Insights into hydrogen atom adsorption on and the electrochemical properties of nitrogen-substituted carbon materials

The nitrogen substitution in carbon materials is investigated theoretically using the density functional theory method. Our calculations show that nitrogen substitution decreases the hydrogen adsorption energy if hydrogen atoms are adsorbed on both nitrogen atoms and the neighboring carbon atoms. On the contrary, the hydrogen adsorption energy can be increased if hydrogen atoms are adsorbed only on the neighboring carbon atoms. The reason can be explained by the electronic structures analysis of N-substituted graphene sheets. Nitrogen substitution reduces the pi electron conjugation and increases the HOMO energy of a graphene sheet, and the nitrogen atom is not stable due to its 3-valent character. This raises an interesting research topic on the optimization of the N-substitution degree, and is important to many applications such as hydrogen storage and the tokamaks device. The electronic structure studies also explain well why nitrogen substitution increases the capacitance but decreases the electron conductivity of carbon electrodes as was experimentally observed in our experiments on the supercapacitor.

A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.

Statistical Analysis of the heavy neutral Atoms measured by IBEX

We investigate the directional distribution of heavy neutral atoms in the heliosphere by using heavy neutral maps generated with the IBEX-Lo instrument over three years from 2009 to 2011. The interstellar neutral (ISN) O&Ne gas flow was found in the first-year heavy neutral map at 601 keV and its flow direction and temperature were studied. However, due to the low counting statistics, researchers have not treated the full sky maps in detail. The main goal of this study is to evaluate the statistical significance of each pixel in the heavy neutral maps to get a better understanding of the directional distribution of heavy neutral atoms in the heliosphere. Here, we examine three statistical analysis methods: the signal-to-noise filter, the confidence limit method, and the cluster analysis method. These methods allow us to exclude background from areas where the heavy neutral signal is statistically significant. These methods also allow the consistent detection of heavy neutral atom structures. The main emission feature expands toward lower longitude and higher latitude from the observational peak of the ISN O&Ne gas flow. We call this emission the extended tail. It may be an imprint of the secondary oxygen atoms generated by charge exchange between ISN hydrogen atoms and oxygen ions in the outer heliosheath.

The thermal decomposition of hydronium jarosite and ammoniojarosite

The thermal decomposition of hydronium jarosite and ammoniojarosite was studied using thermogravimetric analysis and mass spectrometry, in situ synchrotron X-ray diffraction and infrared emission spectroscopy. There was no evidence for the simultaneous loss of water and sulfur dioxide during the desulfonation stage as has previously been reported for hydronium jarosite. Conversely, all hydrogen atoms are lost during the dehydration and dehydroxylation stage from 270 to 400 °C and no water, hydroxyl groups or hydronium ions persist after 400 °C. The same can be said for ammoniojarosite. The first mass loss step during the decomposition of hydronium jarosite has been assigned to the loss of the hydronium ion via protonation of the surrounding hydroxyl groups to evolve two water molecules. For ammoniojarosite, this step corresponds to the protonation of a hydroxyl group by ammonium, so that ammonia and water are liberated simultaneously. Iron(II) sulfate was identified as a possible intermediate during the decomposition of ammoniojarosite (421–521 °C) due to a redox reaction between iron(III) and the liberated ammonia during decomposition. Iron(II) ions were also confirmed with the 1,10-phenanthroline test. Iron(III) sulfate and other commonly suggested intermediates for hydronium and ammoniojarosite decomposition are not major crystalline phases; if they are formed, then they most likely exist as an amorphous phase or a different low temperature phases than usual.

Deposition of hydrocarbon molecules on diamond (001) surfaces : atomic scale modeling

The impact induced chemisorption of hydrocarbon molecules (CH3 and CH2) on H-terminated diamond (001)-(2x1) surface was investigated by molecular dynamics simulation using the many-body Brenner potential. The deposition dynamics of the CH3 radical at impact energies of 0.1-50 eV per molecule was studied and the energy threshold for chemisorption was calculated. The impact-induced decomposition of hydrogen atoms and the dimer opening mechanism on the surface was investigated. Furthermore, the probability for dimer opening event induced by chemisorption of CH, was simulated by randomly varying the impact position as well as the orientation of the molecule relative to the surface. Finally, the energetic hydrocarbons were modeled, slowing down one after the other to simulate the initial fabrication of diamond-like carbon (DLC) films. The structure characteristic in synthesized films with different hydrogen flux was studied. Our results indicate that CH3, CH2 and H are highly reactive and important species in diamond growth. Especially, the fraction of C-atoms in the film having sp(3) hybridization will be enhanced in the presence of H atoms, which is in good agreement with experimental observations. (C) 2002 Elsevier Science B.V. All rights reserved.

Energy dependence of methyl-radical adsorption on diamond (001)-(2×1) surface

The deposition of hyperthermal CH3 on diamond (001)-(2×1) surface at room temperature has been studied by means of molecular dynamics simulation using the many-body hydrocarbon potential. The energy threshold effect has been observed. That is, with fixed collision geometry, chemisorption can occur only when the incident energy of CH3 is above a critical value (Eth). Increasing the incident energy, dissociation of hydrogen atoms from the incident molecule was observed. The chemisorption probability of CH3 as a function of its incident energy was calculated and compared with that of C2H2. We found that below 10 eV, the chemisorption probability of C2H2 is much lower than that of CH3 on the same surface. The interesting thing is that it is even lower than that of CH3 on a hydrogen covered surface at the same impact energy. It indicates that the reactive CH3 molecule is the more important species than C2H2 in diamond synthesis at low energy, which is in good agreement with the experimental observation.

Ion-assisted precursor dissociation and surface diffusion : enabling rapid, low-temperature growth of carbon nanofibers

Growth kinetics of carbon nanofibers in a hydrocarbon plasma is studied. In addition to gas-phase and surface processes common to chemical vapor deposition, the model includes (unique to plasma-exposed catalyst surfaces) ion-induced dissociation of hydrocarbons, interaction of adsorbed species with incoming hydrogen atoms, and dissociation of hydrocarbon ions. It is shown that at low, nanodevice-friendly process temperatures the nanofibers grow via surface diffusion of carbon adatoms produced on the catalyst particle via ion-induced dissociation of a hydrocarbon precursor. These results explain a lower activation energy of nanofiber growth in a plasma and can be used for the synthesis of other nanoassemblies. © 2007 American Institute of Physics.

Formation of carbon nanoscrolls from graphene nanoribbons : a molecular dynamics study

Carbon nanoscrolls (CNSs) are one of the carbon-based nanomaterials similar to carbon nanotubes (CNTs) but are not widely studied in spite of their great potential applications. Their practical applications are hindered by the challenging fabrication of the CNSs. A physical approach has been proposed recently to fabricate the CNS by rolling up a monolayer graphene nanoribbon (GNR) around a CNT driven by the interaction energy between them. In this study, we perform extensive molecular dynamics (MD) simulations to investigate the various factors that impact the formation of the CNS from GNR. Our simulation results show that the formation of the CNS is sensitive to the length of the CNT and temperature. When the GNR is functionalized with hydrogen, the formation of the CNS is determined by the density and distribution of the hydrogen atoms. Graphyne, the allotrope of graphene, is inferior to graphene in the formation of the CNS due to the weaker bonds and the associated smaller atom density. The mechanism behind the rolling of GNR into CNS lies in the balance between the GNR–CNT van der Waals (vdW) interactions and the strain energy of GNR. The present work reveals new important insights and provides useful guidelines for the fabrication of the CNS.

The molecular structure of kaolinite–potassium acetate intercalation complexes: A combined experimental and molecular dynamic simulation study

The kaolinite (Kaol) intercalated with potassium acetate (Ac) was prepared and characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and thermogravimetry. Molecular dynamic simulation was performed to investigate the structure of Kaol–Ac intercalation complex and the hydrogen bonds between Kaol and intercalated Ac andwater using INTERFACE forcefield. The acetate anions andwater arranged in a bilayer structure in the interlayer space of Kaol. The potassium cations distributed in the interlayer space and strongly coordinated with acetate anions aswell aswater rather than keyed into the ditrigonal holes of tetrahedral surface of Kaol. Strong hydrogen bonds formed between the hydrogen atoms of hydroxyl on the octahedral surface and oxygen atoms of both acetate anions and water. The acetate anions andwater also weakly bonded hydrogen to the silica tetrahedral surface through their hydrogen atoms with the oxygen atoms of silica tetrahedral surface.

Jump Reorientation of Water Molecules Confined in Narrow Carbon Nanotubes

We used molecular dynamics (MD) simulations to study the reorientational dynamics of water molecules confined inside narrow carbon nanotubes immersed in a bath of water. Our simulations show that the confined water molecules exhibit bistability in their reorientational relaxation, which proceeds by angular jumps between the two stable states. The angular jump of a water molecule in the bulk involves the breaking of a hydrogen bond with one of its neighbors and the formation of a hydrogen bond with a different neighbor. In contrast, the angular jump of a confined water molecule corresponds to an interchange of the two hydrogen atoms that can form a hydrogen bond with the same neighbor. The free energy barrier between these two states is a few k(B)T. The analytic solution of a simplified two-state jump model that qualitatively explains the reorientational behavior observed in simulations is also presented.

Theoretical studies on penicillins, penicillin sulphones and their 1-oxa-1-dethia and 1-carba-1-dethia analogues: binding specificities of transeptidases and penicillinases

Empirical potential energy calculations have been carried out to determine the preferred conformations of penicillins and penicillin sulphones and their 1-oxa-1-dethia and 1-carba-1-dethia analogues. With the exception of 1-oxa-1-dethia penicillins, all the other compounds favour C2 and the C3 puckered conformations of their five-membered rings. Replacement of C2 methyl groups by hydrogen atoms as in bisnorpenicillin V or oxidation of sulphur in position 1 as in sulphones, makes the C3 puckered form much less favourable. Addition of an amino-acyl group at the C6 atom, however, makes the C3 puckered form more favoured in penicillin G or V and in 1-carba-1-dethia penicillins. Through the replacement of the sulphur atom at position 1 by an oxygen atom or by a -CH2 group increases the non-planarity of the lactam peptide bond, it significantly affects the relative disposition of the C3 carboxyl group with respect to the β-lactam ring. These conformational differences have been correlated with the biological activities of these compounds. The present study suggests that the conformation of the bicyclic ring system may be more important for initial binding with the crosslinking enzyme(s) involved in the biosynthesis of bacterial cell-wall peptidoglycan and that the mode of binding is influenced by the nature of the side-group at the C6 atom. These studies predict, in agreement with experimental results, that the 1-oxa-1-dethia penicillin nulceus is an inhibitor of penicillianses. The study also suggests that the stereospecificities of the crosslinking enzyme(s) and penicillinases are very similar with regard to the nature of the side-group at the 6 atom and the confirmation of the bicyclic ring system. However, the confirmational requirement for the bicyclic ring system appears to be more specific in the former enzyme than in the latter.

Enzyme molecular choreography : studies on soluble inorganic pyrophosphatases

Inorganic pyrophosphatases (PPases, EC 3.6.1.1) hydrolyse pyrophosphate in a reaction that provides the thermodynamic 'push' for many reactions in the cell, including DNA and protein synthesis. Soluble PPases can be classified into two families that differ completely in both sequence and structure. While Family I PPases are found in all kingdoms, family II PPases occur only in certain prokaryotes. The enzyme from baker's yeast (Saccharomyces cerevisiae) is very well characterised both kinetically and structurally, but the exact mechanism has remained elusive. The enzyme uses divalent cations as cofactors; in vivo the metal is magnesium. Two metals are permanently bound to the enzyme, while two come with the substrate. The reaction cycle involves the activation of the nucleophilic oxygen and allows different pathways for product release. In this thesis I have solved the crystal structures of wild type yeast PPase and seven active site variants in the presence of the native cofactor magnesium. These structures explain the effects of the mutations and have allowed me to describe each intermediate along the catalytic pathway with a structure. Although establishing the ʻchoreographyʼ of the heavy atoms is an important step in understanding the mechanism, hydrogen atoms are crucial for the mechanism. The most unambiguous method to determine the positions of these hydrogen atoms is neutron crystallography. In order to determine the neutron structure of yeast PPase I perdeuterated the enzyme and grew large crystals of it. Since the crystals were not stable at ambient temperature, a cooling device was developed to allow neutron data collection. In order to investigate the structural changes during the reaction in real time by time-resolved crystallography a photolysable substrate precursor is needed. I synthesised a candidate molecule and characterised its photolysis kinetics, but unfortunately it is hydrolysed by both yeast and Thermotoga maritima PPases. The mechanism of Family II PPases is subtly different from Family I. The native metal cofactor is manganese instead of magnesium, but the metal activation is more complex because the metal ions that arrive with the substrate are magnesium different from those permanently bound to the enzyme. I determined the crystal structures of wild type Bacillus subtilis PPase with the inhibitor imidodiphosphate and an inactive H98Q variant with the substrate pyrophosphate. These structures revealed a new trimetal site that activates the nucleophile. I also determined that the metal ion sites were partially occupied by manganese and iron using anomalous X- ray scattering.

A study of interaction in the lowest singlet and triplet states of H2

The potential energy curves of the ground state and the first excited state of H2 are examined in terms of the electronic force acting on each nucleus. The results reveal the detailed course of events that occur when two hydrogen atoms with parallel and antiparallel electron spins approach one another from a large internuclear separation.

Reactivation kinetics of boron acceptors in hydrogenated silicon during zero bias anneal

The reactivation kinetics of passivated boron accepters in hydrogenated silicon during zero bias annealing in the temperature range of 65-130 degrees C are reported, For large annealing times and high annealing temperatures, the reactivation process follows second-order kinetics and is rate limited by a thermally activated <(H)over tilde (2)> complex formation process, For short annealing times and low annealing temperatures, the reactivation rate is found to be larger than that due to <(H)over tilde (2)> complex formation alone. We conclude that the faster reactivation is caused by the diffusion of the liberated hydrogen atoms into the bulk as well as <(H)over tilde (2)> complex formation. The effective diffusion coefficient of hydrogen is measured and found to obey the Arrhenius relation with an activation energy (1.41 +/- 0.1) eV. (C) 1997 American Institute of Physics.

Zero-point entropy in 'spin ice'

Common water ice (ice I-h) is an unusual solid-the oxygen atoms form a periodic structure but the hydrogen atoms are highly disordered due to there being two inequivalent O-H bond lengths'. Pauling showed that the presence of these two bond lengths leads to a macroscopic degeneracy of possible ground states(2,3), such that the system has finite entropy as the temperature tends towards zero. The dynamics associated with this degeneracy are experimentally inaccessible, however, as ice melts and the hydrogen dynamics cannot be studied independently of oxygen motion(4). An analogous system(5) in which this degeneracy can be studied is a magnet with the pyrochlore structure-termed 'spin ice'-where spin orientation plays a similar role to that of the hydrogen position in ice I-h. Here we present specific-heat data for one such system, Dy2Ti2O7, from which we infer a total spin entropy of 0.67Rln2. This is similar to the value, 0.71Rln2, determined for ice I-h, SO confirming the validity of the correspondence. We also find, through application of a magnetic field, behaviour not accessible in water ice-restoration of much of the ground-state entropy and new transitions involving transverse spin degrees of freedom.