Elucidation of the molecular and electronic structures of some magic silver clusters Ag<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 8, 18, 20)

Density functional theory (DFT) calculations were carried out to explore the geometric, spectroscopic, and electronic properties of three magic silver clusters Ag_n (n?=?8, 18, and 20) in detail. The computed results show that the global minima of these clusters are compact, near-spherical structures, while other low-lying isomers exhibit oblate or prolate shapes. Vertical ionization energies for the low-lying isomers were also computed and assigned with respect to available experimental values. Although several isomers were predicted to have similar energies, their electronic and vibrational signatures were quite distinctive, meaning that they could be used as fingerprint signals to distinguish between isomers. In addition, the electronic structures of these systems were explored using the phenomenological shell model. Calculations for the coinage metal clusters M₂₀ (M?=?Cu, Ag, Au) indicated that the structures and properties of the Ag cluster are similar to those of the Cu cluster in that both Cu₂₀ and Ag₂₀ prefer a compact structure whereas Au₂₀ prefers to adopt a tetrahedral form.

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Graphical abstract Shell Orbitals of Ag₈ Cluster

     

Stability and electronic properties of praseodymium-doped silicon clusters PrSin (<Emphasis Type="Italic">n</Emphasis> = 12–21)

The neutral PrSi _n (n = 12–21) species considering various spin configurations were systematically studied using PBE0 and B3LYP schemes in combination with relativistic small-core potentials (ECP28MWB) for Pr atoms and cc-pVTZ basis set for Si atoms. The total energy, growth-pattern, equilibrium geometry, relative stability, hardness, charge transfer, and magnetic moments are calculated and discussed. The results reveal that when n < 20, the ground-state structure of PrSi _n evaluated to be prolate clusters. Starting from n = 20, the ground-state structures of PrSi _n are evaluated to be endohedral cagelike clusters. Although the relative stabilities based on various binding energies and different functional is different from each other, the consensus is that the PrSi₁₃, PrSi₁₆, PrSi₁₈, and PrSi₂₀ are more stable than the others, especially the PrSi₂₀. Analyses of hardness show that introducing Pr into Si _n (n = 12–21) elevates the photochemical sensitivity, especially for PrSi₂₀. Calculated result of magnetic moment and charge transfer shows that the 4f electrons of Pr in the clusters are changed, especially in endohedral structures such as PrSi₂₀, in which one electron transfers from 4f to 5d orbital. That is, the 4f electron of Pr in the clusters participates in bonding. The way to participate in bonding is that a 4f electron transfers to 5d orbital. Although the 4f electron of Pr atom participates in bonding, the total magnetic moment of PrSi _n is equal to that of isolated Pr atom. The charge always transfers from Pr atom to Si _n cluster for the ground state structures of PrSi_n (n = 12–19), but charge transfer is reverse for n ≥ 20. The largest charge transfer for endohedral structure reveals that the bonding between Pr and Si _n is ionic in nature and very strong. The fullerenelike structure of PrSi₂₀ is the most stable among all of these clusters and can act as the building blocks for novel functional nanotubes.     

Theoretical study on the structural,vibrational, and thermodynamic properties of the (Br<Subscript>2</Subscript>GaN<Subscript>3</Subscript>)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–4) clusters

The molecular geometries, vibrational properties, and thermodynamic properties of the clusters (Br₂GaN₃) _n (n = 1–4) were studied at the B3LYP/6-311+G* level. The optimized clusters (Br₂GaN₃) _n (n = 2–4) were all found to possess a cyclic structure consisting of Ga atoms bridged by the α-nitrogen of the azide groups. A discussion of the relationships between the geometrical parameters and the degree of oligomerization n is provided. Features in the IR spectra were assigned by vibrational analysis. Trends in thermodynamic properties with temperature and degree of oligomerization n are discussed. Thermodynamic analysis of the gas-phase reaction showed that the formation of the clusters (Br₂GaN₃) _n (n = 2–4) is thermodynamically favorable considering the enthalpies at 298.2 K. The calculated results for the Gibbs free energies were negative, which indicates that the oligomerizations can occur spontaneously at 298.2 K.     

Probing structure,thermochemistry, electron affinity,and magnetic moment of thulium-doped silicon clusters TmSi<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 3–10) and their anions with density functional theory

The most stable structures and electronic properties of TmSi _n (n?=?3–10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi _n and their anions can be regarded as substituting a Si atom of the ground state structure of Si _n?+?1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi _n (n?=?3–10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi _n (n?=?3–10) and their anions do not participate in bonding. The total magnetic moments of TmSi _n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi _n and their anions has been calculated to examine relative stability.     

A first-principles study of Ni<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Pd<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (n = 1 − 5) clusters

A first-principle investigation of structures and properties of Ni _n Pd _n (n=1-5) clusters is presented. For this study, the linear combination of Gaussian-type orbitals auxiliary density functional theory (LCGTO-ADFT) method has been employed. In order to determine the lowest energy structures, several isomers in different spin multiplicities were studied, for each cluster size. Initial structures, for which successive geometry optimization was computed without any constrain, were taken along Born–Oppenheimer molecular dynamics (BOMD) trajectories. To discriminate between minima and transition state structures, harmonic frequency analyses were performed at the optimized structures. Ground state structures, bond lengths, harmonic frequencies, dissociation energy, ionization potential, electron affinity and spin density plots are presented. This work demonstrates, that the Pd atoms prefer to allocate on the surface of the cluster structures whose core is formed by the 3d TM atoms type. Moreover, it has been observed that the ground-state structure spin multiplicity increases as the system size grows. The results of this study contribute to gain insight into how structures and energy properties change with cluster size in bimetallic Pd-based alloys.     

Computational investigation on MB<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (M = Li-Cs,Be-Ba,Sc-La and Ti; <Emphasis Type="Italic">n</Emphasis> = 28 and 38)

Differing from the weakly antiaromatic B₈₀ buckyball, the medium-sized C ₁–B₂₈ and D _2h –B₃₈, as well as their mono- to tetra-anions, are highly aromatic, as indicated by the negative nucleus-independent chemical shifts (NICSs) at their cage centers. The interior cavities and high aromaticity of the B₂₈ and B₃₈ cages render them very promising hosts to accommodate diverse metal atoms. Accordingly, we carried out systematic density functional theory (DFT) computations on the structures, stabilities and electronic properties of metalloborofullerenes MB _n (M?=?Li, Na, K, Rb, Cs, Be, Mg, Ca, Sr, Ba, Sc, Y, La and Ti; n?=?28 and 38). Among them, besides the recently reported M@B₃₈(M?=?Sc, Y and Ti) [Lu et al. (2015) Phys Chem Chem Phys 17:20897–20902], Ti@B₂₈ and M@B₃₈ (M?=?Ca and La) also favor endohedral structures with large binding energies, and are suggested promising targets for experimental applications. Note that Ti@B₂₈ is the first endohedral derivative based on the new B₂₈ fullerene, and La@B₃₈ features the largest metal size inside a B₃₈ cage thus far. These endohedral derivatives, as exemplified by Ca@B₃₈, may exhibit σ and π double aromaticity over the whole cage surface, indicating their considerable stability. In contrast, the other metals prefer to reside at the exterior cage surface, due mainly to the mismatch of their sizes with the boron cages, though the size match is not the only factor to determine their doping form. Furthermore, the infrared absorption spectra and ¹¹B nuclear magnetic resonance spectra of the three new M@B _n complexes were computed to assist future experimental characterization.

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Graphical Abstract Putting more metals into medium-sized boron cages!

     

Density functional theory study on (LiNH<Subscript>2</Subscript>)<Subscript>n</Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–5) clusters

Geometrical structures and relative stabilities of (LiNH₂)_n (n = 1–5) clusters were studied using density functional theory (DFT) at the B3LYP/6-31G* and B3LYP/6-31++G* levels. The electronic structures, vibrational properties, N–H bond dissociation energies (BDE), thermodynamic properties, bond properties and ionization potentials were analyzed for the most stable isomers. The calculated results show that the Li–N and Li–Li bonds can be formed more easily than those of the Li–H or N–H bonds in the clusters, in which NH₂ is bound to the framework of Li atomic clusters with fused rings. The average binding energies for each LiNH₂ unit increase gradually from 142 kJ mol⁻¹ up to about 180 kJ mol⁻¹ with increasing n. Natural bond orbital (NBO) analysis suggests that the bonds between Li and NH₂ are of strong ionicity. Three-center–two-electron Li–N–Li bonding exists in the (LiNH₂)₂ dimer. The N–H BDE values indicate that the change in N–H BDE values from the monomer a1 to the singlet-state clusters is small. The N–H bonds in singlet state clusters are stable, while the N–H bonds in triplet clusters dissociate easily. A study of their thermodynamic properties suggests that monomer a1 forms clusters (b1, c1, d2 and e1) easily at low temperature, and clusters with fewer numbers of rings tend to transfer to ones with more rings at low temperature. E _g, E _HOMO and E _av decrease gradually, and become constant. Ring-like (LiNH₂)_3,4 clusters possess higher ionization energy (VIE) and E _g, but lower values of E _HOMO. Ring-like (LiNH₂)_3,4 clusters are more stable than other types. A comparison of structures and spectra between clusters and crystal showed that the NH₂ moiety in clusters has a structure and spectral features similar to those of the crystal.     

Stereoselective Inhibition of Cholesterol Esterase by Enantiomers of <Emphasis Type="Italic">exo</Emphasis>- and <Emphasis Type="Italic">endo</Emphasis>-2-Norbornyl-<Emphasis Type="Italic">N</Emphasis>–<Emphasis Type="Italic">n</Emphasis>-butylcarbamates

Four stereoisomers of 2-norbornyl-N–n-butylcarbamates are characterized as the pseudo substrate inhibitors of cholesterol esterase. Cholesterol esterase shows enantioselective inhibition for enantiomers of exo- and endo-2-norbornyl-N–n-butylcarbamates. For the inhibitions by (R)-(+)- and (S)-(−)-exo-2-norbornyl-N–n-butylcarbamates, the R-enantiomer is 6.8 times more potent than the S-enantiomer. For the inhibitions by (R)-(+)- and (S)-(−)-endo-2-norbornyl-N–n-butyl-carbamates, the S-enantiomer is 4.6 times more potent than the R-enantiomer. The enzyme-inhibitor complex models have been proposed to explain these different enantioselectivities.     

<Emphasis Type="Italic">Cis</Emphasis>–<Emphasis Type="Italic">trans</Emphasis> photoisomerization properties of GFP chromophore analogs

The photoswitching behaviour of the green fluorescent protein (GFP) chromophore and its analogs opens up exciting horizons for the engineering and development of molecular devices for high sensitivity in vivo studies. In this work we present the synthesis and photophysical study of four GFP chromophore analogs belonging to butenolide and pyrrolinone classes. These chromophores possess an intriguing photoinduced cis–trans isomerization mechanism. Stereochemical structural assignment was unambiguously performed by 1D Nuclear Overhauser Effect NMR measurements. The spectroscopic properties of both cis and trans isomers were studied, and photoconversion quantum yield for cis–trans isomerization was assessed to be in the 0.1–0.4 range. Finally, the ³J_C,H coupling constant in the ¹³C–C=C–H motif was in excellent agreement with theoretical DFT calculations, thus providing a further confirmation of cis–trans photoisomerization of the structurally analog GFP chromophore.     

Well-defined linear Au<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 2–4) chains encapsulated in SWCNTs: a DFT study

One-dimensional (1D) gold nanostructures have been extensively studied due to their potential applications in nanoelectronic devices. Using first-principles calculations, composites consisting of a well-defined linear Au _n (n?=?2–4) chain encapsulated in a (9,0) single-walled carbon nanotube (SWCNT) were studied. The translational energy barrier of a single Au atom in a (9,0) SWCNT was found to be 0.03 eV. This low barrier guaranteed the formation of Au _n @ (9,0) SWCNT (n?=?1–4) composites. Bond lengths, differential charge densities, and electronic band structures of the composites were studied. The average Au–Au bond lengths in the composites were found to be almost the same as those in the corresponding free-standing linear Au _n . The average bond length increased as the number of Au atoms increased. Charge transfer in all of these composites was slight, although a few valence electrons were transferred from the (9,0) SWCNT and the Au chains to intercalations. The conductivities of the encapsulated linear Au _n (n?=?2–4) chains were enhanced to some extent by encapsulating them in the SWCNT.     

Brood cell size of <Emphasis Type="Italic">Apis</Emphasis> <Emphasis Type="Italic">mellifera</Emphasis> modifies the reproductive behavior of <Emphasis Type="Italic">Varroa</Emphasis> <Emphasis Type="Italic">destructor</Emphasis>

We undertook a field study to determine whether comb cell size affects the reproductive behavior of Varroa destructor under natural conditions. We examined the effect of brood cell width on the reproductive behavior of V. destructor in honey bee colonies, under natural conditions. Drone and worker brood combs were sampled from 11 colonies of Apis mellifera. A Pearson correlation test and a Tukey test were used to determine whether mite reproduction rate varied with brood cell width. Generalized additive model analysis showed that infestation rate increased positively and linearly with the width of worker and drone cells. The reproduction rate for viable mother mites was 0.96 viable female descendants per original invading female. No significant correlation was observed between brood cell width and number of offspring of V. destructor. Infertile mother mites were more frequent in narrower brood cells.     

Functional expression of the lipase gene Lip2 of <Emphasis Type="Italic">Pleurotus</Emphasis> <Emphasis Type="Italic">sapidus</Emphasis> in <Emphasis Type="Italic">Escherichia</Emphasis> <Emphasis Type="Italic">coli</Emphasis>

The lipase Lip2 of the edible basidiomycete, Pleurotus sapidus, is an extracellular enzyme capable of hydrolysing xanthophyll esters with high efficiency. The gene encoding Lip2 was expressed in Escherichia coli TOP10 using the gene III signal sequence to accumulate proteins in the periplasmatic space. The heterologous expression under control of the araBAD promoter led to the high level production of recombinant protein, mainly as inclusion bodies, but partially in a soluble and active form. A fusion with a C-terminal His tag was used for purification and immunochemical detection of the target protein. This is the first example of a heterologous expression and periplasmatic accumulation of a catalytically active lipase from a basidiomycete fungus.     

Pistil-function breakdown in a new <Emphasis Type="Italic">S</Emphasis>-allele of European pear, <Emphasis Type="Italic">S</Emphasis><Subscript><Emphasis Type="Italic">21</Emphasis></Subscript>°, confers self-compatibility

European pear exhibits RNase-based gametophytic self-incompatibility controlled by the polymorphic S-locus. S-allele diversity of cultivars has been extensively investigated; however, no mutant alleles conferring self-compatibility have been reported. In this study, two European pear cultivars, ‘Abugo’ and ‘Ceremeño’, were classified as self-compatible after fruit/seed setting and pollen tube growth examination. S-genotyping through S-PCR and sequencing identified a new S-RNase allele in the two cultivars, with identical deduced amino acid sequence as S ₂₁ , but differing at the nucleotide level. Test-pollinations and analysis of descendants suggested that the new allele is a self-compatible pistil-mutated variant of S ₂₁ , so it was named S ₂₁ °. S-genotypes assigned to ‘Abugo’ and ‘Ceremeño’ were S ₁₀ S ₂₁ ° and S ₂₁ °S ₂₅ respectively, of which S ₂₅ is a new functional S-allele of European pear. Reciprocal crosses between cultivars bearing S ₂₁ and S ₂₁ ° indicated that both alleles exhibit the same pollen function; however, cultivars bearing S ₂₁ ° had impaired pistil-S function as they failed to reject either S ₂₁ or S ₂₁ ° pollen. RT-PCR analysis showed absence of S ₂₁ °-RNase gene expression in styles of ‘Abugo’ and ‘Ceremeño’, suggesting a possible origin for S ₂₁ ° pistil dysfunction. Two polymorphisms found within the S-RNase genomic region (a retrotransposon insertion within the intron of S ₂₁ ° and indels at the 3′UTR) might explain the different pattern of expression between S ₂₁ and S ₂₁ °. Evaluation of cultivars with unknown S-genotype identified another cultivar ‘Azucar Verde’ bearing S ₂₁ °, and pollen tube growth examination confirmed self-compatibility for this cultivar as well. This is the first report of a mutated S-allele conferring self-compatibility in European pear.     

Carbohydrate and Ethane Release with <Emphasis Type="Italic">Erwinia carotovora</Emphasis> Subspecies <Emphasis Type="Italic">betavasculorum</Emphasis><Emphasis Type="Italic">–</Emphasis>Induced Necrosis

Erwinia carotovora subspecies betavasculorum, also known as E. betavasculorum and Pectobacterium betavasculorum, is a soil bacterium that has the capacity to cause root rot necrosis of sugarbeets. The qualitatively different pathogenicity exhibited by the virulent E. carotovora strain and two avirulent strains, a Citrobacter sp. and an Enterobacter cloacae, was examined using digital analysis of photographic evidence of necrosis as well as for carbohydrate, ethane, and ethylene release compared with uninoculated potato tuber slices. Visual scoring of necrosis was superior to digital analysis of photographs. The release of carbohydrates and ethane from potato tuber slices inoculated with the soft rot necrosis-causing Erwinia was significantly greater than that of potato tuber slices that had not been inoculated or that had been inoculated with the nonpathogenic E. cloacae and Citrobacter sp. strains. Interestingly, ethylene production from potato slices left uninoculated or inoculated with the nonpathogenic Citrobacter strain was 5- to 10-fold higher than with potato slices inoculated with the pathogenic Erwinia strain. These findings suggest that (1) carbohydrate release might be a useful measure of the degree of pathogenesis, or relative virulence; and that (2) bacterial suppression of ethylene formation may be a critical step in root rot disease formation.     

Rapid induction of <Emphasis Type="Italic">Agrobacterium</Emphasis> <Emphasis Type="Italic">tumefaciens</Emphasis>-mediated transgenic roots directly from adventitious roots in <Emphasis Type="Italic">Panax</Emphasis> <Emphasis Type="Italic">ginseng</Emphasis>

Root segments from seedlings of Panax ginseng produced adventitious roots directly when cultured on 1/2 MS solid medium lacking NH₄NO₃ and containing 3.0 mg l⁻¹ IBA. Using this adventitious root formation, we developed rapid and efficient transgenic root formation directly from adventitious root segments in P. ginseng. Root segments were co-cultivated with Agrobacterium tumefaciens (GV3101) caring β-glucuronidase (GUS) gene. Putative transgenic adventitious roots were formed directly from root segments on medium with 400 mg l⁻¹ cefotaxime and 50 mg l⁻¹ kanamycin. Kanamycin resistant adventitious roots were selected and proliferated as individual lines by subculturing on medium with 300 mg l⁻¹ cefotaxime and 50 mg l⁻¹ kanamycin at two weeks subculture interval. Frequency of transient and stable expression of GUS gene was enhanced by acetosyringon (50 mg l⁻¹) treatment. Integration of transgene into the plants was confirmed by the X-gluc reaction, PCR and Southern analysis. Production of transgenic plants was achieved via somatic embryogenesis from the embryogenic callus derived from independent lines of adventitious roots. The protocol for rapid induction of transgenic adventitious roots directly from adventitious roots can be applied for a new Agrobacterium tumefaciens-mediated genetic transformation protocol in P. ginseng.     

<Emphasis Type="Italic">Carex</Emphasis> × <Emphasis Type="Italic">involuta</Emphasis> and <Emphasis Type="Italic">Carex juncella</Emphasis> in the flora of Slovakia

The paper brings information on an isolated occurrence and morphological characters of Carex × involuta and C. juncella populations in the Vel’ká Fatra Mts. Their presence has been known neither from the territory of Slovakia nor from the whole Western Carpathians till now.     

New family of pectinase genes <Emphasis Type="Italic">PGU1</Emphasis>b–<Emphasis Type="Italic">PGU3b</Emphasis> of the pectinolytic yeast <Emphasis Type="Italic">Saccharomyces bayanus</Emphasis> var. <Emphasis Type="Italic">uvarum</Emphasis>

Using yeast genome databases and literature data, we have conducted a phylogenetic analysis of pectinase PGU genes from Saccharomyces strains assigned to the biological species S. arboricola, S. bayanus (var. uvarum), S. cariocanus, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus, and hybrid taxon S. pastorianus (syn. S. carlsbergensis). Single PGU genes were observed in all Saccharomyces species, except S. bayanus. The superfamily of divergent PGU genes has been documented in S. bayanus var. uvarum for the first time. Chromosomal localization of new PGU1b, PGU2b, and PGU3b genes in the yeast S. bayanus var. uvarum has been determined by molecular karyotyping and Southern hybridization.     

<Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation of <Emphasis Type="Italic">Codonopsis lanceolata</Emphasis> using the <Emphasis Type="Italic">γ-TMT</Emphasis> gene

Efficient transformation of leaf disc-derived callus of Codonopsis lanceolata was obtained using Agrobacterium tumefaciens strain LBA4404 harboring a binary vector, pYBI121, that carries the neomycin phosphotransferase (npt II) gene as a selectable marker. The green shoots recovered from agroinfected explants on selection medium (containing 0.1 mg/l α-naphthaleneacetic acid (NAA), 1 mg/l 6-benzylaminopurine (BAP), 100 mg/l kanamycin, and 250 mg/l cefotaxime) were rooted on Murashige and Skoog (MS) medium supplemented with 2 mg/l IBA and 10 mg/l kanamycin. To optimize the transformation conditions, several factors were assessed, including the co-cultivation period, the duration of pre- and post-culture in darkness and light, the kanamycin concentration, and the Agrobacterium densities. We produced transgenic Codonopsis lanceolata overexpressing γ-tocopherol methyltransferase (γ-TMT) by this protocol. Moreover, the α-tocopherol content of the plants was enhanced by the overexpression of this gene. Bimal Kumar Ghimire and Eun Soo Seong contributed equally to this work.     

Cryopreservation of cell suspension cultures of <Emphasis Type="Italic">Taxus</Emphasis> × <Emphasis Type="Italic">media</Emphasis> and <Emphasis Type="Italic">Taxus floridana</Emphasis>

Different lines of cell suspension cultures of Taxus × media Rehd. and Taxus floridana Nutt. were cryopreserved with a two-step freezing method using a simple and inexpensive freezing container instead of a programmable freezer. Four to seven days old suspension cell cultures were precultured in growth medium supplemented with 0.5 M mannitol for 2 d. The medium was then replaced with cryoprotectant solution (1 M sucrose, 0.5 M glycerol and 0.5 M dimethylsulfoxide) and the cells incubated on ice for 1 h. Before being plunged into liquid nitrogen, cells were frozen with a cooling rate of approximately −1 °C per min to −80 °C. The highest post-thaw cell viability was 90 %. The recovery was line dependent. The cryopreservation procedure did not alter the nuclear DNA content of the cell lines. The results indicate that cryopreservation of Taxus cell suspension cultures using inexpensive freezing container is possible.