Structure of reaction intermediate

Figure 1.20 The structures of reaction intermediates that correspond to Figure 1.19 [22].

The purpose of this section is to describe recent achievements in time-resolved X-ray diffraction from liquids. Keeping the scope of the present chapter in mind, neither X-ray diffraction from solids nor X-ray absorption will be discussed. The majority of experiments realized up to now were performed using optical excitation, although some recent attempts using infrared excitation were also reported. The main topics that have been studied are (1) visualization of atomic motions during a chemical reaction, (2) structure of reaction intermediates in a complex reaction sequence, (3) heat propagation in impulsively heated liquids, and (4) chemical hydrodynamics of nanoparticle suspensions. We hope that the actual state-of-the-art will be illustrated in this way. 

Li Y-F, Y Hata, T Fujii, T Hisano, M Nishihara, T Kurihara, N Esaki (1998) Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. J Biol Chem 273 15035-15044. 

Visualization of Atomic Motions Structure of Reaction Intermediates... 

The unique advantage of the Laue method is that data can be collected rapidly enough to give a freeze-frame picture of the crystal s contents. Typical X-ray data are averaged over the time of data collection, which can be hours, days, or even months, and over the sometimes large number of crystals required to obtain a complete data set. Laue data has been collected with X-ray pulses shorter than 200 picoseconds. Such short time periods for data collection are comparable to half-times for chemical reactions, especially those involving macromolecules, such as enzymatic catalysis. This raises the possibility of determining the structures of reaction intermediates. 

The Incorporation of Added Metal Atoms into Structures of Reaction Intermediates on Catalytic Metal Surfaces... 

The kinetics of reactions on metal surfaces is strongly affected by the structures of reaction intermediates, especially by the incorporated metal adatoms in their structures (Sect 11.5). hi the mid 1970s, Falconer and Madix observed a surface- kinetic explosion for the decomposition of formate and acetate adsorbed on the Ni (110) surface [23, 24], Recently, with the help of STM, TPRS, and XPS, we were able to determine that Ni atoms are incorporated into the structures of the carboxylate intermediates. Remarkably, the incorporation of metal atoms into the carboxylate structure is an important aspect of the origin of the kinetic explosion. 

The first crystal structure of a PLD (from Streptomyces sp.) has been published (I. Leiros, 2000) and is shown in Fig. 11. The positions of two active-site histidines, His-170 and His-448, are indicated and it is proposed that His-170 is the more likely residue to act as the nucleophile and thus be covalently modified during catalysis. This proposal has been confirmed more recently (I. Leiros, 2004) where crystal structures of reaction intermediates were obtained including identification of the catalytic water molecule. 

Obayashi, E., S. Takahashi, and Y. Shiro (1998). Electronic structure of reaction intermediate of cytochrome P450nor in its nitric oxide reduction. 

Figure 3.48. The activation of NH3 by Pt(lll). Reaction energy paths and structures of reaction intermediates and their corresponding transition states. Reaction energy diagram for the transformation of NH3 to Nad.-------NHs --------NHs+Oads NHs+OHads -...

The H-H and C-H activation reactions at lutetium hydride Cp2LuH and the plausible electronic structure of reaction intermediates have been considered using the theory of isolobal analogy of frontier orbitals [52]. 

Coincon, M., Wang, W., Sygusch, J., and Seah, S. Y. K., Crystal structure of reaction intermediates in pyruvate class II aldolase Substrate cleavage, enolate stabilization, and substrate specificity. /. Biol. Chem. 2012,287 (43), 36208-36221. 

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