Erratum: Thermodynamic and Transport Properties of Tetrabutylphosphonium Hydroxide and Tetrabutylphosphonium Chloride-Water Mixtures via Molecular Dynamics Simulation.

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Insight into Cellulose Dissolution with the Tetrabutylphosphonium Chloride-Water Mixture using Molecular Dynamics Simulations.

All-atom molecular dynamics simulations are utilized to determine the properties and mechanisms of cellulose dissolution using the ionic liquid tetrabutylphosphonium chloride (TBPCl)-water mixture, from 63.1 to 100 mol % water. The hydrogen bonding between small and large cellulose bundles with 18 and 88 strands, respectively, is compared for all concentrations. The Cl, TBP, and water enable cellulose dissolution by working together to form a cooperative mechanism capable of separating the cellulose strands from the bundle. The chloride anions initiate the cellulose breakup, and water assists in delaying the cellulose strand reformation; the TBP cation then more permanently separates the cellulose strands from the bundle. The chloride anion provides a net negative pairwise energy, offsetting the net positive pairwise energy of the peeling cellulose strand. The TBP-peeling cellulose strand has a uniquely favorable and potentially net negative pairwise energy contribution in the TBPCl-water solution, which may partially explain why it is capable of dissolving cellulose at moderate temperatures and high water concentrations. The cellulose dissolution declines rapidly with increasing water concentration as hydrogen bond lifetimes of the chloride-cellulose hydroxyl hydrogens fall below the cellulose's largest intra-strand hydrogen bonding lifetime.

Thermodynamic and Transport Properties of Tetrabutylphosphonium Hydroxide and Tetrabutylphosphonium Chloride-Water Mixtures via Molecular Dynamics Simulation.

Thermodynamic, structural, and transport properties of tetrabutylphosphonium hydroxide (TBPH) and tetrabutylphosphonium chloride (TBPCl)-water mixtures have been investigated using all-atom molecular dynamics simulations in response to recent experimental work showing the TBPH-water mixtures capability as a cellulose solvent. Multiple transitional states exist for the water-ionic liquid (IL) mixture between 70 and 100 mol% water, which corresponds to a significant increase in water hydrogen bonds. The key transitional region, from 85 to 92.5 mol% water, which coincides with the mixture's maximum cellulose solubility, reveals small and distinct water veins with cage structures formed by the TBP+ ions, while the hydroxide and chloride ions have moved away from the P atom of TBP+ and are strongly hydrogen bonded to the water. The maximum cellulose solubility of the TBPH-water solution at approximately 91.1 mol% water, appears correlated with the destruction of the TBP's interlocking structure in the simulations, allowing the formation of water veins and channeling structures throughout the system, as well as changing from a subdiffusive to a near-normal diffusive regime, increasing the probability of the IL's interaction with the cellulose polymer. A comparison is made between the solution properties of TBPH and TBPCl with those of alkylimidazolium-based ILs, for which water appears to act as anti-solvent rather than a co-solvent.

On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations.

Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aß16-22 peptide and two of its mutants: Aß16-22(F19V,F20V), which does not form fibrils, and Aß16-22(F19L) which forms fibrils faster than the wild type. We observe that while oligomer formation kinetics depends strongly on the force field, structural properties, such as the most relevant protein-protein contacts, are similar between them. The oligomer formation kinetics obtained with different force fields differ more from each other than the kinetics between aggregating and nonaggregating peptides simulated with a single force field. We discuss the difficulties in comparing atomistic simulations of amyloid oligomer formation with experimental observables.

Translational Entropy and Dispersion Energy Jointly Drive the Adsorption of Urea to Cellulose.

The adsorption of urea on cellulose at room temperature has been studied using adsorption isotherm experiments and molecular dynamics (MD) simulations. The immersion of cotton cellulose into bulk urea solutions with concentrations between 0.01 and 0.30 g/mL led to a decrease in urea concentration in all solutions, allowing the adsorption of urea on the cellulose surface to be measured quantitatively. MD simulations suggest that urea molecules form sorption layers on both hydrophobic and hydrophilic surfaces. Although electrostatic interactions accounted for the majority of the calculated interaction energy between urea and cellulose, dispersion interactions were revealed to be the key driving force for the accumulation of urea around cellulose. The preferred orientation of urea and water molecules in the first solvation shell varied depending on the nature of the cellulose surface, but urea molecules were systematically oriented parallel to the hydrophobic plane of cellulose. The translational entropies of urea and water molecules, calculated from the velocity spectrum of the trajectory, are lower near the cellulose surface than in bulk. As urea molecules adsorb on cellulose and expel surface water into the bulk, the increase in the translational entropy of the water compensated for the decrease in the entropy of urea, resulting in a total entropy gain of the solvent system. Therefore, the cellulose-urea dispersion energy and the translational entropy gain of water are the main factors that drive the adsorption of urea on cellulose.

Theory of wavelet-based coarse-graining hierarchies for molecular dynamics.

We present a multiresolution approach to compressing the degrees of freedom and potentials associated with molecular dynamics, such as the bond potentials. The approach suggests a systematic way to accelerate large-scale molecular simulations with more than two levels of coarse graining, particularly applications of polymeric materials. In particular, we derive explicit models for (arbitrarily large) linear (homo)polymers and iterative methods to compute large-scale wavelet decompositions from fragment solutions. This approach does not require explicit preparation of atomistic-to-coarse-grained mappings, but instead uses the theory of diffusion wavelets for graph Laplacians to develop system-specific mappings. Our methodology leads to a hierarchy of system-specific coarse-grained degrees of freedom that provides a conceptually clear and mathematically rigorous framework for modeling chemical systems at relevant model scales. The approach is capable of automatically generating as many coarse-grained model scales as necessary, that is, to go beyond the two scales in conventional coarse-grained strategies; furthermore, the wavelet-based coarse-grained models explicitly link time and length scales. Furthermore, a straightforward method for the reintroduction of omitted degrees of freedom is presented, which plays a major role in maintaining model fidelity in long-time simulations and in capturing emergent behaviors.

Linear, non-linear and plastic bending deformation of cellulose nanocrystals.

The deformation behaviour of cellulose nanocrystals under bending loads was investigated by using atomistic molecular dynamics (MD) simulations and finite element analysis (FEA), and compared with electron micrographs of ultrasonicated microfibrils. The linear elastic, non-linear elastic, and plastic deformation regions were observed with increasing bending displacements. In the linear elastic region, the deformation behaviour was highly anisotropic with respect to the bending direction. This was due to the difference in shear modulus, and the deformation could be approximated by standard continuum mechanics using the corresponding elastic tensors. Above the linear elastic region, the shear deformation became a dominant factor as the amplitude of shear strain drastically increased. Plastic deformation limit was observed at the bending angle above about 60°, independent of the bending direction. The morphology of the atomistic model of plastically deformed cellulose crystals showed a considerable similarity to the kinked cellulose microfibrils observed by transmission electron microscopy. Our observations highlight the importance of shear during deformation of cellulose crystals and provide an understanding of basic deformations occurring during the processing of cellulose materials.

Classification of precursors in nanoscale droplets.

Molecular precursors, ultrathin films that precede spreading droplets, are still far from being understood, despite intensive study. The inherent microscopic length scales make small-scale experimental techniques and molecular simulation ideal methods to study this phenomenon. Previous work on molecular precursors using nanoscale droplets, however, consistently suffers from incorrect measurement of the dimensions of the precursor film. An alternative method to accurately characterize the precursor film is presented here. In contrast to previous measures, this method (i) allows for easy detection and characterization of precursors and (ii) yields wetting dynamics that agree with experimental observations. Finally, we briefly comment on previous studies whose conclusions may merit reconsideration in light of the present work.

Requirements for the Formation and Shape of Microscopic Precursors in Droplet Spreading.

While the mass transport mechanisms and dynamics of molecular precursors, ultrathin films that precede spreading droplets, are well understood, the requirements for their formation and the reasons for the occurrence of different precursor shapes remain unclear. In this work, we study these requirements using molecular dynamics simulations of spreading droplets and extensive free energy computations. For a simple simulation model, we demonstrate that with growing droplet-substrate attraction, spreading passes succesively through regimes with no precursor, a monolayer precursor, and a continuously growing precursor. We show that the onset of layer formation and the changes in the precursor shape correlate with the free energy of layer formation. On the basis of these findings, we show that a positive spreading coefficient is sufficient but not necessary for precursor formation.

Effect of Water Content in N-Methylmorpholine N-Oxide/Cellulose Solutions on Thermodynamics, Structure, and Hydrogen Bonding.

Native crystalline cellulose is notoriously difficult to dissolve due to its dense hydrogen bond network between chains and weaker hydrophobic forces between cellulose sheets. N-Methylmorpholine N-oxide (NMMO), the solvent behind the Lyocell process, is one of the most successful commercial solvents for the nonderivatized dissolution of cellulose. In this process, water plays a very important role. Its presence at low concentrations allows NMMO to dissolve substantial amounts of cellulose, while at much higher concentrations it precipitates the crystalline fibers. Using all-atom molecular dynamics, we study the thermodynamic and structural properties of ternary solutions of cellulose, NMMO, and water. Using the two-phase thermodynamic method to calculate solvent entropy, we estimate the free energy of dissolution of cellulose as a function of the water concentration and find a transition of spontaneity that is in excellent agreement with experiment. In pure water, we find that cellulose dissolution is nonspontaneous, a result that is due entirely to strong decreases in water entropy. Although the combined effect of enthalpy on dissolution in water is negligible, we observe a net loss of hydrogen bonds, resulting in a change in hydrogen bond energy that opposes dissolution. At lower water concentrations, cellulose dissolution is spontaneous and largely driven by decreases in enthalpy, with solvent entropy playing only a very minor role. When searching for the root causes of this enthalpy decrease, a complex picture emerges in which not one but many different factors contribute to NMMO's good solvent behavior. The reduction in enthalpy is led by the formation of strong hydrogen bonds between cellulose and NMMO's N-oxide, intensified through van der Waals interactions between NMMO's nonpolar body and the nonpolar surfaces of cellulose and unhindered by water at low concentrations due to the formation of efficient hydrogen bonds between water and cellulose.

Automated discovery of reaction pathways, rate constants, and transition states using reactive molecular dynamics simulations.

We provide a methodology for deducing quantitative reaction models from reactive molecular dynamics simulations by identifying, quantifying, and evaluating elementary reactions of classical trajectories. Simulations of the inception stage of methane oxidation are used to demonstrate our methodology. The agreement of pathways and rates with available literature data reveals the potential of reactive molecular dynamics studies for developing quantitative reaction models.

Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations.

Amyloids are associated with diseases, including Alzheimer's, as well as functional roles such as storage of peptide hormones. It is still unclear what differences exist between aberrant and functional amyloids. However, it is known that soluble oligomers formed during amyloid aggregation are more toxic than the final fibrils. Here, we perform molecular dynamics simulations to study the aggregation of the amyloid-ß peptide Aß25-35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Although the three peptides have similar primary sequences, tachykinin peptides, in contrast to Aß25-35, form nontoxic amyloids. Our simulations reveal that the charge of the C-terminus is essential to controlling the aggregation process. In particular, when the kassinin C-terminus is not amidated, the aggregation kinetics decreases considerably. In addition, we observe that the monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations.

Smoothing of contact lines in spreading droplets by trisiloxane surfactants and its relevance for superspreading.

Superspreading, the greatly enhanced spreading of aqueous solutions of trisiloxane surfactants on hydrophobic substrates, is of great interest in fundamental physics and technical applications. Despite numerous studies in the last 20 years, the superspreading mechanism is still not well understood, largely because the molecular scale cannot be resolved appropriately either experimentally or using continuum simulations. The absence of molecular-scale knowledge has led to a series of conflicting hypotheses based on different assumptions of surfactant behavior. We report a series of large-scale molecular dynamics simulations of aqueous solutions of superspreading and non-superspreading surfactants on different substrates. We find that the transition from the liquid-vapor to the solid-liquid interface is smooth for superspreading conditions, allowing direct adsorption through the contact line. This finding complements a study [Karapetsas et al., J. Fluid Mech., 2011, 670, 5-37], which predicts that superspreading can occur if this adsorption path is possible. Based on the observed mechanism, we provide plausible explanations for the influence of the substrate hydrophobicity, the surfactant chain length, and the surfactant concentration on the superspreading phenomenon. We also briefly address that the observed droplet shape is a mechanism to overcome the Huh-Scriven paradox of infinite viscous dissipation at the contact line.

Mechanisms of hydrogen bond formation between ionic liquids and cellulose and the influence of water content.

We study the dynamics of the formation of multiple hydrogen bonds between ionic liquid anions and cellulose using molecular dynamics simulations. We examine fifteen different ionic liquids composed of 1-alkyl-3-methylimidazolium cations ([Cnmim], n = 1, 2, 3, 4, 5) paired with either chloride, acetate or dimethylphosphate. We map the transitions of anions hydrogen bonded to cellulose into different bonding states. We find that increased tail length in the ionic liquids has only a very minor effect on these transitions, tending to slow the dynamics of the transitions and increasing the hydrogen bond lifetimes. Each anion can form up to four hydrogen bonds with cellulose. We find that this hydrogen bond "redundancy" leads to multiply bonded anions having lifetimes three to four times that of singly bound anions. Such redundant hydrogen bonds account for roughly half of all anion-cellulose hydrogen bonds. Additional simulations for [C2mim]Cl, [C2mim]Ac and [C2mim]DMP were performed at different water concentrations between 70 mol% and 90 mol%. It was found that water crowds the hydrogen bond-accepting sites of the anions, preventing interactions with cellulose. The more water that is present in the system, the more crowded these sites become. Thus, if a hydrogen bond between an anion and cellulose breaks, the likelihood that it will be replaced by a nearby water molecule increases as well. We show that the formation of these "redundant" hydrogen bonding states is greatly affected by the presence of water, leading to steep drops in hydrogen bonding between the anions and cellulose.

Atomistic potentials for trisiloxane, alkyl ethoxylate, and perfluoroalkane-based surfactants with TIP4P/2005 and application to simulations at the air-water interface.

The mechanism of superspreading, the greatly enhanced spreading of water droplets facilitated by trisiloxane surfactants, is still under debate, largely because the role and behavior of the surfactants cannot be sufficiently resolved by experiments or continuum simulations. Previous molecular dynamics studies have been performed with simple model molecules or inaccurate models, strongly limiting their explanatory power. Here we present a force field dedicated to superspreading, extending existing quantum-chemistry-based models for the surfactant and the TIP4P/2005 water model ( Abascal et al. J. Chem. Phys. , 2005 , 123 , 234505 ). We apply the model to superspreading trisiloxane surfactants and nonsuperspreading alkyl ethoxylate and perfluoroalkane surfactants at various concentrations at the air-water interface. We show that the developed model accurately predicts surface tensions, which are typically assumed important for superspreading. Significant differences between superspreading and traditional surfactants are presented and their possible relation to superspreading discussed. Although the force field has been developed for superspreading problems, it should also perform well for other simulations involving polymers or copolymers with water.

Coating thickness and coverage effects on the forces between silica nanoparticles in water.

The structure and interactions of coated silica nanoparticles have been studied in water using molecular dynamics simulations. For 5 nm diameter amorphous silica nanoparticles, we studied the effects of varying the chain length and grafting density of polyethylene oxide on the nanoparticle coating's shape and on nanoparticle-nanoparticle effective forces. For short ligands of length n = 6 and n = 20 repeat units, the coatings are radially symmetric while for longer chains (n = 100) the coatings are highly anisotropic. This anisotropy appears to be governed primarily by chain length, with coverage playing a secondary role. For the largest chain lengths considered, the strongly anisotropic shape makes fitting to a simple radial force model impossible. For shorter ligands, where the coatings are isotropic, we found that the force between pairs of nanoparticles is purely repulsive and can be fit to the form (R/2r(core) - 1)(-b) where R is the separation between the center of the nanoparticles, r(core) is the radius of the silica core, and b is measured to be between 2.3 and 4.1.

Multilevel summation for dispersion: a linear-time algorithm for r(-6) potentials.

We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics simulations [R. D. Skeel, I. Tezcan, and D. J. Hardy, J. Comput. Chem. 23, 673 (2002)], to handle dispersion interactions. While dispersion potentials are formally short-ranged, accurate calculation of forces and energies in interfacial and inhomogeneous systems require long-range methods. The MLS method offers some significant advantages compared to the particle-particle particle-mesh and smooth particle mesh Ewald methods. Unlike mesh-based Ewald methods, MLS does not use fast Fourier transforms and is thus not limited by communication and bandwidth concerns. In addition, it scales linearly in the number of particles, as compared with the O(NlogN) complexity of the mesh-based Ewald methods. While the structure of the MLS method is invariant for different potentials, every algorithmic step had to be adapted to accommodate the r(-6) form of the dispersion interactions. In addition, we have derived error bounds, similar to those obtained by Hardy ["Multilevel summation for the fast evaluation of forces for the simulation of biomolecules," Ph.D. thesis, University of Illinois at Urbana-Champaign, 2006] for the electrostatic MLS. Using a prototype implementation, we have demonstrated the linear scaling of the MLS method for dispersion, and present results establishing the accuracy and efficiency of the method.

The role of the cation in the solvation of cellulose by imidazolium-based ionic liquids.

We present a systematic molecular dynamics study examining the roles of the individual ions of different alkylimidazolium-based ionic liquids in the solvation of cellulose. We examine combinations of chloride, acetate, and dimethylphosphate anions paired with cations of increasing tail length to elucidate the precise role of the cation in solvating cellulose. In all cases we find that the cation interacts with the nonpolar domains of cellulose through dispersion interactions, while interacting electrostatically with the anions bound at the polar domains of cellulose. Furthermore, the structure and dimensions of the imidazolium head facilitate the formation of large chains and networks of alternating cations and anions that form a patchwork, satisfying both the polar and nonpolar domains of cellulose. A subtle implication of increasing tail length is the dilution of the anion concentration in the bulk and at the cellulose surface. We show how this decreased concentration of anions in the bulk affects hydrogen bond formation with cellulose and how rearrangements from single hydrogen bonds to multiple shared hydrogen bonds can moderate the loss in overall hydrogen bond numbers. Additionally, for the tail lengths examined in this study we observe only a very minor effect of tail length on the solvation structure and overall interaction energies.

Observed mechanism for the breakup of small bundles of cellulose Iα and Iß in ionic liquids from molecular dynamics simulations.

Explicit, all-atom molecular dynamics simulations are used to study the breakup of small bundles of cellulose Iα and Iß in the ionic liquids [BMIM]Cl, [EMIM]Ac, and [DMIM]DMP. In all cases, significant breakup of the bundles is observed with the initial breakup following a common underlying mechanism. Anions bind strongly to the hydroxyl groups of the exterior strands of the bundle, forming negatively charged complexes. Binding also weakens the intrastrand hydrogen bonds present in the cellulose strands, providing greater strand flexibility. Cations then intercalate between the individual strands, likely due to charge imbalances, providing the bulk to push the individual moieties apart and initiating the separation. The peeling of an individual strand from the main bundle is observed in [EMIM]Ac with an analysis of its hydrogen bonds with other strands showing that the chain detaches glucan by glucan from the main bundle in discrete, rapid events. Further analysis shows that the intrastrand hydrogen bonds of each glucan tend to break for a sustained period of time before the interstrand hydrogen bonds break and strand detachment occurs. Examination of similar nonpeeling strands shows that, without this intrastrand hydrogen bond breakage, the structural rigidity of the individual unit can hinder its peeling despite interstrand hydrogen bond breakage.

Effects of water concentration on the structural and diffusion properties of imidazolium-based ionic liquid-water mixtures.

We have used molecular dynamics simulations to study the properties of three ionic liquid (IL)-water systems: 1-butyl-3-methylimidazolium chloride ([bmim]Cl), 1-ethyl-3-methylimidazolium acetate ([emim][Ac]), and 1,3-dimethylimidazolium dimethylphosphate ([dmim][DMP]). We observe the transition of those mixtures from pure IL to aqueous solution by analyzing the changes in important bulk properties (density) and structural and bonding properties (radial distribution functions, water clustering, hydrogen bonding, and cationic stacking) as well as dynamical properties (diffusion coefficients) at 12 different concentration samplings of each mixture, ranging from 0.0 to 99.95 mol % water. Our simulations revealed across all of the different structural, bonding, and dynamical properties major structural changes consistent with a transition from IL-water mixture to aqueous solution in all three ILs at water concentrations around 75 mol %. Among the structural changes observed were rapid increase in the frequency of hydrogen bonds, both water-water and water-anion. Similarly, at these critical concentrations, the water clusters formed begin to span the entire simulation box, rather than existing as isolated networks of molecules. At the same time, there is a sudden decrease in cationic stacking at the transition point, followed by a rapid increase near 90 mol % water. Finally, the diffusion coefficients of individual cations and anions show a rapid transition from rates consistent with diffusion in IL's to rates consistent with diffusion in water beginning at 75 mol % water. The location of this transition is consistent, for [bmim]Cl and [dmim][DMP], with the water concentration limit above which the ILs are unable to dissolve cellulose.