Hydrogen Complexes Research Articles

Formation and migration energies of a vacancy and an interstitial in a high-purity Si crystal determined by detecting complexes of point defects and hydrogen: Evaluation of activation energies of self-diffusion

Experimental studies to determine the formation energies of vacancies in Si and Ge crystals have been performed since the 1950s, but have been unsuccessful. We studied the formation and migration energies of a vacancy and an interstitial by detecting complexes of point defects and hydrogen atoms by optical absorption measurement. The formation energies of the vacancy and interstitial were found to be 3.85 ± 0.15 and 4.8 + 0.6/−0.4 eV, respectively. The migration energies of the vacancy and interstitial were 0.45 ± 0.04 and 0.49 ± 0.05 eV, respectively. Using these energies, we determined the activation energies of the vacancy- and interstitial-mediated self-diffusion to be 4.30 ± 0.19 and 5.3 + 0.6/−0.4 eV, respectively. The former energy is especially important since there has been no study in which vacancy-mediated diffusion has been successfully determined.

Vacancy–hydrogen complexes in ammonothermal GaN

We have applied positron annihilation spectroscopy to study in-grown vacancy defects in bulk GaN crystals grown by the ammonothermal method. We observe a high concentration of Ga vacancy related defects in n-type samples with varying free electron and oxygen content. The positron lifetimes found in these samples suggest that the Ga vacancies are complexed with hydrogen impurities. The number of hydrogen atoms in each vacancy decreases with increasing free electron concentration and oxygen and hydrogen content. The local vibrational modes observed in infrared absorption support this conclusion.

Tuning the halogen/hydrogen bond competition: a spectroscopic and conceptual DFT study of some model complexes involving CHF2I.

Insight into the key factors driving the competition of halogen and hydrogen bonds is obtained by studying the affinity of the Lewis bases trimethylamine (TMA), dimethyl ether (DME), and methyl fluoride (MF) towards difluoroiodomethane (CHF(2) I). Analysis of the infrared and Raman spectra of solutions in liquid krypton containing mixtures of TMA and CHF(2) I and of DME and CHF(2) I reveals that for these Lewis bases hydrogen and halogen-bonded complexes appear simultaneously. In contrast, only a hydrogen-bonded complex is formed for the mixtures of CHF(2) I and MF. The complexation enthalpies for the C-H⋅⋅⋅Y hydrogen-bonded complexes with TMA, DME, and MF are determined to be -14.7(2), -10.5(5) and -5.1(6) kJ mol(-1), respectively. The values for the C-I⋅⋅⋅Y halogen-bonded isomers are -19.0(3) kJ mol(-1) for TMA and -9.9(8) kJ mol(-1) for DME. Generalization of the observed trends suggests that, at least for the bases studied here, softer Lewis bases such as TMA favor halogen bonding, whereas harder bases such as MF show a substantial preference for hydrogen bonding.

Investigation of H+ implanted Fe-Al alloys

In the present work hydrogen interaction with vacancies was investigated in Fe-Al alloys with various concentration of vacancies. The Fe-Al samples were implanted with low energy H+ ions (100 keV). This procedure introduced high hydrogen concentration into relatively narrow sub-surface region in the depth of ∼500 nm. Variable energy positron annihilation spectroscopy (VEPAS) was employed for investigation of hydrogen interaction with vacancies in the sub-surface region. This study revealed formation of vacancy hydrogen complexes in the sub-surface region. Thermal stability of vacancy-hydrogen complexes was investigated as well.

Intermolecular Interaction in the H2S–H2 Complex: Molecular Beam Scattering Experiments and Ab-Inito Calculations

New molecular beam scattering experiments are reported for the H2S-H2 system recording, under high angular and velocity resolution conditions, the "glory" quantum interference in the velocity dependence of the total cross section. The analysis of the experimental data permits the determination, for the first time, of a spherically averaged intermolecular potential for this system. An evaluation of significant cuts of the potential energy surface, obtained by accurate ab initio CCSD(T) calculations using large basis sets, combined with the analysis of the electronic charge displacement accompanying the formation of H2S-H2, has been also performed in order to rationalize the experimental findings. A direct comparison with the analogous water-hydrogen complex (Belpassi, L. et al. J. Am. Chem. Soc. 2010, 132, 13046), investigated with the same experimental conditions and theoretical methodology, brings to light detailed differences in the intermolecular interaction affecting the observables. In particular, it shows the important fact that the charge transfer (CT) component of the interaction plays a minor role in H2S-H2, whereas it was found to be a crucial stabilization component of the interaction in water-H2, determining the potential energy surface anisotropy and the precise location of the energy minima.

Palladium Clusters Anchored on Graphene Vacancies and Their Effect on the Reversible Adsorption of Hydrogen

The hydrogen storage capacity of nanoporous carbons can be enhanced through metal doping, for instance doping with palladium. However, there are two problems that may limit the positive effect of metal doping on the reversible storage capacity. First, clustering of the metal atoms decreases its effectiveness, which is largest for maximum dispersion. A second problem that is often overlooked is that the desorption of metal–hydrogen complexes may compete favorably with the desorption of hydrogen molecules. Desorption of complexes would spoil the reversible storage of hydrogen in the material. Both problems can be avoided by firmly anchoring the metal atoms and clusters to defects of the carbon substrate, for instance vacancies. With this goal in mind, we have performed density functional calculations to investigate the desorption of hydrogen and of Pd–hydrogen complexes from Pd atoms and clusters supported on pristine graphene and on graphene layers with vacancies. We show that palladium atoms bind much stronger to graphene vacancies, binding energy Eb = 5.13 eV, than to pristine graphene, Eb = 1.09 eV. The Pd atoms tend to nucleate and form clusters around the vacancies and the small Pdn clusters (n = 2–6) also bind strongly, Eb ≈ 5 eV, to the vacancies. However, the Pd–Pd interaction is much smaller than the Pd–vacancy interaction, and therefore, the vacancies favor the dispersion of palladium on the graphene layer. For hydrogen adsobed on Pd atoms and clusters supported on pristine graphene, desorption of Pd–hydrogen complexes competes with desorption of molecular hydrogen. However, for hydrogen adsobed on a Pd atom anchored on a graphene vacancy, the desorption of the PdH2 complex costs 4.2 eV, and therefore, it does not compete with the desorption of molecular hydrogen, which takes place with an energy cost of only 0.2 eV. This shows the beneficial effect that anchoring Pd atoms and clusters to graphene vacancies has on the reversible adsorption/desorption of hydrogen.

A ReaxFF Investigation of Hydride Formation in Palladium Nanoclusters via Monte Carlo and Molecular Dynamics Simulations

Palladium can readily dissociate and absorb hydrogen from the gas phase, making it applicable in hydrogen storage devices, separation membranes, and hydrogenation catalysts. To investigate hydrogen transport properties in Pd on the atomic scale, we derived a ReaxFF interaction potential for Pd/H from an extensive set of quantum data for both bulk and surface properties. Using this potential, we employed a recently developed hybrid grand canonical-Monte Carlo/molecular dynamics (GC-MC/MD) method to derive theoretical hydrogen absorption isotherms in Pd bulk crystals and nanoclusters for hydrogen pressures ranging from 10–1 atm to 10–14 atm, and at temperatures ranging from 300 to 500 K. Analysis of the equilibrated cluster structures reveals the contributing roles of surface, subsurface, and bulk regions during the size-dependent transition between the solid solution α phase and the hydride β phase. Additionally, MD simulations of the dissociative adsorption of hydrogen from the gas phase were conducted to assess size-dependent kinetics of hydride formation in Pd clusters. Hydrogen diffusion coefficients, apparent diffusion barriers, and pre-exponential factors were derived from MD simulations of hydrogen diffusion in bulk Pd. Both the thermodynamic results of the GC-MC/MD method and the kinetic results of the MD simulations are in agreement with experimental values reported in the literature, thus validating the Pd/H interaction potential, and demonstrating the capability of the GC–MC and MD methods for modeling the complex and dynamic phase behavior of hydrogen in Pd bulk and clusters.

Hydrogen–vacancy interaction in bcc iron: ab initio calculations and thermodynamics

The paper presents results of ab initio modelling of formation energies of vacancy–hydrogen complexes VHn and an extended variant of thermodynamic theory describing equilibrium concentrations of such complexes. A single H atom is shifted from vacancy to a neighbouring O-site by 1.19 Å. Two H atoms in a vacancy form a dumbbell with H–H distance of 2.38 Å being much greater than in H2 molecule. Configurations of three, four and five H atoms in a vacancy are more complex, and H–H distances gradually increase showing repulsion between hydrogen atoms. Binding energy of a VHn−1 complex with the next hydrogen atom to form VHn is 0.60, 0.61, 0.39, 0.37 and 0.31 for n = 1–5, which is close to other researchers’ data. These results were used to construct an improved variant of thermodynamic description of vacancy–hydrogen interaction in a bcc solid solution taking into account both binding energies and hydrogen atom configurations in different VHn complexes. Calculations show that at low temperatures most vacancies are bound to several hydrogen atoms, and the equilibrium concentration of vacancies themselves significantly increases, in accordance with existing experiments.

Intermolecular Interaction in the NH3–H2 and H2O–H2 Complexes by Molecular Beam Scattering Experiments: The Role of Charge Transfer

New molecular beam scattering experiments are reported for the ammonia-hydrogen system recording with unprecedented resolution "glory" quantum interferences in the total cross sections. Direct comparison with the analogous water-hydrogen complex, investigated under the same experimental conditions, highlights relevant differences in the intermolecular interaction affecting the observables. Analysis of the electronic charge displacement accompanying formation of both complexes, calculated using very accurate ab initio methods, helps to rationalize the experimental findings and unveils the selective and crucial role of charge transfer in driving water interactions and formation of a weak hydrogen bond.

Vibrational Spectroscopy of Na–H Complexes in ZnO

Sodium acceptors were diffused into ZnO bulk single crystals to a depth of ~1μm, with a near-surface concentration of ~1018–cm3. An O–H local vibrational mode (LVM) was observed at 3304–cm–1, at a temperature of 9 K, in hydrogenated samples. The LVM is attributed to an O–H bond-stretching mode adjacent to a Na acceptor. When deuterium substitutes for hydrogen, a peak is observed at 2466–cm–1. The isotopic frequency ratio is similar to values found in other hydrogen complexes. In the deuterated sample, a sideband at 2461–cm–1 is attributed to a Fermi resonance.

Theoretical prediction of new Kubas four centre H2 complexes involving dimolybdate clusters

A new type of Kubas nonclassical molecular hydrogen complex involving two metallic centers is predicted by extensive DFT calculations, using five accurate functionals. The interaction consists of a four centre bond involving two metal atoms and the H2 molecule, the latter retaining a significant part of its molecular nature. [Mo2Cl8(μ-H2)]2− and [Mo2(CO)8(μ-H2)] are two examples that are found to be stable.

A new theoretical analysis of the cooperative effect in T-shaped hydrogen complexes of CnHm∙∙∙HCN∙∙∙HW with n = 2, m = 2 or 4, and W = F or CN

In this theoretical work, a new idea about cooperativity in intermolecular clusters of CnHm∙∙∙HCN∙∙∙HW stabilized by hydrogen bonds composed by lone-electron pairs (nitrogen) and π clouds (C = C and C ≡ C) as proton acceptors is developed. The structural study and vibrational analysis have pointed out deformations in the intermolecular clusters caused by the HW terminal proton-donor, in which if W = fluorine the largest perturbation occurs. On the contrary, the HCN molecule is considered an intermolecular mediator because its structure is practically unaltered upon the formation of the trimolecular complexes. In order to understand the real contribution of the proton-donor either mediator (HCN) or terminal (HW with W = CN or F), a chemometric analysis was performed uniquely to discover which interaction plays a key role in the collapse of the cooperative effect. The formation of strongest interactions leads to more drastic variations in the energy distribution. In this way, the application of the quantum theory of atoms in molecules (QTAIM) has been extremely important because the hydrogen bond strengths followed by indiciums of covalence were predicted, and therefore the cooperative effect could be understood at last.

Ruthenium Complexes of Triazole-Based Scorpionate Ligands Transfer Hydrogen to Substrates under Base-Free Conditions

The first ruthenium complexes of bulky tris(triazolyl)borate (Ttz) ligands were synthesized, fully characterized, and studied as transfer hydrogenation catalysts. The structures of the complexes we...

Quantum chemical calculations of the structure of hydrogen-bonded sulfuric acid-dimethylformamide complexes

The most characteristic structures of hydrogen-bonded (H2SO4)2, H2SO4-dimethylformamide (DMF) and (H2SO4)2-DMF complexes are obtained by means of B3LYP/cc-pVQZ. The changes in the geometric parameters of the complexes are analyzed and the energy values of the intermolecular interaction are estimated. The electronic mechanism for the formation of hydrogen bonds between molecules is considered. It is shown that complexes of (H2SO4)2-DMF composition are more energy-stable than complex with one H2SO4 molecule. It is established that molecular complexes with very strong hydrogen bonds and complexes with proton transfer can be formed between an acid dimer and N,N-dimethylformamide. It is concluded that protons can be transferred in the gas phase in (H2SO)2-DMF, where the molecules in (H2SO4)2 are bound by three hydrogen bonds.

Crystal Structures, and Magnetic Properties of Cobalt(II) Complexes of N, N’-((1, 10-phenanthroline-2, 9-diyl)bis(methylene))diethanamine)

Two cobalt(II) complexes, CoL(SCN)2 (1) and CoL(N3)2 (2) (L = N, N′-((1,10-phenanthroline-2,9-diyl)bis(methylene))dietha namine), were synthesized and characterized. The crystal structures of both complexes have been determined by X-ray diffraction analysis. Complexes 1 and 2 are neutral molecules and adopt compressed octahedral coordination geometry in which Co(II) ions are coordinated to four nitrogen atoms from ligands and two nitrogen atoms from thiocyanate (for 1) and azide (for 2), respectively. Complex 1 shows two-dimensional chain structure via hydrogen bonds and complex 2 shows three-dimensional structure. The magnetic properties for complexes 1 and 2 have been investigated in the temperature range 2–300 K.

The role of impurity oxygen in hydrogen bubble nucleation in tungsten

The impurity role for hydrogen bubble nucleation is investigated based on first-principles studies of the interaction between impurities (oxygen and carbon), hydrogen and vacancy in tungsten. A new mechanism of hydrogen bubble nucleation is proposed: the interstitial oxygen atom traps multiple hydrogen atoms inducing the appearance of some unstable lattice sites nearby, where the initial vacancy can be created to form vacancy–oxygen–hydrogen complex, whose formation energy is so low that abundant vacancy–oxygen–hydrogen complexes could survive and thus the hydrogen bubble nucleates. This mechanism could provide a sound explanation for the hydrogen bubble nucleation in tungsten (with quite low vacancy concentration) exposed to low-energy (far lower than displacement threshold energy) deuterium ions irradiation. The proposed mechanism should be generally applicable for hydrogen bubble nucleation in other metals with low vacancy concentration.

Cationic complexes of hydrogen with helium.

High-resolution mass spectra of helium nanodroplets doped with hydrogen or deuterium reveal that copious amounts of helium can be bound to H+, H2+, H3+, and larger hydrogen-cluster ions. All conceivable HenHx+ stoichiometries are identified if their mass is below the limit of ≍120 u set by the resolution of the spectrometer. Anomalies in the ion yields of HenHx+ for x=1, 2, or 3, and n≤30 reveal particularly stable cluster ions. Our results for HenH1+ are consistent with conclusions drawn from previous experimental and theoretical studies which were limited to smaller cluster ions. The HenH3+ series exhibits a pronounced anomaly at n=12 which was outside the reliable range of earlier experiments. Contrary to findings reported for other diatomic dopant molecules, the monomer ion (i.e. H2+) retains helium with much greater efficiency than hydrogen-cluster ions.

Remarkable Hydrogen Storage Capacity In Li-Decorated Graphyne: Theoretical Predication

On the basis of first-principles density functional calculations, we predict that Li-decorated graphyne can serve as a promising candidate for hydrogen storage, with a largest storage capacity of 18.6 wt %. The average adsorption energy of hydrogen is about −0.27 eV/H2, indicating that the doped system is an ideal hydrogen storage material at ambient conditions. It is proposed that the polarization mechanism, which stems from the electric field induced by the ionic Li coated on the graphyne, plays a key role in the adsorption of H2 molecules. Furthermore, the formation of the hydrogen–hydrogen complex also stabilizes the adopted hydrogen molecules.

Two new dicopper(II) complexes with oxamido-bridged ligand: Synthesis, crystal structures, DNA binding/cleavage and BSA binding activity

New oxamido-bridged copper(II) complexes, [Cu2(oxbp)(H2O)2(NCS)2] (1) and [Cu2(oxbp)(μ-DMSO)2(NCS)2][Cu2(oxbp)(DMSO)2(NCS)2] (2) (H2oxbp=N,N′-bis(2-(diethylamino)ethyl)oxalamide), were synthesized and characterized by single-crystal X-ray diffraction, elemental analysis, IR, and electronic spectra. X-ray analysis revealed that complex 1 consists of neutral binuclear [Cu2(oxbp)(H2O)2(NCS)2] units which forms a two-dimensional network through intermolecular hydrogen bonds and complex 2 is constructed by neutral [Cu2(oxbp)(μ-DMSO)2(NCS)2] (2a) and [Cu2(oxbp)(DMSO)2(NCS)2] (2b) entities which alternately distribute to form a two-dimensional network by means of quasi μ-DMSO bridge and intermolecular hydrogen bonds. In both 1 and 2, bicopper centers are linked by the “trans-form” oxamido bridges with the distances of 5.272Å for 1 and av. 5.296Å for 2, respectively. The interaction of Cu(II) complexes with DNA was investigated by UV-visible, fluorescence emission spectrometry and agarose gel electrophoresis. The apparent binding constant (Kapp) values of 3.16×105M−1 for 1 and 4.9×105M−1 for 2 suggest moderate intercalative binding modes between the complexes and DNA. Complex 1 displayed efficient oxidative cleavage of supercoiled DNA, which might indicate that the underlying mechanism involves singlet oxygen (1O2) as reactive oxygen species. Complex 2 is characteristic of the involvement of a singlet oxygen-like entity and hydrogen peroxide in the cleavage process. In addition, our present work showed, by fluorescence spectrometry of BSA with complexes, both 1 and 2 bind to BSA with a medium affinity through a static mode which is tentatively assigned binding to Trp134 in BSA.

Experimental and Theoretical Charge Density Distribution in a Host–Guest System: Synthetic Terephthaloyl Receptor Complexed to Adipic Acid

The experimental charge density distributions in a host-guest complex have been determined. The host, 1,4-bis[[(6-methylpyrid-2-yl)amino]carbonyl]benzene (1) and guest, adipic acid (2). The molecular geometries of 1 and 2 are controlled by the presence in the complex of intermolecular hydrogen bonding interactions and the presence in the host 1 of intramolecular hydrogen bonding motifs. This system therefore serves as an excellent model for studying noncovalent interactions and their effects on structure and electron density, and the transferability of electron distribution properties between closely related molecules. For the complex, high resolution X-ray diffraction data created the basis for a charge density refinement using a pseudoatomic multipolar expansion (Hansen-Coppens formalism) against extensive low-temperature (T = 100 K) single-crystal X-ray diffraction data and compared with a selection of theoretical DFT calculations on the same complex. The molecules crystallize in the noncentrosymmetric space group P2(1)2(1)2(1) with two independent molecules in the asymmetric unit. A topological analysis of the resulting density distribution using the atoms in molecules methodology is presented along with multipole populations, showing that the host and guest structures are relatively unaltered by the geometry changes on complexation. Three separate refinement protocols were adopted to determine the effects of the inclusion of calculated hydrogen atom anisotropic displacement parameters on hydrogen bond strengths. For the isotropic model, the total hydrogen bond energy differs from the DFT calculated value by ca. 70 kJ mol(-1), whereas the inclusion of higher multipole expansion levels on anisotropic hydrogen atoms this difference is reduced to ca. 20 kJ mol(-l), highlighting the usefulness of this protocol when describing H-bond energetics.