Polyelectrolytes are linear polymers in which monomer units carry a charge. These charges usually originate from ionizing groups which in aqueous solutions dissociate into multivalent polyion and oppositely charged counter-ions. Ionenes are polyelectro-lytes consisting of hydrophobic methylene strings separated by positively charged qua-ternary nitrogen atoms. They are referred to as x,y-ionenes, where x and y represent the number of methylene groups between adjacent nitrogens (we know e.g. 3,3-, 4,5-, 6,6-, 9,12-ionenes). As the number of methylene groups between positively charged nitro-gens increases, charge-density of ionene decreases and hydrophobicity increases. The aim of this master's thesis was to determine the average structure of 3,3-/6,6-ionene solutions with added halogenide counter-ions (F$^-$ and Br$^-$) with molecular dynamics. The properties of such solutions depend on the charge-density of the ionene and on the type of counter-ions. The latter is known as ion-specific effects. The type of counter-ions determines whether they bind to the charged groups on the ionene due to favoura-ble interactions or remain mobile in the solution. Ion-specific effects are extremely important, as they occur in majority of vital biological processes, e.g., in membrane transport, osmotic regulation, enzymatic activity regulation, adsorption. They also affect the structure and function of proteins, phospholipids, nucleic acids, and polysac-charides. By varying the charge-density of the ionene and the type of added counter-ions we studied the interplay of both effects on the spatial distribution of counter-ions and water molecules around the ionene.
Molecular dynamics is one of the most frequently used types of computer simulations. Simulations in chemistry represent a useful tool for determining the structural, ther-modynamic, dynamic and transport properties of a system, reaction mechanisms and material characteristics. The advantage of simulations is the insight they give us into the events happening at atomic scale while still possessing a high degree of reliability. Such small scales are not accessible to experiments due to high number of particles that make up real matter.
In the first part of my master's thesis, we performed Monte Carlo simulations of Len-nard-Jones fluid, gaseous argon, using our own programme. The same system was simulated by molecular dynamic with GROMACS software. Matching results (ther-modynamic variables, pair distribution functions) of both types of simulation con-firmed that the simulation outcome doesn’t depend on the method used to obtain it.
The main part of our work were simulations of polyelectrolyte solutions. Molecular dynamics simulations of four different systems; aqueous solutions of 3,3- or 6,6-ionene with added F$^-$ or Br$^-$ counter-ions, were performed in GROMACS. OPLS/AA force-field was applied for atomistic treatment of our system. SPC/E water model was used. 10-meres of 3,3- and 6,6-ionene were built and geometrically optimized using Spartan software. Topology was generated by TTPMKTOP server. The charge (+1) was as-signed to the nitrogen atoms exclusively while all the other ionene atoms remained electrically neutral. Pair distribution functions (RDF) between various sites were ob-tained from simulation trajectories. For this purpose, ionene was divided into its con-sisting fragments and each type was treated as an individual group for RDF calcula-tions. This way a detailed insight into orientation and arrangement of water and coun-ter-ions around different parts of ionene molecule was obtained. Radius of hydration and orientation of water molecules in the first hydration shell of counter-ions was de-termined by counter-ion-water oxygen/hydrogen distribution functions. By simultane-ously taking in account all the results the average states of these solutions at equilibri-um were found. We proved that bromides tend to have weakly bound hydration shells from which they lose some of the water molecules upon condensation on ionene chain. Fluorides on the other hand possess tight and compact hydration shell which they al-ways keep intact. We showed that both types of counter-ions condense on 3,3-ionene while the condensation on 6,6-ionene happens only with bromide ions. For each of the four solutions (3,3-/6,6-ionene with F$^-$/Br$^-$ counter-ions) a detailed sketch of the aver-age states at equilibrium was made taking in account the appropriate atomic and ionic radii, molecular geometry of the species involved and SPC/E water model dimensions. In the end Manning’s degree of condensation for both types of ionenes was calculated. We determined that Manning’s counter-ion condensation happens only in the case of 3,3-ionene.
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