Polar atoms solvation structures

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

Examples of empirical descriptors can be considered to be the -+ Taillander index (restricted to substituted benzenes), - second-grade structural parameters (restricted to alkenes), - polar hydrogen factor (restricted to halogenated hydrocarbons), - hydrophobic fragmental constants, - six-position number, Idoux steric constant, -> hydrophilicity index, - adsorbability index, -> bond flexibility index, and -+ atomic solvation parameter. 

The double helix that defines the channel is constructed as a sequence of neutral, but polar and polarizable sources distributed on the z-axis. The same parameters for the interaction of the helical source atoms with the ion are used for each atom. Vibrational structure of the wall-forming helix is not considered at this time the wall of the conduction channel is considered to be rigid. In general, the channel radii used were between 3.2 and 3.6A, values that are close to the solvation radius for a sodium in water. Replica distances used for the sources along the helical axis were of the order of 1.2A to 2.0A. In order to have a distance of about 3A between neighboring atoms on the helix wall, and to make sure that the double strands were uniformly separated from one another, twist angles were determined with eq (4) and generally were found to have values of around 50°. 

Optimization of the valence and dihedral angles yields planar cyclic structures for the 3- to 5-ring intermediates in contrast to a chair conformation for that of the 6-ring. In the cases of n = 4, 5, 6 the oxygen atom is placed almost in the plane of the three C-atoms directly bonded to it. Therefore, an intramolecular solvation of the cationic chain end by methoxy groups which are bonded to the polymer backbone is preferred in the gas phase. The calculations show that for a non-polar solvent such as CH2C12 a decrease in stability of the cyclic intermediates exists. But this decrease does not result in a total break of the intramolecular solvation (Table 13). An equilibrium between open chain and cyclic intermediates must only be taken into account in more polar solvents, due to the competition of intra- and intermolecular solvation. 

Discrete dimers of the head-to-head type have been found in the structures of the Ag+ complex of (145)570 and the Na+ complex of (145)571 respectively. The complexes were recrystallized from carbon tetrachloride. In both complexes each metal is five-coordinated in the cavity provided by one anion, and there is an additional reaction with the second anion [through an Ag+-phenyl interaction or an Na+-carboxylate oxygen atom (Figure 32a)]. When the Na+ complex was crystallized from a solvent of medium polarity, acetone, the head-to-head dimer was recovered.571 In contrast, recrystallization from a polar medium, methanol, gave a monomeric complex in which one methanol of solvation was also present.572 In all of these complexes an intramolecular head-to-tail hydrogen bond was present to hold the ligand in its pseudo-macrocyclic conformation. 

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