Charging termination

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters have been reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins... 

In summary, dendrimers are a unique class of monodispersed synthetic molecules reminiscent of proteins or nucleic acids. If they can be functionalized to be soluble in water with appropriately charged terminal groups, they are generally ideal candidates for gel electrophoretic analyses. 

Ionic polymerizations are characterized by a wide variety of modes of initiation and termination. Unlike radical polymerization, termination in ionic polymerization never involves the bimolecular reaction between two propagating polymer chains of like charge. Termination of a propagating chain occurs by its reaction with the counterion, solvent, or other species present in the reaction system. 

In a similar fashion, the Rotello group reported several protein-mediated assemblies of nanoparticles (Srivastava, Verma, et al. 2005 Verma et al. 2005). Unstable proteins such as chymotrypsin are readily denatured upon prolonged interaction with functionalized nanoparticles because of the exposure of proteins to the hydrophobic layer (Srivastava, Verma, et al. 2005). Addition of a hydrophilic portion to the monolayer by inserting a short tetraethylene glycol between the charged terminal group and hydro-phobic aliphatic chain circumvented this denaturation problem (Hong et al. 2004). 

While the active end of a growing polymeric radical forms a single entity, the active end of an ionically growing polymer involves two species, a charged terminal atom or terminal group of the polymer and, associated with it, an oppositely charged counter-ion. The interaction between these two entities may lead to termination of polymerization, and this event may take place in a variety of ways. 

Dyes in which both charged terminal atoms are not part of a heterocyclic ring are called streptocyanine dyes. An example is 4, which dyes paper in a greenish yellow shade [2],... 

In the hemicyanine dyes, one of the charged terminal atoms is part of a heterocyclic ring, and the other is a nitrogen atom directly linked to the methine chain (5). 

If the second charged terminal atom is also part of a heterocyclic ring, the cyanine dyes are obtained (9). 

A classical molecular dynamics simulation of N3 dissolved in water revealed that six to seven water molecules are hydrogen bonded to the negatively charged terminal nitrogen atoms, (102) with an estimated hydrogen... 

Figure 14 also shows the amino acid residues playing a key role in the proton transport Asp 85, Asp 212, and Tyr 185 with negatively charged terminal groups that are counterions with respect to the positively charged protonated Schiff base Asp 85 and Asp 96 are inner proton acceptor and donor, respectively Arg 82 favors the deprotonation of the retinal Schiff base. The data... 

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