Duurzame energie: biomassa en biobrandstoffen
College 2: Harvesting the light
Photosynthesis → light absorption
What light is available
- Between 400 and 700 nm visible photons
ℎ𝑐
- Energy depends on colour → 𝐸 = 𝜆 = ℎ𝑣
Absorption of light = transition of an e- from one state to another: not all photons can do
this, only photons of a specific energy → right energy corresponds to difference in energy
from HOMO (ground state) and LUMO (excited state)
Single-double bond structures (biomolecules) absorb light from visible region
→ double bonds shift energy of the excited state (decrease) and absorb longer
wavelengths → the lower the energy (due to electron dislocation), the more
conjugated double bonds.
Chlorofyl: difference in R-groups highly influences the absorption spectrum →
Lambert-Beer law: 𝐴 = 𝜀(𝜆) 𝐶 𝐿 en 𝐴 = − log10 𝑇
𝜀 = molar extinction coefficient in 1000 cm2/mole, C = concentration, L = path
length, T = Transmittance = I / I0
The fluid is a pigment in solution.
Different decay processes:
1. Internal conversion = by emitting heat, the molecule decays very fast to lowest
excited state. → Important for chlorofyl because it also occurs between different
electronic states.
2. Decay of the excited state to ground state
a. Internal conversion (decay by heat) → kic = 0.02 ns-1 (probability that it
occurs)
b. Decay by emission of a photon, energy lost by fluorescence → kF = 0.06 ns1
Advantage: we can see photons coming out of the chlorofyl
c. Formation of triplets (decay to triplet state T) → very slow transmission, kT =
0.125 ns-1
, 𝑑𝑁
Rate constant k: 𝑘 = 𝑑𝑡 = −𝑘𝑁 en
𝑁 (𝜏) = 𝑁(0)𝑒 −𝑘𝜏 = 𝑁(0)𝑒 −𝑘/𝑘 (solution rate equation)
N = molecules in excited state.
K smaller → decay longer, k larger → decay shorter.
𝜏 = lifetime = 1/k
→ Different decay pathways (k1 + k2) gives a solution rate equation of:
𝑁 (𝜏) = 𝑁(0)𝑒 −(k1 + k2)𝜏
Quantum yield (Φ) = probability that event occurs per absorbed photon.
Φ1 = relative yield of decay through path 1.
Φ1 = k1 / (k1 + k2 + … + kn)
→ Sum of all decay pathways must be 1.
Lifetime of the excited state of one chlorofyl: = (k)-1 = (kF + kIC + kT)-1
Carotenoids (C40)
Functions:
- Photoprotection
- Light harvesting
- Structure stabilization
Mainly absorb blue photons (350-500 nm)
Role carotenoids in photosynthesis:
Chlorofyl in triplet state is very reactive → react with O2 → danger for DNA, lipids etc.
Carotenoids can react with triplets → decay to ground state without interaction with
oxygen.
,College 3: Transferring and trapping light energy
Second step of photosynthesis: energy transfer.
→ Connecting the pigments to have the energies flowing through the pigments to the
reaction center.
Photosynthetic systems:
1. Light-harvesting antenna: specialized pigment-protein complexes that absorb
sunlight and transfer excited-state energy to reaction center. Bind many pigments.
2. Reaction center: specialized pigment-protein complexes where charge separation
takes place to fix the energy of the excited state. Bind redox-active
pigments/molecules.
→ Why is antenna needed? Because sunlight is diluted energy source. If the reaction center
would be the only thing to take up sunlight energy, the process would be too slow. And the
Reaction Centers and enzymes cost energy to build and maintain. → So with Light-
harvesting antenna more light can be harvested, also under low light intensity conditions.
Diversity in pigments → diversity in antenna structures.
(a) ‘Fused’ Antenna-RC complexes → Antenna and RC are located on the same
polypeptide and cannot be separated with biochemical methods
(b) Core antenna complexes → antenna and RC are closely associated on separate
polypeptides, can be separated with biochemical methods, but they are present in
fixed stoichiometry
(c) Accessory (peripheral) antennas → further away from the RC, presence variable,
often dependent on growing/light conditions
Distance between near-neighbour pigments is similar in every antenna. Most pigments at 10
armstrong, almost no pigments at > 20 A
→ to avoid concentration quenching. At increasing Chl concentration the fluorescence
diminishes. Concentration quenching: average Chl-Chl distance is smaller than 10 A.
Excited states are quenched at high concentration, probably through charge-transfer states
(but not clear what the reason is for concentration quenching).
Protein tunes the absorption properties of the pigments → because they are in solvent
(environment is identical, chemical same molecules), they absorb exactly in the same way.
This makes a broader absorption spectrum → allows to absorb more photons of different
colors.
This is the same for pigments in protein.
Chlorofyl molecules close to eachother can transfer energy from one Chl to another.
→ Another decay pathway (2d): Decay to the excited state.
, → The first chlorofyl (D) decays to ground state, and the chlorofyl next to it (A) goes to
excited state → Dipole-dipole resonant interaction = Förster Resonance Energy transfer
The rate of excitation energy transfer from a donor (D) to an acceptor (A) depends on
several factors:
1. Center-to-center distance between D and A.
a. Dependance: R-6
b. Distance 10-100 A
2. Overlap between the fluorescence emission of the donor and the absorption of the
acceptor → spectral overlap region = where the emission spectra of donor and
acceptor overlap.
3. Mutual orientation of donor and acceptor
Förster equation (short form):
𝑅0 6 𝜅2 ̃ ∗ 𝐹𝐷 (𝑣)
𝜀𝐴 (𝑣) ̃
𝑘𝐷𝐴 = 𝑘 ( ) , 𝑤𝑖𝑡ℎ 𝑅06 = 8.8 ∗ 1017 ∗ 4 ∗ ∫
𝐷
𝑑𝑣̃
𝑅 𝑛 𝑣̃ 4
Compares the energy transfer rate with the radiative rate: measure of energy transfer
efficiency.
Forster radius = 𝑅0 = the distance at which the efficiency of excitation energy transfer is
50%. When R = 𝑅0, the efficiency is 100%. When de distance increases, the efficiency
decreases.
Another decay that can occur (2e): Electron transfer to nearby molecule
In every step of the photosynthetic process there are losses, which causes low efficiency.
1. Absorption of chlorophylls and carotenes → Loss due to the fact that they don’t
absorb the full spectrum of the sunlight. PAR (Photosynthetic Active Radiation)
consists only of visible light.
2. Transmission and reflection → Not all the photons of the right wavelength are
absorbed, because part of them is transmitted and part of them is reflected.
3. Photochemical inefficiency → difference in energy between blue and red photons is
lost as heat, only energy corresponding to red photons can be used for
photosynthesis.
Some cyanobacteria can use far-red light → chlorophylls d and f are made by the bacteria
when they are grown in far-red light. → Can be used in crops to upgrade the yield.
Photophysical efficiency = 37% → Almost identical for all oxygenic photosynthetic
organisms.
Light is not a stable source of energy, because the intensity varies very much. → Important
for photosynthetic organisms to be able to cope with these fluctuations in intensity.
Regulation of light harvesting:
- Saturation of photosynthesis: there is little to no photosynthesis → under tese
conditions the probability to form triplets increases (which can cause O formation).
They avoid this by activating another decay pathway: heat dissipation. Part of the
College 2: Harvesting the light
Photosynthesis → light absorption
What light is available
- Between 400 and 700 nm visible photons
ℎ𝑐
- Energy depends on colour → 𝐸 = 𝜆 = ℎ𝑣
Absorption of light = transition of an e- from one state to another: not all photons can do
this, only photons of a specific energy → right energy corresponds to difference in energy
from HOMO (ground state) and LUMO (excited state)
Single-double bond structures (biomolecules) absorb light from visible region
→ double bonds shift energy of the excited state (decrease) and absorb longer
wavelengths → the lower the energy (due to electron dislocation), the more
conjugated double bonds.
Chlorofyl: difference in R-groups highly influences the absorption spectrum →
Lambert-Beer law: 𝐴 = 𝜀(𝜆) 𝐶 𝐿 en 𝐴 = − log10 𝑇
𝜀 = molar extinction coefficient in 1000 cm2/mole, C = concentration, L = path
length, T = Transmittance = I / I0
The fluid is a pigment in solution.
Different decay processes:
1. Internal conversion = by emitting heat, the molecule decays very fast to lowest
excited state. → Important for chlorofyl because it also occurs between different
electronic states.
2. Decay of the excited state to ground state
a. Internal conversion (decay by heat) → kic = 0.02 ns-1 (probability that it
occurs)
b. Decay by emission of a photon, energy lost by fluorescence → kF = 0.06 ns1
Advantage: we can see photons coming out of the chlorofyl
c. Formation of triplets (decay to triplet state T) → very slow transmission, kT =
0.125 ns-1
, 𝑑𝑁
Rate constant k: 𝑘 = 𝑑𝑡 = −𝑘𝑁 en
𝑁 (𝜏) = 𝑁(0)𝑒 −𝑘𝜏 = 𝑁(0)𝑒 −𝑘/𝑘 (solution rate equation)
N = molecules in excited state.
K smaller → decay longer, k larger → decay shorter.
𝜏 = lifetime = 1/k
→ Different decay pathways (k1 + k2) gives a solution rate equation of:
𝑁 (𝜏) = 𝑁(0)𝑒 −(k1 + k2)𝜏
Quantum yield (Φ) = probability that event occurs per absorbed photon.
Φ1 = relative yield of decay through path 1.
Φ1 = k1 / (k1 + k2 + … + kn)
→ Sum of all decay pathways must be 1.
Lifetime of the excited state of one chlorofyl: = (k)-1 = (kF + kIC + kT)-1
Carotenoids (C40)
Functions:
- Photoprotection
- Light harvesting
- Structure stabilization
Mainly absorb blue photons (350-500 nm)
Role carotenoids in photosynthesis:
Chlorofyl in triplet state is very reactive → react with O2 → danger for DNA, lipids etc.
Carotenoids can react with triplets → decay to ground state without interaction with
oxygen.
,College 3: Transferring and trapping light energy
Second step of photosynthesis: energy transfer.
→ Connecting the pigments to have the energies flowing through the pigments to the
reaction center.
Photosynthetic systems:
1. Light-harvesting antenna: specialized pigment-protein complexes that absorb
sunlight and transfer excited-state energy to reaction center. Bind many pigments.
2. Reaction center: specialized pigment-protein complexes where charge separation
takes place to fix the energy of the excited state. Bind redox-active
pigments/molecules.
→ Why is antenna needed? Because sunlight is diluted energy source. If the reaction center
would be the only thing to take up sunlight energy, the process would be too slow. And the
Reaction Centers and enzymes cost energy to build and maintain. → So with Light-
harvesting antenna more light can be harvested, also under low light intensity conditions.
Diversity in pigments → diversity in antenna structures.
(a) ‘Fused’ Antenna-RC complexes → Antenna and RC are located on the same
polypeptide and cannot be separated with biochemical methods
(b) Core antenna complexes → antenna and RC are closely associated on separate
polypeptides, can be separated with biochemical methods, but they are present in
fixed stoichiometry
(c) Accessory (peripheral) antennas → further away from the RC, presence variable,
often dependent on growing/light conditions
Distance between near-neighbour pigments is similar in every antenna. Most pigments at 10
armstrong, almost no pigments at > 20 A
→ to avoid concentration quenching. At increasing Chl concentration the fluorescence
diminishes. Concentration quenching: average Chl-Chl distance is smaller than 10 A.
Excited states are quenched at high concentration, probably through charge-transfer states
(but not clear what the reason is for concentration quenching).
Protein tunes the absorption properties of the pigments → because they are in solvent
(environment is identical, chemical same molecules), they absorb exactly in the same way.
This makes a broader absorption spectrum → allows to absorb more photons of different
colors.
This is the same for pigments in protein.
Chlorofyl molecules close to eachother can transfer energy from one Chl to another.
→ Another decay pathway (2d): Decay to the excited state.
, → The first chlorofyl (D) decays to ground state, and the chlorofyl next to it (A) goes to
excited state → Dipole-dipole resonant interaction = Förster Resonance Energy transfer
The rate of excitation energy transfer from a donor (D) to an acceptor (A) depends on
several factors:
1. Center-to-center distance between D and A.
a. Dependance: R-6
b. Distance 10-100 A
2. Overlap between the fluorescence emission of the donor and the absorption of the
acceptor → spectral overlap region = where the emission spectra of donor and
acceptor overlap.
3. Mutual orientation of donor and acceptor
Förster equation (short form):
𝑅0 6 𝜅2 ̃ ∗ 𝐹𝐷 (𝑣)
𝜀𝐴 (𝑣) ̃
𝑘𝐷𝐴 = 𝑘 ( ) , 𝑤𝑖𝑡ℎ 𝑅06 = 8.8 ∗ 1017 ∗ 4 ∗ ∫
𝐷
𝑑𝑣̃
𝑅 𝑛 𝑣̃ 4
Compares the energy transfer rate with the radiative rate: measure of energy transfer
efficiency.
Forster radius = 𝑅0 = the distance at which the efficiency of excitation energy transfer is
50%. When R = 𝑅0, the efficiency is 100%. When de distance increases, the efficiency
decreases.
Another decay that can occur (2e): Electron transfer to nearby molecule
In every step of the photosynthetic process there are losses, which causes low efficiency.
1. Absorption of chlorophylls and carotenes → Loss due to the fact that they don’t
absorb the full spectrum of the sunlight. PAR (Photosynthetic Active Radiation)
consists only of visible light.
2. Transmission and reflection → Not all the photons of the right wavelength are
absorbed, because part of them is transmitted and part of them is reflected.
3. Photochemical inefficiency → difference in energy between blue and red photons is
lost as heat, only energy corresponding to red photons can be used for
photosynthesis.
Some cyanobacteria can use far-red light → chlorophylls d and f are made by the bacteria
when they are grown in far-red light. → Can be used in crops to upgrade the yield.
Photophysical efficiency = 37% → Almost identical for all oxygenic photosynthetic
organisms.
Light is not a stable source of energy, because the intensity varies very much. → Important
for photosynthetic organisms to be able to cope with these fluctuations in intensity.
Regulation of light harvesting:
- Saturation of photosynthesis: there is little to no photosynthesis → under tese
conditions the probability to form triplets increases (which can cause O formation).
They avoid this by activating another decay pathway: heat dissipation. Part of the
