Structural organisation in oxide glasses from molecular dynamics modelling

Classical molecular dynamics modelling has been used to obtain new models of 50CaO·50P₂O₅ and 50MgO·50SiO₂ glasses and, together with previously published models of 63CaO·37Al₂O₃, and 50CaO·50SiO₂ glasses, these have been inspected to evaluate structural features. For the first time, models of glasses near the eutectic in three systems, aluminate, silicate, and phosphate, with the same modifier, Ca, have been compared. All have short range order which is similar to that in crystals of the same composition, 5CaO·3Al₂O₃, CaSiO₃ and Ca(PO₃)₂. There is a clear trend in bonding of bridging oxygen to Ca, which is dominant in aluminate glass, common in silicate glass, and absent in phosphate glass. Preliminary results for 50MgO·50SiO₂ glass show unusual behaviour because ~ 5% of oxygen is present as “non-network” oxygen, i.e. bonded only to Mg. The models show broader Qⁿ distributions than seen in NMR experiments, and this remains an area for improvement of MD modelling of glasses. The distributions of Ca in the models have been studied using the pair distribution function T_CaCa(r) which is found to be similar in the three glasses, and also similar to the previous experimental measurement for 50CaO·50SiO₂ glass. The distributions of Ca are markedly different in the glasses compared to the crystals, being isotropic in the former and anisotropic in the latter, which should be a factor in glass forming ability.     

Structural investigation of iron phosphate glasses using molecular dynamics simulation

The current study reports the first molecular dynamics models of iron phosphate glasses. Models were made for xFeO-(100 − x)P₂O₅ glasses with x = 30, 40 and 50 and for xFe₂O₃-(100 − x)P₂O₅ glasses with x = 30 and 40. This study also looks at the effects of mixed Fe²⁺/Fe³⁺ contents. The models are in good agreement with experimental results for nearest-neighbour distances and coordination numbers, and in reasonable agreement with X-ray and neutron diffraction structure factors. As expected the models contain a tetrahedral phosphate network with P-O distances of 1.50 ± 0.01 Å. The network connectivity is dominated by the expected Qⁿ (where n is the number of bridging oxygen) corresponding to the O:P ratio. These are average Qⁿ of 2.3 for 40FeO and 1.0 for 40Fe₂O₃ glasses respectively. Interestingly a small amount of non-network oxygen is found to be present in the 40Fe₂O₃ glass model. The Fe-O coordination is close to 4.5 in both FeO and Fe₂O₃ glass models, with Fe-O bond lengths of 2.12 Å and 1.89 Å respectively. The greater durability of xFe₂O₃-(100 − x)P₂O₅ glasses can be attributed to the lower content of P-O-P bonds and higher bond valence across Fe-O-P bonds. For 40Fe₂O₃ glass the Fe-Fe correlation shows a main peak at 5-6 Å in good agreement with the result from magnetic scattering which was interpreted in terms of speromagnetic order.     

Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations

Peptide and protein self-assembly is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. Sequence repeats from self-assembling proteins may provide useful elementary building blocks of peptide-based nanostructures. Sequences from the adenovirus fiber shaft self-assemble into amyloid-like fibrils outside their native context. In earlier simulations we studied the self-assembly of two shaft sequences, the octapeptide NSGAITIG and the hexapeptide GAITIG. Based on these simulations, cysteine residues were substituted at the first two positions of the octapeptide, yielding amyloid fibrils capable of binding to silver, gold and platinum nanoparticles. Here, we study by implicit-solvent replica-exchange simulations the self-assembly of a longer shaft sequence, the dodecapeptide LSFDNSGAITIG. The simulations provide insights on the molecular organization of the corresponding fibers. Individual molecules tend to adopt hairpin-like conformations in the observed intermolecular β-sheets, in line with the experimentally determined amyloid fiber diameters and the conformation of the peptide in the adenovirus fiber shaft. By analyzing the arrangement of individual peptides in the intermolecular sheets, we suggest possible structural models of the corresponding fibers and interpret their stability by energetic calculations.     

Volume fluctuations in potassium silicate glass studied by molecular dynamics

Potassium-silicate glass, 0.05K₂O·0.95SiO₂, was prepared by molecular dynamics under three different regimes (cooling rates, simulating box sizes) to study their influence to temperature regimes of volume fluctuations. Partial volume fluctuations (VF) were introduced with the help of Voronoi polyhedra tessellation. Dynamic and static fluctuations were suggested as a measure for time- and space-related fluctuations. Separation of the dynamic and static VFs anticipates glass transition. The glass transition was related with the change of the temperature course of the static VFs. The dynamic VFs changed their temperature regimes well below the glass transition and the transition temperature was related with the change of the transport regime. Glass transition cages the atoms but Voronoi polyhedra are definitely shaped well below the glass transition temperature.     

Crystal structure and molecular dynamics simulation of tri-o-thymotide clathrates with thiophene as guest molecule

Tri-o-thymotide (TOT) forms a cage-type clathrate with the thiophene guest molecule in a host:guest ratio of 21. This clathrate crystallizes in the trigonal system (space groupP3₁21). The unit cell, of dimensionsa=b=13.585(4),c=29.914(12)Å, contains 6 TOT and one thiophene molecule. The crystal structure, established by direct methods (R=0.053), indicates that the host cavity has an oblate-ellipsoid shape with a crystallographic twofold axis parallel to the largest dimension of the cage. The guest molecule within the cavity is disordered. Molecular dynamics simulations have been performed and indicate that the guest molecules have hindered molecular freedom around the shortest ellipsoid axis of the cavity, and may produce a dynamic disorder in the cage of the TOT clathrate.     

Structural change of liquid Si15Te85 and Si20Te80 with temperature: Ab initio molecular dynamics simulations

Using ab initio molecular dynamics simulations, the structural and electronic properties of liquid Si₁₅Te₈₅ and Si₂₀Te₈₀ at two temperatures were studied respectively. Compared with available experimental data, the calculated structure factors are acceptable. From symmetry arguments, the calculated partial bond-angle distribution functions suggest that with increasing temperature the extensive tetrahedral network structures persist longer in liquid Si₂₀Te₈₀ than those do in liquid Si₁₅Te₈₅. Our results indicate that the local tetrahedral structure around Si atoms and the Peierls-like distorted local atomic structure around Te atoms both play important roles in the structural change of liquid Si₂₀Te₈₀ and Si₁₅Te₈₅, which also suggest that the mechanisms of the structural change upon cooling in liquid Si₂₀Te₈₀ and Si₁₅Te₈₅ are of no essential difference. The results of DOS and LDOS indicate that the variation of the dip in DOS at E_F mainly results from the change of Te p orbitals.     

Molecular dynamics simulation of radiation damage in glasses

Molecular dynamics simulations of the ballistic effects arising from displacement cascades in glasses have been investigated in silica and in a SiO₂-B₂O₃-Na₂O glass. In both glasses the T-O-T′ angle (where T and T′ are network formers) diminishes, despite radiation causes opposite effects: while the ternary glass swells and silica becomes denser. We show that radiation-induced modifications of macroscopic glass properties result from structural change at medium/range, reflecting an increasing disorder and internal energy of the system. A local thermal quenching model is proposed to account for the effects of ballistic collisions. The core of a displacement cascade is heated by the passage of the projectile, then rapidly quenched, leading to a process that mimics a local thermal quenching. The observed changes in both the mechanical and structural properties of glasses eventually reach saturation at 2 10¹⁸ α/g as the accumulated energy increases. The passage of a single projectile is sufficient to reach the maximum degree of damage, confirming the hypothesis postulated in the swelling model proposed by J.A.C. Marples.     

Dipolar relaxation of propylene glycol molecular cluster confined in carbon nanotubes of different chiralities—computer simulation study

We performed fully atomistic molecular dynamics simulation of propylene glycol molecules confined in single-walled carbon nanotubes of similar diameters but different chiralities to study the effect of the nanotube surface geometry on dipolar relaxation characteristic of the studied system. We show that it follows stretched exponential characteristic and that the chirality of the nanotube considerably affects thermal activation characteristic of the process.     

Influence of ambient gases on the morphology and photoluminescence of ZnO nanostructures synthesized with nickel oxide catalyst

The morphology and luminescence properties of ZnO nanowires synthesized using NiO catalyst in a chemical vapor deposition system under different growth ambient have been studied. ZnO nanostructures were prepared in nitrogen, ammonia and hydrogen ambient and characterized using X-ray diffraction, scanning electron microscopy, transmission electron microscopy and photoluminescence. Growth in nitrogen ambient yields ZnO nanoneedles while growth with ammonia and hydrogen ambient ends up with ZnO nanowires. Presence of the Ni tip at the end in either morphology indicated the involvement of vapor–liquid–solid growth mechanism. Enhanced green emission in ZnO nanowires implies the presence of a high density of oxygen vacancies. Influence of the ambient gases on the morphology and optical properties of ZnO nanostructures is discussed.     

Rapid synthesis of tin-doped indium oxide microcrystals in supercritical water using hydrazine as reducing agent

Tin-doped indium oxide (ITO) microcrystals were successfully synthesized in supercritical water (SCW) using hydrazine (N₂H₄) as a reducing agent. Using a mixture of tin and indium hydroxides prepared at pH = 9.4 as a precursor, ITO microcrystals were synthesized at temperatures 400–450 °C under pressures 25–30 MPa. Synthesizing in SCW effectively shortened the time required to synthesize the ITO microcrystals to below 30 mins. The effect of reducing agents (ethanol, formic acid, and N₂H₄) and reaction conditions on the formation of ITO particles were investigated, and it was found that N₂H₄, which is superior to ethanol and formic acid, played a key role in the doping of the In₂O₃ structure with Sn⁴⁺ to form ITO particles with a blue color. Addition of N₂H₄ possibly depleted the oxygen in the In(Sn)OOH structure, accelerating the formation of cubic In₂O₃ and introduced Sn⁴⁺ into the structure along with the creation of oxygen vacancies. It was also found that the high temperatures and the properties of the SCW, such as ion product, strongly affected the morphology of the ITO particles and the Sn⁴⁺ doping. Based on these results, a mechanism has been proposed for the synthesis of ITO particles under SCW conditions. This study demonstrates that due to the unique properties of SCW, the synthesis of doped oxides in SCW is a plausible alternative method.     

Comparison of the crystal structure and molecular models of N,N-diisobutyl-2-(octylphenylphosphinyl)acetamide (CMPO)

The crystal structure of N,N-diisobutyl-2-(octylphenylphosphinyl)acetamide, or CMPO was recently determined. The compound crystallizes in the space group P2₁/c witha=13.446(6),b=22.280(7),c=17.217(7) Å, =92.07(4)°, andD _calc=1.05 g/cm³ forZ=8 @20°C). Molecular mechanics, molecular dynamics, and MNDO calculations were also performed on CMPO utilizing the SYBYL¹ suite of programs. The results from these calculations are compared to the crystal structure and to similar calculations performed on CMPO using ALCHEMY^2,3. In general, the results from the calculations agree fairly well with the parameters from the crystal structure.     

Effect of boron oxide addition on the Nd environment in a Nd-rich soda-lime aluminoborosilicate glass

The environment of Nd³⁺ ions has been studied using optical absorption spectroscopy and EXAFS at the Nd L₃-edge, in a series of soda lime aluminoborosilicate glasses with increasing B₂O₃ content. The proportion of BO₄ units has been determined by ¹¹B MAS NMR in an equivalent glass series with La³⁺ ions replacing the majority of Nd³⁺ ions, and complementary information has been obtained by measuring the Nd³⁺ decay fluorescence times in these latter glasses. In these glasses with low Al₂O₃ content, the R′ ratio, with R′ = [Na₂O^exc] / [B₂O₃] and [Na₂O^exc] = [Na₂O] − [Al₂O₃] − [ZrO₂], plays a key role in controlling the structural organization and crystallization resistance, in a similar way as the R ratio in the Dell and Bray model of sodium borosilicate glasses. At R′ > 0.5, the Nd³⁺ ions are located in a mixed silicate-borate environment and, by slow cooling of the melt, they tend to crystallize within a silicate apatite phase close to the Ca₂Nd₈(SiO₄)₆O₂ composition. At R′ < 0.5, the structural results are compatible with Nd³⁺ ions located in a borate-type environment (not excluding Si neighbors), and, by slow cooling of the melt, they segregate with Ca²⁺ ions within a Si-depleted separated borosilicate phase.     

Multifractal nature of heterogeneous dynamics and structures in glass forming ionic liquids

Complex dynamics and structures of ionic liquids exemplified in 1-ethyl-3-methylimidazolium nitrate (EMIM-NO₃) are examined by molecular dynamics simulations. Correlation length of the radial charge distribution function and density distribution function show different temperature dependence. Density profiles are obtained from the accumulated positions visited by ions during the MD runs. The profile originating from the coexistence of layered structures of density (density wave) and those of charges (charge density wave), shows complicated heterogeneity, which is proven to be multifractal in nature. Thus, present is more than one characteristic length scale together with their mixing. The multifractal density profiles are formed by the multifractal walks with fast and slow ions. Generally, the coexistence of different length scales due to the different species or the different local structures can be the mechanism to form similar multifractal dynamics and structures.     

Explanations of the optical absorption and ESR spectrum for tetragonal Ni+ centers in CuAlS2:Ni+ crystals

In this paper, the optical absorption and electron spin resonance (ESR) spectrum of Ni⁺‐doped CuAlS₂ crystals have been studied by using a double spin‐orbit (SO) coupling approximation model, where the effects due to the SO coupling of the central metal 3d¹ ion and those of ligands are included. From this model, the formulas of the ESR g factors g_‖, g_⊥ and hyperfine structure constants A_‖, A_⊥ for 3d¹ ions in the tetragonal MX₄ clusters are constructed. The optical absorption and ESR parameters for Cu⁺ sites of CuAlS₂ have been calculated. The results obtained show that Ni⁺ ions substitute for Cu⁺ ions sites. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Study of the nucleation and growth of TiO2 and ZnO thin films by means of molecular dynamics simulations

The nucleation and growth of titanium dioxide (TiO₂) and zinc oxide (ZnO) thin films on Fe₂O₃ (hematite), Al₂O₃ (α-alumina) and SiO₂ (α-quartz) are studied by molecular dynamics simulations. The results show the formation of a strong interface region between the substrate and the film in the six systems studied here. A combination of polycrystalline and amorphous phases are observed in the TiO₂ films grown on the three substrates. ZnO deposition on the Fe₂O₃ and Al₂O₃ crystals yields a monocrystalline film growth. The ZnO film deposited on the SiO₂ crystal exhibits less crystallinity. The simulation results are compared with experimental results available in the literature.     

Crystal growth experiments in the systems Ni2MSbO6 (M = Sc,In) using chemical vapour transport reactions: Ni2InSbO6 and NiSb2O6 crystals in the millimetre range

Endothermic chemical vapour transport (CVT) reactions of Ni₂MSbO₆ (M = Sc, In), using a temperature gradient of 1313 → 1233 K and HgCl₂, HgBr₂, PtCl₂ or TeCl₄ as transport agents, led to growth of Ni₂InSbO₆ single crystals in the millimetre range, whereas in the case of Ni₂ScSbO₆ an incongruent dissolution of the solid in the source region was observed, leading to the formation of single crystals of the ternary phase NiSb₂O₆ in the sink region. The crystal structures of the obtained crystals were refined from single crystal X‐ray data with high precision [Ni₂InSbO₆: R3, Z = 3, a = 5.21640(10) Å, c = 14.0142(3) Å, 1279 structure factors, 33 parameters, R[F² > 2σ(F²)] = 0.0189; NiSb₂O₆: P4₂/mnm, Z = 2, a = 4.63910(10) Å, c = 9.2182(2) Å, 500 structure factors, 19 parameters, R[F² > 2σ(F²)] = 0.0145]. Ni₂InSbO₆ crystallizes in a corundum‐related structure, NiSb₂O₆ in the trirutile structure type. Spontaneous polarization and the ferroelectric transition temperature were estimated from the atomic arrangement and cation displacement along the polar axis in Ni₂InSbO₆. Magnetic measurements on Ni₂InSbO₆ evidence an antiferromagnetic transition near T_N = 74 K, with significant magnetic frustration.     

Epitaxial growth of tin oxide film on TiO2(1 1 0) using molecular beam epitaxy

Growth of tin oxide thin films using molecular beam epitaxy in a pyrolyzed nitrogen dioxide atmosphere on a titanium dioxide (1 1 0) substrate was investigated using X-ray photoelectron spectroscopy (XPS), electron diffraction, and atomic force microscopy (AFM). Properties of deposited films were studied for their dependence on substrate temperature and oxidation gas pressure. Analyses using XPS data revealed that tin atoms were fully oxidized to Sn⁴⁺ and SnO₂ films were grown epitaxially in deposition conditions of substrate temperatures of 627 K or higher and NO₂ pressure greater than 3×10⁻³ Pa. At a substrate temperature of 773 K, a smooth surface with atomic steps was visible in the SnO₂ films, but above or below this temperature, fine grains with crystal facets or porous structures appeared. At pressures of 8×10⁻⁴ to 3×10⁻⁴ Pa, the randomly oriented SnO phase was dominantly grown. Further decreasing the pressure, the Sn metal phase, which was epitaxially crystallized at less than 500 K, was also grown.     

Changes in molecular dynamics of the tri-ethylene glycol dimethacrylate monomer upon polymerization

The dielectric behavior of the tri-ethylene glycol dimethacrylate monomer was investigated by dielectric relaxation spectroscopy after isothermal polymerization at different temperatures and compared with the unreacted monomer. The relaxation process associated with the monomer glass transition slightly deviates to lower frequencies/higher temperatures in partial polymerized samples. Additionally, it is stronger depleted the higher the polymerization temperature, vanishing after a temperature where the polymerization reached completion. A secondary relaxation process related with localized mobility with the appearance of an excess wing in the bulk monomer previously studied in a narrower frequency range, becomes better defined after partial polymerization due to the depletion of the main relaxation process. Its location and activation energy is independent of the polymerization temperature. Whereas its intensity does not change significantly upon polymerization, the decrease of the intensity of the glass transition process could be taken as a degree of conversion. A αβ splitting scenario was drawn that maintains its pattern in the partial polymerized systems relatively to the bulk monomer. The fragility parameter of the bulk monomer was recalculated (m = 85), slightly increasing when the monomer left unreacted co-exists with the newly formed polymer.