Chemical Arguments Research Articles

Molecular Symmetry and Art: Visualizing the Near-Symmetry of Molecules in Piet Mondrian's De Stijl.

Symmetry and shape are essential aspects of molecular structure and how we interpret molecules and their properties. We, as chemists, are comfortable with pictorial representations of structure, in which some nuance is lost-investigating molecular shape numerically by looking at how closely it fits a reference, such as a plane, or a set of vectors or coordinates, is informative, though far from engaging. Often relationships between chemical structure and derived values are obscured. Taking our inspiration from Piet Mondrian's Compositions, we have depicted the symmetry information encoded within 3D data as blocks of color, to show clearly how chemical arguments and resultant molecular distortion may contribute to symmetry. Great art gives us a new perspective on the world; as a pastiche, this art may allow us to look at familiar molecules, such as porphyrins, in a new light, understanding how their shape and properties are intertwined.

Molecular Symmetry and Art: Visualizing the Near‐Symmetry of Molecules in Piet Mondrian's De Stijl

AbstractSymmetry and shape are essential aspects of molecular structure and how we interpret molecules and their properties. We, as chemists, are comfortable with pictorial representations of structure, in which some nuance is lost—investigating molecular shape numerically by looking at how closely it fits a reference, such as a plane, or a set of vectors or coordinates, is informative, though far from engaging. Often relationships between chemical structure and derived values are obscured. Taking our inspiration from Piet Mondrian's Compositions, we have depicted the symmetry information encoded within 3D data as blocks of color, to show clearly how chemical arguments and resultant molecular distortion may contribute to symmetry. Great art gives us a new perspective on the world; as a pastiche, this art may allow us to look at familiar molecules, such as porphyrins, in a new light, understanding how their shape and properties are intertwined.

May We Use Chemical Arguments to Distinguish between Possible Space‐Groups? Description of the Crystal Structure of an Inclusion Compound in Space Groups P1 or P‐1

AbstractThe structure of the inclusion compound of 1‐(3‐hydroxy‐4‐{(E)‐[(2‐hydroxyphenyl)methylidene]amino}phenyl)ethan‐1‐one – a light‐sensitive guest molecule, with 4,4′‐cyclohexylidenebisphenol as light‐stable host molecule was studied at 293 and 200 K. At room temperature the crystal structure may be described in space group P‐1, with one of the two guest molecules disordered occupying a crystallographic inversion center or in space group P1, avoiding the need for disorder description. One of the ordered guest molecules is connected by H‐bonds to a water molecule and a host molecule. The other guest molecule has the role of filling space. The distinction between the structures in the two space groups is discussed from a crystallographic and from chemical interactions point of view. The crystal structure at low temperature justifies the chemical arguments regarding the true space group.

Altering Microbiomes with Hydroxyapatite Nanoparticles: A Metagenomic Analysis.

Hydroxyapatite (HAp), the most abundant biological material among mammals, has been recently demonstrated to possess moderate antibacterial properties. Metagenomics provides a series of tools for analyzing the simultaneous interaction of materials with larger communities of microbes, which may aid in optimizing the antibacterial activity of a material such as HAp. Here, a microbiome intrinsic to the sample of sandy soil collected from the base of an African Natal plum (Carissa macrocarpa) shrub surrounding the children’s sandbox at the Arrowhead Park in Irvine, California was challenged with HAp nanoparticles and analyzed with next-generation sequencing for hypervariable 16S ribosomal DNA base pair homologies. HAp nanoparticles overwhelmingly reduced the presence of Gram-negative phyla, classes, orders, families, genera and species, and consequently elevated the relative presence of their Gram-positive counterparts. Thermodynamic, electrostatic and chemical bonding arguments were combined in a model proposed to explain this selective affinity. The ability of amphiphilic surface protrusions of lipoteichoic acid in Gram-positive bacteria and mycolic acid in mycobacteria to increase the dispersibility of the bacterial cells and assist in their resistance to capture by the solid phase is highlighted. Within the Gram-negative group, the variability of the distal, O-antigen portion of the membrane lipopolysaccharide was shown to be excessive and the variability of its proximal, lipid A portion insufficient to explain the selectivity based on chemical sequence arguments. Instead, flagella-driven motility proves to be a factor favoring the evasion of binding to HAp. HAp displayed a preference toward binding to less pathogenic bacteria than those causative of disease in humans, while taxa having a positive agricultural effect were largely captured by HAp, indicating an evolutionary advantage this may have given it as a biological material. The capacity to selectively sequester Gram-negative microorganisms and correspondingly alter the composition of the microbiome may open up a new avenue in environmental and biomedical applications of HAp.

Vinylacetylene synthesis with a low power submerged carbon arc in n-hexane

A low power carbon arc (12–18 W) struck between two graphite electrodes submerged in n-hexane has produced selectively vinylacetylene as the main product. Vinylacetylene was identified through its electronic absorption spectrum, the HPLC-DAD analysis and its precipitation as silver vinylacetylide. The HPLC analysis has revealed that the main by-product accompanying vinylacetylene is 1,3-butadiene and small amounts of diacetylene and divinylacetylene. The formation of other important by-products detected using also GC-MS (e.g., indene, naphthalene and some others) were discussed also in an astrochemical perspective. In contrast, a higher power submerged carbon arc in n-hexane struck at 108–216 W, yields an abundant mixture of polyynes accompanied by PAHs by-products. In the two arc regimes two mechanism are effective in producing selectively different products. In the low power arc regime, vinylacetylene is formed by the pyrolysis of acetylene primarily produced from n-hexane cracking in the arc. Chemical thermodynamics arguments also explain the vinylacetylene formation in low power arc conditions and diacetylene (and higher polyynes) in a higher power arc conditions.

DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search.

Protein searching and binding to specific sites on DNA is a fundamentally important process that marks the beginning of all major cellular transformations. While the dynamics of protein-DNA interactions in in vitro settings is well investigated, the situation is much more complex for in vivo conditions because the DNA molecules in live cells are packed into chromosomal structures where they are undergoing strong dynamic and conformational fluctuations. In this work, we present a theoretical investigation on the role of DNA looping and DNA conformational fluctuations in the protein target search. It is based on a discrete-state stochastic analysis that allows for explicit calculations of dynamic properties, which is also supplemented by Monte Carlo computer simulations. It is found that for stronger nonspecific interactions between DNA and proteins the search occurs faster on the DNA looped conformation in comparison with the unlooped conformation, and the fastest search is observed when the loop is formed near the target site. It is also shown that DNA fluctuations between the looped and unlooped conformations influence the search dynamics, and this depends on the magnitude of conformational transition rates and on which conformation is more energetically stable. Physical-chemical arguments explaining these observations are presented. Our theoretical study suggests that the geometry and conformational changes in DNA are additional factors that might efficiently control the gene regulation processes.

Criteria for Realizing Room-Temperature Electrical Transport Applications of Topological Materials.

The unusual electronic states found in topological materials can enable a new generation of devices and technologies, yet a long-standing challenge has been finding materials without deleterious parallel bulk conduction. This can arise either from defects or thermally activated carriers. Here, the criteria that materials need to meet to realize transport properties dominated by the topological states, a necessity for a topological device, are clarified. This is demonstrated for 3D topological insulators, 3D Dirac materials, and 1D quantum anomalous Hall insulators, though this can be applied to similar systems. The key parameters are electronic bandgap, dielectric constant, and carrier effective mass, which dictate under what circumstances (defect density, temperature, etc.) the unwanted bulk state will conduct in parallel to the topological states. As these are fundamentally determined by the basic atomic properties, simple chemical arguments can be used to navigate the phase space to ultimately find improved materials. This will enable rapid identification of new systems with improved properties, which is crucial to designing new material systems and push a new generation of topological technologies.

Orbital and spectral characterization of the benchmark T-type brown dwarf HD 19467B

Context.Detecting and characterizing substellar companions for which the luminosity, mass, and age can be determined independently is of utter importance to test and calibrate the evolutionary models due to uncertainties in their formation mechanisms. HD 19467 is a bright and nearby star hosting a cool brown dwarf companion detected with radial velocities and imaging, making it a valuable object for such studies.Aims.We aim to further characterize the orbital, spectral, and physical properties of the HD 19467 system.Methods.We present new high-contrast imaging data with the SPHERE and NaCo instruments. We also analyze archival data from the instruments HARPS, NaCo, HIRES, UVES, and ASAS. Furthermore, we use proper motion data of the star from HIPPARCOSandGaia.Results.We refined the properties of the host star and derived an age of 8.0+2.0−1.0Gyr based on isochrones, gyrochronology, and chemical and kinematic arguments. This age estimate is slightly younger than previous age estimates of ~9–11 Gyr based on isochrones. No orbital curvature is seen in the current imaging, radial velocity, and astrometric data. From a joint fit of the data, we refined the orbital parameters for HD 19467B, including: a period of 398+95−93yr, an inclination of 129.8+8.1−5.1deg, an eccentricity of 0.56 ± 0.09, a longitude of the ascending node of 134.8 ± 4.5 deg, and an argument of the periastron of 64.2+5.5−6.3deg. We assess a dynamical mass of 74+12−9MJ. The fit with atmospheric models of the spectrophotometric data of the companion indicates an atmosphere without clouds or with very thin clouds, an effective temperature of 1042+77−71K, and a high surface gravity of 5.34+0.8−0.9dex. The comparison to model predictions of the bolometric luminosity and dynamical mass of HD 19467B, assuming our system age estimate, indicates a better agreement with the Burrows et al. (1997, ApJ, 491, 856) models; whereas, the other evolutionary models used tend to underestimate its cooling rate.

Thermodynamic Inhibition in Chemostat Models : With an Application to Bioreduction of Uranium.

We formulate a mathematical model of bacterial populations in a chemostat setting that also accounts for thermodynamic growth inhibition as a consequence of chemical reactions. Using only elementary mathematical and chemical arguments, we carry this out for two systems: a simple toy model with a single species, a single substrate, and a single reaction product, and a more involved model that describes bioreduction of uranium[VI] into uranium[IV]. We find that in contrast to most traditional chemostat models, as a consequence of thermodynamic inhibition the equilibria concentrations of nutrient substrates might depend on their inflow concentration and not only on reaction parameters and the reactor's dilution rate. Simulation results of the uranium degradation model indicate that thermodynamic growth inhibition quantitatively alters the solution of the model. This suggests that neglecting thermodynamic inhibition effects in systems where they play a role might lead to wrong model predictions and under- or over-estimate the efficacy of the process under investigation.

Selectivity of Bedaquiline reacting with different polypeptide chains. Theoretical approach

ABSTRACTIn this article, we take a theoretical approach to analyse the pharmaceutical activity of Bedaquiline. This pharmaceutical agent has proved to be efficacious for tuberculosis treatment; however, it also shows toxic effects for human beings. Therefore, by simulating (DFT-ADMP) reactions, this study has reproduced the chemical activity of this substance, when faced with fragments of polypeptides coming from different sources; for example, the cellular wall of the Koch basilum or the corresponding chain from human albumin cells. Bedaquiline's preference for glutamate and arginine is demonstrated on the basis of chemical arguments and we propose the design of a Fullerene-Bedaquiline complex with low toxic effects.

Chemical Abundances along the 1G Sequence of the Chromosome Maps: The Globular Cluster NGC 3201*

Abstract The Hubble Space Telescope (HST) UV Legacy Survey of Galactic Globular Clusters (GCs) has investigated multiple stellar populations by means of the “chromosome map” (ChM) diagnostic tool that maximizes the separation between stars with different chemical compositions. One of the most challenging features revealed by ChM analysis is the apparent inhomogeneity among stars belonging to the first population, a phenomenon largely attributed to He variations. However, this explanation is not supported by uniformity in the p-capture elements of these stars. The HST survey has revealed that the GC NGC 3201 shows exceptionally wide coverage in the parameter of the ChM. We present a chemical abundance analysis of 24 elements in 18 giants belonging to the first population of this GC and having a wide range in . As far as the p-capture elements are concerned, the chemical abundances are typical of first-generation (1G) stars, as expected from the location of our targets in the ChM. Based on radial velocities and chemical abundance arguments, we find that the three stars with the lowest values are binary candidates. This suggests that at least those stars could be explained with binarity. These results are consistent with evidence inferred from multiband photometry that evolved blue stragglers (BSs) populate the bluest part of the 1G sequence in the ChM. The remaining 15 spectroscopic targets show a small range in the overall metallicity by ∼0.10 dex, with stars at higher values having higher absolute abundances. We suggest that a small variation in metals and binarity governs the color spread of the 1G in the ChM and that evolved BSs contribute to the bluest tail of the 1G sequence.

Thermal decomposition of ammonium perchlorate using Monte Carlo methods

ABSTRACTOne of the most intriguing aspects of ammonium perchlorate (AP) decomposition is its incomplete decomposition at low temperatures, in which the decomposition halts at a level of approximately 30%. Various theories have been proposed to explain this observation based on physical and chemical arguments. Here we consider the notion that geometry itself might contribute to this limiting value. Percolation theory involves the “connectedness” of a geometric lattice, and a network is said to percolate if it is connected continuously end-to-end. It has been demonstrated that in a cubic lattice, percolation occurs at a site density of ~31.1%, remarkably similar to the limiting void fraction in AP. A Monte Carlo (MC) algorithm using simple rules has been developed and applied to particle decomposition. The MC simulations result in porosity evolutions that are reminiscent of actual AP behavior in terms of the overall limiting porosity which is developed, the effect of particle size, and the sigmoidal time response.

Turning copper metal into a Weyl semimetal

A search for new topological quantum systems is challenging due to the requirement of nontrivial band connectivity that leads to protected surface states of electrons. Progress in this field was primarily due to a realization of a band inversion mechanism between even and odd parity states that was proven to be very useful in both predicting many such systems and our understanding of their topological properties. Despite many proposed materials that assume the band inversion between $s$ and $p$ (or $p/d$, $d$/$f$) electrons, here, we explore a different mechanism where the occupied $d$ states subjected to a tetrahedral crystal field produce an active ${t}_{2g}$ manifold behaving as a state with an effective orbital momentum equal to $\ensuremath{-}1$, and pushing ${j}_{\mathrm{eff}}=1/2$ doublet at a higher energy. Via hybridization with nearest-neighbor orbitals realizable, e.g., in a zinc-blende structural environment, this allows a formation of odd parity state whose subsequent band inversion with an unoccupied $s$ band becomes possible, prompting us to look for the compounds with ${\mathrm{Cu}}^{+1}$ ionic state. Chemical valence arguments coupled to a search in the materials database of zinc-blende-like lattice space groups ${T}_{d}^{2}$ ($F\overline{4}3m$) lead us to systematically investigate electronic structures and topological properties of CuY ($Y=\text{F}$, Cl, Br, I) and $\mathrm{Cu}X\mathrm{O}$ ($X=\text{Li}$, Na, K, Rb) families of compounds. Our theoretical results show that CuF displays a behavior characteristic of an ideal Weyl semimetal with 24 Weyl nodes at the bulk Brillouin zone. We also find that other compounds, CuNaO and CuLiO, are the $s\text{\ensuremath{-}}d$ inversion-type topological insulators. Results for their electronic structures and corresponding surfaces states are presented and discussed in the context of their topological properties.

Bentonitas da Formação Irati no setor sul da Bacia do Paraná

Este artigo tem como objetivo identificar e apresentar argumentos mineralógicos e químicos que demonstrem a existência de níveis de bentonitas inseridos na Formação Irati, em afloramentos a leste da cidade de Aceguá, sul do Rio Grande do Sul. Tratam-se de níveis com pequena espessura (em média 4 cm) e grande extensão lateral, constituídos de argilitos maciços branco-acinzentados a esverdeados que, em campo, contrastam com os folhelhos que compõem a Formação Irati. As bentonitas da Formação Irati se caracterizam por serem compostas predominantemente por Ca-montmorilonita e formam a matriz fina da rocha, na qual se encontram dispersos cristais primários, ou magmáticos, com tamanho não superior a areia muito fina. Entre os principais minerais primários identificados e representativos do ambiente vulcânico explosivo, encontram‑se pseudomorfos de β-quartzo, sanidina, biotita, zircão, apatita e ilmenita, além de fragmentos de quartzo e feldspatos (splinters). Mais raramente, encontram-se fragmentos de meso e macrocharcoals dentro das camadas de bentonita, que contrastam com a maturidade e tipo de matéria orgânica não vegetal do folhelho Irati. Com base na geoquímica da rocha e na cristaloquímica da montmorilonita neoformada nos níveis de bentonita, infere-se sobre a natureza do vulcanismo precursor. Ambas as metodologias apontam que nesse período as cinzas vulcânicas que alcançaram a Bacia do Paraná originaram-se de vulcanismo com composição intermediária, em concordância com o que é conhecido sobre as manifestações da Província Vulcânica Choiyoi Inferior, sincrônica com a sedimentação da Formação Irati na Bacia do Paraná.

Large-Area Elemental Imaging Reveals Van Eyck's Original Paint Layers on the Ghent Altarpiece (1432), Rescoping Its Conservation Treatment.

A combination of large-scale and micro-scale elemental imaging, yielding elemental distribution maps obtained by, respectively non-invasive macroscopic X-ray fluorescence (MA-XRF) and by secondary electron microscopy/energy dispersive X-ray analysis (SEM-EDX) and synchrotron radiation-based micro-XRF (SR μ-XRF) imaging was employed to reorient and optimize the conservation strategy of van Eyck's renowned Ghent Altarpiece. By exploiting the penetrative properties of X-rays together with the elemental specificity offered by XRF, it was possible to visualize the original paint layers by van Eyck hidden below the overpainted surface and to simultaneously assess their condition. The distribution of the high-energy Pb-L and Hg-L emission lines revealed the exact location of hidden paint losses, while Fe-K maps demonstrated how and where these lacunae were filled-up using an iron-containing material. The chemical maps nourished the scholarly debate on the overpaint removal with objective, chemical arguments, leading to the decision to remove all skillfully applied overpaints, hitherto interpreted as work by van Eyck. MA-XRF was also employed for monitoring the removal of the overpaint during the treatment phase. To gather complementary information on the in-depth layer build-up, SEM-EDX and SR μ-XRF imaging was used on paint cross sections to record micro-scale elemental maps.

Large‐Area Elemental Imaging Reveals Van Eyck's Original Paint Layers on the Ghent Altarpiece (1432), Rescoping Its Conservation Treatment

AbstractA combination of large‐scale and micro‐scale elemental imaging, yielding elemental distribution maps obtained by, respectively non‐invasive macroscopic X‐ray fluorescence (MA‐XRF) and by secondary electron microscopy/energy dispersive X‐ray analysis (SEM‐EDX) and synchrotron radiation‐based micro‐XRF (SR μ‐XRF) imaging was employed to reorient and optimize the conservation strategy of van Eyck's renowned Ghent Altarpiece. By exploiting the penetrative properties of X‐rays together with the elemental specificity offered by XRF, it was possible to visualize the original paint layers by van Eyck hidden below the overpainted surface and to simultaneously assess their condition. The distribution of the high‐energy Pb‐L and Hg‐L emission lines revealed the exact location of hidden paint losses, while Fe‐K maps demonstrated how and where these lacunae were filled‐up using an iron‐containing material. The chemical maps nourished the scholarly debate on the overpaint removal with objective, chemical arguments, leading to the decision to remove all skillfully applied overpaints, hitherto interpreted as work by van Eyck. MA‐XRF was also employed for monitoring the removal of the overpaint during the treatment phase. To gather complementary information on the in‐depth layer build‐up, SEM‐EDX and SR μ‐XRF imaging was used on paint cross sections to record micro‐scale elemental maps.

Self-similarity in the chemical evolution of galaxies and the delay-time distribution of SNe Ia

Recent improvements in the age dating of stellar populations and single stars allow us to study the ages and abundance of stars and galaxies with unprecedented accuracy. We here compare the relation between age and \alpha-element abundances for stars in the solar neighborhood to that of local, early-type galaxies. We find both relations to be very similar. Both fall into two regimes with a flat slope for ages younger than ~9 Gyr and a steeper slope for ages older than that value. This quantitative similarity seems surprising, given the different types of galaxies and scales involved. For the sample of early-type galaxies we also show that the data are inconsistent with literature delay time distributions of either single or double Gaussian shape. The data are consistent with a power law delay time distribution. We thus confirm that the delay time distribution inferred for the Milky Way from chemical evolution arguments also must apply to massive early-type galaxies. We also offer a tentative explanation for the seeming universality of the age-[\alpha/Fe] relation as the manifestation of averaging of different stellar populations with varying chemical evolution histories.

Crystal and magnetic effects of selected substitutions of Ni for Fe and for Co in the orthorhombic MnFe0.35Co0.65P compound

Both series of MnFe0.35−xCo0.65NixP and MnFe0.35Co0.65−xNixP orthorhombic compounds were analyzed for their structural characteristics versus x and versus temperature, as well for the changes induced to the magnetic behaviors (ordering temperature, saturation magnetization, magnetic entropy change). The operated Ni substitutions lead to decrease the Curie point closer to room temperature, especially when Ni substitutes to Co. However, in both systems, the saturation magnetization evolves unexpectedly. Even if remaining rather weak, the corresponding changes of magneto-caloric entropy at the transition are significantly increased, being more than twice and three times the initial value for Ni substituted to Fe and to Co respectively. Chemical and topological arguments are then proposed to discuss the noticeable difference of behaviors observed between the hexagonal (e.g. MnFeP1−xAsx) and the orthorhombic (e.g. MnFe1−xCoxP) series of polytype pnictides.

Two-Dimensional (2D) Correlation Analysis and the Search for Intermediates: A Strictly Mathematical Approach to an Important Mechanistic Question

In situ spectroscopic studies of metal-mediated syntheses of new and previously unstudied systems are being increasingly used to better understand speciation and mechanistic aspects. These types of experiments give rise to an interesting question: namely, can one deduce from in situ data alone, and with no a priori chemical knowledge (i.e. chemical assignments), which pure component spectral estimates correspond to intermediates? In the present contribution, a statistical 2D correlation analysis is introduced to solve this problem for unicyclic catalytic systems. Such a methodological development achieves two goals: (1) it allows the experimentalist to concentrate on the most meaningful information at the outset of a new exploratory study (focus on the species directly associated with the catalysis), and (2) it helps to free the experimentalist from chemical bias and prejudice, i.e. believing that a specific organometallic species has to be an intermediate due to one or more chemical arguments, when in fact it may be just a side product or spectator species in the metal-mediated synthesis. The 2D correlation analysis is first tested with a numerically simulated data set and then with a real in situ FTIR data set from an unmodified rhodium-catalyzed hydroformylation. The resulting statistical 2D correlation analysis provides a clear and correct answer.

First principles calculations of (La,Mg)2Ni7 hydrides

Between interstitial metal hydrides, such as LaNi5H6, and ionic complex such as Mg2NiH4, a large family of (La,Mg)–Ni hydrides exists, exhibiting intermediate electronic properties. Using first principles calculations, a systematic investigation of the electronic properties of these (La,Mg)NiyHx hydrides was performed.In the present work, we focus on the calculated preferential H sites. A comparison between geometrical and chemical arguments, leads to a general trend which governs the stability of the hydrides of the (La–Mg)–Ni compound family, namely that the Mg substituted hydrides are less stable. As an example, the (La,Mg)2Ni7Hx hydrides are fully presented. Crystallographic features and possible ordered hydride description are compared with available experimental data.