp3-
hybridized carbon atom.
Quoted from Figure 4.3 of Organic
Chemistry by G.M. Loudon (a) (b)
p orbital 21
Bonding molecular orbitals
in ETHYLENE
The p-bonds in ethylene

p orbital
Overlap of p orbital to
form boding and
antibonding π-molecular antibonding
orbitals. The π-bond is
formed when two
electrons occupy the
bonding π-molecular
orbital.
p2 – p1

__ __
ENERGY

bonding
wave peak

wave trough

Quoted from Figure 4.5 of Organic Chemistry by G.M. Loudon 22

Bond Length

The following generalizations can be made about bond length:

1. Bond lengths between atoms of a given type decrease with the amount of
multiple bonding. Thus, bond lengths for carbon-carbon bonds are in the
order C-C > C =C > C=C _

2. Bond lengths tend to increase with the size of the bonded atoms. This
effect is most dramatic as we proceed down the periodic table. Thus, a C-
H bond is shorter then a C-F bond, which is shorter then a C-Cl bond. Since
bond length is the distance between the center of bonded atoms, it is
reasonable that larger atoms should form longer bonds.

3. When we make comparisons within a given row of the periodic table, bonds
of a certain type (single, double, or triple) between a given atom and a
series of other atoms become shorter with increasing electro negativity.
Thus, the C-F bond in H3C-F is shorter then the C-C bond in H3C-CH3. This
effect occurs because a more electronegative atoms has a greater
attraction for the electrons of the bonding partner, and therefore ‘pulls it
closer,’ than a less electronegative atom.
Quoted from Organic Chemistry by G.M. Loudon
23
 Bonding in Aliphatic Hydrocarbons

single bonds double bonds

(alkanes) (alkenes)
C-H sp2 orbital
σ−bonds sp2
orbitals

p orbital

p orbital

sp3-1s σ-bond

π-molecular
bonding orbital

sp3-sp3 σ-bond

Adapted from Organic Chemistry by G.M. Loudon

24