Hydrogen Positions Research Articles

Geometrical features, stability and hydrogen positions in (Al2Cu)n clusters

The phase equilibria of the Al-Cu alloys have been well-established, with the Al2Cu being a crucial component of the phase diagram. Constructing an atomic model with a 2:1 stoichiometric ratio of Al and Cu holds significance for further investigating the local structures of the alloy phases. Here, we employ the GA-DFT method to explore the structural potential energy surfaces of (Al2Cu)n clusters (n = 1–6). The results reveal that the (Al2Cu)n evolve from hollow cages to more densely packed configurations, with Al atoms relatively more concentrated and Cu atoms becoming more dispersed throughout the structures. The Eb and Δ2E analyses show that the (Al2Cu)3 has a higher stability than that of its neighbors, and the AIMD simulations demonstrate that it can maintain the structural integrity at 700 K. The molecular orbitals reveal that 21 valence electrons of the (Al2Cu)3 fill superatomic orbits resulting in an electronic configuration of 1S21P61D102S21F1, which is also confirmed by the density of states. The good stability of the (Al2Cu)3 allows the bonding of the H atom to it without causing significant deformation changes in the parent geometry, in which the H tends to preferentially locate at Al sites. The deformation of structures is particularly obvious when H is close to Cu atom.

Structure and dynamics of the active site of hen egg-white lysozyme from atomic resolution neutron crystallography.

Hen egg-white lysozyme (HEWL) is a widely used model protein in crystallographic studies and its enzymatic mechanism has been extensively investigated for decades. Despite this, the interaction between the reaction intermediate and the catalytic Asp52, as well as the orientation of Asn44 and Asn46 side chains, remain ambiguous. Here, we report the crystal structures of perdeuterated HEWL and D2O buffer-exchanged HEWL from 0.91 and 1.1Å resolution neutron diffraction data, respectively. These structures were obtained at room temperature and acidic pH, representing the active state of the enzyme. The unambiguous assignment of hydrogen positions based on the neutron scattering length density maps elucidates the roles of Asn44, Asn46, Asn59, and nearby water molecules in the stabilization of Asp52. Additionally, the identification of hydrogen positions reveals unique details of lysozyme's folding, hydrogen (H)/deuterium (D)exchange, and side chain disorder.

Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II.

Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.

Hydrogen incorporation mechanism in the lower-mantle bridgmanite

Abstract Bridgmanite, the most abundant mineral in the lower mantle, can play an essential role in deep-Earth hydrogen storage and circulation processes. To better evaluate the hydrogen storage capacity and its substitution mechanism in bridgmanite occurring in nature, we have synthesized high-quality single-crystal bridgmanite with a composition of (Mg0.88Fe0.052+Fe0.053+Al0.03)(Si0.88Al0.11H0.01)O3 at nearly water-saturated environments relevant to topmost lower mantle pressure and temperature conditions. The crystallographic site position of hydrogen in the synthetic (Fe,Al)-bearing bridgmanite is evaluated by a time-of-flight single-crystal neutron diffraction scheme, together with supporting evidence from polarized infrared spectroscopy. Analysis of the results shows that the primary hydrogen site has an OH bond direction nearly parallel to the crystallographic b axis of the orthorhombic bridgmanite lattice, where hydrogen is located along the line between two oxygen anions to form a straight geometry of covalent and hydrogen bonds. Our modeled results show that hydrogen is incorporated into the crystal structure via coupled substitution of Al3+ and H+ simultaneously exchanging for Si4+, which does not require any cation vacancy. The concentration of hydrogen evaluated by secondary-ion mass spectrometry and neutron diffraction is ~0.1 wt% H2O and consistent with each other, showing that neutron diffraction can be an alternative quantitative means for the characterization of trace amounts of hydrogen and its site occupancy in nominally anhydrous minerals.

Mapping Hydrogen Positions along the Proton Transfer Pathway in an Organic Crystal by Computational X-ray Spectra.

Understanding proton transfer (PT) dynamics in condensed phases is crucial in chemistry. We computed a 2D map of N 1s X-ray photoelectron/absorption spectroscopy (XPS/XAS) for an organic donor-acceptor salt crystal against two varying N-H distances to track proton motions. Our results provide a continuous spectroscopic mapping of O-H···N↔O-··· H+-N processes via hydrogen bonds at both nitrogens, demonstrating the sensitivity of N 1s transient XPS/XAS to hydrogen positions and PT. By reducing the O-H length at N1 by only 0.2 Å, we achieved excellent theory-experiment agreement in both XPS and XAS. Our study highlights the challenge in refining proton positions in experimental crystal structures by periodic geometry optimizations and proposes an alternative scaled snapshot protocol as a more effective approach. This work provides valuable insights into X-ray spectra for correlated PT dynamics in complex crystals, benefiting future experimental studies.

Molecular dynamics study on the effect of hydrogen on the plastic behavior of α-Fe crack tip

In this paper, the unilateral tension of α-Fe in the local region of the crack tip are simulated by molecular dynamics method, the plastic deformation behaviors and hydrogen embrittlement mechanism of the crack tip under different hydrogen concentration and hydrogen positions are analyzed. The results show that for the hydrogen-containing models, there exists a critical hydrogen concentration c0 that can make the plasticity of the α-Fe material reduce greatly. For the crack-free model, the main hydrogen embrittlement mechanism is adsorption-induced dislocation emission (AIDE), and the critical hydrogen concentration c0 is 0.3%. When the hydrogen concentration cH<c0, the plastic deformation mechanism is mainly dominated by phase transformation; when cH≥c0, the plastic deformation mechanism is phase transformation at low strains and dislocation motion at high strains. For the cracked model, the main mechanism of hydrogen embrittlement is hydrogen-enhanced local plasticity at the crack tip, with a critical c0 of 1.7%. When cH<c0, the plastic deformation mechanism of the model is a combination of phase transformation and dislocation; when cH≥c0, the plastic deformation mechanism is controlled by phase transformation. When the hydrogen is far away from the crack tip, the local mechanical behavior of the crack tip does not change significantly, while when hydrogen gathered at the crack tip, the addition of a small amount of hydrogen atoms will make the fracture strain decrease rapidly, which shows a mechanism of hydrogen-enhanced strain-induced vacancies (HESIV). A saturation value of hydrogen concentration at the crack tip is confirmed in this paper, when the local hydrogen concentration exceeds this saturation value, the plastic behaviour tends to be stable. The influence of hydrogen atoms distribution on the crack initiation behavior was determined by atomic configuration analysis.

Study of hydrogen injection strategy on fuel mixing characteristics of a free-piston engine

The formation of the gas mixture in the cylinder has a significant effect on the combustion and emission of the engine. The main difference between a conventional engine and a free piston engine is that the piston movement mode is different. Therefore, a new coupled iterative method is adopted in this paper to study the injection position and duration of hydrogen fuel in a free piston engine where diesel fuels hydrogen, and reveal its influence on gas mixing and combustion in the cylinder of a free piston engine. The results show that it is suitable to spray hydrogen 55 mm from TDC. At this time, the mass fraction of H2 in the cylinder is relatively uniform, the cumulative heat release is about 620 J, and the pressure and temperature are relatively low, which are 7.2 MPa and 1529 K respectively. The duration of hydrogen injection is 0.4 ms, at this time, the mixing degree in the cylinder and the gas flow speed are better, although there is a little shortage of unburned equivalent ratio, but this has little impact on the overall, and the final cumulative heat release reaches 655 J.

Impact of surface treatments on the electron affinity of nitrogen-doped ultrananocrystalline diamond

In recent years, various forms of nanocrystalline diamond (NCD) have emerged as an attractive group of diamond/graphite mixed-phase materials for a range of applications from electron emission sources to electrodes for neural interfacing. To tailor their properties for different uses, NCD surfaces can be terminated with various chemical functionalities, in particular hydrogen and oxygen, which shift the band edge positions and electron affinity values. While the band edge positions of chemically terminated single crystal diamond are well understood, the same is not true for nanocrystalline diamond, which has uncontrolled crystallographic surfaces with a variety of chemical states as well as graphitic grain boundary regions. In this work, the relative band edge positions of as-grown, hydrogen terminated, and oxygen terminated nitrogen-doped ultrananocrystalline diamond (N-UNCD) are determined using ultraviolet photoelectron spectroscopy (UPS), while the band bending is investigated using photoelectrochemical measurements. In contrast to the widely reported negative electrode affinity of hydrogen terminated single crystal diamond, our work demonstrates that hydrogen terminated N-UNCD exhibits a positive electron affinity owing to the increased surface and bulk defect densities. These findings elucidate the marked differences in electrochemical properties of hydrogen and oxygen terminated N-UNCD, such as the dramatic changes in electrochemical capacitance.

Optimal position and distribution mode for on-site hydrogen electrolyzers in onshore wind farms for a minimal levelized cost of hydrogen (LCoH)

Abstract. Storing energy is a major challenge in achieving a 100 % renewable energy system. One promising approach is the production of green hydrogen from wind power. This work proposes a method for optimizing the design of wind–hydrogen systems for existing onshore wind farms in order to achieve the lowest possible levelized cost of hydrogen (LCoH). This is done by the application of a novel Python-based optimization model that iteratively determines the optimal electrolyzer position and distribution mode of hydrogen for given wind farm layouts. The model includes the costs of all required infrastructure components. It considers peripheral factors such as existing and new roads, necessary power cables and pipelines, wage and fuel costs for truck transportation, and the distance to the point of demand (POD). Based on the results, a decision can be made whether to distribute the hydrogen to the POD by truck or pipeline. For a 23.4 MW onshore wind farm in Germany, a minimal LCoH of EUR 4.58 kgH2-1 at an annual hydrogen production of 241.4 tH2a-1 is computed. These results are significantly affected by the position of the electrolyzer, the distribution mode, varying wind farm and electrolyzer sizes, and the distance to the POD. The influence of the ratio of electrolyzer power to wind farm power is also investigated. The ideal ratio between the rated power of the electrolyzer and the wind farm lies at around 10 %, with a resulting capacity factor of 78 % for the given case. The new model can be used by system planners and researchers to improve and accelerate the planning process for wind–hydrogen systems. Additionally, the economic efficiency, hence competitiveness, of wind–hydrogen systems is increased, which contributes to an urgently needed accelerated expansion of electrolyzers. The results of the influencing parameters on the LCoH will help to set development goals and indicate a path towards a cost-competitive green wind–hydrogen system.

Enhancing hydrogen positions in X-ray structures of transition metal hydride complexes with dynamic quantum crystallography.

Hirshfeld atom refinement (HAR) is a method which enables the user to obtain more accurate positions of hydrogen atoms bonded to light chemical elements using X-ray data. When data quality permits, this method can be extended to hydrogen-bonded transition metals (TMs), as in hydride complexes. However, addressing hydrogen thermal motions with HAR, particularly in TM hydrides, presents a challenge. At the same time, proper description of thermal vibrations can be vital for determining hydrogen positions correctly. In this study, we employ tools such as SHADE3 and Normal Mode Refinement (NoMoRe) to estimate anisotropic displacement parameters (ADPs) for hydrogen atoms during HAR and IAM refinements performed for seven structures of TM (Fe, Ni, Cr, Nb, Rh and Os) and metalloid (Sb) hydride complexes for which both the neutron and the X-ray structures have been determined. A direct comparison between neutron and HAR/SHADE3/NoMoRe ADPs reveals that the similarity between neutron hydrogen ADPs and those estimated with NoMoRe or SHADE3 is significantly higher than when hydrogen ADPs are refined with HAR. Regarding TM-H bond lengths, traditional HAR exhibits a slight advantage over the other methods. However, combining NoMoRe/SHADE3 with HAR results in a minor decrease in agreement with neutron TM-H bond lengths. For the Cr complex, for which high-resolution X-ray data were collected, an investigation of resolution-related effects was possible.

Refining hydrogen positions in the complex beam-sensitive hydrated mineral bulachite

Refining hydrogen positions in the complex beam-sensitive hydrated mineral bulachite

Locating Hydrogen Positions for COF-300 by Cryo-3D Electron Diffraction.

Covalent organic frameworks (COFs) have wide-ranging applications, and their host-guest interactions play an essential role in the achievement of COF functions. To investigate these host-guest interactions, it is necessary to locate all atoms, especially hydrogen atoms. However, it is difficult to determine the hydrogen atomic positions in COFs because of the complexities in synthesizing high-quality large single crystals. Three-dimensional electron diffraction (3D ED) has unique advantages for the structural determination of nanocrystals and identification of light atoms. In this study, it was demonstrated for the first time that the hydrogen atoms of a COF, not only on the framework but also on the guest molecule, can be located by 3D ED using continuous precession electron diffraction tomography (cPEDT) under cryogenic conditions. The host-guest interactions were clarified with the location of the hydrogen atoms. These findings provide novel insights into the investigation of COFs.

Locating Hydrogen Positions for COF‐300 by Cryo‐3D Electron Diffraction

Locating Hydrogen Positions for COF‐300 by Cryo‐3D Electron Diffraction

Quantum Crystallography and Complementary Bonding Analysis of Agostic Interactions in Titanium Amides

AbstractAgostic interactions involving titanium are textbook examples for C−H bond activation. Therefore, it is surprising that there is no study in the literature in which the hydrogen atom in the C−H⋅⋅⋅Ti interaction has been determined reliably, although nearly all the criteria for assessing the strength and character of the agostic interaction depend on the hydrogen atom and its position. Here, we demonstrate with quantum crystallographic techniques how hydrogen atoms in a series of three titanium amides can indeed be localized accurately and precisely based on routine single‐crystal X‐ray diffraction data. Once the hydrogen positions have been established, theoretical and experimentally fitted bonding analyses reveal that the C−H⋅⋅⋅Ti interaction becomes stronger with increasing inter‐ligand London dispersion stabilization of bulky alkyl groups.

Hirshfeld Atom Refinement of Metal-Organic Complexes: Treatment of Hydrogen Atoms Bonded to Transition Metals.

Hydrogen positions in hydrides play a key role in hydrogen storage materials and high-temperature superconductors. Our recently published study of five crystal structures of transition-metal-bound hydride complexes showed that using aspherical atomic scattering factors for Hirshfeld atom refinement (HAR) resulted in a systematic elongation of metal-hydrogen bonds compared to using spherical scattering factors with the Independent Atom Model (IAM). Even though only standard-resolution X-ray data was used, for the highest-quality data, we obtained excellent agreement between the X-ray and the neutron-derived bond lengths. We present an extended version of this study including 10 crystal structures of metal-organic complexes containing hydrogen atoms bonded to transition-metal atoms for which both X-ray and neutron data are available. The neutron structures were used as a benchmark, and the X-ray structures were refined by applying Hirshfeld atom refinement using various basis sets and DFT functionals in order to investigate the influence of the technical aspects on the length of metal-hydrogen bonds. The result of including relativistic effects in the Hamiltonian and using a cluster of multipoles simulating interactions with a crystal environment during wave function calculations was examined. The effect of the data quality on the final result was also evaluated. The study confirms that a high quality of experimental data is the key factor allowing us to obtain significant improvement in transition metal (TM)-hydrogen bond lengths from HAR in comparison with the IAM. Individual adjustments and better choices of the basis set can improve hydrogen positions. Average differences between TM-H bond lengths obtained with various DFT functionals upon including relativistic effects or between double-ζ and triple-ζ basis sets were not statistically significant. However, if all bonds formed by H atoms were considered, significant differences caused by different refinement strategies were observed. Finally, we examined the refinement of atomic thermal motions. Anisotropic refinement of hydrogen thermal motions with HAR was feasible only in some cases, and isotropically refined hydrogen thermal motions were in similar agreement with neutron values whether obtained with HAR or with the IAM.

Locating anionic hydrogen in Ba3(Yb,Lu)2O5H2: A combined approach of X-ray diffraction, crystal chemistry, and DFT calculations

By a combination of x-ray diffraction, structural chemistry, and DFT calculations, the presence and location of anionic hydrogen in the two new, layered lanthanide oxyhydrides, Ba3Ln2O5H2 (Ln ​= ​Yb, Lu) is inferred. Single crystals of the compounds have been synthesized from a molten barium flux with the addition of small amounts of BaH2. These phases crystallize in space group I4/mmm (#139, Z ​= ​2) with lattice parameters a ​= ​4.3336(2) Å and c ​= ​22.7197(6) Å, and a ​= ​4.3291(1) Å and c ​= ​22.597(1) Å, respectively. The Ba3Ln2O5H2 phases comprise two different structural moieties: a perovskite double layer of stoichiometry Ba2Ln2O5H− formed by corner-connected LnO5 tetragonal bi-pyramids with a terminating hydrogen anion, and a puckered rocksalt-type (BaH)+ layer that is stretched along the c-axis. DFT calculations were used to arrive at hydrogen positions that minimize energy and are consistent with structural chemistry principles. Furthermore, the calculations show that the valence band edge is dominated by oxygen 2p orbitals with hydrogen 1s states admixed. The conduction band is formed by barium 5d-orbitals and Lu (Yb) 5d-orbitals. These are characteristics of materials with anionic H−. These new phases are isostructural with the Ba3Ln2O5Cl2 (Ln ​= ​Gd–Lu) family of compounds with the chlorine atom in the same apical position as the hydrogen atom. Steric effects limit the size of the lanthanide ion for Ba3Ln2O5H2.

The Gastropod Shell Structure as a Blueprint for a Periodic System: A New Theory for Element Configurations

The purpose of this article is to propose a new design for the periodic table of elements. The new design is based on a three-dimensional (3D) model of the gastropod shell structure and presents a mechanism of the formation of elements that reflects the laws of nature that guide the formation of the gastropod shell, electron orbitals, and element structure. The author also identifies challenges associated with the current standard periodic table, such as the positions of hydrogen, helium, lanthanides, and actinides. The author’s research is a response to the IUPAC’s request, dating back to 2016, to settle unresolved disputes surrounding the current standard periodic table. Hence, the author proposes the “Gastropod Shell Model”, which presents the periodic system in 2D and 3D snail shells based on a hypothesized unifying principle guiding the formation of elements: the universal unified theory that considers the spiral and vortex forms as the bridge between energy and matter. The author was able to position hydrogen, helium, lanthanides, and actinides uniquely in their proposed periodic system to solve problems associated with their positions in the standard periodic table. Readers will be interested in uncovering the “hypothesized unifying principle guiding the formation of elements”.

Hydrous wadsleyite crystal structure up to 32 GPa

Abstract Hydroxylation of wadsleyite, β-(Mg,Fe)2SiO4, is associated with divalent cation defects and well known to affect its physical properties. However, an atomic-scale understanding of the defect structure and hydrogen bonding at high pressures is needed to interpret the influence of water on the behavior of wadsleyite in the mantle transition zone. We have determined the pressure evolution of the wadsleyite crystal symmetry and structure, including all O∙∙∙O interatomic distances, up to 32 GPa using single-crystal X-ray diffraction on two well-characterized, Fe-bearing (Fo90) samples containing 0.25(4) and 2.0(2) wt% H2O. Both compositions undergo a pressure-dependent monoclinic distortion from orthorhombic symmetry above 9 GPa, with the less hydrous sample showing a larger increase in distortion at increased pressures due to the difference in compressibility of the split M3 site in the monoclinic setting arising from preferred vacancy ordering at the M3B site. Although hydrogen positions cannot be modeled from the X-ray diffraction data, the pressure evolution of the longer O1∙∙∙O4 distance in the structure characterizes the primary hydrogen bond length. We observe the hydrogen-bonded O1∙∙∙O4 distance shorten gradually from 3.080(1) Å at ambient pressure to about 2.90(1) Å at 25 GPa, being still much longer than is defined as strong hydrogen bonding (2.5–2.7 Å). Above 25 GPa and up to the maximum pressure of the experiment at 32.5 GPa, the hydrogen-bonded O1∙∙∙O4 distance decreases no further, despite the fact that previous spectroscopic studies have shown that the primary O-H stretching frequencies continuously drop into the regime of strong hydrogen bonding (&amp;lt;3200 cm–1) above ~15 GPa. We propose that the primary O1-H∙∙∙O4 hydrogen bond in wadsleyite becomes highly nonlinear at high pressures based on its deviation from frequency-distance correlations for linear hydrogen bonds. One possible explanation is that the hydrogen position shifts from being nearly on the long O1-O4 edge of the M3 site to a position more above O1 along the c-axis.

The change of hydrogen position on π-conjugated bridge to affect NLO property of D(–NH2)-π(DHTPs)-A(–NO2) system

The donor-π-conjugated bridge-acceptor (D-π-A) is a classical framework to design high-performance organic electro-optical materials. In this work, based on the π-conjugated dihydrotetraazapentacenes (DHTPs), four isomers (1–4) with D(–NH2)-π(DHTPs)-A(–NO2) framework are designed and characterized. The 2 and 3 originate from single-hydrogen migration of 1, and 4 derives from double-hydrogen migration of 1. Significantly, the change of hydrogen position on DHTPs bridge can affect their nonlinear optics (NLO) property. Compared with the first hyperpolarizability (βtot) (4.08 × 103a.u.) of 1, the 6.90 × 103-2.56 × 104 a.u. of 2–4 are enhanced. More interestingly, the 4 has largest βtot value of 2.56 × 104, which is approximately equal to the sum of 6.90 × 103 a.u. of 2 and 1.82 × 104 a.u. of 3. Furthermore, the change of hydrogen position on DHTPs brings some distinctive changes in their geometric structure, nucleus-independent chemical shifts (NICS) value, natural population analysis (NPA) charge, UV–vis absorption spectrum along with its other electronic property that might be beneficial to explore their structure–property relationships.

About One Numerical Method for Finding the Positions of Hydrogen and Oxygen Nuclei in a Water Cluster

About One Numerical Method for Finding the Positions of Hydrogen and Oxygen Nuclei in a Water Cluster