organic dyes
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5/19/2018 Organic Dyes
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Organic Dyes, Conjugation, and
the Chemistry of Vision
Franois G. Amar
Department of ChemistryUniversity of Maine
April 29, 2010
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5/19/2018 Organic Dyes
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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!
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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
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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
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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
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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
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Light
! The spectrum of white light is obtained
when white light is dispersed through a
prism
UV IR
remember ROYG BIV
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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
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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:
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5/19/2018 Organic Dyes
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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.
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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
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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?
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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.
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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.
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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.
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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!
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Absorption of light (h$) by 11-cis-retinal
HCH3
C
CH3
CH3
H
C
C C
C C
C C
C NH+
CH3
H
CH3
H
H
11 12
H
H
CH3 C
CH3
CH3
C
C C
C C
C C
C NH+
CH3
H
CH3
H
H
11 12
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11-cis-retinalbound to the opsin protein
H
H
CH3 C
CH3
CH3
C
C C
C C
C C
C NH+
CH3
H
CH3
H
H
11 12
Opsin protein in the
retina of the eye
Before a photon isabsorbed by the retinal
molecule, it is in the cis
conformation shown here.
HCH3
C
CH3
CH3
H
C
C C
C C
C C
C NH+
CH3
H
CH3
H
H
11 12
After absorption of a photon, the
molecule undergoes a large amplitude
rearrangement to the trans
conformation. The resulting change in
the retinal protein is transmitted as an
electrical signal to the brain:
PHOTON RECEIVED HERE
h$
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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.
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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.
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