Non-bridging Oxygen Atoms Research Articles

A Raman-spectroscopic study of indentation-induced structural changes in technical alkali-borosilicate glasses with varying silicate network connectivity

We report on the deformation behavior of a series of glasses in the ternary alkali-borosilicate system. Vickers indentation was applied to different samples and structural changes were studied by micro-Raman spectroscopy. Selected sodium- and potassium-borosilicate glasses, a soda-lime silicate glass and pure vitreous SiO2 were chosen as models for technical glasses, as their varying content of non-bridging oxygen atoms affects the connectivity of the silicate and borate sub-networks. Indentation experiments were performed with different loads and two different load times in order to analyze the response of the two sub-networks in the studied glasses.The measured Raman spectra show distinct indentation-induced changes in the glass structure. These changes depend not only on the borate concentration, but also on the silicate sub-network's connectivity and reflect anomalous (densification-driven) and normal (shear-driven) deformation mechanisms. Using vitreous SiO2 as reference material, indentation-induced structural changes were also correlated to hydrostatic compression experiments from the literature in order to develop a more detailed picture of the apparent evolution of the local compaction in and around the indent.

Luminescence of intrinsic localized states in alkali silicate glasses excited by pulsed electron beam

The exposure of pulsed electron beam was applied for exciting the luminescence of two types of localized electronic states (so-called L-centers) in the Na2O-K2O-CaO-SiO2 glasses with varied Na/K relation. The recorded luminescence spectra clearly exhibit the line-type fine structure. It was shown that this fine structure of spectra reflects the interaction of electron excitations both with local vibrations of nonbridging oxygen atoms and with phonon modes of the glassy network during the radiative relaxation of the triplet state of L-centers. The appearance of additional “mixed” vibrations discussed and interpreted in terms of the expanded model of an L-center.

Defects and localized states in silica layers implanted with lead ions

The luminescence of silica films and glasses implanted with Pb+ ions was studied by means of time-resolved photoluminescence spectroscopy under synchrotron excitation. The ion-modified silica layers are “metal–dielectrics“ composites the oxide part of which is represented by amorphous micro-heterogeneous phase with variable Pb2+ions. Two groups of emission centers are identified: such as: (1) radiation-induced oxygen-deficient centers (ODCs) and non-bridging oxygen atoms (NBOs) in the SiO2 matrix and (2) localized electronic states (LS) of the amorphous lead–silicate phase.

Mixed Network Former Effects in Oxide Glasses: Spectroscopic Studies in the System (M2O)1/3[(Ge2O4)x(P2O5)1–x]2/3

The structure of mixed-network former glasses in the system (M2O)0.33[(Ge2O4)x(P2O5)1–x]0.67.(M = Na, K) has been studied by 31P and 23Na high-resolution and dipolar solid state nuclear magnetic resonance (NMR) techniques, O-1s X-ray photoelectron spectroscopy, and Raman spectroscopy. Using an iterative fitting procedure, a quantitative structural model has been developed that is consistent with all of the experimental data and which provides a detailed description of network connectivities, network modification processes, and spatial cation distributions. Formation of heteroatomic P–O–Ge linkages is generally preferred over homoatomic P–O–P and Ge–O–Ge linkages, as shown by a detailed comparison with a random linkage model. An exception occurs in glasses with low germanium contents (x = 0.2) where a pronounced nonlinear dependence of the glass transition temperature on x can be related to a cross-linking of the sodium ultraphosphate network by fully polymerized germanium species, possibly including also 5- and 6-fold coordination states. At higher x values, the Ge component is modified as well, however, the fraction of anionic nonbridging oxygen atoms bound to germanium is always lower than expected for proportional modifier sharing between both network formers. Rather, the phosphate component is preferentially modified by the cations, leading to the formation of P(1) units at high x values. Consequently, the local coordination of the cations is dominated by phosphorus, as is clearly evident from the 23Na{31P} rotational echo double resonance (REDOR) results. This preferred association, combined with the formation of P(1) units, results in partially clustered cation distributions, which can be detected by 23Na spin echo decay spectroscopy. Finally, the joint interpretation of all of the data from NMR, Raman, XPS, and thermal analysis measurements offers indirect evidence for the formation of higher germanium coordination states in this glass system.

Effects of quartz grain size distribution on the structure of porcelain glaze

This paper discusses the effects of quartz grain size on the structure of porcelain ceramic glazes. Individual compositions of white opaque ceramic glaze for sanitary ware contained quartz powder of different grain sizes from 8.33µm to 0.27µm. The structure of the glazes was analyzed using FTIR spectroscopy of the phase composition and microscopic imaging using SEM–EDAX and confocal laser scanning microscopy. It was shown that the use of quartz of a very fine grain size increases the degree of disordering of the glaze by increasing the number of non-bridging oxygen atoms.

Topology and glass structure evolution in (BaO)x((B₂O₃)₃₂(SiO₂)₆₈)(100-x) ternary--evidence of rigid, intermediate, and flexible phases.

We examine variations in the glass transition temperature (T(g)(x)), molar volume (V(m)(x)), and Raman scattering of titled glasses as a function of modifier (BaO) content in the 25% < x < 48% range. Three distinct regimes of behavior are observed; at low x, 24% < x < 29% range, the modifier largely polymerizes the backbone, T(g)(x) increase, features that we identify with the stressed-rigid elastic phase. At high x, 32% < x < 48% range, the modifier depolymerizes the network by creating non-bridging oxygen (NBO) atoms; in this regime T(g)(x) decreases, and networks are viewed to be in the flexible elastic phase. In the narrow intermediate x regime, 29% < x < 32% range, T(g)(x) shows a broad global maximum almost independent of x, and Raman mode scattering strengths and mode frequencies become relatively x-independent, V(m)(x) show a global minimum, features that we associate with the isostatically rigid elastic phase, also called the intermediate phase. In this phase, medium range structures adapt as revealed by the count of Lagrangian bonding constraints and Raman mode scattering strengths.

The structural role of manganese ions in soil active silicate–phosphate glasses

Silicate–phosphate glasses of SiO2P2O5K2OMgOCaO system containing manganese ions were synthesized by the melt-quenching technique and were investigated to obtain information about the influence of Mn-cations on the glass structure and their chemical activity. Structural properties were studied using X-ray method, FTIR and Raman spectroscopies. The chemical activity of analyzed glasses in the 2wt.% citric acid solution was measured by chemical analysis (ICP-AES, EDS) and SEM observations.It has been found that increasing amount of MnO2 in the structure of investigated glasses causes their gradual depolymerization. This process is more apparent in the case of the silico-oxygen subnetwork than phospho-oxygen one. This is related to increasing amounts of SiO4 tetrahedra containing two nonbridging oxygen atoms in silico-oxygen subnetwork. It has been also found that the presence of “weaker” chemical bonds of SiOMn type in comparison to SiOCa and SiOMg bonds is responsible for the increase in solubility of the analyzed silicate–phosphate glasses in conditions simulating natural soil environment.

Structural Particulars of Iron-Containing Borosilicate Glasses

The behavior of iron in the structure of sodium iron-containing borosilicate glasses with different ratio of the glass-forming and modifying ions was studied by Mossbauer and vibrational spectroscopy. It was found that the distribution of the modifying ions differs between different types of structural species in the structure of the initial and iron-containing sodium borosilicate glasses. The addition of iron decreases the BO4 tetrahedra fraction and increases the BO3 triangles fraction and the fraction of the structural species Q 2 and Q 3 containing nonbridging oxygen atoms. This is accompanied by the destruction of mixed silicon borate rings and the formation of the bridging bonds Si–O–Fe3+ and nonbridging bonds Si–O−, coordinated by Fe2+ ions.

Aqueous Methane in Slit-Shaped Silica Nanopores: High Solubility and Traces of Hydrates

Equilibrium molecular dynamic simulations were employed to investigate the methane solubility in water confined between two parallel silica surfaces. The solid substrate was obtained from β-cristobalite; all nonbridging oxygen atoms were protonated. The resultant surface density of OH groups was ∼4.54 sites per nm2. The simulations were conducted at constant temperature, 300 K, and at increasing bulk methane pressure for pores of width 1.0 nm. For bulk systems, these thermodynamic conditions are outside the window of methane hydrates stability. Methane solubility in confined water was found to far exceed that in bulk systems. The increase in tangential pressure, observed under confinement, cannot solely explain the marked increase in solubility predicted by our simulations. Most likely, the structure of confined water favors the sequestration of methane. The excess chemical potential for methane was found to significantly decrease within the confined water compared with that in the bulk phase. On the basis of the cage adsorption hypothesis for hydrate nucleation, the predicted solubility of methane in the confined water (up to ∼0.05 mol fraction) is large enough to suggest the possible formation of methane hydrates. Indeed, analysis of simulation data shows the presence of amorphous cages of hydrogen-bonded water that host a single methane molecule. Within the limits of our simulations, these amorphous cages last for only short times. Perhaps the pores considered are too narrow to allow the formation of stable methane hydrates, and perhaps longer simulations would allow us to observe the formation of a hydrate nucleus. The large methane solubility in confined water predicted by our simulations might have consequences for hydraulic fracturing and other technological processes.

Spectroscopic Observation of Fractal Packing of Oxygen in Variably Modified Glassy Tetrahedral Networks.

The spatial distribution of bridging and nonbridging oxygen atoms in silicate glass networks with a wide range of connectivity is studied using (17)O nuclear magnetic resonance spin-lattice relaxation spectroscopy. The results demonstrate a mass fractal spatial distribution of both oxygen species in the network at the nanometer length scale. The fractal dimension increases with increasing relative fraction of these oxygen species and reaches a maximum value of ∼2.6. Such locally fractal character of the structural network is key to the understanding of the apparently anomalous transport, relaxation, and localization properties that are the hallmarks of the glassy state.

Site-Directed Mutagenesis Maps Interactions That Enhance Cognate and Limit Promiscuous Catalysis by an Alkaline Phosphatase Superfamily Phosphodiesterase

Catalytic promiscuity, an evolutionary concept, also provides a powerful tool for gaining mechanistic insights into enzymatic reactions. Members of the alkaline phosphatase (AP) superfamily are highly amenable to such investigation, with several members having been shown to exhibit promiscuous activity for the cognate reactions of other superfamily members. Previous work has shown that nucleotide pyrophosphatase/phosphodiesterase (NPP) exhibits a >10⁶-fold preference for the hydrolysis of phosphate diesters over phosphate monoesters, and that the reaction specificity is reduced 10³-fold when the size of the substituent on the transferred phosphoryl group of phosphate diester substrates is reduced to a methyl group. Here we show additional specificity contributions from the binding pocket for this substituent (herein termed the R' substituent) that account for an additional ~250-fold differential specificity with the minimal methyl substituent. Removal of four hydrophobic side chains suggested on the basis of structural inspection to interact favorably with R' substituents decreases phosphate diester reactivity 10⁴-fold with an optimal diester substrate (R' = 5'-deoxythymidine) and 50-fold with a minimal diester substrate (R' = CH₃). These mutations also enhance the enzyme's promiscuous phosphate monoesterase activity by nearly an order of magnitude, an effect that is traced by mutation to the reduction of unfavorable interactions with the two residues closest to the nonbridging phosphoryl oxygen atoms. The quadruple R' pocket mutant exhibits the same activity toward phosphate diester and phosphate monoester substrates that have identical leaving groups, with substantial rate enhancements of ~10¹¹-fold. This observation suggests that the Zn²⁺ bimetallo core of AP superfamily enzymes, which is equipotent in phosphate monoester and diester catalysis, has the potential to become specialized for the hydrolysis of each class of phosphate esters via addition of side chains that interact with the substrate atoms and substituents that project away from the Zn²⁺ bimetallo core.

An EPR investigation of SiOx films with columnar structure

The results of electron paramagnetic resonance (EPR) study of obliquely deposited porous SiOx films before and after thermal annealing in vacuum at 950°C are presented. The low intensity slightly asymmetrical and featureless EPR line with a g-value of 2.0044 and a linewidth of 0.77mT has been detected in as-sputtered films and attributed to dangling bonds of silicon atoms in amorphous SiOx domains with x=0.8. Successive annealing results in decreasing this line and the appearance of an intense EPR line with g=2.0025, linewidth of 0.11mT and a hyperfine doublet with 1.6mT splitting. According to the parameters this spectrum has been attributed to the EX center, a hole delocalized over four non-bridging oxygen atoms grouped around a Si vacancy in SiO2. The impact of chemical treatment before annealing and duration of anneals on the defect system is discussed.

Stabilities of the Divalent Metal Ion Complexes of a Short-Chain Polyphosphate Anion and Its Imino Derivative

The stability constants of ML-type complexes of the two linear triphosphate ligand anion analogues triphosphate ( {text{P}}_{ 3} {text{O}}_{10}^{5 - } ) and diimidotriphosphate ( {text{P}}_{ 3} {text{O}}_{ 8} ( {text{NH}})_{2}^{5 - } ) were investigated thermodynamically using potentiometric titrations according to Schwarzenbach’s procedure. The stability constants of the ML-type complexes of different divalent metal ions with {text{P}}_{ 3} {text{O}}_{ 8} ( {text{NH}})_{2}^{5 - } are larger than those of the corresponding complexes with {text{P}}_{ 3} {text{O}}_{10}^{5 - } because of the greater basicity of the imino group. The order of the stability constants for the ML-type complexes follows the Irving–Williams order, indicating that only non-bridging oxygen atoms are coordinated directly to the different metal ions in both ligands, and that the imino groups cannot participate in coordination to the metal ions. In the complexation reactions of the Ca2+, Sr2+, Ba2+– {text{P}}_{ 3} {text{O}}_{10}^{5 - } and Cu2+, Zn2+, Ni2+– {text{P}}_{ 3} {text{O}}_{ 8} ( {text{NH}})_{2}^{5 - } systems, each metal ion forms an enthalpically stable complex, and there was no suggestion of a conspicuous entropic effect based on the chelate effect. Monodentate complexes that are strongly coordinated with the ligands were therefore formed, whereas entropically stable bidentate complexes were formed in the complexation reactions of the Cu2+, Zn2+, Ni2+– {text{P}}_{ 3} {text{O}}_{10}^{5 - } and Ca2+, Ba2+, Sr2+– {text{P}}_{ 3} {text{O}}_{ 8} ( {text{NH}})_{2}^{5 - } systems. According to the HSAB concept, hard metal cations such as Ca2+, Ba2+ and Sr2+ should bind to the harder oxygen atoms rather than the softer nitrogen atoms of the imidopolyphosphate anions, preventing direct coordination to the imino nitrogen atom.Graphical Electronic supplementary materialThe online version of this article (doi:10.1007/s10953-013-0099-2) contains supplementary material, which is available to authorized users.

Role of B2O3 on the Viscosity and Structure in the CaO-Al2O3-Na2O-Based System

The effect of B2O3 on the viscosity and structure in the calcium-aluminate melt flux system containing Na2O was studied. An increase in the B2O3 content at fixed CaO/Al2O3 ratio lowered the viscosity. Higher CaO/Al2O3 ratio at fixed B2O3 content also decreased the viscosity. The alumino-borate structures were confirmed through Fourier transformed infrared (FTIR) and Raman spectroscopy and consisted of [AlO4]-tetrahedral structural units, [BO3]-triangular structural units, and [BO4]-tetrahedral structural units, which could be correlated to the viscosity. At fixed CaO/Al2O3 ratio, B2O3 additions decreased the [AlO4]-tetrahedral structural units and transformed the 3-D network structures such as pentaborate and tetraborate into 2-D network structures of boroxol and boroxyl rings by breaking the bridged oxygen atoms (O0) to produce non-bridged oxygen atoms (O−) leading to a decrease in the molten flux viscosity. At fixed B2O3 contents and higher CaO/Al2O3 ratio, 3-D complex network structures become 3-D simple and 2-D isolated network structures, resulting in lower viscosities. The apparent activation energy for viscous flow varied from 132 to 249 kJ/mol according to the composition of B2O3 and CaO/Al2O3 ratio.

Formation of S–Cl Phosphorothioate Adduct Radicals in dsDNA S-Oligomers: Hole Transfer to Guanine vs Disulfide Anion Radical Formation

In phosphorothioate-containing dsDNA oligomers (S-oligomers), one of the two nonbridging oxygen atoms in the phosphate moiety of the sugar-phosphate backbone is replaced by sulfur. In this work, electron spin resonance (ESR) studies of one-electron oxidation of several S-oligomers by Cl2(•-) at low temperatures are performed. Electrophilic addition of Cl2(•-) to phosphorothioate with elimination of Cl(-) leads to the formation of a two-center three-electron σ(2)σ*(1)-bonded adduct radical (-P-S-̇Cl). In AT S-oligomers with multiple phosphorothioates, i.e., d[ATATAsTsAsT]2, -P-S-̇Cl reacts with a neighboring phosphorothioate to form the σ(2)σ*(1)-bonded disulfide anion radical ([-P-S-̇S-P-](-)). With AT S-oligomers with a single phosphorothioate, i.e., d[ATTTAsAAT]2, reduced levels of conversion of -P-S-̇Cl to [-P-S-̇S-P-](-) are found. For guanine-containing S-oligomers containing one phosphorothioate, -P-S-̇Cl results in one-electron oxidation of guanine base but not of A, C, or T, thereby leading to selective hole transfer to G. The redox potential of -P-S-̇Cl is thus higher than that of G but is lower than those of A, C, and T. Spectral assignments to -P-S-̇Cl and [-P-S-̇S-P-](-) are based on reaction of Cl2(•-) with the model compound diisopropyl phosphorothioate. The results found for d[TGCGsCsGCGCA]2 suggest that [-P-S-̇S-P-](-) undergoes electron transfer to the one-electron-oxidized G, healing the base but producing a cyclic disulfide-bonded backbone with a substantial bond strength (50 kcal/mol). Formation of -P-S-̇Cl and its conversion to [-P-S-̇S-P-](-) are found to be unaffected by O2, and this is supported by the theoretically calculated electron affinities and reduction potentials of [-P-S-S-P-] and O2.

Influence of lanthanum on borosilicate glass structure: A multinuclear MAS and MQMAS NMR investigation

The physical and chemical properties of silicate glasses containing rare-earth elements (REEs), either as dopants or at higher concentrations, are sensitive to the REE structural and chemical environment. An unambiguous role of REEs in the glass structure still remains difficult to define because many configurations may exist and are strongly composition-dependent. The structural configuration of lanthanum and its interactions with sodium and calcium are examined here in borosilicate glasses. The impact of lanthanum and calcium substituted for sodium on the boron speciation is investigated by 11B MAS NMR. The resulting 29Si MAS NMR spectra and their interpretations are discussed. A quantitative approach of 17O MQMAS NMR data with the reconstruction of 17O NMR parameter distributions provides an overview of lanthanum distribution and its interactions with the other cations in the vitreous network. No clustering of lanthanum atoms is observed; they are uniformly distributed in the glass structure, surrounded by about 6 non-bridging oxygen atoms and mixed with sodium and calcium atoms to the detriment of the number of BO4 groups. These data provide a better understanding of the addition of rare earths in the glass and of the conditions favorable to their uniform distribution in soda-lime borosilicate glass matrices.

Sp-2-propylthio-ATP-α-B and Sp-2-propylthio-ATP-α-B,β-γ-dichloromethylene are novel potent and specific agonists of the human P2Y11 receptor

The human P2Y11 nucleotide receptor mRNA was found in virtually all human tissues, and the receptor serves many physiological roles, such as immune response regulation. The Ala-87-Thr-P2Y11 receptor single nucleotide polymorphism was linked to increased risk for acute myocardial infarction. To facilitate the development of new therapeutic applications involving cells expressing several P2 receptor subtypes, the availability of specific and potent agonists is mandatory. Here, we synthesized a series of novel adenine nucleotide derivatives, based upon the potent P2Y11 receptor agonists AR-C67085. Features of the novel nucleotide derivatives are a propylthio substitution at C2-adenine and a Pα-borano or Pα-thio substitution of non-bridging oxygen atom. The latter substitutions introduce a chiral center at the α-phosphate. Sp-isomers of Pα-borano- and Rp-isomers of Pα-thio-substituted nucleotides are preferred by the P2Y11 receptor. As recently reported by us, diastereoselectivity of the P2Y11 receptor is opposite to that of the P2Y1 receptor. Therefore, we exploit this characteristic to increase nucleotide selectivity. At the P2Y11 receptor, the Sp-isomers of 2-propylthio-ATP-α-B (2B) and 2-propylthio-ATP-α-B,β-γ-dichloromethylene (4B) were the most potent of the novel nucleotide series, with EC50 values of 0.03μM for both, being ca. 80-fold more potent than 2-propylthio-ATP and ATP (EC50=2.6μM). We conclude that the borano-substitution at the α-phosphate of 2-propylthio-ATP enhances nucleotide potency at the P2Y11 receptor. The combination with a Pβ-Pγ-dichloromethylene group in 4B results in a nucleotide, which shows higher selectivity for the P2Y11 receptor over the P2Y1 receptor than 2B making it the most promising of the novel P2Y11 receptor agonists.

Structure–property correlations in highly modified Sr, Mn-borate glasses

Highly modified borate glasses with the composition (1−2x)MnO–x(SrO–B2O3) (x=0.46, 0.42, 0.36, 0.25, and 0.20) were prepared and investigated by Raman, infrared (IR), and electron paramagnetic resonance (EPR) spectroscopy. Optical properties were studied in regard to photoluminescence, optical absorption, and refractive index. The Mn2+/Mn3+ equilibrium was shifted towards the divalent manganese ion as a result of the strongly reducing melting conditions employed in this work, which facilitate the preparation of transparent glasses with up to 80mol% total SrO and MnO content. Changes in the optical and physical properties within this glass series were related to structural variations. The structure of glasses with relatively low MnO content was found to involve mainly trigonal [BØ2O]− and tetrahedral [BØ4]− metaborate groups, which are replaced progressively by pyroborate [B2O5]4− and orthoborate [BO3]3− triangular units upon increasing MnO content. At the highest modification level (x=0.20) the structure is built of orthoborate isomeric species in triangular [BO3]3− and tetrahedral [BØ2O2]3− configuration. The latter species form [B3O9]9− rings, which reestablish some degree of network connectivity, as they involve three bridging and six non-bridging oxygen atoms, and this is reflected by the increase of the glass transition temperature for x=0.25 over x=0.20. Micro-Raman measurements showed structural inhomogeneities in these glasses due to chemical isomerization processes involving short- and medium-range order structures. Also, increasing MnO content was shown to cause MnO-clustering in the glasses as revealed by luminescence and EPR measurements.

Sirna Analogs Containing Phosphorodithioate Substitutions

Chemically synthesized short interfering RNAs (siRNAs) mediate gene silencing in sequence-specific manner by utilizing the endogenous mechanism of RNA interference (RNAi). Synthetic siRNAs are often modified for improving their potency, stability, and for reducing undesirable “off-target” effects. Modification of the internucleotide bond in RNA chain, involving substitution of a single non-bridging phosphate oxygen with sulfur leads to the phosphorothioate (PS) derivatives of RNA. Substitution of both non-bridging phosphate oxygen atoms with sulfur gives rise to a phosphorodithioate (PS2) internucleotide linkage. We used a novel type of PS2-siRNA duplexes and tested their silencing activity, stability, and cellular up-take in comparison to PS- or unmodified duplexes. PS2-siRNAs show the A-type structure, characteristic for double-stranded RNA. Incorporation of PS2 substitutions into siRNA duplexes increases their serum stability. Gene silencing effect is strand- and position-dependent, with certain molecules showing significantly higher activity than PS or unmodified siRNAs. PS2 modifications are promising candidates in RNAi research and in therapeutic applications.

Use of a novel 5'-regioselective phosphitylating reagent for one-pot synthesis of nucleoside 5'-triphosphates from unprotected nucleosides.

5'-Triphosphates are building blocks for enzymatic synthesis of DNA and RNA. This unit presents a protocol for convenient synthesis of 2'-deoxyribo- and ribonucleoside 5'-triphosphates (dNTPs and NTPs) from any natural or modified base. This one-pot synthesis can also be employed to prepare triphosphate analogs with a sulfur or selenium atom in place of a non-bridging oxygen atom of the α-phosphate. These S- or Se-modified dNTPs and NTPs can be used to prepare diastereomerically pure phosphorothioate or phosphoroselenoate nucleic acids. Even without extensive purification, the dNTPs or NTPs synthesized by this method are of high quality and can be used directly in DNA polymerization or RNA transcription. Synthesis and purification of the 5'-triphosphates, as well as analysis and confirmation of natural and sulfur- or selenium-modified nucleic acids, are described in this protocol unit.