Reaction mechanisms femtosecond studies

A fundamental goal of chemical research has always been to understand the reaction mechanisms leading to specific reaction products. Reaction mechanisms, in turn, are a consequence of the structural dynamics of molecules participating in the chemical process, with atomic motions occurring on the ultrafast timescale of femtoseconds (10 s) and picoseconds (10" s). Although kinetic studies often allow reaction mechanisms as well as the kind and properties of reaction intermediates to be determined, the obtained information is not sufficient to deduce the ultrafast molecular dynamics. Because these ultrafast motions are the essence of every chemical process, detailed knowledge about their nature is of fundamental importance. 

Yang H, Asplund MC, Kotz KT, Wilkens MJ, Frei H, Harris CB. Reaction mechanism of silicon-hydrogen bond activation studied using femtosecond to nanosecond IR spectroscopy and ab initio methods. J Am Chem Soc 1998 120(39) 10154-10165. 

We first discuss the overall chemical process predicted, followed by a discussion of reaction mechanisms. Under the simulation conditions, the HMX was in a highly reactive dense fluid phase. There are important differences between the dense fluid (supercritical) phase and the solid phase, which is stable at standard conditions. Namely, the dense fluid phase cannot accommodate long-lived voids, bubbles, or other static defects, since it has no surface tension. Instead numerous fluctuations in the local environment occur within a timescale of 10s of femtoseconds. The fast reactivity of the dense fluid phase and the short spatial coherence length make it well suited for molecular dynamics study with a finite system for a limited period of time. Under the simulation conditions chemical reactions occurred within 50 fs. Stable molecular species were formed in less than a picosecond. We report the results of the simulation for up to 55 picoseconds. Figs. 11 (a-d) display the product formation of H2O, N2, CO2 and CO, respectively. The concentration, C(t), is represented by the actual number of product molecules formed at the corresponding time (. Each point on the graphs (open circles) represents a 250 fs averaged interval. The number of the molecules in the simulation was sufficient to capture clear trends in the chemical composition of the species studied. These concentrations were in turn fit to an expression of the form C(/) = C(l- e ), where C is the equilibrium concentration and b is the effective rate constant. From this fit to the data, we estimate effective reaction rates for the formation of H2O, N2, CO2, and CO to be 0.48, 0.08,0.05, and 0.11 ps, respectively. 

The impact which femtosecond spectroscopy is also having on the study of the reaction mechanisms of biological systems is finally illustrated by an investigation of the cis/trans isomerization of rhodopsin 66 —> 67,... 

The reaction pathways by which the net transfer of a hydrogen atom from an amine to a photoexcited ketone has been extensively examined in the nanosecond [23, 25-30], picosecond [20, 22, 31-33], and femtosecond [24] time domains. The following mechanism, as it pertains to the photochemical reduction of benzophenone (Bp) by N, A-dimethylaniline (DMA), is derived from these numerous studies. Only an overview of the mechanism will be presented. The details of the studies leading to the mechanism will not be given for specifics, the reader is referred to the original literature. 

The product we monitor is again the I atom using femtosecond-resolved mass spectrometry (the other product is the Bzl species). We also monitor the initial complex evolution. The initial femtosecond pulse prepares the system in the transition state of the harpoon region, that is, Bz+h. The iodine atom is liberated either by continuing on the harpoon PES and/or by electron transfer from iodine (I2-) to Bz+ and dissociation of neutral I2 to iodine atoms. We have studied the femtosecond dynamics of both channels (Fig. 17) by resolving their different kinetic energies and temporal behavior. The mechanism for the elementary steps of this century-old reaction is now clear. 

Three main tendencies have been underlined in recent studies of structure and action mechanism ofbacterial photosynthetic reaction centers. The crystallographic structure of the reaction centers from Rps. viridis and Rb. spheroids was initially determined to be 2.8 and 3 A resolutions (Michel and Deisenhofer et al., 1985 Allen et al., 1986). Resolution and refinement of these structures have been subsequently extended to 2.2, 2.3 and 2.6 A. (Rees et al., 1989 Stowell et al., 1997, Fyfe and Johns, 2000 Rutherford and Faller, 2001). Investigations of the electronic structure of donor and acceptor centers in the ground and exited states by modern physical methods with a combination ofpico-and femtosecond kinetic techniques have become more precise and elaborate. Extensive experimental and theoretical investigations on the role of orbital overlap and protein dynamics in the processes of electron and proton transfer have been done. All the above-mentioned research directions are accompanied by extensive use of methods of sit-directed mutagenesis and substitution of native pigments for artificial compounds of different redox potential. 

Earlier studies on dye-sensitized Ti02 reported nanosecond time constants for the injection kinetics [16, 40-42]. These results were obtained indirectly from the measurement of the injection quantum yield and implicitly assumed that the interfacial electron transfer reaction was competing only with the decay of the dye excited state. Other studies were based on the same assumption but used measurements of the dye fluorescence lifetime, which provided picosecond-femtosecond time resolution [43-45]. Direct time-resolved observation of the buildup of the optical absorption due to the oxidized dye species S+ has been employed in more recent studies [46-51]. This appears to be a more reliable way of monitoring the charge injection process as it does not require any initial assumption on the sensitizing mechanism. 

Photo-induced reaction on a metal surface usually consists of several elementary reactions and it is difficult to model the whole reaction process. However, any reactions need to be triggered by electronic excitation. As stated in Section 20.1.4, the major mechanism is indirect excitation thus we focus on modeling the indirect excitation reaction. Since desorption from the surface is one of the simplest processes and can be a prototype for other complex surface reactions, DIET or DIME are clearly the best to study [10, 48, 53, 57, 96]. In photochemistry, continuous wave or nanosecond lasers lead to DIET, where desorption increase linearly with fluence. In contrast, the DIMET process is caused by intense and short laser pulses on the picosecond or femtosecond time scale, with nonlinear dependence on fluence. Since the fluence is proportional to the number of created hot electrons in the bulk, linear... 

This chapter has gathered together the current understanding of retinal photoisomerization in visual and archaeal rhodopsins mainly from the experimental point of view. Extensive studies by means of ultrafast spectroscopy of visual and archaeal rhodopsins have provided an answer to the question, What is the primary reaction in vision We now know that it is isomerization from 11-cis to all-trans form in visual rhodopsins and from all-trans to 13-cis form in archaeal rho-dopsin. Femtosecond spectroscopy of visual and archaeal rhodopsins eventually captured their excited states and, as a consequence, we now know that this unique photochemistry takes place in our eyes and in archaea. Such unique reactions are facilitated in the protein environment, and recent structural determinations have further improved our understanding on the basis of structure. In parallel, vibrational analysis of primary intermediates, such as resonance Raman and infrared spectroscopies, have provided insight into the isomerization mechanism. 

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