scholarly journals Selenium Minerals: Structural and Chemical Diversity and Complexity

Minerals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 455 ◽  
Author(s):  
Vladimir G. Krivovichev ◽  
Sergey V. Krivovichev ◽  
Marina V. Charykova
Keyword(s):  
Chemical Elements ◽  
Structural Complexity ◽  
Essential Element ◽  
Closed Shell ◽  
Unit Cell ◽  
Chemical Diversity ◽  
Near Surface ◽  
International Mineralogical Association ◽  
Chemical Complexity ◽  
Essential Components

Chemical diversity of minerals containing selenium as an essential element has been analyzed in terms of the concept of mineral systems and the information-based structural and chemical complexity parameters. The study employs data for 123 Se mineral species approved by the International Mineralogical Association as of 25 May 2019. All known selenium minerals belong to seven mineral systems with the number of essential components ranging from one to seven. According to their chemical features, the minerals are subdivided into five groups: Native selenium, oxides, selenides, selenites, and selenates. Statistical analysis shows that there are strong and positive correlations between the chemical and structural complexities (measured as amounts of Shannon information per atom and per formula or unit cell) and the number of different chemical elements in a mineral. Analysis of relations between chemical and structural complexities provides strong evidence that there is an overall trend of increasing structural complexity with the increasing chemical complexity. The average structural complexity for Se minerals is equal to 2.4(1) bits per atom and 101(17) bits per unit cell. The chemical and structural complexities of O-free and O-bearing Se minerals are drastically different with the first group being simpler and the second group more complex. The O-free Se minerals (selenides and native Se) are primary minerals; their formation requires reducing conditions and is due to hydrothermal activity. The O-bearing Se minerals (oxides and oxysalts) form in near-surface environment, including oxidation zones of mineral deposits, evaporites and volcanic fumaroles. From the structural viewpoint, the five most complex Se minerals are marthozite, Cu(UO2)3(SeO3)2O2·8H2O (744.5 bits/cell); mandarinoite, Fe2(SeO3)3·6H2O (640.000 bits/cell); carlosruizite, K6Na4Na6Mg10(SeO4)12(IO3)12·12H2O (629.273 bits/cell); prewittite, KPb1.5ZnCu6O2(SeO3)2Cl10 (498.1 bits/cell); and nicksobolevite, Cu7(SeO3)2O2Cl6 (420.168 bits/cell). The mechanisms responsible for the high structural complexity of these minerals are high hydration states (marthozite and mandarinoite), high topological complexity (marthozite, mandarinoite, carlosruizite, nicksobolevite), high chemical complexity (prewittite and carlosruizite), and the presence of relatively large clusters of atoms (carlosruizite and nicksobolevite). In most cases, selenium itself does not play the crucial role in determining structural complexity (there are structural analogues or close species of marthozite, mandarinoite, and carlosruizite that do not contain Se), except for selenite chlorides, where stability of crystal structures is adjusted by the existence of attractive Se–Cl closed-shell interactions impossible for sulfates or phosphates. Most structurally complex Se minerals originate either from relatively low-temperature hydrothermal environments (as marthozite, mandarinoite, and carlosruizite) or from mild (500–700 °C) anhydrous gaseous environments of volcanic fumaroles (prewittite, nicksobolevite).

scholarly journals Tellurium Minerals: Structural and Chemical Diversity and Complexity

Minerals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 623
Author(s):  
Vladimir G. Krivovichev ◽  
Sergey V. Krivovichev ◽  
Marina V. Charykova
Keyword(s):  
Statistical Analysis ◽  
Chemical Weathering ◽  
Chemical Elements ◽  
Structural Complexity ◽  
Ore Deposits ◽  
Chemical Diversity ◽  
Mineral Species ◽  
Hydrothermal Solutions ◽  
Informational Entropy ◽  
Reducing Conditions

The chemical diversity and complexity of tellurium minerals were analyzed using the concept of mineral systems and Shannon informational entropy. The study employed data for 176 Te mineral species known today. Tellurium minerals belong to six mineral systems in the range of one-to-six species-defining elements. For 176 tellurium minerals, only 36 chemical elements act as essential species-defining constituents. The numbers of minerals of main elements are calculated as follows (the number of mineral species is given in parentheses): O (89), H (48), Cu (48), Pb (43), Bi (31), S (29), Ag (20), Fe (20), Pd (16), Cl (13), and Zn (11). In accordance with their chemistry, all Te minerals are classified into five types of mineral systems: tellurium, oxides, tellurides and intermetalides, tellurites, and tellurates. A statistical analysis showed positive relationships between the chemical, structural, and crystallochemical complexities and the number of essential species-defining elements in a mineral. A positive statistically significant relationship between chemical and structural complexities was established. It is shown that oxygen-free and oxygen-bearing Te minerals differ sharply from each other in terms of chemical and structural complexity, with the first group of minerals being simpler than the second group. The oxygen-free Te minerals (tellurium, tellurides, and intermetallides) are formed under reducing conditions with the participation of hydrothermal solutions. The most structurally complex oxygen-bearing Te minerals originate either from chemical weathering and the oxidation of ore deposits or from volcanic exhalations (Nabokoite).

scholarly journals Jahn-Teller Distortion and Cation Ordering: The Crystal Structure of Paratooite-(La), a Superstructure of Carbocernaite

Minerals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 370
Author(s):  
Sergey V. Krivovichev ◽  
Taras L. Panikorovskii ◽  
Andrey A. Zolotarev ◽  
Vladimir N. Bocharov ◽  
Anatoly V. Kasatkin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Chemical Elements ◽  
South Australia ◽  
Structural Complexity ◽  
Cation Ordering ◽  
Teller Distortion ◽  
Chemical Complexity ◽  
Distorted Octahedral ◽  
Jahn Teller ◽  
Cation Sites

The crystal structure of paratooite-(La) has been solved using crystals from the type locality, Paratoo copper mine, near Yunta, Olary Province, South Australia, Australia. The mineral is orthorhombic, Pbam, a = 7.2250(3) Å, b = 12.7626(5) Å, c = 10.0559(4) Å, V = 927.25(6) Å3, and R1 = 0.063 for 1299 unique observed reflections. The crystal structure contains eight symmetrically independent cation sites. The La site, which accommodates rare earth elements (REEs), but also contains Sr and Ca, has a tenfold coordination by seven carbonate groups. The Ca, Na1, and Na2 sites are coordinated by eight, eight, and six O atoms, respectively, forming distorted CaO8 and Na1O8 cubes, and Na2O6 octahedra. The Cu site is occupied solely by copper and possess a distorted octahedral coordination with four short (1.941 Å) and two longer (2.676 Å) apical Cu–O bonds. There are three symmetrically independent carbonate groups (CO3)2− with the average <C–O> bond lengths equal to 1.279, 1.280, and 1.279 Å for the C1, C2, and C3 sites, respectively. The crystal structure of paratooite-(La) can be described as a strongly distorted body-centered lattice formed by metal cations with (CO3)2− groups filling its interstices. According to the chemical and crystal-structure data, the crystal-chemical formula of paratooite-(La) can be described as (La0.74Ca0.11Sr0.07)4CuCa(Na0.75Ca0.15)(Na0.63)(CO3)8 or REE2.96Ca1.59Na1.38CuSr0.28(CO3)8. The idealized formula can be written as (La,Sr,Ca)4CuCa(Na,Ca)2(CO3)8. The structure of paratooite is a 1 × 2 × 2 superstructure of carbocernaite, CaSr(CO3)2. The superstructure arises due to the ordering of the chemically different Cu2+ cations, on one hand, and Na+ and Ca2+ cations, on the other hand. The formation of a superstructure due to the cation ordering in paratooite-(La) compared to carbocernaite results in the multiple increase of structural complexity per unit cell. Therefore, paratooite-(La) versus carbocernaite represents a good example of structural complexity increasing due to the increasing chemical complexity controlled by different electronic properties of mineral-forming chemical elements (transitional versus alkali and alkaline earth metals).

scholarly journals Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure

2020 ◽  
Author(s):  
Tianming Yao ◽  
Ming-Hsu Chen ◽  
Stephen R. Lindemann
Keyword(s):  
Microbial Diversity ◽  
Structural Complexity ◽  
Structure And Function ◽  
Microbial Consortia ◽  
Carbohydrate Structure ◽  
High Dilution ◽  
Chemical Complexity ◽  
Metabolic Interactions ◽  
And Function

ABSTRACTDietary fibers are major substrates for the colonic microbiota, but the structural specificity of these fibers for the diversity, structure, and function of gut microbial communities are poorly understood. Here, we employed an in vitro sequential batch fecal culture approach to determine: 1) whether the chemical complexity of a carbohydrate structure influences its ability to maintain microbial diversity in the face of high dilution pressure and 2) whether substrate structuring or obligate microbe-microbe metabolic interactions (e.g. exchange of amino acids or vitamins) exert more influence on maintained diversity. Sorghum arabinoxylan (SAX, complex polysaccharide), inulin (low-complexity oligosaccharide) and their corresponding monosaccharide controls were selected as model carbohydrates. Our results demonstrate that complex carbohydrates stably sustain diverse microbial consortia. Further, very similar final consortia were enriched on SAX from the same individual’s fecal microbiota across a one-month interval, suggesting that polysaccharide structure is more influential than stochastic alterations in microbiome composition in governing the outcomes of sequential batch cultivation experiments. SAX-consuming consortia were anchored by Bacteroides ovatus and retained diverse consortia of >12 OTUs; whereas final inulin-consuming consortia were dominated either by Klebsiella pneumoniae or Bifidobacterium sp. and Escherichia coli. Furthermore, auxotrophic interactions were less influential in structuring microbial consortia consuming SAX than the less-complex inulin. These data suggest that carbohydrate structural complexity affords independent niches that structure fermenting microbial consortia, whereas other metabolic interactions govern the composition of communities fermenting simpler carbohydrates.IMPORTANCEThe mechanisms by which gut microorganisms compete for and cooperate on human-indigestible carbohydrates of varying structural complexity remain unclear. Gaps in this understanding make it challenging to predict the effect of a particular dietary fiber’s structure on the diversity, composition, or function of gut microbiomes, especially with inter-individual variability in diets and microbiomes. Here, we demonstrate that carbohydrate structure governs the diversity of gut microbiota under high dilution pressure, suggesting that such structures may support microbial diversity in vivo. Further, we also demonstrate that carbohydrate polymers are not equivalent in the strength by which they influence community structure and function, and that metabolic interactions among members arising due to auxotrophy exert significant influence on the outcomes of these competitions for simpler polymers. Collectively, these data suggest that large, complex dietary fiber polysaccharides structure the human gut ecosystem in ways that smaller and simpler ones may not.

scholarly journals Analysis of a large food chemical database: chemical space, diversity, and complexity

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 993 ◽  
Author(s):  
J. Jesús Naveja ◽  
Mariel P. Rico-Hidalgo ◽  
José L. Medina-Franco
Keyword(s):  
Natural Products ◽  
Chemical Space ◽  
Structural Complexity ◽  
Chemical Diversity ◽  
Chemical Structures ◽  
Novel Approach ◽  
Chemical Database ◽  
Protein Interactome ◽  
Limited Basis ◽  
Future Direction

Background: Food chemicals are a cornerstone in the food industry. However, its chemical diversity has been explored on a limited basis, for instance, previous analysis of food-related databases were done up to 2,200 molecules. The goal of this work was to quantify the chemical diversity of chemical compounds stored in FooDB, a database with nearly 24,000 food chemicals. Methods: The visual representation of the chemical space of FooDB was done with ChemMaps, a novel approach based on the concept of chemical satellites. The large food chemical database was profiled based on physicochemical properties, molecular complexity and scaffold content. The global diversity of FooDB was characterized using Consensus Diversity Plots. Results: It was found that compounds in FooDB are very diverse in terms of properties and structure, with a large structural complexity. It was also found that one third of the food chemicals are acyclic molecules and ring-containing molecules are mostly monocyclic, with several scaffolds common to natural products in other databases. Conclusions: To the best of our knowledge, this is the first analysis of the chemical diversity and complexity of FooDB. This study represents a step further to the emerging field of “Food Informatics”. Future study should compare directly the chemical structures of the molecules in FooDB with other compound databases, for instance, drug-like databases and natural products collections. An additional future direction of this work is to use the list of 3,228 polyphenolic compounds identified in this work to enhance the on-going polyphenol-protein interactome studies.

scholarly journals Experimental and Numerical Analysis of Additively Manufactured Inconel 718 Coupons With Lattice Structure

2020 ◽  
Vol 142 (6) ◽  
Author(s):  
Sarwesh Parbat ◽  
Zheng Min ◽  
Li Yang ◽  
Minking Chyu
Keyword(s):  
Heat Transfer ◽  
Steady State ◽  
Pressure Drop ◽  
Inconel 718 ◽  
Lattice Structure ◽  
Unit Cell ◽  
Common Vertex ◽  
Constant Wall Temperature ◽  
Near Surface ◽  
Smooth Channel

Abstract In the present paper, two lattice geometries suitable for near surface and double wall cooling were developed and tested. The first type of unit cell consisted of six ligaments of 0.5 mm diameter joined at a common vertex near the middle. The second type of unit cell was derived from the first type by adding four mutually perpendicular ligaments in the middle plane. Two lattice configurations, referred to as L1 and L2, respectively, were obtained by repeating the corresponding unit cell in streamwise and spanwise directions in an inline fashion. Test coupons consisting of these lattice geometries embedded inside rectangular cooling channel with dimensions of 2.54 mm height, 38.07 mm width, and 38.1 mm in length were fabricated using Inconel 718 powder and selective laser sintering (SLS) process. The heat transfer and pressure drop performance was then evaluated using steady-state tests with constant wall temperature boundary condition and for channel Reynolds number ranging from 2800 to 15,000. The lattices depicted a higher heat transfer compared with a smooth channel and both the heat transfer and pressure drop increased with a decrease in the porosity from L1 to L2. Steady-state conjugate numerical results revealed formation of prominent vortical structures in the inter-unit cell spaces, which diverted the flow toward the top end wall and created an asymmetric heat transfer between the two end walls. In conclusion, these lattice structures provided an augmented heat transfer while favorably redistributing the coolant within channel.

Formation and paleontologic recognition of structures caused by marine annelids

Paleobiology ◽  
1977 ◽  
Vol 3 (4) ◽  
pp. 389-403 ◽  
Author(s):  
Thomas E. Ronan
Keyword(s):  
Function Analysis ◽  
Structural Complexity ◽  
Soft Sediment ◽  
Water Interface ◽  
Surface Material ◽  
Near Surface ◽  
Sedimentary Structures ◽  
Biogenic Structures ◽  
Sediment Mixing ◽  
Feeding Function

Laboratory and field collected sediments were x-rayed to document the array of biogenic sedimentary structures produced by the burrowing and feeding behavior of six species of marine intertidal annelid (Glycera robusta, Nephtys caecoides, Pectinaria californiensis, Notomastus magnus, Eupolymnia crescentis, and Cirriformia spirabrancha). Polychaete burrows were found to vary greatly in structural complexity with both errant (N. magnus) and relatively sessile forms (C. spirabrancha) producing a variety of biogenic structures. Sediment mixing by the tentacle-feeding polychaete C. spirabrancha was observed by sequentially x-raying an experimental field enclosure stratified with an opaque substance. The experiment demonstrates that tentacle-feeding polychaetes can influence the topography of the sediment-water interface and transport substantial amounts of near surface material downward.Criteria by which fossil biogenic sedimentary structures, presumably produced by soft-bodied organisms, can be assigned a feeding function have been advanced by Walker (1972). Some of the assumptions inherent in feeding function analysis were applied, with varying degrees of success, to the biogenic structures of modern soft-sediment polychaetes.

scholarly journals Changes in energetic metabolism of Biomphalaria glabrata (Mollusca, Planorbidae) in response to exogenous calcium

2016 ◽  
Vol 77 (2) ◽  
pp. 304-311 ◽  
Author(s):  
L. D. Silva ◽  
V. C. S. Amaral ◽  
M. C. Vinaud ◽  
A. M. Castro ◽  
H. H. A. Rezende ◽  
...  
Keyword(s):  
Organic Acids ◽  
High Performance ◽  
Chemical Elements ◽  
Essential Element ◽  
Biomphalaria Glabrata ◽  
Control Group ◽  
Limiting Factor ◽  
Energetic Metabolism ◽  
Significant Difference ◽  
Commercial Kits

Abstract Calcium is considered an essential element for the metabolism of aquatic snail Biomphalaria glabrata (Say, 1818), intermediate host of Schistosoma mansoni Sambon, 1907 in Brazil, and represents a limiting factor to its distribution and adaptation to the environment. This study investigated the effect of different concentrations of exogenous CaCO3 on the energetic metabolism of B. glabrata for better understanding the physiological interference of chemical elements dissolved in the environment with the physiology of this species. Sixty-day-old snails were distributed into six groups, five exposed to different concentrations of CaCO3 (20, 40, 60, 80 and 100 mg/L) and a control group. The exposure to CaCO3 was assessed over time, with analysis of 15 snails of each group in the following intervals: 1, 14, 21 or 30 days for hemolymph extraction. Concentrations of calcium and glucose in the hemolymph were determined by commercial kits, and organic acids were extracted using an ion exchange column and analyzed by high-performance liquid chromatography. Concentration of calcium in the hemolymph showed no significant difference (p>0.05) from the control group and between the concentrations tested. Concentration of glucose decreased (p<0.05) in the treatments of exposure to 20 and 40 mg/L and increased when exposed to 80 and 100 mg/L CaCO3 compared to control and to other concentrations tested over 30 days. The organic acids pyruvate, oxaloacetate, citrate, succinate, fumarate, beta-hydroxybutyrate and lactate presented increased concentrations, while propionate and acetoacetate, decreased concentrations, when exposed to CaCO3 compared to control. Considering the influence of different periods of exposure to CaCO3, on the 14th day, there were stronger alterations in the metabolism of B. glabrata. In conclusion, exposure to CaCO3 reduced the concentration of glucose, which is metabolized into pyruvate, the final product of glycolysis, and also influenced the energetic metabolism pathways, indicating an aerobic or partially anaerobic functioning.

Ladders of information: what contributes to the structural complexity of inorganic crystals

2018 ◽  
Vol 233 (3-4) ◽  
pp. 155-161 ◽  
Author(s):  
Sergey V. Krivovichev
Keyword(s):  
Crystal Structures ◽  
Inorganic Compounds ◽  
Structural Complexity ◽  
Unit Cell ◽  
Shannon Information ◽  
Topological Complexity ◽  
Crystal Chemical ◽  
Quantitative Estimates ◽  
Hydration State ◽  
Inorganic Crystals

AbstractComplexity is one of the important characteristics of crystal structures, which can be measured as the amount of Shannon information per atom or per unit cell. Since complexity may arise due to combination of different factors, herein we suggest a method of ladder diagrams for the analysis of contributions to structural complexity from different crystal-chemical phenomena (topological complexity, superstructures, modularity, hydration state, etc.). The group of minerals and inorganic compounds based upon the batagayite-type [M(TO4)ϕ] layers (M=Fe, Mg, Mn, Ni, Zn, Co; T=P, As; ϕ=OH, H2O) is used as an example. It is demonstrated that the method allows for the quantitative estimates of various contributions to the complexity of the whole structure.

scholarly journals GEOCHEMICAL ATLASES OF EUROPE PRODUCED BY THE EUROGEOSURVEYS GEOCHEMISTRY EXPERT GROUP: STATE OF PROGRESS AND POTENTIAL USES

2017 ◽  
Vol 43 (5) ◽  
pp. 2350
Author(s):  
A. Demetriades ◽  
C. Reimann ◽  
M. Birke ◽  
R. Salminen ◽  
W. De Vos ◽  
...  
Keyword(s):  
Ground Water ◽  
Chemical Elements ◽  
Stream Water ◽  
Geochemical Data ◽  
Expert Group ◽  
Data Quality Control ◽  
Grazing Land ◽  
Water Geochemistry ◽  
Near Surface ◽  
Physico Chemical

An ‘Atlas’ is a collection of maps usually published in a book form. A ‘Geochemical Atlas’ is a thematic special purpose atlas with maps describing the geographical distribution of chemical elements and other physico-chemical parameters in different natural sample media, such as stream sediment, overbank or floodplain sediment, stream water, ground water, soil, plants, etc. Because our standard of living and health depend closely on the chemistry of near-surface materials, such atlases that provide data on the state of our environment are important for policy and decision makers, but also for researchers and citizens alike. The EuroGeoSurveys Geochemistry Expert Group is dedicated to provide harmonised multi-purpose geochemical data bases, and has already published the Geochemical Atlas of Europe, and is in the process of preparing the Atlas of Ground water Geochemistry of Europe, and the Atlas of Agricultural and Grazing Land Soils. An important aspect is that all raw data, quality control information, statistics, maps and interpretation texts are freely available for downloading through the internet.

scholarly journals GPAHex-A synthetic biology platform for Type IV–V glycopeptide antibiotic production and discovery

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Min Xu ◽  
Wenliang Wang ◽  
Nicholas Waglechner ◽  
Elizabeth J. Culp ◽  
Allison K. Guitor ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Antibiotic Production ◽  
Structural Complexity ◽  
Fold Increase ◽  
Building Blocks ◽  
Chemical Diversity ◽  
Glycopeptide Antibiotics ◽  
Gram Positive Bacteria ◽  
Type Iv

Abstract Glycopeptide antibiotics (GPAs) are essential for the treatment of severe infectious diseases caused by Gram-positive bacteria. The emergence and spread of GPA resistance have propelled the search for more effective GPAs. Given their structural complexity, genetic intractability, and low titer, expansion of GPA chemical diversity using synthetic or medicinal chemistry remains challenging. Here we describe a synthetic biology platform, GPAHex (GPA Heterologous expression), which exploits the genes required for the specialized GPA building blocks, regulation, antibiotic transport, and resistance for the heterologous production of GPAs. Application of the GPAHex platform results in: (1) a 19-fold increase of corbomycin titer compared to the parental strain, (2) the discovery of a teicoplanin-class GPA from an Amycolatopsis isolate, and (3) the overproduction and characterization of a cryptic nonapeptide GPA. GPAHex provides a platform for GPA production and mining of uncharacterized GPAs and provides a blueprint for chassis design for other natural product classes.

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