Study on the Mixed ZnO Clusters and Ring-Like ZnO Ions

The pure Zn_m (m?=?2–10), mixed Zn_mO_m (m?=?1–10), Zn_mO_10??m (m?=?1–9) clusters and the univalent and divalent ring-like Zn_mO_m (m?=?2–10) cluster ions are systematically investigated by using Amsterdam density functional (ADF) program with Triple-zeta with two polarization functions basis set in conjunction with self-consistent field. Our calculated results show that the Zn₄ and Zn₇ clusters are the magic clusters. The structures of the Zn_mO_m (m?=?1–10) clusters evolve from two-dimension to three-dimension after m?=?8. For the Zn_mO_10??m (m?=?1–9) clusters, the Zn-rich structures evolve gradually from three-dimension to plane with an increase in the O ratios. The Zn₅O₅ cluster with equal ratio has a two dimensional structure. In the O-rich clusters, the O dimers can be easily detached from them. The O and Zn atoms partly adopt sp² and sp hybridization, respectively, in the ring-like Zn_mO_m (m?=?2–10) clusters and their ions. Gain and loss charge would affect the degree of hybridization and change their geometries. Their structural changes can be explained by valence bond theory.     

A Systematic Search for Structures and Stabilities of Asymmetric Clusters (HfInN<Subscript>3</Subscript>)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1-6)

In order to find single source precursors (SSP), the structures, relative stabilities, and IR spectra of small asymmetric clusters (HFInN₃) _n (n = 1–6) are systematically investigated by means of the density functional theory at the B3LYP level. The obtained geometries show that the frameworks of clusters (HFInN₃) _n (n = 2–6) prefer to be 2n-membered ring with alternating indium and α-nitrogen atoms. The averaged binding energies reveal that all of asymmetric clusters (HFInN₃) _n (n = 1–6) can continue to gain energy as the cluster size n increasing. The second-order difference of energy (Δ₂E) and the HOMO-LUMO energy gap (E_gap) as a function of the cluster size n both exhibit a pronounced even-odd alternation phenomenon. The influences of cluster size n and temperature T on the thermodynamic properties of clusters are discussed. Judged by enthalpies and Gibbs free energies, the formations of the most stable clusters (HFInN₃) _n (n = 2–6) from the monomer are thermodynamically favorable in the range of 200–800 K.     

Computational Studies on the Mo-Doped Gold Nanoclusters Au<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Mo(<Emphasis Type="Italic">n</Emphasis> = 1–10): Structures,Stabilities and Magnetic Properties

The geometric structures, relative stabilities, magnetic properties of Mo-doped gold clusters Au _n Mo(n = 1–10) have been investigated at the PBE1PBE/def2TZVP level of theory. The results show that molybdenum doping has a significant effect on the geometric structures and electronic properties of Au _n Mo(n = 1–10) clusters. For the lowest energy structures of Au _n Mo(n = 1–10), the two dimensional to three dimensional transition occurs at cluster size n ≥ 8, and their relative stabilities exhibit odd–even oscillation with the change of Au atom number. It is found that charge in corresponding Au _n Mo clusters transfers from Mo atom to Au _n host in the size range n = 1–7, whereas the charge in opposition direction in the size range n = 8–10. In addition, the magnetic properties of Au _n Mo clusters are enhanced after doping single Mo atom into the corresponding gold clusters. Our results are valuable for the design of magnetic material.     

Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble

Representing the 3D structures of ligands in virtual screenings via multi-conformer ensembles can be computationally intensive, especially for compounds with a large number of rotatable bonds. Thus, reducing the size of multi-conformer databases and the number of query conformers, while simultaneously reproducing the bioactive conformer with good accuracy, is of crucial interest. While clustering and RMSD filtering methods are employed in existing conformer generators, the novelty of this work is the inclusion of a clustering scheme (NMRCLUST) that does not require a user-defined cut-off value. This algorithm simultaneously optimizes the number and the average spread of the clusters. Here we describe and test four inter-dependent approaches for selecting computer-generated conformers, namely: OMEGA, NMRCLUST, RMS filtering and averaged-RMS filtering. The bioactive conformations of 65 selected ligands were extracted from the corresponding protein:ligand complexes from the Protein Data Bank, including eight ligands that adopted dissimilar bound conformations within different receptors. We show that NMRCLUST can be employed to further filter OMEGA-generated conformers while maintaining biological relevance of the ensemble. It was observed that NMRCLUST (containing on average 10 times fewer conformers per compound) performed nearly as well as OMEGA, and both outperformed RMS filtering and averaged-RMS filtering in terms of identifying the bioactive conformations with excellent and good matches (0.5 < RMSD < 1.0 Å). Furthermore, we propose thresholds for OMEGA root-mean square filtering depending on the number of rotors in a compound: 0.8, 1.0 and 1.4 for structures with low (1–4), medium (5–9) and high (10–15) numbers of rotatable bonds, respectively. The protocol employed is general and can be applied to reduce the number of conformers in multi-conformer compound collections and alleviate the complexity of downstream data processing in virtual screening experiments.     

Synthesis and magnetic properties of solid solutions In<Subscript>1–<Emphasis Type="Italic">x</Emphasis></Subscript>Ga<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>Sb〈Mn〉

Manganese-doped solid solutions In_1–x Ga _x Sb (x = 0.05, 0.1, 0.5, 0.9, 0.95) were synthesized. It was found that, in samples of the compositions In_0.95Ga_0.05Sb〈Mn〉 and In_0.05Ga_0.95Sb〈Mn〉, a homogeneous substitutional solid solution forms, into which manganese-containing clusters are incorporated. The clusters are mainly located at crystal lattice defects—grain boundaries and dislocations. The ferromagnetic properties of the obtained samples at room temperature and higher are caused by clusters Mn_1+x Sb, the effective size of which is about 180–300 nm.     

Crystal structure and conduction of BICUTIVOX

Existence boundaries, structure, and transport parameters were studied for Bi₄V_{2 ? x} Cu _x/2Ti _x/2O_{11 ? x} solid solutions. Doping levels within x = 0.025–0.15 distort the C2/m crystal lattice (this lattice is characteristic of individual the Bi₄V₂O₁₁ phase) and lowers its symmetry to triclinic. The solid solutions with 0.25 ≤ x ≤ 0.30 crystallize in tetragonal space group I4/mmm. High-temperature X-ray diffraction and dilatometry measurements for Bi₄V_{2 ? x} Cu _x/2Ti _x/2O_{11 ? x} (x ≤ 0.35) solid solutions verified the existence of three structural varieties within 298–1023 K. Electrical conductivity of BICUTIVOX was studied by impedance spectroscopy as a function of temperature, composition, and oxygen partial pressure. Equivalent circuits of cells were analyzed. Features of electrical conductivity versus temperature for the structural varieties are noted. Above 873 K, the solid solutions samples with x = 0.05 have the highest conductivity. At lower temperatures, higher conductivities are in the solid solutions that retain the γ phase in the low-temperature region. The dominant oxygen-ion conduction mechanism was discovered in the solid solutions.     

DFT study of small aluminum and boron hydrides: isomeric composition and physical properties

The structure, energetics, and physical properties, including rotational constants, characteristic vibrational temperatures, dipole moment, static polarizability, HOMO-LUMO gap, formation enthalpy and collision diameter of different isomeric forms of atomic Al _n H _m and B _n H _m clusters with n = 1..4 and all feasible m numbers are studied within the density functional theory framework. The search of isomer structures has been accomplished using multistep hierarchical algorithm. Temperature dependences of thermodynamic functions (enthalpy, entropy and specific heat capacity) have been calculated both for the individual isomers and for the ensemble of isomers with equilibrium composition for each class of clusters, taking into account the anharmonicity of cluster vibrations and the contribution of excited electronic states. The prospects of the application of small atomic Al _n H _m and B _n H _m clusters as the components of energetic and hydrogen storage materials are also discussed.     

First principle study of magnetic and electronic properties of single X (X = Al,Si) atom added to small carbon clusters (C<Subscript> <Emphasis Type="Italic">n</Emphasis> </Subscript>X, <Emphasis Type="Italic">n</Emphasis> = 2–10)

In this paper, the magnetic and electronic properties of single aluminum and silicon atom added to small carbon clusters (C_nX; X = Al, Si; n = 2–10) are studied in the framework of generalized-gradient approximation using density functional theory. The calculations were performed for linear, two dimensional and three dimensional clusters based on full-potential local-orbital (FPLO) method. The total energies, HOMO–LUMO energy gap and total magnetic moments of the most stable structures are presented in this work. The calculations show that C_nSi clusters have more stability compared to C_nAl clusters. In addition, our magnetic calculations were shown that the C_nAl isomers are magnetic objects whereas C_nSi clusters are nonmagnetic objects.     

Spatial Structure,Electron Energy Spectrum,and Growth of HfSi<Stack><Subscript><Emphasis Type="Italic">n</Emphasis></Subscript><Superscript>−</Superscript></Stack> Clusters (<Emphasis Type="Italic">n</Emphasis> = 6–20)

The optimized spatial structure and calculated electronic spectra of anionic clusters HfSi _n ^? (n = 6–20) are presented. The calculations have been performed by the density functional theory method. By comparing the calculated and available experimental data, the spatial structures of the clusters detected in the experiment have been determined. It has been established that the formation of endohedral structures begins with n = 12, when a stable structure of a prism encapsulating a hafnium atom is formed. Clusters with n = 12 and 16 have increased stability and are basic for the construction of clusters with a close number of silicon atoms.     

Theoretical investigation on the geometries and electronic properties of cesium–silicon CsSi<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 2–12) clusters

The structures, relative stabilities, and electronic properties of pure Si _n and Cs-doped silicon clusters (n = 2–12) are systematically investigated using the density functional theory at the B3LYP level. The optimized structures indicated that the lowest-energy structures of CsSi _n are similar to those of pure Si _n clusters and prefer the 3-dimensional configuration for n = 3–12. The relative stabilities of CsSi _n clusters are analyzed based on the averaged binding energy, fragmentation energy, second-order energy difference, and HOMO–LUMO energy gap. It is found that CsSi₆ and CsSi₉ are the magic clusters, and the doping of Cs atom reduces the chemical stabilities of Si _n frame. The Mulliken population analysis pointed out that the charges in the corresponding CsSi _n clusters always transfer from Cs atom to Si _n host in the range of 0.80–0.91 electron. In addition, the partial density of states, infrared, and Raman spectra is discussed.     

Crystal Chemistry of Lithium Intermetallic Compounds: A Survey

The structural chemistry of lithium intermetallic compounds that are formed in Li–М binary systems where М = Ca, Sr, Ba, Mg, Zn, Cd, and Hg is surveyed. It is for the first time that the crystal structures of intermetallic compounds are classified in terms of polyhedral precursor metal clusters (in the program package ToposPro). The precursor metal clusters of crystal structures are identified using the algorithms of partitioning structural graphs into cluster structures and via the design of the basal 3D network of the structure in the form of a graph whose nodes correspond to the positions of the centers of precursor clusters. Tetrahedral precursor metal clusters M₄ are identified for the crystal structures LiZn₃-oC4, LiMg₃-hP2, LiCd₃-hP2, LiHg₃-hP8, (LiMg₃)(Li₂Mg₂)-tI16, Li₂Zn₂-cF16, Li₂Cd₂-cF16, Li₂Hg₂-cP2, Li₃Cd-cF4, and Li₃Hg-cF16; tetrahedral metal clusters M₄ are found for the framework structures with spacer atoms Sr(Li₂Sr₂)-tP20, Ca₂(Li₄)-cF24, and Ca₂(Li₄)-cP12; tetrahedral metal clusters M₄ and rings M₆, for framework structures Ba₃Li₂(Li₁₀)-hP30 and Ba₃Li₂(Li₄In₆)-hP30; icosahedral metal clusters M13 for the framework structure Li(Zn₁₃)-cF112; bilayer tetrahedral metal clusters 0@М₄@M₂₂ for the framework structure Li₂₃Sr₆-cF116; and deltahedra М₁₇ and deltahedra М₃₀, for framework structures Sr₄Li₁₄ [Sr(Sr₄Li₁₂)] [(Sr₂ (Sr₈Li₁₈)]-tI252 and Ba₄Li₁₄ [Ba(Ba₄Li₁₂)][(Ba₂ (Ba₈Li₁₈)]-tI252. The scenario of crystal structure self-assembly from precursor metal clusters S₃⁰ in intermetallic compounds is reconstituted as: primary chain S₃¹→ microlayer S₃²→ microframework S₃³.     

Electrical percolation in micellar sodium dodecyl sulfate solutions. a phenomenological consideration

Effects of electrical percolation accompanying variations in overall surfactant concentration с have been studied by the example of micellar sodium dodecyl sulfate solutions. It has been found that, in the studied concentration range of 0.001–1.2 M, dependences of electrical conductivity K on c may exhibit at least three break points, with the dK/dc derivatives changing in the vicinities of these points. At two of these points, which are reliably identified and correspond to critical micelle concentrations (CMC₁ and CMC₂), they decrease. At the third concentration, lying between CMC₁ and CMC₂, the dK/dc derivative increases. A substantiated assumption has been put forward that this break point, at which the dK/dc derivative increases, results from the clustering of micelles and the appearance of channels with a higher specific conductivity, which is provided by the contribution from the electrical conductivity of the diffuse and dense parts of micelle electrical double layers, upon the formation of clusters. The ionic surfactant concentration that corresponds to the break point at which the dK/dc value increases has been denoted as the critical percolation concentration.     

Specific detection and effective inhibition of a single bacterial species <Emphasis Type="Italic">in situ</Emphasis> using peptide mineralized Au cluster probes

Increasingly serious microbial infections call for the development of new simpler methods for the precise diagnosis and specific inhibition of such pathogens. In this work, a peptide mineralized Au cluster probe was applied as a new simplified strategy to both recognize and inhibit a single bacteria species of Staphylococcus aureus (S. aureus) simultaneously. The probes are composed of peptides and Au clusters. Moreover, the peptides specifically target S. aureus cells and the Au clusters provide fluorescent imaging and have an antibacterial effect. These new probes enable the simultaneous specific detection and effective destruction S. aureus cells in situ.     

Geometries,stabilities, electronic and magnetic properties of small aluminum cluster anions doped with cobalt: A density functional theory study

The geometrical structures, relative electronic and magnetic properties of small Al_nCo^– (1 ≤ n ≤ 9) clusters are systematically investigated within the framework of density functional theory at the BPW91 level. The single Co doping can dramatically affect the ground state geometries of the 1 Al_n+1^- clusters. At the same time, the resulting geometries show that the lowest energy Al_nCo^– clusters prefer to be three dimensional structures. Here, the relative stabilities are investigated in terms of the calculated average binding energies, fragmentation energies, and second-order energy differences. Moreover, the result of the highest occupiedlowest unoccupied molecular orbital energy gaps indicates that Al₆Co^– clusters have the highest chemical stability for Al_nCo^– (1 ≤ n ≤ 9) clusters. Furthermore, the natural population analysis reveals that the charges in Al_nCo^– clusters transfer from the Al frames to the Co atom. Additionally, the analyses of the local and total magnetic moments of the Al_nCo^– clusters show that the magnetic effect mainly comes from the Co atom.     

Study on the Geometric and Electronic Structures of Al<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Si<Subscript><Emphasis Type="Italic">m</Emphasis></Subscript> (n = 3, 4, 5; m = 1, 2, 3, 4) Clusters

Genetic algorithm combined with the semi-empirical Hamitonian AM1/PM3 is used to search the low energy isomers of Al _n Si _m (n = 3, 5, m ≤ 3 and n = 4, m ≤ 4) and the charged clusters with 20 and 28 valence electrons. The candidate structures were optimized by the density functional theory PBE0 and B3LYP models with the triply split basis sets including polarization functions. The electronic structures show that Al–Si binary clusters behave like metal clusters. The molecular orbitals accord with that predicted by the jellium model, and the electron localization function shows the valence electrons are delocalized over the entire clusters. The clusters having 20 and 28 valence electrons exhibit pronounced stabilities and large energy gaps. The 20 valence electrons of Al₄Si₂ and Al₃Si₃ ⁺, Al₅Si^? form closed shells 1S ²1P ⁶2S ²1D ¹⁰. Al₄Si₄ and Al₅Si₃ ^? have oblate structures and the P, D, F levels spilt considerably in these clusters. The electron density distributions suggest that doping silicon in the aluminum clusters enhances the stability considerably.     

Electronic Structure and Relative Stabilities of 10- and 12-Vertex. <Emphasis Type="Italic">Closo</Emphasis>and <Emphasis Type="Italic">Nido</Emphasis>-Heteroborane Clusters of Ga,Ge, and As Elements

A DFT method with the B3LYP functional and the 6-311++G(d,p) diffuse basis set is used to predict geometries, relative stabilities, electronic structures, and the bonding of closo- and nido-Ga_mB_n–mH _n ^2? , Ge_mB_n–mH _n ^m?2 , and As_mB_n–mH _n ^{2 m?2} (n = 10, 12 and m = 1, 2) Clusters are obtained by replacing BH with isolobal GaH, GeH⁺, and AsH²⁺ fragments, keeping the same skeleton electron pairs (SEP). Based on the polyhedral skeletal electron pairs theory (PSEPT), closo and nido structures are predicted and can be of significant interest for experimentalists working in the field of heteroboranes. Different cluster stabilities are studied according to Gimarc′s and Williams′ rules, where our calculations show that the monosubstituted clusters deviate from these rules, giving rise to open structures. As₂B₈H _n ²⁺ as 10-vertex structures lead to nido-type clusters, however, Ge_mB_n–mH _n ^m?2 (n = 10, 12 and m = 1, 2) give rise to closo isomers with close energies. All optimized structures exhibit large HOMO–LUMO gaps suggesting a good kinetic stability, thus predicting their isolation and characterization.     

Composition of essential oils of four <Emphasis Type="Italic">Hedychium</Emphasis>species from Vietnam

Background

Vietnam is a country blessed with many medicinal plants widely used as food and for medicinal purposes, and they contain a host of active substances that contribute to health. However, the analysis of chemical constituents of these plant species has not been subject of literature discussion.

Results

In this study, the chemical compositions of essential oils of four Hedychium species, obtained by hydrodistillation, were determined by means of gas chromatography-flame ionization detector (GC-FID) and gas chromatography–mass spectrometry (GC-MS) techniques. Individually, α-pinene (52.5%) and β-pinene (31.8%) were present in the leaf oil of Hedychium stenopetalum Lodd., while linalool (45.2%), (E)-nerolidol (8.7%) and α-pinene (5.0%) were identified in the root. The leaf of Hedychium coronarium J. König was characterized by α-pinene (20.0%), linalool (15.8%), 1,8-cineole (10.7%), α-pinene (10.1%) and α-terpineol (8.6%); while α-pinene (23.6%), α-humulene (17.1%) and β-caryophyllene (13.0%) were identified in the root. Hedychium flavum Roxb., gave oil whose major compounds were α-pinene (22.5%), α-humulene (15.7%) and β-caryophyllene (10.4%) in the leaf; α-humulene (18.9%), β-caryophyllene (11.8%) and α-pinene (11.2%) in the stem, as well as α-pinene (21.8%), linalool (17.5%) and 1,8-cineole (13.5%) in the root. The main constituents of Hedychium ellipticum Buch.-Ham. ex Smith were (E)-nerolidol (15.9%), α-pinene (11.8%) and bornyl acetate (9.2%) in the leaf with 1,8-cineole (40.8%), α-pinene (18.3%) and α-pinene (11.0%) occurring in the root.

Conclusions

Ubiquitous monoterpenes and sesquiterpenes were identified as characteristic markers for Hedychium species. This work is of great importance for the evaluation of Hedychium essential oils grown in Vietnam.

     

Matrix Assisted and/or Laser Desorption Ionization Quadrupole Ion Trap Time-of-Flight Mass Spectrometry of WO<Subscript>3</Subscript> Clusters Formation in Gas Phase. Nanodiamonds,Fullerene, and Graphene Oxide Matrices

The formation of W _x O _y ^+●/-● clusters in the gas phase was studied by laser desorption ionization (LDI) and matrix assisted laser desorption ionization (MALDI) of solid WO₃. LDI produced (WO₃) _n ^{+ ●/- ●} (n = 1-7) clusters. In MALDI, when using nano-diamonds (NDs), graphene oxide (GO), or fullerene (C₆₀) matrices, higher mass clusters were generated. In addition to (WO₃) _n ^-● clusters, oxygen-rich or -deficient species were found in both LDI and MALDI (with the total number of clusters exceeding one hundred ≈ 137). This is the first time that such matrices have been used for the generation of(WO₃) _n ^+●/-● clusters in the gas phase, while new high mass clusters (WO₃) _n ^-● (n = 12-19) were also detected.

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Graphical Abstract

     

Structural,Electronic and Tunable Magnetic Properties of Transition Metal Doped Rh<Subscript>8</Subscript> Cluster from First Principles Calculation

The configurations, electronic and magnetic properties of the Rh₇M (M?=?3d, 4d transition metal) are systematically investigated within the framework of the generalized gradient approximation density-functional theory (DFT-GGA). The results indicated that the ground state structures of Rh₇M (M?=?3d) clusters prefer to a bicapped octahedron configuration, while the Rh₇M (M?=?4d) clusters present a different degree of geometry reconstruction relative to the perfect cubic structure of Rh₈ cluster. In most cases, the doped clusters show relatively higher stability, indicating that impurity atoms could stabilize the pure Rh₈ cluster; the Rh₇M (M?=?3d, 4d) have smaller frontier orbital energy gaps in comparison to the host. The magnetic moments of Rh₇M (M?=?3d, 4d) exhibit a tunable magnetism with range from 3μ_B to 13μ_B and the Fe atom doping enhances the magnetic moment of mixed cluster.     

Palladium clusters Pd<Subscript>4</Subscript>(SR)<Subscript>4</Subscript>(OAc)<Subscript>4</Subscript> and Pd<Subscript>6</Subscript>(SR)<Subscript>12</Subscript> (R = Bu,Ph): Structure and properties

The structures of the Pd₄(SBu)₄(OAc)₄ (I) and Pd₆ (SBu)₁₂ (II) palladium clusters are determined by the X-ray diffraction method. For cluster I: a = 8.650(2), b = 12.314(2), c = 17.659(4) Å, α = 78.03(3)°, β = 86.71(2)°, γ = 78.13(3)°, V = 1800.8(7) ų, ρcalcd = 1.878 g/cm³, space group P \(\bar 1\), Z = 4, N = 3403, R = 0.0468; for structure II: a = 10.748(2), b = 12.840(3), c = 15.233(3) Å, α = 65.31(3)°, β = 70.10(3)°, γ = 72.91(3)°, V = 1767.4(6) ų, ρ calcd = 1.605 g/cm³, space group P \(\bar 1\), Z = 1, N = 3498, R = 0.0729. In cluster I, four Pd atoms form a planar cycle. The neighboring Pd atoms are bound by two acetate or two mercaptide bridges (Pd…Pd 2.95–3.23 Å, Pd…Pd angles 87.15°–92.85°). In cluster II, the Pd atoms form a planar six-membered cycle with Pd···Pd distances of 3.09–3.14 Å, the PdPdPd angles being 118.95°–120.80°. The Pd atoms are linked in pairs by two mercaptide bridges. The formation of clusters I and II in solution is proved by IR spectroscopy and calorimetry. Analogous clusters are formed in solution upon the reaction of palladium(II) diacetate with thiophenol.