Janna K. Maranas

Investigating the specificity of peptide adsorption on gold using molecular dynamics simulations

We report all-atom molecular dynamics simulations following adsorption of gold-binding and non-gold-binding peptides on gold surfaces modeled with dispersive interactions. We examine the dependence of adsorption on both identity of the amino acids and mobility of the peptides. Within the limitations of the approach, results indicate that when the peptides are solvated, adsorption requires both configurational changes and local flexibility of individual amino acids. This is achieved when peptides consist mostly of random coils or when their secondary structural motifs (helices, sheets) are short and connected by flexible hinges. In the absence of solvent, only affinity for the surface is required: mobility is not important. In combination, these results suggest the barrier to adsorption presented by displacement of water molecules requires conformational sampling enabled through mobility.

A comparison of united atom, explicit atom, and coarse-grained simulation models for poly(ethylene oxide).

We compare static and dynamic properties obtained from three levels of modeling for molecular dynamics simulation of poly(ethylene oxide) (PEO). Neutron scattering data are used as a test of each models accuracy. The three simulation models are an explicit atom (EA) model (all the hydrogens are taken into account explicitly), a united atom (UA) model (CH(2) and CH(3) groups are considered as a single unit), and a coarse-grained (CG) model (six united atoms are taken as one bead). All three models accurately describe the PEO static structure factor as measured by neutron diffraction. Dynamics are assessed by comparison to neutron time of flight data, which follow self-motion of protons. Hydrogen atom motion from the EA model and carbon/oxygen atom motion from the UA model closely follow the experimental hydrogen motion, while hydrogen atoms reinserted in the UA model are too fast. The EA and UA models provide a good description of the orientation properties of C-H vectors measured by nuclear magnetic resonance experiments. Although dynamic observables in the CG model are in excellent agreement with their united atom counterparts, they cannot be compared to neutron data because the time after which the CG model is valid is greater than the neutron decay times.

Comparison of explicit atom, united atom, and coarse-grained simulations of poly(methyl methacrylate).

We evaluate explicit atom, united atom, and coarse-grained force fields for molecular dynamics simulation of poly(methyl methacrylate) (PMMA) by comparison to structural and dynamic neutron scattering data. The coarse-grained force field is assigned based on output of the united atom simulation, for which we use an existing force field. The atomic structure of PMMA requires the use of two types of coarse-grained beads, one representing the backbone part of the repeat unit and the other representing the side group. The explicit atom description more closely resembles dynamic experimental data than the united atom description, although the latter provides a reasonable approximation. The coarse-grained description provides structural and dynamic properties in agreement with the united atom description on which it is based, while allowing extension of the time trajectory of the simulation.

Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics.

We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala(10), Ser(10), Thr(10), Arg(10), Lys(10), and Gln(10)], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movement and flexibility of the peptide within a given conformation. Low conformational movement indicates stability of a given conformation and leads to less adsorption than homopolypeptides with faster conformational movement. Likewise, low flexibility within a given conformation also leads to less adsorption. Neither amino acid affinities nor dynamic considerations alone predict surface coverage; rather both quantities must be considered in peptide adsorption to gold surfaces.

Dynamic evolution in coarse-grained molecular dynamics simulations of polyethylene melts

We test a coarse-grained model assigned based on united atom simulations of C50 polyethylene to seven chain lengths ranging from C76 to C300. The prior model accurately reproduced static and dynamic properties. For the dynamics, the coarse-grained time evolution was scaled by a constant value [t=alphatCG] predictable based on the difference in intermolecular interactions. In this contribution, we show that both static and dynamic observables have continued accuracy when using the C50 coarse-grained force field for chains representing up to 300 united atoms. Pair distribution functions for the longer chain systems are unaltered, and the chain dimensions present the expected N0.5 scaling. To assess dynamic properties, we compare diffusion coefficients to experimental values and united atom simulations, assign the entanglement length using various methods, examine the applicability of the Rouse model as a function of N, and compare tube diameters extracted using a primitive path analysis to experimental values. These results show that the coarse-grained model accurately reproduces dynamic properties over a range of chain lengths, including systems that are entangled.

Why are coarse-grained force fields too fast? A look at dynamics of four coarse-grained polymers

Coarse-grained models decrease the number of force sites and thus reduce computational requirements for molecular simulation. While these models are successful in describing structural properties, dynamic evolution is faster than the corresponding atomistic simulations or experiments. We consider coarse-grained models for four polymers and one polymer mixture, where accurate dynamics are obtained by scaling to match the mean-squared displacements of the corresponding atomistic descriptions. We show that the required scaling is dictated by local friction and that this scaling is only valid after the onset of continuous motion.

Differences between polymer/salt and single ion conductor solid polymer electrolytes

PEO/salts and PEO-based ionomers have been previously investigated for battery applications. Although both contain a PEO backbone, reports so far show different polymer dynamics, cation solvation, and ion conduction mechanisms. The different properties may be attributed to their lattice energy, ion content, molecular weight, and molecular structure. As the ion identities from which this information has been obtained differ, we have used molecular dynamics simulation to study a PEO/salt system that has identical cations and anions as a PEO-based ionomer previously studied in our group. This enables us to isolate the effect of covalent bonding of the anion to the backbone. Our study shows that the ionomer structure reduces PEO flexibility, PEO mobility, and cation solvation. In the PEO/salt, PEO segments crosslinking via ion aggregation does not occur because the anions are not incorporated in the polymer. The absence of ionic crosslinking results in PEO mobility evenly distributed along the polymer backbone in contrast to the gradient mobility exhibited in the PEO-based ionomer. Due to the more mobile PEO chains in the PEO/salt, ion transport is controlled by the dynamics of the polymer matrix, whereas ion hopping is more important within more rigid ionomer systems. To improve cation mobility in the PEO/salt, the focus should be on polymer dynamics. For the PEO-based ionomer, additional attention should be focused on attaining cation states that promote cation hopping.

Scaling behavior and local structure of ion aggregates in single-ion conductors

Single-ion conductors are attractive electrolyte materials because of their inherent safety and ease of processing. Most ions in a sodium-neutralized PEO sulfonated-isophthalate ionomer electrolyte exist as one dimensional chains, restricted in dimensionality by the steric hindrance of the attached polymer. Because the ions are slow to reconfigure, atomistic MD simulations of this material are unable to adequately sample equilibrium ion structures. We apply a novel coarse-graining scheme using a generalized-YBG procedure in which the polymer backbone is completely removed and implicitly represented by the effective potentials of the remaining ions. The ion-only coarse-grained simulation allows for substantial sampling of equilibrium aggregate configurations. We extend the wormlike micelle theory to model ion chain equilibrium. Our aggregates are random walks which become more positively charged with increasing size. Defects occur on the string-like structure in the form of “dust” and “knots,” which form due to cation coordination with open sites along the string. The presence of these defects suggest that cation hopping along open third-coordination sites could be an important mechanism of charge transport using ion aggregates.

Hydration Control of the Mechanical and Dynamical Properties of Cellulose

The mechanical and dynamical properties of cellulose, the most abundant biomolecule on earth, are essential for its function in plant cell walls and advanced biomaterials. Cellulose is almost always found in a hydrated state, and it is therefore important to understand how hydration influences its dynamics and mechanics. Here, the nanosecond-time scale dynamics of cellulose is characterized using dynamic neutron scattering experiments and molecular dynamics (MD) simulation. The experiments reveal that hydrated samples exhibit a higher average mean-square displacement above ∼240 K. The MD simulation reveals that the fluctuations of the surface hydroxymethyl atoms determine the experimental temperature and hydration dependence. The increase in the conformational disorder of the surface hydroxymethyl groups with temperature follows the cellulose persistence length, suggesting a coupling between structural and mechanical properties of the biopolymer. In the MD simulation, 20% hydrated cellulose is more rigid than the dry form, due to more closely packed cellulose chains and water molecules bridging cellulose monomers with hydrogen bonds. This finding may have implications for understanding the origin of strength and rigidity of secondary plant cell walls. The detailed characterization obtained here describes how hydration-dependent increased fluctuations and hydroxymethyl disorder at the cellulose surface lead to enhancement of the rigidity of this important biomolecule.

Does decreasing ion–ion association improve cation mobility in single ion conductors?

We report on poly(ethylene oxide) based single ion conductors for solid polymer electrolytes. The widely agreed upon vehicle for cation movement in PEO-based solid polymer electrolytes is the single cation, in which the cation is solvated by PEO ether oxygens. Here we report a different vehicle that becomes active with strong anion-cation interactions. In the common perspective, increasing ion-ion interactions would increase ion association, decrease cation solvation, and disable cation movement. Decreasing these interactions would have the opposite effect. We vary cation-anion interaction strength, using anion charge delocalization in molecular dynamics simulations. This creates a series of systems with levels of ion aggregation from single cations (weak interaction) to mostly ion aggregates (strong interaction). Although in the weak model single cations are faster than those in ion pairs and aggregates, with stronger interactions a different mechanism emerges. Paired cations move the fastest by visiting different anion partners in succession. The importance of this observation lies in the possibility of decoupling cation movement from polymer motion, which is required to prevent dendrite formation in both Li and Na ion batteries.