Upendra Natarajan

The self-association behaviour of atactic poly(methacrylic acid) (a-PMA) in water was investigated by atomistic molecular dynamics (MD) simulations. Simulations show that interchain association of a-PMA occurs only in its un-neutralised form, by hydrogen bonding between -COOH groups, which is in agreement with the experimental observation. Chain conformations, dihedral angle distributions, hydration behaviour, scattering structure factor and enthalpy-of-hydration (i.e. aqueous solvation) were analysed as a function of concentration for un-neutralised PMA, across dilute to concentrated regimes. The average Rg of the chain remains unaffected in solution and also for amorphous undissolved a-PMA phase, confirming the occurrence of the approximate theta-solution condition for the first time, as revealed by simulations, in a polar hydrogen-bonding polymer aqueous solution. Chain hydration behaviour and scattering structure factor show significant changes in concentrated regime. Scattering intensity collapse occurs in concentrated PMA solution, due to the existence of the swollen regime captured for the first time by explicit-MD-simulations. The hydration of PMA is driven by H-bonding, specifically between H atoms of the COOH groups and O atoms of water molecules in the closest coordination shell. The enthalpy of hydration of PMA is dominated by PMA-water interactions (charges and H-bonding). The thermodynamic contributions of PMA-PMA and PMA-water interactions towards the electrostatics as well as the dispersion components of the total solvation-enthalpy become more favourable than water-water interactions.

We have investigated the interaction of dodecyltrimethylammonium chloride (DoTA) micelle with weak polyelectrolytes, poly(acrylic acid) and poly(methacrylic acid). Anionic as well as un-ionized forms of the polyelectrolytes were studied. Polyelectrolyte-surfactant complexes were formed within 5-11 ns of the simulation time and were found to be stable. Association is driven purely by electrostatic interactions for anionic chains whereas dispersion interactions also play a dominant role in the case of un-ionized chains. Surfactant headgroup nitrogen atoms are in close contact with the carboxylic oxygens of the polyelectrolyte chain at a distance of 0.35 nm. In the complexes, the polyelectrolyte chains are adsorbed on to the hydrophilic micellar surface and do not penetrate into the hydrophobic core of the micelle. Polyacrylate chain shows higher affinity for complex formation with DoTA as compared to polymethacrylate chain. Anionic polyelectrolyte chains show higher interaction strength as compared to corresponding un-ionized chains. Anionic chains act as polymeric counterion in the complexes, resulting in the displacement of counterions (Na⁺ and Cl^-) into the bulk solution. Anionic chains show distinct shrinkage upon adsorption onto the micelle. Detailed information about the microscopic structure and binding characteristics of these complexes is in agreement with available experimental literature.

Structural and dynamic properties of aqueous solution of atactic poly(acrylic) acid (PAA) in dilute, semi-dilute and concentrated regimes were studied by fully atomistic molecular dynamics simulations with explicit solvent description, as a function of polymer concentration c (i.e. volume fraction φp) and charge density f. PAA size (Rg, R) decreases with φp in semi-dilute and concentrated regimes, due to increase in counter-ion condensation. For all values of f, in dilute regime (c < c*) chains are expanded and in semi-dilute regime (c*< c < c**) chains are in contact with each other, while for c ≅ c** aggregates comprising of few PAA chains occur (at f = 0.2, 0.4 and 0.7). Number of PAA intrachain h-bonds is greater than PAA–PAA interchain h-bonds at all values of f and φp. The number of h-bonds between carboxylic acid groups and carboxylate groups remain unaffected by φp. The Na+ ion self-diffusion coefficient shows linear decrease with concentration for f < 1 and exponential decrease for f = 1. The PAA self-diffusion coefficient shows power law decrease with concentration for f < 1 and exponential decrease for f = 1. Aggregation of chains is favoured due to PAA–PAA interactions with increase in concentration. Our simulation results are in agreement with experiments and coarse-grained simulations in the literature.

Polyelectrolytes are useful in a variety of applications such as detergents, consumer care, electrochemical devices, solid-state reference electrode, water treatment, paper production, contact lenses, drug delivery systems, tissue engineering and biosensors. The behaviour of polyelectrolytes in solution is influenced by stereochemistry. The influence of tacticity on conformations of carboxylate anionic polyelectrolytes isotactic poly(acrylic acid) (i-PAA) and syndiotactic poly(acrylic acid) (s-PAA) in water was investigated by explicit solvent atomistic molecular dynamics (MD) simulations using different generic force-fields (CHARMM27, GROMOS 53a6) and water models (SPC-E and TIP4P). Simulations with uniformly distributed charges were performed using 20, 30, and 60 repeat unit chains of i-PAA and s-PAA. CHARMM27 FF with SPC/E water model correctly depict the helical conformational structure of the i-PAA (tg + = 76%) in comparison with experimental data (tg + = 72%). Simulation results show i-PAA to be helical as compared to s-PAA which is extended (trans), in qualitative agreement with experimental data on i-PAA and s-PMA. Counter-ion condensation is stronger for i-PAA which may be partly responsible for its helical conformation. The novelty of the present work is the origin of the conformational behaviour of the anionic polyelectrolyte with such information having potential biological applications such as gene therapy. Abbreviations: i-PAA: isotactic-poly(acrylic acid); s-PAA: syndiotactic-poly(acrylic acid); s-PMA: syndiotactic-poly(methacrylic acid); PEA: Poly(ethacrylic acid); SPC: Simple Point Charge; SPC/E: Extended Simple Point Charge; ST2: Based on the Ben-Naim and Stillinger model; TIPS: A Set of Transferable Intermolecular Potential function; TIP3P: Three-point Transferable Intermolecular Potential; TIP4P, TIP4P-Ew, TIP4P/Ice, TIP4P/2005: Four-point Transferable Intermolecular Potential, for Ewald technique, for Ice, reparametrised original TIP4P model, respectively; TIP5P: Five-point Transferable Intermolecular Potential; R g: Radius-of-gyration; R: End-to-end distance; RDF: Radial Distribution Function; RB: Ryckaert-Bellemans; COM: Centre-of-Mass; CHARMM: Chemistry at HARward Macromolecular Mechanics; GROMOS: GROningen MOlecular Simulation; GROMACS: GROningen MAchine for Chemical Simulations; MD: Molecular Dynamics; PME: Particle Mesh Ewald; LINCS: LINear Constraint Solver; VR: Velocity Rescaling; NPT: Constant Number of particle, Pressure, and Temperature; NVT: Constant Number of particle, Volume, and Temperature; L-J: Lennard-Jones; vdW: van der Waals; FF, FF1, FF2: Force-Field, Force-Field 1, Force-Field 2 respectively; f Charge fraction or charge density or degree-of-ionisation; ACF: Autocorrelation Function.

We present the GB-OBC model as an approach for implicit-solvent MD simulations of a synthetic macromolecule in water. The model is tested and found to be successful in reproducing the chain dimensions and predicting the free energy of solvation of carboxylic acid vinyl polymers. The influence of stereochemistry and the hydrophobic nature of the polymer was investigated as a function of chain length (20 < N < 600) for poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMA). The dimensionless parameters of the GB-OBC model were parameterized to be applicable to PAA and PMA. Scaling relations for chain dimensions obtained using implicit-solvent MD simulations in this study are in good agreement with those from experiments, theory of solvated chains in good solvents, and all-atom MD simulations in explicit water. Results show that ⟨Rg2⟩/NL2 is greater for the atactic chain as compared to the isotactic chain, for PAA as well as PMA. ⟨Rg2⟩/NL2 values of chains attain constancy in water for N = 200, with the values being greater for PMA. The PMA chain is conformationally more perturbed than the PAA chain, for both isotactic and atactic stereochemistry. The solvation free energy ΔGhyd of PAA and PMA in water is negative for all chain lengths (N = 20-600) and becomes more favorable with an increase in molecular weight. The ΔGhyd values for isotactic and atactic chains are identical at lower values of N but differ slightly for N > 300. Irrespective of the hydrophobic nature of the polymer, the atactic chain is thermodynamically more soluble in water as compared to the isotactic chain. The isotactic chain is less hydrophilic as compared to the atactic chain due to the closer proximity of the COOH groups along the backbone. This implicit solvent method is an effective way to accurately simulate the configurational properties and solvation of synthetic polymers in water.

Molecular dynamics simulations of polyelectrolyte poly(acrylic acid) at infinitely dilute conditions in aqueous solutions containing up to 6 vol% ethanol were performed with explicit solvent and counter-ion description for varying degree of neutralisation. In the range of ethanol concentration employed, this study shows a swelling in the case of non-ionised chain, chain collapse for 25% ionised system, minimal swelling for 50% ionised chain and no significant change in conformation for 75-100% ionised chains. Ethanol interacts with non-ionised residues via hydrogen bonding and is found to be dominant in the solvation cage surrounding them, whereas no such interaction is seen with ionised residues. Thus, chains with higher charge densities show a preference for the aqueous environment in comparison to ethanol and hydrogen bonding to water is unaltered. For chains with lower charge density, a reduction in the hydrogen bonding with water is seen with an increase in ethanol concentration. © 2013 Taylor & Francis.

A modeling approach based on sequential stages of pressure compression (NPT) and constant volume (NVT) molecular dynamics (MD) simulations was used effectively for generation of models of glassy samples of poly(phenylene oxide) PPO. Starting from a large periodic simulation box the samples were brought down to the desired density using NPT simulations and also NVT simulations for energy and structural relaxation. The GROMOS 45a3 force-field, with appropriate intermolecular potentials for PPO, was used to model the interatomic interactions. The PPO glassy phase was studied by independently generating 9 samples with different numbers of chains (for the chains of repeat units 15, 25 and 40). Structural analysis included dihedral angle distribution, intra-chain and inter-chain radial distribution functions, radius-of-gyration and torsion angle distributions, free volume and the orientation distributions of intra-chain and inter-chain phenylene rings. The simulated solubility parameter was in excellent agreement with experimental data for PPO. This computational study of the glassy phase of PPO is an extension of earlier studies by others on single, unperturbed chains of PPO.

Atomistic molecular dynamics simulations of copolymers of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMA) in dilute aqueous solution were performed as a function of charge density, in explicit solvent medium and counterions. The studied polyelectrolytes follow a general behavior of chain expansion with charge density until a point where the repulsion between the electrostatic charges between the anionic residues is effectively neutralized by the counterions. The average persistence length is found to increase and levels off at higher charge densities, and the values imply the chains to be flexible. With increase in PMA content in the chain, counterions show increased correlation with chain backbone and a systematic reduction in the number of water molecules in the first hydration shell. The intermittent hydrogen-bond correlation function for the hydrogen bonds between the chain residues and water decays faster for PAA chain as compared to PMA, indicating a rigid hydration layer for the latter. The shorter H-bond lifetimes coupled with the slower relaxation indicate that MA-water H-bonds break more easily than those of AA-water H-bonds, but the water molecules remain in the vicinity of the chain because of slow diffusivity and can easily reform the bonds. © 2012 American Chemical Society.

Molecular dynamic simulations of anionic polyelectrolyte poly(acrylic acid) (PAA) in water–ethanol solution, specifically Li+-PAA and Cs+-PAA, were carried out across the solvent composition range 0 ≤ фeth ≤ 0.9. Chain collapse (i.e. shrinkage) occurs with increase in фeth for both types of counter-ion systems and in agreement with the experiments. The qualitative difference in the collapse point is in agreement with experimental results, with counter-ion specific chain collapse of PAA following the order Li+ > Cs+. With increase in фeth the number of hydrogen-bonds between PAA and water decreases while that between PAA and ethanol increases. At higher level of ethanol content in solution, ethanol molecules displace water molecules from the vicinity of the chain. The analysis of the radial distribution functions shows that counter-ion binding distance of Li+ to chain is lesser as compared to that of Cs+, as well as a higher coordination number exhibited by Li+. Thus, as compared to Cs+-PAA, greater number of contact ion pairs formed between Li+ and PAA induce chain collapse more easily. The coordination of Li+ to PAA is better than that of Cs+ throughout the фeth range, which could be the reason for the greater extent of PAA chain shrinkage observed in the case of Li+. Binding of water molecule to PAA units is stronger in the case of Cs+. The backbone dihedral trans probability of both systems displayed a decrease with фeth indicating chain shrinkage. The relaxation time of H-bonds between PAA and EtOH is greater for Li+-PAA as compared to Cs+-PAA system. The enhancement of counter-ion pairs formation is found to be directly responsible for the solvent composition at which chain collapse occurs in the particular system.