Active sites face atoms

Example Yon can monitor improper torsion angles to determine wh ich side of a substrate m olecn le faces the active site of a protein. Select three atoms on the substrate molecule and a fourth in the active site. These atom s define an improper torsion angle. Save th is selection as a named selection. Then observe a plot of this improper torsion angle (in the Molecular Dynam ics Results dialog... 

Adsorbed molecules are more strongly held at the sites where the weakest metal-metal bonding is to be found, and these conespond to the active sites of Langmuir. A demonstration of this effect was found in smdies of the adsorption of H2S from a H2S/H2 mixture on a single crystal of copper of which die separate crystal faces had been polished and exposed to die gas. The formation of copper sulphide first occuiTed on die [100] and [110] planes at a lower H2S partial pressure dran on die more densely packed [111] face. Thus die metal atoms which are less strongly bonded to odrer metal atoms can bond more strongly to die adsorbed species from die gas phase. 

NADH. These experiments were pioneering with respect to contemporary enzymology, especially with regard to early recognition that coenzymes are held within enzyme active sites in stereochemically preferred ways. One typically utilizes NADH that contains a tritium or deuterium atom in the 4R or 45 position, and the success or failure of substrate deuteration/tritiation indicates the stereochemistry. Westheimer has tabulated the known examples of dehydrogenases that exhibit specificity for a particular face of NADH. Creighton and Murthy have reproduced this tabulation in their comprehensive review on the stereochemistry of enzyme-catalyzed reactions at carbon. 

The detection of other molecules, such as ammonia, requires the use of a porous catalytic metal. To obtain a gas response from the NH3 molecule, it is believed that active sites of triple points are required where the molecules are in contact with the metal, insulator, and ambient [30, 31]. It has been shown that gas species such as hydrogen atoms or protons also diffuse out onto the exposed oxide surface in between the metal grains [Figure 2.1(b)] [32, 33]. Furthermore, Lofdahl et al. have performed experiments that provide clear evidence that hydrogen atoms or protons also diffuse under the metal from the triple point [34]. The hollow structure of the metal surface facing the insulator has been revealed by Abom et al. [35]. 

In contrast, structure-insensitive reactions are those for which turnover frequency under fixed conditions does not depend or depends slightly on the surface crystalline anisotropy of clusters of varying size or of single crystals exposing different faces. For these kinds of reactions, all accessible surface atoms can be considered as equally active sites (Boudart, 1981 and 1995). 

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