Elementary Structural Units Research Articles

Quasi-stable structures in equilibrium dense bismuth melt: Experimental and first principles theoretical studies

Near the melting temperature, equilibrium bismuth melt is characterized by structural features that are absent in equilibrium monatomic simple liquids. In the present work, the structure of bismuth melt is studied by X-ray diffraction experiments and quantum chemical calculations. The presence of quasi-stable structures in the melt has been found, the lifetime of which exceeds the structural relaxation time of this melt. It is shown that these structures are characterized by a low degree of ordering and spatial localisation. It was found that up to 50% of the atoms in the melt can be involved in the formation of these structures. The elementary structural units of these structures are triplets of regular geometry with the characteristic lengths 3.25 Å and 4.7 Å as well as with the characteristic angles 45∘ and 90∘. The characteristic lengths of these triplets are fully consistent with correlation lengths associated with the short-range order in bismuth melt.

Water-Soluble Ionic Metal-Organic Polyhedra as a Versatile Platform for Enzyme Bio-immobilization.

Metal-organic polyhedra (MOPs) can act as elementary structural units for the design of modular porous materials; however, their association with biological systems remains greatly restricted by their typically low stabilities and solubilities in water. Herein, we describe the preparation of novel MOPs bearing either anionic or cationic groups and exhibiting a high affinity for proteins. Simple mixing of the protein bovine serum albumin (BSA) and ionic MOP aqueous solutions resulted in the spontaneous formation of MOP-protein assemblies, in a colloidal state or as solid precipitates depending on the initial mixing ratio. The versatility of the method was further illustrated using two enzymes, catalase and cytochrome c, with different sizes and isoelectric points (pI's) below and above 7. This mode of assembly led to the high retention of catalytic activity and enabled recyclability. Furthermore, the co-immobilization of cytochrome c with highly charged MOPs resulted in a substantial 44-fold increase of its catalytic activity.

A Mini-Review on the Synthesis of Pyrazinoindole: Recent Progress and Perspectives

: The diverse library of biologically active organic compounds is composed majorly of heterocyclic compounds. Nature provides a variety of pharmacologically active compounds consisting of N-heterocycle motif, such as Noscapine (anti-cancer), Morphine (analgesic), Chelerythrine (antibacterial), etc. which are the elementary structural units of marketed drugs in the present era. One such “N-heterocyclic” promising building block which has gained the attention of chemists is Pyrazinoindoles and the inflating interest in this moiety is a result of the three-fused heterocyclic ring structure subsuming an indolic nucleus in it. Fused-polycyclic structural core is necessary to synthesize potential multi-functional drugs, which is evident from indole (an example of fused five and sixmembered ring structure) being an exemplary and established privileged template in medicinal chemistry. In the literature, Pyrazino-fused indoles have been found documented regarding their biological activities and therapeutic uses, particularly as antifungal, antibacterial, serotonergic receptor inhibitor, central nervous system depressants, anticonvulsants, antihistaminic, protein kinase C inhibitors, anti-depressants and so on. Although various synthesis strategies are available in the literature, yet the medical relevance of the Pyrazinoindoles demands the development of versatile and simple novel methodologies. This review features a comprehensive overview of the recent developments in synthetic approaches and therapeutic applications of Pyrazinoindoles based scaffolds.

Formation process and pervaporation of high aluminum ZSM-5 zeolite membrane with fluoride-containing and organic template-free gel

The formation progress of the high aluminum ZSM-5 zeolite membrane was investigated and characterized with the organic template-free and fluoride-containing initial synthesis gel. The nano spherical Silicalite-1 seed crystals were dissolved into amorphous by the fluoride-containing precursor synthesis gel. The amorphous contained elementary structural units (TO4) and isolated five-membered ring structure of MFI zeolites. These were retained to provide the nucleation sites for high aluminum ZSM-5 zeolite. The ZSM-5 zeolite nucleus was grown into fine needle-like ZSM-5 zeolites, which were gradually grown into twin crystals, aggregation and compact ZSM-5 zeolites layer on the support without the organic template initial synthesis gel. In addition, the high aluminum ZSM-5 zeolite membranes kept the identical morphology and structure for separation of high concentration acetic acid (H2O/HAc) or inorganic acid (1 M H2SO4) aqueous mixtures by XRD, SEM and NMR characterization. Furthermore, the membrane had a good dehydration performance and acid-stability by pervaporation. The flux and separation factor of the membrane for 10 wt% H2O/HAc mixtures were 0.98 kg∙m−2∙h−1 and 3200 at 348 K, respectively.

Recurring Patterns and Blueprints of Industrial Symbioses as Structural Units for an IT Tool

Industrial Symbiosis (IS) deals with the set-up of advanced circular/cascading systems, in which the energy and material flows are prolonged for multiple material and energetic (re-)utilization within industrial systems. To facilitate the technology-enabling environment of IS systems, this work deals with the identification of recurring patterns in IS systems of specific IS case studies and deduction of elementary blueprints and structural units, setting an initial cornerstone to pool and synthesize existing IS knowledge and to deploy this knowledge base in an Information Technology (IT)-supported IS tool, which would remarkably advance the scope of action and development of IS systems. An explorative cross-case analysis was conducted by investigating 80 IS case studies in depth in order to illuminate recurring (key) patterns in IS systems by generalizing and abstracting IS main structures, compositions, resource exchange activities and measures. It has been shown that similar IS sectoral partnerships and resource exchanges have recurrently formed in different regions and hence, generalizable patterns can be deduced. This study identified common IS compositions, sector clusters and key/core/anchor entities and synthesized a content basis for a database of an IS resource exchange catalog based on existing/available IS information, which can be used in an IT-supported IS tool. It contains information of specific IS resource exchanges, broken down by industrial sectors, differentiating providing and receiving sectors and which respective exchanged waste flows were processed into which secondary material/product. Once this fundamental information/data base is incorporated and applied in an IT-supported IS tool, it enables the facilitated recommendation of potential IS partners and IS actions to optimize existing IS cases or to initiate IS development. Especially, first IS germ cells of (key) entities can be derived and connected to each other considering individual circumstances and (geographical) business environments.

Phonon traces in glassy vibrations

A numerical approach, based on a local comparative projectional analysis onto symmetry modes of elementary structural units of glasses and their crystalline counterparts, is developed and used for the analysis of atomic vibrations in glasses in terms of phonons for the entire frequency range. The results of such an analysis shed light on the origin of the modes in the controversial low-frequency range, including the boson-peak region. Comparative analyses undertaken for glass, lattice-glass, and polycrystalline models reveal the role of different types of disorder in atomic vibrations.

Comparison of Two Elementary Nanomembranes Cells for Gas Mixture Separation Problem

In this paper we have considered two versions of elementary cells for creating a nanomembrane, which will be used to separate natural gas into different gas components. Calculated trajectories of helium atoms and methane molecules interacting with elementary structural units of the membrane are presented. The model is based on a discrete approach to describe the interaction of a structure with atoms and molecules.

Identification of the elementary structural units of the DNA damage response

Histone H2AX phosphorylation is an early signalling event triggered by DNA double-strand breaks (DSBs). To elucidate the elementary units of phospho-H2AX-labelled chromatin, we integrate super-resolution microscopy of phospho-H2AX during DNA repair in human cells with genome-wide sequencing analyses. Here we identify phospho-H2AX chromatin domains in the nanometre range with median length of ∼75 kb. Correlation analysis with over 60 genomic features shows a time-dependent euchromatin-to-heterochromatin repair trend. After X-ray or CRISPR-Cas9-mediated DSBs, phospho-H2AX-labelled heterochromatin exhibits DNA decondensation while retaining heterochromatic histone marks, indicating that chromatin structural and molecular determinants are uncoupled during repair. The phospho-H2AX nano-domains arrange into higher-order clustered structures of discontinuously phosphorylated chromatin, flanked by CTCF. CTCF knockdown impairs spreading of the phosphorylation throughout the 3D-looped nano-domains. Co-staining of phospho-H2AX with phospho-Ku70 and TUNEL reveals that clusters rather than nano-foci represent single DSBs. Hence, each chromatin loop is a nano-focus, whose clusters correspond to previously known phospho-H2AX foci.

Cooperation and competition between halogen bonding and van der Waals forces in supramolecular engineering at the aliphatic hydrocarbon/graphite interface: position and number of bromine group effects.

Herein, the photophysical properties of two π-conjugated thienophenanthrene derivatives (6,9- and 5,10-DBTD) are reported. Their self-assembled monolayers in aliphatic hydrocarbon solvents under different concentrations were investigated by scanning tunneling microscopy on a graphite surface. The STM results revealed that the self-assembled structures of the two geometrical isomers exhibited absolutely different behaviors. At the aliphatic solvent/graphite interface, 6,9-DBTD produced almost a single stable coassembled linear structure, except for that with n-tridecane as the solvent. However, the self-assembly of 5,10-DBTD showed structural diversity, and it presented a gradient variety through increasing the chain length of the aliphatic solvents as well as the solution concentration. All ordered self-assembled adlayers critically depend on not only the interchain van der Waals (vdW) interactions, but also on multiple intermolecular interactions, including BrO[double bond, length as m-dash]C and BrS hetero-halogen bonds, homo-BrBr interactions, and HBr and HO hydrogen bonds. We proposed that the cooperation and competition of the intermolecular interactions involving a Br atom and interchain vdW forces induce this structural variety. Density functional theory calculations support to unravel the different elementary structural units based on halogen bonds and hydrogen bonds and were useful tools to dissect and explain the formation mechanism.

Behavior of sodium borosilicate glasses under compression using molecular dynamics.

We have performed classical molecular dynamics simulations in order to study the changes under compression in the local and medium range structural properties of three sodium borosilicate glasses with varying sodium content. These glasses have been isostatically compressed up to 20 GPa and then decompressed in order to analyze the different mechanisms that affect densification, alongside with the permanent modifications of the structure after a full compression/decompression cycle. The results show that the atomic packing is the prominent characteristic that governs the amount of densification in the glass, as well as the setup of the permanent densification. During compression, the bulk modulus increases linearly up to approximately 15 GPa and more rapidly for higher pressures, a behavior which is reflected on the rate of increase of the average coordination for B and Na. Radial distribution functions at different pressures during the cycle help to quantify the amount of distortions in the elementary structural units, with a pronounced shortening of the Na-Na and Na-O bond lengths during compression. A subsequent decomposition of the glassy matrix into elementary Voronoi volumes verifies the high compressibility of Na-rich regions.

Molecular architecture of silk fibroin of Indian golden silkmoth, Antheraea assama.

The golden silk spun by Indian golden silkmoth Antheraea assama, is regarded for its shimmering golden luster, tenacity and value as biomaterial. This report describes the gene coding for golden silk H-fibroin (AaFhc), its expression, full-length sequence and structurally important motifs discerning the underlying genetic and biochemical factors responsible for its much sought-after properties. The coding region, with biased isocodons, encodes highly repetitious crystalline core, flanked by a pair of 5′ and 3′ non-repetitious ends. AaFhc mRNA expression is strictly territorial, confined to the posterior silk gland, encoding a protein of size 230 kDa, which makes homodimers making the elementary structural units of the fibrous core of the golden silk. Characteristic polyalanine repeats that make tight β-sheet crystals alternate with non-polyalanine repeats that make less orderly antiparallel β-sheets, β-turns and partial α-helices. Phylogenetic analysis of the conserved N-terminal amorphous motif and the comparative analysis of the crystalline region with other saturniid H-fibroins reveal that AaFhc has longer, numerous and relatively uniform repeat motifs with lower serine content that assume tighter β-crystals and denser packing, which are speculated to be responsible for its acclaimed properties of higher tensile strength and higher refractive index responsible for golden luster.

Thematic integration of spatial data on natural landscape elements in GIS

Three different types of integration of spatial data on natural landscape components are introduced: spatial, geographic, and thematic. Thematic integration is the process of combining data carried out on the basis of the integrated hierarchical genetic classification of natural landscapes-systems. Natural landscape-systems are regarded as elementary structural units of the earth’s landscape envelope comprised of interacting elements (basic ones – rock, air, waters, and living organisms, and derivative one – soil) with relatively homogenous genetic properties. The result of the thematic integration is represented in GIS as one polygon spatial data layer with joined table of attribute data. The layer produces the systemic landscape maps, namely maps of landscapes of different hierarchical levels and maps of natural landscape component properties. Currently the concept, technology, and tools of the thematic integration of spatial data on natural landscape components are tested and developed in the prosess of landscape mapping of Saratov oblast, Russia. Scale of the basic topographic map, which was used, is 1 : 1500 000.

Development of structural element precedent of technological process in computer-aided design

Based on the methodology of building of the intelligent system of TP design, a new approach to the transformation of information on structural and technological characteristics of the part and of 3D part model and representation of it in the form of elementary constructive modules structural units of a surface to form automatically alternative TP variants on a complex of qualitative and quantitative criteria. Each constructive surface module is represented in the database of module CAM of the intelligent system for constructing TP with records of all possible transitions.

Impact of Alkaline Cement-Dust Pollution on BorealPinus sylvestrisForest Communities: A Study at the Bryophyte Synusiae Level

The elementary structural units where changes of plant communities come about are synusiae and studies of successional processes induced by external factors should focus on that scale. Synusia is a structural part of a plant community inhabiting a special microhabitat, with a specific floristic composition and consisting of species that belong to the same stratum and that do not differ fundamentally in either periodicity or way of exploitation of their environment. We studied the responses of the moss synusiae to the cement kiln dust pollution in Myrtillus site-type forests in the vicinity of the Kunda cement plant (North Estonia). The synusiae were clustered into eight societies. The species content of the bryophyte synusiae changed completely along the alkaline pollution gradient. Synusiae of Dicranum polysetum—Pleurozium schreberi, Aulacomnium palustre—Hylocomium splendens and Ptilium crista-castrensis—Hylocomium splendens societies, characteristic of unpolluted forests, were replaced gradually by the ...

Investigation of Self-Diffusion and Structure in Calcium Aluminosilicate Slags by Molecular Dynamics Simulation

Molecular dynamics simulation is applied to investigate the mechanism and variation of self-diffusion in calcium aluminosilicate slags. The self-diffusion coefficients are calculated for eleven slag compositions with varying Al2O3/SiO2 ratios at a fixed CaO content. In practice, the results of the study are relevant to the significant changes in transport phenomenon caused by the changes in chemical composition during continuous casting of steels containing high amounts of dissolved aluminum. The cooperative movement between O atoms and network formers is discussed since [AlO4] and [SiO4] tetrahedra are the elementary structural units in the CaO-Al2O3-SiO2 (CAS) slag system. The diffusivities for four atomic types are affected by the degree of polymerization (DOP) of slag network characterized by the proportions of non-bridging oxygen (NBO) and Qn species in the system. On the other hand, a sudden increase in 5-coordinated Al as network modifiers in high alumina regions slightly increases the self-diffusion coefficient for Al. As another structural defect, oxygen tricluster plays an important role in the behavior of self-diffusion for O atoms, while the diffusivity for Ca is deeply influenced by its bonding and coordinating conditions.

Combined vibrational multipolar analyses and ab initio cluster description of glasses: Toward structural insights in vitreous v-P2O5

In a study of the v-P2O5 glassy structure, we discuss the complementarity of experimental and combined vibrational spectroscopies, namely infrared and polarized Raman scattering, using vibrational multipolar decomposition (VMD) analysis and ab initio calculations of local structures and vibrational spectra. VMD is a rigorous method that relates multiple vibrational spectroscopic activities of an isotropic medium to the point group symmetry of its elementary structural units (ESU) [see G. Guimbretière et al., J. Phys. Chem. C 112 (2008) 17906]. These ESUs are molecule-like and can be efficiently modeled using ab initio cluster calculations. Information obtained by both analytical techniques is compared and discussed. Finally a detailed spectroscopic assignment is proposed.

X-ray diffraction and the development of the mineral crystal chemistry

After the epochal experience of Friedrich and Knipping suggested and interpreted by Laue, the scene rapidly moved to England where the young Bragg correctly explained the results of the Munich discovery and showed how to use X-rays to determine the arrangement of atoms in crystals and, in few years, actually derived the structures of several inorganic compounds. Their comparison permitted Bragg to assert that crystals are composed of “inelastic spheres in contact” and that “it is possible to assign to the sphere representing an atom… a constant diameter.” The development of these concepts by various authors (Wasastjerna, Goldschmidt, …) led to the well-known Table of ionic radii by Pauling, who—at the same time—proposed the rules for the stability of ionic compounds, based on the concept of coordination polyhedra as building elementary modules of inorganic compounds. The stability rules of Pauling, as well as the conception, formulated by Bragg, of the structures of complex oxides as characterized by ‘close packing’ of oxygen anions, were the main guiding lines in the ‘trial and error’ procedures to determine the atomic arrangements in minerals and in inorganic compounds in general. The increasing number of known structures raised the need for proper classification schemes, largely based on elementary structural units (as the silicon tetrahedra in silicates) and the various ways of their connection. At the same time the wide basis of structural data and the increased precision and accuracy of those data stimulated the revision of the old compilations of ionic radii as well as a re-formulation of the Pauling’s rule of valence-bond balance. Examples are presented of the application of the crystal chemical concepts to some important mineralogical, geochemical and geophysical problems. An explosive growth of structural knowledge in the last decades of the twentieth century was stimulated by the new techniques of data collection, the high speed of computing and the advent of direct methods of structure solution, which resulted not only in an enormous increase in the number of known structures, but also in unraveling very complex arrangements. This increasing structural knowledge accompanied and stimulated the development of a new way to look at the arrangements of inorganic compounds, based on their modular aspects. The concept of assembling different, geometrically compatible modules, mainly structural layers, to build up complex structures has been very productive; in fact it not only consented a deep knowledge of the structural relationships inside wide families of natural and synthetic compounds, but also favored the solution of complex structural problems and permitted careful previsions of new possible structural arrangements. Few lines of future developments of the crystal chemical study of minerals are briefly presented and discussed: ‘synergy’ between mineralogists and material chemists; computational simulations of structural arrangements; new experimental approach through automated electron diffraction tomography.

Effect of ovarian steroids on gene expression related to synapse assembly in serotonin neurons of macaques

Dendritic spines are the elementary structural units of neural plasticity. In a model of hormone replacement therapy (HT), we sought to determine the effect of estradiol (E) and progesterone (P) on gene expression related to synapse assembly in a laser-captured preparation enriched for serotonin neurons from rhesus macaques. Microarray analysis was conducted (n = 2 animals/treatment), and the results were confirmed for pivotal genes with qRT-PCR on additional laser-captured material (n = 3 animals/treatment). Ovariectomized rhesus macaques were treated with placebo, E, or E + P via Silastic implants for 1 month. The midbrain was obtained, sectioned, and immunostained for tryptophan hydroxylase (TPH). TPH-positive neurons were laser captured using an arcturus laser dissection microscope (Pixel II). RNA from laser-captured serotonin neurons was hybridized to Rhesus Affymetrix GeneChips for screening purposes. There was a twofold or greater change in the expression of 63 probe sets in the cell adhesion molecule (CAM) category, and 31 probe sets in the synapse assembly category were similarly altered in E- and E + P-treated animals. qRT-PCR assays showed that E treatment induced a significant increase in ephrin receptor A4 (EPHA4) and in integrin A8 (ITGA8) but not in ephrin receptor B4 (EPHB4) or integrin B8 (ITGB8) expression. E also increased expression of cadherin 11 (CDH11), neuroligin 3 (NLGN3), neurexin 3 (NRXN3), syndecan 2 (SCD2), and neural cell adhesion molecule (NCAM) compared with placebo. Supplemental P treatment suppressed E-induced gene expression. In summary, ovarian steroids target gene expression of adhesion molecules in serotonin neurons that are important for synapse assembly.

Ovarian steroids increase glutamatergic related gene expression in serotonin neurons of macaques

Dendritic spines are the elementary structural units of neuronal plasticity and their proliferation and stabilization involve components of glutamate neurotransmission. In a model of hormone replacement therapy (HT), we sought the effect of estradiol (E) and progesterone (P) on gene expression related to glutamate neurotransmission in a laser captured preparation enriched for serotonin neurons from rhesus macaques. Microarray analysis was conducted (n=2 animals/treatment) and then confirmed for pivotal genes with qRT-PCR on additional laser captured material (n=3 animals/treatment). Ovariectomized rhesus macaques were treated with either placebo, E or E+P via Silastic implants for 1month prior to euthanasia. The midbrain was obtained, sectioned and immunostained for TPH. TPH-positive neurons were laser captured using an Arcturus Laser Dissection Microscope (Pixel II). RNA from laser captured serotonin neurons (n=2 animals/treatment) was hybridized to Rhesus Affymetrix GeneChips for screening purposes. There was a 2-fold or greater change in the expression of 28 probe sets related to glutamate processes in E and E+P treated animals. Quantitative (q) RT-PCR was conducted for 11 genes with a custom Taqman PCR array containing monkey specific primers and analyzed with ANOVA followed by Bonferroni's test. The log of the relative expression values indicated that in general, the responses to E and E+P were similar. Comparison of the relative expression or log relative expression in Ovx-controls to combined E and E+P treated groups with t-tests showed a significant increase in AMPA1 (GRIA1), AMPA2 (GRIA2), AMPA4 (GRIA4), NMDA2a (GRIN2A), metabotrophic glutamate receptor (GRM1), glutamine synthetase (GLUL), glutamate dehydrogenase (GLUD), glutamate cysteine ligase modifier subunit (GCLM), the glutamate transporter 2 (SLC1A2) and the glutamate transporter 3 (SLC1A3) with steroid treatment. There was no effect of steroid treatment on gene expression of the glutamate cysteine ligase catalytic subunit (GCLC). These data suggest that ovarian steroids target gene expression of ionotrophic and metabotrophic glutamate receptors in serotonin neurons. These receptors are present on dendritic spines and are necessary for spine maturation. The mRNAs coding for glutamate-related enzymes and transporters are likely derived from astrocytes or glutamate-containing terminals. Their induction by ovarian steroids indicates a complex upregulation of multiple components in the glutamate cycle and antioxidation, in addition to spine proliferation.

Thermoelectric and other phenomena in structures with nonequilibrium charge carriers and nanoparticles

The results of investigations of thermoelectric and other physical phenomena in semiconductor structures with n-p junctions are presented for the conducting direction. The direction of the heat transport is opposite to that observed for the “conventional” Peltier effect, and its magnitude is much higher. The possible parameters of thermoelectric cooling devices based on this effect are estimated. The sizes of elementary structural units in condensed phases are estimated. The thermoelectric, electrogravitational, and other phenomena in substances, the charge carriers in which are multimolecular nanocomplexes—the other-phase nuclei, are described.