Occupation Of Different Sites Research Articles

Hydrodynamics in kinetically constrained lattice-gas models.

Kinetically constrained models are lattice-gas models that are used for describing glassy systems. By construction, their equilibrium state is trivial and there are no equal-time correlations between the occupancy of different sites. We drive such models out of equilibrium by connecting them to two reservoirs of different densities, and we measure the response of the system to this perturbation. We find that under the proper coarse-graining, the behavior of these models may be expressed by a nonlinear diffusion equation, with a model- and density-dependent diffusion coefficient. We find a simple approximation for the diffusion coefficient, and we show that the relatively mild discrepancy between the approximation and our numerical results arises due to non-negligible correlations that appear as the system is driven out of equilibrium, even when the density gradient is infinitesimally small. Similar correlations appear when such kinetically constrained models are driven out of equilibrium by applying a uniform external force. We suggest that these correlations are the reason for the same discrepancy between the approximate diffusion coefficient and the numerical results for a broader group of models-nongradient lattice-gas models-for which kinetically constrained models are arguably the simplest example thereof.

Structural and spectroscopic features of Ca9M(PO4)7 (M = Al3+, Lu3+) whitlockites doped with Pr3+ ions

In this work we present the structural and spectroscopic properties of Ca9M(PO4)7 (M = Al, Lu) whitlockite compounds doped with Pr3+ ions. The Al containing samples were prepared by the citrate route, while the Lu based samples were prepared by standard solid state reaction. The structural properties were investigated by XRD measurements and Rietveld analysis. Detailed spectroscopic properties like emission and excitation spectra, luminescence kinetics and luminescence temperature quenching were measured to determine the influence of different trivalent host metal on the Pr3+ ions. Pr3+ enter in the three Ca2+ sites in the Ca9Al(PO4)7 compounds, creating some defect to compensate the charge mismatch, whereas in the Ca9Lu(PO4)7 Pr3+ ions occupy four Ca2+/Lu3+ sites, where no charge compensation is needed. The emission spectra are similar for both materials. Efficient quenching of the 1D2 emission was observed, while the 3P0 emission remains stable for all dopant concentrations. Decay times were found to be non-single exponential due to the occupation of different sites by the Pr3+ ions. The luminescence temperature quenching measurements have revealed that two different mechanisms (multi-phonon relaxation and cross-relaxation processes) are responsible for the emission quenching.

Selective Production of Reactive and Nonreactive Oxygen Atoms on Pd(001) by Rotationally Aligned Oxygen Molecules

Sticking together: The occupation of different sites by oxygen atoms that are produced by the dissociation of O(2) on Pd(100) is determined by the initial rotational alignment of the parent molecules. The atom locations are characterized by different chemical reactivities in the reaction with CO to form CO(2) (see picture), which are followed by synchrotron radiation (SR) experiments with a supersonic molecular beam (SMB).

Applications of Tailored Ferrocenyl Molecules as Electrochemical Probes of Biochemical Interactions

The development of electrochemical probes useful for investigating the occupancy by other molecules of sites on complex proteins such as human serum albumin (HSA) is described. Ferrocenyl-(oxoethylene)-fatty acid compounds of different fatty acid chain length probed different binding sites on HSA. The interaction could be changed from one primarily with a drug binding site, when the probe was ferrocene methanol, to one predominantly with medium-chain fatty acid binding sites, by adding an (oxoethylene)-fatty acid substituents. Finally, the interaction could be changed to one interacting primarily with high-affinity long-chain fatty acid binding sites, as the fatty acid chain length in ferrocene-(oxoethylene)-fatty acid molecules increased. These results strongly implied that the binding could be further tailored by relatively simple modifications to the probe, for example, by changing the balance of hydrophobicity and hydrophilicity. The possibility of a procedure using mass-produced electrochemical cells to determine the fractional occupancy of different sites on HSA is demonstrated.

Crystal Structure, Electronic Structure, and Luminescence of Cs2KYF6:Pr3+.

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Crystal Structure, Electronic Structure, and Luminescence of Cs2KYF6:Pr3+

AbstractThe crystal structure, electronic states and VUV spectroscopic behaviour of Cs2KYF6 doped with Pr3+ ions have been investigated both by experimental and theoretical methods. Cs2KYF6 (${\rm F}m{\bar 3}m$, Z = 4, a = 945.5(3) pm, R1all = 0.0297) crystallizes with the cubic elpasolite type of structure. The local relaxation of the activator ions in the host lattices has been calculated by the projector augmented wave method (computer code VASP). The electronic states have been calculated using a spin density functional procedure based on the atomic sphere approximation (computer code ASW). VUV spectroscopic measurements show fast 4f15d1 → 4f2 emission of nanosecond duration as well as slow 4f2 → 4f2 emission depending on the excitation energy which indicates the occupation of different sites in the host lattice. This assumption was verified by a recently developed quantum mechanical method. The combination of the experimental and the theoretical results show that the Pr3+ ions are occupying three different sites, namely the Y3+ and the Cs+ site as well as the K+ site.

Weak Polar Interactions Confer Albumin Binding Site Selectivity for Haloether Anesthetics

Enflurane and isoflurane are structural isomers with different anesthetic potencies and side effects. It is not clear whether these differences are produced by differing occupancy of common protein binding sites or by occupancy of different sites, but the very similar molecular properties make the latter possibility unlikely. In this study, the authors examined binding site selectivity of these anesthetics in human serum albumin (HSA). Binding of isoflurane and enflurane with HSA was determined with isothermal titration calorimetry. Competition with known ligands (propofol) allowed localization of binding sites within the HSA molecule. Molecular properties of isoflurane and enflurane were calculated. Isoflurane binds HSA with higher affinity but smaller total enthalpy than enflurane. Enthalpogram analysis suggested that isoflurane bound a single site, whereas enflurane bound two. Competition experiments indicated that enflurane and isoflurane share one binding site, which also binds propofol. The additional enflurane site binds propofol but not isoflurane. Increased salt concentration decreased the affinity for isoflurane but not for enflurane. The dipole moment of isoflurane is higher than that of enflurane, and the isoflurane binding site is more polar. These data indicate two binding sites of different character for the haloether anesthetics on HSA. One site is more polar and prefers isoflurane, presumably because of its larger dipole. The second site prefers the less polar enflurane. Therefore, weak polar interactions confer considerable selectivity, and differences in drug action may arise from occupancy of different protein sites.

Unanticipated guest motion during a phase transition in a ferroelastic inclusion compound.

Urea inclusion compounds (UICs) have been used as tools to understand ferroelastic domain switching and molecular recognition during crystal growth. Although the vast majority of UICs contain helical arrangements of host H-bonds, those containing guests with the formula X(CH(2))(6)Y (X, Y = Br, Cl, CN, NC) adopt an alternative P2(1)/n packing mode in which the host molecules exist as stacked loops of urea hexamers. Such structures may be further separated into two classes, ones distorted away from hexagonal symmetry along [100] (Br(CH(2))(6)Br, Br(CH(2))(6)Cl, and Cl(CH(2))(6)Cl) and those distorted along [001] (e.g. NC(CH(2))(6)CN). In each of these systems, guests exist as equilibrium mixtures of gauche conformers whose populations control the direction and magnitude of the observed distortion. Such UICs are potentially ferroelastic, but the n-glide requires that domains are not related by a simple rotation-translation mechanism as in the helical systems. Ferroelastic (degenerate) domain reorientation would necessitate a large-scale reorganization of the urea framework and rupture of numerous H-bonds. Coupled with distortions of 2 to 10%, this mechanism-based barrier to domain switching has precluded observation of this phenomenon. To prepare ferroelastic UICs with minimal distortions from hexagonal symmetry, attempts were made to form solid solutions of UICs containing guests from the two classes. This failed, however: solid solution formation of the stacked loop form is usually possible within a series (e.g. with Cl(CH(2))(6)Cl and Br(CH(2))(6)Br), but not between series (e.g. Cl(CH(2))(6)Cl and NC(CH(2))(6)CN). Crystals of Cl(CH(2))(6)CN/urea, in which a single guest contains substituents from each class, are distorted along [001] by only 0.5% from hexagonal symmetry at 298 K and exhibit ferroelastic domain reorientation at high forces. At -66 degrees C, Cl(CH(2))(6)CN/urea undergoes a topotactic phase transition that is unexpectedly nontopochemical. The structure of the low-temperature phase, including the orientation of the methylene chain, closely matches the structures of UICs distorted by 10% along [100] (e.g. Cl(CH(2))(6)Cl/urea). In this transition, small conformation changes of guests give rise to large-scale guest translations of approximately 5.5 A down the channel axis, even though an analogous gauche-to-gauche jump is well established in closely related materials that adopt either high- or low-temperature forms (e.g. NC(CH(2))(6)CN/urea, Cl(CH(2))(6)Cl/urea). The large guest displacement during this transition explains the difficulty in preparing solid solutions of the P2(1)/n form with guests of formula X(CH(2))(6)Y from two different series (e.g. Cl(CH(2))(6)Cl and NC(CH(2))(6)CN). This failure arises not from the different orientations of guest-induced strain, but from preferential occupation of different sites along the channel by the two types of guests. The subtlety of this process and of the interactions involved highlights the difficulty in using simple considerations of isomorphism to design new materials.

An NMR Investigation of Lithium Occupancy of Different Sites in the Oxide Superconductor LiTi2O4 and Related Compounds

The changes in lithium site occupancy as LiTi2O4 changes phase through the spinel to ramsdellite solid state phase transition are monitored by a 6Li NMR investigation of quenched samples, using magic angle spinning. Other lithium/titanium/oxygen compounds are studied as references for lithium environments. The 8a/16d 3:1 partition of lithium in Li4Ti5O12 is confirmed quantitatively. Lithium is found in several environments as a function of quenching temperature, and we discuss the assignment of the NMR responses to these different environments. These NMR studies, along with diffraction measurements, confirm that the spinel to ramsdellite transition is indirect, with two phases of changing composition coexisting between the spinel and the ramsdellite LiTi2O4 forms.

Coverage- and temperature-dependent site occupancy of carbon monoxide on Rh(111) studied by high-resolution core-level photoemission

High-resolution core-level photoemission is used to study structural aspects for the molecular adsorption of CO on the Rh(111) single-crystal surface, and in particular to derive the adsorption sites. The site sensitivity of the core-level binding energy and the fact that the core level photoemission signal is proportional to the adsorbate coverage make it possible to study quantitatively how the occupation of different sites changes with temperature and/or CO coverage. For the CO Rh(111) adsorption system we find two sites (on-top and three-fold hollow) to be occupied by the CO molecules. At coverages up to 0.33 ML only on-top sites are occupied, whereas at higher coverages a mixture of three-fold hollow and on-top sites are found. The distribution between these two sites is found to depend strongly on temperature. Quantitative studies of these reversible, temperature-dependent site changes have been carried out for a number of CO coverages. For coverages between 0.33 and ∼0.54 ML, increasing the temperature results in part of the molecules moving from on-top to three-fold hollow sites. This change is strongest for a (4 × 4) structure formed at 0.5 ML where an order-disorder transition is observed at a temperature of 120 K. For coverages above ∼0.54 ML, increasing the temperature leads instead to a decrease of the relative occupation of the three-fold hollow sites. For coverages below 0.33 ML, the molecules occupy on-top sites at all temperatures.

Acceleration of unisite catalysis of mitochondrial F1-adenosinetriphosphatase by ATP, ADP and pyrophosphate--hydrolysis and release of the previously bound [gamma-32P]ATP.

The effect of ATP, ADP and pyrophosphate (PPi) on hydrolysis and release of [gamma-32P]ATP bound to the high-affinity catalytic site of soluble F1 from bovine heart mitochondria under unisite conditions [Grubmeyer, C., Cross, R. L. & Penefsky, H. S. (1982) J. Biol. Chem. 257, 12092-12100] was studied. In accord with the previous data, it was observed that millimolar concentrations of ATP or ADP added to F1 undergoing unisite hydrolysis of [gamma-32P]ATP accelerated its hydrolysis. PPi also produced a hydrolytic burst of a fraction of the previously bound [gamma-32P]ATP; kinetic data suggested that for production of optimal hydrolysis by PPi of the bound [gamma-32P]ATP, two binding sites with apparent Kd of 27 microM and 240 microM must be filled. The extent of the hydrolytic burst induced by MgPPi was lower than that induced by ADP and ATP. In F1 in which PPi had produced a hydrolytic burst of the bound [gamma-32P]ATP, the addition of ATP induced a second burst of hydrolysis. By filtration experiments and enzyme trapping, it was also studied whether ATP, ADP and PPi produce release of the tightly bound [gamma-32P]ATP. At millimolar concentrations, ATP and ADP brought about release of about 25% of the previously bound [gamma-32P]ATP. At micromolar concentrations, ADP accelerated the hydrolysis of the previously bound [gamma-32P]ATP but not its release. Hence, the hydrolytic and release reactions could be separated, indicating that the two reactions require the occupancy of different sites in F1. With PPi, no release of the tightly bound [gamma-32P]ATP was observed. The ADP induced hydrolysis and release of the F1-bound [gamma-32P]ATP were inhibited by sodium azide to the same extent (60%). Since release of ATP from a high-affinity catalytic site of F1 represents the terminal step of oxidative phosphorylation, the data illustrate that the binding energy of substrates to F1 is critical to the ejection of ATP into the media. The failure of PPi to induce release of [gamma-32P]ATP bound to F1 under unisite conditions is probably due to its lower binding energy.

Iron sites in the FeCr ordered sigma phase

FeCr and Fe(CrNiMnMo) structurally ordered σ-phases have been studied. The Mossbauer parameters corresponding to the different crystallographic sites of iron atoms have been established. The spectral components have been attributed on the basis of both the order of symmetry around the sites and of an estimation of the isomer shift as a function of the number of Cr atoms n.n. of Fe atoms. Iron occupation of different sites obtained in this way are in good agreement with previous X-ray and synchrotron radiation diffraction results.

Diffusion and sorption in zeolites—I. A Markov process formulation

A molecular model is used for describing diffusion and sorption of a single component in a one-dimensional pore. A state space is defined in terms of the occupancy of different sites of an individual pore. The process of diffusion and sorption is then formulated for the first time as a Markov process. This results in a system of simultaneous linear equations whose solution gives important insights into the process of diffusion and sorption in zeolites. The obtained using this novel procedure are shown to be consistent with earlier results. The Markov process formulation can be extended to cover more complex cases which will be treated in later parts of this series.

A comparison of phototautomerism in different sites of free-base porphin (H 2P) in n-alkane crystals

Selective laser-induced phototautomerism of free-base porphin in different n-alkanes ( n-hexane, n-heptane, n-octane, nnonane, n-decane, n-undecane and n-dodecane) has been used to identify tautomer splittings in a number of sites in polycrystalline samples at 2 K. Pairs or lines arising from the two molecular orientations in each site can be reversibly transformed into each other. In the odd n-alkanes the occupation of different sites was not dependent on the rate at which the samples were frozen, but in the even n-alkanes metastable sites were only occupied following rapid quenching.

CO on Ru (001): Electron stimulated desorption and its correlation with other measurements

Electron stimulated desorption (ESD) of CO on Ru (001) leads to emission of CO+ and O+ ions from the same adsorption states. Following earlier work on this system, a correlated study of its ESD behaviour together with LEED, Δϕ, and TPD measurments has been carried out. The filling of the two states found earlier can be seen in ESD also. The dividing line between the high and low energy states is different in room temperature adsorption on the one hand, and desorption or equilibrium measurements at elevated temperatures on the other, which is explained by incomplete attainment of equilibrium in the layer under the first condition. The behaviour of the ESD ion currents with coverage showstthat part of the molecules occupying high energy sites in the ordered layer of intermediate coverage are shifted to less favourable sites at higher coverage, so that the full layer consists of a mixture of states due to the occupation of different sites in the compressed layer, possibly accompanied by lateral interactions. ESD also suggests that the high energy sites are the on-top sites rather than the threefold sites.