Treatment Of Hydrogen Research Articles

Empirical Hydrogen‐Bond Potential Functions—An Old Hat Reconditioned

The accurate description of hydrogen-bond interactions is of vital importance for the computational modeling of biological systems. Standard force field (FF) as well as semiempirical quantum mechanical (SQM) methods are now known to have considerable problems with the accurate description of hydrogen bonds. It was found that the performance of SQM methods can be greatly improved with empirical hydrogen-bond correction terms. In the first part of this work we review the improvements developed during the recent revival of dedicated hydrogen-bond terms, also in the light of earlier FF-related work. The second part presents new findings connected to open questions in this field, namely, a study on the importance of angular and torsional information, a scheme how to avoid atom-type-defined target angles and a reduced version of our DH(+) model for the application to force-field methods and physically motivated protein-ligand scoring functions. Our results highlight the importance of using a complete geometric description (including angular and torsional coordinates) for the accurate treatment of hydrogen bonding. The reduced DH(+) model-applied to a modified version of the UFF force field-shows a much improved accuracy for non-covalent interactions also with FF methods, with gains in accuracy by more than one order of magnitude.

The extinction properties of long gamma-ray burst host galaxies from H and He i recombination lines★

In this paper we show how a self-consistent treatment of hydrogen and helium emission line fluxes of the hosts of long gamma-ray bursts can result in improved understanding of the dust properties in these galaxies. In particular, we find that even with modest signal to noise spectroscopy we can differentiate different values for R_V, the ratio of total to selective extinction. The inclusion of Paschen and Brackett lines, even at low signal to noise, greatly increase the accuracy of the derived reddening. This method is often associated with strong systematic errors, caused by the need for multiple instruments to cover the wide wavelength range, the requirement to separate stellar hydrogen absorption from the nebular emission, and because of the dependancy of the predicted line fluxes on the electron temperature. We show how these three systematic errors can be negated, by using suitable instrumentation (in particular X-shooter on the Very Large Telescope) and wide wavelength coverage. We demonstrate this method using an extensive optical and near-infrared spectroscopic campaign of the host galaxy of gamma-ray burst 060218 (SN 2006aj), obtained with FORS1, UVES and ISAAC on the VLT, covering a broad wavelength range with both high and low spectral resolution. We contrast our findings of this source with X-shooter data of a star forming region in the host of GRB 100316D, and show the improvement over existing published fluxes of long GRB hosts.

Non-equilibrium calcium ionisation in the solar atmosphere

Our aim is to determine the dominant processes and timescales for the ionisation equilibrium of calcium under solar chromospheric conditions. The study is based on numerical simulations with the RADYN code, which includes hydrodynamics, radiative transfer, and a detailed non-equilibrium treatment of hydrogen, calcium, and helium. The simulations are characterised by upwards propagating shock waves, which cause strong temperature fluctuations and variations of the ionisation degree of calcium. The passage of a hot shock front leads to a strong net ionisation of Ca II, rapidly followed by net recombination. The relaxation timescale of the Ca ionisation state is found to be of the order of a few seconds at the top of the photosphere and 10 to 30 s in the upper chromosphere. Generally, the timescales are significantly reduced in the wakes of hot shock fronts. The timescales can be reliably determined from a simple analysis of the eigenvalues of the transition rate matrix. The timescales are dominated by the radiative recombination from Ca III into the metastable Ca II energy levels of the 4d 2D term. These transitions depend strongly on the density of free electrons and therefore on the (non-equilibrium) ionisation degree of hydrogen, which is the main electron donor. The ionisation/recombination timescales derived here are too long for the assumption of an instantaneous ionisation equilibrium to be valid and, on the other hand, are not long enough to warrant an assumption of a constant ionisation fraction. Fortunately, the ionisation degree of Ca II remains small in the height range, where the cores of the H, K, and the infrared triplet lines are formed. We conclude that the difference due to a detailed treatment of Ca ionisation has only negligible impact on the modelling of spectral lines of Ca II and the plasma properties under the conditions in the quiet solar chromosphere.

THE EFFECT OF SODIUM HYDROGEN PHOSPHATE/ CITRIC ACID MIXTURES ON PHYTOREMEDIATION BY ALFALFA & METALS AVAILABILITY IN SOIL

The effect of sodium hydrogen phosphate/citric acid mixtures on enhancing phytoremediation of heavy metal-contaminated soil by alfalfa (Medicago sativa L.) and the changes of metal availability in soils were investigated. Alfalfa plants grew healthily in heavy metals-contaminated soils (collected from molybdenum mine) for 30 days. The heavy metal content was determined by ICP-OES. In this paper, it was found that: the phytoextraction efficiency of alfalfa plants was enhanced after the sodium hydrogen phosphate/citric acid mixtures were added into soil. As usual, the phosphorus can promote plants to accumulate more biomass (increasing 0.35%-24.62%) even if the availability of metals to extraction were increased by citric acid in the soil. With the treatment of sodium hydrogen phosphate/citric acid mixtures, the bioconcentration factor (BCF) values of alfalfa plants and the acid soluble fractions of heavy metals in soils were increased. The translocation factor (TF) values of all alfalfas in heavy metals were low, but the TF of As, Cr, Hg, Mo tended to increase with sodium hydrogen phosphate/citric acid mixtures. In other words, both the availability and the biological- validity of heavy metals in soils were increased after sodium hydrogen phosphate/citric acid mixtures were added into soils.

Hydrogen and helium in the late phase of supernovae of Type IIb

Supernovae of Type IIb contain large fractions of helium and traces of hydrogen, which can be observed in the early and late spectra. Estimates of the hydrogen and helium mass and distribution are mainly based on early-time spectroscopy and are uncertain since the respective lines are usually observed in absorption. Constraining the mass and distribution of H and He is important to gain insight into the progenitor systems of these SNe. We implement a NLTE treatment of hydrogen and helium in a three-dimensional nebular code. Ionisation, recombination, (non-)thermal electron excitation and H$\alpha$ line scattering are taken into account to compute the formation of H$\alpha$, which is by far the strongest H line observed in the nebular spectra of SNe IIb. Other lines of H and He are also computed but are rarely identified in the nebular phase. Nebular models are computed for the Type IIb SNe 1993J, 2001ig, 2003bg and 2008ax as well as for SN 2007Y, which shows H$\alpha$ absorption features at early times and strong H$\alpha$ emission in its late phase, but has been classified as a SN Ib. We suggest to classify SN 2007Y as a SN IIb. Optical spectra exist for all SNe of our sample, and there is one IR nebular observation of SN 2008ax, which allows an exploration of its helium mass and distribution. We develop a three-dimensional model for SN 2008ax. We obtain estimates for the total mass and kinetic energy in good agreement with the results from light-curve modelling found in the literature. We further derive abundances of He, C, O, Ca and $^{56}$Ni. We demonstrate that H$\alpha$ absorption is probably responsible for the double-peaked profile of the [O {\sc i}] $\lambda\lambda$ 6300, 6363 doublet in several SNe IIb and present a mechanism alternative to shock interaction for generating late-time H$\alpha$ emission of SNe IIb.

Low Temperature Synthesis of Vertically Aligned Carbon Nanotubes with Electrical Contact to Metallic Substrates Enabled by Thermal Decomposition of the Carbon Feedstock

Growth of vertically aligned carbon nanotube (CNT) carpets on metallic substrates at low temperatures was achieved by controlled thermal treatment of ethylene and hydrogen at a temperature higher than the substrate temperature. High-resolution transmission electron microscopy showed that nanotubes were crystalline for a preheating temperature of 770 degrees C and a substrate temperature of 500 degrees C. Conductive atomic force microscopy measurements indicated electrical contact through the CNT carpet to the metallic substrate with an approximate resistance of 35 kOmega for multiwall carpets taller than two micrometers. An analysis of the activation energies indicated that thermal decomposition of the hydrocarbon/hydrogen gas mixture was the rate-limiting step for low-temperature chemical vapor deposition growth of CNTs. These results represent a significant advance toward the goal of replacing copper interconnects with nanotubes using CMOS-compatible processes.

Treatment of low concentration hydrogen by electrochemical pump or proton exchange membrane fuel cell

Proton exchange membrane fuel cell (PEMFC) can produce electricity through electrochemical reaction of hydrogen with oxygen with the use of a membrane and electrode assembly (MEA). In other words, the hydrogen pressure difference between the anode and cathode can produce electricity via an electrochemical process. Conversely, when we supply electricity to MEA from an external power source, we can pump up or separate hydrogen from the low-pressure anode to the high-pressure cathode, according to the principle of “concentration cell”. By the way, PEMFC cannot use the fuel completely, because a cell potential decreases and electrode material may corrode when most of the fuel is consumed. Therefore the fuel released from PEMFC should be treated safely. The depleted hydrogen from PEMFC can be recovered by the electrochemical hydrogen pump, or further can be used as a fuel for the power generation by PEMFC, even though the cell voltage might be low. In this study we preliminarily measured the voltage–current characteristics of hydrogen pump and PEMFC changing the hydrogen concentration from 99.99% to 1%, as another option to platinum catalytic combustion of low concentration hydrogen. Moreover we could successfully treat the low concentration hydrogen by electrochemical pump or PEMFC, for the widely changing hydrogen concentration and mixture flow rate. The gas chromatography confirmed the hydrogen concentration of the treated gas to be 1000 ppm at most.

The Important Role of Lone-Pairs in Force Field (MM4) Calculations on Hydrogen Bonding in Alcohols

An expanded treatment of hydrogen bonding has been developed for MM4 force field calculations, which is an extension from the traditional van der Waals-electrostatic model. It adds explicit hydrogen-bond angularity by the inclusion of lone-pair directionality. The vectors that account for this directionality are placed along the hydrogen acceptor and its chemically intuitive electron pairs. No physical lone-pairs are used in the calculations. Instead, an H-bond angularity function, and a lone-pair directionality function, are incorporated into the hydrogen-bond term. The inclusion of the lone-pair directionality results in improved accuracy in hydrogen-bonded geometries and interaction energies. In this work is described hydrogen bonding in alcohols, and also in water and hydrogen fluoride dimer. The extension to other compounds such as aldehydes, ketones, amides, and so on is straightforward and will be discussed in future work. The conformational energies of ethylene glycol are discussed.

Treatment of Low Concentration Hydrogen by use of Proton Exchange Membrane

Proton exchange membrane fuel cell (PEMFC) can hardly react a hundred percent of fuel, because a cell potential becomes zero if all of the fuel is consumed at PEMFC. Therefore a small amount of fuel is always released from PEMFC. The exhausted H2 should be treated for safety. iave-Vcel characteristics were measured changing hydrogen concentration from 99.99% to 1%. Moreover, Vcell of the constant voltage control was selected from the measured Vcell-iave characteristics, the low concentration hydrogen could be treated under Vcell =0.15 - 0.3V by hydrogen pump and Vcell =0.4 - 0.6V by PEMFC. The exhaust hydrogen was reduced to the hydrogen concentration of several tens of ppm.

Inelastic neutron scattering study of hydrogen in d8-THF∕D2O ice clathrate

In situ neutron inelastic scattering experiments on hydrogen adsorbed into a fully deutrated tetrahydrofuran-water ice clathrate show that the adsorbed hydrogen has three rotational excitations (transitions between J=0 and 1 states) at approximately 14 meV in both energy gain and loss. These transitions could be unequivocally assigned since there was residual orthohydrogen at low temperatures (slow conversion to the ground state) resulting in an observable J=1-->0 transition at 5 K (kT=0.48 meV). A doublet in neutron energy loss at approximately 28.5 meV is interpreted as J=1-->2 transitions. In addition to the transitions between rotational states, there are a series of peaks that arise from transitions between center-of-mass translational quantum states of the confined hydrogen molecule. A band at approximately 9 meV can be unequivocally interpreted as a transition between translational states, while broad features at 20, 25, 35, and 50-60 meV are also interpreted to as transitions between translational quantum states. A detailed comparison is made with a recent five-dimensional quantum treatment of hydrogen in the smaller dodecahedral cage in the SII ice-clathrate structure. Although there is broad agreement regarding the features such as the splitting of the J=1 degeneracy, the magnitude of the external potential is overestimated. The numerous transitions between translational states predicted by this model are in poor agreement with the experimental data. Comparisons are also made with three simple exactly solved models, namely, a particle in a box, a particle in a sphere, and a particle on the surface of a sphere. Again, there are too many predicted features by the first two models, but there is reasonable agreement with the particle on a sphere model. This is consistent with published quantum chemistry results for hydrogen in the dodecahedral 5(12) cage, where the center of the cage is found to be energetically unfavorable, resulting in a shell-like confinement for the hydrogen molecule wave function. These results demonstrate that translational quantum effects are very significant and a classical treatment of the hydrogen molecule dynamics is inappropriate under such conditions.

Validation of the COSMO-RS electrostatics by Monte-Carlo simulations

The conductor-like screening model for real solvents (COSMO-RS) meanwhile is widely accepted as a novel and efficient tool for the predictive simulation of fluid phase thermodynamics based on quantum chemical calculations for the individual compounds. In COSMO-RS all molecular interactions are described as local interactions of surface segments and quantified by the local surface polarization charge densities which are known from the quantum chemical simulation of the compounds in a virtual conductor (COSMO). The statistical thermodynamics of the interacting segments is solved in COSMO-RS by an accurate and efficient self-consistency algorithm. While the treatment of hydrogen bonding and dispersive interactions as local surface interactions appears to be justified by the local nature of these interactions, the local description of the electrostatics in COSMO-RS is somewhat counter-intuitive, because the Coulomb electrostatics is longer ranged and non-local in its nature. This has been a frequent topic of criticism of the COSMO-RS theory. In order to check the validity of the local description of electrostatics we compare the results of MC simulations and COSMO-RS calculations for dipolar and quadrupolar compounds of the same shape and very similar σ-profiles. According to the COSMO-RS theory such two compounds should have very similar interactions in the liquid phase, which is a bit counterintuitive from the perspective of the conventional molecular simulation. For this purpose different simplified CO 2-shaped and spherical pseudo-molecules with a variety of different charge distributions have been consistently treated by COSMO-RS and by MC simulation applying a 2-center or 1-center Lennard–Jones model, respectively, in the MC-simulations. The comparison reveals that the results for the average electrostatic interaction energies and for the vapour pressures resulting from both simulation methods are in satisfying agreement. This indicates the validity of the local description of electrostatics and hence gives further confirmation of the fundaments of the COSMO-RS theory.

A critical review of the Energy Policy Act of 2005's treatment of hydrogen

The paper analyzes the Energy Policy Act's goals and proposed action in Title VIII, the section dedicated to hydrogen. It then assesses whether or not the resources dedicated to this cause are sufficient to overcome the obstacles facing the commercial use of hydrogen and fuel cells.

Multicentered integrated QM:QM methods for weakly bound clusters: An efficient and accurate 2-body:many-body treatment of hydrogen bonding and van der Waals interactions

An efficient integrated QM:QM technique for the description of weakly bound clusters is presented. The computational technique described here takes advantage of the recently developed multicentered (MC) integrated QM:QM methods and reliably describes hydrogen bonding and van der Waals interactions by treating all 2-body interactions with a high-level QM method and the many-body interactions with a low-level QM method. Even for small clusters of He, Ne, HF, and water, the MC QM:QM methods are typically 1–3 orders of magnitude faster than the high-level method while introducing an error of less than 1% in the interaction energy.

High-temperature treatment of hydrogen loaded GeO 2:SiO 2 glasses for photonic device fabrication

High-temperature treatment of hydrogen loaded silica- and germanium doped silica glass, also referred to as OH flooding, has been studied. The removal mechanism of hydroxyl groups in silica glass, during OH flooding, occurs by formation and diffusion of molecular hydrogen, while in germanium doped silica the main diffusion mechanism is attributed to diffusion of molecular water. UV exposure of OH flooded and non-treated germanium doped silica samples, from a ArF laser at 193 nm, show large changes in the asymmetric stretching vibration of Si–O–Si bridges, indicating compaction of the glass network. In addition, the thermal relaxation kinetics of the UV induced compaction are found to be similar for non-treated samples and OH flooded samples.

Dyes and other colorants in microtechnique and biomedical research

Dyes and other colorants in microtechnique and biomedical research

Irreversible hydrogen quantum dynamics and anomalous scattering behavior in liquids and solids

We report on neutron–proton Compton scattering experiments on various hydrogen containing materials like water, an organic polymer and an ionic metal hydride. Furthermore, results of an electron–proton Compton scattering experiment on the polymer are presented. The results reveal a strong decrease of the scattering integral intensities due to the protons in these materials. Thus far these effects have found no common explanation based on existing condensed matter theories. Rather, they invoke the existence of quantum correlations (also called quantum entanglement—QE) and decoherence between the particles. Of particular importance in the present context is the fact that the interaction time of the probe (i.e. neutron or electron) must be of the same order of magnitude as the decay of the coherence (also called decoherence) of the correlated particles. The found experimental effects and their possible explanations may have far reaching consequences for condensed matter physics and in particular for the theoretical treatment of hydrogen containing materials.

Molecular dynamics with quantum transitions for proton transfer: Quantum treatment of hydrogen and donor–acceptor motions

The mixed quantum/classical molecular dynamics with quantum transitions (MDQT) method is extended to treat the donor–acceptor vibrational motion as well as the hydrogen motion quantum mechanically for proton transfer reactions. The quantum treatment of both the hydrogen and the donor–acceptor motions requires the calculation of two-dimensional vibrational wave functions. The MDQT surface hopping method incorporates nonadiabatic transitions among these adiabatic vibrational states. This approach is applied to a model representing intramolecular proton transfer within a phenol-amine complex in liquid methyl chloride. For this model, the rates and kinetic isotope effects are the same within statistical uncertainty for simulations in which only the hydrogen motion is treated quantum mechanically and simulations in which both the hydrogen and the donor–acceptor vibrational motions are treated quantum mechanically. The analysis of these simulations elucidates the fundamental issues arising from a quantum mechanical treatment of the donor–acceptor vibrational motion as well as the hydrogen motion. This insight is relevant to future mixed quantum/classical molecular dynamics simulations of proton and hydride transfer reactions in solution and in enzymes.

Alcohols, ethers, carbohydrates, and related compounds. IV. Carbohydrates.

Ab initio calculations [B3LYP/6-311++G(2d,2p)] have been carried out on 84 conformations of 12 different sugars (hexoses), in both pyranose and furanose forms, with the idea of generating a data base for carbohydrate structural energies that may be used for developing the predictive value of molecular mechanics calculations for carbohydrates. The average value for the apparent gas phase anomeric effect for a series of 31 pairs of pyranose conformations was found to be 1.83 kcal/mol (vs. 2.67 kcal/mol with a smaller basis set used in earlier calculations). In developing MM4 to reproduce these data, it was necessary first to have good energies for simple alcohols and ethers, together with an adequate treatment of hydrogen bonding, and then to include the anomeric effect, and the ethylene glycol type system, as was previously recognized. It was also found that the so-called delta-2 effect, long recognized in carbohydrates, must be explicitly included, in order to obtain acceptable results. When a force field that included all of these items as developed from the small molecules based on the MM4 hydrocarbon force field was applied without any parameter adjustment to the set of hexopyranose and furanose conformations mentioned earlier, the E(beta) - E(alpha) was found to have an average value of 1.88 kcal/mol, versus 1.74 for the quantum calculations. The signed average and RMS deviations of the MM4 from the QM results were +0.15 and 0.87 kcal/mol.

Properties and Composition of the Wastes of Monoethanolamine Treatment of Hydrogen to Remove Carbon Dioxide

The properties and composition of the wastes of monoethanolamine treatment of pyrolysis hydrogen to remove carbon dioxide and their effect on corrosion of ferrous and non-ferrous metals in various media were studied.

Experience in revamping the ethanolamine gas treatment unit

Positive experience in use of contact devices of the VNIIUS—14 type in ethanolamine treatment to remove hydrogen sulfide from gases has been covered relatively extensively in the press. The results of experience with the LUKOIL—Permnefteorgsintez OJSC L—24/6 plant are reported here: faultless operation of two absorbers for MEA treatment of hydrogen—containing gas and absorber for treatment of hydrocarbon gas for seven years.