Hydrogen bonding displacement model

Fig. 3.15 Model for allosteric inhibition of a protein-DNA complex by a polyamide-inter-calator conjugate. (Top) The GCN4 homodimer (yellow) is displaced by the intercalating moiety (green) of the polyamide conjugate. Blue and red spheres represent pyrrole and imidazole amino acids, respectively. The blue diamond represents / -alanine. (Bottom, left) Hydrogen-bonding model of an eight-ring hairpin polyamide-intercalator conjugate...

Thomas et al. [72] used a modified force microscope in which a compensatory force was applied to the probe to keep its displacement at zero. With this system they studied interactions between organomercaptan molecules with CH3, NH2, or COOH end groups. All measurements were performed in dry nitrogen. From SEM-measured tip radii and pull-off force they calculated the work of adhesion using the DMT model. They found that the work of adhesion values qualitatively scaled as expected for van der Waals, hydrogen bonding,... 

Abstract This chapter describes the experimentai compiement of theoretical models of the microscopic mechanism of ferroelectric transitions. We use the hydrogen-bonded compounds as examples, and attempt to show that the new experimental data obtained via recently developed high resolution nuclear magnetic resonance techniques for solids clearly support the hypothesis that the transition mechanism must involve lattice polarizability (i.e. a displacive component), in addition to the order/disorder behaviour of the lattices. 

An examination of the stereochemistry of the H+ ion is complicated by a number of factors. Because it has no electron core, hydrogen is difficult to locate using X-rays which are scattered by electrons. In earlier structure determinations its presence was often ignored because it made no contribution to the X-ray diffraction pattern and could not therefore be located. Even when H is included in the model, its position can rarely be accurately determined and in any case the centre of its electron density is usually displaced from the nucleus towards the donor anion by around 20 pm. Accurate positions of the H+ nuclei can be found using neutron diffraction which has provided sufficient information to reveal the essential characteristics of hydrogen bond geometries, but in many of the structures determined by X-ray diffraction the positions of the H cations have had to be inferred from the positions of their neighbouring anions. 

Figure 71 shows the 13C spectra of pyridine at different loading levels and after a pretreatment with HC1. It is seen that the resonance of the y carbon of pyridine (middle peak) is very sensitive to its chemical state, and Maciel et al. developed a model of pyridine exchange between Bronsted, Lewis, and hydrogen-bonding acid sites as well as the physisorbed state. The same authors used the 15N signal of a fixed quantity of adsorbed pyridine as a kind of urface indicator. Pyridine is displaced by n-butylamine according to the sequence... 

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