210867737
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.
40491295
Fast and facile dissolution of cellulose with tetrabutylphosphonium hydroxide containing 40 wt% water.
Tetrabutylphosphonium hydroxide containing 40 wt% water dissolved 20 wt% cellulose at the final concentration within 5 minutes under mild stirring at 25 °C.
94643879
Assessment of phosphonium ionic liquid-dimethylformamide mixtures for dissolution of cellulose
This paper reports a new method for dissolving cellulose based on phosphonium ionic liquids (PILs). The method has the potential to produce novel cellulosic and cellulose composite materials in an environmentally friendly way. PILs with melting points less than 100 °C and mixtures of dimethylformamide and PILs were used, and are recommended here, due to their negligible vapour pressure, limited reactivity, high thermal stability, and their ability to be easily recycled. The effect of the mass percent of PILs along with the comparison of the effects of different ionic liquids on the viscosity of mixtures are discussed. The limited reactivity of PILs can be used to do chemical reaction on cellulose in the presence of ionic liquids without encountering the problem of incorporation of ionic liquids in the reactions. However, if need be the PILs could also be incorporated into cellulose composites by intramolecular interactions.
30654212
Observed mechanism for the breakup of small bundles of cellulose Iα and Iβ 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 Iβ 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.
98230473
Disintegration and dissolution kinetics of wood chips in ionic liquids
Abstract Ionic liquids are able to dissolve polysaccharides and lignin, but there is only scarce knowledge about the dissolution of native wood. In the present paper, wood was dissolved by the ionic liquid 1-ethyl-3-methylimidazolium acetate (EMIMAc). A quantitative balance of the dissolved compounds is presented and the investigations are complemented by in situ microscopy of native wood in EMIMAc. The resulting dissolution kinetics in EMIMAc reveals distinct differences between spruce and beech. While particles of 0.1–0.5 mm of spruce dissolve slowly (up to 40% after 24 h), beech is dissolved more efficiently (75% after 24 h and 90% after 72 h). Wood chips of 10 mm length show similar dissolution kinetics and lignin yields of up to 10%. Microscopic studies reveal a disintegration of wood in EMIMAc into cells with large specific surface area, and differences in dissolution between spruce and beech were observed. These findings explain the size-independent dissolution of wood in EMIMAc and may open up new opportunities for the pretreatment of wood in ionic liquids.
9867186
Multi-scale processes of beech wood disintegration and pretreatment with 1-ethyl-3-methylimidazolium acetate/water mixtures
BackgroundThe valorization of biomass for chemicals and fuels requires efficient pretreatment. One effective strategy involves the pretreatment with ionic liquids which enables enzymatic saccharification of wood within a few hours under mild conditions. This pretreatment strategy is, however, limited by water and the ionic liquids are rather expensive. The scarce understanding of the involved effects, however, challenges the design of alternative pretreatment concepts. This work investigates the multi length-scale effects of pretreatment of wood in 1-ethyl-3-methylimidazolium acetate (EMIMAc) in mixtures with water using spectroscopy, X-ray and neutron scattering.ResultsThe structure of beech wood is disintegrated in EMIMAc/water mixtures with a water content up to 8.6 wt%. Above 10.7 wt%, the pretreated wood is not disintegrated, but still much better digested enzymatically compared to native wood. In both regimes, component analysis of the solid after pretreatment shows an extraction of few percent of lignin and hemicellulose. In concentrated EMIMAc, xylan is extracted more efficiently and lignin is defunctionalized. Corresponding to the disintegration at macroscopic scale, SANS and XRD show isotropy and a loss of crystallinity in the pretreated wood, but without distinct reflections of type II cellulose. Hence, the microfibril assembly is decrystallized into rather amorphous cellulose within the cell wall.ConclusionsThe molecular and structural changes elucidate the processes of wood pretreatment in EMIMAc/water mixtures. In the aqueous regime with >10.7 wt% water in EMIMAc, xyloglucan and lignin moieties are extracted, which leads to coalescence of fibrillary cellulose structures. Dilute EMIMAc/water mixtures thus resemble established aqueous pretreatment concepts. In concentrated EMIMAc, the swelling due to decrystallinization of cellulose, dissolution of cross-linking xylan, and defunctionalization of lignin releases the mechanical stress to result in macroscopic disintegration of cells. The remaining cell wall constituents of lignin and hemicellulose, however, limit a recrystallization of the solvated cellulose. These pretreatment mechanisms are beyond common pretreatment concepts and pave the way for a formulation of mechanistic requirements of pretreatment with simpler pretreatment liquors.
24787479
Theoretical Insights into the Role of Water in the Dissolution of Cellulose Using IL/Water Mixed Solvent Systems.
The use of certain ionic liquids (ILs) as pretreatment solvents for lignocellulosic biomass has gained great interest in recent years due to the IL's capacity for efficient cellulose dissolution in aqueous solution as compared to other common pretreatment techniques. A fundamental understanding on how these ILs in aqueous environments act on cellulose, particularly at lower IL concentrations with water as a cosolvent, is essential for optimizing pretreatment efficiency, lowering pretreatment cost, and improving IL recyclability. The IL 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]) is one of the most efficient cellulose solvents known, greatly altering cellulose structure for improved enzymatic saccharification. To understand the role of water as a cosolvent with [C2C1Im][OAc], we investigated the dissolution mechanism of microcrystalline cellulose, type Iβ, in different [C2C1Im][OAc]:water ratios at room (300 K) and pretreatment (433 K) temperatures using all atom molecular dynamics (MD) simulations. These simulations show that 80:20 ratios of [C2C1Im][OAc]:water should be considered as "the tipping point" above which [C2C1Im][OAc]:water mixtures are equally effective on decrystallization of cellulose by disrupting the interchain hydrogen bonding interactions. Simulations also reveal that the resulting decrystallized cellulose from 100% [C2C1Im][OAc] begins to repack in the presence of water but into a less crystalline, or more amorphous, form.
15881414
Fast parallel algorithms for short-range molecular dynamics
Abstract Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.
37345574
A force field for molecular simulation of tetrabutylphosphonium amino acid ionic liquids.
An all-atom force field was set up for a new class of ionic liquids (ILs), tetrabutylphosphonium amino acid, on the basis of the AMBER force field with determining parameters related to the phosphorus atom and modifying several parameters. Ab initio quantum chemical calculations were employed to obtain molecular geometries, infrared frequencies, and torsion energy profiles. Atom partial charges were obtained by using the one-conformation, two-step restraint electrostatic potential approach. Molecular dynamics simulation was carried out in the isothermal-isobaric ensemble for 14 tetrabutylphosphonium amino acid ILs at two temperatures to validate the force field against the experimental densities and heat capacities at constant pressure. Computed thermodynamic properties are in good agreement with available experimental values. Moreover, radial distribution functions were investigated to depict the microscopic structures of these ILs.
1635054
Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids.
OPLS-AA force field parameters have been developed and validated for use in the simulation of 68 unique combinations of room temperature ionic liquids featuring 1-alkyl-3-methylimidazolium [RMIM] (R = Me, Et, Bu, Hex, Oct), N-alkylpyridinium [RPyr], and choline cations, along with Cl(-), PF6(-), BF4(-), NO3(-), AlCl4(-), Al2Cl7(-), TfO(-), saccharinate, and acesulfamate anions. The new parameters were fit to conformational profiles from gas-phase ab initio calculations at the LMP2/cc-pVTZ(-f)//HF/6-31G(d) theory level and compared to experimental condensed-phase structural and thermodynamic data. Monte Carlo simulations of the ionic liquids gave relative deviations from experimental densities of ca. 1-3% at 25 °C for most combinations and also yielded close agreement over a temperature range of 5 to 90 °C. Predicted heats of vaporization compared well with available experimental data and estimates. Transferability of the new parameters to multiple alkyl side-chain lengths for [RMIM] and [RPyr] was determined to give excellent agreement with charges and torsion potentials developed specific to desired alkyl lengths in 35 separate ionic liquid simulations. As further validation of the newly developed parameters, the Kemp elimination reaction of benzisoxazole via piperidine was computed in 1-butyl-3-methylimidazolium hexafluorophosphate [BMIM][PF6] using mixed quantum and molecular mechanics (QM/MM) simulations and was found to give close agreement with the experimental free energy of activation.
9757894
A general purpose model for the condensed phases of water: TIP4P/2005.
A potential model intended to be a general purpose model for the condensed phases of water is presented. TIP4P/2005 is a rigid four site model which consists of three fixed point charges and one Lennard-Jones center. The parametrization has been based on a fit of the temperature of maximum density (indirectly estimated from the melting point of hexagonal ice), the stability of several ice polymorphs and other commonly used target quantities. The calculated properties include a variety of thermodynamic properties of the liquid and solid phases, the phase diagram involving condensed phases, properties at melting and vaporization, dielectric constant, pair distribution function, and self-diffusion coefficient. These properties cover a temperature range from 123 to 573 K and pressures up to 40,000 bar. The model gives an impressive performance for this variety of properties and thermodynamic conditions. For example, it gives excellent predictions for the densities at 1 bar with a maximum density at 278 K and an averaged difference with experiment of 7 x 10(-4) g/cm3.
18285536
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.
488073
Reversible multiple time scale molecular dynamics
The Trotter factorization of the Liouville propagator is used to generate new reversible molecular dynamics integrators. This strategy is applied to derive reversible reference system propagator algorithms (RESPA) that greatly accelerate simulations of systems with a separation of time scales or with long range forces. The new algorithms have all of the advantages of previous RESPA integrators but are reversible, and more stable than those methods. These methods are applied to a set of paradigmatic systems and are shown to be superior to earlier methods. It is shown how the new RESPA methods are related to predictor–corrector integrators. Finally, we show how these methods can be used to accelerate the integration of the equations of motion of systems with Nose thermostats.
28666966
Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation.
Long-range dispersion interactions have a critical influence on physical quantities in simulations of inhomogeneous systems. However, the perceived computational overhead of long-range solvers has until recently discouraged their implementation in molecular dynamics packages. Here, we demonstrate that reducing the cutoff radius for local interactions in the recently introduced particle-particle particle-mesh (PPPM) method for dispersion [Isele-Holder et al., J. Chem. Phys., 2012, 137, 174107] can actually often be faster than truncating dispersion interactions. In addition, because all long-range dispersion interactions are incorporated, physical inaccuracies that arise from truncating the potential can be avoided. Simulations using PPPM or other mesh Ewald solvers for dispersion can provide results more accurately and more efficiently than simulations that truncate dispersion interactions. The use of mesh-based approaches for dispersion is now a viable alternative for all simulations containing dispersion interactions and not merely those where inhomogeneities were motivating factors for their use. We provide a set of parameters for the dispersion PPPM method using either ik or analytic differentiation that we recommend for future use and demonstrate increased simulation efficiency by using the long-range dispersion solver in a series of performance tests on massively parallel computers.
18365139
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
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.
94849208
Error estimates on averages of correlated data
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.
19789166
A modified TIP3P water potential for simulation with Ewald summation.
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.
18350153
GLYCAM06: A generalizable biomolecular force field. Carbohydrates
A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small‐molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both α‐ and β‐anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas‐phase properties of an array of small test molecules, condensed‐phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
26703003
Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.
Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion.
122571492
Time-averaged mean square displacement for switching diffusion.
We consider a classic two-state switching diffusion model from a single-particle tracking perspective. The mean and the variance of the time-averaged mean square displacement (TAMSD) are computed exactly. When the measurement time (i.e., the trajectory duration) is comparable to or smaller than the mean residence times in each state, the ergodicity breaking parameter is shown to take arbitrarily large values, suggesting an apparent weak ergodicity breaking for this ergodic model. In this regime, individual random trajectories are not representative while the related TAMSD curves exhibit a broad spread, in agreement with experimental observations in living cells and complex fluids. Switching diffusions can thus present, in some cases, an ergodic alternative to commonly used and inherently non-ergodic continuous-time random walks that capture similar features.
13597501
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
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.
99733626
Maintenance-Free Cellulose Solvents Based on Onium Hydroxides
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 ...
30979610
Hydrogen bonds in aqueous electrolyte solutions: statistics and dynamics based on both geometric and energetic criteria.
We have investigated the statistics and dynamics of hydrogen bonds in a concentrated aqueous electrolyte solution and also in pure water by means of molecular dynamics simulations. Both geometric and energetic definitions are employed for the existence of a hydrogen bond. The present study extends our earlier work on the structure and dynamics of hydrogen bonds where only the geometric definition was used [A. Chandra, Phys. Rev. Lett. 85, 768 (2000)]. In the presence of ions, like the earlier results for geometric definition, the energetic definition is also found to give a lower number of hydrogen bonds per water molecule and a wider distribution, a slightly faster rate of breaking and a slower rate of structural relaxation of hydrogen bonds. The results are explained in terms of a decrease of the potential of mean force between water molecules, an enhanced population of hydrogen bonded water pairs in the vicinity of the dividing surface that separates the hydrogen bonded and nonbonded states and an increase of the friction on translational and rotational motion of water molecules in the presence of ions.
89614663
Resolving the hydrogen bond dynamics conundrum
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...
4337032
Hydrogen-bond kinetics in liquid water
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.
93656110
The reorientation mechanism of hydroxide ions in water: A molecular dynamics study
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.
96395448
A jump motion of small molecules in glassy polymers: A molecular dynamics simulation
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.
98062248
Diffusion of penetrants in amorphous polymers: A molecular dynamics study
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.
5003128
Second-Generation ReaxFF Water Force Field: Improvements in the Description of Water Density and OH-Anion Diffusion.
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.
10769069
Geometry controlled anomalous diffusion in random fractal geometries: looking beyond the infinite cluster.
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.
17953666
Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate
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.
93109588
Mechanism of Tetraalkylammonium Headgroup Degradation in Alkaline Fuel Cell Membranes
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.
98591945
Reactivity of ionic liquids
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).
101414800
Relative Chemical Stability of Imidazolium-Based Alkaline Anion Exchange Polymerized Ionic Liquids
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...
46542537
Comparing reduced partial charge models with polarizable simulations of ionic liquids.
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.