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.

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title: Fast and facile dissolution of cellulose with tetrabutylphosphonium hydroxide containing 40 wt% water.
abstract: Tetrabutylphosphonium hydroxide containing 40 wt% water dissolved 20 wt% cellulose at the final concentration within 5 minutes under mild stirring at 25 °C.

title: Assessment of phosphonium ionic liquid-dimethylformamide mixtures for dissolution of cellulose
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title: Observed mechanism for the breakup of small bundles of cellulose Iα and Iβ in ionic liquids from molecular dynamics simulations.
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title: Disintegration and dissolution kinetics of wood chips in ionic liquids
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title: Theoretical Insights into the Role of Water in the Dissolution of Cellulose Using IL/Water Mixed Solvent Systems.
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title: Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids.
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title: Reversible multiple time scale molecular dynamics
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title: Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation.
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title: Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
abstract: A numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated. The relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration. The method is applied to a molecular dynamics simulation of a liquid of 64 n-butane molecules and compared to a simulation using generalized coordinates. The method should be useful for molecular dynamics calculations on large molecules with internal degrees of freedom.

title: Error estimates on averages of correlated data
abstract: We describe how the true statistical error on an average of correlated data can be obtained with ease and efficiency by a renormalization group method. The method is illustrated with numerical and analytical examples, having finite as well as infinite range correlations.

title: A modified TIP3P water potential for simulation with Ewald summation.
abstract: The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for molecular dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have Lennard-Jones parameters, thus making the model independent of the combining rules used for the calculation of nonbonded, heteroatomic interaction energies, and limiting the number of Lennard-Jones calculations required. Under these conditions, this model provides accurate density (rho = 0.997 g/ml) and heat of vaporization (DeltaH(vap) = 10.53 kcal/mol) at 25 degrees C and 1 atm, but also provides improved structure in the second peak of the O-O radial distribution function and improved values for the dielectric constant (epsilon(0) = 89) and the diffusion coefficient (D = 4.0 x 10(-5) cm(2)/s) relative to the original parametrization. Like the original parameterization, however, this model does not show a temperature density maximum. Several similar models are considered with the additional constraint of trying to match the performance of the optimized potentials for liquid simulation atom force field to that obtained when using the simulation conditions under which it was originally designed, but no model was entirely satisfactory in reproducing the relative difference in free energies of hydration between the model compounds, phenol and benzene. Finally, a model that incorporates a long-range correction for truncated Lennard-Jones interactions is presented, which provides a very accurate dielectric constant (epsilon(0) = 76), however, the improvement in this estimate is on the same order as the uncertainty in the calculation.

title: GLYCAM06: A generalizable biomolecular force field. Carbohydrates
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title: Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.
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title: Time-averaged mean square displacement for switching diffusion.
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title: Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
abstract: BackgroundThe Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.ResultsThe work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.ConclusionsAvogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

title: Maintenance-Free Cellulose Solvents Based on Onium Hydroxides
abstract: Here, we report maintenance-free cellulose solvents that dissolve much cellulose within a few minutes under mild conditions even in the presence of water. We have examined a series of aqueous solutions of tetraalky-phosphonium and tetraalkyl-ammonium hydroxides to clarify the effect of cation species on cellulose dissolving. Aqueous solutions of the many hydroxides examined here were found to dissolve cellulose at room temperature, and electrostatic interaction and/or steric hindrance of component ions are suggested to affect the cellulose-dissolving ability. In spite of increasing water content after dissolution of wet cellulose, the water content automatically reduced to less than 60% just by keeping the filtrated solution in the air. The solvation state of cellulose in aqueous onium hydroxide solutions is discussed with 13C NMR chemical shift of cellobiose signals in these solutions. They dissolve cellulose only when the 13C NMR signal of the carbon atom at the 12 position of cellobiose is 64.8 ppm or ...

title: Hydrogen bonds in aqueous electrolyte solutions: statistics and dynamics based on both geometric and energetic criteria.
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title: Resolving the hydrogen bond dynamics conundrum
abstract: This paper analyzes dynamic properties of hydrogen bonds in liquid water. We use molecular dynamics simulation to calculate different probability densities that govern the time evolution of the formation and rupture of hydrogen bonds. We provide analytical connections between these functions. Excellent agreement with our simulation results is observed. We prove transition state theory rate constant to be identical to the inverse of the associated mean first passage time (hydrogen bond lifetime). Hence, the analysis establishes its Arrhenius temperature dependence. We give the explicit relation between reactive flux correlation function for the relaxation dynamics of hydrogen bonds, and their first passage time probability densities. All the different observations in the existing literature, associated with various estimates of hydrogen bonding times in liquid water that are affected (or not affected) by particular bond criteria, as well as by different definitions of hydrogen bond lifetimes applied in sim...

title: Hydrogen-bond kinetics in liquid water
abstract: HYDROGEN bonds play a crucial role in the behaviour of water1–4; their spatial patterns and fluctuations characterize the structure and dynamics of the liquid5–7. The processes of breaking and making hydrogen bonds in the condensed phase can be probed indirectly by a variety of experimental techniques8, and more quantitative information can be obtained from computer simulations9. In particular, simulations have revealed that on long timescales the relaxation behaviour of hydrogen bonds in liquid water exhibit non-exponential kinetics7,10–13, suggesting that bond making and breaking are not simple processes characterized by well defined rate constants. Here we show that these kinetics can be understood in terms of an interplay between diffusion and hydrogen-bond dynamics. In our model, which can be extended to other hydrogen-bonded liquids, diffusion governs whether a specific pair of water molecules are near neighbours, and hydrogen bonds between such pairs form and persist at random with average lifetimes determined by rate constants for bond making and breaking.

title: The reorientation mechanism of hydroxide ions in water: A molecular dynamics study
abstract: Classical molecular dynamics simulations with a polarizable force field indicate two major structural motifs for the aqueous bulk solvation of OH−: a four- and a five-coordinated solvent hydrogen bond donor to OH− in addition to a weak solvent hydrogen bond acceptor by OH−. A two-step mechanism for the reorientation of OH− in water is proposed: first, the reorientation of OH− is initiated by the coupled translation with the water molecules in its first solvation shell; second, the OH− relaxes to the minimum energy configuration. The first step is the rate-limiting one for this mechanism.

title: A jump motion of small molecules in glassy polymers: A molecular dynamics simulation
abstract: Motions of small molecules in an amorphous polymer below its glass transition temperature Tg have been studied using molecular dynamics simulation. An infinite length chain model having 600 interacting sites, each representing a CH2 unit, is used. The system, which is composed of the infinite length chain and ten spherical molecules representing oxygen, is examined at 30 deg below Tg. Although most of the molecules are trapped by cages created by the chain, a molecule reveals clear jump motions. During the jump, no significant change is found in the local free volume as well as in the nonbonded energy acting on the molecule. Potential energy surfaces for the molecules clearly show the cooperative process of jump and chain motions: a generation of a vacant cage and a channel which connects two cages. It is found that the molecule passes through the channel without significant energy barrier and concentration of free volume.

title: Diffusion of penetrants in amorphous polymers: A molecular dynamics study
abstract: Molecular dynamics calculations are performed that simulate the diffusion of penetrant molecules through an amorphous polymer. For the polymer and the penetrant molecules, model potentials are chosen that approximate polyethylene and methane, respectively. The simulations extend over several hundred picoseconds. The results indicate that permeation proceeds by a hopping mechanism: The penetrants dwell in voids in the polymer matrix for a considerable time and perform fast jumps between neighboring voids. A potential scaling technique based on the fact that individual jump events are activated processes is presented by which the calculation of penetrant self‐diffusion coefficients is speeded up.

title: Second-Generation ReaxFF Water Force Field: Improvements in the Description of Water Density and OH-Anion Diffusion.
abstract: Hydronium (H3O+) and hydroxide (OH-) ions have anomalously large diffusion constants in aqueous solutions due to their combination of vehicular and Grotthuss hopping diffusion mechanisms. An improvement of the ReaxFF reactive water force field on the basis of our first-generation water force field (water-2010) is presented to describe the proton transfer (PT) mechanisms of H3O+ and OH- in water. Molecular dynamics simulation studies with the water-2017 force field support the Eigen-Zundel-Eigen mechanism for PT in acidic aqueous solution and reproduce the hypercoordinated solvation structure of the OH- in a basic environment. In particular, it predicts the correct order of the diffusion constants of H2O, H3O+, and OH- and their values are in agreement with the experimental data. Another interesting observation is that the diffusion constants of H3O+ and OH- are close to each other at high concentration due to the strong correlation between OH- ions in basic aqueous solution. On the basis of our results, it is shown that ReaxFF provides a novel approach to study the complex acid-base chemical reactions in aqueous solution with any pH value.

title: Geometry controlled anomalous diffusion in random fractal geometries: looking beyond the infinite cluster.
abstract: We investigate the ergodic properties of a random walker performing (anomalous) diffusion on a random fractal geometry. Extensive Monte Carlo simulations of the motion of tracer particles on an ensemble of realisations of percolation clusters are performed for a wide range of percolation densities. Single trajectories of the tracer motion are analysed to quantify the time averaged mean squared displacement (MSD) and to compare this with the ensemble averaged MSD of the particle motion. Other complementary physical observables associated with ergodicity are studied, as well. It turns out that the time averaged MSD of individual realisations exhibits non-vanishing fluctuations even in the limit of very long observation times as the percolation density approaches the critical value. This apparent non-ergodic behaviour concurs with the ergodic behaviour on the ensemble averaged level. We demonstrate how the non-vanishing fluctuations in single particle trajectories are analytically expressed in terms of the fractal dimension and the cluster size distribution of the random geometry, thus being of purely geometrical origin. Moreover, we reveal that the convergence scaling law to ergodicity, which is known to be inversely proportional to the observation time T for ergodic diffusion processes, follows a power-law ∼T(-h) with h < 1 due to the fractal structure of the accessible space. These results provide useful measures for differentiating the subdiffusion on random fractals from an otherwise closely related process, namely, fractional Brownian motion. Implications of our results on the analysis of single particle tracking experiments are provided.

title: Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate
abstract: The aims of this study were to identify thermophilic microbial communities that degrade green waste in the presence of the ionic liquids (IL) tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate and examine preservation methods for IL-tolerant communities. High-solids incubations with stepwise increases in IL concentration were conducted to enrich for thermophilic IL-tolerant communities that decomposed green waste. 16S rRNA sequencing of enriched communities revealed microorganisms capable of tolerating high levels of IL. Cryogenic preservation of enriched communities reduced the IL tolerance of the community and decreased the relative abundance of IL-tolerant organisms. The use of cryoprotectants did not have an effect on microbial activity on green waste of the stored community. A successful approach was developed to enrich communities that decompose green waste in thermophilic high-solids environments in the presence of IL. Alternative community storage and revival methods are necessary for maintenance and recovery of IL-tolerant communities. The enriched communities provide a targeted source of enzymes for the bioconversion of IL-pretreated green waste for conversion to biofuels.

title: Mechanism of Tetraalkylammonium Headgroup Degradation in Alkaline Fuel Cell Membranes
abstract: Cationic headgroups such as tetramethylammonium (TMA) undergo degradation in alkaline conditions through two different mechanisms. In the first mechanism, a hydroxide ion performs an SN2 attack on the methyl groups and directly forms methanol. In the second mechanism, an ylide (trimethylammonium methylide) and a water molecule are formed by the abstraction of a proton from a methyl group. The ylide subsequently reacts with water to form methanol. Both pathways have the same overall barrier as observed in our reaction path calculations with density functional theory. The ylide mechanism is verified by H−D exchange observed between the aqueous phase and the cationic head group. We also discuss the effect of the medium and the water content on the calculated reaction barriers. Good solvation of the head-groups and hydroxide ions is essential for the overall chemical stability of alkaline membranes.

title: Reactivity of ionic liquids
abstract: Ionic liquids are becoming widely used in synthetic organic chemistry and yet relatively little attention has been paid to the intrinsic reactivity of these low temperature molten salts. Clues to the non-innocent nature of many ionic liquids are contained in the reports of altered reactivity of dissolved substrates, unexpected catalytic activity and unforeseen by-product formation. In this review, we focus on the reactivity of ionic liquids, as opposed to reactivity in ionic liquids (although discussion of the latter is often included where it aids understanding of the former).

title: Relative Chemical Stability of Imidazolium-Based Alkaline Anion Exchange Polymerized Ionic Liquids
abstract: We thoroughly investigate and quantify the chemical stability of an imidazolium-based alkaline anion exchange polymerized ionic liquid (PIL), poly(1-[(2-methacryloyloxy)ethyl]-3-butylimidazolium hydroxide) (poly(MEBIm-OH), over a broad range of humidities, temperatures, and alkaline concentrations using the combined techniques of electrochemical impedance spectroscopy and nuclear magnetic resonance spectroscopy. High chemical stability was observed under dry conditions (10% RH) at 30 °C, humid and saturated conditions up to 80 °C, and even in mild alkaline conditions ([KOH] 1 M). Under these conditions, we suggest an imidazolium ring-opening mechanism as the primary degradation pathway, based on a detailed analysis of the 1H NMR spectra. Similar to poly(MEBIm-OH), other alkaline anion (carbonate (CO32–) and bicarbonate (HCO3–)) exchange PILs were als...

title: Comparing reduced partial charge models with polarizable simulations of ionic liquids.
abstract: Molecular ionic liquids are typically characterized by strong electrostatic interactions resulting in a charge ordering and retardation of their translational and rotational behaviour. Unfortunately, this effect is often overestimated in classical molecular dynamics simulations. This can be circumvented in a twofold way: the easiest way is to reduce the partial charges of the ions to sub-integer values of ±0.7-0.9 e. The more realistic model is to include polarizable forces, e.g. Drude-oscillators, but it comes along with an increasing computational effort. On the other hand, charge-scaled models are claimed to take an average polarizability into account. But do both models have the same impact on structure and dynamics of molecular ionic liquids? In the present study several molecular dynamics simulations of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate are performed with different levels of polarization as well as with varying charge scaling factors of 0.74 to 0.90. The analysis of the structural and dynamical results are performed in different levels: from the atomic point of view over the molecular level to collective properties determined by the complete sample.