A1 Substitution Research Articles

Enhancement of the Long-Wavelength Sensitivity of Optogenetic Microbial Rhodopsins by 3,4-Dehydroretinal

Electrogenic microbial rhodopsins (ion pumps and channelrhodopsins) are widely used to control the activity of neurons and other cells by light (optogenetics). Long-wavelength absorption by optogenetic tools is desirable for increasing the penetration depth of the stimulus light by minimizing tissue scattering and absorption by hemoglobin. A2 retinal (3,4-dehydroretinal) is a natural retinoid that serves as the chromophore in red-shifted visual pigments of several lower aquatic animals. Here we show that A2 retinal reconstitutes a fully functional archaerhodopsin-3 (AR-3) proton pump and four channelrhodopsin variants (CrChR1, CrChR2, CaChR1, and MvChR1). Substitution of A1 with A2 retinal significantly shifted the spectral sensitivity of all tested rhodopsins to longer wavelengths without altering other aspects of their function. The spectral shift upon substitution of A1 with A2 in AR-3 was close to that measured in other archaeal rhodopsins. Notably, the shifts in channelrhodopsins were larger than those measured in archaeal rhodopsins and close to those in animal visual pigments with similar absorption maxima of their A1-bound forms. Our results show that chromophore substitution provides a complementary strategy for improving the efficiency of optogenetic tools.

2-propanol photodegradation over molybdates: effects of chemical compositions and electronic structures

A new kind of photocatalysts, ABi(MoO4)2 (A = Na, Ag), were prepared by a traditional solid-state reaction method. The samples were characterized by x-ray diffraction, UV–Vis diffuse reflectance spectroscopy, N2 adsorption–desorption measurement and scanning electron microscopy. The results showed that ABi(MoO4)2 (A = Na, Ag) were all crystallized in a tetragonal system with the space group I41/a. However, the substitution of A1+ cations with different elemental compositions imposed significant effects on their electronic structures and photocatalytic performance. The photocatalytic activities were evaluated by photo-oxidation of gaseous 2-propanol. It was found that NaBi(MoO4)2 showed a higher activity than AgBi(MoO4)2. Theoretically, calculated band structures and density of states by the plane-wave density functional theory revealed that the different photophysical and photocatalytic properties of ABi(MoO4)2 (A = Na, Ag) can possibly be ascribed to their different electronic structures.

Study on the interaction between 4-(2-diethylamino-ethylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile and DNA by molecular spectra

The binding geometry of a heterocyclic compound, 4-(2-diethylamino-ethylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile ( A1) to CT DNA was studied by molecular spectroscopy. Deduced from SYBR Green–DNA melt curve, UV–vis spectroscopy, and fluorescence studies, there were two different interaction mechanisms involved in the whole interaction process depending on the R-value ( R, the molar ratio of A1 to CT DNA base pairs). The value R = 0.20 was the turning point. The induced circular dichroism (ICD) spectra of A1 complexed with CT DNA, poly[(G-C) 2] and poly[(A-T) 2] showed when R ≤ 0.20, A1 intercalated into CT DNA and the intercalation orientation of A1 to the dyad axis of DNA double-helix was heterogeneous. When R > 0.20, stacking of A1 on surface helix of DNA occurred driven by the protonation of amidogen group in the N, N-diethyldiamine substitution of A1, which was illustrated by the changes of A1–DNA geometry in different pH solutions. The intrinsic circular dichroism (CD) spectra showed the conformation of DNA converted from the B-form to A-like conformation due to the A1 intercalation.

Solid-state29Si MAS NMR studies of illite and illite-smectite from shale

A new method to extract quantitative information from poorly resolved 29 Si magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of natural mixed-layer illite-smectite (I-S) clays is presented. The Si-Al distribution in layered aluminosilicates are used to link the intensities of 29 Si resonances from all Q 3 (nAl) sites (n = 0, 1, 2, 3) to the tetrahedral layer aluminum substitution by applying Loewenstein9s aluminum avoidance principle (no Al-O-Al linkages) extended to ensure a homogeneous distribution of charge. In addition, correlations between 29 Si chemical shifts and the A1 substitution are established for illite resonances by computer fitting of well-resolved phyllosilicate spectra. Combination of these two constraints led to a general procedure for iterative fitting of 29 Si MAS NMR spectra of clay minerals containing high-charge (illite-like) and low-charge (smectite-like) sites. The applicability of the new method is demonstrated for two I-S samples from Cambrian black shale in the Baltic area and two I-S samples from Upper Jurassic oil-source rock in the Central Trough of the North Sea. In combination with data from XRD and chemical analysis, the results from 29 Si MAS NMR enables determination of the composition for the entire I-S particles.

Ga/Al substitutions in synthetic kaolinites and smectites

AbstractThe Ga for A1 substitution in kaolinites and smectites was studied using clay synthesis from initial gels having an (Al + Ga)/Si ratio of kaolinites andMGa = Ga/(Ga + A1) ratio ranging from 0 to 1. Only kaolinite was obtained for MGa in the range 0-0.10. For higher MGa, synthesized clays were both kaolinite and beidellite, or pure beidellites. The evolution of b cell parameters, and the appearance of avAI-OH-Ga absorption band at 3600 cm-1in FFIR spectra, proves the progressive substitution of AI by Ga in kaolinite. The low substitution of AI by Ga in kaolinite can be correlated with the large difference in ionic radii between Al3+and Ga3+which causes a large increase in cell dimensions. By contrast, the incorporation of Ga in smectites is easy and can be complete.

Ga/Al Substitutions in Synthetic Kaolinites and Smectites

The Ga for A1 substitution in kaolinites and smectites was studied using clay synthesis from initial gels having an (AI + Ga)/Si ratio of kaolinites and MGa = Ga/(Ga + A1) ratio ranging from 0 to 1. Only kaolinite was obtained for MGa in the range 0-0.10. For higher MGa, synthesized clays were both kaolinite and beidellite, or pure beidellites. The evolution of b cell parameters, and the appearance of a vAI-OH-Ga absorption band at 3600 cm -1 in FFIR spectra, proves the progressive substitution of AI by Ga in kaolinite. The low substitution of AI by Ga in kaolinite can be correlated with the large difference in ionic radii between AI 3+ and Ga 3§ which causes a large increase in cell dimensions. By contrast, the incorporation of Ga in smectites is easy and can be complete.

Cathodoluminescence and trace element zoning in quartz phenocrysts and xenocrysts

Quartz phenocrysts and xenocrysts are a common component of volcanic rocks but rarely contribute to our understanding of magmatic or eruptive processes due to an apparent internal chemical and structural homogeneity. Scanning electron microscopy cathodoluminescence imaging (SEM-CL) and secondary ion mass spectroscopy (ion microprobe) analysis (SIMS) are used here to demonstrate that quartz crystals in volcanic rocks show hitherto unrecognised internal structural and chemical zoning. Two contrasting crystal morphologies have been studied. Porphyritic euhedral bipyramidal quartz crystals in dacite from Bonne Nuit Bay, Jersey, UK show fine-scale growth zoning in SEM-CL. Zones are narrow (1–40 μm wide), planar, parallel to crystal faces, and overgrow more broadly zoned, rounded cores. These crystals are interpreted to have formed at small degrees of undercooling by diffusion-controlled growth. Quiescent magma conditions are indicated by the preservation of an Al-rich diffusive boundary layer which has not been removed by melt shearing during convection. In contrast, rounded and embayed porphyritic quartz grains in a quartz dacite from the Esperanza Mine, E1 Salvador, northern Chile show broad internal SEM-CL zones with irregular boundaries, some of which are truncated by grain margins indicating dissolution. Crystal rounding may occur by dissolution or melting due to thermal or thermal-chemical disequilibrium with surrounding melt, and embayments by gas bubble enhanced convective dissolution are consistent with the development of incipient ocelli textures (strings of amphibole inclusions adjacent to quartz rims). Several episodes of rounding can be recognised in some xenocrysts. Ion microprobe (SIMS) analysis of quartz from both samples shows that A1 contents are higher in areas of bright CL emission. Previous studies of CL in quartz have suggested that several factors control luminescence. Although A1 substitution for Si in SiO4 tetrahedra may be partly responsible for SEM-CL zoning recorded in volcanic quartz, additional mechanisms (including the effect of growth rate on defect density) probably also play a major role.

Cathodoluminescence of quartz from sandstones; interpretation of the UV range by determination of trace element distributions and fluid-inclusion P-T-X properties in authigenic quartz

Other| August 01, 1996 Cathodoluminescence of quartz from sandstones; interpretation of the UV range by determination of trace element distributions and fluid-inclusion P-T-X properties in authigenic quartz Christelle Demars; Christelle Demars CREGU, Vandoeuvre-les-Nancy, France Search for other works by this author on: GSW Google Scholar Maurice Pagel; Maurice Pagel Search for other works by this author on: GSW Google Scholar Etienne Deloule; Etienne Deloule Search for other works by this author on: GSW Google Scholar Philippe Blanc Philippe Blanc Search for other works by this author on: GSW Google Scholar American Mineralogist (1996) 81 (7-8): 891–901. https://doi.org/10.2138/am-1996-7-812 Article history first online: 02 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Search Site Citation Christelle Demars, Maurice Pagel, Etienne Deloule, Philippe Blanc; Cathodoluminescence of quartz from sandstones; interpretation of the UV range by determination of trace element distributions and fluid-inclusion P-T-X properties in authigenic quartz. American Mineralogist 1996;; 81 (7-8): 891–901. doi: https://doi.org/10.2138/am-1996-7-812 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentBy SocietyAmerican Mineralogist Search Advanced Search Abstract Quartz overgrowths from Keuper sandstones of the Paris basin were examined using cathodoluminescence (CL) microscopy and spectroscopy coupled with a scanning electron microscope (SEM). With the use of standard cold CL equipment, it was observed that the emission of authigenic quartz is much less intense than that of detrital quartz grains, but a reversal of intensity was observed with scanned CL in the 200-800 nm range. The main CL emission band of diagenetic quartz is at 330-340 nm in the UV range, with other bands in the visible range. The determination of trace element distributions in authigenic quartz by in situ analyses and by SIMS imagery reveals the correlation of the 330-340 nm emission band with the highest A1 and Li contents. The cathodoluminescence emission of diagenetic quartz in the UV range appears to be influenced by the coupled substitution of A1 and Li into the crystal. Two explanations are suggested: (1) Al, Li, or both serve as activators, and (2) the incorporation of Al and Li causes lattice defects that lead to an enhancement of the intrinsic luminescence. Trace element analyses and fluid-inclusion studies revealed that quartz overgrowths precipitated from a fluid that partially originated from an Li-enriched primary brine derived from eastern Triassic evaporites of the Paris basin. The specific CL emission band in the UV range can be linked to the diagenetic environment. The chemistry of the fluids appears to be the essential parameter, whereas precipitation temperatures do not influence the occurrence of such emissions. This content is PDF only. Please click on the PDF icon to access. First Page Preview Close Modal You do not currently have access to this article.

Magnetic and thermal properties of TbMn 2 and Tb(Mn 1 − xA1 x) 2 compounds

The effects of A1 substitution for Mn on the magnetic and thermal properties of TbMn 2 have been studied by measuring the temperature dependence of the magnetization, the thermal expansion and the specific heat of Tb(Mn 1 − x A1 x ) 2 compounds. It has been revealed that the substitution of A1 remarkably suppresses the magnetization, resulting in the disappearance of the sharp peak in the thermomagnetic curve characteristic of the helimagnetic transition of TbMn 2. The magnetic specific heat and the magnetic entropy of TbMn 2 and Tb(Mn 0.9A1 0.1) 2 were estimated. A1 substitution wipes out the λ-type peak of the specific heat for TbMn 2. The nature of the magnetic state and the magnetic phase transition in the A1-substituted system is discussed.

Rotationally Disordered Illite/Smectite in Paleozoic K-Bentonites

AbstractThe three-dimensional crystal structure of rotationally disordered illite/smectite (I/S) in K-bentonite samples from the Appalachian basin and neighboring areas is described using the parameters of 1) P0, the proportion of zero-degree layer stacking rotations, such as in the polytype series 1Md-1M; 2) Pcv, the proportion of 2:1 layers with cis-vacant (cv) octahedral sites that are randomly interstratified with trans-vacant (tv) layers; and 3) P60 the proportion of layers with n·60° rotations (as opposed to n·120°) in the rotated layers. These parameters were determined by computer modeling of experimental randomly oriented powder X-ray diffraction patterns.The proportion of cv interstratification in the I/S increases with A1 and decreases with Mg and Fe content. The proportion of n·60° rotations in the rotated layers increases with Mg and Fe content. The cv 120° disordered structure correlates with tetrahedral A1 for Si substitution and increasing tetrahedral charge. The tv n·60° disordered structures correlate with octahedral Mg for A1 substitution. The data indicate that the type of unit cell and nature of rotational disorder in I/S is controlled by the octahedral Mg content. The three-dimensional structures do not show any systematic correlation with Reichweite and percent expandability as determined from diffraction patterns of oriented sample preparations.

Density Functional Calculations on Model Clusters of Zeolite-.beta.

The substitution of silicon by aluminum at different tetrahedral sites of zeolite-@ in the presence of H+ and Na+ has been investigated by density functional calculations on pentameric model clusters. It is found that the relative substitution energies are within a narrow range, which is 1.4 kcal/mol in the presence of proton and 0.7 kcal/mol in the presence of Na+. For the protonated case, the A1 substitution is the least favored at sites associated with two four-membered rings. The structure of the A104 unit is considerably distorted in the protonated clusters due to the formation of a strong OH bond. The sodium ion has a less significant effect on the geometry of the A104 unit, since it forms much weaker bonds with two 0 atoms.

Fine structure analyses of the Drosophila and Saccharomyces heat shock factor--heat shock element interactions.

Heat shock genes are activated by the binding of the heat shock transcription factor (HSF) to heat shock elements (HSEs), consisting of arrays of the 5-bp unit NGAAN arranged as inverted repeats. Here, we have investigated the interaction of the 5-bp unit with HSFs of Drosophila and Saccharomyces. Mutations within the conserved, central trinucleotide GAA reduce the relative binding affinity of both HSFs. In addition, the base at position 1 (N1) also influences binding, with a strong preference for an A at this position. Methylation interference initially indicated that HSF contacts A1 in the minor groove, but interacts with the immediately adjacent base G2 in the major groove. Further characterization of this apparently abrupt minor to major groove transition by substitution of A1 with an inosine, shows that HSF contacts A1 in the major groove. We offer an explanation for this apparent contradiction and propose that HSF recognizes the HSE primarily through contacts within the major groove of the DNA helix. Finally, based on these observations and a re-evaluation of the base frequencies and criteria for consensus sequence assignment, we propose that the sequence AGAAN more accurately represents the consensus HSE motif.

Properties and distribution of iron oxides and their association with minor elements in the soils of south‐western Australia

SUMMARYIron oxides from 39 soils derived from various parent materials in south‐western Australia have been studied using a variety of techniques. Goethite and hematite were the only two Fe oxides present. The goethite/(goethite+hematite) ratio ranged from 0.18 to 1.0, and was highest in soils on acidic igneous rocks, decreasing for soils on alluvial and mafic parent materials. In a few soils derived from acid rocks only goethite was present. The redness rating of soils increased linearly with increasing amount of hematite. Al substitution in goethite ranged from 13 to 35 mol%, with higher values for soils on acid igneous rocks (median value = 26 mol%) than for soils on mafic (19 mol%) and alluvial (17 mol%) parent materials. Substitution of A1 in hematite ranged from 4 to 23 mol%, and was greatest in soils on mafic parent materials (median value = 12 mol% A1). A1 substitution in hematite was about half of that in associated goethite. The dehydroxylation temperature for goethite increased linearly with increasing A1 substitution. Goethite and hematite had similar crystal sizes (c. 20 nm), and both were in the form of irregular plates.Dissolution with 1 M HCl of iron oxides concentrated from the soils by 5 M NaOH digestion could be described both by the Cube Root Law and by Kabai's equation. Only one straight line was obtained for the dissolution data using Kabai's equation for samples containing both goethite and hematite, in contrast to the results of other workers. Major proportions of the Co, Cr, Cu, Mn, Ni and Zn in the soils were concentrated with the iron oxides, and the dissolution kinetics of these elements indicate that some may be present in the structure of the iron oxides.

Ab-initio molecular orbital calculations on the siting of aluminium in the Theta-1 framework: Some general guidelines governing the site preferences of aluminium in zeolites

Ab-initio molecular orbital calculations are utilized to obtain the preferred tetrahedral (T) sites for substitution of Si by AI in the Theta 1-framework. Using a method developed by Derouane and Fripiat ( Zeolites 1985, 5, 165), it is shown that the T1 and T4 sites of Theta 1 are the favored sites for A1 substitution. A survey of preferred Al substitution sites for Theta 1, ZSM-5, and ferrierite indicates that Al preferentially substitutes into sites having the highest average TO bond lengths and the lowest average TOT bond angles. It is suggested, however, that the use of the crystallographic TO bond lengths may lead to errors in the substitution trend, and, hence, it is preferable to discuss favored Al substitution sites in terms of TOT angles alone. Analysis of preferred Al substitution sites as the sole criteria of average TOT angle around a particular T site is shown to give rise to a slightly different substitution pattern than that obtained via the method proposed by Derouane and Fripiat.

57Fe Mössbauer effect study of highly substituted aluminum hematites: determination of the magnetic hyperfine field distributions

A number of synthetic α-(Fe 1− c Al c ) 2O 3 compounds with c ranging between 0.095 and 0.282 have been investigated by the Mössbauer effect technique at room temperature and at 80 K and two compositions ( c = 0.181 and 0.263) at variable temperature between 80 and 480 K. The results obtained by fitting two different magnetic hyperfine field distribution approaches are compared and the dependence of the hyperfine parameters on the A1 substitution and on the temperature is discussed.

The effect of substitution of A1 on the magnetic properties of Nd/sub 16/Fe/sub 78/B/sub 6/ permanent magnets

The temperature dependence of the anisotropy field H/sub A/ and of the coercivity of the mixed crystal series Nd/sub 16/(Fe/sub 1-x/Al/sub x/)/sub 78/B/sub 6/ was measured between 100 K and the Curie temperature T/sub c/. The intrinsic properties (like T/sub c/(x), H/sub A/(x) but also the lattice constants and the concentration dependence of the spin reorientation temperature) indicate that a part of the A1 enters indeed into the 2/14/1 lattice. The coercivity increases with increasing A1 content. The analysis of a correlation between /sub x/H/sub c/ and H/sub A/ gives hints of a decoupling between the grains due to the A1, but it shows also the limits of such attempts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Refinement of the Crystal Structure of A Monoclinic Ferroan Clinochlore

AbstractA monoclinic IIb-2 clinochlore from Washington, D.C., contrary to previous studies, is primarily a ferroan rather than a ferrian chlorite. Disorder of tetrahedral Si,Al cations is indicated because of unsuccessful structural refinements in subgroup symmetries. The true space group is C2/m. Slight ordering of Mg, Fe2+, and Fe3+ over octahedra M(l) and M(2) within the 2:1 layer (mean M-O,OH = 2.092 and 2.084 Å, respectively), complete ordering of trivalent Al into the centrosymmetric octahedron M(4) of the interlayer sheet (M-OH = 1.929 Å), and ordering of primarily divalent cations (Mg and Fe) into the two interlayer M(3) octahedra (M-OH = 2.117 Å) exist. The excess of negative charge above unity due to tetrahedral substitution of Al for Si (1.378 atoms) is compensated entirely within the octahedral sheet of the 2:1 layer.Ordering of a trivalent cation into one octahedron in the interlayer should be universal for all stable trioctahedral chlorites. In this specimen the ordering is due to (1) minimization of cation-cation repulsion by layer offsets which provide more space around the trivalent element, and (2) energy minimization by localization of the source of positive charge on the interlayer sheet in one octahedron rather than two. In other structures or for different compositions additional factors can be important also. Most chlorites of the IIb and Ib (β = 90°) types are expected to show disorder of the tetrahedral cations. The b positioning of interlayer and layer provides no preferential driving force for concentration of Si and A1 in any tetrahedron as a consequence of the expected ordering of the interlayer cations. The monoclinic IIb-2 polytype is less abundant in nature than the triclinic IIb-4 and IIb-6 structures, because only half as many possible superpositions of layers exist that will produce monoclinic symmetry. Crystallization factors must also be important, because the IIb-2 chlorite is much less abundant than predicted by this purely geometrical argument.

The crystal chemistry of the amphiboles. III: Refinement of the crystal structure of a sub-silicic hastingsite

SummaryThree-dimensional counter-diffractometer data and a full-matrix least-squares method have been used to refine the crystal structure of a sub-silicic hastingsite in the space group C2/m. The chemical composition of the amphibole is with ceil parameters a = 9·8659(4), b = 18·0139(8), c = 5·3545(2)Å, and β = 105·082(1)°. Unit weights were used throughout the refinement and the final R-factor for 1263 observed non-equivalent reflections was 4.1%. The mean tetrahcdral bond length for aluminous amphiboles varies linearly with the total amount of tetrahedral A1. Curves are derived relating individual mean bond lengths with A1 occupancy. The positional disorder on the A-site of the aluminous amphiboles appears to be partly related to the amount of substitution of A1 into the T(2) tetrahedron.

Minerals from the charnockite series of Amaravathi, Andhra Pradesh, South India

SummaryThe potash feldspar in the charnockites is orthoclase and they are inferred to have been formed around 700 °C. A twin-law study of the plagioclase indicates an igneous origin of the charnockites and pyroxene granulites. The KD values of the coexisting pyroxenes in the granulites are appropriate to equilibrium at 670 °C. A substantial substitution of A1 for Si in the values of the coexisting pyroxenes in the granulites are appropriate to equilibrium at 670 °C. A substantial substitution of A1 for Si in the Z group in all mafic minerals studied also indicates relatively high temperatures of formation. Almandine is pyroperich, a result of high pressure. The charnockites and pyroxene granulites are inferred to be formed under conditions of high pressure and temperature.

Differences between silica and silica-alumina gels II. A proposed mechanism for the gelation and syneresis of these gels

An ionic mechanism for the gelation of silica and silica-alumina gels is proposed as explanation of the very rapid gelation occurring within a certain pH range. The intermicellar bonds are hydrogen bonds and the condensation reaction is believed to be a slow reaction. This reaction is the essential feature of the syneresis, or aging, process in silica gel. Interruption of this process by introduction of an acidic medium causes rupture of the hydrogen bonds which, in turn, results in smaller particles, higher density and higher surface area. In the case of silica-alumina gel the properties of the alumina overshadow those of the silica groups. Thus, the most important reaction occurring during syneresis is the rupture of the hydrogen bonds joining alumina groups to silica groups. This reaction, furthermore, is accelerated by hydroxyl ions. As a result, increased syneresis time and/or exchange with slightly basic media give smaller particles and, therefore, greater surface area. Acidic exchange media promote the condensation reaction, thus giving increased particle size. In the case of silica-alumina gels decreased density invariably accompanies increased surface area ( i.e., decreased particle size). This is contrary to the effect found in silica gels. The explanation lies in the fact that the silica-alumina micelles are charged particles. An important consequence of the proposed theory is that the alumina particles must be “terminal” groups. Thus the base exchange properties of such gels do not arise by substitution of A1 for Si in tetrahedral groups.