Richard P. Matthews

Competitive pi interactions and hydrogen bonding within imidazolium ionic liquids

In this paper we have explored the structural and energetic landscape of potential π(+)-π(+) stacked motifs, hydrogen-bonding arrangements and anion-π(+) interactions for gas-phase ion pair (IP) conformers and IP-dimers of 1,3-dimethylimidazolium chloride, [C1C1im]Cl. We classify cation-cation ring stacking as an electron deficient π(+)-π(+) interaction, and a competitive anion on-top IP motif as an anion-donor π(+)-acceptor interaction. 21 stable IP-dimers have been obtained within an energy range of 0-126 kJ mol(-1). The structures have been found to exhibit a complex interplay of structural features. We have found that low energy IP-dimers are not necessarily formed from the lowest energy IP conformers. The sampled range of IP-dimers exhibits new structural forms that cannot be recovered by examining the ion-pairs alone, moreover the IP-dimers are recovering additional key features of the local liquid structure. Including dispersion is shown to impact both the relative energy ordering and the geometry of the IPs and IP-dimers, however the impact is found to be subtle and dependent on the underlying functional.

The impact of anion electronic structure: similarities and differences in imidazolium based ionic liquids

In this paper the structural and energetic landscapes of ion-pair dimer conformers of 1,3-dimethylimidazolium based ionic liquids have been explored ([C1C1im][A])2, A = Cl(-), [NO3](-), [MeSO4](-), [OTf](-) and [BF4](-)). A common low-energy conformer has been selected for full electronic structure analysis. We have compared and contrasted each cluster based on the relative hydrogen bonding ability (β-value) of the anion, which varies experimentally as Cl(-) > [NO3](-) ≈ [MeSO4](-) > [OTf](-) ≈ [BF4](-). Correlations between experimental β-values, computed binding energies, charge transfer and various hydrogen bonding data have been made and outliers have been explained in terms of environmental effects present in the liquid phase. This is most evident in the structurally similar [MeSO4](-) and [OTf](-) anions that have very similar hydrogen bonding motifs, but significantly different β-values. Moreover, detailed analysis of the cluster molecular orbitals, for each anion, reveals a subtle interplay between two modes of interaction, an in-plane traditional H-bonding and inter-planar anion-π interaction. Inter-planar anion-π interactions are particularly prominent for the [NO3](-) cluster. We have rationalized how the full range of interactions could impact on the structuring of ILs at surfaces and the effect these may have on viscosity.

Influence of Rigidity and Knot Complexity on the Knotting of Confined Polymers.

We employ computer simulations and thermodynamic integration to analyze the effects of bending rigidity and slit confinement on the free energy cost of tying knots, ΔFknotting, on polymer chains under tension. A tension-dependent, nonzero optimal stiffness κmin exists, for which ΔFknotting is minimal. For a polymer chain with several stiffness domains, each containing a large amount of monomers, the domain with stiffness κmin will be preferred by the knot. A local analysis of the bending in the interior of the knot reveals that local stretching of chains at the braid region is responsible for the fact that the tension-dependent optimal stiffness has a nonzero value. The reduction in ΔFknotting for a chain with optimal stiffness relative to the flexible chain can be enhanced by tuning the slit width of the 2D confinement and increasing the knot complexity. The optimal stiffness itself is independent of the knot types we considered, while confinement shifts it toward lower values.

Influence of fluctuating membranes on self-assembly of patchy colloids.

A coarse-grained computational model is used to investigate the effect of a fluid membrane on patchy-particle assembly into biologically relevant structures motivated by viral cores and clathrin. For cores, we demonstrate a nonmonotonic dependence of the promotion of assembly on membrane stiffness. If the membrane is significantly deformable, cores are enveloped in buds, although this effect is suppressed for very flexible membranes. In the less deformable regime, we observe no marked enhancement for cores, even for strong adhesion to the surface. For clathrinlike particles, we again observe the formation of buds, whose morphology depends on membrane flexibility.

Effect of Bending Rigidity on the Knotting of a Polymer under Tension

A coarse-grained computational model is used to investigate how the bending rigidity of a polymer under tension affects the formation of a trefoil knot. Thermodynamic integration techniques are applied to demonstrate that the free-energy cost of forming a knot has a minimum at nonzero bending rigidity. The position of the minimum exhibits a power-law dependence on the applied tension. For knotted polymers with nonuniform bending rigidity, the knots preferentially localize in the region with a bending rigidity that minimizes the free energy.

Experimentally Consistent Ion Association Predicted for Metal Solutions from Free Energy Simulations

The calculation of association constants from computer simulations has historically been complicated because of difficulties in validating metal ion force fields for solution simulations. Here we develop a method that produces a force field for divalent metal ions in metal sulfate solutions (i.e., Mg(2+)SO(4)(2-), Ca(2+)SO(4)(2-), Mn(2+)SO(4)(2-), Fe(2+)SO(4)(2-), Co(2+)SO(4)(2-), Ni(2+)SO(4)(2-), Cu(2+)SO(4)(2-), and Zn(2+)SO(4)(2-)). Using free energy of perturbation calculations, we are able to calibrate the potential of mean force W(r) for these metal sulfate solutions. The calibrated free energy profiles then allow us to produce association constants for contact, solvent-shared, and solvent-separated ion pairs that are in excellent agreement with available ultrasonic and dielectric spectroscopic data. This metal solution force field is accurate for the calculation of relative free energies from physical and biophysical computer simulations.

Structures and pathways for clathrin self-assembly in the bulk and on membranes

We present a coarse-grained model of clathrin that is simple enough to be computationally tractable yet includes key observed qualitative features: a triskelion structure with excluded volume between legs; assembly of polymorphic cages in the bulk; formation of buds on a membrane. We investigate the assembly of our model using both Monte Carlo simulations and molecular dynamics with hydrodynamic interactions, in the latter employing a new membrane boundary condition. In the bulk, a range of known clathrin structures are assembled. A membrane budding pathway involving the coalescence of multiple small clusters is identified.

Dynamics of self-assembly of model viral capsids in the presence of a fluctuating membrane.

A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are presented, showing the effect of varying interaction strength, membrane stiffness, and membrane viscosity. Furthermore, the effect of hydrodynamic interactions is investigated. Attraction to a membrane may promote assembly, including for subunit interaction strengths for which it does not occur in the bulk, and may also decrease single-core assembly time. The membrane budding rate is strongly increased by hydrodynamic interactions. The membrane deformation rate is important in determining the finite-time yield. Higher rates may decrease the entropic penalty for assembly and help guide subunits toward each other but may also block partial cores from being completed. For increasing subunit interaction strength, three regimes with different effects of the membrane are identified.

Conformational flexibility of sulphur linked saccharides a possible key to their glycosidase inhibitor activity

We investigate the reasons why sulphur linked saccharides are good inhibitors of retaining β-glycosidases. A comparison of the conformational space and electronic profile of the oxygen and sulphur linked oligosaccharides using HF/6-31G* * reveals that they are electronically very similar and have identical conformational preferences. However, the conformational barriers separating the minima are at least 3 kcal mol− 1 lower for the sulphur linkage implying a greater conformational flexibility. Furthermore, we find using natural bond orbital analysis that the sulphur linkage is significantly less open to acid hydrolysis than the oxygen, found in the natural sugar on which retaining β-glycosidases act. Our nanosecond molecular dynamics studies of Bacillus agaradhaerens glycosidase reveal that the thio-cellotriose binds the enzyme 6 kcal mol− 1more strongly than does cellotriose. A comparison of the conformational space of the sulphur linkage with that of the oxygen glycosidic linkage provides an explanation for the stronger binding which appears to be due to the greater flexibility of the sulphur glycosidic linkage.

Experimental validation of calculated atomic charges in ionic liquids

A combination of X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy has been used to provide an experimental measure of nitrogen atomic charges in nine ionic liquids (ILs). These experimental results are used to validate charges calculated with three computational methods: charges from electrostatic potentials using a grid-based method (ChelpG), natural bond orbital population analysis, and the atoms in molecules approach. By combining these results with those from a previous study on sulfur, we find that ChelpG charges provide the best description of the charge distribution in ILs. However, we find that ChelpG charges can lead to significant conformational dependence and therefore advise that small differences in ChelpG charges (<0.3 e) should be interpreted with care. We use these validated charges to provide physical insight into nitrogen atomic charges for the ILs probed.