Defining And Understanding Femtochemistry Biology Essay


Chemical reactions are ultrafast processes, and the study of these elementary chemical steps has been termed "femtochemistry" . A The essence of the chemical industry and indeed of life is the making and breaking of molecular bonds. The elementary steps in bond making and breaking occur on the time scale of molecular vibrations and rotations, the fastest period of which is ≈10 femtoseconds (10−14 s). Chemical reactions are, therefore, ultrafast primary aim of this field is to develop an understanding of chemical reaction pathways at a molecular level. Given this information, one can better conceive of new methods to control the outcome of a chemical reaction. Because chemical reaction

pathways for all but the simplest of reactions are complex, this field poses challenges both theoretically and experimentally. Nevertheless, much progress is being made, and systems as complex as biomolecules can now be investigated in great detail. In the following, we will present results from theoretical and experimental efforts to probe deeply into the nature of chemical reactions in complex systems. The topic of femtochemistry is surveyed from both theoretical and experimental points of view. Theoretical approaches for treating femtosecond chemical phenomena in condensed phases are featured along with prospects for laser-controlled chemical reactions by using tailored ultrashort chirped pulses. An experimental study of the photoisomerization of retinal in the protein bacteriorhodopsin is discussed with an aim to gain insight into the potential energy surfaces on which this remarkably efficient and selective reactions proceeds.Thus " Femtochemistry is the science that studies chemical reactions on extremely short timescales, approximately 10-15 seconds (one femtosecond, hence the name)."

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The actual atomic motions involved in chemical reactions had never been observed in real time despite the rich history of chemistry over two millennia. Chemical bonds break, form, or geometrically change with awesome rapidity. Whether in isolation or in any other phase, this ultrafast transformation is a dynamic process involving the mechanical motion of electrons and atomic nuclei. The speed of atomic motion is ~1 km/second and, hence, to record atomic-scale dynamics over a distance of an angström, the average time required is ~100 femtoseconds (fs). The very act of such atomic motions as reactions unfold and pass through their transition states is the focus of the field of femtochemistry. With fs time resolution we can "freeze" structures far from equilibrium and prior to their vibrational and rotational motions, or reactivity.

In over a century of development, ultrafast pulsed-laser techniques have made direct exploration

of this temporal realm a reality. A femtosecond laser probe pulse provides the shutter speed for freezing nuclear motion with the necessary spatial resolution. The finite speed of light translates the difference in path length into a difference in arrival time of the two pulses at the sample; 1 micron corresponds to 3.3 fs. The individual snapshots combine to produce a complete record of the continuous time evolution-a motion picture, or a movie-in what may be termed femtoscopy.

In femtochemistry, studies of physical, chemical, or biological changes are at the fundamental

timescale of molecular vibrations: the actual nuclear motions. Moreover, the fs timescale is unique for the creation of coherent molecular wave packets on the

atomic scale of length, a basic problem rooted in the development of quantum mechanics and the duality of matter. Superposition of a number of separate wave functions of appropriately chosen phases can produce the spatially localized and moving coherent wave packet. The packet has a well-defined (group) velocity and position which now makes it analogous to a moving classical marble, but at atomic resolution, and without violation of the uncertainty principle. In this way, localization in time and in space are simultaneously achievable for reactive and nonreactive systems.

Fig. 1 Timescales. The relevance to physical, chemical, and biological changes. The fundamental limit of the vibrational motion defines the regime for femtochemistry.

This powerful concept of coherence lies at the core of femtochemistry and was a key advance in

observing the dynamics. The realization of its importance and its detection by selectivity in both preparationand probing were essential in all studies, initially of states and orientations, and culminating inatomic motions in reactions. Laser-induced fluorescence was the firstprobe used, but later we invoked mass spectrometry and nonlinear optical techniques. Now, numerous methods of probing are known and used in laboratories around the world; Coulomb explosion is the most recent powerful probe for arresting reactive intermediates. Applications of femtochemistry have spanned the different types of chemical bonds-covalent, ionic, dative and metallic, and the weaker ones, hydrogen and van der Waals bonds. The studies have continued to address the varying complexity of molecular systems, from diatomics to proteins and DNA.

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Fig. 2 Areas of study in femtochemistry.

Founder(Father) of Femtochemistry:

Femtochemistry, a word coined by Nobel Prize winner "Dr. Ahmed Zewail," describes the field of chemistry that studies the making and breaking of chemical bonds.  Chemical bonds are the glue which actually holds atons together.  Actually understanding these bonds gives scientists a better understanding of how chemical reactions take place.  And understanding how chemical reactions take place may allow scientists to manipulate these bonds insuch a way as to create entirely new molecules. 

However, to actually study these bonds taking place (or being destryoed) needs a camera. A fast one. An extremely fast one.  One so fast that it could take stop-action pictures of two atoms approaching each other and forming a chemical bond.  How fast is that? A few hundred femtoseconds.  And what's a femtosecond?  Fast. One femtosecond is one millionth of one billionth of a second.  For example, if you moved at the speed of light for one femtosecond, you'd only travel 30 micrometers, or 0.0012 inches.  In fact, a femtosecond is so quick (or short) that light couldn't even get a third of the way across a human hair.

So Dr. Ahmed created a camera quick enough to "photograph" these chemical binds taking place. Now working at Caltech, Dr. Ahmed and other scientists are studying various biological systems, such as how oxygen binds to hemoglobin in the blood or how retinal in the eye triggers excitation of the optical nerve to create vision.  Dr. Ahmed's current research is looking into how his work in femtochemistry can create new disease treatments and even prevention.


The range of applications to different systems and phases in many laboratories around the world is extensive and beyond the purpose of this report. Let us examine few of them:

Elementary reactions and transition states:

The focus here was on the studies of elementary reactions. Some of these have already been discussed above. The dynamics are generally of three classes:

1. Dynamics of bond breakage

2. Dynamics of the (saddle-point) transition state

3. Dynamics of (bimolecular) bond breakage/bond formation

Organic chemistry:

With the integration of mass spectrometry into femtochemistry experiments, the field of organic reaction mechanisms became open to investigations of multiple transition states and reaction intermediates.The technique of fs-resolved kinetic-energy-time-of-flight (KETOF) provided a new dimension to the experiment-correlations of time, speed, and orientation which elucidate the scalar and vectorial dynamics. The examples of reactions include:

1. Isomerization reactions

2. Pericyclic addition and cleavage reactions

3. Diels-Alder/sigmatropic reactions

4. Norrish-type I and II reaction

5. Nucleophilic substitution (SN) reactions

6. Extrusion reactions

7. β-Cleavage reactions

8. Elimination reactions

9. Valence structure isomerization

10. Reactive intermediates

11. Electron and proton transfer

Here, we examined both bimolecular and intramolecular electron transfer reactions, and these studies were the first to be made under solvent-free conditions. We also studied the transfer in clusters and in solutions. For proton transfer, three classes of reactions were of interest, those of bimolecular and intramolecular reactions, and those involving double proton transfer (base-pair models):

1. Bimolecular electron transfer reactions

2. Intramolecular electron transfer and folding reactions

3. Acid-base bimolecular reactions

4. Intramolecular hydrogen-atom transfer

5. Tautomerization reactions: DNA base-pair models

Inorganic and atmospheric chemistry:

We extended the applications of femtochemistry to complex inorganic reactions of organometallics. Organometallic compounds have unique functions and properties which are determined by the dynamics of metal-metal (M-M) and metal-ligand (M-L) bonding. The timescales for cleavage of such bonds determine the product yield and the selectivity in product channels. They also establish the nature of the reactive surface: ground-state versus excited-state chemistry. Similarly, we studied the dynamics of chlorine atom production from OClO, a reaction of relevance to ozone depletion.

The mesoscopic phase: clusters and nanostructures:

We have studied different types of reactions under microscopic solvation condition in clusters. These include:

1. Reactions of van der Waals complexes

2. Unimolecular reactions

3. Bimolecular reactions

4. Recombination, caging reactions

5. Electron and proton transfer reactions

6. Isomerization reactions

The condensed phase: dense fluids, liquids, and polymers:

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In this area of research, we have focused our efforts on the study of reactions in dense fluids and comparison with dynamics in liquids. By varying the solvent density, we could study the femtosecond dynamics from gas-phase conditions to the condensed phase of liquid-state density. Accordingly, we could observe the influence of solute-solvent collisions on reaction dynamics in real time. We also did studies in liquid solutions for some of the systems examined in the gas phase: bond breakage and caging; valence structure isomerization; and double proton transfer. Similarly, we studied systems of nanocavities and polymers. Some highlights include:

1. Dynamics of the gas-to-liquid transition region (T1 and T2)

2. Dynamics of bimolecular (one-atom) caging

3. Dynamics of microscopic friction

4. Dynamics in the liquid state

5. Dynamics of energy flow in polymers

6. Dynamics of small and large molecules in cyclodextrins


Three areas of study are discussed here:

1. Transient structures from ultrafast electron diffraction (UED):

Electron diffraction of molecules in their ground state has been a powerful tool over the past 50 years, and both electron and X-ray methods are now being advanced in several laboratories for the studies of structural changes. We have reported the latest advance in UED, by which major challenges were surmounted: the very low number densities of gas samples; the absence of the long-range order that is present in crystals, which enhances coherent interference; and the daunting task of determining in situ the zero-of-time when diffraction changes are on the ps and sub-ps timescale. With UED, we have been able to study molecular structures and branching ratios of final products on the ps timescale. The change in diffraction from before to after a chemical reaction was observe. This leap in our ability to record structural changes on the ps and shorter timescales bodes wellfor many future applications to complex molecular systems, including biological systems. We havecompleted a new apparatus equipped with diffraction detection and also with mass spectrometry. Thisuniversal system is capable of studying complex systems in the gas and other phases. It holds great promise with opportunities for the future.

Biological dynamics:

There have been important contributions to femtobiology, and these include: studies of the elementarysteps of vision; photosynthesis; protein dynamics; and electron and proton transport in DNA. In pro-teins such as those of photosynthetic reaction centers and antennas, hemoglobins, cytochromes, and rhodopsin, a femtosecond event, bond-breaking, twisting, or electron transfer occurs. There exist global and coherent nuclear motions, observed in these complex system


The key to the explosion of research can perhaps be traced to three pillars of femtochemistry.

1. Time resolution: Reaching the transition-state limit:

Three points are relevant:

(i) The improvement of nearly ten orders of magnitude in time resolution, from the (milli)microsecond timescale to present femtosecond resolution, opened the door to studies of new phenomena and to new discoveries;

(ii) The transition state, the cornerstone of reactivity, could be clocked as a molecular species, providing a real foundation to the hypothesis of Arrhenius, Eyring, and Polanyi for ephemeral species and leading the way to numerous new studies. Extensions will be made to study transition-state dynamics in complex systems, but the previous virtual status of the transition state has now given way to experimental reality;

(iii) Inferences deduced from "rotational periods" as clocks in uni- and bimolecular reactions can now be replaced by the actual clocking of the nuclear (vibrational) motion. This is particularly important when a chemical phenomenon such as "concertedness" is involved or the timescale of complexes or intermediates is many vibrational periods. Moreover, the uncertainty principle was thought to represent a severe limit of the utility of shorter time resolution; coherence was not part of the thinking in deciphering fs nuclear motion, as detailed above and summarized below:

Atomic-scale resolution:

Two points are relevant:

(i) The transition from kinetics to dynamics. On the femtosecond timescale, one can see the coherent nuclear motion of atoms-oscillatory or quantized steps instead of exponential decays or rises. This was proved to be the case for bound, quasi-bound, or unbound systems and in sim- ple (diatomics) and in complex systems (proteins);

(ii) The issue of the uncertainty principle. The thought was that the pulse was too short in time, thus broad in energy by the uncertainty principle ∆t∆E ~h but localization is consistent with the two uncertainty relationships, and coherence is the key.h The energy uncertainty ∆E should be compared with bond energies: ∆E is 0.7 kcal/mol for a 60 fs pulse.

Generality of the approach:

Three points are relevant:

(i) In retrospect, the femtosecond timescale was just right for observing the "earliest dynamics" at the actual vibrational timescale of the chemical bond.

(ii) The time resolution offers unique opportunities when compared with other methods. Processes often appear complex because we look at them on an extended timescale, during which many steps in the process are integrated.

(iii) The methodology is versatile and general, as evidenced by the scope of applications in different phases and of different systems. It is worth noting that both excited and ground state reactions can be studied. It has been known for some time that the use of multiple pulses can populate the ground state of the system and, therefore, the population and coherence of the system can be monitored. The use of Coherent Anti-Stokes Raman Spectroscopy (CARS), Degenerate Four-Wave Mixing (DFWM), simulated Raman scattering (SRS), π-pulses, or the use of direct IR excitation are some of the approaches possible.


As the ability to explore shorter and shorter timescales has progressed from the millisecond to the present stage of widely exploited femtosecond capabilities, each step along the way has provided surprising discoveries, new understanding, and new mysteries. Our desperate efforts in this field over a century have develop areas of study and the scope of applications. Developments will continue, and new directions of research will be pursued. Surely, studies of transition states and their structures in chemistry and biology will remain active for exploration in new directions, from simple systems to complex enzymes and proteins, and from probing to controlling of matter-femtochemistry, femtobiology, and femtophysics. Additionally, there will be studies involving the combination of the "three scales", namely time, length, and number. We should see extensions to studies of the femtosecond dynamics of single molecules and of molecules on surfaces (e.g., using STM). Combined time/length resolution will provide unique opportunities for making the important transition from molecular structures to dynamics and to functions. We may also see that all of femtochemistry can be done at micro-to-nano Kelvin temperatures, utilizing lasers and other cooling techniques. It seems that on the femtosecond to attosecond timescale we are reaching the "inverse" of the Big Bang time, with the human heartbeat "enjoying" the geometric average of the two limits. Perhaps we are approaching a universal limit of time!