The molecular dynamics study of lithium ion conduction in phosphate glasses and the role of non-bridging oxygen

Molecular dynamics (MD) simulation of lithium phosphate (Li2O-P2O5) glasses with varying Li2O content has been carried out. Two different P-O distances corresponding to phosphorus coordination with bridging oxygen (BO) and non-bridging oxygen (NBO) were identified in the simulated glasses. NBO-BO interconversion or bond switching was noted, which results in a dynamic equilibration of the tetrahedral phosphate units (P-n, n = 1,3 indicates the number of bridging oxygen atoms in the coordination of phosphorus). The NBO-BO bond switching is mildly activated with an effective activation barrier of 0.03-0.05 eV. Lithium ion jumps do not appear to be strongly coupled to bond switching. But the number of Li+ ions coordinated to an optimum number of NBOs and the number of Li+ ions jumping out of their sites appear to be correlated. Detailed analysis was made of the dynamics of P-n species and new insights have been obtained regarding ion migration in network-modified phosphate glasses.

Raman spectral studies of borate glasses

Raman spectroscopic measurements in borate glasses have been reviewe. The review shows that the technique is useful in identifying the structural groups present in the borate on the basis of the Krogh-Moe hypothesis. Vitreous B2O3 and alkali borates are extensvvely studied and a satisfactory assignment of bands is possible by a careful consideration of the literature. A cation effect on the borate netwoork is observed. Availaable measurements on binary borates other than alkali borates and on ternary borates are limited and more work is required to identify the structural modifications that take place with composition. Mixed alkali effect is reported only lithium-caesium borade and shows the formation of non-bridging oxygens, destroying the six-membered rings when Li2O is replaced by Cs2O. Fast ionic glasses (alkali borates containing alkali halides) yield the same Raman spectra as the alkali borates, except when the alkali is a fluoride.

Ion transport studies in lithium phospho-molybdate glasses containing Cl- ion

Ion conducting glasses in xLiCl-20Li(2)O-(80-x) 0.80P(2)O(5)-0.20MoO(3)] glass system have been prepared over a wide range of composition (X = 5, 10, 15, 20 and 25 mol%). The electrical conductivity and dielectric relaxation of these glasses were analyzed using impedance spectroscopy in the frequency range of 10 Hz-10 MHz and in the temperature range of 313-353 K. D.c. activation energies extracted from Arrhenius plots using regression analysis, decreases with increasing LiCl mol%. A.c. conductivity data has been fitted to both single and double power law equation with both fixed and variable parameters. The increased conductivity in the present glass system has been correlated with the volume increasing effect and the coordination changes that occur due to structural modification resulting in the creation of non-bridging oxygens (NBO's) of the type O-Mo-O- bonds in the glass network. Dielectric relaxation mechanism in these glasses is analyzed using Kohlrausch-Williams-Watts (KWW) stretched exponential function and stretched exponent (beta) is found to be insensitive to temperature.

一种宽带拉曼放大碲酸盐玻璃的拉曼散射特性

The flattening and broadening effects of Ga2O3, GeO2, P2O5 in TeO2-BaCO3-SrCO3- Nb2O5 (TBSN) glass system were studied. The results showed that P2O5 can broaden the vibration band in Raman spectra and Ga2O3, GeO2 can flatten the spectra compared with TBSN glass. And also, they can extend the main vibration band and decrease the vibration intensity of 730 cm^-1 and 780 cm^-1 nonbridging oxygen connected with Te. They also make for the decrease of flatness in 600-870 cm^-1 vibration band and GeO2 has larger effect than Ga2O3 in weakening the vibration of nonbridging oxygen.

Changes of physical properties of glass surfaces exposed to KNO3 vapors

Modifications of glass surfaces were studied after exposure of samples to an atmosphere resulting from the decomposition of molten KNO3. The diffusion coefficient of K+ ions migrating into the surfaces of float glass and synthesized glasses doped with up to 5 wt% SnO2 was calculated by the Boltzmann-Matano technique. The Vickers hardness and the refractive index increase with exposure time. Infrared spectra show that the migration of K+ is responsible for an increase in the number of non-bridging oxygens in the exposed samples. The spectra of the synthesized glasses present evidences that their surfaces undergo crystallization during the exposure. All results lead to the conclusion that the presence of tin in the glasses hinders the diffusion of K+ ions, thus affecting the Vickers hardness, the refractive index and the infrared spectra. It is shown that the exposure method can be used as an alternative process to promote the K+ migration into glass surfaces. (c) 2006 Elsevier B.V. All rights reserved.

Structural studies in lead germanate glasses: EXAFS and vibrational spectroscopy

The Raman, IR absorption and EXAFS spectra at the Ge K-edge and Pb LIII-edge of eight lead germanate glasses, with general formula xPbO(1-x)GeO2 with x = 0.20, 0.25, 0.33, 0.40, 0.50, 0.53, 0.56 and 0.60, have been measured. The occurrence of [GeO6] units besides [GeO4] could not be deduced unambiguously from the data. The vibrational and EXAFS data agree with a progressive depolymerization of the network. Starting from all Ge atoms linked to four bridging oxygens in GeO2 (x = 0), the number of tetrahedral units with one or two non-bridging oxygens increases with x. At low content, Pb2+ ions act as modifiers in the germanate structure, but to a lesser extent than an equivalent number of alkaline ions. © 1993.

Atomic mutagenesis of the ribosomal Sarcin-Ricin-Loop to study EF-G GTPase activation

Translocation factor EF-G, possesses a low basal GTPase activity, which is stimulated by the ribosome. One potential region of the ribosome that triggers GTPase activity of EF-G is the Sarcin-Ricin-Loop (SRL) (helix 95) in domain VI of the 23S rRNA. Structural data showed that the tip of the SRL closely approaches GTP in the active center of EF-G, structural probing data confirmed that EF-G interacts with nucleotides G2655, A2660, G2661 and A2662.1-3 The exocyclic group of adenine at A2660 is required for stimulation of EF-G GTPase activity by the ribosome as demonstrated using atomic mutagenesis.4 Recent crystal structures of EF-G on the ribosome, gave more insights into the molecular mechanism of EF-G GTPase activity.5 Based on the structure of EF-Tu on the ribosome1, the following mechanism of GTPase activation was proposed: upon binding of EF-G to the ribosome, the conserved His92 (E.coli) changes its position, pointing to the γ-phosphate of GTP. In this activated state, the phosphate of residue A2662 of the SRL positions the catalytic His in its active conformation. It was further proposed that the phosphate oxygen of A2662 is involved in a charge-relay system, enabling GTP hydrolysis. In order to test this mechanism, we use the atomic mutagenesis approach, which allows introducing non-natural modifications in the SRL, in the context of the complete 70S ribosome. Therefore, we replaced one of the non-bridging oxygens of A2662 by a methyl group. A methylphosphonat is not able to position or activate a histidine, as it has no free electrons and therefore no proton acceptor function. These modified ribosomes were then tested for stimulation of EF-G GTPase activity. First experiments show that one of the two stereoisomers incorporated into ribosomes does not stimulate GTPase activity of EF-G, whereas the other is active. From this we conclude that indeed the non-bridging phosphate oxygen of A2662 is involved in EF-G GTPase activation by the ribosome. Ongoing experiments aim at revealing the contribution of this non-bridging oxygen at A2662 to the mechanism of EF-G GTPase activation at the atomic level.

Atomic mutagenesis of the ribosomal Sarcin-Ricin-Loop to study EF-G GTPase activation

Translocation factor EF-G, possesses a low basal GTPase activity, which is stimulated by the ribosome. One potential region of the ribosome that triggers GTPase activity of EF-G is the Sarcin-Ricin-Loop (SRL) (helix 95) in domain VI of the 23S rRNA. Structural data showed that the tip of the SRL closely approaches GTP in the active center of EF-G, structural probing data confirmed that EF-G interacts with nucleotides G2655, A2660, G2661 and A2662.1-3 The exocyclic group of adenine at A2660 is required for stimulation of EF-G GTPase activity by the ribosome as demonstrated using atomic mutagenesis.4 Recent crystal structures of EF-G on the ribosome, gave more insights into the molecular mechanism of EF-G GTPase activity.5 Based on the structure of EF-Tu on the ribosome1, the following mechanism of GTPase activation was proposed: upon binding of EF-G to the ribosome, the conserved His92 (E.coli) changes its position, pointing to the γ-phosphate of GTP. In this activated state, the phosphate of residue A2662 of the SRL positions the catalytic His in its active conformation. It was further proposed that the phosphate oxygen of A2662 is involved in a charge-relay system, enabling GTP hydrolysis. In order to test this mechanism, we use the atomic mutagenesis approach, which allows introducing non-natural modifications in the SRL, in the context of the complete 70S ribosome. Therefore, we replaced one of the non-bridging oxygens of A2662 by a methyl group. A methylphosphonat is not able to position or activate a histidine, as it has no free electrons and therefore no proton acceptor function. These modified ribosomes were then tested for stimulation of EF-G GTPase activity. First experiments show that one of the two stereoisomers incorporated into ribosomes does not stimulate GTPase activity of EF-G, whereas the other is active. From this we conclude that indeed the non-bridging phosphate oxygen of A2662 is involved in EF-G GTPase activation by the ribosome. Ongoing experiments aim at revealing the contribution of this non-bridging oxygen at A2662 to the mechanism of EF-G GTPase activation at the atomic level.

Tail bridging vs. patchiness

The subject of this thesis are the interactions between nucleosome core particles (NCPs). NCPs are the primary storage units of DNA in eucaryotic cells. Each NCP consists of a core of eight histone proteins and a strand of DNA, which is wrapped around about two times. Each histone protein has a terminal tail passing over and between the superhelix of the wrapped DNA. Special emphasis was placed on the role of the histone tails, since experimental ndings suggest that the tails have a great in uence on the mutual attraction of the NCPs. In those experiments Mangenot et al. observe a dramatic change in the con guration of the tails, which is accompanied by evidence of mutual attraction between NCPs, when a certain salt concentration is reached. Existing models used in the theoretical approaches and in simulations focus on the description of the histone core and the wrapped DNA, but neglect the histone tails. We introduce the multi chain complex as a new simulation model. Here the histone core and the wrapping DNA are modelled via a charged sphere, while the histone tails are represented by oppositely charged chains grafted on the sphere surface. We start by investigating the parameter space describing a single NCP. The Debye-Huckel potential is used to model the electrostatic interactions and to determine the e ective charge of the NCP core. This value is subsequently used for a study of the pairinteraction of two NCPs via an extensive Molecular Dynamics study. The monomer distribution of the full chain model is investigated. The existence of tail bridges between the cores is demonstrated. Finally, by discriminating between bridging and non-bridging con gurations, we can show that the effect of tail bridging between the spheres does indeed account for the observed attraction. The full chain model can serve as a model to study the acetylation of the histone tails of the nucleosome. The reduction of the charge fraction of the tails, that corresponds to the process of acetylation, leads to a reduction or even the disappearance of the attraction. A recent MC study links this e ect to the unfolding of the chromatin ber in the case of acetylated histone tails. In this case the acetylation of the histone tails leads to the formation of heterochromatin, and one could understand how larger regions of the genetic information could be inactivated through this mechanism.

Hyalotekite, (Ba,Pb,K)(4)(Ca,Y)(2)Si-8(B,Be)(2)(Si,B)(2)O28F, a Tectosilicate Related to Scapolite: New Structure Refinement, Phase Transitions and a Short-Range Ordered 3B Superstructure

Hyalotekite, a framework silicate of composition (Ba,Pb,K)(4)(Ca,Y)(2)Si-8(B,Be)(2) (Si,B)(2)O28F, is found in relatively high-temperature(greater than or equal to 500 degrees C) Mn skarns at Langban, Sweden, and peralkaline pegmatites at Dara-i-Pioz, Tajikistan. A new paragenesis at Dara-i-Pioz is pegmatite consisting of the Ba borosilicates leucosphenite and tienshanite, as well as caesium kupletskite, aegirine, pyrochlore, microcline and quartz. Hyalotekite has been partially replaced by barylite and danburite. This hyalotekite contains 1.29-1.78 wt.% Y2O3, equivalent to 0.172-0.238 Y pfu or 8-11% Y on the Ca site; its Pb/(Pb+Ba) ratio ranges 0.36-0.44. Electron microprobe F contents of Langban and Dara-i-Pioz hyalotekite range 1.04-1.45 wt.%, consistent with full occupancy of the F site. A new refinement of the structure factor data used in the original structural determination of a Langban hyalotekite resulted in a structural formula, (Pb1.96Ba1.86K0.18)Ca-2(B1.76Be0.24)(Si1.56B0.44)Si8O28F, consistent with chemical data and all cations with positive-definite thermal parameters, although with a slight excess of positive charge (+57.14 as opposed to the ideal +57.00). An unusual feature of the hyalotekite framework is that 4 of 28 oxygens are non-bridging; by merging these 4 oxygens into two, the framework topology of scapolite is obtained. The triclinic symmetry of hyalotekite observed at room temperature is obtained from a hypothetical tetragonal parent structure via a sequence of displacive phase transitions. Some of these transitions are associated with cation ordering, either Pb-Ba ordering in the large cation sites, or B-Be and Si-B ordering on tetrahedral sites. Others are largely displacive but affect the coordination of the large cations (Pb, Ba, K, Ca). High-resolution electron microscopy suggests that the undulatory extinction characteristic of hyalotekite is due to a fine mosaic microstructure. This suggests that at least one of these transitions occurs in nature during cooling, and that it is first order with a large volume change. A diffuse superstructure observed by electron diffraction implies the existence of a further stage of short-range cation ordering which probably involves both (Pb,K)-Ba and (BeSi,BB)-BSi.

Raman spectroscopic study of a hydroxy-arsenate mineral containing bismuth-atelestite Bi2O(OH)(AsO4)

The Raman spectrum of atelestite Bi2O(OH)(AsO4), a hydroxy-arsenate mineral containing bismuth, has been studied in terms of spectra-structure relations. The studied spectrum is compared with the Raman spectrum of atelestite downloaded from the RRUFF database. The sharp intense band at 834 cm-1 is assigned to the 1 AsO43- (A1) symmetric stretching mode and the three bands at 767, 782 and 802 cm-1 to the 3 AsO43- antisymmetric stretching modes. The bands at 310, 324, 353, 370, 395, 450, 480 and 623 cm-1 are assigned to the corresponding ν4 and ν2 bending modes and Bi-O-Bi (vibration of bridging oxygen) and Bi-O (vibration of non-bridging oxygen) stretching vibrations. Lattice modes are observed at 172, 199 and 218 cm-1. A broad low intensity band at 3095 cm-1 is attributed to the hydrogen bonded OH units in the atelestite structure. A weak band at 1082 cm-1 is assigned to  (Bi-OH) vibration.

Single crystal Raman spectroscopy of natural leiteite ZnAs2O4 and in comparison with the synthesised mineral

The oriented single crystal Raman spectrum of leiteite has been obtained and the spectra related to the structure of the mineral. The intensities of the observed bands vary according to orientation allowing them to be assigned to either Ag or Bg modes. Ag bands are generally the most intense in the CAAC spectrum, followed by ACCA, CBBC, and ABBA whereas Bg bands are generally the most intense in the CBAC followed by ABCA. The CAAC and ACCA spectra are identical, as are those obtained in the CBBC and ABBA orientations. Both cross-polarised spectra are identical. Band assignments were made with respect to bridging and non-bridging As-O bonds.

The synthesis, characterization, X-ray structure and magnetism of dinuclear-based bis[μ-(1,1,3,3-tetracyano-2-ethoxypropenido-κ2N,N′) (1,1,3,3-tetracyano-2-ethoxypropenido-κN)(2,2′-bipyridine)copper(II)] organized in alternating chains via semi-coordinating Cu–N distances

The monoanionic ligand 1,1,3,3 tetracyano-2 ethoxypropenide (tcnoet) is reported with its Cu(II)–bpy complex of formula [Cu2(µ-tcnoet)2(tcnoet)2(bpy)2]. The structure has been determined using X-ray diffraction and features an alternating chain with bridging tcnoet ligands. One ligand acts as a bidentate, dinucleating ligand with one short Cu–N and one medium Cu–N bond, whereas the other tcnoet is largely monodentate, albeit with a very weak interdimer Cu–N bond. Despite the arrangement in dinuclear units, further arranged into linear chains through the non-bridging tcnoet ligand, the compound shows no significant magnetic exchange, as deduced from magnetic susceptibility down to 4 K. Ligand-field, IR and EPR spectra in the solid state and in frozen solution are reported and are consistent with the overall structure.

A structural study of Li2S---B2S3 glasses by neutron diffraction

The radial distribution functions (RDFs) of five xLi2S.(1 - x)B2S3 glasses (x = 0.55, 0.60, 0.67, 0.71 and 0.75) have been determined from neutron diffraction experiments performed at the Institut Laue-Langevin, Grenoble. These glasses are prepared by casting a molten mixture of boron, sulphur and Li2S inside a controlled atmosphere glovebox. Addition of the Li2S Modifier is found gradually to suppress all peaks corresponding to interatomic distances > 3.5 angstrom, which implies that the structural entities present in these glasses become segmented, and therefore more ionic, as x increases. The assumption of the existence of four main structural entities based on four- and three-coordinated borons (the latter carrying bridging and/or non-bridging sulphurs) accounts for all the peaks present in the RDFs as a function of composition. Furthermore, in the most modified glass (x = 0.75), that which contains only 'isolated' BS33- triangles, there seems to be evidence for either octahedral or tetrahedral coordination of Li+ by S- ions

Distribution of ionic charge carriers and migration barriers in binary alkali silicate glasses

Likely spatial distributions of network-modifying (and mobile) cations in (oxide) glasses are discussed here. At very low modifier concentrations, the ions form dipoles with non-bridging oxygen centres while, at higher levels of modification, the cations tend to order as a result of Coulombic interactions. Activation energies for cation migration are calculated, assuming that the ions occupy (face-sharing) octahedral sites. It is found that conductivity activation energy decreases markedly with increasing modifier content, in agreement with experiment.