Abstract
All-atom molecular dynamics is used to investigate the structural, energetic, and dynamical properties of polyacrylamide (PAM) oligomers of different lengths solvated in pure glycerol, a 90:10 glycerol–water mixture, and pure water. We predict that the oligomers’ globular structure is obtained only when the modeling strategy considers the solvent as a continuous background. Meanwhile, for all-atom modeled solvents, the glycerol solutions display a strong tendency of trapping the oligomers in instantaneous elongated random coiled structures that remain locked-in over tens of nanoseconds. In pure water, the oligomers acquire considerably shorter random coiled structures of increased flexibility. The all-atom force field, generalized amber force field, is modified by including restrained electrostatic potential atomic charges for both glycerol and PAM. Three PAM oligomer lengths containing 10, 20, and 30 monomers are considered in detail by monitoring the radius of gyration, end-to-end distance, intra-potential energy, and solvent–oligomer interaction energies for decades of nanoseconds. The density and radial distribution function of glycerol solutions are calculated when modeled with the modified atomic charges, showing a very good agreement with the experimental results at temperatures around 300 K. Glycerol has multiple applications, including its use in gel formation for PAM gel electrophoresis. Our findings are relevant for the design of sensors based on microfluidics and tailored pharmaceutical buffer solutions.
Highlights
Polyacrylamide (PAM) is a biocompatible and water-soluble polymer that can be tailored to meet a broad range of industrial applications, most of them based on its well above room temperature, glass transition temperature of 400 K.1,2 The polymer is synthesized either as a simple linear chain or as a cross-linked structure
We present extensive all-atom Molecular Dynamics (MD) simulations of PAM oligomers of various molecular weights solvated in pure glycerol, pure water, and mixed glycerol–water (90:10) by weight
The n-PAM properties presented below result from a 298 K thermalization Langevin-MD44 lasting 1 ns–5 ns depending on the size, followed by a production NVE-MD of 50 ns for every n-PAM size in either the implicit solvent corresponding to glycerol or 90:10 glycerol–water
Summary
Polyacrylamide (PAM) is a biocompatible and water-soluble polymer that can be tailored to meet a broad range of industrial applications, most of them based on its well above room temperature, glass transition temperature of 400 K.1,2 The polymer is synthesized either as a simple linear chain or as a cross-linked structure. Polyacrylamide (PAM) is a biocompatible and water-soluble polymer that can be tailored to meet a broad range of industrial applications, most of them based on its well above room temperature, glass transition temperature of 400 K.1,2. PAM increases the viscosity of water and belongs to the super water-absorbent polymer (SAP) family. PAM forms a soft gel used in gel electrophoresis for protein separation. PAM is hydrophilic and can form aqueous solutions of very high concentrations.. PAM is hydrophilic and can form aqueous solutions of very high concentrations.3 Because of their gel-like properties, these aqueous solutions are employed as flocculants in the removal of suspended particles from sewage and industrial effluents such as paper mill wastewater. PAM increases the viscosity of other fluids and may be the cause of unexpected turbulent scitation.org/journal/adv behavior in the flow of otherwise viscoelastic fluids at low Reynolds numbers. Through the highly reactive amide NH2 groups, the polymer can be chemically modified to produce cationic or anionic polymers, which are useful in mineral-processing and metallurgical operations for the separation of metals from residues. PAM increases the viscosity of other fluids and may be the cause of unexpected turbulent scitation.org/journal/adv behavior in the flow of otherwise viscoelastic fluids at low Reynolds numbers.
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