organic dyes

5/19/2018 Organic Dyes

1/20

Organic Dyes, Conjugation, and

the Chemistry of Vision

Franois G. Amar

Department of ChemistryUniversity of Maine

April 29, 2010


2/20

A little history

!

Blue indigo dye (blue jeans) was obtained

from the indigo plant by the Romans who

called this pigment vitrum. It has the

molecular formula: C16H10N2O2.

! The famouspurple of Tyreis a dibromo

indigo extracted (very expensively) from aspecies of marine molluscs!


3/20

Conjugation of Single and Double Bonds

C=C-C=C-C=C

This characteristic is called

conjugation

Dyes have extensive networks of alternating #

single and double bonds


4/20

The structure of blue indigo

!

Molecular formula determined in 1840 by

Dumas

!

Synthesized in 1870 by Baeyer&Emmerling

N

C

C

C

C

N

HH

H

H

HOH

H

H

H

H O


5/20

Atomic

Orbitals

of Carbon

Atomic

Orbitals

of Carbon

CC

sp2sp2sp2sp2

2p 2p

bonding to Hs bonding to Hs

Carbon has sp2hybrid orbitals in ethylene

H2C=CH2

!

!

"

"

Molecular

Orbitals

C=C


6/20

The $-to-$* transition

Ground state configuration

of the C=C double bond: (")2(!)2.

Bond order = (4-0)/2 = 2

!

!

"

"

light absorbed

C=C

Excited state configuration

of the C-C bond: (")2(!)1(!)1.

Bond order = (3-1)/2 = 1

!

!

"

E=h$

"

C-C


7/20

Light

! The spectrum of white light is obtained

when white light is dispersed through a

prism

UV IR

remember ROYG BIV


8/20

Two important formulas

!

%$ = c

lamda x nu = speed of light

!

Ephoton= h$

%is the wavelength of the light in meters

$is the frequency of the light in cycles per second

(cps or Hz)

his Plancks constant (= 6.626x10-34 Js)

c= 2.997x108m/s


9/20

Absorption of light and color

abs(nm)

Color of absorbed light

Color of object

400 Blue Yellow

500

Green

Red600 Yellow Blue

700 Red Green

Shine white light on a yellow solution and yellow light gets through:

Shine blue light on a yellow solution and no light gets through:


10/20

Organic dyes are conjugated molecules

Ethylene ( CH2=CH2 ) absorbs at %=165 nm,

Butadiene ( CH2=CH-CH=CH2 ) absorbs at %=217 nm (UV)

&-caroteneabsorbs at %= 500 nm (absorbs green, looks

orange):

CH3

H3C

H3C

H3C

CH3

CH3

CH3

CH3CH3

CH3

As the number of alternating single and double bonds in a

molecule increases (increasing amount of conjugation), the

energy of the absorbed light (energy difference between !

and !* orbitals decreases), as shown on the next slide.


11/20

General formula: H-(CH=CH)n

-H

n=1: ethylene is H-(CH=CH)-H or CH2=CH2

n=2: 1,3-butadiene is H-(CH=CH-CH=CH)-H

or CH2=CH-CH=CH2 )

n=4: 1,3,5-hexatriene is H-(CH=CH-CH=CH-CH=CH)-Hor CH2=CH-CH=CH-CH=CH2 )

n=6: 1,3,5,7,9,11-dodecahexaene is

CH2=CH-CH=CH-CH=CH-CH=CH-CH=CH-CH=CH 2

Excited state (!*)

Ground state (!)

n= 1 2 4 6

%(nm) = 165 217 286 345


12/20

Some other organic dyes

O

OH

OH

HO

OH

OH

N+

N CH

NH2

H3C

N

CH3

H

Mauve: the

first synthetic

dye

Cyanidin

(bluish-red color

in cranberries)

+

How many conjugated double bonds are in each

of these dyes?


13/20

A closer look: notation for double bonds

cis and trans refer to systems which have one H and one othergroup

attached to each carbon of the double bond.

C

H

C

H

H

H

C

H

CH3

H3C

H

C

C

CH3

H

H3C

H

C

1 4

4

1

This molecule is called "cis-2-butene" . "cis"means that the non-H unitsstuck to the carbons of the double bond are on the same side.

2 3

2 3

This molecule is called "trans-2-butene" . The 2-butene partmeans that a double bond between C atoms starts with C#2 and

ends at C#3. "trans"means that the non-H units stuck to thecarbons of the double bond are diagonal away from each other.

Ethylene is planar (in the plane of the paper) and rigid becausethe !bond (above & below the plane) resists rotation.


14/20

Electron micrograph of cone and rod cells

The retina of the eye has about 1 billion rod cells (longer, blue objects in this

false-color picture) which are sensitive to low light levels but not to color. The

3 million cone cells--shaded green--are responsible for color vision.


15/20

The active molecule in cones & rods : 11-cis-retinal

11-cis-retinal, shown below, is made in the body from !-caroteneand,

when bound to the retinal protein, opsin, forms the active light sensitive

compound of the eye, rhodopsin.

H

H

CH3 C

CH3

CH3

C

C C

C C

C C

C NH+

CH3

H

CH3

H

H

11 12

The carbons numbered 11 and 12 in the box are linked

by a double bond with a cis conformation.


16/20

Absorption of light (h$) by 11-cis-retinal

HCH3

C

CH3

CH3

H

C

C C

C C

C C

C NH+

CH3

H

CH3

H

H

H

H

CH3 C

CH3

CH3

C

C C

C C

C C

C NH+

CH3

H

CH3

H

H

11 12

11 12

cis tra ns

11-c is- ret ina l

absorbs a photon, breaking

the -bond at the C11

position, allowing the

molecule to rotate from the

cis to the trans

conformation

h!


17/20

Absorption of light (h$) by 11-cis-retinal

HCH3

C

CH3

CH3

H

C

C C

C C

C C

C NH+

CH3

H

CH3

H

H

11 12

H

H

CH3 C

CH3

CH3

C

C C

C C

C C

C NH+

CH3

H

CH3

H

H

11 12


18/20

11-cis-retinalbound to the opsin protein

H

H

CH3 C

CH3

CH3

C

C C

C C

C C

C NH+

CH3

H

CH3

H

H

11 12

Opsin protein in the

retina of the eye

Before a photon isabsorbed by the retinal

molecule, it is in the cis

conformation shown here.

HCH3

C

CH3

CH3

H

C

C C

C C

C C

C NH+

CH3

H

CH3

H

H

11 12

After absorption of a photon, the

molecule undergoes a large amplitude

rearrangement to the trans

conformation. The resulting change in

the retinal protein is transmitted as an

electrical signal to the brain:

PHOTON RECEIVED HERE

h$


19/20

What about color vision?

blue green red

400 500 600 700

%(nm)

Shifted absorption

spectrum of retinal in

different kinds of cone

cells (adapted from ST, p.

903)

11-cis-retinalbound to three slightly different proteins in the cone cells uses

the same mechanism but is more sensitive to (more likely to absorb) one of

the three colors shown than the others.


20/20

Fluorescence and fluorescent dyes

Some dyes can absorb at short wavelength (high energy)

and then lose some of that energy internally before re-

emitting the light at a longer wavelength.

absorption of

UV lightemission of

visible light

relaxationS1

S0

Typically a molecule may

absorb in the UV and re-

emit in the visible, making

the object to which it is

bound appear to glow.

Brighteners in laundrydetergents operate on this

principle. Fluorescent lights

also use the principle of

emitting light at lower

energy than the initial

excitation of the molecule.

organic dyes

Documents

chhor ch2

cc5192018 organic dyes

997x108ms5192018 organic

blue light

cc bond

yellow light

c double bond

speed of light