Chapter 4


PHOTO PHARMACOLOGY
Ibn al-Baitar’s major contribution is Kitāb Al-jāmiu li-mufradāt
al-adwiya wa al-aghdhiya which greatly influenced the works of
prohetic sayings of photolytic fruits, especially in the Near East, in
and out of the Islamic world. It was a pharmacopoeia (pharmaceutical
encyclopedia) listing 1,400 plants, foods, and drugs. The book also
contains references to 150 other previous Arabic authors as well as 20
previous Greek authors.
Ibn al-Baitar also provides detailed photo-chemical information on the
Rosewater and Orangewater production. He mentions: The scented Shurub
(Syrup) was often extracted from flowers and rare leaves, by means of
using hot oils and fat, they were later cooled in cinnamon oil. The
oils used were also extracted from sesame and olives. Ethereal oil was
produced by joining various resorts, the steam from these resorts
condensed and combined and its scented droplets were used as perfume
and mixed to produce the most costly medicines
Photodissociation, photolysis, or photodecomposition is a chemical
reaction in which a chemical compound is broken down by photons. It is
defined as the interaction of one or more photons with one target
molecule.
Photodissociation is not limited to visible light. Any photon with
sufficient energy can affect the chemical bonds of a chemical
compound. Since a photon's energy is inversely proportional to its
wavelength, electromagnetic waves with the energy of visible light or
higher, such as ultraviolet light, x-rays and gamma rays are usually
involved in such reactions.
Photolysis in photosynthesis
Photolysis is part of the light-dependent reactions of photosynthesis.
The general reaction of photosynthetic photolysis can be given as:
H2A + 2 photons (light) 2e- + 2H+ + A
The chemical nature of "A" depends on the type of organism. In purple
sulfur bacteria, hydrogen sulfide (H2S) is oxidized to sulfur (S). In
oxygenic photosynthesis, water (H2O) serves as a substrate for
photolysis resulting in the generation of diatomic oxygen (O2) from
carbon dioxide (CO2). This is the process which returns oxygen to
earth's atmosphere. Photolysis of water occurs in the thylakoids of
cyanobacteria and the chloroplasts of green algae and plants.
 Energy transfer models
The conventional, semi-classical, model describes the photosynthetic
energy transfer process as one in which excitation energy hops from
light-capturing pigment molecules to reaction center molecules
step-by-step down the molecular energy ladder.
The effectiveness of photons of different wavelengths depends on the
absorption spectra of the photosynthetic pigments in the organism.
Chlorophylls absorb light in the violet-blue and red parts of the
spectrum, while accessory pigments capture other wavelengths as well.
The phycobilins of red algae absorb blue-green light which penetrates
deeper into water than red light, enabling them to photosynthesize in
deep waters. Each absorbed photon causes the formation of an exciton
(an electron excited to a higher energy state) in the pigment
molecule. The energy of the exciton is transferred to a chlorophyll
molecule (P680, where P stands for pigment and 680 for its absorption
maximum at 680 nm) in the reaction center of photosystem II via
resonance energy transfer. P680 can also directly absorb a photon at a
suitable wavelength.
Photolysis during photosynthesis occurs in a series of light-driven
oxidation events. The energized electron (exciton) of P680 is captured
by a primary electron acceptor of the photosynthetic electron transfer
chain and thus exits photosystem II. In order to repeat the reaction,
the electron in the reaction center needs to be replenished. This
occurs by oxidation of water in the case of oxygenic photosynthesis.
The electron-deficient reaction center of photosystem II (P680*) is
the strongest biological oxidizing agent yet discovered, which allows
it to break apart molecules as stable as water.
The water-splitting reaction is catalyzed by the oxygen evolving
complex of photosystem II. This protein-bound inorganic complex
contains four manganese ions, plus calcium and chloride ions as
cofactors. Two water molecules are complexed by the manganese cluster,
which then undergoes a series of four electron removals (oxidations)
to replenish the reaction center of photosystem II. At the end of this
cycle, free oxygen (O2) is generated and the hydrogen of the water
molecules has been converted to four protons released into the
thylakoid lumen.
These protons, as well as additional protons pumped across the
thylakoid membrane coupled with the electron transfer chain, form a
proton gradient across the membrane that drives photophosphorylation
and thus the generation of chemical energy in the form of adenosine
triphosphate (ATP). The electrons reach the P700 reaction center of
photosystem I where they are energized again by light. They are passed
down another electron transfer chain and finally combine with the
coenzyme NADP+ and protons outside the thylakoids to NADPH. Thus, the
net oxidation reaction of water photolysis can be written as:
2H2O + 2NADP+ + 8 photons (light) 2NADPH + 2H+ + O2
The free energy change (ΔG) for this reaction is 102 kilocalories per
mole. Since the energy of light at 700 nm is about 40 kilocalories per
mole of photons, approximately 320 kilocalories of light energy are
available for the reaction. Therefore, approximately one-third of the
available light energy is captured as NADPH during photolysis and
electron transfer. An equal amount of ATP is generated by the
resulting proton gradient. Oxygen as a byproduct is of no further use
to the reaction and thus released into the atmosphere.
 Quantum models
In 2007 a quantum model was proposed by Graham Fleming and his
co-workers which includes the possibility that photosynthetic energy
transfer might involve quantum oscillations, explaining its unusually
high efficiency.]
According to Fleming there is direct evidence that remarkably
long-lived wavelike electronic quantum coherence plays an important
part in energy transfer processes during photosynthesis, which can
explain the extreme efficiency of the energy transfer because it
enables the system to sample all the potential energy pathways, with
low loss, and choose the most efficient one.
This approach has been further investigated by Gregory Scholes and his
team at the University of Toronto, which in early 2010 published
research results that indicate that some marine algae make use of
quantum-coherent electronic energy transfer (EET) to enhance the
efficiency of their energy harnessing.
 Photolysis in the atmosphere
Photolysis also occurs in the atmosphere as part of a series of
reactions by which primary pollutants such as hydrocarbons and
nitrogen oxides react to form secondary pollutants such as peroxyacyl
nitrates. See photochemical smog.
The two most important photodissociaton reactions in the troposphere
are firstly:
O3 + hν → O2 + O(1D) λ < 320 nm
which generates an excited oxygen atom which can react with water to
give the hydroxyl radical:
O(1D) + H2O → 2OH
The hydroxyl radical is central to atmospheric chemistry as it
initiates the oxidation of hydrocarbons in the atmosphere and so acts
as a detergent.
Secondly the reaction:
NO2 + hν → NO + O
is a key reaction in the formation of tropospheric ozone.
The formation of the ozone layer is also caused by photodissociation.
Ozone in the Earth's stratosphere is created by ultraviolet light
striking oxygen molecules containing two oxygen atoms (O2), splitting
them into individual oxygen atoms (atomic oxygen). The atomic oxygen
then combines with unbroken O2 to create ozone, O3. In addition,
photolysis is the process by which CFCs are broken down in the upper
atmosphere to form ozone-destroying chlorine free radicals.
 Astrophysics.
In astrophysics, photodissociation is one of the major processes
through which molecules are broken down (but new molecules are being
formed). Because of the vacuum of the interstellar medium, molecules
and free radicals can exist for a long time. Photodissociation is the
main path by which molecules are broken down. Photodissociation rates
are important in the study of the composition of interstellar clouds
in which stars are formed.
Examples of photodissociation in the interstellar medium are (hν is
the energy of a single photon of frequency ν):
 Atmospheric Gamma Ray Bursts
Currently orbiting satellites detect an average of about one gamma-ray
burst per day. Because gamma-ray bursts are visible to distances
encompassing most of the observable universe, a volume encompassing
many billions of galaxies, this suggests that gamma-ray bursts must be
exceedingly rare events per galaxy.
Measuring the exact rate of Gamma Ray bursts is difficult, but for a
galaxy of approximately the same size as the Milky Way, the expected
rate (for long GRBs) is about one burst every 100,000 to 1,000,000
years. Only a few percent of these would be beamed towards Earth.
Estimates of rates of short GRBs are even more uncertain because of
the unknown beaming fraction, but are probably comparable.
A gamma-ray burst in the Milky Way, if close enough to Earth and
beamed towards it, could have significant effects on the biosphere.
The absorption of radiation in the atmosphere would cause
photodissociation of nitrogen, generating nitric oxide that would act
as a catalyst to destroy ozone.
The atmospheric photodissasociation
•       N2 -> 2N
•       O2 -> 2O
•       CO2 -> C + 2O
•       H2O -> 2H + O
would yield
•       NO2 (consumes up to 400 Ozone molecules)
•       CH2 (nominal)
•       CH4 (nominal)
•       CO2
(incomplete)
According to a 2004 study, a GRB at a distance of about a kiloparsec
could destroy up to half of Earth's ozone layer; the direct UV
irradiation from the burst combined with additional solar UV radiation
passing through the diminished ozone layer could then have potentially
significant impacts on the food chain and potentially trigger a mass
extinction. The authors estimate that one such burst is expected per
billion years, and hypothesize that the Ordovician-Silurian extinction
event could have been the result of such a burst.
There are strong indications that long gamma-ray bursts preferentially
or exclusively occur in regions of low metallicity. Because the Milky
Way has been metal-rich since before the Earth formed, this effect may
diminish or even eliminate the possibility that a long gamma-ray burst
has occurred within the Milky Way within the past billion years. No
such metallicity biases are known for short gamma-ray bursts. Thus,
depending on their local rate and beaming properties, the possibility
for a nearby event to have had a large impact on Earth at some point
in geological time may still be significant.
 Multiple photon dissociation
Single photons in the infrared spectral range usually are not
energetic enough for direct photodissociation of molecules. However,
after absorption of multiple infrared photons a molecule may gain
internal energy to overcome its barrier for dissociation. Multiple
photon dissociation (MPD, IRMPD with infrared radiation) can be
achieved by applying high power lasers, e.g. a carbon dioxide laser,
or a free electron laser, or by long interaction times of the molecule
with the radiation field without the possibility for rapid cooling,
e.g. by collisions. The latter method allows even for MPD induced by
black body radiation, a technique called Blackbody infrared radiative
dissociation
References
Huff, Toby (2003). The Rise of Early Modern Science: Islam, China, and
the WesCambridge University Press
Russell McNeil, Ibn al-Baitar, Malaspina University-College.
Smith, A. L. (1997). Oxford dictionary of biochemistry and molecular
biology. Oxford [Oxfordshire]: Oxford University Press.
"Photosynthesis – the synthesis by organisms of organic chemical
compounds, esp. carbohydrates, from carbon dioxide using energy
obtained from light rather than the oxidation of chemical compounds."
D.A. Bryant & N.-U. Frigaard (2006). "Prokaryotic photosynthesis and
phototrophy illuminated". Trends Microbiol 14 (11): 488–96.
Nealson KH, Conrad PG (1999). "Life: past, present and future".
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 354 (1392): 1923–39..
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1692713.
"World Consumption of Primary Energy by Energy Type and Selected
Country Groups, 1980–2004" (XLS). Energy Information Administration.
July 31, 2006. http://www.eia.doe.gov/pub/international/iealf/table18.xls.
Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998). "Primary
production of the biosphere: integrating terrestrial and oceanic
components". Science 281 (5374): 237–40.
doi:10.1126/science.281.5374.237. PMID 9657713.
“Photosynthesis,” McGraw-Hill Encyclopedia of Science and Technology,
Olson JM (2006). "Photosynthesis in the Archean era". Photosyn. Res. 88 (2)
Buick R (2008). "When did oxygenic photosynthesis evolve?". Philos.
Trans. R. Soc. Lond., B, Biol. Sci. 363 (1504)
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid.
Rodríguez-Ezpeleta, Naiara; Henner Brinkmann, Suzanne C Burey,
Béatrice Roure, Gertraud Burger, Wolfgang Löffelhardt, Hans J Bohnert,
Hervé Philippe, B Franz Lang (2005-07-26). "Monophyly of primary
photosynthetic eukaryotes: green plants, red algae, and glaucophytes".
Current Biology: CB 15 (14) http://www.ncbi.nlm.nih.gov/pubmed/.
Gould SB, Waller RF, McFadden GI (2008). "Plastid evolution". Annu Rev
Plant Biol 59: 491–517..
Anaerobic Photosynthesis, Chemical & Engineering News, Kulp TR, Hoeft
SE, Asao M, Madigan MT, Hollibaugh JT, Fisher JC, Stolz JF, Culbertson
CW, Miller LG, Oremland RS (2008). "Arsenic(III) fuels anoxygenic
photosynthesis in hot spring biofilms from Mono Lake, California".
Science 321 (5891)