In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates.

Advances in sample preparation, ion sources and mass spectrometer technology have enabled the detection and characterisation of intact proteins. The challenges associated include an appropriately soft ionisation event, efficient transmission and detection of the often delicate macromolecules. Ambient ion sources, in particular, offer a wealth of strategies for analysis of proteins from solution environments, and directly from biological substrates. The last two decades have seen rapid development in this area. Innovations include liquid extraction surface analysis, desorption electrospray ionisation and nanospray desorption electrospray ionisation. Similarly, developments in native mass spectrometry allow protein-protein and protein-ligand complexes to be ionised and analysed. Identification and characterisation of these large ions involves a suite of hyphenated mass spectrometry techniques, often including the coupling of ion mobility spectrometry and fragmentation techniques. The latter include collision, electron and photon-induced methods, each with their own characteristics and benefits for intact protein identification. In this review, recent developments for in situ protein analysis are explored, with a focus on ion sources and tandem mass spectrometry techniques used for identification.

Effect of ultrasonic field on the enzyme activities and ion balance of potential pathogen Saccharomyces cerevisiae.

OBJECTIVES: This study aimed at investigating the enzyme activities and ion concentrations in potential pathogen S.cerevisiae upon ultrasonic treatment. METHODS: The activities of ATPase and antioxidase were identified by ATPase, SOD, and CAT assay kits following the instructions. Extracellular Ca2+ and K+ concentrations were determined in an atomic absorption spectrometer with calcium and potassium hollow-cathode lamps as radiation sources. RESULTS: SOD and CAT activities were enhanced by relatively low ultrasonic power at early time points and reduced to lower levels. Total ATPase, Na+/K+-ATPase, and Ca2+/Mg2+-ATPase activities were reduced by ultrasonic field, with higher reducing rate at stronger ultrasonic power and early time points. In addition, ultrasonic field disturbed the Ca2+ and K+ balances in S.cerevisiae cells. CONCLUSIONS: Ultrasonic field resulted in the reduce even the lost of S.cerevisiae cell viability.

Pion effects in flattening filter-free radiation beams.

Flattening filter-free radiation beams have higher dose rates that significantly increase the ion recombination rate in an ion chamber's volume and lower the signal read by the chamber-electrometer pair. The ion collection efficiency correction (P(ion)) accounts for the loss of signal and subsequently changes dosimetric quantities when applied. We seek to characterize the changes to the percent depth dose, tissue maximum ratio, relative dose factor, absolute dose calibration, off-axis ratio, and the field width. We measured P(ion) with the two-voltage technique and represented P(ion) as a linear function of the signal strength. This linear fit allows us to correct measurement sets when we have only gathered the high voltage signal and to correct derived quantities. The changes to dosimetric quantities can be up to 1.5%. Charge recombination significantly affects percent depth dose, tissue maximum ratio, and off-axis ratio, but has minimal impact on the relative dose factor, absolute dose calibration, and field width.

Determination of lead ion removal from a flowing electrolyte in the presence of a magnetic field using Raman spectroscopy.

PURPOSE: The authors report on the development of a new, noninvasive method to efficiently remove metal ions in aqueous solution flowing in a tube and to quantify the concentrations of those ions. Such a technique could be used to remove toxic ions in the interiors of arteries and veins in patients intoxicated by the ingestion of metal ions. METHODS: A magnetic field is applied to an aqueous electrolyte flowing in a specially designed rectangular cell in order to deflect the ion trajectories and concentrate them at one side of a cell. Once the ions are concentrated, they can be removed. Raman spectroscopy is used to promptly determine the concentration of the removed lead ions. RESULTS: It is possible to increase, on one side of the cell, the ion concentration by more than 80% with respect to the average concentration; the removed ions were taken from this high concentration region. This approach is a rapid, efficient, and noninvasive method for the removal of ions in aqueous solution. Raman spectroscopy was found to be a suitable technique to determine the amount of removed ions. CONCLUSIONS: The results indicate that the ion concentration can be increased more than 80% in a region where they can be removed. The increment in the ion concentration produced by the deflection due to the magnetic field, together with the use of Raman spectroscopy, allows for a rapid analysis of the removed ions without any previous preparation. The proposed method is a potentially useful method for metal ion separation of interest in the medical physics field.

Simulation of the charge migration in DNA under irradiation with heavy ions.

A computer model to simulate the processes of charge injection and migration through DNA after irradiation by a heavy charged particle was developed. The most probable sites of charge injection were obtained by merging spatial models of short DNA sequence and a single 1 GeV/u iron particle track simulated by the code RITRACKS (Relativistic Ion Tracks). Charge migration was simulated by using a quantum-classical nonlinear model of the DNA-charge system. It was found that charge migration depends on the environmental conditions. The oxidative damage in DNA occurring during hole migration was simulated concurrently, which allowed the determination of probable locations of radiation-induced DNA lesions.

Sunlight-driven reduction of silver ion to silver nanoparticle by organic matter mitigates the acute toxicity of silver to Daphnia magna.

Due to the unique antibacterial activities, silver nanoparticles (AgNPs) have been extensively used in commercial products. Anthropogenic activities have released considerable AgNPs as well as highly toxic silver ion (Ag(+)) into the aquatic environment. Our recent study revealed that ubiquitous natural organic matter (NOM) could reduce Ag(+) to AgNP under natural sunlight. However, the toxic effect of this process is not well understood. In this work, we prepared mixture solution of Ag(+) and AgNPs with varied Ag(+)% through the sunlight-driven reduction of Ag(+) by NOM and investigated the acute toxicity of the solutions on Daphnia magna. Formation of AgNPs was demonstrated and characterized by comprehensive techniques and the fraction of unconverted Ag(+) was determined by ultrafiltration-inductively coupled plasma mass spectrometry determination. The formation of AgNPs enhanced significantly with the increasing of solution pH and cumulative photosynthetically active radiation of sunlight. The toxicity of the resulting solution was further investigated by using freshwater crustacean D. magna as a model and an 8hr-median lethal concentration (LC50) demonstrated that the reduction of Ag(+) by NOM to AgNPs significantly mitigated the acute toxicity of silver. These results highlight the importance of sunlight and NOM in the fate, transformation and toxicity of Ag(+) and AgNPs, and further indicate that the acute toxicity of AgNPs should be mainly ascribed to the dissolved Ag(+) from AgNPs.

Effect of magnetic field inhomogeneity on ion cyclotron motion coherence at high magnetic field.

A three-dimensional code based on the particle-in-cell algorithm modified to account for the inhomogeneity of the magnetic field was applied to determine the effect of Z(1), Z(2), Z(3), Z(4), X, Y, ZX, ZY, XZ(2) YZ(2), XY and X(2)-Y(2) components of an orthogonal magnetic field expansion on ion motion during detection in an FT-ICR cell. Simulations were performed for magnetic field strengths of 4.7, 7, 14.5 and 21 Tesla, including experimentally determined magnetic field spatial distributions for existing 4.7 T and 14.5 T magnets. The effect of magnetic field inhomogeneity on ion cloud stabilization ("ion condensation") at high numbers of ions was investigated by direct simulations of individual ion trajectories. Z(1), Z(2), Z(3) and Z(4) components have the largest effect (especially Z(1)) on ion cloud stability. Higher magnetic field strength and lower m/z demand higher relative magnetic field homogeneity to maintain cloud coherence for a fixed time period. The dependence of mass resolving power upper limit on Z(1) inhomogeneity is evaluated for different magnetic fields and m/z. The results serve to set the homogeneity requirements for various orthogonal magnetic field components (shims) for future FT-ICR magnet design.

Keto-enol tautomerization and intermolecular proton transfer in photoionized cyclopentanone dimer in the gas phase.

Time-of-flight mass spectra of cyclopentanone and its clusters cooled in a supersonic jet expansion have been measured following 4-, 3-, and 2-photon ionizations by the 2nd, 3rd, and 4th harmonic wavelengths, respectively, of a Q-switched Nd:YAG laser. The mass spectra reveal signatures of energetically favored keto to enol tautomerization of the molecular ion leading to intermolecular proton transfer, and this observation is found sharply dependent on the ionization wavelengths used. Electronic structure calculation predicts that in spite of the energetic preference, keto-enol conversion barrier of isolated molecular ion is high. However, the barrier is significantly reduced in a CH⋯O hydrogen-bonded dimer of the molecule. The transition states associated with tautomeric conversion of both cyclopentanone monomer and dimer cations have been identified by means of intrinsic reaction co-ordinate calculation. In a supersonic jet expansion, although a weakly bound dimer is readily generated, the corresponding cation and also the protonated counterpart are observed only for ionization by 532 nm. For other two ionization wavelengths, these species do not register in the mass spectra, where the competing reaction channels via α-cleavage of the ring become dominant. In contrast to the report of a recent study, we notice that the intact molecular ion largely survives fragmentations when ionized from the 2-photon resonant 3p Rydberg state as intermediate using nanosecond laser pulses, and the corresponding resonant 3-photon ionization spectrum has been recorded probing the intact molecular ion.

Non-adiabatic molecular dynamics investigation of photoionization state formation and lifetime in Mn²âº-doped ZnO quantum dots.

The unique electronic structure of Mn(2+)-doped ZnO quantum dots gives rise to photoionization states that can be used to manipulate the magnetic state of the material and to generate zero-reabsorption luminescence. Fast formation and long non-radiative decay of this photoionization state is a necessary requirement for these important applications. In this work, surface hopping based non-adiabatic molecular dynamics are used to demonstrate the fast formation of a metal-to-ligand charge transfer state in a Mn(2+)-doped ZnO quantum dot. The formation occurs on an ultrafast timescale and is aided by the large density of states and significant mixing of the dopant Mn(2+) 3dt2 levels with the valence-band levels of the ZnO lattice. The non-radiative lifetime of the photoionization states is also investigated.

Time-dependent density functional theory for ion diffusion in electrochemical systems.

We introduce a generic form of time-dependent density functional theory (TDDFT) to describe ion diffusion in electrochemical systems to account for steric effects and electrostatic correlations neglected in the Poisson-Nernst-Planck equations. An efficient numerical algorithm is proposed to analyze the charging kinetics of electric double layers in model electrochemical systems that consist of spherical ions in a dielectric continuum confined between two planar electrodes. By comparing the theoretical predictions from TDDFT and conventional electrokinetic methods for constant-voltage charging of the model electrochemical cells, we demonstrate that thermodynamic non-ideality plays a pivotal role in electrodiffusion even at relatively low electrolyte concentrations, and this effect cannot be captured by the lattice-gas model for the excluded volume effects. In particular, TDDFT predicts 'wave-like' variation of the ionic density profiles that has not been identified in previous investigations. At conditions where there are no significant correlations between electric double layers from opposite electrodes, the charging kinetics follows an exponential behavior with a linear dependence of the relaxation time on the cell thickness in excellent agreement with the equivalent circuit model. However, the conventional electrokinetic model breaks down when the electrodes are at small separation, in particular for systems with low ionic strength or high charging voltage. We also find that ionic screening retards the charging kinetics at low salt concentrations, but has the opposite effect at large salt concentrations.

An efficient enzymatic modification of cordycepin in ionic liquids under ultrasonic irradiation.

A comparative study of the immobilized Candida antarctica lipase B (Novozym 435)-catalyzed acylation of cordycepin with vinyl acetate in ionic liquids (ILs) under ultrasonic irradiation and shaking was conducted. The application of ultrasonic irradiation instead of shaking during acylation resulted in an enhanced reaction rate and a higher level of substrate conversion. Among the various ILs examined, 1-butyl-3-methylimidazolium tetrafluorobrate ([C4MIm][BF4]) was the best medium for the reaction because it produced the highest substrate conversion. In [C4MIm][BF4], the optimal ultrasonic power, water activity, and reaction temperature were 120 W, 0.33, and 50 °C, respectively. The acylation of cordycepin in [C4MIm][BF4] proved to be regioselective under both conditions: the C5'-OH was acylated. Novozym 435 exhibited a much higher operational stability in [C4MIm][BF4], and 58.0% of its original activity was maintained after ten reuse cycles under ultrasonic irradiation. Compared with the cordycepin, the rate of adenosine deaminase-catalyzed deamination was greatly reduced when the 5'-OH was substituted by acetyl group. These results demonstrated that the combined application of ultrasonic irradiation and IL as a medium was an efficient approach for the enzymatic modification of cordycepin.

Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase.

Photon activation of ions in the visible and ultraviolet range attracts a growing interest, partly for its promising applications in tandem mass spectrometry. However, this task is not trivial, as it requires notably high brilliance photon sources. Hence, most of the work in that field has been performed using lasers. Synchrotron radiation is a source continuously tunable over a wide photon energy range and which possesses the necessary characteristics for ion activation. This review focuses on the array of applications of synchrotron radiation in photon activation of ions ranging from near UV to soft X-rays.

Experimental analysis of general ion recombination in a liquid-filled ionization chamber in high-energy photon beams.

PURPOSE: To study experimentally the general ion recombination effect in a liquid-filled ionization chamber (LIC) in high-energy photon beams. METHODS: The general ion recombination effect on the response of a micro liquid ion chamber (microLion) was investigated with a 6 MV photon beam in normal and SRS modes produced from a Varian(®) Novalis Tx(TM) linear accelerator. Dose rates of the linear accelerator were set to 100, 400, and 1000 MU∕min, which correspond to pulse repetition frequencies of 60, 240, and 600 Hz, respectively. Polarization voltages applied to the microLion were +800 and +400 V. The relative collection efficiency of the microLion response as a function of dose per pulse was experimentally measured with changing polarization voltage and pulse repetition frequencies and was compared with the theoretically calculated value. RESULTS: For the 60 Hz pulse repetition frequency, the experimental relative collection efficiency was not different from the theoretical one for a pulsed beam more than 0.3% for both polarization voltages. For a pulsed radiation beam with a higher pulse repetition frequency, the experimental relative collection efficiency converged to the theoretically calculated efficiency for continuous beams. This result indicates that the response of the microLion tends toward the response to a continuous beam with increasing pulse repetition frequency of a pulsed beam because of low ion mobility in the liquid. CONCLUSIONS: This work suggests an empirical method to correct for differences in general ion recombination of a LIC between different radiation fields. More work is needed to quantitatively explain the LIC general ion recombination behavior in pulsed beams generated from linear accelerators.

Contribution of recollision ionization to the cross-shaped structure in nonsequential double ionization.

With the three-dimensional classical ensemble model, we investigate the correlated electron emission in nonsequential double ionization (NSDI) of argon atoms by few-cycle laser pulses. Our calculations well reproduce the experimentally observed cross-shaped structure in the correlated two-electron momentum spectrum [ Nature Commun. 3, 813 (2012)]. By tracing these NSDI trajectories, we find that besides the process of recollision-induced excitation with subsequent ionization just before the next field maximum, the recollision ionization also significantly contributes to the cross-shaped structure.

Nanometer-scale mapping of irreversible electrochemical nucleation processes on solid Li-ion electrolytes.

Electrochemical processes associated with changes in structure, connectivity or composition typically proceed via new phase nucleation with subsequent growth of nuclei. Understanding and controlling reactions requires the elucidation and control of nucleation mechanisms. However, factors controlling nucleation kinetics, including the interplay between local mechanical conditions, microstructure and local ionic profile remain inaccessible. Furthermore, the tendency of current probing techniques to interfere with the original microstructure prevents a systematic evaluation of the correlation between the microstructure and local electrochemical reactivity. In this work, the spatial variability of irreversible nucleation processes of Li on a Li-ion conductive glass-ceramics surface is studied with ~30 nm resolution. An increased nucleation rate at the boundaries between the crystalline AlPO4 phase and amorphous matrix is observed and attributed to Li segregation. This study opens a pathway for probing mechanisms at the level of single structural defects and elucidation of electrochemical activities in nanoscale volumes.

Stochastic ion acceleration by beating electrostatic waves.

A study is presented of the stochasticity in the orbit of a single, magnetized ion produced by the particle's interaction with two beating electrostatic waves whose frequencies differ by the ion cyclotron frequency. A second-order Lie transform perturbation theory is employed in conjunction with a numerical analysis of the maximum Lyapunov exponent to determine the velocity conditions under which stochasticity occurs in this dynamical system. Upper and lower bounds in ion velocity are found for stochastic orbits with the lower bound approximately equal to the phase velocity of the slower wave. A threshold condition for the onset of stochasticity that is linear with respect to the wave amplitudes is also derived. It is shown that the onset of stochasticity occurs for beating electrostatic waves at lower total wave energy densities than for the case of a single electrostatic wave or two nonbeating electrostatic waves.

Molecular switch for tuning ions across nanopores by an external electric field.

Active control of ion transport in nanoscale channels is attracting increasing attention. Recently, experimental and theoretical results have verified that depending on the charged surface of nanopores, the solution inside nanopores can contain either negative or positive ions, which does not happen in macroscale channels. However, the control of the surface chemistry of synthetic nanopores is difficult and the design of nanotubes with novel recognition mechanisms that regulate the ionic selectivity of negative and positive charges remains a challenge. We present here a design for an ion-selective nanopore that is controllable by external charges. Our molecular dynamics simulations show that this remarkable selectivity can be switched from predominantly negative to positive ions and that the magnitude of the ionic flux can be varied by changing the distance of the external charges. The results suggest that the hydration structures around ions play a prominent role in the selectivity process, which is tuned by the external charge. These studies may be useful for developing ways to control the behavior, properties and chemical composition of liquids and provide possible technical applications for nanofluidic field effect transistors.

Ion-acoustic solitary waves and shocks in a collisional dusty negative-ion plasma.

We study the effects of ion-dust collisions and ion kinematic viscosities on the linear ion-acoustic instability as well as the nonlinear propagation of small-amplitude solitary waves and shocks (SWS) in a negative-ion plasma with immobile charged dusts. The existence of two linear ion modes, namely the "fast" and "slow" waves, is shown, and their properties are analyzed in the collisional negative-ion plasma. Using the standard reductive perturbation technique, we derive a modified Korteweg-de Vries-Burger (KdVB) equation which describes the evolution of small-amplitude SWS. The profiles of the latter are numerically examined with parameters relevant for laboratory and space plasmas where charged dusts may be positively or negatively charged. It is found that negative-ion plasmas containing positively charged dusts support the propagation of SWS with negative potential. However, the perturbations with both positive and negative potentials may exist when dusts are negatively charged. The results may be useful for the excitation of SWS in laboratory negative-ion plasmas as well as for observation in space plasmas where charged dusts may be positively or negatively charged.

Ion-conserving Poisson-Boltzmann theory.

It is well known that the Poisson-Nernst-Planck (PNP) theory and the classical Gouy-Chapman theory are inconsistent at a high applied voltage. For solving this problem, we propose an ion-conserving Poisson-Boltzmann theory, which shows remarkable agreement with the numerical PNP solutions, even at a high applied voltage. In other words, we have found the exact analytical solutions for steady PNP equations; we believe that this finding greatly contributes to understanding surface science between solids and liquids.

Delayed double ionization as a signature of Hamiltonian chaos.

We analyze the dynamical processes behind delayed double ionization of atoms subjected to strong laser pulses. Using reduced models, we show that these processes are a signature of Hamiltonian chaos which results from the competition between the laser field and the Coulomb attraction to the nucleus. In particular, we exhibit the paramount role of the unstable manifold of selected periodic orbits which lead to a delay in these double ionizations. Among delayed double ionizations, we consider the case of recollision excitation with subsequent ionization (RESI) and, as a hallmark of this mechanism, we predict oscillations in the ratio of RESI to double ionization yields versus laser intensity. We discuss the significance of the dimensionality of the reduced models for the analysis of the dynamical processes behind delayed double ionization.