Kinetic lattice grand canonical Monte Carlo simulation for ion current calculations in a model ion channel system

An algorithm in which kinetic lattice grand canonical Monte Carlo simulations are combined with mean field theory (KLGCMC/MF) is presented to calculate ion currents in a model ion channel system. In this simulation, the relevant region of the system is treated by KLGCMC simulations, while the rest of the system is described by modified Poisson-Boltzmann mean field theory. Calculation of reaction field due to induced charges on the channel/water and membrane/water boundaries is carried out using a basis-set expansion method [Im and Roux, J. Chem. Phys. 115, 4850 (2001)]. Calculation of ion currents, electrostatic potentials, and ion concentrations, as obtained from the KLGCMC/MF simulations, shows good agreement with Poisson-Nernst-Planck (PNP) theory predictions when the channel and membrane have the same dielectric constant as water. If the channel and membrane have a lower dielectric constant than water, however, there is a considerable difference between the KLGCMC/MF and PNP predictions. This difference is attributed to the reaction field, which is missing in PNP theory. It is demonstrated that the reaction field as well as fixed charges in the channel play key roles in selective ion transport. Limitations and further development of the current KLGCMC/MF approach are also discussed.     

Monte Carlo simulation of ion transport in non-linear ion mobility spectrometry

A program for Monte Carlo simulation of ion transport in non-linear ion mobility spectrometry, also known as field asymmetric ion mobility spectrometry (FAIMS) or differential mobility spectrometry (DMS), has been developed. Simulations are based on elastic collisions between the ions and the gas particles, and take into account the effects of flow dynamics and asymmetric electric fields. Using this program, the separation and diffusion of the ions moving in a planar DMS filtration gap are demonstrated. Ion focusing in a cylindrical filtration gap is also confirmed. A characteristic compensation voltage is found to provide insight for understanding separation in non-linear ion mobility spectrometry. The simulation program is used to study the characteristics of non-linear ion mobility spectrometry, the effect of the carrier gas flow, and the dependence of the compensation voltage and nonlinear mobility coefficient (α) on the applied asymmetric electric field.     

Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study

The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.     

Quantitative selected ion flow tube mass spectrometry: The influence of ionic diffusion and mass discrimination

Selected ion flow tube mass spectrometry, (SIFT-MS), involves the partial conversion of mass-selected precursor ions to product ions in their reactions with the trace gases in an air sample that is introduced into helium carrier gas in a flow tube. The precursor and product ions are then detected and counted by a downstream quadrupole mass spectrometer. Quantification of particular trace gases is thus achieved from the ratio of the total count rate of the product ions to that for the precursor ions. However, it is important to appreciate that in this ion chemistry the light precursor ions (usually H3O+ ions) are invariably converted to heavier product ions. Hence, the product ions diffuse to the flow tube walls more slowly and thus they are more efficiently transported to the downstream mass spectrometer sampling orifice. This phenomenon we refer to as diffusion enhancement. Further, it is a well-known fact that discrimination can occur against ions of large mass-to-charge ratio, (m/z), in quadrupole mass spectrometers. If not accounted for, diffusion enhancement usually results in erroneously high trace gas concentrations and mass discrimination results in erroneously low concentrations. In this experimental investigation, we show how both these counteracting effects can be accounted for to increase the accuracy of SIFT-MS quantification. This is achieved by relating the currents of ions of various m/z that arrive at the downstream mass spectrometer sampling orifice disc to their count rates at the ion detector after mass analysis. Thus, both diffusion enhancement and mass discrimination are parameterized as a function of m/z and these are combined to provide an overall discrimination factor for the particular analytical instrument.     

Coupled ion and network dynamics in polymer electrolytes: Monte Carlo study of a lattice model

Monte Carlo simulations are used to study ion and polymer chain dynamic properties in a simplified lattice model with only one species of mobile ions. The ions interact attractively with specific beads in the host chains, while polymer beads repel each other. Cross linking of chains by the ions reduces chain mobilities which in turn suppresses ionic diffusion. Diffusion constants for ions and chains as a function of temperature follow the Vogel-Tammann-Fulcher (VTF) law with a common VTF temperature at low ion concentration, but both decouple at higher concentrations, in agreement with experimental observations. Our model allows us to introduce pressure as an independent variable through calculations of the equation of state using the quasichemical approximation, and to detect an exponential pressure dependence of the ionic diffusion.     

Realistic modeling of ion cloud motion in a Fourier transform ion cyclotron resonance cell by use of a particle-in-cell approach

Using a 'Particle-In-Cell' approach taken from plasma physics we have developed a new three-dimensional (3D) parallel computer code that today yields the highest possible accuracy of ion trajectory calculations in electromagnetic fields. This approach incorporates coulombic ion-ion and ion-image charge interactions into the calculation. The accuracy is achieved through the implementation of an improved algorithm (the so-called Boris algorithm) that mathematically eliminates cyclotron motion in a magnetic field from digital equations for ion motion dynamics. It facilitates the calculation of the cyclotron motion without numerical errors. At every time-step in the simulation the electric potential inside the cell is calculated by direct solution of Poisson's equation. Calculations are performed on a computational grid with up to 128 x 128 x 128 nodes using a fast Fourier transform algorithm. The ion populations in these simulations ranged from 1000 up to 1,000,000 ions. A maximum of 3,000,000 time-steps were employed in the ion trajectory calculations. This corresponds to an experimental detection time-scale of seconds. In addition to the ion trajectories integral time-domain signals and mass spectra were calculated. The phenomena observed include phase locking of particular m/z ions (high-resolution regime) inside larger ion clouds. A focus was placed on behavior of a cloud of ions of a single m/z value to understand the nature of Fourier transform ion cyclotron resonance (FTICR) resolution and mass accuracy in selected ion mode detection. The behavior of two and three ion clouds of different but close m/z was investigated as well. Peak coalescence effects were observed in both cases. Very complicated ion cloud dynamics in the case of three ion clouds was demonstrated. It was found that magnetic field does not influence phase locking for a cloud of ions of a single m/z. The ion cloud evolution time-scale is inversely proportional to magnetic field. The number of ions needed for peak coalescence depends quadratically on the magnetic field.     

Monte Carlo simulation of ion transport in ion mobility spectrometry

A program for simulation of ion trajectories in ion mobility spectrometry (IMS) instruments has been developed and incorporated into SIMION 7.0 [Int. J. Mass Spectrom. 200 (2000) 3–25]. Simulations were based on elastic collisions between ions and gas particles and conducted for an IMS drift tube. The program was validated by comparing the reduced mobility of helium ions derived from the simulation with the experimental data for helium ions in neon drift gas in low electric fields. Typical IMS parameters, including pressure, temperature, and flow rate of the drift gas were taken into account in the simulations. The program demonstrates capabilities of generating IMS spectra and predicting ion transport efficiency and separating ions. For the IMS drift tube studied, a correlation between imperfection of the electric field distribution and low resolution has been observed.     

Theoretical and numerical analysis of the behavior of ions injected into a quadrupole ion trap mass spectrometer

A numerical simulation method has been developed for the analysis of trapping ions injected into an ion trap mass spectrometer. This method was applied to clarify the effects of the following parameters on trapping efficiencies: (1) initial phase of the radio frequency (RF) drive voltage, (2) ion injection energy, and (3) RF peak voltage while injecting ions. The following conclusions were obtained by theoretical and simulation approaches. 1. The second and third dominant oscillations contribute significantly to the trapping mechanism of the injected ions, even for low q values. 2. A formula relating the operating parameters, which gives the maximum trapping efficiency, is derived. 3. Based on the above-mentioned formula, an advanced injection method is proposed, in which the RF peak voltage is decreased while injecting ions. The ability of this method to solve the problem of unequal sensitivity among different ion species is indicated by numerical simulation. Copyright 2000 John Wiley & Sons, Ltd.     

Method for improved secondary ion yields in cluster secondary ion mass spectrometry

A method to increase useful yields of organic molecules is investigated by cluster secondary ion mass spectrometry (SIMS). Glycerol drops were deposited onto various inkjet‐printed arrays and the organic molecules in the film were rapidly incorporated into the drop. The resulting glycerol/analyte drops were then probed with fullerene primary ions under dynamic SIMS conditions. High primary ion beam currents were shown to aid in the mixing of the glycerol drop, thus replenishing the probed area and sustaining high secondary ion yields. Integrated secondary ion signals for tetrabutylammonium iodide and cocaine in the glycerol drops were enhanced by more than a factor of 100 compared with an analogous area on the surface, and a factor of 1000 over the lifetime of the glycerol drop. Once the analyte of interest is incorporated into the glycerol microdrop, the solution chemistry can be tailored for enhanced secondary ion yields, with examples shown for cyclotrimethylenetrinitramine (RDX) chloride adduct formation. In addition, depositing localized glycerol drops may enhance analyte secondary ion count rates to high enough levels to allow for site‐specific chemical maps of molecules in complex matrices such as biological tissues. Published in 2010 by John Wiley & Sons, Ltd.     

Computer simulation of ion recombination in irradiated nonpolar liquids

A review of the results of computer simulation of the diffusion controlled recombination of ions is presented. The ions generated in clusters of two and three pairs of oppositely charged ions were considered. The recombination kinetics and the ion escape probability at infinite time with and without external electric field have been computed. These results are compared with the calculations based on the single-pair theory.     

Lattice dynamics to trigger low temperature oxygen mobility in solid oxide ion conductors

SrFeO(2.5) and SrCoO(2.5) are able to intercalate oxygen in a reversible topotactic redox reaction already at room temperature to form the cubic perovskites Sr(Fe,Co)O(3), while CaFeO(2.5) can only be oxidized under extreme conditions. To explain this significant difference in low temperature oxygen mobility, we investigated the homologous SrFeO(2.5) and CaFeO(2.5) by temperature dependent oxygen isotope exchange as well as by inelastic neutron scattering (INS) studies, combined with ab initio (DFT) molecular dynamical calculations. From (18)O/(16)O isotope exchange experiments we proved free oxygen mobility to be realized in SrFeO(x) already below 600 K. We have also evidence that low temperature oxygen mobility relies on the existence of specific, low energy lattice modes, which trigger and amplify oxygen mobility in solids. We interpret the INS data together with the DFT-based molecular dynamical simulation results on SrFeO(2.5) and CaFeO(2.5) in terms of an enhanced, phonon-assisted, low temperature oxygen diffusion for SrFeO(3-x) as a result of the strongly reduced Fe-O-Fe bond strength of the apical oxygen atoms in the FeO(6) octahedra along the stacking axis. This dynamically triggered phenomenon leads to an easy migration of the oxide ions into the open vacancy channels and vice versa. The decisive impact of lattice dynamics, giving rise to structural instabilities in oxygen deficient perovskites, especially with brownmillerite-type structure, is demonstrated, opening new concepts for the design and tailoring of low temperature oxygen ion conductors.     

Cross sections and ion kinetic energy analysis for the electron impact ionization of acetylene

Using a Nier-type electron impact ion source in combination with a double focusing two sector field mass spectrometer, partial cross sections for electron impact ionization of acetylene are measured for electron energies up to 1000 eV. Discrimination factors for ions are determined using the deflection field method in combination with a three-dimensional ion trajectory simulation of ions produced in the ion source. Analysis of the ion yield curves obtained by scanning the deflectors allows the assignment of ions with the same mass-to-charge ratio to specific production channels on the basis of their different kinetic energy distributions. This analysis also allows to determine, besides kinetic energy distributions of fragment ions, partial cross sections differential in kinetic energy. Moreover a charge separation reaction, the Coulomb explosion of the doubly charged parent ions C2H2++ into the fragment ions C2H+ and H+, is investigated and its mean kinetic energy release (KER=3.88 eV) is deduced.     

The influence of drift gas composition on the separation mechanism in traveling wave ion mobility spectrometry: insight from electrodynamic simulations

The influence of three different drift gases (helium, nitrogen, and argon) on the separation mechanism in traveling wave ion mobility spectrometry is explored through ion trajectory simulations which include considerations for ion diffusion based on kinetic theory and the electrodynamic traveling wave potential. The model developed for this work is an accurate depiction of a second-generation commercial traveling wave instrument. Three ion systems (cocaine, MDMA, and amphetamine) whose reduced mobility values have previously been measured in different drift gases are represented in the simulation model. The simulation results presented here provide a fundamental understanding of the separation mechanism in traveling wave, which is characterized by three regions of ion motion: (1) ions surfing on a single wave, (2) ions exhibiting intermittent roll-over onto subsequent waves, and (3) ions experiencing a steady state roll-over which repeats every few wave cycles. These regions of ion motion are accessed through changes in the gas pressure, wave amplitude, and wave velocity. Resolving power values extracted from simulated arrival times suggest that momentum transfer in helium gas is generally insufficient to access regions (2) and (3) where ion mobility separations occur. Ion mobility separations by traveling wave are predicted to be effectual for both nitrogen and argon, with slightly lower resolving power values observed for argon as a result of band-broadening due to collisional scattering. For the simulation conditions studied here, the resolving power in traveling wave plateaus between regions (2) and (3), with further increases in wave velocity contributing only minor improvements in separations.     

Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: a proton conducting electrolytic component in fuel cells

Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.     

Single-phase P2-type layered oxide with Cu-substitution for sodium ion batteries

The development of high-performance layered oxide cathodes for sodium ion batteries (SIBs) continues to facing be hindered by severe challenges to date.Herein,a single-phase P2-Na_(0.67)Mn_(0.6)Ni_(0.2)Co_(0.1)Cu_(0.1)O_2(NMNCC) comprising multiple-layer-oriented stacked nanoflakes is designed and synthesized via a simple sol-gel method.The large lattice parameters ensure a large three-dimensional frame,which enables the diffusion of sodium ions.Owing to its optimal morphology structure modulation transition metal substitution strategy,the MNCC electrode delivers a reversible capacity of 131.3 mAh g~(-1) at 0.1 C with retention of 86.7%after 200 cycles.In addition,it provides an initial capacity of 86.7 mAh g~(-1),and a retention of 80.0%after 500 cycles even at a current density of up to 1 A g~(-1).The stable single-phase structure and slight volume shrinkage observed after Na~+extraction further delay structural degradation.High Na~+mobility and low Na~+diffusion resistance are also guarantee the excellent rate performance of the NMNCC electrode.Thus,we determine that the NMNCC cathode is significant in the advancement of promising novel layered oxide cathodes.     

Transport of ions through tubes in a stream of flowing gas

The theoretical analysis and experimental investigations of phenomena connected with the transport of ions in regions devoid of external electric field were performed. The movement of ions in such regions is caused by gas flow. Due to diffusion, recombination and mutual repulsion the concentration of transported ions in the space outside the ionization source drops. The influence of these phenomena was analyzed using simplified ions balance equations taking into account a specific mechanisms of ion losses. A full system of balance equations describing a combined effect of diffusion, recombination and repulsion was also solved. The results of theoretical considerations were confirmed experimentally by measuring currents, for which the charge carriers were ions transported through metal tubes. The measurements were performed for the case when the ions of both polarities were present in the gas as well as for swarms consisting of positive ions only. The possibility of ion transport between parts of the measurement system connected to different potentials was also investigated. The method used for this purpose involved the application of the metal tubes connected to variable potential as an intermediate element.     

Interpreting ion fluxes to channel arrays in monolayers

The exponentially decaying permeability model interprets the chronoamperometric currents arising from Tl+ reduction at a Hg electrode covered with a phospholipid monolayer (DOPC) containing gramicidin monomer by combining three processes: (i) the diffusion of an ion to a membrane surface with an array of channels, (ii) the conformational dynamics of the individual channels, and (iii) the passage of the ion through the channels. The introduction of a variable permeability allows us to uncouple the diffusion from the heterogeneous processes, given that the concentration of a species at the active surface can be obtained by semi-integration of the currents. Consideration of a reverse step for the dehydration process at the mouth of the channel allows the analysis of potential steps away from diffusion-limited conditions where a Nernstian-like behavior of the relevant parameter is observed. The model has been successfully applied to data with all trans retinol or benzo-alpha-pyrene as additive to the phospholipid monolayer and to monolayers without any additive at all.     

Thermodynamics and kinetics of hydroxide ion formation in 12 CaO x 7 Al2O3

We have examined the thermodynamics and kinetics of hydroxide (OH-) ions that formed in cages of 12 CaO x 7 Al2O3 (C12A7) with nanoporous structures. It is confirmed using thermogravimetric-evolved gas analyses (TG-EGA) that hydration in C12A7 is mediated by a reaction between an oxide (O2-) ion in the cage and an H2O molecule in the atmosphere to form two OH- ions in the cages. To simply and exactly quantify the OH- content from infrared absorption measurements of OH-stretching band, we propose a method combined with a thermodynamic analysis, allowing the simultaneous determination of the molar extinction coefficient of the OH-band, enthalpy, and entropy for the hydration. Hydration enthalpy in C12A7 is extremely high compared with other oxides and was enhanced by the marked instability of O2- ion in the cage. Consequently, high solubility of OH- ion is retained up to unusually high temperatures. Furthermore, we determined diffusion coefficients of species relevant to the hydration process and demonstrated that inward diffusion of OH- ions is the rate-determining process.     

An insight into the structure,conductivity and ion dynamics of Sr-Sm co-doped ceria oxygen ion conductors: Effect of defect interaction

In this work, we investigate the structure, conductivity and ion dynamics of mixed di and tri-valent doped Ce_0.8Sm_0.2-xSr_xO_2-δ (x = 0–0.2) oxygen ion conductors. The lattice parameter and root mean square strain are significantly affected by the ionic radius of dopants and their solubility into ceria lattice. Due to the solubility limit of Sr²⁺ ions, SrCeO₃ phase increases with the doping concentration of Sr²⁺. The increase of Sr²⁺ ions into ceria lattice promotes the formation of large defect clusters by expense of formed oxygen vacancies. The coulombic interaction between oxygen vacancies with substituted dopant cations enhances with Sr²⁺ ions due to decrease of the value of dielectric constant of the compositions. The defect interaction significantly affects the conductivity values by means of increase of SrCeO₃ phase and defect clusters. The conductivity values are found to be consistent with the migration and association energy. The scaled spectra of dielectric tangent loss and real part of complex conductivity confirm the temperature and defect interaction independent nature of hoping mechanism in the compositions.