C.G. Jesudason, A.J.P. Agung
The simulation results from a basic polyelectrolyte chain consisting of an anionic string of 150 univalent negatively charged particles connected under various harmonic-like potential interactions with each other in the presence of a similar number of positive and free counter ions found in Jesudason et al. (EPJE 30:341-350, 2009) forms the focal point for further discussion on chain models based on a survey of more recent developments in general polyelectrolyte theory. The topics discussed include persistence length definition, forcefields and methods of controlling simulation parameters, and thermodynamics. The data for the basic system was derived for the temperature range 0.1-10.0 in reduced units (corresponding to ξ = 10-0.1); the augmented data involves a 360 monomer chain. The data include the total and Coulombic energies, radial distribution functions, radii of gyration, end-to-end distances and snapshots of the system which are all discussed anew. Polyelectrolyte systems have been overwhelmingly associated with biophysical interpretations, but here it is suggested that these detailed studies and the consequent theoretical formulations could be extended further afield; non-biological ionic liquid systems with catalytic and energy storage applications are some of many other possibilities. However, the approach used by MD simulations to validate ionic liquid systems as carriers of molecules with catalytic moieties often refer to CPMD and DFT quantum methods, which is not the current norm as judged by the literature in especially coarse grained polyelectrolyte MD. The quantum approach could also be used for more detailed analysis of biophysical systems where one trend seems to be that the incorporation of details in simulations accounts for phenomena not explicable in coarser grained MD, for instance if conventional atomic ionic charges are assigned to all atom modeling. This is illustrated by a linear chain modeling a DNA polymer using different charge and size assignments for the same linear charge density. The trends are such that it might be expected that some form of routine standardization of force fields in the spirit of the Jorgensen OPLS-AA method that incorporates quantum calculations specific to a system will be implemented as a routine as refinements are seen to lead to more comprehensive rationalization. © 2013 Springer Science+Business Media New York.
Chemistry Department, Science Faculty, University of Malaya, 50603 Kuala Lumpur, Pantai Valley, Malaysia; Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast, BT7 1NN, United Kingdom; Sumatera Institute of Technology (ITERA), Kota Baru Lampung South, Lampung Province, Sumatera, Indonesia