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(Chem) Spectroscopy: Photodissociation

 
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Joseph Cho
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PostPosted: Fri Dec 15, 2006 4:20 pm    Post subject: (Chem) Spectroscopy: Photodissociation Reply with quote






Photodissociation
by Joseph Cho, Georgetown University
15 December 2006

Have you ever wondered how living organisms, such as plants, gather energy from the sun? The most common answer you may hear is the word “photosynthesis” - the process by which light energy becomes chemical energy. While this answer is correct and very important, there are also other processes that occur to make life possible. One of these processes is the interaction between invisible light and the molecules of living cells.
Ultraviolet (UV) radiation is a special type of invisible light that biological molecules absorb. You may be wondering what exactly happens when these molecules absorb such radiation. When a molecule absorbs ultraviolet radiation, an electron is promoted from its ground state energy level (low) to an excited state energy level (high). An excited electron can either return to its ground state by releasing energy in the form of a photon or by transforming electronic energy into vibrational energy. If vibrational energy increases enough, the molecule breaks apart, resulting in a process known as photodissociation. This process allows promoted electrons to return to the ground state energy level and creates two molecular fragments. Photodissociation may also prevent electrons from staying in an “excited” energy state for too long which could be harmful for a living cell.
To get a better picture of what happens during photodissociation, think of the biological molecule as a pinball machine and the electrons as the balls inside. The ultraviolet radiation is like the spring plunger that launches the balls up to the top of the pinball machine. In some instances the ball goes straight to the top of the machine and in other cases the ball only travels to the middle of the machine. A ball at the top can either roll to the bottom of the machine (game over…try again ) or roll to the middle where it may bounce between two obstacles, earning you many point . For the sake of illustration, pretend that this particular pinball machine is defective and the only way a ball in the middle of the machine can get to the bottom is by bouncing around (vibrating) until the pinball machine breaks in half. We are now left with a ball at the bottom of a broken pinball machine. While in real-life a broken pinball machine is of little use, in living cells these “broken pinball machine pieces” may actually be more valuable. Now that we have this pinball machine analogy, let’s return to the biological molecule and take a deeper look.
There are several excited state energy levels that electrons in a biological molecule can occupy. Two notable levels are the ππ* (pi pi star) and π* (pi sigma star) excited states. The energy levels of these two excited states vary with different molecules. The energy levels of these two excited states also vary depending on the bond length the excited electrons occupy. In some cases the ππ* excited state is higher in energy than the π* excited state and in other cases the opposite is true. The electrons of a biological molecule can be promoted to either excited state. If electrons are promoted to the ππ* excited state they can transfer to the π* excited state by absorbing more energy (UV radiation) or by crossing over at special places called conical intersection. These intersections are where the two energy levels overlap due to the varying bond lengths that the two excited electrons occupy. Once the electrons are in the π* excited state, photodissociation may occur.


Recent studies conducted by scientists at the University of Bristol demonstrate the role of π* excited states play in the photodissociation of biological molecules. By working backwards from the broken molecule pieces these researchers were able to show that there are discrete sets of broken pieces that corresponded to different vibrational energies of the biological molecule in the π* excited state. In terms of the pinball analogy, scientists were able to extrapolate how the balls were bouncing around prior to the pinball machine breaking by observing the broken pieces. Furthermore when many pinball machine pieces were compared with one another, small groups appeared. The groups were defined by the direction these broken pinball machine pieces recoiled and the initial speed of the broken pieces. The different groups of pinball machine pieces formed because the balls were bouncing at different energy levels.
It is now understood that the π* excited state plays a key role in photodissociation. In corroboration, discrete sets of broken molecules arise from the various vibrational levels of the π* excited state. However the purpose of photodissociation in biological molecules remains unclear. While there is speculation that photodissociation occurs to create new molecules for the living cell or to protect it from dangerous photoreactions, clear evidence is lacking. Until further studies confirm the purpose of photodissociation, we can only assume that there must be some importance that drives biological molecules to undergo this process. After all, it would be absurd to assume that Mother Nature is in the business of breaking pinball machines just for fun.

Reference:
The Role of π* Excited States in the Photodissociation of Heteroaromatic Molecules
M. N. R. Ashfold,* B. Cronin, A. L. Devine, R. N. Dixon, M. G. D. Nix
Science 16 June 2006:
Vol. 312. no. 5780, pp. 1637 - 1640
DOI: 10.1126/science.1125436


Questions to explore further this topic:

What is light?

http://imagers.gsfc.nasa.gov/ems/visible.html
http://cse.ssl.berkeley.edu/light/measure.html

What is photosynthesis?

http://www.emc.maricopa.edu/fa.....ookPS.html
http://www.cix.co.uk/~argus/Dr.....mation.htm

What is light energy?

http://imagine.gsfc.nasa.gov/d.....atoms.html

What is chemical energy?

http://kevingilmore46407.tripod.com/id13.html

What is invisible light?

http://imagine.gsfc.nasa.gov/d.....ctrum.html
http://www.mhschool.com/scienc.....i?quiz=101

What are molecules?

http://en.wikipedia.org/wiki/Molecule

What are cells?

http://www.cellsalive.com/

What is ultraviolet (UV) radiation?

http://imagers.gsfc.nasa.gov/ems/uv.html

What are electrons?

http://web.jjay.cuny.edu/~acarpi/NSC/3-atoms.htm
http://www.aip.org/history/electron/jjhome.htm

What are ground state and excited state energy levels?

http://imagine.gsfc.nasa.gov/d.....atoms.html


What is a photon?

http://www.colorado.edu/physic.....sers2.html
http://www.play-hookey.com/opt.....stics.html

What is electronic energy?

http://www.hydepark.gp.school......ectrum.htm

What is vibrational energy?

http://www.pha.jhu.edu/~ggaspa.....kinerg.htm

What is photodissociation?

http://en.wikipedia.org/wiki/Photodissociation

What is a pinball machine?

http://en.wikipedia.org/wiki/Pinball

What is a chemical bond?

http://hyperphysics.phy-astr.g...../bond.html

What is the bond length?

http://www.science.uwaterloo.c.....ondel.html

What is a conical intersection?

http://www.ch.ic.ac.uk/hunt/re....._ci_2.html

GAMES

http://www.nasa.gov/audience/f.....index.html
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adedios
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Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Mon Dec 15, 2008 1:05 pm    Post subject: Reply with quote

Dianne O. Atienza Molecular Spectroscopy Paper

Femtosecond Raman Spectroscopy Tracking of Structural Evolution in Stilbene Photoisomerization


Chemical reactions are often associated with molecular rearrangements, energy barrier that impedes the product formation and brief stops in energy valleys along the way from reactants to products. However, continuous observation as to how these molecules choreograph to form a product are seldom observed and is often limited to an oversimplified reaction coordinate that usually neglects significant molecular motions across the molecular framework.

Since early 20th century, chemical reactions are only depicted as how energy of molecules increase or decrease as bonds are broken or formed but none or only few gave a detailed picture of how reactants orient to proceed to the product formation. Such hurdle can be attibuted to the extremely short time reacting molecules spend in the unstable regions of reaction pathways so majority of the experimental observations of reacting molecules were made on relatively stable molecules which are in usual cases the intial and final states of reactants and products.

However, it was found out that molecular rearrangements in chemical reactions occur on a time comparable to nuclear vibrational periods (10 fs to 1 ps). Thereby, making spectroscopy particularly Raman spectroscopy a viable means in observing molecular rearrangement.

In the paper published by Takeuchi et. al., they have presented the structural evolution of cis-stilbene ultrafast photoisomerization using femtosecond time-domain Raman Spectroscopy. The femtosecond time- domain offers effective probing of complicated multidimensional reaction coordinate which cannot be tracked by conventional vibrational spectroscopy such as a typical Raman spectroscopy. Conventional spontaneous Raman is applicable only to pico or slower processes that utilizes long and narrow-band pulses (signals) to achieve sufficient resolution (output). Recently, this drawback was resolved by the introduction of stimulated Raman process with femtosecond pulses.

Takeuchi et.al. chose the well studied ultrafast olefinic photoisomerization of cis-stilbene which exhibits nearly a barrierless bond twisting in the excited state that is complete within ~ 1 ps. They mapped out vibrational motions not directly involved in the twisting of its double and consider probing unstable regions related to twisting of C=C bonds to determine the structural changes made by cis-stilbene.

Unstable regions of a reaction coordinate (path) can be probed by determining the connections between what is happening in the reaction and the more stable states. In a light assisted reaction, photo excites the molecules from stable ground states to higher electronic excited states. This light absorption will be used to probe the difference between ground and excited states and if enough points on the ground-state surface is determined, this will enable the mapping of the excited-state surface. Takeuchi et. al work, on the otherhand, has the reaction taking place on the excited state surface while the ground state surface serves as the point of reference. The region of the accessible part of the upper surface directly above the region of stability on the reference surface is the so called Frank-Codon region. A light pulse excited the stilbene up to this region and after a short delay, another light pulse was employed but this time is to determine the progress of the reaction in the reaction coordinate.

In order to map the unstable regions of the potential energy surface, spectroscopic methods such as Raman Spectroscopy employ more than one absorption or emission event and/ or both. The closer or more comparable the time resolution in mapping the unstable regions of the potential energy surface the more accurate and reliable will be the observed result. Takeuchi et.al. used femtosecond time domain enabling them not only to follow the reaction coordinate but also confirm these observations with the changes in the vibrational modes of stilbene during the twisting of the double bonds from cis to trans conformation. They probed the vibrational motion in terms of time instead of frequency which enables them to observe the evolution of vibration.

This work of Takeuchi et. al. provides as a new approach and perspective in understanding how each atom in the reactants moves during product formation. Also, this shows the integration of a new method that will enable us to track the pathways a molecule undergoes to transform itself to its product form.

*What is Spectroscopy?

http://www.ipedia.net/information/spectroscopy

http://imagine.gsfc.nasa.gov/d.....scopy.html

*What is Raman Spectroscopy?

http://www.princetoninstrument.....raman.aspx

*What is photoisomerization?

http://www.chemistrydaily.com/.....merization

*What is Frank Codon region?

http://www.smallscalechemistry.....oscopy.pdf

http://ocw.mit.edu/NR/rdonlyre...../w4_a2.pdf

*What is a stilbene?

http://faculty.physics.tamu.ed.....ilbene.pdf

*What is Potential Enegy Surface?

*http://www.cmbi.kun.nl/tutorials/cheminf/mopac/rxc.html

*http://www.phys.uit.no/~inge/ttp5/concept-of-pes.htm

Main Reference

Takeuchi et.al. Spectroscopic Tracking of Structural Evolution in Ultrafast Stilbene Photoisomerization. Science 322, 1073 (2008)

Blank, D. A. A Sideways Glance at Chemical Reactivity. Science 322, 1056 (2008)
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