Fractional Site Occupancy Research Articles

Fractional Site Occupation of Hf5-xNbxGe4: Crystallographic Investigation and Thermodynamic Modeling.

For Abstract see ChemInform Abstract in Full Text.

Effects of an external electrical field on the polarization of growing organic crystals: a theoretical study

In certain non-ferroelectric molecular crystals a static external electrical field applied during the growth in the high vacuum may induce effects of permanent poling or depoling through interaction with dipolar molecules getting attached to crystal faces. In centrosymmetric crystal structures a field may effect a substantial deviation from a 50%:50% fractional site occupation with respect to the molecular dipole orientation. For channel-type inclusion compounds the electric field may affect growth sectors as such as to annihilate polarity in one sector and to enhance polarity in symmetry related sectors. Numerical simulations are given to show the change in the spatial distribution of polarity, including its temperature dependence.

Fractional site occupation of Hf 5− xNb xGe 4: crystallographic investigation and thermodynamic modeling

The binary compound Hf 5Ge 4 (structure type Sm 5Ge 4, oP36, Pnma) was found to form an extended ternary solid solution Hf 5− x Nb x Ge 4 with 0⩽ x⩽3.8. This solid solution was investigated by X-ray diffraction employing powder- as well as single crystal methods. Structure refinements at several different compositions within the phase revealed strongly preferred site occupation by Nb at the three crystallographically independent metal sites of the Sm 5Ge 4-type structure yielding an almost stepwise substitution mechanism of the two transition metals. Chemical bonding and site occupation are discussed on the basis of extended Hückel calculations performed on Hf 5Ge 4, and site volumes (Dirichlet domains) as well as atomic orbital occupations (site potentials) are correlated with the observed substitution mechanism. A thermodynamic model based on the compound energy formalism was developed in order to link the observed substitution mechanism to thermodynamic properties (Gibbs energies) of the different sublattices formed by the crystallographically independent sites.

Effect of cerium doping on the micro-structure and electrical properties of sol-gel derived Pb 1.05(Zr 0.53− δCe δTi 0.47)O 3 ( δ≤10 at.%) thin films

We have studied the effect of Ce on the phase formation behavior, surface morphology and electrical properties of sol-gel derived PZT thin films. Ce doping has been found to have a dramatic influence on the surface morphology and electrical characteristics of PZT thin films. Up to 1 at.% doping content Ce is found to improve the dielectric and ferroelectric properties and also optimal Ce doping is found to be effective in reducing the leakage current density and increasing the dielectric breakdown strength of PZT thin films. The fractional site occupancy of Ce ion has been predicted theoretically and the validity of the prediction has been investigated by XPS analysis. We have observed that Ce ions can exist both in +3 and +4 valence states. Up to 1 at.% content Ce predominantly enters into the A site with +3 valence state and acts as a donor dopant. The observed variation in microstructure and electrical properties have been discussed to be due to the fractional site occupancy of Ce ion either in A or B site, as a function of Ce doping content in PZT thin films.

Nb xTa 7− xS 2 ( x=2.73), a structurally distinct (Nb,Ta)-rich sulfide obtaining its stability from the dissimilar cohesive energy of the two metals

Nb x Ta 7− x S 2 ( x=2.73) has been prepared by application of high temperature synthesis techniques. The structure was determined by single crystal X-ray diffraction at ambient temperature to be orthorhombic, space group Pnma ( Z=4) with a=547.08(5), b=1971.33(9), c=1030.25(7) pm. Nb x Ta 7− x S 2 represents the metal-richest member of a series of phases with composition (Nb,Ta) n S 4. It is the only phase of its class that has no counterpart in one of the adjacent binary systems and is structurally related with the Ta-rich rather than the Nb-rich sulfides. Icosahedral (Nb,Ta) 13 clusters fused into pentagonal antiprismatic metal columns are the characteristic motif of the structure. The trend of the fractional site occupancies of the non-randomly distributed metal atoms can be conclusively rationalized on the basis of calculated total Mulliken overlap populations. Enrichment of the metal with the higher cohesive energy, namely Ta, is highly correlated with the strength of M–M interactions which differ significantly at the various crystallographic sites in this structurally distinguished metal-rich sulfide.

An improved azo chromophore for optical NO2 sensing

In previous studies, the response to NO2 of a number of substituted azobenzenes was characterised for sensitivity and kinetics over a range of temperatures. These studies indicated that the optimal sensor of this sort must be based on a chromophore with a binding energy for the target gas of approximately 70 kJ mol−1. Here, we present data for the best chromophore which has resulted, dispersed in an addition-cure polysiloxane matrix. We characterise the activation energy for the binding of NO2 to the azobenzene sites and report measurements of the response time of thin films from which the diffusion constant of NO2 in the matrix is deduced. We report on the behaviour of the films when operated in the cycled mode. We present quartz-crystal microbalance data allowing absolute calibration of the fractional site occupancy in a related system.

Simulation of Atomic Distribution of Guest Atoms in Layered 1T-TiS2Crystal using Monte Calro Method and Its Effect on the Magnetic Properties and Local Structures

Monte Carlo simulations of atomic distribution of intercalated guest atoms in the layered 1T-TiS 2 have been performed by taking into account attractive or repulsive pair-interactions between the neighboring guest atoms in the a -axis plane and along the c -axis of the crystal lattice (lattice size for computation: 18×18×6). X-ray diffraction patterns are calculated from the atomic distributions obtained using four kinds of pair-interactions, in qualitative agreement with the experimental data of the 2 a ×2 a ×2 c short-range ordered structure for x =0.15, and superlattices of \(2\sqrt{3}a\times 2a\times 2c\) for x =0.25 and \(\sqrt{3}a\times\sqrt{3}a\times 2c\) for x =0.333 with fractional site occupancy in Fe x TiS 2 . From the calculated atomic distributions, we have evaluated the number of neighboring guest atoms, the formation of clusters, and percolation cluster, as well as its dimension, all of which are responsible for the dynamical relaxation behaviors of the thermoremanent magnetization observed...

Montecarlo Simulation of Intercalated Atomic Distributions in Layered Dichalcogenide

Atomic distributions of intercalated guest atoms into layered dichalcogenide have been simulated taking into account the interactions between the first and second nearest neighboring guest atoms in the triangular lattices stacked with 6 layers (lattice size 18 × 18 × 6) using a MonteCarlo method. With these distributions, the X-ray patterns of Fe x TiS2 with x = 0.25 having the 2√a × 2a × 2c superlattice with the fractional site occupancy have been reproduced qualitatively by averaging the intensities for different patterns obtained by different random seeds.

Structur–Composition Relations and Fractional Site Occupancy of New M5Ge4 Compounds in the System Ge–Ta–Zr

The new ternary phases Zr4−xTa1+xGe4 (0.1<x<0.4) and Zr2+xTa3−xGe4 (0.1<x<1.1) were prepared from the elements by arc melting and subsequent induction heating at 1400–1450°C. Single-crystal X-ray diffraction was used to determine their structures and to refine mixed site occupancies. Zr4−xTa1+xGe4 was found to crystallize in the monoclinic space group P21/c (structure type: U2Mo3Si4) and the compound Zr2−xTa3−xGe4 shows orthorhombic symmetry (space group Pnma, structure type: Sm5Ge4). The close structural relationship between the two structures is discussed. Both phases exhibit pronounced differential fractional site occupancy of Ta and Zr on the metal sites and considerable composition ranges. Extended Hückel calculations were performed for various site occupancy models and Mulliken overlap populations for the different lattice sites of each structure were calculated for these models. The correlation of the cumulated Mulliken overlap populations and the atomic orbital populations with the actual site occupancies is discussed.

Phosphate ion partially relieves the cooperativity of effector binding in D-3-phosphoglycerate dehydrogenase without altering the cooperativity of inhibition.

The binding of L-serine to phosphoglycerate dehydrogenase from E. coli displays elements of both positive and negative cooperativity. In addition, the inhibition of enzymatic activity by L-serine is also cooperative with Hill coefficients greater than 1. However, phosphate buffer significantly reduces the cooperative effects in serine binding without affecting the cooperativity of inhibition of activity. The maximal degree of inhibition and fluorescence quenching in Tris buffer occurs when an average of two serine binding sites out of four are occupied. This value increases to three out of the four sites at maximal levels of inhibition and quenching in phosphate buffer. The increase from two to three sites appears to be due to the ability of phosphate to reduce the site to site cooperative effects and render each ligand binding site less dependent on each other. The correlation between the level of inhibition and the fractional site occupancy indicates that in Tris buffer, one serine is bound to each interface at maximal effect. In the presence of phosphate, the order of binding appears to change so that both sites at one interface fill before the first site at the opposite interface is occupied. In each case, there is a good correlation between serine binding, conformational change at the regulatory site interfaces, and inhibition of enzyme activity. The observation that phosphate does not appear to have a similar effect on the cooperativity of inhibition of enzymatic activity suggests that there are two distinct cooperative pathways at work: one path between the four serine binding sites, and one path between the serine binding sites and the active sites.

Novel Quaternary Metal-Rich Phosphides: Stabilization by Differential Fractional Site Occupancies and Polar Intermetallic Bonding

The new phosphide Hf5Nb5Ni3P5 has been prepared by arc-melting of a pressed stoichiometric mixture of HfP, Nb, and Ni. Single crystals suitable for the structure determination were obtained after annealing in an induction furnace at 1350 °C. Hf5Nb5Ni3P5 crystallizes in the hexagonal space group P62m (No. 189). The early transition metal atoms Hf and Nb are found on three crystallographically different sites, with refined occupancies of 100% Hf for the M1, 59.5(4)% Hf and 40.5(4)% Nb for the M2, and 13.1(6)% Hf and 86.9(6)% Nb for the M3 site. Small variations of the Hf to Nb ratio are possible, occurring with significantly different lattice parameters. The early transition elements form a three-dimensional framework with numerous M−M (M = Hf, Nb) interactions, including Ni and P in its trigonal prismatic voids. The differential fractional site occupancies can be understood on the basis of the different preferences of Hf and Nb to form M−M, M−Ni, and M−P bonds. The metallic character is confirmed by the P...

A modeling framework for the study of protein glycosylation

The key step in the asparagine-linked glycosylation of secretory proteins is the transfer of oligosaccharide from a dolichol precursor to the polypeptide at an Asp-X-Ser/Thr (NXS/T) consensus sequence. It is often the case, both in cultured cells and in vivo, that this reaction does not occur for every molecule of a given protein. Thus, the cell may create two protein populations, one bearing and one lacking oligosaccharide, for each potential glycosylation site. We present a structured kinetic modeling framework of the initial glycosylation event based on a balance of available glycosylation sites through the region of endoplasmic reticulum lumen proximal to the membrane. Oligosaccharyltransferase, a multimeric protein complex, catalyzes the sugar transfer. This enzyme is integral to the endoplasmic reticulum membrane, and it is thought to act cotranslationally. The nascent polypeptide may also fold in such a way as to prevent glycosylation from occurring. The net result is a potentially complex spatial and temporal relationship among translation, glycosylation, and other cotranslational events. Model results predict how fractional glycosylation site occupancy may depend on protein synthesis rate, oligosaccharyldolichol availability, and mRNA elongation rate. Although we are currently unable to quantitatively compare predicted to experimentally obtained fractional site occupancy, we are able to determine qualitative trends which may be confirmed experimentally.

Model for the high-temperature oxygen-ordering thermodynamics in YBa2Cu3O6+x: Inclusion of electron spin and charge degrees of freedom.

A lattice-gas model for the high-temperature oxygen-ordering thermodynamics in ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6+\mathit{x}}$ is presented, which assumes constant effective pair interactions between oxygen atoms and includes in a simple fashion the effect of the electron spin and charge degrees of freedom. This is done using a commonly utilized picture relating the creation of mobile electron holes and unpaired spins to the insertion of oxygen into the basal plane. The model is solved using the nearest-neighbor square approximation of the cluster-variation method. In addition, preliminary Monte Carlo results using next-nearest-neighbor interactions are presented. The model is compared to experimental results for the thermodynamic response function, kT(\ensuremath{\partial}x/\ensuremath{\partial}\ensuremath{\mu}${)}_{\mathit{T}}$ (\ensuremath{\mu} is the chemical potential), the number of monovalent copper atoms, and the fractional site occupancies. The model drastically improves the agreement with measured values of kT(\ensuremath{\partial}x/\ensuremath{\partial}\ensuremath{\mu}${)}_{\mathit{T}}$ as compared to bare lattice-gas models. Additionally, the monovalent copper count, in contrast to the standard lattice-gas models, is determined self-consistently and agrees qualitatively with experiment.

Substitution behavior of Mn, Cr, and Zr in ternary and quaternary alloys of TiAl

The fractional lattice site occupation of Mn, Cr and Zr in TiAl alloys was determined using the ALCHEMI (atom location by channeling enhanced microanalysis) method in transmission electron microscopy. The alloys were (in atomic per cent) 49.5Ti–49.5Al–1Mn, 48Ti–50Al–2Mn, 48ti–47.5Al–5Mn, 48Ti–49Al–3Cr, and 49Ti–49Al–1Zr–1Cr. The Mn substitutes randomly in the TiAl lattice and the Cr favors slightly the Al sites. In the quaternary alloy, Cr favors slightly Al sites and Zr occupies exclusively Ti sites.

Kinetics of vasoconstrictor action of endothelins.

Endothelin peptides (Et) induce slowly developing and long-lasting contractions of rat aortic strips with a rank order of potency (Et-1 = Et-2 greater than sarafotoxin S6b greater than Et-3) consistent with the involvement of an EtA-like receptor subtype. A similar profile of action is observed for Et-induced intracellular [Ca2+]i mobilization in cultured aortic myocytes. Modeling the association of Et-1 to its receptor shows that, at concentrations which produce large increases in tension, Et-1 associates rapidly to its receptors and that a slow rate of association is not responsible for the slow rate of tension development. Action of endothelins on [Ca2+]i was studied using isolated cultured aortic myocytes and compared with that of angiotensin II and vasopressin. Results show that three vasoconstrictors produce similar and rapid changes in [Ca2+]i. The rate-limiting step for the contractile action of Et is a postreceptor event probably distal to early changes in [Ca2+]i. Biological responses to Et are usually characterized by a relative insensitivity to the peptide as compared with Kd values determined in binding experiments. Data presented show that insensitivity of the early [Ca2+]i responses to Et could be accounted for by the fact that the responses develop under nonequilibrium conditions. Tension amplitude seems also to be determined by non-equilibrium binding conditions. It correlates with the fraction of the Et-1 binding sites occupied 20 s after addition of the peptide and not to the fractional site occupancy at the time of maximum tension development.(ABSTRACT TRUNCATED AT 250 WORDS)

Changes in a fractional site occupancy as an effect of an oxygen ordering on the basal CuO plane in YBa2Cu3Ox

X-ray diffraction and thermogravimetric (TGA) studies have been carried out on orthorhombic YBa2Cu3Ox samples obtained by the reoxygenation of tetragonal samples. Thermogravimetric measurements performed in 100% oxygen provided data for the oxygen content (x) on the CuO basal planes. At fixed x higher than 6.8, samples obtained by different final heat treatments show different amounts of orthorhombic distortion (higher values for samples with higher degree of ordering). The orthorhombic distortion and oxygen content data have been used for the estimation of fractional site occupancy of O(1) and O(5) sites∗∗The site notation is the same as in Jorgensen's et al.2 paper. of YBa2Cu3Ox on the basis of Bakker's et al. 8theory. Differences in fractional site occupancy are obtained for samples with different degree of ordering.

Statistical analysis of electron channelling microanalytical data for the determination of site occupancies of impurities

Abstract A novel method for determining the concentration and distribution across sites of substitutional impurities in crystals is described, as an alternative to the usual ratio method of atom location by the channelling enhanced microanalysis (ALCHEMI) technique. The integrated X-ray counts for emission from impurity and host atom species under strong zone-axis diffraction conditions are analysed using standard multivariate statistical procedures. This enables both the total concentration and the fractional site occupancy of the impurity species to be determined, together with quantitative estimates of the uncertainties in these quantities. This method of analysis is illustrated through the determination of the site occupancy of Fe in a Cr2MnO4 spinel. Advantages of this technique include reduced sensitivity both to the effects of delocalization and to the effects of experimental errors compared with standard ALCHEMI analyses.

Multi-analyte immunoassay

Immunoassays rely on the molecular recognition properties possessed by antibodies to measure substances defined by a particular structure. They can therefore be defined as “structurally specific”, as distinct from “functionally specific” assays, e.g. bioassays, which compare the biological effects of substances which are functionally similar, but which may differ in molecular structure. Within the broad class of “immunoassays”, two subclasses may be distinguished, differing in their design. These may be described as “competitive” and “non-competitive”, respectively, reflecting their dependence on the use of optimal concentrations of antibody which are either very small or very large. It is demonstrable that “non-competitive” assays are those relying on measurement of occupied antibody binding sites following reaction with analyte; conversely “competitive” assays rely on measurement of unoccupied sites. In certain assay designs, it may be shown that fractional antibody binding site occupancy is independent of (a) antibody concentration, and (b) sample volume. Such assays may be termed “ambient analyte immunoassays”. This concept has been exploited in the development of free hormone and drug assays, and currently underlines the development of salivary “dip-stick” assays in the Author's Department. The concept is also being exploited in the development of “multi-analyte” immunoassay systems, enabling the simultaneous measurement of tens or even hundreds of substances simultaneously in the same small sample. These systems depend on measurement of fractional antibody occupancy using two different labels: one labeling the “sensing” antibody, the second labeling a “developing antibody”, selected to react either with occupied or unoccupied sites on the “sensing” antibody. The ratio of signals emitted by the two labeled antibodies reveals the analyte concentration to which the sensing antibody has been exposed. An array of sensing antibodies, each labeled with the same fluorescent label, is scanned (by a laser), and the fluorescent signal ratio emitted from each discrete antibody couplet in the array measured. Multi-analyte immunoassay systems of this kind are likely to totally transform medical diagnosis in the foreseeable future and are also likely to be of value in the analysis of complex protein mixtures deriving from recombinant DNA technologies.

Oxygen-vacancy ordering in the YBa2Cu3Oz basal plane studied by the cluster variation method

The cluster variation method is used to calculate a phase diagram for a two-dimensional Ising model representing the Cu2O plane of the high-Tc superconductor YBa2Cu3Oz. Both first (V1 and second-neighbor (V2) interactions are considered, withV2/V1= −1/2; At high temperatures, the transition from the disordered (tetragonal) to the ordered (orthorhombic) phase is second-order. A tricritical point is found below which phase separation occurs. Fractional site occupancy and second-neighbor pair correlations are calculated as a function of temperature. The relevance of the model to the thermodynamics of ordering in the high-Tc compound is discussed.

A theory for the width of the Coulomb gap

The results of two different calculations of the mean width Eg of the Coulomb gap are presented. The calculations are performed for the 'lattice model' used by Efros and Shklovskii (1975) in which the fractional site occupation K and the disorder energy W0 are parameters which may be varied independently. The authors determine approximations to the ground state first by stabilising the system against single-electron transfers, and second by direct minimisation of the total energy. Eg is found to depend on W0 as Eg varies as Ec((Ec/W0+Ec))1(d-1)/ where d is the dimensionality, and is either two or three. The dependence on K of Eg differs slightly for the two methods.