Coordination Number Of Atoms Research Articles

Influence of charge on conformations, inter-molecular structure and thermodynamics of symmetric polystyrene-block-polymethacrylic acid (PS-b-PMA) polyelectrolyte micelle in aqueous solution

ABSTRACT The various aspects of molecular structure, kinetics, and thermodynamics of symmetric polystyrene-b-poly(methacrylic acid) (PS-b-PMA) block copolymer micelle in salt-free aqueous solution as a function of degree-of-ionisation (f) of PMA (corona) block was investigated by explicit molecular dynamics (MD) simulations. Micelle size increases linearly with f in a qualitative agreement with simulation results in the literature. With increase in charge density of the corona-forming PMA chain block, the micelle becomes more spherical, and there is a decrease in the surface area of micelle core and an increase in the favourable interactions among the PS chains. The structure of the micelle changes with f. The behaviour of the RDF’s of core and corona PMA atoms and the enthalpy of solvation show that the interactions among the segments of the core PS blocks are insensitive to variation in f. The atom density profiles, solvation enthalpy, and coordination number of PMA-Na+ and Water-Na+ pairs reveal the existence of the micelle in the ‘osmotic regime’ in agreement with results from experiments and mean-field theory in literature. The significance of electrostatic interactions on the kinetics of formation, structural aspects, and thermodynamics of micellisation is shown. The characteristics of PMA-b-PS micelle are compared with those of PAA-b-PS.

Regulation of the coordination number of Zn single atoms to boost electrochemical sensing of H2O2.

Compared with transition metals with partially occupied 3d orbitals, Zn has a filled 3d10 configuration, which severely restricts electron mobility and hence usually renders Zn2+ intrinsically inactive for electrochemical sensing. Metal single-atom catalysts are a new kind of sensing material. Owing to their unique coordination structure and high atomic utilization rate, metal single-atom catalysts show unique properties, which makes them promising for use in the field of electrochemical sensing. However, whether Zn single atoms are active sites remains to be elucidated. In this study, we prepared nitrogen-doped carbon (NC) materials by pyrolyzing ZIF-8 at high temperatures and reported that when the pyrolysis temperature was 800 °C, many Zn single atoms with Zn-N4 coordination structures remained in the NC material. Even when the pyrolysis temperature is increased to 1000 °C, a small number of Zn single atoms remain, and the coordination structure changes from Zn-N4 to Zn-N3. Furthermore, unexpectedly, both residual Zn single atoms showed electrocatalytic activity for H2O2 reduction. In particular, the electrocatalytic activity was significantly enhanced after the coordination structure was changed from Zn-N4 to Zn-N3. Density functional theory (DFT) calculations indicate that the coordination structure of Zn-N3 optimizes the adsorption and desorption strength of oxygen-containing species in the electrocatalytic reaction process, which lowers the energy barrier of the rate-determining step and increases the detection sensitivity of H2O2 nearly 4.1 times. This study revealed new properties of Zn single atoms for the electrocatalytic reduction of H2O2 and developed a strategy to increase the electrocatalytic activity of metal single-atom catalysts through coordination number regulation, which lays the foundation for the use of Zn single atoms in the field of electrochemical sensing and provides ideas for the design of new highly active sensing materials.

The Reconstruction of Pt(001) Surface and the Shell-Like Reconstruction of the Vicinal Pt(001) Surfaces Revealed by Neural Network Potential.

In this work, a highly accurate neural network potential (NNP) is presented, named PtNNP, and the exploration of the reconstruction of the Pt(001) surface and its vicinal surfaces with it. Contrary to the most accepted understanding of the Pt(001) surface reconstruction, the study reveals that the main driving force behind Pt(001) quasi-hexagonal reconstruction is not the surface stress relaxation but the increased coordination number of the surface atoms resulting in stronger intralayer binding in the reconstructed surface layer. In agreement with experimental observations, the optimized supercell size of the reconstructed Pt(001) surface contains (5×20) unit cells. Surprisingly, the reconstruction of the vicinal Pt(001) surfaces leads to a smooth shell-like surface layer covering the whole surface and diminishing sharp step edges.

Pressure-Induced Structural Phase Transitions and Photoluminescence Properties of Micro/Nanocrystals HoF3.

HoF3 crystals of varying sizes and morphologies were synthesized by controlling the amount of water. As the water content gradually decreased, the size of the crystals reduced, transforming from microcrystals to approximately 100 nm nanocrystals with unique morphologies. At room temperature, the pressure-induced phase transitions, and photoluminescence (PL) properties of HoF3 micro/nanocrystals are studied using in situ high-pressure PL technique. The PL spectra show that the HoF3 micro/nanocrystals exhibit two structural phase transformations at 5 (6 GPa for NCs) and 12 GPa. Nanoparticles have higher fluorescence intensity, which initially increases and then decreases with changes in pressure. Based on first-principles calculations, HoF3 transforms from an orthorhombic structure to a hexagonal structure during the phase transition, with the coordination number of holmium atoms increasing from 9 to 11. The high-pressure Raman spectra on lattice modes also confirmed the existence of the two phase transitions. This work not only provides precise structural changes but also facilitates the understanding of two typical structures of rare-earth trifluoride (REF3), which may play an important role in the application of the RE family.

Insights of the Multimode Orientation-Dependent Initial Oxidation of Aluminum by First-Principles Theory Calculations.

A fundamental understanding of the oxidation mechanisms of aluminum (Al) alloys is of great importance for its applications in corrosion, catalysis, sensors, etc. In this work, we systematically investigated the first-stage oxidation behaviors of three low-index Al facets with O coverage up to two monolayers (ML) by using density-functional theory (DFT). The large negative adsorption energies indicated favorable oxidation on all three facets. However, distinctive structural and electronic changes induced by the adsorption of oxygen have led to different oxidation modes. More specifically, the oxidation process proceeded by "intercalating" into the subsurface region along the (111) plane out of the (110) facet with spontaneous O ingress into (110) far below one ML, as revealed by the electron density distribution, whereas the oxide ad-layer grew in a "layer-by-layer" mode on Al(111) and (001) facets. Moreover, various Al-O complexes with different atomic coordination numbers (CN), configurations, and sizes may be indicators of the tendency of an Al surface to be oxidized. Besides, the oxide phases formed on (111)/(001) and (110) assembled the Al-O bond distribution within α-Al2O3 and γ-Al2O3, respectively.

Photoluminescent Lanthanide(III) Complexes Based on 2-[((4-Chlorophenyl)amino)methylene]-5,5-dimethylcyclohexane-1,3-dione

Five coordination compounds of the general formula [LnL2(NO3)3]n (Ln3+ = Eu (I), Sm (II), Tb(III), Dy (IV), and Gd (V)) are synthesized from 2-[((4-chlorophenyl)amino)methylene]-5,5-dimethylcyclohexane-1,3-dione (L). The crystal structures of the ligand and complex III are determined by X-ray diffraction (XRD) of single crystals (CIF files CCDC nos. 2298715 (L) and 2298716 (III)). Complex III is polymeric due to the bidentate-bridging coordination of the ligand by the oxygen atoms of the cyclohexanedione fragment, and the coordination number of the central atom is ten. According to the phase XRD data, all synthesized polycrystalline compounds are isostructural to the single crystals of complex III. The photoluminescence properties of the ligand and coordination compounds in the polycrystalline state are studied. The energy transfer from the ligand to lanthanide(III) ion is shown to proceed via the “antenna” mechanism in the case of the europium(III), samarium(III), and terbium(III) compounds. Among the series of the complexes, the highest quantum yield is observed for compound I (21.9%), and the sensibilization efficiency of the europium(III) complex is 43.5%.

Strained Cu(111) surface can be catalytic efficient for C–C coupling in CO2 electrochemical reduction

It is well accepted that the Cu(100) surface is catalytic active for C–C coupling in CO2 reduction. However, the (100) surface is less active for the preceding CO* formation process and, most importantly, less stable than other surfaces. In this work, we investigate the relationship between catalytic effects and general factors such as coordination number and spacing (strain) of the Cu surface atoms. We find that the former affects the CO* formation only and the latter affects both the CO* formation and the subsequent C–C coupling. Among all the strained surfaces with larger atomic spacing, the more stable Cu(111) surface is extraordinary and outperforms Cu(100) and the high index surfaces for CO2 reduction to C2 on Cu.

Electromechanical properties and piezoelectric potentials of one-dimensional GaN nanostructures: A bond relaxation investigation

From the viewpoint of atomic bond relaxation, an analytical approach was put forward to elucidate the physical origins of crystal size and cross-sectional shape dependency of piezoelectric potentials in GaN nanowires and nanotubes. It is demonstrated that (i) size-induced increase in piezoelectric potential is attributed to the coupling effect of the rising piezoelectric coefficient and both the reducing dielectric constant and elastic constant caused by the surface atomic coordination number loss, bond energy perturbation, and surface-to-volume ratio rising; (ii) as the number of sides for polygonal nanowires or nanotubes with the same equivalent radius decreases, the surface-to-volume ratio rises, and the piezoelectric potential increases; and (iii) the nanotubes can generate a piezoelectric potential higher than their nanowire counterparts due to their larger surface-to-volume ratios. The proposed formulation offers a scientific basis for the fabrication, optimization, and modulation of one-dimensional GaN-based piezoelectric nanometer devices.

Effect of fly ash and nano Silica on the formation and evolution of Calcium Silicate Hydrate in Portland Cement during hydration process

Recently, the trend of replacing cement with mineral admixtures in concrete has witnessed increasing interest in the construction industry due to the reduction in embodied energy and CO2 emissions. However, the addition of these admixtures in Portland Cement (PC) affected the formation as well as the structure of the hydration product Calcium-Silicate-Hydrate (C-S-H), which is reflected in the mechanical and durability properties of cement concrete. In the present study, nano-silica (NS) and a mixture of fly ash (FA) and NS were replaced into PC (PC + 0.5 % NS, PC + 1 % NS, PC + 0.5 % NS + 20 % FA and PC + 1 % NS + 40 % FA) to systematically study the formation and structural evolution of hydration products, namely C-S-H, at atomic and micro-scales at the early stage of hydration (3 days) and a later stage of hydration (90 days). The formation and structure of C-S-H were analyzed to correlate the microstructure development by using XRD, Rietveld technique, FESEM, TEM, FTIR and nano-scale mechanical properties by employing the nanoindentation techniques. Atomic Pair Distribution Function (PDF) is used to understand the effect of admixtures on the C-S-H structure from atomic point of view. PDF shows the structural modification of C-S-H such as different polyhedral, separation of intralayer/interlayer, pair/bond length, coordination number of atoms corresponding to the addition of additives with hydration age. Also, porosity measurements show increasing or decreasing porosity during hydration with additives. It is observed that the contribution of low-density C-S-H (LD C-S-H) is greater than that of high-density C-S-H (HD C-S-H) in the beginning days, whereas HD C-S-H more than LD C-S-H in the latter days of hydration. The elastic modulus increased from 15.44 GPa to 19.82 GPa and the hardness decreased from 0.41 GPa to 0.35 GPa of LD C-S-H in early days, whereas elastic modulus decreased from 34.84 GPa to 29.33 GPa and the hardness increased from 0.75 GPa to 0.83 GPa of HD C-S-H in the latter stage due to addition of additives. However, both increased for LD C-S-H and HD C-S-H for each corresponding mixture during hydration. The present study reported the formation and microstructural modifications of C-S-H and the correlation with nano-mechanical properties due to addition of nano or micro-sized admixtures (nano silica and fly ash) in the cement system. This correlation helps to develop low-energy cement composites by tailoring cement systems with desired properties.

Tunable Ag-Ox coordination for industrial-level carbon-negative CO2 electrolysis

The electrochemical CO2 reduction (eCO2RR) is promising for eliminating CO2, generate valuable chemicals and utilize spare electricity. However, its industrialization is greatly hindered by low CO2 single-pass conversion efficiency (SPCE) in alkaline/neutral electrolytes, and poor compatibility between the electrolysis and intermittent energy system. Herein, a carbon-negative acidic eCO2RR system is developed using acidic-tolerant Ag based metal-organic frameworks (Ag-MOFs), achieving a high Faradaic efficiency of CO above 97 % in a broad working window of 10–400 mA cm−2 for unsaturated Ag-O2 clusters, and a high CO2 SPCE of 46.3 % even under industrial-level 400 mA cm−2. Being connected to solar cells, the acidic eCO2RR system displays a remarkable solar-to-chemical efficiency of 19.74 %, offering great potential for industrial eCO2RR directly driven by renewable energy. Specifically, the CO/HCOOH selectivity could be manipulated by adjusting the coordination number of Ag atoms in Ag-MOFs, and thus a Pourbaix-diagram is proposed to explain the tunable selectivity theoretically.

Molecular dynamics simulation of the influence of nanocutting parameters on microstructure of AISI M2

Molecular dynamics simulation has become the main analysis method of ultra precision machining of various materials. In this research, molecular dynamics method was used to explore the influence of nanocutting parameters on amorphous atoms, atomic coordination numbers, atomic strain and dislocations of AISI M2 workpiece. LAMMPS was used to construct the molecular dynamics model for CBN tool cutting AISI M2. The polycrystalline model of the workpiece contained 12 grains and iron, chromium and tungsten atoms. The polycrystalline model of the tool contained 3 grains and boron and nitrogen atoms. Tersoff, EAM, Morse and L-J potential energy functions were used to characterize the interaction between atoms. The following results were obtained through 8 groups of simulation experiments: (1) Both cutting speed and cutting depth promoted the amorphous transformation of workpiece atoms. (2) Under the extrusion of the tool, atoms with high coordination numbers were produced in the contact area between the tool and the workpiece. (3) The cutting depth was positively correlated with the average strain of workpiece atoms. Large strain atoms mainly occurred in the cutting area and gradually extended into the workpiece. (4) 1/2 < 111> dislocation was the most common dislocation form in nanocutting. This research plays a rich role in molecular dynamics simulation of nanocutting polycrystalline alloys.

Theoretical study of the effects of surface Cu coordination environment on CO2 hydrogenation to CH3OH

The coordination environment of Cu (the coordination number and arrangement of surface atoms) plays an important role in CO2 hydrogenation to CH3OH. Compared with the extensive studies of the effects of coordination number, the comprehensive effects of coordination number and arrangement of surface atoms were seldom explored in literature. To unravel the effects of surface Cu coordination environment on CO2 hydrogenation to CH3OH, the adsorption and reaction behaviors of H2 and CO2 on Cu(111), (100), (110) and (211) with different coordination numbers and arrangement of surface Cu were systematically calculated by density functional theory (DFT) and kinetic Monte Carlo (kMC) simulation. It was found that the adsorption energies of intermediates in CO2 hydrogenation on Cu surfaces increase with the decrease of coordination number. When the Cu coordination numbers are similar, the charge density on the open surface derived from the different atom arrangement becomes larger and leads to stronger interaction with intermediates than that on the compact one. DFT calculation and kMC simulation indicate that methanol formation pathway follows CO2*→HCOO*→HCOOH*→H2COOH*→H2CO*→CH3O*→CH3OH* on four Cu facets; CO formation is via CO2 direct dissociation on Cu(111), (100) and (110) but COOH* dissociation on (211). The low-coordinated surface Cu with more openness on Cu(211) is the highly active site for CO2 hydrogenation to CH3OH with high turnover of frequency (3.71 × 10−4 s−1) and high selectivity (87.17 %) at 600 K, PCO2 = 7.5 atm and PH2 = 22.5 atm, which is much higher than those on Cu(111), (100) and (110). This work unravels the effects of coordination environment on CO2 hydrogenation at the molecular level and provides an important insight into the design and development of catalysts with high performance in CO2 hydrogenation to CH3OH.

Unraveling Hydrogen Adsorption on Transition Metal-Doped [Mo3S13]2- Clusters: Insights from Density Functional Theory Calculations.

Molecular and dissociative hydrogen adsorption of transition metal (TM)-doped [Mo3S13]2- atomic clusters were investigated using density functional theory calculations. The introduced TM dopants form stable bonds with S atoms, preserving the geometric structure. The S-TM-S bridging bond emerges as the most stable configuration. The preferred adsorption sites were found to be influenced by various factors, such as the relative electronegativity, coordination number, and charge of the TM atom. Notably, the presence of these TM atoms remarkably improved the hydrogen adsorption activity. The dissociation of a single hydrogen molecule on TM[Mo3S13]2- clusters (TM = Sc, Cr, Mn, Fe, Co, and Ni) is thermodynamically and kinetically favorable compared to their bare counterparts. The extent of favorability monotonically depends on the TM impurity, with a maximum activation barrier energy ranging from 0.62 to 1.58 eV, lower than that of the bare cluster (1.69 eV). Findings provide insights for experimental research on hydrogen adsorption using TM-doped molybdenum sulfide nanoclusters, with potential applications in the field of hydrogen energy.

First-principles definition of ionicity and covalency in molecules and solids.

The notions of ionicity and covalency of chemical bonds, effective atomic charges, and decomposition of the cohesive energy into ionic and covalent terms are fundamental yet elusive. For example, different approaches give different values of atomic charges. Pursuing the goal of formulating a universal approach based on firm physical grounds (first-principles or non-empirical), we develop a formalism based on Wannier functions with atomic orbital symmetry and capable of defining these notions and giving numerically robust results that are in excellent agreement with traditional chemical thinking. Unexpectedly, in diamond-like boron phosphide (BP), we find charges of +0.68 on phosphorus and -0.68 on boron atoms, and this anomaly is explained by the Zintl-Klemm nature of this compound. We present a simple model that includes energies of the highest occupied cationic and lowest unoccupied anionic atomic orbitals, coordination numbers, and strength of interatomic orbital overlap. This model captures the essential physics of bonding and accurately reproduces all our results, including anomalous BP.

The analysis of extension evolution law and damage behavior characteristic for line microcracks on Si3N4 bearing balls

To predict the relation between extension evolution law and damage of line microcracks on silicon nitride bearing balls. Firstly, the 3D point cloud features of line microcracks are obtained based on multi-image 3D reconstruction. Next, the point cloud diagram data is optimized to fit the molecular dynamics geometric model of line microcracks extension process. Then, according to the Si3N4 molecular dynamics deep learning potential, the molecular dynamics mechanical model is established. Finally, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used to numerically solve the extension evolution of line microcracks. The experiment result shows that from the change analysis of single-layer surface mesh, the microcracks extension is concentrated in the central region of the indentation. The new microcracks spread along both sides of the original microcracks. After uniformly distributed load is applied to line microcracks, there is a phenomenon of concentrated swirling microcracks formation under the indentation region. By analyzing the atomic coordination number nephogram, the microcracks extension occurs when the proportion of amorphous atoms is up to 7 % during loading. And the plastic deformation occurs when the proportion of amorphous atoms is dropped to 6 % during unloading. In addition, in the process of indentation loading, plastic deformation and slip zone occur on Si3N4 bearing balls surface. However, the strain is accumulated in the middle region during unloading. The slip zone moves inward and becomes thin, and the elastic deformation partially is recovered.

Pressure-induced phase transitions of intermetallic TMBe2 (TM = Zr and Hf) from first-principles calculations

High-pressure stable structures of intermetallic TMBe2 (TM = Zr and Hf) have been fully explored up to 40 GPa using particle swarm structure searches combined with first-principles calculations. The resulting findings show that both intermetallics undergo a structure transition from the ambient-pressure layered AlB2-type structure to a uniform orthorhombic Cmcm structure at 4.5 GPa and 13.8 GPa, respectively. The significant volume collapses under high pressure indicate that the structural transitions of two intermetallics are typical first-order. During the pressure-induced phase transition process, the formation of newly folded Be hexagonal rings in the high-pressure Cmcm structure with unusual change of coordination numbers of TM atoms was attributed to the alternating distortions of the layer-like Be hexagonal rings in ambient AlB2-type structure. The contributions of atomic orbitals near the Fermi level changes correspondingly before and after the structural phase transition, demonstrated by an analyses of electronic band structures and density of states. An obvious degeneracy of TM-d orbitals in the new high-pressure Cmcm structure was further revealed. Additionally, a systematic comparative analysis of mechanical parameters and anisotropic distributions of TMBe2 intermetallics with two structures was performed.

Improving Quantum Chemical Solvation Models by Dynamic Radii Adjustment for Continuum Solvation (DRACO).

We present the Dynamic Radii Adjustment for COntinuum solvation (DRACO) approach, which employs precomputed atomic partial charges and coordination numbers of the solute atoms to improve the solute cavity. As such, DRACO is compatible with major solvation models, improving their performance significantly and robustly at virtually no extra cost, especially for charged solutes. Combined with the purely electrostatic CPCM and COSMO models, DRACO reduces the mean absolute deviation (MAD) of the solvation free energy by up to 4.5 kcal mol-1 (67%) for a large data set of polar and ionic solutes. Even in combination with the highly empirical universal solvation model (SMD), DRACO substantially reduces the MAD for charged solutes by up to 1.5 kcal mol-1 (39%), while neutral solutes are slightly improved (0.2 kcal mol-1 or 16%). We present an interface of DRACO with two computationally efficient atomic charge models that enables fully automated, out-of-the-box calculations with the widely used program packages Orca and TurboMole.

A Metal Coordination Number Determined Catalytic Performance in Manganese Borides for Ambient Electrolysis of Nitrogen to Ammonia.

A new strategy that can effectively increase the nitrogen reduction reaction performance of catalysts is proposed and verified by tuning the coordination number of metal atoms. It is found that the intrinsic activity of Mn atoms in the manganese borides (MnBx) increases in tandem with their coordination number with B atoms. Electron-deficient boron atoms are capable of accepting electrons from Mn atoms, which enhances the adsorption of N2 on the Mn catalytic sites (*) and the hydrogenation of N2 to form *NNH intermediates. Furthermore, the increase in coordination number reduces the charge density of Mn atoms at the Fermi level, which facilitates the desorption of ammonia from the catalyst surface. Notably, the MnB4 compound with a Mn coordination number of up to 12 exhibits a high ammonia yield rate (74.9 ± 2.1µg h-1 mgcat -1) and Faradaic efficiency (38.5 ± 2.7%) at -0.3V versus reversible hydrogen electrode (RHE) in a 0.1 m Li2SO4 electrolyte, exceeding those reported for other boron-related catalysts.

Fundamental Understanding of Hydrogen Evolution Reaction on Zinc Anode Surface: A First-Principles Study

HighlightsThe reaction mechanisms of hydrogen evolution reaction (HER) on various crystal surfaces of zinc anode have been systematically investigated by first-principle calculations.Both the thermodynamic and kinetic aspects of HER have been studied to reveal the relative HER activity of several crystal surface of zinc anode.The generalized coordination number of surface Zn atoms are proposed as a key descriptor of HER activity of Zn anode.

Guanidinium Vanadate [C(NH2)3]3VO4·2H2O Revealing Enhanced Second-Harmonic Generation and Wide Band Gaps.

A new guanidinium-templated vanadate, [C(NH2)3]3VO4·2H2O, has been synthesized in a phase-pure form. It crystallizes in a noncentrosymmetric polar space group, Cc, and the crystal structure is built upon a framework of guanidinium, vanadate tetrahedra, and water molecules linked by hydrogen bonds. Notably, optical measurements reveal that the material exhibits an approximately 9.6-fold enhancement in second-harmonic generation efficiency compared to its phosphate analogue. The enhancement can be attributed to the increased geometrical distortion of the VO4 tetrahedra. Furthermore, we found that the coordination number of the central vanadium atom significantly affects the optical band gaps. Among various coordination numbers, the 4-coordinate VO4 tetrahedra are found to be more favorable for widening the optical band gap of materials compared to the 5- and 6-coordinate vanadium polyhedra, as demonstrated by this work.