1943 Pure Appl. Chem., Vol. 82, No. 10, pp. 1943–1955, 2010. doi:10.1351/PAC-CON-09-10-41 © 2010 IUPAC, Publication date (Web): 1 August 2010 Molecular dynamics study of the hydrophobic 6,6-ionene oligocation in aqueous solution with sodium halides* Maksym Druchok 1 and Vojko Vlachy 2,‡ 1 Institute for Condensed Matter Physics, Svientsitskii 1, 79011 Lviv, Ukraine; 2 Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia Abstract: An explicit water molecular dynamics (MD) simulation is presented of a solution modeling aliphatic 6,6-ionene oligocations mixed with low-molecular-weight electrolytes. In all cases, the co-ions were sodium cations and the counterions were fluoride, chloride, bro- mide, or iodide anions. The simple point charge/extended (SPC/E) model was used to de- scribe water. The results of the simulation at T = 278 K (the data for 298 K were obtained earlier) and T = 318 K are presented in the form of pair distributions between various atoms and/or between ions in the system. We were interested in how temperature variation modi- fies the ion-specific effects, revealed by the various pair distribution functions (PDFs). The results were compared with previous calculations for the less hydrophobic 3,3-ionene solu- tions. Simulations of 6,6-ionene solutions containing mixtures of fluoride and iodide counter- ions at T = 298 K were also presented. Keywords: 3,3-ionene oligocations; 6,6-ionene oligocations; molecular dynamics; pair distri- bution functions; simple point charge/extended model. INTRODUCTION Polyelectrolytes are polymers containing groups that can ionize in an appropriate solvent (for a review, see refs. [1–6]). They have complex properties and find many applications in industry [7]. Their theo- retical description is most often based on the cylindrical cell model; see, for example, [1,2] or the Manning condensation approach [8,9]. These macromolecules contain ionic and hydrophobic groups and can therefore serve as prototypes for biological materials, such as nucleic acids and proteins. In this paper, we model the properties of cationic polyelectrolytes called ionenes. Aliphatic x,y-ionenes can be prepared with varying degree of hydrophobicity; x and y refer to the numbers of methylene groups be- tween the two quaternary ammonium atoms. Interestingly, even very hydrophobic 10,10-ionenes are soluble in water [10]. So far, the 3,3-, 4,5-, 6,6-, and 6,9-ionenes have been examined using different experimental methods [11–18]. The x,y-ionenes, therefore, form a homologous series, which allows the study of the effect of increasing hydrophobicity on the polyion–counterion interaction. A better under- standing of this effect, accompanied by the hydration and dehydration of interacting ionic species, is of considerable importance for the biological sciences. *Paper based on a presentation at the 31 st International Conference on Solution Chemistry (ICSC-31), 21–25 August 2009, Innsbruck, Austria. Other presentations are published in this issue, pp. 1855–1973. ‡ Corresponding author