Tetrahedral Arrangement Research Articles

Insight into a pure spinel Co3O4 and boron, nitrogen, sulphur (BNS) tri-doped Co3O4-rGO nanocomposite for the electrocatalytic oxygen reduction reaction.

The intricate problems concerning energy require innovative solutions. Herein, we propose a smart composite nano system that can be used in a sustainable and dichotomous manner to resolve energy crises. The current study describes a new way to synthesize a pure spinel cobalt oxide (Co3O4) and boron (B), nitrogen (N), and sulfur (S) tri-doped Co3O4-reduced graphite oxide (rGO) nanocomposite (CBNS). A hydrothermal method has been used for the synthesis of these nanomaterials. The synthesized nanocomposite was characterized by UV-visible spectroscopy, X-ray diffraction (XRD), Raman spectroscopy, scanning electron microscopy (SEM), X-ray absorption spectroscopy (XAS), and transmission electron microscopy (TEM). The XRD results showed the formation of Co3O4 and B, N, S doped nanocomposite with high purity and crystallinity. XAS analysis elucidates the formation of spinel Co3O4 with tetrahedral and octahedral arrangement of cobalt ions. The peaks at 2.50 Å and 3.07 Å are due to the Co-Co bonding. The electrocatalytic oxygen reduction (ORR) was successfully implemented using these nanocomposites. The electrochemical study exhibits the better activity of the B, N, and S tri-doped Co3O4-rGO nanocomposite due to the mutual effect of B, N and S. The synthesized catalyst has maximum current density of 9.97 mA cm-2 with onset potential (Eonset) of 0.98 V in alkaline medium.

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity.

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis2 complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis2 is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.

Beryllium ion coordination in Ammonia, methanol and water solvents

• Be is a key component of materials indispensable in today’s industries and its solvation behavior is a topic of interest. • The study highlight the coordination behavior of beryllium ion with water, ammonia and methanol solvents. • Fitting procedure to obtain Binding energy convergence. • Temperature effects on the isomeric distribution for each cluster size. • MP2 method as reliable method to describe the solvation process around cations. The solvation of B e 2 + [ M g N H 3 n = 1 - 10 ] 2 + cation in ammonia, methanol and water has been studied at Ab initio MP2 level using cluster models in which the solvent molecules have been distributed between the first and second solvation shells. In all cases, the first solvation sphere results to be saturated with four solvent molecules in a tetrahedral arrangement. The second shell contains instead up to 8,12 and 16 ligands in the case of methanol, water and ammonia, respectively. Solvent molecules in the second solvation shell serve to stabilizes the structures through the formation of a number of hydrogen bonds and improves the agreement with the available experimental data. From obtained distances values it can be deduced that beryllium ion establishes with the solvent molecules, inside the first coordination shell, bonds of covalent nature (less than1.8Å) which are longer than those with the magnesium ion. Using a fitting procedure, binding energy values of 29.2, 46.9 and 68.6 kcal/mol, for ammonia, water and methanol clusters, have been obtained, respectively. The clustering enthalpies and free energies have been also evaluated. Temperature effects on the isomeric distribution for each cluster and for all considered solvents, have been calculated in the range of 25–40 K and results show that only the tetracoordinated systems are populate.

Using Car-Parrinello simulations and microscopic order descriptors to reveal two locally favored structures with distinct molecular dipole moments and dynamics in ambient liquid water

Water is essential for life and technological applications, mainly for its unique thermodynamic and dynamic properties, often anomalous or counterintuitive. These anomalies result from the hydrogen-bonds fluctuations, as evidenced by studies for supercooled water. However, it is difficult to characterize these fluctuations under ambient conditions. Here, we fill this knowledge gap thanks to the Car-Parrinello ab initio molecular dynamics (MD) simulation technique. We calculate the local structural order parameter ζ, quantifying the coordination shells separation, and find two locally-favored structures or states: High-ζ and Low-ζ. On average, High-ζ molecules have a tetrahedral arrangement, with four hydrogen bonds, and the first and the second coordination shell well separated. The Low-ζ molecules are less connected, partially merging the first and the second shells. The appearance of isosbestic points in the radial distribution functions and the collective density fluctuations at different length scales and timescales reveal that the two-state model, consistent with available experimental data for supercooled water, also holds under ambient conditions, as we confirm by analyzing the vibrational spectrum of both types of water molecules. Significant consequences of the structural differences between the two states are that High-ζ molecules have a dipole moment 6 % higher than Low-ζ. At the same time, Low-ζ structures are more disordered and with more significant angular fluctuations. These differences are also reflected in the dynamics under ambient conditions. The Low-ζ molecules decorrelate their reorientation faster than High-ζ and merge their coordination shells within 0.2 ps, while the High-ζ preserve the shell separation for longer times. Our analysis shows that first-principle calculations make predictions under ambient conditions calling for new and definitive experiments confirming the two-state model.

Structure of a subnanometer-sized semiconductor Cd14Se13 cluster

Structure of a subnanometer-sized semiconductor Cd14Se13 cluster

Four new tin(II), uranyl(II), vanadyl(II), and zirconyl(II) alloxan biomolecule complexes: synthesis, spectroscopic and thermal characterizations

ABSTRACT. The alloxan as a biomolecule ligand has been utilized to synthesize thermodynamically and kinetically stabilized four new tin(II), uranyl(II), vanadyl(II), and zirconyl(II) complexes. In the complexes, tin(II) ion present is in tetrahedral arrangement, zirconyl and vanadyl(II) ions present are in square pyramid feature but uranyl(II) ion present is in octahedral arrangement and all are coordinated by two bidentate alloxan ligand in complexes. The synthesized alloxan ligand coordinate with central metal(II) ion through oxygen in position C2=O and the nitrogen in position N1 developing a 4-membered chelate ring. Synthesized Sn(II), UO2(II), VO(II), and ZrO(II) complexes via bidentate ligand have been accurately described by various spectroscopic techniques like elemental analysis (C, H, N, metal), conductivity measurements, FT-IR, UV-Vis, 1H-NMR, and TGA. The kinetic thermodynamic parameters such as: E*, ΔH*, ΔS* and ΔG* were calculated using Coats and Redfern and Horowitz and Metzger equations.
 
 KEY WORDS: Alloxan, Metal ions, Spectroscopy, Ligand, Coordination, Thermogravimetry
 
 Bull. Chem. Soc. Ethiop. 2022, 36(2), 373-385. 
 DOI: https://dx.doi.org/10.4314/bcse.v36i2.11

Spectroscopic studies, DFT calculations, cytotoxicity activity, and docking stimulation of novel metal complexes of Schiff base ligand of isonicotinohydrazide derivative

In this elucidation, the reactivity of isonicotinohydrazide derivative (3)(L) was reacted with the nitrate salts of Cr(III), Fe(III), Co(II), Ni(II), Cu(II), and Zn(II) to afford the corresponding stable metal coordination compounds. The synthesized metal coordination compounds were confirmed through physicochemical and analytical analysis such as elemental analysis, UV‐Visible, FT‐IR, TGA, Mass,1H NMR, XRD, magnetic, and molar conductance analysis. All complexes exhibit distorted octahedral geometry except Zn(II) complex which has a distorted tetrahedral arrangement. Both the thermal stability and the kinetic parameter for all complexes were elucidated via TGA analysis and Coats‐Redfern method. XRD study suggested that the complexes have a partially amorphous structure which was further confirmed by calculating the crystallinity index. Moreover, the synthesized metal complexes exhibited excellent cytotoxicity activity contra lung cancer cells (A549) and liver cancer cells (HepG2) using neutral red uptake assay. The complexes of Fe(III), Ni(II), and Zn(II) showed higher cytotoxic effect than doxorubicin againstA549andHepG2cells for 24 h incubation. Furthermore, the Cr(III), Co(II), Zn(II), and Cu(II) coordination compounds showed more inhibitory influence when treated withA549andHepG2cells for 48 h incubation. The biological studies of these complexes were confirmed through molecular docking studies with different proteins such as (PDB ID: 2ITO) and (PDB ID: 5H38) and showed low binding energy and shortage bond length with different amino acids. Also, computational calculations of all metal complexes were carried out utilizing DFT/B3LYP/LANL2DZ basis set to detect the FMO, ESP, MEP, and physical descriptor's of them and confirms their reactivity.

Crystalline phase transitions and water-soluble complexes of copper(I) 2-hydroxyethanethiolate

The coordination polymer copper(I) 2-hydroxyethanethiolate, (CuSCH2CH2OH)n, though insoluble in all common solvents, dissolved readily in basic aqueous solutions of the thiolate anion (HOCH2CH2S–) of 2-mercaptoethanol to form a single species: the tetranuclear cluster [Cu4(µ-SCH2CH2OH)6]2–. From this solution were grown X-ray quality single crystals of copper(I) 2-hydroxyethanethiolate. This compound underwent a hitherto unknown crystal phase transition at ca. 6 °C, from point group P212121 to Pna21, with noticeable changes in the geometry of the Cu-S layer and in the orientation of the alkylthiolate side chains. When the bulky base tetrabutylammonium hydroxide was employed in the aqueous thiolate solution used to dissolve (CuSCH2CH2OH)n, the water-soluble polynuclear copper(I) complex bis(tetrabutylammonium) hexakis(µ-2-hydroxyethanethiolato) tetracuprate(I), [(C4H9)4N]2[Cu4(µ-SCH2CH2OH)6], could be isolated as X-ray quality crystals. Structural characterization of this complex revealed a tetrahedral arrangement of copper(I) centers with thiolates bridging the edges of the tetrahedra. On standing, this complex degraded to a larger polynuclear Cu(I) sulfide cluster.

Anomalies and Local Structure of Liquid Water from Boiling to the Supercooled Regime as Predicted by the Many-Body MB-pol Model.

For the past 50 years, researchers have sought molecular models that can accurately reproduce water's microscopic structure and thermophysical properties across broad ranges of its complex phase diagram. Herein, molecular dynamics simulations with the many-body MB-pol model are performed to monitor the thermodynamic response functions and local structure of liquid water from the boiling point down to deeply supercooled temperatures at ambient pressure. The isothermal compressibility and isobaric heat capacity show maxima near 223 K, in excellent agreement with recent experiments, and the liquid density exhibits a minimum at ∼208 K. A local tetrahedral arrangement, where each water molecule accepts and donates two hydrogen bonds, is found to be the most probable hydrogen-bonding topology at all temperatures. This work suggests that MB-pol may provide predictive capability for studies of liquid water's physical properties across broad ranges of thermodynamic states, including the so-called water's "no man's land" which is difficult to probe experimentally.

Structural changes of interfacial water upon fluid-ripple-gel phase transitions of bilayers

All atom molecular dynamics simulations of fully hydrated dimyristoylphosphatidylcholine lipid bilayers are performed for total 9.45 μs showing a fluid to a ripple to a gel phase transition. Changes in the radial distribution functions and angular distribution functions of the interface water (IW) signify a shift from a distorted tetrahedral to a tetrahedral arrangement upon decrease in temperature at the gel phase. The potential of mean forces of the IW follow two cross-overs near both phase transitions unlike the BW. Our analyses reveal a strong correlation between bilayer phase transitions and the structural properties of the IW.

Structural characteristics of low-density environments in liquid water.

The existence of two structural forms in liquid water has been a point of discussion for a long time. A phase transition between these two forms of liquid water has been proposed based on evidence from molecular simulations, and experiments have also been very recently able to track the proposed transition of the low-density liquid form to the high-density liquid form. We propose to use the average angle an oxygen atom makes with its neighbors to describe the structural environment of a water molecule. The distribution of this order parameter is observed to have two peaks with one peak at ∼109.5^{∘}, corresponding to the internal angle of a regular tetrahedron, indicating tetrahedral arrangement. The other peak corresponds to an environment with a tighter arrangement of neighboring molecules. The distribution of O-O-O angles is decomposed into two skewed distributions to estimate the fractions of the two liquid forms in water. A good similarity is observed between the temperature and pressure trends of fractions of locally favored tetrahedral structure (LFTS) form estimated using the new order parameter and the reports in the literature, over a range of temperatures and pressures. We also compare the structural environments indicated by different order parameters and find that the order parameter proposed in this paper captures the structure of first solvation shell of the LFTS accurately.

NaCl salt effect on water structure: a Monte Carlo simulation study

ABSTRACT Monte Carlo simulations and the nearest neighbour approach have been employed in the present study to investigate the effect of NaCl salt on the local structure of water at ambient conditions. The calculations are performed at increasing concentration of NaCl starting from C = 0.5 m up to 6 m. We investigate the influence of ions on the tetrahedral structure and the hydrogen-bonded network of water. The analysis shows that increasing salt concentration results in a reduction of the tetrahedral arrangement of water in favour of a non-tetrahedral arrangement. The use of the nearest neighbour approach allows us to determinate the origin and angular characteristics of this non-tetrahedral structure. Moreover it is demonstrated that compared to Na+, Cl− ion has a larger effect on the tetrahedral structure of water.

Zinc(II) and cobalt(II) complexes with unusual coordination of mixed imidazole-1,2,4-triazole ligand in a protonated cationic form

Zinc(II) and cobalt(II) molecular coordination compounds with the mixed-donor 1-(4-(1H-imidazol-1-yl)benzyl)-1H-1,2,4-triazole were prepared and their crystal structure was determined by single crystal X-ray diffraction analysis. Both metal cations are in a slightly distorted tetrahedral arrangement, the heterocyclic ligand is coordinated via 1,2,4-triazole nitrogen atoms at position 4 of the ring, consistent with the localization of a negative charge at this atom, according to DFT calculations. Upon coordination, the ligand undergoes protonation with the formation of rare examples of transition metal coordination compounds with the cationic ligands. Zinc(II) complex demonstrated ligand-centered photoluminescence with the maximum near 302 nm upon excitation at 264 nm.

Structural and theoretical studies on copper(II) and zinc(II) complexes with a 9-anthraldehyde-derived thiosemicarbazone

Complexes [Cu(ATPh)2]·H2O (1) and [Zn(ATPh)2] (2) were obtained with 9-anthraldehyde-N(3)-phenyl thiosemicarbazone (HATPh). The g|| ≈ 2.15 and A|| ≈ 180 G EPR parameters of complex (1) are compatible with two nitrogen and two sulfur donor atoms in a nearly square planar geometry. The first excited state of complex (1) is not emissive due to fluorescence quenching by the paramagnetic copper(II) ion. The crystal structure of [Zn(ATPh)2]·2DMF (2a) shows that in 2a the anionic thiosemicarbazone ligands are attached to the metal through the NS chelating system in a distorted tetrahedral arrangement. Computational studies revealed that the S1 → S0 emission of complex (2) is attributed to anthracene, the emission band involving two electronic transitions centered at the anthracene rings. The HOMO-1 → LUMO transition is characterized as a ligand-to-ligand charge transfer (LLCT) between anthracene groups, which contributes with 12% and an intra-ligand charge transfer transition (ILCT) centered in the anthracene group of one of the ligands, which contributes with 77% to the emission band. The emission intensity of complex (2) is lower than that of the free thiosemicarbazone, but the presence of two ligand molecules in the complex increases the fluorescence efficiency and the computed fluorescence rate constant for 2 is ∼ 600-fold higher than that of the free ligand.

Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment.

Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant Haliangium ochraceum encapsulin:encapsulated ferritin complex using cryo–electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.

Regulating Optical Activity and Anisotropic Second-Harmonic Generation in Zero-Dimensional Hybrid Copper Halides.

Structural engineering permits the introduction of chirality into organic-inorganic hybrid metal halides (HMHs), which creates a promising and exclusive material for applications in various optoelectronics. However, the optical activity regulation of chiral HMHs remains largely unexplored. In this work, we have synthesized two pairs of lead-free chiral HMHs with a zero-dimensional tetrahedral arrangement, i.e., (R- and S-1-(1-naphthyl)ethylammonium)2CuCl4 and (R- and S-1-(2-naphthyl)ethylammonium)2CuCl4. The magnitude of optical activity in these HMHs can be efficiently modulated as a result of the different magnetic transition dipole moments. Furthermore, these HMHs exhibited effective second-harmonic generation (SHG) and distinct SHG-circular dichroism (CD), with (R-1-(1-naphthyl)ethylammonium)2CuCl4 having an anisotropy factor (gSHG-CD) of up to 0.41. This work not only provides insights into regulating the optical activity and anisotropic SHG effect of lead-free chiral HMHs but also confirms the feasibility of SHG-CD spectroscopy as a promising tool for characterizing the intrinsic optical activity of chiral materials.

Structural diversity of CuZn2InSe4 quaternary chalcogenides: electronic and phonon properties from first principles.

First principles simulations are utilized to calculate the electronic and vibrational properties of several metastable structural phases of the CuZn2InSe4 quaternary chalcogenide, including stanite, kesterite, primitive mixed CuAu, wurtzite-stanite, and wurtzite-kesterite lattices. We find that although each phase is formed by nearest cation-chalcogen bonds, the structural diversity due to cation and polyhedral arrangements has direct consequences in the electronic structure. The simulations further indicate that hybrid functionals are needed to account for the s–p and p–d orbital hybridization that is found around the Fermi level, which leads to much enhanced energy band gaps when compared with standard exchange-correlation approaches. We also find that the thermal conductivities for all phases are relatively low, and the main scattering channel comes from a low frequency optical band hybridized with acoustic phonons. Given that CuZn2InSe4 is a material from a larger class of quaternary chalcogenides, other materials may exhibit similar electronic and vibrational properties, which may be useful for electronic and thermal management applications.

Evaluation of the efficiency of divalent cobalt and copper chelates based on isatin derivatives and thiosemicarbazide ligands as inhibitors for the corrosion of Sabic iron in acidic medium

Divalent cobalt and copper chelates of the two ligands 1-(1-ethoxycarbonylmethyl-2-oxoindolin-3-ylidene) thiosemicarbazide ( EOIT ) and 1-(1-benzyl-2-oxoindolin-3-ylidene) thiosemicarbazide ( BOIT ) are the target compounds of the current study. Identification of the structures and geometries of these compounds have been performed using the possible physicochemical and analytical instruments. Elemental analysis, molar conductance and thermal analysis assured the composition of the four chelates to be [Co(BOIT)Cl]•1·.5H 2 O ( BOIT-Co ), [Cu(BOIT)Cl] ( BOIT-Cu ), [Co(EOIT)Cl 2 (H 2 O)]•5H 2 O ( EOIT-Co ) and [Cu(EOIT)Cl]•Cl ( EOIT-Cu ) which was further confirmed by the measurement of mass spectra. The architecture arrangement of the ligand atoms around Co and Cu centers has been determined depending on the UV–Vis spectral measurements and calculation of µ eff values. This proved that the copper compounds were square planer whereas the cobalt complexes were tetrahedral or octahedral arrangements. These compounds were examined as corrosion inhibitors for Sabic iron in 1.0 M HCl solution using potentiodynamic polarization, electrochemical impedance spectroscopy, mass-loss and scanning electron microscopy techniques. The acquired outcomes disclosed that the examined compounds were found to have high inhibition efficiencies (% IEs) which were dependent on their concentrations and composition. The obtained high % IEs (83–87% at concentration of 400 mg/l) were interpreted by strong adsorption of the compounds’ molecules on the iron surface and such adsorption was discovered to follow Langmuir adsorption isotherm. At the same concentration, the % IEs are slightly increased in the order: EOIT-Cu > BOIT-Cu > EOIT-Co > BOIT-Co . Finally, the investigational results obtained from all employed techniques were in a good consistent with each other.

Quasi-water layer sandwiched between hexagonal ice and wall and its influences on the ice tensile stress.

The presence of a quasi-water/premelting layer at the interface between wall and ice when the temperature (T) is below the melting point was extensively observed in experiments. In this work, molecular dynamics simulations are performed to analyze the underlying physics of the quasi-water layer and the effects of the layer on the ice tensile stress. The results indicate that each molecule and its four nearest neighbours in the quasi-water layer representing an equilibrium structure gradually form a tetrahedral ice-like arrangement from an unstructured liquid-like structure along the direction away from the wall. The average density of the quasi-water layer is equal to or higher than the bulk density of water at T ≥ 240 K or T ≤ 240 K respectively, and reaches 1.155 g cm-3 at T = 210 K, suggesting a structural correlation with the high-density liquid phase of water. Depending on the temperature and wall wettability, the thickness of the quasi-water layer (Hq) ranges from ∼2 Å to ∼25 Å. For prescribed hydrophilic walls, Hq increases monotonically with temperature, and is almost proportional to(Tm - T)-1/3, where Tm is the melting temperature of ice. Hq keeps an almost constant value (2 Å) as the temperature increases and rises sharply after passing a threshold temperature of T ≈ 250 K. In the joint effects of the wall wettability and quasi-water layer's thickness, the ice tensile stress decreasing monotonically at a larger temperature shows an upward trend and then reduces to almost a constant value as the wall changes from a hydrophobic to a hydrophilic one. The results reveal the potential development of anti-icing/de-icing techniques by heating the wall or modifying its surface to increase Hq.

In Silico Elucidation of Molecular Picture of Water-Choline Chloride Mixture.

Choline chloride (ChCl) is a component of several deep eutectic solvents (DESs) having numerous applications. Recent studies have reported manifold promising use of aqueous choline chloride solution as an alternative to DES, where water plays the role of the hydrogen-bond donor. The characteristic physical properties of the DESs and aqueous DES originate from the "inter-" and intraspecies hydrogen-bond network formed by the constituents. However, a detailed molecular-level picture of choline chloride and water mixture is largely lacking in the literature. This motivates us to carry out extensive all-atom molecular dynamics simulations of the ChCl-water mixture of varying compositions. Our analyses clearly show an overall increase in the interspecies association with an increase in ChCl concentration. At higher concentrations, the trimethylammonium groups of choline are stabilized by a nonpolar interaction, whereas the hydroxyl groups preferentially interact with water. Chloride ions are found to be involved in two types of interactions: one where chloride ions intercalate two or more choline cations, and the other one where they are surrounded by five to six water molecules forming solvated chloride ions. However, the relative fractions of these two types of associations depend on the concentration of ChCl in the mixture. Another important structural aspect is the disruption of the hydrogen-bonded water network due to the presence of both choline cations and chloride ions. However, chloride ions participate to partially restore the tetrahedral arrangement of partners around water molecules.