Non-bridging Oxygen Atoms Research Articles

Void Deformation and Breakup in Shearing Silica Glass

We study shear deformation and breakup of voids in silica glass using molecular dynamics simulations. With an increase in the shear strain, two kinds of defects--threefold-coordinated silicon and nonbridging oxygen atoms--appear as spherical voids deform elastically into ellipsoidal shapes. For shear strains epsilon>15%, nanocracks appear on void surfaces and voids deform plastically into a threadlike structure. Nanocracks are nucleated by the migration of threefold-coordinated Si and nonbridging O on -Si-O-Si-O- rings. For epsilon>40%, the threadlike structures break up into several fragments.

Barium borosilicate glass as a matrix for the uptake of dyes

Barium borosilicate (BBS) and sodium borosilicate (SBS) glass samples, prepared by the conventional melt-quench method, were used for the uptake of Rhodamine 6G dye from aqueous solution. The experimental conditions were optimized to get maximum uptake and was found to be 0.4 mg of dye per gram of BBS glass sample. For the same network former to modifier ratio, barium borosilicate glasses are found to have improved extent of uptake for the dye molecules from aqueous solutions compared to sodium borosilicate glasses. Based on 29Si MAS NMR studies on these glasses, it is inferred that significantly higher number of non-bridging oxygen atoms present in barium borosilicate glasses compared to sodium borosilicate glasses is responsible for its improved uptake of Rhodamine 6G dye. 11B MAS NMR studies have confirmed the simultaneous existence of boron in BO 3 and BO 4 configurations in both barium borosilicate and sodium borosilicate glasses. The luminescence studies have established that the dye molecule is incorporated into the glass matrix through ion exchange mechanism by replacing the exchangeable ions like Na +/Ba 2+ attached with the non-bridging oxygen atoms present in the glass.

Structure of barium chloride-oxide tellurite glasses

Abstract New barium chloride-oxide tellurite glasses, BaCl 2 – BaO – TeO 2 , are studied by means of quantum-chemical modeling and Raman spectroscopy and a model of glass network is developed. The model allows one to relate the glass structure and vibrational properties (in particular, vibrational frequencies and Raman intensities) with the glass composition. Continuous network of barium chloride-oxide tellurite glass is proved to be formed mainly by structural groups of three types, TeO 4 trihedral bipyramids, O 2 Te O trihedral pyramids and O 3 Te – O - tetrahedra. No structural groups of any other type are necessary for the continuous network being built. Barium and chlorine atoms form no covalent bonds in the glass network occurring as Ba 2 + and Cl - ions in interstitial sites. Interpretation of Raman spectra of barium chloride-oxide tellurite glasses in the 550 – 850 cm - 1 range is suggested. In particular, the Raman band near 760 cm - 1 characteristic of these glasses is shown to be caused by both stretching vibrations of Te O double bonds of nonbridging oxygen atoms in O 2 Te O groups and stretching vibrations of Te – O - bonds of negatively charged nonbridging oxygen atoms in O 3 Te – O - groups. The model can be applied to analyze vibrational spectra of barium chloride-oxide tellurite glasses of various compositions.

XPS and magnetic studies of vanadium tellurite glassses

A series of tellurite glasses containing vanadium with nominal composition xV 2O 5–(1 − x)TeO 2, where x = 0.1, 0.2, 0.3, and 0.4, have been prepared by melt quenching technique and investigated using X-ray photoelectron spectroscopy (XPS) and magnetization techniques. The Te 3d core level spectra show asymmetry and therefore were fitted with two contributions one from Te ions in TeO 4 trigonal bipyramid (tbp) configuration and the other from Te ions in TeO 3 trigonal pyramid (tp) configuration. Quantitative analysis of the areas of both components support the model of a change of TeO 4 tbp to TeO 3 tp upon V 2O 5 addition. The V 2p core level spectra did not show any asymmetry and were fitted with a single component corresponding to V 5+ while the O 1s core level spectra show slight asymmetry on the higher binding energy side of the main peak and were fitted with two contributions, one due to bridging oxygen (BO) atoms and the other due to non-bridging oxygen (NBO) atoms. The fraction of NBO, determined from these spectra, is found to increase with increasing V 2O 5 content suggesting the formation of TeO 3 units and also that V 2O 5 is acting as a glass modifier in this glass series. The magnetic susceptibility data for these glasses follow a Curie–Weiss behavior ( M/ H = C/( T − θ)) which also indicates the presence of some V ions existing in a magnetic state, i.e., a valence state other than that of the non-magnetic state V 5+. The ratios of V 4+/V total as determined from magnetic susceptibility measurements assuming only the presence of magnetic V 4+ and non-magnetic V 5+ ions vary from 0.030 to 0.037. These ratios are too small to be detected by XPS measurements and this is why no asymmetry is observed in the V2p spectra of these glasses.

Elastic Properties of Potassium Borate Glass in a Wide Composition Range Studied by Brillouin Scattering

The elastic properties of potassium borate glass, xK2O·(100 - x)B2O3, where x is the molar composition of K2O in mol %, have been investigated by Brillouin scattering spectroscopy over a wide composition range of 2 ≤x ≤42 mol %. From the observed values of longitudinal sound velocity, the elastic constant has been determined and compared with that of lithium borate glass. The sound velocity increases with increasing x below x = 30; however, for a further increase in x, it decreases owing to the softening caused by the formation and increase in the number of nonbridging oxygen atoms. The absorption coefficient also increases markedly above x = 30 owing to the scattering of acoustic waves by nonbridging oxygen atoms. The temperature dependences of both sound velocity and absorption coefficient of 14K2O·86B2O3 show a markedly change at approximately the glass transition temperature Tg of 395 °C.

DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus

BackgroundA novel DNA phosphorothioate modification (DNA sulfur modification), in which one of the non-bridging oxygen atoms in the phosphodiester bond linking DNA nucleotides is exchanged by sulphur, was found to be genetically determined by dnd or dnd-counterpart loci in a wide spectrum of bacteria from diverse habitats. A detailed mutational analysis of the individual genes within the dnd locus in Streptomyces lividans responsible for DNA phosphorothioation was performed and is described here. It should be of great help for the mechanistic study of this intriguing system.ResultsA 6,665-bp DNA region carrying just five ORFs (dndA-E) was defined as the sole determinant for modification of the DNA backbone in S. lividans to form phosphorothioate. This provides a diagnostically reliable and easily assayable Dnd (DNA degradation) phenotype. While dndA is clearly transcribed independently, dndB-E constitute an operon, as revealed by RT-PCR analysis. An efficient mutation-integration-complementation system was developed to allow for detailed functional analysis of these dnd genes. The Dnd- phenotype caused by specific in-frame deletion of the dndA, C, D, and E genes or the enhanced Dnd phenotype resulting from in-frame deletion of dndB could be restored by expression vectors carrying the corresponding dnd genes. Interestingly, overdosage of DndC or DndD, but not other Dnd proteins, in vivo was found to be detrimental to cell viability.ConclusionDNA phosphorothioation is a multi-enzymatic and highly coordinated process controlled by five dnd genes. Overexpression of some proteins in vivo prevented growth of host strain, suggesting that expression of the gene cluster is strictly regulated in the native host.

Physical and structural properties of some bismuth borate glasses

Glasses in the system ( x/2)Bi 2O 3–( x/2)Nb 2O 5–(1 − x)Na 2B 4O 7, 0 ≤ x ≤ 0.3, have been prepared by the melt quenching technique. Elastic properties and Debye temperature ( θ D) have been investigated using sound velocity measurements at 4 MHz. The ultrasonic parameters along with the IR spectroscopic studies have been employed to study the role of Bi 2O 3, and Nb 2O 5 on the structure of Na 2B 4O 7 glass. The density, the molar volume, the sound velocities, and the glass transition temperatures of these samples have been found to be compositional dependent. The results indicate that Bi 2O 3, and Nb 2O 5 act as a network modifier in the range 0 ≤ x ≤ 0.15, while beyond x = 0.15, Nb 2O 5 acts as a network former which affects the diborate units that mainly consist the strong borate network. These results are interpreted in terms of the transformation of NbO 6 into NbO 4, the increase in the number of non-bridging oxygen atoms, and the substitution of longer bond lengths of Bi–O, and Nb–O in place of shorter B–O bond. The observed compositional dependence of the elastic moduli is interpreted in terms of the effect of Bi 2O 3, and Nb 2O 5 on the Boron-coordination number of the glass structure and to the relatively large electron–phonon anharmonic interactions.

Effect of pressure on the refractive index and relative density of the CaO·Al2O3·6SiO2 glass

The refractive index for glass of the CaO · Al2O3 · хSiO2 system with х = 6 in the range of pressures up to 6.0 GPa was measured using a polarization-interference microscope and an apparatus with diamond anvils. The changes in the relative density characterizing the compressibility of glass were estimated from the measured refractive indices within the framework of the theory of photoelasticity. The data were compared with the previous data for glasses of the same system with х = 2 and 4. The most compressible of the three glasses in the range 2.0–6.0 GPa was the CaO · Al2O3 · 6SiO2 glass. For glasses with х = 2, 4 and 6 we calculated the degrees of polymerization of silicon–aluminum–oxygen network, NBO/T (NBO – non-bridging oxygen), which are determined as the ratio of the number of gram-ions of non-bridging oxygen atoms to the total number of gram-ions of network formers. The structure–chemical parameter NBO/T was calculated with due regard for the formation of triclusters and highly coordinated aluminum. The degree of polymerization of the CaO · Al2O3 · хSiO2 glasses increases with increasing х, which agrees with the change of their relative density under pressure.

The structure of calcium metaphosphate glass obtained from x-ray and neutron diffractionand reverse Monte Carlo modelling

The short range structure of (CaO)0.5(P2O5)0.5 glass has been studied using x-ray and neutron diffraction and modelled using thereverse Monte Carlo method. Using this combination of techniques has allowed sixinteratomic correlations to be distinguished and fitted to obtain a set of bond lengthsand coordination numbers that describe the structure of the glass. The glassconsists of metaphosphate chains of phosphate tetrahedra and each phosphateunit has two non-bridging oxygen atoms available for coordination with Ca. TheCa–O correlation was fitted with two peaks at 2.35 and 2.86 Å, representing a broaddistribution of bond lengths. The total Ca–O coordination is 6.9 and is consistent withdistorted polyhedral units such as capped octahedra or capped trigonal prisms. It isfound that most non-bridging oxygen atoms are bonded to two calcium atoms. Allof these observations are consistent with Hoppe’s model for phosphate glasses.Furthermore, the medium range order is revealed to consist of phosphate chainsintertwined with apparently elongated clusters of Ca ions, and the Ca–O and Ca–Pcorrelations contributed significantly to the first sharp diffraction peak in x-raydiffraction.

Network structure and thermal property of a novel high temperature seal glass

In this study, novel glasses based on SrO–La2O3–Al2O3–B2O3–SiO2 system are investigated for solid oxide fuel and electrolyzer cells. The network structure evolution of the glasses with increasing B2O3:SiO2 ratio was studied using Raman spectroscopy. The thermal properties of the glasses, including glass transition temperature T g and glass softening temperature T d , were studied using dilatometry. The thermal stability of the glasses was investigated using X-ray diffraction. The study shows that as the B2O3:SiO2 ratio increases, the SrO–La2O3–Al2O3–B2O3–SiO2 glass micro-heterogeneity and the amount of non-bridging oxygen atoms increase. Correspondingly, the T g of the SrO–La2O3–Al2O3–B2O3–SiO2 glasses changes from 635 to 775°C, and the T d changes from 670 to 815°C. Glass thermal stability decreases with B2O3:SiO2 ratio increase. The glass without B2O3 is thermally stable after being kept at 850°C for 200 hrs.

Structure of TeO2·B2O3 glasses inferred from infrared spectroscopy and DFT calculations

Glasses in the system (1 − x )TeO 2 · x B 2 O 3 glasses (with x = 0.3 and 0.4) have been prepared from melt quenching method. The structural changes were studied by FTIR spectroscopy and DFT calculations. From the analysis of the FTIR spectra it is reasonable to assume that when increasing boron ions content the tetrahedral [BO 4 ] units are gradually replaced by trigonal [BO 3 ] units. The increase in the number of non-bridging oxygen atoms would decrease the connectivity of the glass network, would depolymerize of borate chains and would necessite quite a radical rearrangement of the network formed by the [TeO 6 ] octahedral. This is possible considering that tellurium dioxide brings stoichiometrically two oxygen atoms in [TeO 4 ] and needs an additional oxygen atom for the formation of [TeO 6 ] octahedra. This additional oxygen atom is evidently taken off from the boron co-ordination and thus boron atoms transfer their [BO 4 ] co-ordination into [BO 3 ] co-ordination. We used the FTIR spectroscopic data in order to compute two possible models of the glasses matrix. We propose two possible structural models of building blocks for the formation of continuous random network glasses used by density functional theory (DFT) calculations.

Low-frequency Raman scattering in alkali tellurite glasses

Raman scattering has been employed to study the alkali-cation size dependence and the polarization characteristics of the low-frequency modes for the glass-forming tellurite mixtures, 0·1M2O–0·9TeO2 (M = Na, K, Rb and Cs). The analysis has shown that the Raman coupling coefficient alters by varying the type of the alkali cation. The addition of alkali modifier in the tellurite network leads to the conversion of the TeO4 units to TeO3 units with a varying number of non-bridging oxygen atoms. Emphasis has also been given to the low-frequency modes and particular points related to the low-frequency Raman phenomenology are discussed in view of the experimental findings.

Raman and NMR study of bioactive Na2O–MgO–CaO–P2O5–SiO2 glasses

The results of a structural study combining NMR and Raman spectroscopy of several melt-derived glasses in the system Na2O–MgO–CaO–P2O5–SiO2 are presented. The Raman spectra show clear changes in the Si–O–Si vibrational modes (related to the bridging oxygen atoms, BO) and also verify the presence of non-bridging oxygen atoms (NBO), also named terminal oxygens. The intensity of the Si–O–NBO stretching mode depends on the cation concentration. It can be concluded from the NMR studies that the MgO-containing samples have orthophosphate units charge-compensated by Ca2+ and Mg2+. The silicate matrix also contains both types of two-valent cations and consists of Q2 and Q1 units. Similarly, the Na2O-containing samples contain isolated orthophosphate units in a silicate matrix (Q2 and Q3 units), both charge-compensated by mixed cations Ca2+ and Na+. These experimental data were compared with theoretical parameters given by the Stevels model, which is a suitable tool for understanding bioactive behavior of these glasses. Furthermore, results of the in vitro tests carried out in simulated body fluids are presented and compared with both Raman and NMR structural data.

Effects of nickel on network structure and thermal properties of a new solid oxide cell seal glass

Successful seal design relies on good understanding of glass network structure and the corresponding impact on glass thermophysical properties. This study is focused on effects of nickel replacement of glass formers SiO 2 and B 2O 3 and glass modifier SrO on SrO La 2O 3 Al 2O 3 B 2O 3 SiO 2 glass network structure and thermal properties. Glass structure local ordering was studied by Raman spectroscopy. Glass network connectivity was formulated to compare glass structure evolution with nickel addition for different compositions. Glass transition temperature and dilatometric softening temperature were evaluated by dilatometry. Glass thermal stability was studied by X-ray diffraction. Nickel behaves as a glass modifier in the studied glass system and decreases glass network connectivity. However, nickel can increase or decrease glass transition temperature and dilatometric softening temperature depending on the specific composition. Overall, nickel addition degrades glass thermal stability by increasing the amount of non-bridging oxygen atoms and devitrification.

Structure-guided Mutational Analysis of the OB, HhH, and BRCT Domains of Escherichia coli DNA Ligase

NAD(+)-dependent DNA ligases (LigAs) are ubiquitous in bacteria and essential for growth. LigA enzymes have a modular structure in which a central catalytic core composed of nucleotidyltransferase and oligonucleotide-binding (OB) domains is linked via a tetracysteine zinc finger to distal helix-hairpin-helix (HhH) and BRCT (BRCA1-like C-terminal) domains. The OB and HhH domains contribute prominently to the protein clamp formed by LigA around nicked duplex DNA. Here we conducted a structure-function analysis of the OB and HhH domains of Escherichia coli LigA by alanine scanning and conservative substitutions, entailing 43 mutations at 22 amino acids. We thereby identified essential functional groups in the OB domain that engage the DNA phosphodiester backbone flanking the nick (Arg(333)); penetrate the minor grove and distort the nick (Val(383) and Ile(384)); or stabilize the OB fold (Arg(379)). The essential constituents of the HhH domain include: four glycines (Gly(455), Gly(489), Gly(521), Gly(553)), which bind the phosphate backbone across the minor groove at the outer margins of the LigA-DNA interface; Arg(487), which penetrates the minor groove at the outer margin on the 3 (R)-OH side of the nick; and Arg(446), which promotes protein clamp formation via contacts to the nucleotidyltransferase domain. We find that the BRCT domain is required in its entirety for effective nick sealing and AMP-dependent supercoil relaxation.

Molecular Dynamics Simulation of Interaction between Supercritical CO2 Fluid and Modified Silica Surfaces

The structural and dynamical properties of the supercritical CO2 fluid confined in the slit nanopores with the hydroxylated and silylated amorphous silica surfaces have been studied using molecular dynamics (MD) simulation. The amorphous bulk silica was obtained by a melt-quench MD simulation technique and the modified silica surfaces were artificially created by the attachment of hydrogen (−OH model) and trimethysilane (−Si(CH3)3 model) to the nonbridging oxygen atoms on the silica surfaces. The VdW interaction potential between the CO2 molecule and the hydroxylated silica surface was determined based on the ab initio quantum mechanics (QM) computation. The adsorption potential distributions of CO2 on the two modified silica surfaces were examined in order to evaluate the different surface interaction characteristics. The density profiles, the radial distribution functions, as well as the interfacial dynamics properties (self-diffusion coefficients and residence time) for the confined supercritical CO2 fluid have been simulated. It is demonstrated that the hydroxylated silica surface gives a stronger confining effect on the supercritical CO2 fluid as compared with the silylated surface. The remarkable impact on the supercritical CO2 fluid from the hydroxylated silica surface can be attributed to the H-bonding interaction between CO2 molecules and surface silanol groups. The analysis of the vibrational density of states of the confined supercritical CO2 fluid reveals the phenomena of the spectral shifts and the Fermi resonance in compaison with the bands in unconfined supercritical CO2. This spectrum behavior is associated with the enhanced interaction from the functional groups on silica surfaces.

The Mixed-Network Former Effect in Phosphate Glasses: NMR and XPS Studies of the Connectivity Distribution in the Glass System (NaPO3)1−x(B2O3)x

The structural organization of sodium borophosphate glasses with composition (NaPO3)1−x(B2O3)x (0.0 ≤ x ≤ 0.3) has been investigated by X-ray photoelectron spectroscopy (XPS), as well as single- and double-resonance 11B and 31P magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. O-1s XPS data provides a quantitative distinction between B−O−B, B−O−P, and P−O−P linkages as well as nonbridging oxygen atoms. 11B and 31P MAS NMR data indicate that within the compositional region 0 ≤ x ≤ 0.20 the entire boron inventory is present in the form of anionic BO4− units, resulting in the repolymerization of an equivalent fraction of the phosphate units (conversion of anionic metaphosphate (P(2)) into neutral branching groups (P(3)) species. Both XPS as well as 31P{11B} and 11B{31P} rotational echo double resonance (REDOR) NMR results reveal strong interactions between the two network formers boron oxide and phosphorus oxide, resulting in the dominant formation of B−O−P linkages. In addition, the ...

Structural Role and Distribution of Alkali and Alkaline-Earth Cations in Rare Earth-Rich Aluminoborosilicate Glasses

The structure of a seven oxide aluminoborosilicate simplified nuclear glass, bearing a high amount of neodymium or lanthanum oxide (16 wt%), alkali and alkaline earth cations is studied. Nd3+ or La3+ are supposed to simulate the trivalent lanthanides and minor actinides present in nuclear wastes. In the studied glass composition, lanthanide ions have a modifying role and are located in highly depolymerized regions of the structure as shown by neodymium optical absorption and EXAFS spectroscopies. Both alkali and alkaline earth cations are present around Nd3+ ions enabling their stabilization in glass structure near non-bridging oxygen atoms (NBOs). We show that both the nature of alkali R+ and alkaline earth R'2+ cations and the K = [R'O]/([R2O]+[R'O]) ratio can greatly influence the structure of the aluminoborosilicate glass network. Three glass series were prepared for which: (i) K ratio was varied from 0 to 0.5 (Na+ and Ca2+ being respectively the only alkali and alkaline-earth cations), (ii) the nature of R+ cation was varied from Li+ to Cs+ (Ca2+ being the only alkaline earth cation and K = 0.3), (iii) the nature of R'2+ cation was varied from Mg2+ to Ba2+ (Na+ being the only alkali cation and K = 0.3). 27Al MAS NMR spectroscopy results show that (AlO4)- units are preferentially charge compensated by alkali cations rather than by alkaline-earth cations. Both R+ and R’2+ cations can compensate (BO4)- units. Nevertheless, whereas the proportion N4 of (BO4)- units increases with the size of R'2+ cations, the evolution of N4 with R+ cation size for glasses of the R series is not monotonous. The evolution of sodium ions distribution trough glass structure is followed by 23Na MAS NMR spectroscopy.

Mg2+‐Assisted Catalysis by B. stearothermophilus TrpRS is Promoted by Allosteric Effects

Mg2+ ion accelerates TrpRS‐catalyzed Trp activation ~105 fold, providing 35% of the reduction in ΔG‡. This catalytic contribution is achieved indirectly, by interactions from active‐site lysine residues to the non‐bridging phosphate oxygen atoms that coordinate the Mg2+, lengthening metal‐oxygen distances and weakening interaction with the triphosphate. This electrostatic compromise is coupled to an endergonic twist of the anticodon‐binding domain relative to the active site, whose unfavorable energetics arise from long‐range interactions, and which leads to (exergonic) untwisting during the catalytic step. We investigated these interactions quantitatively, determining mutant effects in multi‐variant thermodynamic cycles with [ATP]‐dependent Michaelis‐Menten kinetics and Mn2+ for Mg2+ substitution. These cycles confirm the coupling of lysines to metal coordination and rule out a proposed interaction between the metal and the nearly invariant aspartate, D146. The two lysine residues most strongly coupled to the metal bind the PPi leaving group; the third interacts with the Pα phosphate. Coupling was also observed for a remote mutation, F37I, which affects both kcat and the use of Mn2+. Tηεσειντεραχτιℴνσ αρε χℴνσιστεντ ωιτη στραιν αρισινγ φρℴμ αν υνφαϖℴραβλε χℴνφℴρματιℴν νεχεσσαρψ τℴ ασσεμβλε τηε αχτιϖε σιτε αρℴυνδδ A TΠ ανδ ωηιχη εσταβλισηεσ α δελιχατε βαλανχε ℴφ ελεχτρℴστατιχ ανδ μεχηανιχαλ φℴρχεσ τηατ στραιν τηε σχισσιλε Πα‐O‐Pβ linkage. Supported by NIGMS 48519 and 45295.

Structure and thermal properties of yttrium alumino-phosphate glasses

The structure and thermal properties of yttrium alumino-phosphate glasses, of nominal composition(Y2O3)0.31−z(Al2O3)z(P2O5)0.69 with , were studied by using a combination of neutron diffraction,27Al and 31P magic angle spinning nuclear magnetic resonance, differential scanning calorimetryand thermal gravimetric analysis methods. The Vickers hardness of the glasseswas also measured. The data are compared to those obtained for pseudo-binaryAl2O3–P2O5 glasses and the structure of all these materials is rationalized interms of a generic model for vitreous phosphate materials in whichY3+ and Al3+ act as modifying cations that bind only to the terminal (non-bridging) oxygen atoms ofPO4 tetrahedra. The results are used to help elucidate the phenomenon ofrare-earth clustering in phosphate glasses which can be reduced by substitutingAl3+ ions forrare-earth R3+ ions at fixed modifier content.