Models of the structure

Table 2. Predicted intrinsic and apparent pKa values for the Cys403 residue in Yersinia phosphatase for different models of the structure the data refer to a temperature of 293 K and an ionic strength corresponding to 150 mM of monovalent salt. See the text for the detailed description of the conditions under which each pK estimation was made. The experimentally determined value is 4.67 [39]...

Singer, S. J., and Nicolson, G. L., 1972. The fluid mosaic model of the structure of cell membranes. Science 175 720-731. 

The proposed model of the structure of oxyfluoride melts corresponds with the conductivity results shown in Fig. 69. The specific conductivity of the melt drops abruptly and asymptotically approaches a constant value with the increase in tantalum oxide concentration. This can be regarded as an additional indication of the formation of oxyfluorotantale-associated polyanions, which leads to a decrease in the volume in which light ions, such as potassium and fluorine, can move. The formation of the polyanions can be presented as follows ... 

These new facts about electrical phenomena can be incorporated into our particle model of the structure of matter if we again allow some... 

This model of the structure of orientationally crystallized samples based on experimental data is in good agreement with the results of the foregoing thermodynamic analysis which resulted in relationships describing the formation of two structures, FCC and ECC, during the crystallization of strongly oriented melts of flexible-chain polymers. 

Kee, R.J., Miller, J.A., Evans, G.H., and Dixon-Lewis, G., A computational model of the structure and extinction of strained, opposed flow, premixed methane-air flames, Proc. Combust. Inst., 22, 1479, 1988. 

The mechanism of the coupling between ATP hydrolysis and Ca transport is determined by the spatial relationship of the phosphorylation and ATP binding domains of the Ca -ATPase to the Ca channel involved in the translocation of calcium. Two alternative coupling mechanisms have been proposed, based on two rather different hypothetical models of the structure of the Ca -ATPase. In the conformational coupling mechanism the energy transfer between ATP hydrolysis and transport involves a mechanical coupling over long distances between... 

Taylor C, Kelly RG, Neurock M. 2009b. First principles modeling of the structure and reactivity of water at the metal/water interface. Submitted. 

Figure 1.4 Left panel Space filing model of the structure of bacterial dihydrofolate reductase with methotrexate bound to the active site. Right panel Close-up view of the active site, illustrating the structural complementarity between the ligand (methotrexate) and the binding pocket. See color insert. Source Courtesy of Nesya Nevins.

Figure 1.4 Top panel Space filing model of the structure of bacterial dihydrofolate reductase with...

Figure 21 Space-filling model of the structure with the lowest overall energy showing the amino acid side chains hindering axial approach to Nin. Color code C, light blue H, white N, dark blue O, red Ni11,...

Fig. 12.3. Model of the structure of Tc-CTL-1, based on the known crystal structure of rat MBP-A. Model created by Dr Nick Mullin and published in Loukas etal. (1999).

Thus a quantitative model of the structure would probably require to consider a third phase (three-phase system). 

Equation (2.33) now defines the double layer in the final model of the structure of the electrolyte near the electrode specifically adsorbed ions and solvent in the IHP, solvated ions forming a plane parallel to the electrode in the OHP and a dilfuse layer of ions having an excess of ions charged opposite to that on the electrode. The excess charge density in the latter region decays exponentially with distance away from the OHP. In addition, the Stern model allows some prediction of the relative importance of the diffuse vs. Helmholtz layers as a function of concentration. Table 2.1 shows... 

In the second half of the nineteenth century the structural theory of organic chemistry was developed. It led to the concept that chemical, physical and biological properties of all kinds must vary with structural change. The earliest structure-property relationships (SPR) were qualitative. With the development of methods of quantitative measurement of these properties data accumulated. Attempts were then made to develop quantitative models of the structural dependence of these properties. These methods for the quantitative description of structural effects will now be described. 

Fig. 8.11 Illustration of the basic steps followed by the Molecular Fragment Replacement method to build a model of the structure of the protein Dinl.

As was shown, the planar conductivity of the film can be increased by immersing the substratum with the film in the ethanol-water (1 1) solution of LiNOs (0.1 mol/liter) for a short time. Then the film should be washed in water and allowed to dry. After such treatment the conductivity becomes 500 times greater and reaches the value 6x10 (Q/cm)". This increase may be due to the fact that in considering the second general model of the structure of this polymer it could be assumed that some additional quantity of Li cations might be absorbed into the ionic sphere of SO- groups, so that the total amount of Li in the electrolytic layers increases, and the conductivity then also increases. 

None of the models address the question of how the main chains are packed, and details of crystallinity are neither factored into nor predicted by mathematical models of the structure and properties of Nafion. Chains packed in crystalline arrays are usually considered to be rigid within the context of certain properties for example, with regard to diffusion, crystallites are viewed as impenetrable obstacles. F NMR studies indicate otherwise. Molecular motions that do not significantly alter symmetry can in fact occur in polymer crystals. It would seem, for example, that the response of the Nafion structure to applied stress would depend on the flexibility of the polymer backbone, a certain fraction of which is incorporated in crystalline regions. On the other hand. Starkweather showed that the crystallinity and swelling of Nafion are not correlated. 

Figure 18. Schematic model of the structure of Pt particles on an voltammogram in relation to the electrode potential. The hydrogen, double layer, and oxide regions are based on cyclic voltammetry. The lattice disorder decreases in the order D>A>C>B." (Reproduced with permission from ref 40. Copyright 1993 ElsevierSequoia S.A., Lausanne.)...

The state of our understanding of the physics of chromatin folding is such that the current knowledge about the structure and interaction of the basic components of chromatin— histones and DNA—enables us to develop the first quantitative models of the structure and dynamics of the chromatin fiber. Even so, these models are still at a very rudimentary stage data on the interaction of the histone tails... 

The simplest model of the structure of the metal-solution interphase is the Helmholtz compact double-layer model (1879). According to this model, all the excess charge... 

The NH3 treatment for 120 min completed the clusterization of the Re species as shown in Figure 10.9. The CN of the Re-Re bonds was 5.210.3 (0.276 0.002 nm) (Table 10.7). A desorphon peak of N2 in TPD of the NHs-treated Re/HZSM-5 catalyst appeared at around 673 K, which indicates that the Re cluster possesses N atoms supplied by the NH3 treatment [73]. The amount of N2 evolved was 1.2 N2 per Reio. DFT modeling of the structure of the Re cluster based on the structural parameters obtained by FXAFS analysis revealed the formation of an N-interstitial Reio cluster in the HZSM-5 pore (structure is illustrated in Scheme 10.4) [73]. N atoms at the edge and hollow sites of the Re cluster never stabilized the Re cluster framework with the Re-Re bonds at 0.276 nm. Adsorption of nitrogen atoms on the exterior surface of the Re cluster also did not reproduce the Re-Re bond distances. 

Organic chemistry is a very visual subject, but most of us have difficulty visualizing a structure in three dimensions. Making a 3-D model of the structure allows you to detect finer points of conformation, steric hindrance, and so on. Making a model also helps you find those Ccirbons with incorrect numbers of bonds. 

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