Coordination Number Of Atoms Research Articles

Pressure-induced phase transition and electronic structure evolution in layered semimetal HfTe2

Motivated by the recent experimental work, the pressure-induced structural transition of well-known two-dimensional (2D) 1T-HfTe2 was investigated up to 50 GPa through the advanced CALYPSO structure search technique combined with the first-principles calculations. Our calculations suggested that the 1T-HfTe2 will first transform to C2/m phase at 3.6 GPa with a volume reduction of 7.6% and then to phase at 9.6 GPa with a volume collapse of 4.6%. The occurrences of 3D C2/m and phases mainly originated from the enhanced Te–Te interlayer coupling and the drastic distortions of Hf–Te polyhedrons in phase under compression. Concomitantly, the coordination number of Hf atoms increased from six in to eight in C2/m and eventually to nine in at elevated pressure. The metallic and semimetallic nature of C2/m and phases were characterized, and the evidence of the reinforced covalent interactions of Te–Hf and Te–Te orbitals in these two novel high-pressure phases were manifested by the atom-projected electronic DOS and Bader charge.

How Crystallographic Orientation‐Induced Fibrinogen Conformation Affects Platelet Adhesion and Activation on TiO2 (Adv. Healthcare Mater. 13/2023)

Crystal Surfaces Crystallographic orientation, and therefore the arrangement and coordination number of surface atoms, defines the surface energy and wettability, subsequently controlling the cellular response to blood-contacting biomaterials. Depending on the crystallographic orientation of TiO2 (rutile) surfaces, fibrinogen adsorbs typically in a trinodular and/or globular conformation, determining platelet adhesion and activation. Rutile surface crystallographic orientation may determine the risk of blood clotting. This work is highlighted in article 2202508 by Klaus D. Jandt and co-workers.

Atomic structure evolution and linear regression fitting models for pre-breakdown electric field strength of FCC, BCC and HCP metal nano-emitters under high electric field from PIC-ED–MD simulations

Multi-scale and multi-physics simulations are carried out for nano-emitters consisting of FCC (Al, Cu and Au), BCC (V, Mo and W) and HCP (Ti, Zn and Zr) metals, using hybrid electrodynamics coupled with molecular dynamics-particle in cell simulations (PIC-ED–MD). We show that the tilting of the nano-emitter at low temperature and small electric field (E-field) is mainly caused either by the movement of partial dislocations at the apex of the nanotip or by the elastic local distortions of atomic registries away from their ideal lattice sites (FCC/BCC/HCP). At high E-field, the intense resistive heating due to the strong electron emission leads to the direct melting of the apex of nano-emitters. For nano-emitters consisting of low melting point metals such as Al, Zn and Au, the thermal runaway is driven by the elongation, thinning and necking of the molten region. Meanwhile, the elongation, thinning and sharpening produce the nano-protrusion at the apex of metal nano-emitters, and the detachment of atoms or atomic clusters from the nano-protrusion mainly contributes to the thermal runaway event for refractor metals such as Ti, Zr, Mo and W. The critical E-field strength of metal nano-emitters is found to be strongly correlated with structural parameters (atomic coordination number of liquid and equilibrium lattice constant), thermodynamic quantities (cohesive energy and enthalpy of evaporation) and phase transition temperatures (melting point and boiling point). These correlations enable us to establish either single-variable linear fitting models or multi-variable linear regression models to predict the critical E-field value for metal nano-emitters with good credibility.

Insights to the fracture toughness, damage tolerance, electronic structure, and magnetic properties of carbides M2C (M = Fe, Cr)

The fracture toughness, damage tolerance, electronic structure, and magnetic properties of M2C (M = Fe, Cr) carbides were analyzed using first-principles calculations. Calculations of formation energy and modulus of elasticity indicate that a Cr/Fe ratio of 1/3 is a critical threshold which triggers a significant increase in the corresponding stability and related mechanical properties. Cr atomic content enhances the crack resistance, while Cr has a significantly detrimental effect on damage resistance. The electronic properties demonstrated that the Cr atom content enhances the metallic, ionic and covalent bonding. Furthermore, the reduction in the coordination number of Fe atoms is the main reason for the reduction in the local magnetic moment of the low-spin Cr atoms, which is strongly supported by the electronic structure. These studies provide detailed insights into Cr-containing carbides, providing valuable theoretical and technological information for the knowledge-based design and prediction of the mechanical properties of chromium-containing iron-based materials.

Effects of electron-donating ability of binding sites on coordination number: the interactions of a cyclic Schiff base with copper ions.

The stepwise addition of Cu2+ ions to the nonplanar cyclic Schiff base 5,9,14,18-tetramethyl-1,4,10,13-tetraazacyclooctadeca-5,8,14,17-tetraene-7,16-dione (H4daaden, C18H28N4O2), yields a one-end-open dinuclear copper chelate. The pyridine adduct of the dinuclear copper chelate, namely, [μ-6,11-dimethyl-7,10-diazahexadeca-5,11-diene-2,4,13,15-tetraolato(4-)](pyridine)dicopper(II), [Cu2(C16H20N2O4)(C5H5N)], was characterized by single-crystal X-ray crystallography. The two CuII atoms of the copper chelate display different coordination modes, i.e. inner-N2O2 and outer-O2O2. The Cu atom which is bonded in the outer-O2O2 mode is axially bonded to a pyridine molecule, which suggests that the electron-donating ability of the O2O2 site to the Cu atom is poor. As a result, the O2O2-bonded Cu atom has a coordination number of five, showing square-bipyramidal geometry around the Cu atom. The N2O2-coordinated site provides sufficient electron density to the other Cu atom to be stabilized with a coordination number of four, showing square-planar geometry around the Cu atom. The electron-donating ability of the ligand coordination sites plays a key role in determining the coordination number of the Cu atoms of the dicopper chelate.

An investigation on creep deformation and mechanical properties of a polycrystalline Fe-based alloy: a molecular dynamics study

In this work, Molecular dynamics (MD) simulation was carried out to uncover the mechanism of creep deformation in FeCrAl alloys. The MD results indicated that the rise in the amount of Cr and Al leads to the increase of creep rate in the samples. Moreover, under a constant temperature (1000 K) and alloying composition (FeCr15Al4), the increase of applied stress altered the creep mechanism from Coble mode to grain boundary sliding, followed by dislocation creep, which was accompanied with the appearance of tertiary creep stage in the strain-time curves. Considering the stress exponent values, it was found that the applied stress of 1-1.5 GPa is a transition value from Coble creep to dislocation creep. It was also unveiled that the atomic coordination number in the grain boundaries was averagely lower than the grain interiors, indicating that the boundaries were potential sites for the atomic motion and the defect nucleation. Finally, in comparison with the applied stress and temperature, the creep deformation is less sensitive to the alloying composition and grain size.

First principles investigations of structural and electronic properties of Ga-doped ZnZrOx solid solutions for catalytic reduction of CO2

ZnZrOx and gallium-doped ZnZrOx solid solutions exhibit excellent catalytic properties for the hydronation of CO2 to methanol. However, the details of the structures and catalytic properties are not fully understood. Herein, density functional theory has been used to explore the structural, electronic and catalytic properties of ZnZrOx and gallium-doped ZnZrOx catalysts. We used zinc-doped Zr sites of tetragonal ZrO2 with different Zn concentrations as a model to simulate the ZnZrOx solid solution. For the Ga-doped ZnZrOx catalysts, Zr atoms were substituted by Ga atoms. The doping of Zn atoms in ZrO2 reduce the coordination numbers of Zr atoms. Heavily Zn-doped ZrO2 systems do not maintain the tetragonal structure and, hence, deviate from the perfect tetragonal phase. At ∼29.16% Zn concentration, the bandgap of ZnZrOx has been reduced from 4.45 to 2.45 eV. The insertion of Ga in ZnZrOx solid solutions shifts the conduction band edges back, increasing the bandgap of the solid solutions. The Ga doping improves the CO2 adsorption ability of ZnZrOx solid solutions and efficiently dissociates the H2 molecules. On the surface of Ga-Zn doped ZrO2(101), the hydrogenation of CO2 to methanol via the formate pathway is more favorable than the CO pathway.

Cobalt single atom anchored on N-doped carbon nanoboxes as typical single-atom catalysts (SACs) for boosting the overall water splitting

Single-atom catalysts (SACs) are considered one of the promising strategies to achieve efficient energy conversion, due to their advantage of both maximum atomic utilization and minimum catalyst cost. However, finding a balance between increasing the atom loading and preventing the agglomeration of metal single atoms is a current research hotspot. Herein, we have developed single-atom cobalt embedded in N-doped carbon nanoboxes as high-efficiency bifunctional electrocatalysts for overall water splitting in alkaline/acidic electrolytes. Due to the reliable metal-nonmetal bonds between the Co single atom and the substrate carbon, where the uniformly dispersed Co atoms could be effectively and stably riveted on the carbon nanoboxes, and the as-prepared electrocatalyst possesses high mass loading of single Co atoms (∼10.2 wt%). In addition, the systematic X-ray absorption fine structure (XAFS) and density functional theory (DFT) calculations were performed to further investigate the relationship between coordination number, configuration and electrocatalytic properties of Co single atoms and N atoms. Based on the above results, the presence of Co atoms induces the formation of pyrr-N and possesses Co@CNB-N4 configuration with HER overpotential of 45 mV, comparable to Pt/C (20 wt%). As for OER, Co@CNB-N4 still has satisfactory catalytic performance, superior to the benchmark catalyst RuO2. Thus, this work builds a bridge to understand the impact of metal single atoms and substrate configuration on catalytic performance and opens a door to the successful synthesis of SACs with high loading of non-precious metal atoms, high atomic utilization and electrocatalytic activity.

Novel three-dimensional TiO2 structure with a unique quasi-direct band gap for photocatalysts.

Motivated by fundamental interests and practical applications, three-dimensional (3D) photocatalysts are a fascinating area of research in clean energy. Based on first-principles calculations, we predicted three new 3D polymorphs of TiO2: δ-, ε-, and ζ-TiO2. Our results indicate that the band gaps of TiO2 decrease almost linearly with an increase in the coordination number of Ti. Moreover, δ-TiO2 and ζ-TiO2 are semiconductors, whereas ε-TiO2 is a metal, and the lowest energy of ζ-TiO2 is a quasi-direct band gap semiconductor with a distinctive band gap of 2.69 eV, calculated by the HSE06 level. In addition, the calculated imaginary part of the dielectric function indicates that the optical absorption edge is located in the visible light region, suggesting that the proposed ζ-TiO2 may be a good photocatalyst candidate. Importantly, ζ-TiO2 with the lowest energy is dynamically stable, and phase diagrams based on total energies at a specific pressure indicate that ζ-TiO2 can be synthesized from rutile TiO2 at high-pressure conditions.

Coordination engineering of atomically dispersed zirconium on graphene for the oxygen reduction reaction.

We study the effect of boron and sulfur doping on graphene with atomically dispersed zirconium as an electrocatalyst for the oxygen reduction reaction (ORR) by using density functional theory (DFT). The use of Zr as a metal center offers a highly stable catalyst due to the high electronegativity difference between Zr and its ligand. The origin of the ORR activity improvement has been investigated thoroughly. Here, we proposed a novel geometric descriptor for an atomically dispersed zirconium on a nitrogen-doped graphene catalyst with an axial oxygen ligand, which is the fractional coordination number of the Zr atom. We found that the fractional coordination number can successfully describe the shift of the dz2 band center in the doped compound, which is related to the binding energy of the Zr to the O ligand. We also found that the oxygen ligand is mobile during the adsorption process of ORR intermediates, and hence it is imperative for the axial oxygen ligand to bind neither too strongly nor too weakly to the Zr atom. The coordination engineering strategy can successfully enhance the ORR activity, shifting the ORR overpotential from 0.75 V and 0.92 V to 0.33 V and 0.32 V. This study provides new insights into the origin of ORR activity by connecting the novel geometric descriptor to the electronic structure and finally it is connected to the ORR activity.

Dissolution mechanism of Fe3O4 scale by 1-hydroxyethane-1,1-diphosphonic acid: an ab initio molecular metadynamics study.

Using the ab initio molecular metadynamics method, the adsorption of the structure of 1-hydroxyethane-1,1-diphosphonic acid (HEDP) on the Fe3O4 surface and subsequent detachment of Fe atoms from the surface were simulated, and the dissolution mechanism by which HEDP dissolves Fe3O4 scale at room temperature while other organic acids cannot was elucidated. The adsorbed hydroxyl groups, water and HEDP on the Fe3O4 surface play a synergistic role in detaching the Fe ions, which increases the coordination number of the Fe atoms and weakens the original Fe-O bond strength. In addition, the strong coordination ability and flexible molecular structure of HEDP also facilitate dissolution of Fe3O4 scale by breaking down the chemical bonds and forming Fe-HEDP complexes. The free energy surface for the dissolution reaction shows a low barrier, and the descaling reaction is easily accomplished.

NMR chemical shift of confined 129Xe: coordination number, paramagnetic channels and molecular dynamics in a cryptophane-A biosensor.

Advances in hyperpolarisation and indirect detection have enabled the development of xenon nuclear magnetic resonance (NMR) biosensors (XBSs) for molecule-selective sensing in down to picomolar concentration. Cryptophanes (Crs) are popular cages for hosting the Xe "spy". Understanding the microscopic host-guest chemistry has remained a challenge in the XBS field. While early NMR computations of XBSs did not consider the important effects of host dynamics and explicit solvent, here we model the motionally averaged, relativistic NMR chemical shift (CS) of free Xe, Xe in a prototypic CrA cage and Xe in a water-soluble CrA derivative, each in an explicit H2O solvent, over system configurations generated at three different levels of molecular dynamics (MD) simulations. We confirm the "contact-type" character of the Xe CS, arising from the increased availability of paramagnetic channels, magnetic couplings between occupied and virtual orbitals through the short-ranged orbital hyperfine operator, when neighbouring atoms are in contact with Xe. Remarkably, the Xe CS in the present, highly dynamic and conformationally flexible situations is found to depend linearly on the coordination number of the Xe atom. We interpret the high- and low-CS situations in terms of the magnetic absorption spectrum and choose our preference among the used MD methods based on comparison with the experimental CS. We check the role of spin-orbit coupling by comparing with fully relativistic CS calculations. The study outlines the computational workflow required to realistically model the CS of Xe confined in dynamic cavity structures under experimental conditions, and contributes to microscopic understanding of XBSs.

C(spn)−X (n=1–3) Bond Activation by Iron

AbstractThe iron‐catalyzed oxidative addition of C(spn)−X bonds (n=1–3 and X=H, CH3, Cl) in archetypal model substrates H3C−CH2−X, H2C=CH−X and HC≡C−X to Fe(CO)4was investigated using relativistic density functional theory at ZORA‐OPBE/TZ2P. The C(spn)−X bonds become substantially stronger going from C(sp3)−X to C(sp2)−X to C(sp)−X, whereas the oxidative addition reaction barrier decreases along this series. Our activation strain and energy decomposition analyses expose that the decreased reaction barrier for the oxidative addition going fromsp3tosp2tospstems from a relief of the destabilizing (steric) Pauli repulsion between the catalyst and substrate. This originates from the decreasing coordination number of the carbon atom that goes from four in C(sp3)−X to three in C(sp2)−X to two in C(sp)−X. In analogy with our previous results on palladium‐catalyzed oxidative additions, this enhances the stabilizing catalyst–substrate interaction, which is able to overcome the more destabilizing strain associated with the stronger C(spn)−X bonds. This work again demonstrates that iron‐based catalysts can resemble the behavior of their well‐known palladium analogs in the oxidative addition step of cross‐coupling reactions.

Solvent-Solute Interaction Effect on Permeation Flux through Forward Osmosis Membranes Investigated by Non-Equilibrium Molecular Dynamics.

The relationship between the solvent-solute interaction and permeation properties is fundamental in the development of the forward osmosis (FO) membrane. In this study, we report on the quantitative reproduction of the permeation flux, which has different solvent-solute interactions, through the modeled FO membrane by non-equilibrium molecular dynamics (NEMD). The interaction effect was investigated by changing the interatomic interaction between the solute and the solvent. The calculated permeation through the semi-permeable modeled FO membrane, in which the interaction between solvent and solution is equal to that between solutions, was consistent with the theoretical curve derived from the combination of the permeation flux and Van't Hoff equations. These results validate the NEMD for the evaluation of permeation in FO. On the other hand, the permeation is much derived from the theoretical values when the interaction between the solvent and solute atoms is relatively large. However, the simulated permeation was consistent with the theoretical curve, correcting the solution concentration by the coordination number of the solvent atoms to the solute atoms. Our results imply that permeation flux through the FO membrane is significantly changed by the interaction between the solute and the solvent and can be theoretically predicted by calculating the coordination number of the solvent to the solute, which can be readily estimated by equilibrium molecular dynamics simulation.

Boosting hydrogenation properties of Pt single-atom catalysts via tailoring the electronic structures by coordination number regulation

Clarifying the relationship of single metal atom coordination structures and catalytic properties is crucial for the fine-design of highly-efficient catalysts, but systematically manipulating the coordination structure (e.g., coordination numbers (CN) of metal atoms) without changing atomic dispersion is challenging. Herein, we develop a precursor-atomization strategy for the synthesis of single-atom catalysts (SACs) and further precisely tailor Pt-N CN by changing the pyrolysis sequence and atmosphere. It is found that as Pt-N CN decreases (from Pt-N5 to Pt-N3), the electron density of Pt atoms increases and the energy barrier for H2 dissociation decreases, thus achieving a ∼550-fold increase in activity of selective hydrogenation of 3-nitrophenylacetylene (reduction of nitro group while maintaining the highly sensitive alkyne group), successfully breaking the selectivity-activity seesaw. Additionally, Pt-N3 SACs also show remarkably broad applicability for the hydrogenation of nitroarenes (even for iodo-nitrobenzene) due to its unique heterolytic cleavage path of H2 and preferential adsorption of nitro group.

Beyond single-crystal surfaces: The GAL21 water/metal force field.

Solvent effects are notoriously difficult to describe for metallic nanoparticles (NPs). Here, we introduce GAL21 which is the first pairwise additive force field that is specifically designed to modulate the near chemisorption energy of water as a function of the coordination numbers of the metallic atoms. We find a quadratic dependence to be most suitable for capturing the dependence of the adsorption energy of water on the generalized coordination number (GCN) of the metal atoms. GAL21 has been fitted against DFT adsorption energies for Cu, Ag, Au, Ni, Pd, Pt, and Co on 500 configurations and validated on about 3000 configurations for each metal, constructed on five surfaces with GCNs varying from 2.5 to 11.25. Depending on the metals, the root mean square deviation is found between 0.7kcal mol-1 (Au) to 1.6kcal mol-1 (Ni). Using GAL21, as implemented in the open-source code CP2K, we then evaluate the solvation energy of Au55 and Pt55 NPs in water using thermodynamic integration. The solvation free energy is found to be larger for Pt than for Au and systematically larger than 200kcal mol-1, demonstrating the large impact of solvent on the surface energetics of NPs. Still, given that the amorphous NPs are both, the most stable and the most solvated ones, we do not predict a change in the preferred morphology between the gas-phase and in water. Finally, based on a linear regression on three sizes of NPs (from 38 to 147), the solvation energy for Au and Pt surface atoms is found to be -5.2 and -9.9kcal mol-1, respectively.

Dual Pt-Ni atoms dispersed on N-doped carbon nanostructure with novel (NiPt)-N4C2 configurations for synergistic electrocatalytic hydrogen evolution reaction

Single-atom catalysts with high atomic utilization efficiency, well-defined active centers, and catalytic sites with low atomic coordination numbers are promising to boost electrocatalytic performance. Dual-atom catalysts (DACs) with neighboring heteroatoms are expected to exert the synergistic effect of the two atoms, further improving the activity. Herein, we report a PtNi-NC catalyst consisting of PtNi dual atoms anchored on a nitrogen-doped carbon substrate synthesized through atomic layer deposition. X-ray absorption spectroscopy confirms the existence of the PtNi dual atoms. The as-prepared PtNi-NC catalyst exhibits extraordinary catalytic activity, with an overpotential of 30 mV for hydrogen evolution reaction (HER) in acidic media at a current density of 10 mA cm−2, which is comparable to that of commercial 20 wt% Pt/C. Notably, PtNi-NC possesses a much higher mass activity, about 21 times, than 20 wt% Pt/C. Density functional theory calculations reveal that PtNi dual atoms generate a synergistic effect by modulating the local electronic structure and optimizing the charge distribution, contributing to optimized adsorption properties and enhanced electrocatalytic performance. This work provides a new avenue for the fabrication of DACs, revealing their potential applications in electrocatalytic HER and beyond.

New Quaternary Compounds R3Ni0.5SiS7 (R – Y, Sm, La) with the La3Mn0.5SiS7 Structure

The new sulfides Y3Ni0.5SiS7, Sm3Ni0.5SiS7, and La3Ni0.5SiS7 exist in the quasi-ternary systems Y2S3 – NiS – SiS2, Sm2S3 – NiS – SiS2, and La2S3 – NiS – SiS2, respectively, for which the isothermal sections at 770 K were investigated. The crystal structure of the sulfides was determined by the X-ray powder method. It belongs to the La3Mn0.5SiS7 structure type (S.G. Р63; Pearson symbol hP23), with the lattice parameters а = 0.97643(4) nm; с = 0.56377(4) nm (Y3Ni0.5SiS7), а = 0.99599(8) nm; с = 0.56583(5) nm (Sm3Ni0.5SiS7), and а = 1.02830(6) nm; с = 0.57412(4) nm (La3Ni0.5SiS7). The structure of obtained sulfides is as follows: Y, Sm, and La atoms are located in the 6с site and center trigonal prisms with two additional S atoms. Ni atoms occupy the 2а site (0.5 occupancy) and have octahedral surrounding of S atoms. The coordination number of Si atoms (the 2b site) is 4. The Ni-centered octahedra form infinite chains [Ni 6S]n.

Substrate-Mediated Borophane Polymorphs through Hydrogenation of Two-Dimensional Boron Sheets.

The two-dimensional boron monolayer (borophene) stands out from the two-dimensional atomic layered materials due to its structural flexibility and tunable electronic and mechanical properties from a large number of allotropic materials. The stability of pristine borophene polymorphs could possibly be improved via hydrogenation with atomic hydrogen (referred to as borophane). However, the precise adsorption structures and the underlying mechanism are still elusive. Employing first-principles calculations, we demonstrate the optimal configurations of freestanding borophanes and the ones grown on metallic substrates. For freestanding borophenes, the energetically favored hydrogen adsorption sites are sensitive to the polymorphs and corresponding coordination numbers of boron atoms. With various metal substrates, the hydrogenation configurations of borophenes are modulated significantly, attributed to the overlap between B pz and H s orbitals. These findings provide a deep insight into the hydrogenating borophenes and facilitate the stabilization of two-dimensional boron polymorphs by engineering hydrogen adsorption sites and concentrations.

Correlation between the activity of Fe@ (N, S, and P) doped graphene catalysts and the coordination environment: A density functional theory study

Transition metal-doped graphene single-atom catalysts exhibit great application prospects for catalyzing hydrogen evolution applications. However, the precise timing and control of the activity of central atoms is a key problem to ensure the further development of catalysts. Revealing the correlation between the catalytic activity of the central atom and the coordination environment (atomic species, coordination number, and geometric configuration) is regarded as quite crucial for solving this key problem. Along these lines, in this work, Fe as the central atom and N, S, and P doped porous graphene (DPG) as the matrix material were used to systematically study the correlation between the coordination environment and the stability, catalytic activity of the catalyst. From the acquired results, it was demonstrated that: (1) The binding strength between the Fe atom and the N-atom DPG is the highest, and the anchoring strength of the Fe atom on two-element doping doped graphene is relatively low. Under the tetrad coordination condition, the catalyst doped with S and P atoms showed excellent performance in hydrogen evolution and water activation. A moderate correlation between the hydrogen evolution performance (ΔGH∗, EA, and ΔGOH∗) and d-band electronic properties (d-CU and d-SE) under single element doping (four and three coordination) was also detected. In addition, a certain correlation between the Fe atom outer-shell electron (3d 4s) and the hydrogen evolution performance was found. A weak correlation between the electronic properties of the double element doped graphene and the hydrogen evolution performance was also confirmed from our simulations. The results are of great significance for the regulation of the single-atom catalyst activity.