Single Hydrogen Atom Research Articles

Hydrogen in the approximant i-TiZrHf: The energy state, charge, and diffusion

The energy of hydrogen dissolution in different tetrahedral pores of a 1/1 approximant of the icosahedral TiZrHf quasicrystal has been determined in terms of the density functional theory and ab initio pseudopotentials. At low and high degrees of loading of TiZrHf with hydrogen, the charges of atoms involved in the system and the Mayer bond order have been calculated for all possible M-M and M-H pairs. The diffusion coefficient of a single hydrogen atom in the system under study has been estimated numerically.

Structural, energetic, and electronic properties of hydrogenated aluminum arsenide clusters

The chemisorptions of hydrogen on aluminum arsenide clusters are studied with density functional theory (DFT). The on-top site is identified to be the most favorable chemisorptions site for hydrogen. And the Al-top site is the preferred one in the most cases for one hydrogen adsorption in (AlAs) n (n = 2, 5, 6, 8–15) clusters. Top on the neighboring Al and As atoms ground-state structures are found for two hydrogen adsorption on (AlAs) n except for (AlAs)2 cluster. The Al–As bond lengths decrease generally as the size of the cluster increases. And there is a slight increase in the mean Al–As bond lengths after H adsorption on the lowest-energy sites of the most AlAs clusters. In general, the binding energy of H and 2H are both found to decrease with an increase in the cluster size. And the result shows that large binding energies (BE) of a single hydrogen atom on small AlAs clusters and large highest occupied and lowest unoccupied molecular-orbital gaps for (AlAs)H and (AlAs)3H make these species behaving like magic clusters. Calculations on two hydrogen atoms on (AlAs) n clusters show large BE for (AlAs) n H2 with an odd number of n. The stability of these complexes is further studied from the fragmentation energies. (AlAs)7H2 and (AlAs)9H2 clusters are again suggested to be the stable clusters. On the other hand both the fragmentation energy and the binding energy for (AlAs)13H are close to the lowest values.

A combined combinatorial and pKa-based approach to ligand protonation states

The protonation of the ligand molecule and the protein binding site has a significant influence on the results obtained by protein-ligand docking. Due to the inability of X-ray crystallography to resolve the hydrogen atom in protein and protein complex structures, the correct protonation for the protein and the ligand has to be assigned on a theoretical basis before the structures can be used. Because of the local environment inside the binding site and because of the influence of the ligand and the protein onto each other, the ligand protonation can differ from the protonation one would expect for the ligand in solution under physiological conditions. Hence for protein-ligand docking different protonation states of the ligand have to be taken into account. Our recently introduced structure preparation tool SPORES [1] used a rule based method to generate a standard protonation for each ligand molecule and afterwards generated different protonation states in a combinatorial way by adding and removing single hydrogen atoms belonging to predefined functional groups. Docking of all these protonation states of a given ligand molecule often led to scoring problems due to the different number of hydrogen interactions formed by the different protomers of the ligand molecule. To overcome these problems two methods to filter highly charged and unstable protonation states from the docking were implemented. One based on the difference between the standard protonation of the ligand and the actual protonation state and one based on pKa values calculated with ChemAxon's MARVIN software [2]. Here we present a new approach in which the ligand atoms considered for the combinatorial method not chosen from predefined functional groups but according to the calculated pKa values which leads to a wider variety but with a smaller overall number of protonation states.

Interactions between hydrogen impurities and vacancies in Mg and Al: A comparative analysis based on density functional theory

Using first-principles methods we have studied the interactions between hydrogen impurities and vacancies in hcp Mg and fcc Al. We find that single vacancies can, in principle, host up to 9 H atoms in Mg and 10 in Al, not 12 as recently reported in the case of Al. The difference between our results and the results in previous work is attributed to a more appropriate definition of the trapping energy of hydrogen impurities in vacancies. The concentration of hydrogen-vacancy complexes depends on the amount of hydrogen dissolved in the metal, which in turn is dictated by the hydrogen chemical potential ${\ensuremath{\mu}}_{\text{H}}$. We evaluated the concentration of all relevant hydrogen-vacancy complexes as a function of ${\ensuremath{\mu}}_{\text{H}}$, corresponding to different H loading conditions---ranging from low pressures to high pressures of ${\text{H}}_{2}$ gas, up to hydrogen plasma conditions. Our analysis reveals fundamental differences in the characteristics of the hydrogen-vacancy interaction between Mg and Al. In the case of Al, up to 15% of H atoms are trapped in single vacancies in the form of H-vacancy complexes even for very low values of ${\ensuremath{\mu}}_{\text{H}}$. The trapping effect slows down the diffusion of H atoms in Al by more than an order of magnitude. While interactions between vacancies and single hydrogen atoms are therefore clearly important, interactions with multiple H atoms and related mechanisms (such as hydrogen-induced superabundant vacancy formation) are predicted to occur in Al only at very high values of ${\ensuremath{\mu}}_{\text{H}}$. In the case of Mg, the effects of H trapping in single vacancies are negligible for low values of ${\ensuremath{\mu}}_{\text{H}}$ due to the relatively low formation energy of isolated interstitial H. However, vacancies containing multiple H atoms and related mechanisms such as hydrogen-induced superabundant vacancy formation are predicted to occur in Mg at much lower values of ${\ensuremath{\mu}}_{\text{H}}$ than in Al. We estimate that, at room temperature, the critical pressure of an ${\text{H}}_{2}$ gas to induce hydrogen-enhanced (superabundant) vacancy formation is $\ensuremath{\sim}1\text{ }\text{GPa}$ in Mg and $\ensuremath{\sim}10\text{ }\text{GPa}$ in Al.

Collisions with biomolecules embedded in small water clusters

We have studied fragmentation of water embedded adenosine 5'-monophosphate (AMP) anions after collisions with neutral sodium atoms. At a collision energy of 50 keV, loss of water molecules from the collisionally excited cluster ions is the dominant process and fragmentation of the AMP itself is almost completely prohibited if the number of attached water molecules is larger than 13. However, regardless of the initial number of water molecules attached to the ion, capture of an electron, i.e. formation of a dianion, always leads to loss of a single hydrogen atom accompanied by evaporation of water molecules. This damaging effect becomes more important as the size of the water cluster increases, which is just the opposite to the protective behavior observed for collision induced dissociation (CID) without electron transfer. For both cases, the loss of water molecules within the experimental time frame is qualitatively well described by means of a common model of an evaporative ensemble. These simulations, however, indicate that characteristically different distributions of internal energy are involved in CID and electron capture induced dissociation.

Electron capture induced dissociation of water embedded nucleotide anions

We have studied fragmentation of the hydrated nucleotide anion adenosine 5'-monophosphate after collisions with neutral sodium atoms. Regardless of the initial number (≤ 16) of water molecules attached to the ion, dianion formation always leads to water evaporation as well as loss of a single hydrogen atom, possibly from the adenine part. This damaging effect becomes more important as the number of initially attached water molecules increases, which is just the opposite to the protective behavior observed for collision induced dissociation processes without electron transfer.

Atomic-Scale Templates Patterned by Ultrahigh Vacuum Scanning Tunneling Microscopy on Silicon

The ultrahigh vacuum (UHV) scanning tunneling microscope (STM) enables patterning and characterization of the physical, chemical, and electronic properties of nanostructures on surfaces with atomic precision. On hydrogen-passivated Si(100) surfaces, selective nanopatterning with the STM probe allows the creation of atomic-scale templates of dangling bonds surrounded by a robust hydrogen resist. Feedback-controlled lithography, which can remove a single hydrogen atom from the Si(100):H surface, demonstrates high-resolution nanopatterning. The resulting patterns can be used as templates for a variety of materials to form hybrid silicon nanostructures while maintaining a pristine background resist. The versatility of this UHV-STM nanolithography approach has led to its use on a variety of other substrates, including alternative hydrogen-passivated semiconductor surfaces, molecular resists, and native oxide resists. This review discusses the mechanisms of STM-induced hydrogen desorption, the postpatterning deposition of molecules and materials, and the implications for nanoscale device fabrication.

Effect of Hydrogen Atoms on the Structures of Trinuclear Metal Carbonyl Clusters: Trinuclear Manganese Carbonyl Hydrides

The structures of the trinuclear manganese carbonyl hydrides H(3)Mn(3)(CO)(n) (n = 12, 11, 10, 9) have been investigated by density functional theory (DFT). Optimization of H(3)Mn(3)(CO)(12) gives the experimentally known structure in which all carbonyl groups are terminal and each edge of a central Mn(3) equilateral triangle is bridged by a single hydrogen atom. This structure establishes the canonical distance 3.11 A for the Mn-Mn single bond satisfying the 18-electron rule. The central triangular (mu-H)(3)Mn(3) unit is retained in the lowest energy structure of H(3)Mn(3)(CO)(11), which may thus be derived from the H(3)Mn(3)(CO)(12) structure by removal of a carbonyl group with concurrent conversion of one of the remaining carbonyl groups into a semibridging carbonyl group to fill the resulting hole. The potential energy surface of H(3)Mn(3)(CO)(10) is relatively complicated with six singlet and five triplet structures. One of the lower energy H(3)Mn(3)(CO)(10) structures has one of the hydrogen atoms bridging the entire Mn(3) triangle and the other two hydrogen atoms bridging Mn-Mn edges. This H(3)Mn(3)(CO)(10) structure achieves the favored 18-electron configuration with a very short MnMn triple bond of 2.36 A. The other low energy H(3)Mn(3)(CO)(10) structure retains the (mu-H)(3)Mn(3) core of H(3)Mn(3)(CO)(12) but has a unique six-electron donor eta(2)-mu(3) carbonyl group bridging the entire Mn(3) triangle similar to the unique carbonyl group in the known compound Cp(3)Nb(3)(CO)(6)(eta(2)-mu(3)-CO). For H(3)Mn(3)(CO)(9) a structure with a central (mu(3)-H)(2)Mn(3) trigonal bipyramid lies >20 kcal/mol below any of the other structures. Triplet structures were found for the unsaturated H(3)Mn(3)(CO)(n) (n = 11, 10, 9) systems but at significantly higher energies than the lowest lying singlet structures.

Magic behavior and bonding nature in hydrogenated aluminum phosphide clusters

Interaction of hydrogen with aluminum phosphide clusters has been investigated using the density functional method of Becke's three-parameter hybrid functional with the nonlocal correlation of Lee, Yang, and Parr. Berny structural optimization and frequency analyses are performed with the basis of 6–311 + G(d). Our results show large binding energies of a single hydrogen atom on small AlP clusters and large highest occupied and lowest unoccupied molecular–orbital gaps for (AlP)H and (AlP) 5H making these species behave like magic clusters. Calculations on two hydrogen atoms on AlP clusters show large binding energies for (AlP) n H 2 with n = 1, 3, 5, and 7. In general the binding energy of H and 2H are both found to decrease with an increase in the cluster size. And the calculations also suggest that hydrogen should be dissociated on (AlP) 2 and (AlP) 3.

Single or double hydrogen atom transfer in the reaction of metal – Associated phenolic acids with •OH radical: DFT study

Results of quantum chemical calculations based on B3LYP/6-31+G* are reported for 3,4-dihydroxyphenylpyruvic acid (3,4-DHPPA), 3,4-dihydroxycinnamic acid (3,4-DHCA) and 3,4-dihydroxybenzoic acid (3,4-DHBA) chelated with Cu 2+, Mg 2+ and Ca 2+. These results are discussed in regard to the capacity of these phenolic acids (PAs) to scavenge free radicals in the presence or the absence of a metal ion. The O H bond dissociation enthalpies, the HOMO eigenvalues, the NBO charges and the structural changes are parameters that seem to be the best indicators of the antiradical property of these PAs. These parameters indicate that the antioxidant activity of the PAs are ordered as follows: 3,4-DHPPA > 3,4-DHCA > 3,4-DHBA. The C 7 C 8 double bond, and the O 8H 8···O 9 intramolecular hydrogen bond present in the side chain are influential in determining this activity. We also showed that the chelation with a metal ion led to the oxidation of the PAs and the reduction of the metal ion, a behaviour evidenced by charge transfer from the PAs to the ion. This tendency is more pronounced for the copper ion for which we registered a charge transfer of roughly 1.02e. Chelation with a metal ion led to important structural changes at the site of chelation and contributed to the decrease of the Bond Dissociation Enthalpy (BDE). It greatly facilitated the hydrogen atom transfer and consequently enhanced the antioxidant activity of the PAs.

Molecular Dynamics Simulation of the Chemical Interaction between Hydrogen Atom and Graphene

We report the chemical interaction between a single hydrogen atom and graphene via a classical molecular dynamics simulation using a modified Brenner empirical bond order potential. Three interactions, that is, adsorption, reflection, and penetration, are observed in our simulation. The rates of the interactions depend on the incident energy of the hydrogen atom and the graphene temperature. This dependence can be explained by the following mechanisms: (1) The hydrogen atom experiences a repulsive force due to π electrons. (2) The graphene adsorbs the hydrogen atom and transforms its structure to an “overhang” configuration such as the sp 3 state. (3) The expansion of the six-membered ring causes the loss of the kinetic energy of the hydrogen atom during penetration.

High‐throughput approaches towards the definitive identification of pharmaceutical drug metabolites. 1. Evidence for an ortho effect on the fragmentation of 4‐benzenesulfinyl‐3‐methylphenylamine using electrospray ionisation mass spectrometry

A 50 m/z unit loss from protonated 4-benzenesulfinyl-3-methylphenylamine has been observed and investigated using electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS). It was hypothesised that the specific fragmentation was affected by the presence of an ortho methyl group in relation to the sulfoxide functionality, i.e. an ortho effect influences the preferred dissociation pathway. This was because the des-methyl homologue did not display a 50 m/z unit loss. This fragmentation was shown to be a two-step process with sequential losses of a hydroxyl radical and a thiol radical. Molecular modelling calculations showed that the most favourable site of protonation for 4-benzenesulfinyl-3-methylphenylamine was the sulfoxide oxygen, which would facilitate the loss of a hydroxyl radical. Subsequent deuterium-exchange experiments confirmed that the loss was a hydroxyl radical and afforded definitive assignment of the site of protonation. Furthermore, the involvement of a single exchangeable hydrogen atom in the overall 50 m/z unit loss was demonstrated. Thus, supportive evidence was provided for the involvement of the ortho methyl group in the second stage of the fragmentation, leading to the loss of the thiol radical. Accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS), verified the elemental formulae of the individual losses. The ion structure following the 50 m/z unit loss was proposed to be a protonated aminofluorene and was supported by comparing the product ion spectrum of commercially available protonated 2-aminofluorene with the MS4 data of protonated 4-benzenesulfinyl-3-methylphenylamine. Fragmentation mechanisms are proposed. The relevance of the loss with regards to pharmaceutical drug metabolite identification is discussed.

Electronic effects induced by single hydrogen atoms on the Ge(001) surface

The properties of an isolated dangling bond formed by the chemisorption of a single hydrogen atom on a dimer of the Ge(001) surface are investigated by first-principles density functional theory (DFT) calculations, and scanning tunneling microscopy (STM) measurements. Two stable atomic configurations of the Ge-Ge-H hemihydride with respect to the neighboring bare Ge-Ge dimers are predicted by DFT. For both configurations, the unpaired electron of the HGe(001) system is found to be delocalized over the surface, rendering the isolated dangling bond of the hemihydride unoccupied. However, local surface charge accumulation, such as may occur during STM imaging, leads to the localization of two electrons onto the hemihydride dangling bond. The calculated surface densities of states for one of the charged Ge-Ge-H hemihydride configurations are found to be in good agreement with atomic-resolution STM measurements on n-type Ge(001). Comparison with a Si-Si-H hemihydride of the Si(001) surface shows similarities in structural properties, but substantial differences in electronic properties.

Hydrogen−Deuterium Exchange in Bulk LiBH4

Because of its apparent simplicity, diffusion of hydrogen in solids can be regarded as a general model system for diffusion. However, only rudimentary knowledge exists for the dynamics of hydrogen in complex hydrides. Insight into the specific diffusion process is given by hydrogen-deuterium exchange experiments. Thermogravimetry and Raman spectroscopy are used to measure the hydrogen-deuterium exchange during the decomposition of LiBH4. At a temperature of 523 K the self-diffusion constant of deuterium in LiBH4 is estimated to be D approximately 7 x 10(-14) m(2) s(-1). A careful analysis of the Raman spectra shows that hydrogen is statistically exchanged by deuterium in LiBH4; i.e., the diffusing species is assumed to be the single hydrogen atom.

TRAP is a more sensitive assay than FRAP for evaluation of human plasma antioxidant capacity in response to acute coffee intake

This study aimed to evaluate the plasma antioxidant capacity (AC) in response to acute coffee intake using two assays based on different mechanisms: single electron transfer (Ferric ion Reducing Antioxidant Parameter) and hydrogen atom transfer (Total Radical‐trapping Antioxidant Parameter). Nine healthy subjects drank 200 mL of instant coffee or water after overnight fast, with 7d interval between treatments. Blood was drawn before (baseline) and 90 min after treatment. Plasma AC was evaluated by FRAP and TRAP at both time points. Albumin, bilirubin and uric acid levels were also measured. At baseline, FRAP and TRAP were correlated (r = 0,86, p < 0.001), and both FRAP and TRAP were correlated with uric acid (r = 0.88 and r = 0.91, p < 0.001, respectively). After coffee ingestion, FRAP and TRAP values increased 1.7 and 8.7%, whereas after water ingestion, FRAP and TRAP decreased 1.3 and 3.0%, respectively. Net percent increase in response to coffee intake was significantly higher (p < 0.02) for TRAP (11.7%) than for FRAP (3.0%). Changes in FRAP and TRAP were not correlated with those of uric acid, bilirubin and albumin levels, indicating that these endogenous components do not contribute to the antioxidant response to coffee intake. Although FRAP and TRAP assays were both able to detect the increase in plasma AC after coffee intake, TRAP showed to be a more sensitive assay. Financial support: CBP&D Café, CNPq, FAPERJ (Brazil).

Theoretical Study of Neutral, Anionic, and Cationic Uracil−Ag and Uracil−Au Systems: Nonconventional Hydrogen Bonds

The interaction of Ag and Au with uracil has been studied using the B3LYP density-functional approach. Neutral, cationic, and anionic systems were analyzed in order to study the influence of the atomic charge on bond formation. This interaction becomes stronger as the charge increases. In the case of neutral systems, a weak association is present. In the case of cations, the interaction is mainly electrostatic. The extra electron of the anions is localized on the metal atom. Consequently, nonconventional hydrogen bonds are formed. The ionization energy of uracil-Ag and uracil-Au is lower than the corresponding values for the metal atoms and uracil molecule, while the electron affinity is higher for uracil-Ag and uracil-Au than the analogous values for the isolated Ag, Au, and uracil. This might have significance for further experiments and possibly for applications, where the movement of the electrons is important. In the case of uracil-Ag and uracil-Au (anions), it may be possible to induce the detachment of one electron from the anion and also to remove a single hydrogen atom. It is possible that tight competition exists between the H dissociation and electron aloofness.

Hydrogen Diffusion Behavior in Perfect <EM>δ</EM>-Pu Metal

The diffusion behavior of hydrogen atom in perfect δ-Pu metal was studied with density functional theory (DFT) and periodical model. The stablest site for hydrogen is the octahedral interstitial site. A single hydrogen atom has the minimum embedding energy about -3.12 and -2.22 eV in the octahedral interstitial site of fcc δ-Pu at non-spin polarization and spin-polarization levels, respectively. The embedding energy in tetrahedral interstitial site is little larger than that in tetrahedral interstitial site. Hydrogen atom in δ-Pu crystal most preferably diffuses along the path linked with different interstitials. The diffusion barrier along the path from octahedral interstitial site to tetrahedral interstitial site is 1.06 eV. The diffusion barrier along the reverse path is 0.38 eV. In addition, the diffusion barrier along the path from tetrahedral interstitial site to tetrahedral interstitial site is 1.83 eV, and the path from octahedral interstitial site to octahedral interstitial site corresponds to the highest diffusion barrier.

Smoke Emissions in Fires

Emission of smoke from various fire sizes and fuels has been examined using data from the literature. The data used for the examination were for the fully ventilated combustion of the mixed fuels of all compositions and for non-mixed single hydrogen atom containing fuels, without highly fire-retarded compositions. The combustion data used were for the smaller (0.008 m 2 in area) and larger (0.911-m 2 area) pool-like configuration. The data were also used for the combustion of fuels in vertical wall-like configuration consisting of single panel (0.31-m long and 0.10-m wide) and parallel panels (each panel 2.4m long and 0.60-m wide separated by 0.30-m and 4.9-m long and 1.1-m wide separated by 0.53-m). The examination of these data show that the average smoke emission rate, S G � , depends on the fire size, expressed as the average chemical heat release rate, ch

Single hydrogen atoms on the Si(001) surface

Chemisorption of a single hydrogen atom on the $n$-type Si(001) surface is investigated by scanning tunneling microscopy (STM) and first-principles density functional theory (DFT) calculations. The STM experiments show that the formation of a hemihydride induces static buckling of the neighboring Si-Si dimers and suggest that different buckling configurations of these dimers are observed at negative and positive biases. They also show that the appearance of an isolated Si-Si-H hemihydride on Si(001) exhibits a complex voltage dependence with the brightness of the dangling bond of the hemihydride changing significantly at negative sample bias. DFT calculations predict two stable, ground state atomic configurations for the hemihydride on Si(001). These correspond to parallel and antiparallel configurations of the Si-Si-H hemihydride with respect to the neighboring bare Si-Si dimers. In order to understand the bias-dependent appearance in the STM images of the $n$-type Si(001) surface, we include the effect of hemihydride charging due to tip-induced band bending. In filled state, the STM images are shown to result from the electronic and structural features that originate from the charge-dependent parallel configuration. In empty state, the energetics and STM measurements support the charge independent antiparallel configuration, while either structure can produce simulated images consistent with experiment.

Cation-Modulated Electron-Transfer Channel: H-Atom Transfer vs Proton-Coupled Electron Transfer with a Variable Electron-Transfer Channel in Acylamide Units

The mechanism of proton transfer (PT)/electron transfer (ET) in acylamide units was explored theoretically using density functional theory in a representative model (a cyclic coupling mode between formamide and the N-dehydrogenated formamidic radical, FF). In FF, PT/ET normally occurs via a seven-center cyclic proton-coupled electron transfer (PCET) mechanism with a N-->N PT and an O-->O ET. However, when different hydrated metal ions are bound to the two oxygen sites of FF, the PT/ET mechanism may significantly change. In addition to their inhibition of PT/ET rate, the hydrated metal ions can effectively regulate the FF PT/ET cooperative mechanism to produce a single pathway hydrogen atom transfer (HAT) or a flexible proton coupled electron transfer (PCET) mechanism by changing the ET channel. The regulation essentially originates from the change in the O...O bond strength in the transition state, subject to the binding ability of the hydrated metal ions. In general, the high valent metal ions and those with large binding energies can promote HAT, and the low valent metal ions and those with small binding energies favor PCET. Hydration may reduce the Lewis acidity of cations, and thus favor PCET. Good correlations among the binding energies, barrier heights, spin density distributions, O...O contacts, and hydrated metal ion properties have been found, which can be used to interpret the transition in the PT/ET mechanism. These findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide useful information for a greater understanding of PT/ET cooperative mechanisms, and a possible method for switching conductance in nanoelectronic devices.