title: Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution.
abstract: We demonstrate that different sets of Lennard-Jones parameters proposed for the Na(+) ion, in conjunction with the empirical combining rules routinely used in simulation packages, can lead to essentially different equilibrium structures for a deprotonated poly-L-glutamic acid molecule (poly-L-glutamate) dissolved in a 0.3M aqueous NaCl solution. It is, however, difficult to discriminate a priori between these model potentials; when investigating the structure of the Na(+)-solvation shell in bulk NaCl solution, all parameter sets lead to radial distribution functions and solvation numbers in broad agreement with the available experimental data. We do not find any such dependency of the equilibrium structure on the parameters associated with the Cl(-) ion. This work does not aim at recommending a particular set of parameters for any particular purpose. Instead, it stresses the model dependence of simulation results for complex systems such as biomolecules in solution and thus the difficulties if simulations are to be used for unbiased predictions, or to discriminate between contradictory experiments. However, this opens the possibility of validating a model specifically in view of analyzing experimental data believed to be reliable.
authors.affiliation: Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP 92208, FR-44322 Nantes Cedex 3, France.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Marchand
authors.affiliation: Institut des Sciences Moléculaires (ISM), Université de Bordeaux, Bât A12, FR-33405 Talence Cedex, France.
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Soetens
authors.affiliation: Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP 92208, FR-44322 Nantes Cedex 3, France.
authors.forename: Denis
authors.initials: D
authors.lastname: Jacquemin
authors.affiliation: Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
authors.forename: Philippe A
authors.initials: PA
authors.lastname: Bopp
mesh_terms: D002412:Cations / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D011099:Polyglutamic Acid / Q000737:chemistry*; D012965:Sodium Chloride / Q000737:chemistry*; D012996:Solutions; D014867:Water / Q000737:chemistry
chemical_list: D002412:Cations; D012996:Solutions; D014867:Water; D011099:Polyglutamic Acid; D012965:Sodium Chloride