Neutral charge group

Figure 4 Neutral charge groups in a nucleotide from GROMOS. Groups are indicated by a line enclosing the atoms in each group.

Figure 6 Neutral charge group constructed from backbone phosphate group and mobile counterion. The geometric center of the group is shown along with the switching region. The radii of atoms in the phosphate group are reduced in size for clarity. This arrangement shows the counterion at 6 A from the P.

Analysis of only selected parts of the system during the validation phase of research is a dangerous exercise and can lead to erroneous conclusions. We illustrate this by means of results from an unpublished 500 ps simulation on the Drew—Dickerson dodecamer sequence in its canonical form, surrounded by 2000 SPG waters in a hexagonal box. In this simulation, each counterion was associated with a phosphate group to form a neutral charge group and was restrained by a hemiharmonic potential centered at 6 A with a force constant of... 

Defining (neutral) charge groups makes the electrostatic interaction a dipolar interaction, which has a I /r distance dependence. 

In some systems, such as lake and river waters, the suspended inorganic particles may be coated by biological polymers, termed humic substances, which prevent flocculation by either steric or electrostatic mechanisms. These can also interact with added inorganic salts (31) that can neutralize charged functional groups on these polymers. 

In an ideal SEC separation, the mechanism is purely sieving, with no chemical interaction between the column matrix and the sample molecules. In practice, however, a small number of weakly charged groups on the surface of all TSK-GEL PW type packings can cause changes in elution order from that of an ideal system. Fortunately, the eluent composition can be varied greatly with TSK-GEL PW columns to be compatible with a wide range of neutral, polar, anionic, and cationic samples. Table 4.8 lists appropriate eluents for GFC of all polymer types on TSK-GEL PW type columns (11). 

For some nonionic, nonpolar polymers, such as polyethylene glycols, normal chromatograms can be obtained by using distilled water. Some more polar nonionic polymers exhibit abnormal peak shapes or minor peaks near the void volume when eluted with distilled water due to ionic interactions between the sample and the charged groups on the resin surface. To eliminate ionic interactions, a neutral salt, such as sodium nitrate or sodium sulfate, is added to the aqueous eluent. Generally, a salt concentration of 0.1-0.5 M is sufficient to overcome undesired ionic interactions. 

To be contrasted with a negatively charged metal surrounded by positively charged groups. The idea of neutral ligands with donor lone pairs will be considered in due course. 

Ion binding reduces the repulsive forces between the charged groups on the polyanion but, unless the counterions are site-bound, the repulsive osmotic forces are not affected. At full neutralization the coulombic forces along the polymer chain become zero. However, the polymer does not contract, because the osmotic forces remain unless, of course, all the cations become site-bound. (Of course, in the case of a free weak acid the concentration of mobile hydrogen ions is very small and the polymer adopts a compact form.)... 

Another interesting application area of PHMD simulations is to investigate electrostatic interactions in the unfolded states of proteins. A traditional view that unfolded proteins adopt random conformational states that are devoid of electrostatic and hydrophobic interactions, are recently challenged by experimental data [20, 69], REX-CPHMD folding simulations of the 35 residue C-terminal subdomain of the villin headpiece domain revealed a significant deviation from the standard pKa values for several titratable residues. Additional simulations, in which a charged group is neutralized confirmed the existence of specific electrostatic interactions in the unfolded states (JK and CLB, manuscript in preparation). 

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