Ultra-high pressure liquid chromatography-mass spectrometry for plant metabolomics: a systematic comparison of high-resolution quadrupole-time-of-flight and single stage Orbitrap mass spectrometers.

The response of Arabidopsis to stress caused by mechanical wounding was chosen as a model to compare the performances of high resolution quadrupole-time-of-flight (Q-TOF) and single stage Orbitrap (Exactive Plus) mass spectrometers in untargeted metabolomics. Both instruments were coupled to ultra-high pressure liquid chromatography (UHPLC) systems set under identical conditions. The experiment was divided in two steps: the first analyses involved sixteen unwounded plants, half of which were spiked with pure standards that are not present in Arabidopsis. The second analyses compared the metabolomes of mechanically wounded plants to unwounded plants. Data from both systems were extracted using the same feature detection software and submitted to unsupervised and supervised multivariate analysis methods. Both mass spectrometers were compared in terms of number and identity of detected features, capacity to discriminate between samples, repeatability and sensitivity. Although analytical variability was lower for the UHPLC-Q-TOF, generally the results for the two detectors were quite similar, both of them proving to be highly efficient at detecting even subtle differences between plant groups. Overall, sensitivity was found to be comparable, although the Exactive Plus Orbitrap provided slightly lower detection limits for specific compounds. Finally, to evaluate the potential of the two mass spectrometers for the identification of unknown markers, mass and spectral accuracies were calculated on selected identified compounds. While both instruments showed excellent mass accuracy (<2.5ppm for all measured compounds), better spectral accuracy was recorded on the Q-TOF. Taken together, our results demonstrate that comparable performances can be obtained at acquisition frequencies compatible with UHPLC on Q-TOF and Exactive Plus MS, which may thus be equivalently used for plant metabolomics.

Vaporization behaviour and some thermodynamic properties of the Pd-In, Pd-Pb, Pd-Sn systems

In this study, the vaporization behaviour of solid Pd-rich phases in the Pd-Pb, Pd-In and Pd-Sn systems was investigated by Knudsen-effusion-cell coupled with mass-spectrometry. The Pb, Pd, In vapor pressures [no Sn(g) has been detected in the vapor of Pd-Sn system] were evaluated in the temperatures range 1190-1563 K from the ion intensities measured over two-phases regions. Thermodynamic quantities were derived from vapor pressure data. In particular, for the Pd-Sn binary, the intermediate phase Pd7Sn2, the existence of which has been recently proposed, has been studied here for the first time. Furthermore, preliminary thermochemical data are presented for the diatomic intermetallic molecules PdSn and PdPb, which have been for the first time identified in the vapors in equilibrium over liquid solutions of appropriate composition at higher temperatures (1935-2025 K). (C) 2000 Elsevier Science Ltd. All rights reserved.

Analysis and quantification of vitamin D metabolites in serum by ultra-performance liquid chromatography coupled to tandem mass spectrometry and high-resolution mass spectrometry: a method comparison and validation.

RATIONALE: The aim of the work was to develop and validate a method for the quantification of vitamin D metabolites in serum using ultra-high-pressure liquid chromatography coupled to mass spectrometry (LC/MS), and to validate a high-resolution mass spectrometry (LC/HRMS) approach against a tandem mass spectrometry (LC/MS/MS) approach using a large clinical sample set. METHODS: A fast, accurate and reliable method for the quantification of the vitamin D metabolites, 25-hydroxyvitamin D2 (25OH-D2) and 25-hydroxyvitamin D3 (25OH-D3), in human serum was developed and validated. The C3 epimer of 25OH-D3 (3-epi-25OH-D3) was also separated from 25OH-D3. The samples were rapidly prepared via a protein precipitation step followed by solid-phase extraction (SPE) using an HLB μelution plate. Quantification was performed using both LC/MS/MS and LC/HRMS systems. RESULTS: Recovery, matrix effect, inter- and intra-day reproducibility were assessed. Lower limits of quantification (LLOQs) were determined for both 25OH-D2 and 25OH-D3 for the LC/MS/MS approach (6.2 and 3.4 µg/L, respectively) and the LC/HRMS approach (2.1 and 1.7 µg/L, respectively). A Passing & Bablok fit was determined between both approaches for 25OH-D3 on 662 clinical samples (1.11 + 1.06x). It was also shown that results can be affected by the inclusion of the isomer 3-epi-25OH-D3. CONCLUSIONS: Quantification of the relevant vitamin D metabolites was successfully developed and validated here. It was shown that LC/HRMS is an accurate, powerful and easy to use approach for quantification within clinical laboratories. Finally, the results here suggest that it is important to separate 3-epi-25OH-D3 from 25OH-D3. Copyright © 2012 John Wiley & Sons, Ltd.

New Radicals and new applications of Dynamic Nuclear Polarization of biological systems

Dynamic Nuclear Polarization (DNP) is an emerging technique that could revolutionize the NMR study of small molecules at very low concentrations by the increase in sensitivity that results from transfer of polarization between electronic and nuclear spins. Although the underlying physics has been known for a long time, in the last few years there has been a lot of excitement on the chemistry and biology NMR community caused by the demonstration that the highly polarized nuclei that are prepared in solid state at very low temperatures (1-2 K) could be rapidly transferred to liquid samples at room temperature and studied in solution by conventional NMR techniques. In favorable cases several order of magnitude increases in sensitivity have been achieved. The technique is now mature enough that a commercial instrument is available. The efficiency of DNP depends on two crucial aspects: i) the efficiency of the nuclear polarization process and ii) the efficiency of the transfer from the initial solid state to the fluid state in which NMR is measured. The preferred areas of application (iii) will be dictated by situations in which the low concentration of the sample or its intrinsic low receptivity are the limiting factors .

Freezing of 4He and its liquid-solid interface from density functional theory

We show that, at high densities, fully variational solutions of solidlike types can be obtained from a density functional formalism originally designed for liquid 4He . Motivated by this finding, we propose an extension of the method that accurately describes the solid phase and the freezing transition of liquid 4He at zero temperature. The density profile of the interface between liquid and the (0001) surface of the 4He crystal is also investigated, and its surface energy evaluated. The interfacial tension is found to be in semiquantitative agreement with experiments and with other microscopic calculations. This opens the possibility to use unbiased density functional (DF) methods to study highly nonhomogeneous systems, like 4He interacting with strongly attractive impurities and/or substrates, or the nucleation of the solid phase in the metastable liquid.

Liquid-gas phase transition in nuclear matter from realistic many-body approaches

The existence of a liquid-gas phase transition for hot nuclear systems at subsaturation densities is a well-established prediction of finite-temperature nuclear many-body theory. In this paper, we discuss for the first time the properties of such a phase transition for homogeneous nuclear matter within the self-consistent Green's function approach. We find a substantial decrease of the critical temperature with respect to the Brueckner-Hartree-Fock approximation. Even within the same approximation, the use of two different realistic nucleon-nucleon interactions gives rise to large differences in the properties of the critical point.

Design of Optical Systems With Extended Depth of Field: an Educational Approach to Wavefront Coding Techniques

A practical activity designed to introduce wavefront coding techniques as a method to extend the depth of field in optical systems is presented. The activity is suitable for advanced undergraduate students since it combines different topics in optical engineering such as optical system design, aberration theory, Fourier optics, and digital image processing. This paper provides the theoretical background and technical information for performing the experiment. The proposed activity requires students able to develop a wide range of skills since they are expected to deal with optical components, including spatial light modulators, and develop scripts to perform some calculations.

Statistical dynamics of dislocation systems: The influence of dislocation-dislocation correlations.

During plastic deformation of crystalline materials, the collective dynamics of interacting dislocations gives rise to various patterning phenomena. A crucial and still open question is whether the long range dislocation-dislocation interactions which do not have an intrinsic range can lead to spatial patterns which may exhibit well-defined characteristic scales. It is demonstrated for a general model of two-dimensional dislocation systems that spontaneously emerging dislocation pair correlations introduce a length scale which is proportional to the mean dislocation spacing. General properties of the pair correlation functions are derived, and explicit calculations are performed for a simple special case, viz pair correlations in single-glide dislocation dynamics. It is shown that in this case the dislocation system exhibits a patterning instability leading to the formation of walls normal to the glide plane. The results are discussed in terms of their general implications for dislocation patterning.

Chemical and mineralogical changes in a Brazilian Rhodic Paleudult under different land use and managements

Changes in land use and management can affect the dynamic equilibrium of soil systems and induce chemical and mineralogical alterations. This study was based on two long-term experiments (10 and 27 years) to evaluate soil used for no-tillage maize cultivation, with and without poultry litter application (NTPL and NTM), and with grazed native pasture fertilized with cattle droppings (GrP), on the chemical and mineralogical characteristics of a Rhodic Paleudult in Southern Brazil, in comparison with the same soil under native grassland (NGr). In the four treatments, soil was sampled from the 0.0-2.5 and 2.5-5.0 cm layers. In the air-dried fine soil (ADFS) fraction (∅ < 2 mm), chemical characteristics of solid and liquid phases and the specific surface area (SSA) were evaluated. The clay fraction (∅ < 0.002 mm) in the 0.0-2.5 cm layer was analyzed by X-ray diffraction (XRD) after treatments for identification and characterization of 2:1 clay minerals. Animal waste application increased the total organic C concentration (COT) and specific surface area (SSA) in the 0.0-2.5 cm layer. In comparison to NGr, poultry litter application (NTPL) increased the concentrations of Ca and CECpH7, while cattle droppings (GrP) increased the P and K concentrations. In the soil solution, the concentration of dissolved organic C was positively related with COT levels. With regard to NGr, the soil use with crops (NTM and NTPL) had practically no effect on the chemical elements in solution. On the other hand, the concentrations of most chemical elements in solution were higher in GrP, especially of Fe, Al and Si. The Fe and Al concentrations in the soil iron oxides were lower, indicating reductive/complexive dissolution of crystalline forms. The X-ray diffraction (XRD) patterns of clay in the GrP environment showed a decrease in intensity and reflection area of the 2:1 clay minerals. This fact, along with the intensified Al and Si activity in soil solution indicate dissolution of clay minerals in soil under cattle-grazed pasture fertilized with animal droppings.

Fluctuations in finite systems: fluctuations in fluids in thermocapillary motion

We compute nonequilibrium correlation functions about the stationary state in which the fluid moves as a consequence of tangential stresses on the liquid surface, related to a varying surface tension (thermocapillary motion). The nature of the stationary state makes it necessary to take into account that the system is finite. We then extend a previous analysis on fluctuations about simple stationary states to include some effects related to the finite size of the sample.

Static and dynamic structure of liquid metals: Role of the different parts of the interaction potential

The influence of different parts of the interaction potential on the microscopic behavior of simple liquid metals is investigated by molecular dynamics simulation. The role of the soft-core repulsive, short-range attractive, and long-range oscillatory forces on the properties of liquid lithium close to the triple point is analyzed by comparing the results from simulations of identical systems but truncating the potential at different distances. Special attention is paid to dynamic collective properties such as the dynamic structure factors, transverse current correlation functions, and transport coefficients. It is observed that, in general, the effects of the short-range attractive forces are important. On the contrary, the influence of the oscillatory long-range interactions is considerably less, being the most pronounced for the dynamic structure factor at long wavelengths. The results of this work suggest that the influence of the attractive forces becomes less significant when temperature and density increase.

Metastable liquid-liquid phase transition in a single-component system with only one crystal phase and no density anomaly

We investigate the phase behavior of a single-component system in three dimensions with spherically-symmetric, pairwise-additive, soft-core interactions with an attractive well at a long distance, a repulsive soft-core shoulder at an intermediate distance, and a hard-core repulsion at a short distance, similar to potentials used to describe liquid systems such as colloids, protein solutions, or liquid metals. We showed [Nature (London) 409, 692 (2001)] that, even with no evidence of the density anomaly, the phase diagram has two first-order fluid-fluid phase transitions, one ending in a gas¿low-density-liquid (LDL) critical point, and the other in a gas¿high-density-liquid (HDL) critical point, with a LDL-HDL phase transition at low temperatures. Here we use integral equation calculations to explore the three-parameter space of the soft-core potential and perform molecular dynamics simulations in the interesting region of parameters. For the equilibrium phase diagram, we analyze the structure of the crystal phase and find that, within the considered range of densities, the structure is independent of the density. Then, we analyze in detail the fluid metastable phases and, by explicit thermodynamic calculation in the supercooled phase, we show the absence of the density anomaly. We suggest that this absence is related to the presence of only one stable crystal structure.

Liquid-liquid phase transition for soft-core attractive potential

Using event-driven molecular dynamics simulations, we study a three-dimensional one-component system of spherical particles interacting via a discontinuous potential combining a repulsive square soft core and an attractive square well. In the case of a narrow attractive well, it has been shown that this potential has two metastable gas-liquid critical points. Here we systematically investigate how the changes of the parameters of this potential affect the phase diagram of the system. We find a broad range of potential parameters for which the system has both a gas-liquid critical point C1 and a liquid-liquid critical point C2. For the liquid-gas critical point we find that the derivatives of the critical temperature and pressure, with respect to the parameters of the potential, have the same signs: they are positive for increasing width of the attractive well and negative for increasing width and repulsive energy of the soft core. This result resembles the behavior of the liquid-gas critical point for standard liquids. In contrast, for the liquid-liquid critical point the critical pressure decreases as the critical temperature increases. As a consequence, the liquid-liquid critical point exists at positive pressures only in a finite range of parameters. We present a modified van der Waals equation which qualitatively reproduces the behavior of both critical points within some range of parameters, and gives us insight on the mechanisms ruling the dependence of the two critical points on the potential¿s parameters. The soft-core potential studied here resembles model potentials used for colloids, proteins, and potentials that have been related to liquid metals, raising an interesting possibility that a liquid-liquid phase transition may be present in some systems where it has not yet been observed.

Dynamic properties of Lennard Jones fluids and liquid metals

The dependence of the dynamic properties of liquid metals and Lennard-Jones fluids on the characteristics of the interaction potentials is analyzed. Molecular-dynamics simulations of liquids in analogous conditions but assuming that their particles interact either through a Lennard-Jones or a liquid-metal potential were carried out. The Lennard-Jones potentials were chosen so that both the effective size of the particles and the depth of the potential well were very close to those of the liquid-metal potentials. In order to investigate the extent to which the dynamic properties of liquids depend on the short-range attractive interactions as well as on the softness of the potential cores, molecular-dynamics simulations of the same systems but assuming purely repulsive interactions with the same potential cores were also performed. The study includes both singleparticle dynamic properties, such as the velocity autocorrelation functions, and collective dynamic properties, such as the intermediate scattering funcfunctions, and collective dynamic properties, such as the intermediate scattering functions, the dynamic structure factors, the longitudinal and transverse current correlations, and the transport coefficients.