Selective detection of cyanogen halides by BN nanocluster: a DFT study

The electronic sensitivity and adsorption behavior toward cyanogen halides (X–CN; X?=?F, Cl, and Br) of a B₁₂N₁₂ nanocluster were investigated by means of density functional theory calculations. The X-head of these molecules was predicted to interact weakly with the BN cluster because of the positive σ-hole on the electronic potential surface of halogens. The X–CN molecules interact somewhat strongly with the boron atoms of the cluster via the N-head, which is accompanied by a large charge transfer from the X–CN to the cluster. The change in enthalpy upon the adsorption process (at room temperature and 1 atm) is about ?19.2, ?23.4, and ?30.5 kJ mol^?1 for X?=?F, Cl, and Br, respectively. The LUMO level of the BN cluster is largely stabilized after the adsorption process, and the HOMO–LUMO gap is significantly decreased. Thus, the electrical conductivity of the cluster is increased, and an electrical signal is generated that can help to detect these molecules. By increasing the atomic number of X, the signal will increase, which makes the sensor selective for cyanogen halides. Also, it was indicated that the B₁₂N₁₂ nanocluster benefits from a short recovery time as a sensor.     

Anticorrosion mechanism of Cr-doped nickel-base alloy in Br/O environment: a DFT study

ABSTRACT

Density functional theory was used to investigate the anticorrosion mechanism of Cr-doped nickel-base alloy in Br/O environment. The adsorption properties including adsorption energy, bond length and electron structure of Br/O on Ni and Cr-doped Ni surfaces have been investigated. We find that the O atom has bigger adsorption activity than the Br atom. The oxide film can be preferentially formed on the Cr-doped nickel-base alloy surface under the coexistence of Br and O atoms. By exploring the interactions between Br and NiO (111) or Cr₂O₃ (100) surfaces, we demonstrate that oxide films could prevent Br from erosion. Results indicate that Cr₂O₃ has stronger corrosion resistance than NiO. The corrosion resistance mechanism of Cr-doped nickel-base alloy is summarised into two processes, i.e. competitive adsorption and adsorption inhibition.     

Exohedral and endohedral adsorption of alkaline earth cations in BN nanocluster

Adsorption of three alkaline earth cations inside and outside of a B₁₂N₁₂ nano-cage in aqueous medium was investigated using density functional theory. The results obtained are discussed in terms of thermodynamic, geometric, and electronic properties. Based on the calculation of enthalpy changes at 298 K and 1 atm, the adsorption of the considered cations was found to be exothermic outside the cluster while it is endothermic inside. It was also found that the exohedral adsorption favorability of the cluster increases in the series: Ca²⁺?<?Mg²⁺?<<?Be²⁺ with Gibbs free energy changes in the range of ?0.08 to ?1.53 eV at B3LYP/6-31G (d) level of theory. Overall, interaction of the cations with the cluster influences the electronic properties of the cluster through stabilizing the HOMO and LUMO as well as reducing the energy gap between them. However, the electronic properties changed much more in the case of endohedral adsorption in comparison with the exohedral adsorption.     

A DFT study on the sensing behavior of a BC2N nanotube toward formaldehyde

We investigated the viability of using a BC₂N nanotube to detect formaldehyde (H₂CO) molecule by means of B3LYP and M06 density functionals. The results indicate that the molecule is weakly adsorbed on the intrinsic BC₂N nanotube releasing energy of 0.8 kcal mol^-1 (at B3LYP/6-31G(d)) without significant effect on the HOMO-LUMO energy gap and electrical conductivity of the tube. Thus, H₂CO cannot be detected using this intrinsic nanotube. To overcome this problem, a carbon atom of the tube wall was substituted by a Si atom. It was demonstrated that the Si-doped tube cannot only strongly adsorb the H₂CO molecule, but also may effectively detect its presence because of the increase in the electric conductivity of the tube.     

DFT studies of acrolein molecule adsorption on pristine and Al- doped graphenes

The ability of pristine graphene (PG) and Al-doped graphene (AlG) to detect toxic acrolein (C₃H₄O) was investigated by using density functional calculations. It was found that C₃H₄O molecule can be adsorbed on the PG and AlG with adsorption energies about ?50.43 and – v30.92 kcal mol^?1 corresponding to the most stable configurations, respectively. Despite the fact that interaction of C₃H₄O has no obvious effects on the of electronic properties of PG, the interaction between C₃H₄O and AlG can induce significant changes in the HOMO/LUMO energy gap of the sheet, altering its electrical conductivity which is beneficial to sensor designing. Thus, the AlG may be sensitive in the presence of C₃H₄O molecule and might be used in its sensor devices. Also, applying an external electric filed in an appropriate orientation (almost stronger than 0.01 a.u.) can energetically facilitate the adsorption of C₃H₄O molecule on the AlG.     

A large gap opening of graphene induced by the adsorption of CO on the Al-doped site

We investigated CO adsorption on the pristine, Stone-Wales (SW) defected, Al- and Si- doped graphenes by using density functional calculations in terms of geometric, energetic and electronic properties. It was found that CO molecule is weakly adsorbed on the pristine and SW defected graphenes and their electronic properties were slightly changed. The Al- and Si- doped graphenes show high reactivity toward CO, so calculated adoption energies are about ?11.40 and ?13.75 kcal mol^?1 in the most favorable states. It was found that, among all the structures, the electronic properties of Al-doped graphene are strongly sensitive to the presence of CO molecule. We demonstrate the existence of a large E_g opening of 0.87 eV in graphene which is induced by Al-doping and CO adsorption.     

NH3 on a BC3 nanotube: effect of doping and decoration of aluminum

The adsorption of the NH₃ molecule was investigated on pristine, Al-doped and Al-decorated BC₃ nanotubes (BC₃NT) using density functional theory calculations. It was found that NH₃ prefers to be adsorbed on a B atom of the tube wall, releasing energy of 1.02 eV. Al-doping increases the acidity of the tube surface and, therefore, its reactivity toward NH₃ so that the released energy in this case is about 1.62 eV, while decorating the BC₃NT with Al atom decreases the acidity and reactivity. Although Al-doping has no significant effect on the electronic properties of the BC₃NT, Al-decoration significantly reduces its HOMO/LUMO energy gap from 2.37 to 1.16 eV so that the tube becomes an n-type semiconductor. However, we believe that the acidity of the BC₃NTs may be controlled by doping or decoration of Al atoms.     

Nitrous oxide adsorption on pristine and Si-doped AlN nanotubes

Using density functional theory, we studied the adsorption of an N₂O molecule onto pristine and Si-doped AlN nanotubes in terms of energetic, geometric, and electronic properties. The N₂O is weakly adsorbed onto the pristine tube, releasing energies in the range of ?1.1 to ?5.7 kcal mol^-1. The electronic properties of the pristine tube are not influenced by the adsorption process. The N₂O molecule is predicted to strongly interact with the Si-doped tube in such a way that its oxygen atom diffuses into the tube wall, releasing an N₂ molecule. The energy of this reaction is calculated to be about ?103.6 kcal mol^-1, and the electronic properties of the Si-doped tube are slightly altered.     

Fluorination of BC3 nanotubes: DFT studies

We have studied the adsorption of atomic and molecular fluorines on a BC₃ nanotube by using density functional calculations. It was found that the adsorption of atomic fluorine on a C atom of the tube surface is energetically more favorable than that on a B atom by about 0.97 eV. The adsorption of atomic fluorine on both C and B atoms significantly affects the electronic properties of the BC₃ tube. The HOMO-LUMO energy gap is considerably reduced from 2.37 to 1.50 and 1.14 eV upon atomic F adsorption on B and C atoms, respectively. Molecular fluorine energetically tends to be dissociated on B atoms of the tube surface. The associative and dissociative adsorption energies of F₂ were calculated to be about ?0.42 and ?4.79 eV, respectively. Electron emission density from BC₃ nanotube surface will be increased upon both atomic and molecular fluorine adsorptions due to work function decrement.     

Tailoring the Field Distribution of ZnO by Polyaniline for SPR-Based Fiber Optic Detection of Hardness of the Drinking Water

Due to the industrial development, drinking water is getting polluted by disposing several waste products of the industries. Hardness is one of the prominent impurities in drinking water which is mainly due to the presence of carbonate and bicarbonate ions (CO₃ ^2? and HCO₃ ^?) in it. Here, we present the synthesis of the zinc oxide (ZnO) and polyaniline (PANI) nanocomposite for the detection and estimation of hardness of the drinking water. The chemical formula of such a nanocomposite is defined in terms of the fraction of polyaniline nanoparticles reinforced in ZnO matrix and is derived as ZnO_(1???x)PANI _x (0?≤?x?≤?0.9); x is the composition ratio. Silver and ZnO_(1???x)PANI _x layers are coated over the unclad core of the optical fiber so as to create the four layer system as that of Kretschmann configuration SPR structure. The working principle involves the change in dielectric constant of (ZnO_(1???x)PANI _x ) by CO₃ ^2? or HCO₃ ^? ions in aqueous atmosphere. Due to the strong interaction of the sensing surface to the CO₃ ^2? and HCO₃ ^? ions, a red shift in the SPR spectrum is observed in the concentration range 0–200 μg/l. The sensitivity of the sensor depends on the composition ratio of the nanocomposite and has been found to be maximum for the composition ratio lying in the range 0.45–0.60. This has been further confirmed in terms of the enhancement of the electric field density and found to be in agreement with the experimental value. The sensitivity of the sensor with optimum value of the composition ratio is 0.094 and 0.065 nm/(μg/l) for CO₃ ^2? and HCO₃ ^?, respectively. The sensor is highly selective to CO₃ ^2? and HCO₃ ^?. The sensor has advantages of online monitoring and remote sensing of water quality because the probe is fabricated over an optical fiber.     

A density functional study of chemical,magnetic and thermodynamic properties of small palladium clusters

Structural, chemical, magnetic and thermodynamic properties of palladium clusters Pd_n with n = 2–11 are studied using density functional methods. The average bond length, entropy, enthalpy and polarisability are observed to increase as the cluster grows in size. The binding energy per atom also increases with cluster size. Stability function and atom addition energy change predict that Pd₄, Pd₆ and Pd₉ are relatively more stable than their neighbouring clusters. Electron affinity, electronegativity and electrophilicity values suggest that larger clusters have stronger tendency to accept electrons, thereby supporting the relative stability of Pd₄ and Pd₆. Chemical hardness is also seen to decrease with cluster size, which suggests that large clusters are more prone to changes in their electronic structure. The magnetic properties of these clusters are reported.     

Rational Improvement of Peptide Affinity to Human Pregnancy-Related Serine Protease HtrA3 PDZ Domain by Introducing a Halogen Bond to the Domain–Peptide Complex Interface

The pregnancy-related serine protease HtrA3 plays an important role in human placental development and has recently been recognized as a potential therapeutic target in the treatment of cancer. Previously, a C-terminal pentapeptide FGRWV^–COOH was identified to bind at the PDZ domain of HtrA3 with a moderate affinity. Here, based on the high-resolution complex crystal structure of HtrA3 PDZ domain with the pentapeptide ligand we successfully introduced a rationally designed halogen bond to the complex interface by substituting R₄-hydrogen atom of the indole moiety of peptide Trp_-1 residue with a halogen atom. High-level theoretical calculations suggested that bromine is the best choice that can render strong interaction energy for the halogen bond and can confer high affinity to the PDZ–peptide complex. Fluorescence spectroscopy characterizations revealed that the resulting R₄-brominated peptide (K _d = 0.15 ± 0.03 μM) exhibited 12-fold affinity improvement relative to its nonhalogenated counterpart (K _d = 1.8 ± 0.4 μM). In contrast, the PDZ-binding affinity of R₆-brominated peptide (K _d = 1.2 ± 0.1 μM), a negative control that was unable to form the halogen bond according to theoretical investigations, did not change substantially as compared to the nonhalogenated peptide.     

Selective hydrogenolysis of raw glycerol to 1,2-propanediol over Cu–ZnO catalysts in fixed-bed reactor

The catalytic properties of Cu–ZnO catalysts for glycerol hydrogenolysis to 1,2-propanediol (1,2-PDO) were tested in a fixed-bed reactor at 250 °C and 2.0 MPa H₂. The relation between composition, surface properties, and catalytic performance of glycerol hydrogenation of Cu–ZnO catalysts was studied using nitrogen adsorption (BET methods), XRD, H₂ temperature-programmed reduction, and N₂O chemisorptions. It was found that there was a close link between the surface CuO amount of Cu–ZnO catalyst and the reactivity for glycerol hydrogenation. The Cu–ZnO catalyst (Cu/Zn = 1.86) which had the highest surface Cu amount showed the best catalytic activity for glycerol hydrogenolysis. Furthermore, Cu–ZnO catalyst presented good stability and remarkable catalytic activity for glycerol hydrogenolysis to 1,2-PDO using raw glycerol derived from the fat saponification as feedstock.     

Methane adsorption and hydrogen atom abstraction at diatomic radical cation metal oxo clusters: first-principles calculations

A thermochemical assessment of the C–H bond activation of methane over a series of monoxide MO^?+ radical cations (M = Be, Mg, Ca, Sr, Ti, Cr, Fe, Ni, Zn, Pd and Pt) is presented in this paper within a hybrid density functional theory framework. Although all oxo clusters could implement chemisorption, only three (MgO^?+, CaO^?+ and SrO^?+) could spontaneously perform H transfer. The stabilisation of methane at the adsorption stage, which was accompanied by partial electron transfers (0.026–0.210 e) from methane to the radical cation, was found to be a key player in the exergonic CH₄/MO^?+ reaction systems. The thermodynamic favourability followed the order of CrO^?+ < TiO^?+ < FeO^?+ < PtO^?+ < PdO^?+ < NiO^?+ < ZnO^?+ < MgO^?+ < SrO^?+ < CaO^?+ < BeO^?+ as understood from the free energy changes. The activation barriers ranged from 6.86 kcal/mol (SrO^?+) to 37.29 kcal/mol (TiO^?+). The density of states implied that a promising radical cation system was able to maintain its occupied molecular orbital on the O atom while reserving the metal atom for the unoccupied one.     

One-Step Preparation and Fluorescence Enhancement Effect in SiO2/Eu2+ Doped with Ag Nanowires

Eu²⁺ single-doped SiO₂ (SiO₂/Eu²⁺) and Eu²⁺, Ag nanowires co-doped SiO₂ (SiO₂/Eu²⁺–Ag) luminescent nanomaterials were prepared by an efficient one-step sol–gel method. Their microstructure and optical properties were characterized, and the fluorescence enhancement of Eu²⁺ by Ag nanowires was investigated. The experimental results indicate that the average diameter of Ag nanowires doped is 12.5 nm, and the length–diameter ratio is 30. The Ag nanowires cannot only enhance the light absorption of SiO₂/Eu²⁺ in the range of 230–350 nm, but also reduce the fluorescence lifetime of Eu²⁺. More importantly, the emission intensity is enhanced after doping Ag nanowires, and the red shift phenomenon of the emission spectrum is observed, red shift occurs between 10 and 56 nm. The highest fluorescence intensity is accessed under the Ag doping concentration of 0.10 %. Additionally, the emission of SiO₂/Eu²⁺ with 0.10 % of Ag doping at 456 nm is 16 times stronger than that of pure SiO₂/Eu²⁺. The present results indicate that the fluorescence enhancement is attributed to the local field enhancement and the increased radiative decay rates induced by Ag nanowires.     

Tracing carbon monoxide uptake by Clostridium ljungdahlii during ethanol fermentation using 13C-enrichment technique

Conversion of synthesis gas (CO and H₂) to ethanol can be an alternative, promising technology to produce biofuels from renewable biomass. To distinguish microbial utilization of carbon source between fructose and synthesis gas CO and to evaluate biological production of ethanol from CO, we adopted the ¹³C-enrichment of the CO substrate and hypothesized that the residual increase in δ¹³C of the cell biomass would reflect the increased contribution of ¹³C-enriched CO. Addition of synthesis gas to live culture medium for ethanol fermentation by Clostridum ljungdahlii increased the microbial growth and ethanol production. Despite the high ¹³C-enrichment in CO (99 atom % ¹³C), however, microbial δ¹³C increased relatively small compared to the microbial growth. The uptake efficiency of CO estimated using the isotope mass balance equation was also very low: 0.0014 % for the low CO and 0.0016 % for the high CO treatment. Furthermore, the fast production of ethanol in the early stage indicated that the presence of sugar in fermentation medium would limit the utilization of CO as a carbon source by C. ljungdahlii.     

Zwitterion l-cysteine adsorbed on the Au20 cluster: enhancement of infrared active normal modes

The study reported herein addressed the structure, adsorption energy and normal modes of zwitterion l-cysteine (Z-cys) adsorbed on the Au₂₀ cluster by using density functional theory (DFT). It was found that four Z-cys are bound to the Au₂₀ apexes preferentially through S atoms. Regarding normal modes, after adsorption of four Z-cys molecules, a more intense infrared (IR) peak is maintained around 1,631.4 cm^?1 corresponding with a C=O stretching mode, but its intensity is enhanced approximately six times. The enhancement in the intensity of modes between 0 to 300 cm^?1 is around 4.5 to 5.0 times for normal modes that involve O–C=O and C-S bending modes. Other two normal modes in the range from 300 to 3,500 cm^?1 show enhancements of 6.0 and 7.4 times. In general, four peaks show major intensities and they are related with normal modes of carboxyl and NH₃ groups of Z-cys.     

Spectroscopic evidence for an all-ferrous [4Fe–4S]<Superscript>0</Superscript> cluster in the superreduced activator of 2-hydroxyglutaryl-CoA dehydratase from <Emphasis Type="Italic">Acidaminococcus </Emphasis><Emphasis Type="Italic">fermentans</Emphasis>

The key enzyme of the fermentation of glutamate by Acidaminococcus fermentans, 2-hydroxyglutarylcoenzyme A dehydratase, catalyzes the reversible syn-elimination of water from (R)-2-hydroxyglutaryl-coenzyme A, resulting in (E)-glutaconylcoenzyme A. The dehydratase system consists of two oxygen-sensitive protein components, the activator (HgdC) and the actual dehydratase (HgdAB). Previous biochemical and spectroscopic studies revealed that the reduced [4Fe–4S]⁺ cluster containing activator transfers one electron to the dehydratase driven by ATP hydrolysis, which activates the enzyme. With a tenfold excess of titanium(III) citrate at pH 8.0 the activator can be further reduced, yielding about 50% of a superreduced [4Fe–4S]⁰ cluster in the all-ferrous state. This is inferred from the appearance of a new Mössbauer spectrum with parameters δ = 0.65 mm/s and ΔE _Q = 1.51–2.19 mm/s at 140 K, which are typical of Fe(II)S₄ sites. Parallel-mode electron paramagnetic resonance (EPR) spectroscopy performed at temperatures between 3 and 20 K showed two sharp signals at g = 16 and 12, indicating an integer-spin system. The X-band EPR spectra and magnetic Mössbauer spectra could be consistently simulated by adopting a total spin S _t = 4 for the all-ferrous cluster with weak zero-field splitting parameters D = ?0.66 cm^?1 and E/D = 0.17. The superreduced cluster has apparent spectroscopic similarities with the corresponding [4Fe–4S]⁰ cluster described for the nitrogenase Fe-protein, but in detail their properties differ. While the all-ferrous Fe-protein is capable of transferring electrons to the MoFe-protein for dinitrogen reduction, a similar physiological role is elusive for the superreduced activator. This finding supports our model that only one-electron transfer steps are involved in dehydratase catalysis. Nevertheless we discuss a common basic mechanism of the two diverse systems, which are so far the only described examples of the all-ferrous [4Fe–4S]⁰ cluster found in biology.     

HdrC2 from Acidithiobacillus ferrooxidans Owns Two Iron–Sulfur Binding Motifs But Binds Only One Variable Cluster Between [4Fe–4S] and [3Fe–4S]

The heterodisulfide reductase complex HdrABC from Acidithiobacillus ferrooxidans was suggested to own novel features that act in reverse to convert the sulfane sulfur of GS _n H species (n > 1) into sulfite in sulfur oxidation. The HdrC subunit is potentially encoded by two different highly upregulated genes sharing only 29 % identity in A. ferrooxidans grown in sulfur-containing medium, which were named as HdrC1 and HdrC2, respectively and had been confirmed to contain iron–sulfur cluster by expression and characterization, especially the HdrC1 which had been showed to bind only one [4Fe–4S] cluster by mutations. However, the mutations of the HdrC2 remain to be done and the detailed binding information of it is still unclear. Here, we report the expression, mutations, and molecular modeling of the HdrC2 from A. ferrooxidans. This HdrC2 had two identical motifs (Cx₂Cx₂Cx₃C) containing total of eight cysteine residues potentially for iron–sulfur cluster binding. This purified HdrC2 was exhibited to contain one variable cluster converted between [4Fe–4S] and [3Fe–4S] according to different conditions by the UV-scanning and EPR spectra. The site-directed mutagenesis results of these eight residues further confirmed that the HdrC2 in reduction with Fe²⁺ condition loaded only one [4Fe–4S]⁺ with spin S = 1/2 ligated by the residues of Cys73, Cys109, Cys112, and Cys115; the HdrC2 in natural aeration condition lost the Fe atom ligated by the residue of Cys73 and loaded only one [3Fe–4S]⁰ with spin S = 0; the HdrC2 in oxidation condition loaded only one [3Fe–4S]⁺ with spin S = 1/2. Molecular modeling results were also in line with the experiment results.