Quantum chemical study on 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) and some of its constitutional isomers

Presently, certain isomeric compounds of NTO and their tautomers have been investigated by performing density functional theory (DFT) calculations at B3LYP/6-31G(d,p) and ROB3P86/6-311G(d,p) levels and also ab initio calculations at RHF/6-311G(d,p) level. The optimized geometries, vibrational frequencies, electronic structures and some thermodynamical values for the presently considered NTO isomers have been obtained in their ground states. Also, detonation performances were evaluated by the Kammlet-Jacobs equations, based on the calculated densities and heat of formation values. The homolytic bond dissociation energies (BDEs) (at ROB3P86/6-311G(d,p) level) of NNO(2) and CNO(2) for the molecules were calculated. Moreover, aromatic character of NTO and its isomers and tautomers were investigated by performing NICS calculations using the gauge invariant atomic orbital (GIAO) approach at the B3LYP/6-31G(d,p) and B3LYP/cc-pVDZ levels.     

Ab initio and DFT studies on nitrosoguanidine tautomers

Isolated nitrosoguanidine tautomers have been subjected to 6-31G(d,p), 6-31G(d,p) /(MP2), B3LYP/6-311G(d,p) and B3LYP/6-311++G(d,p) type quantum chemical analyses in the gas phase. The geometrical features and energetics of some conformers of the tautomers are reported. The nitrosimine form has the highest stability than the others and the diazoic acid form is the least stable one. The nitrosoimine form has the highest HOMO and LUMO energies. Whereas, the nitrosamine form possesses the lowest HOMO and the diazoic acid form has the lowest LUMO energies.     

Fluorescence-based transient state monitoring for biomolecular spectroscopy and imaging

To increase read-out speed, sensitivity or specificity, an often applied strategy in fluorescence-based biomolecular spectroscopy and imaging is to simultaneously record two or more of the fluorescence parameters: intensity, lifetime, polarization or wavelength. This review highlights how additional, to-date largely unexploited, information can be extracted by monitoring long-lived, photo-induced transient states of organic dyes and their dynamics. Two major approaches are presented, where the transient state information is obtained either from fluorescence fluctuation analysis or by recording the time-averaged fluorescence response to a time-modulated excitation. The two approaches combine the detection sensitivity of the fluorescence signal with the environmental sensitivity of the long-lived transient states. For both techniques, proof-of-principle experiments are reviewed, and advantages, limitations and possible applications for biomolecular cellular biology studies are discussed.     

Adsorption of single Ag and Cu atoms on regular and defective MgO(0 0 1) substrates: an ab initio study

The DFT slab calculations were performed for Ag and Cu atoms adsorbed on both regular and defective MgO(0 0 1) substrates. Both metal atoms and surface O vacancies (F_s centers) were distributed uniformly with a concentration of one Ag, Cu or F_s per 2×2 surface supercell. Surface O²⁻ ions are energetically more preferable for metal-atom adsorption on a regular substrate as compared to Mg²⁺ ions. The nature of the interaction between Ag or Cu adatoms and a defectless MgO substrate is physisorption (despite the difference in the adsorption energies: 0.62 vs. 0.39 eV per Cu and Ag adatom, respectively). Above the F_s centers, metal atoms are bounded much stronger when compared with regular O²⁻ sites (2.4  vs. 2.1 eV per Cu and Ag adatoms, respectively). This is accompanied by a substantial charge transfer towards each adatom (Δq_Cu=0.41e and Δq_Ag=0.32e) as well as a formation of partly covalent Me-F_s bonds across the interface (Mulliken bond populations p_Cu-Fs=0.25e and p_Ag-Fs=0.33e).     

Ab initio and TD-DFT study of the structural and spectroscopic properties of C30H10 as a new buckybowl

In this study, the structural and spectroscopic properties of the C₃₀H₁₀ as a sub-fullerene and a new buckybowl was carried out by quantum mechanical computations using B3LYP method and 6–311++G(d,p) basis set. All of the parameters were evaluated by density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were described which revealed different charge transfer possibilities for the molecule. The chemical shifts (δ, ppm) were predicted for ¹H and ¹³C atoms using GIAO method. Natural bond orbital (NBO) analysis was carried out to picture the charge transfer between the localized bonds and lone pairs. The Fukui function (FF) for local reactivity of C₃₀H₁₀ was calculated and related discussions were done.     

DFT study of the coverage effects for Al adsorption on Si(1 1 1) surfaces

Density functional theory (DFT) calculations have been carried out to investigate the interactions between the Si(1 1 1) surface and the Al adatoms. Different adsorption sites and coverage effects have been considered. For low Al coverage, the threefold-filled adsorption site is the most energy favored site. With the increase of Al coverage, adatom-adatom interactions become increasingly important and Al atomic chains or clusters are formed. With the clean Si(1 1 1) surface of metallic feature, we found that 1/3 ML Al adsorption leads to a semiconducting surface. The results for the electronic behavior suggest the formation of the polarized covalent bonding between the Al adatom and the Si(1 1 1) surface.     

Ab initio investigation on a promising transparent conductive oxide, Nb:SnO2

The effects of Nb dopant on the lattice structure, thermal, electronic, and optical properties of rutile-phased SnO₂ were investigated via ab initio calculations. The corresponding effects of Sb and Ta dopants were also studied for comparison. Results indicated that after SnO₂ was doped with Nb, the differences in ionic radii, electron configurations, and electronegativities between the native element and the heterogeneous dopant led to the variations in lattice structure, thermal stability, and electron distribution, while the tetragonal symmetry of the rutile phase is conserved. The partially filled bands around E_f originated from Nb dopant led to the severe enhancement of conductivity, electron excitation in infrared region, and the consequent optical properties except for the band gaps and the selection rule restricting the electron excitation in the visible light region. Therefore, the visible transparency of Nb:SnO₂ is expected to be comparable with or even better than Ta:SnO₂.     

A comparative study of the reported performance of ab initio protein structure prediction algorithms

Protein structure prediction is one of the major challenges in bioinformatics today. Throughout the past five decades, many different algorithmic approaches have been attempted, and although progress has been made the problem remains unsolvable even for many small proteins. While the general objective is to predict the three-dimensional structure from primary sequence, our current knowledge and computational power are simply insufficient to solve a problem of such high complexity.Some prediction algorithms do, however, appear to perform better than others, although it is not always obvious which ones they are and it is perhaps even less obvious why that is. In this review, the reported performance results from 18 different recently published prediction algorithms are compared. Furthermore, the general algorithmic settings most likely responsible for the difference in the reported performance are identified, and the specific settings of each of the 18 prediction algorithms are also compared.The average normalized r.m.s.d. scores reported range from 11.17 to 3.48. With a performance measure including both r.m.s.d. scores and CPU time, the currently best-performing prediction algorithm is identified to be the I-TASSER algorithm. Two of the algorithmic settings--protein representation and fragment assembly--were found to have definite positive influence on the running time and the predicted structures, respectively. There thus appears to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.     

Cis-trans isomerization and optical laser writing in new heterocycle based azo-polyurethanes

Three new azo-polyurethanes containing the s-triazolo[3,4-b]thiadiazole heterocycle have been prepared and characterized. The polymers showed glass transition temperatures between 183 °C and 232 °C and a moderate to good thermal stability in air. The thermal cis-trans isomerization around the azo group was analyzed in solution and the kinetic constant of this process was calculated.One of the synthesized polymers was processed in form of thin films (thickness was 1.2 μm) and some experiments of optical laser writing were performed on it: three different surface relief gratings (SRGs) structures were realized at micrometer scale (a square, a concentric square pattern and a grating) indicating this polymer as an interesting candidate for the azo-lithography.     

Surface effects on mode-I crack tip fields: A numerical study

Surface energy often significantly influences the deformation and failure behavior of materials and devices at the nanoscale. However, how it alters the local deformation around a crack tip remains unclear. In the present paper, we investigate the surface effects on the near-tip fields of a mode-I blunt crack (or notch). The theory of surface elasticity is incorporated into the finite element method. It is found that when the curvature radius of the crack root shrinks to nanometers, surface effects considerably affect the local stress distributions near the crack tip. We also calculate the J-integral, which is almost independent of surface effects except when the integral path approaches the crack tip. This demonstrates that surface effects are localized in a small zone around the crack tip, where the classical fracture mechanics solutions neglecting surface effects should be modified.     

Ab initio molecular dynamics simulation for the insertion process of Si and Ca atoms into C74

A large-scale ab initio molecular dynamics simulation for the insertion process of silicon and calcium atoms into C₇₄ is carried out for the first time by using the all-electron mixed-basis approach, where a one-electron wave function is expressed by superposing plane waves and numerical atomic orbitals. The present numerical results show that a silicon atom with more than a 40 eV kinetic energy can be inserted into C₇₄ through the center of a six-membered ring with a very short relaxation time of about 40 fs, and a calcium atom can be inserted with a 120 eV kinetic energy with a rather long relaxation time (>540 fs).     

A study on the aromaticity and kinetic stability of fullerene C38 isomers and their molecular ions

The aromaticity of the fullerene C₃₈ isomers and their molecular ions is examined by the topological resonance energy (TRE) method. The aromaticity order obtained by the TRE method is compared with relative energies found in DFT calculation results reported in literature. It is found that all C₃₈ isomers exhibit antiaromaticity when in the neutral state. However, they are highly aromatic in the hexaanionic states. The minimum bond resonance energy (min BRE) method is utilized to estimate the kinetically stability of the C₃₈ isomers and their molecular ions. According to the min BRE method, C₃₈ isomers are only have kinetic stability in penta- and hexavalent molecular anionic states.     

On the conformational disorder of PHTP:oligothiophene inclusion compounds: A semi-empirical and ab initio study

A study at the semi-empirical and ab initio level of models of the supramolecular architecture of perhydrotriphenylene and terthiophene (PHTP:T3) inclusion compound shows that the observed conformational disorder in this kind of molecular systems is subject to some constraints, the most important is that there exists an important degree of order inside the nanochannels preventing free rotational orientation of the T3 guest molecules as well as free distribution in the axial direction of the channels. For trigonal channels, T3 guests distort in two (planar and non-planar) configurations, depending on size factors of the nanochannels and small changes from the trigonal to orthorhombic symmetry favour the planar configuration of the guest molecule.     

Effects of some organic pollutants on the exopolysaccharides (EPSs) produced by some Pseudomonas spp. strains

In this study, isolation and characterization of exopolysaccharides produced by Pseudomonas aeruginosa B1, P. fluorescens B5, P. stutzeri B11 and P. putida B15 which had been seen to produce exopolymers of potential interest in biotechnological applications were examined. To initiate the observation of the organic pollutants–polymer interactions, the yield and properties of their extracellular polysaccharide were researched. The exopolysaccharide production by these strains during growth in nutrient broth medium (control) was 41–75 mg L⁻¹. Also, P. aeruginosa B1, P. fluorescens B5, P. stutzeri B11 and P. putida B15 had exhibited high production of EPSs in presence of various organic pollutants (2,4-D, benzene, BTX and gasoline, respectively) in mineral salt medium (MSM) as a sole carbon source. EPS production by the 4 strains ranged from 40 mg L⁻¹ to 8 mg L⁻¹. Monosaccharide composition of EPS produced by these cultures were analyzed by HPLC. Results indicated that EPSs of strains contained neutral sugars and acetylated amino sugars. The neutral sugars in the EPS were mainly composed of glucose, arabinose, glycerol, ribose. The presence of galactronic acid, N-acetyl-d-galactosamin and N-acetyl-d-glucosamine indicated the acidic nature of the polysaccharide. Glycerol was the basic structural unit of EPS produced by the strains except P. stutzeri B11 (MSM with 1% BTX). Strain B1 (in NB medium) was found to be composed of neutral sugars (100%) while strain B1 [in MSM medium with 0.2% (v/v) 2.4-D] contained neutral sugars (70.0%), acetylated amino sugars (30.0%). Also, EPS content of strain B5 (in the NB medium) was neutral sugars (99.8%), acetylated amino sugars (0.2%) while the strain B5 [in MSM medium containing the 1% (v/v) benzene] was found to contain neutral sugars (99.9%), acetylated amino sugars (0.1%). However, EPS monomer composition by strain B11 was detected as neutral sugars (99.77%), acetylated amino sugars (0.23%) in NB medium while the strain B11 [in MSM medium with 1% (v/v) BTX] contained neutral sugars (98.2%) and acetylated amino sugars (1.8%). Lastly, in NB medium by strain B15 was found to contain neutral sugars (99.9%) and acetylated amino sugars (0.1%) while in MSM medium in the presence of 1% (v/v) gasoline it was found to contain neutral sugars (83.6%), acetylated amino sugars (16.4%). Monomer composition of control EPSs changed to different structures in the presence of various organic pollutants. Diversities of organic compounds as carbon source affected the monomer composition of EPS produced by some Pseudomonas spp. cultures.     

Ab initio study on the lattice instability of silicon and aluminum under [0 0 1] tension

Two different single crystals, Si with the diamond structure and Al with face-centered-cubic, are subjected to [0 0 1] tension in ab initio molecular dynamics (static) simulations based on Bachelet–Hammann–Schlüter (BHS) pseudopotential. Not only the ideal tensile strength under isotropic Poisson contraction, but also the crystal stability and bifurcation to anisotropic contraction are discussed in terms of the elastic stiffness matrix and the change in the charge density. The ideal tensile strengths are overestimated to as high as =0.18, σ=18.7 GPa for Si and =0.25, σ=23.5 GPa for Al, respectively. These values are inconsistent with the experimentally observed characteristics such as the hardness of Al being lower than that of Si. The elastic stiffness matrix reveals that the crystals become unstable at far lower strain and stress, =0.094, σ=10.7 GPa for Si and =0.055, σ=5.65 GPa for Al, and bifurcate to the lower energy pass of the anisotropic contraction. The change in the electronic structure suggests that nucleation/passage of a partial dislocation would take place in the bifurcated anisotropic contraction. Thus the instability point indicates the onset of the nonelastic deformation and is much more important than the ideal tensile strength.     

A study of atomic layer deposited LiAlxOy films on Mg-Li alloys

LiAl_xO_y films with thicknesses of 65-200 nm were deposited by the atomic layer deposition (ALD) technique on the LZ101 Mg-Li alloy. The ALD-deposited LiAl_xO_y films exhibit an amorphous structure and have an atomic ratios of Li:Al:O = 1:1:2. The potentio-dynamic polarization tests show that the corrosion resistance of Mg-Li alloys can be significantly improved due to the dense and pinhole-free structure as well as the excellent coverage and conformity of the ALD-deposited LiAl_xO_y films.     

Experimental study of the effect of loading condition on fracture surface contact features and crack closure behavior in a carbon steel

To better understand the crack closure effect in the fatigue process, influence of fatigue stress amplitude and R ratio on the contact features of fracture surfaces in an annealed carbon steel was studied via two special experimental approaches: (i) the collection of the fracture debris fallen from the crack surfaces, and (ii) the direct observation of the contact zones on the fracture surface through an ink dyeing method. The results of this study show that the change of fatigue CMOD value as a function of a/W ratio depends strongly on the loading condition; the fatigue stress amplitude and R ratio are the major factors that determine the contacting status between the mating fracture surfaces; the severity of the fracture surface contact can also be characterized by the dropping rate of the fracture debris particles collected during the fatigue test.     

Photocatalytic degradation of NOx gases using TiO2-containing paint: a real scale study

An indoor car park was appropriately equipped in order to test the de-polluting efficiency of a TiO(2)-containing paint in an indoor polluted environment, under real scale configuration. Depollution tests were performed in an artificially closed area of the parking, which was polluted by a car exhaust during the testing period. The ceiling surface of the car park was covered with white acrylic TiO(2)-containing paint (PP), which was developed in the frame of the EU project 'PICADA' (Photocatalytic Innovative Coverings Application for Depollution Assessment). The closed area was fed with car exhaust gases. As soon as the system reached steady state, the UV lamps were turned on for 5h. The difference between the final and the initial steady state concentration indicates the removal of the pollutants due to both the photocatalytic paint and car emission reduction. Results showed a significant photocatalytic oxidation of NO(x) gases. The photocatalytic removal of NO and NO(2) was calculated to 19% and 20%, respectively, while the photocatalytic rate (microgm(-2)s(-1)) ranged between 0.05 and 0.13 for NO and between 0.09 and 0.16 for NO(2).     

Novel silicon-carbon fullerene-like nanostructures: an Ab initio study on the stability of Si54C6 and Si60C6 clusters

Silicon fullerene like nanostructures with six carbon atoms on the surface of Si60 cages by substitution, as well as inside the cage at various symmetry orientations have been studied within the generalized gradient approximation to density functional theory. Full geometry optimizations have been performed without any symmetry constraints using the Gaussian 03 suite of programs and the LANL2DZ basis set. Thus, for the silicon atom, the Hay-Wadt pseudopotential with the associated basis set are used for the core electrons and the valence electrons, respectively. For the carbon atom, the Dunning/Huzinaga double zeta basis set is employed. Electronic and geometric properties of the nanostructures are presented and discussed in detail. It was found that optimized silicon-carbon fullerene like nanostructures have increased stability compared to bare Si60 cage and the stability depends on the orientation of carbon atoms, as well as on the nature of bonding between silicon and carbon atoms and also on the carbon-carbon bonding.     

Study on ZnO thin films deposited on sol-gel grown ZnO buffer by RF magnetron sputtering

ZnO thin films with preferential C-orientation and dense microstructure have been prepared using RF magnetron sputtering method by the insertion of a sol-gel grown ZnO buffer layer. The XRD results show that the C-orientation of the film deposited on ZnO buffer is obviously better than that deposited directly on lime-glass substrate. With an increase of the RF power from 100 to 380 W, C-orientation of the films with ZnO buffer improves and the grain size increases. When the RF power equals 550 W, the orientation of the film changes to (1 0 0) and the grain size decreases. The crystalline and microstructure quality of the films can be improved after annealing, however, the grain size is not much dependent on the annealing temperature in the range of 560-610 °C.