Structure and electronic properties of native and defected gallium nitride nanotubes

Structure and electronic properties of GaN nanotubes (GaNNTs) are investigated by using ab initio density functional theory. By full optimization, the optimized structures (bond-lengths and angles between them) of zigzag GaNNTs (n,0) and armchair GaNNTs (n,n) (4<n<11) are calculated. The difference between nitrogen ring diameter and gallium ring diameter (buckling distance) and semiconducting energy gap in term of diameter for zigzag and armchair GaNNTs have also been calculated. We found that buckling distance decreases by increasing nanotube diameter. Furthermore, we have investigated the effects of nitrogen and gallium vacancies on structure and electronic properties of zigzag GaNNT (5,0) using spin dependent density functional theory. By calculating the formation energy, we found that N vacancy in GaNNT (5,0) is more favorable than Ga vacancy. The nitrogen vacancy in zigzag GaNNT induces a 1.0μB magnetization and makes a polarized structure. We have shown that in polarized GaNNT a flat band near the Fermi energy splits to occupied spin up and unoccupied spin down levels.     

Essay: reflections on Physical Review Letters

During my tenure as APS Editor-in-Chief Physical Review Letters changed from a journal whose authors were mostly from the U.S. to one whose authors were mostly from abroad. I encouraged authors to publicize their work even before their papers were accepted for publication. And I sought to raise the quality of the papers that were published even higher than before.     

Influence of Halogen Substitution in the Ligand Sphere on the Antitumor and Antibacterial Activity of Half‐sandwich Ruthenium(II) Complexes [RuX(η6‐arene)(C5H4N‐2‐CH=N‐Ar)]+

New complexes [(η⁶‐p‐cymene)Ru(C₅H₄N‐2‐CH=N–Ar)X]PF₆ [X = Br ( 1 ), I ( 2 ); Ar = 4‐fluorophenyl ( a ), 4‐chlorophenyl ( b ), 4‐bromophenyl ( c ), 4‐iodophenyl ( d ), 2,5‐dichlorophenyl ( e )] were prepared, as well as 3a – 3e (X = Cl) and the new complexes [(η⁶‐arene)RuCl(N‐N)]PF₆ (arene = C₆H₅OCH₂CH₂OH, N‐N = 2,2′‐bipyridine ( 4 ), 2,6‐(dimethylphenyl)‐pyridin‐2‐yl‐methylene amine ( 5 ), 2,6‐(diisopropylphenyl)‐pyridin‐2‐yl‐methylene amine ( 6 ); arene = p‐cymene, N‐N = 4‐(aminophenyl)‐pyridin‐2‐yl‐methylene amine ( 7 )]. X‐ray diffraction studies were performed for 1a , 1b , 1c , 1d , 2b , 5 , and 7 . Cytotoxicities of 1a – 1d and 2 were established versus human cancer cells epithelial colorectal adenocarcinoma (Caco‐2) (IC₅₀: 35.8–631.0 μM), breast adenocarcinoma (MCF7) (IC₅₀: 36.3–128.8.0 μM), and hepatocellular carcinoma (HepG2) (IC₅₀: 60.6–439.8 μM), 3a – 3e were tested against HepG2 and Caco‐2, and 4 – 7 were tested against Caco‐2. 1 – 7 were tested against non‐cancerous human epithelial kidney cells. 1 and 2 were more selective towards tumor cells than the anticancer drug 5‐fluorouracil (5‐FU), but 3a – 3e (X = Cl) were not selective. 1 and 2 had good activity against MCF7, some with lower IC₅₀ than 5‐FU. Complexes with X = Br or I had moderate activity against Caco‐2 and HepG2, but those with Cl were inactive. Antibacterial activities of 1a , 2b , 3a , and 7 were tested against antibacterial susceptible and resistant Gram‐negative and ‐positive bacteria. 1a , 2b , and 3a showed activity against methicillin‐resistant S. aureus (MIC = 31–2000 μg · mL^–1).     

Structures of anti,Z-4,4-dimethyl-3-thiosemicarbazide, syn,E,Z-2,4-dimethyl-3-thiosemicarbazide and syn,E-1-cyclopentano-3-thiosemicarbazone

The structures of three alkyl derivatives of thiosemicarbazide are described: anti,Z-4,4-dimethyl-3-thiosemicarbazide (1), syn,E,Z-2,4-dimethyl-3-thiosemicarbazide (2), and syn,E-1-cyclopentano-3-thiosemicarbazone (3). Crystal data: for 1: triclinic, P-1 (#2), a = 5.802(1)Å, b = 6.935(1)Å, c = 8.104(2)Å, = 78.35(1)°, = 82.13(1)°, = 70.71(1)°, and Z = 2; for 2: orthorhombic, Pbca (#61), a = 9.417(3)Å, b = 8.624(2)Å, c = 15.169(3)Å, and Z = 8; for 3: triclinic, P-1 (#2), a = 6.068(3)Å, b = 8.145(4)Å, c = 8.666(5)Å, = 83.75(4)°, = 86.16(5)°, = 74.07(4)°, and Z = 2. In general, molecules are linked by N–H···S hydrogen bonds with sulfurs accepting two or three hydrogen bonds. Structures 2 and 3, which adopt the syn conformation, form N–H···N intramolecular hydrogen bonds. The solid-state structures are consistent with their infrared and proton nuclear magnetic resonance spectra.     

Protein–small molecule docking with receptor flexibility in iMOLSDOCK

We have earlier reported the iMOLSDOCK technique to perform ‘induced-fit’ peptide–protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein–ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/.     

Combined experimental and theoretical study on aromatic hydroxylation by mononuclear nonheme iron(IV)-oxo complexes

The hydroxylation of aromatic compounds by mononuclear nonheme iron(IV)-oxo complexes, [FeIV(Bn-tpen)(O)]2+ (Bn-tpen=N-benzyl-N,N',N'-tris(2-pyridylmethyl)ethane-1,2-diamine) and [FeIV(N4Py)(O)]2+ (N4Py=N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine), has been investigated by a combined experimental and theoretical approach. In the experimental work, we have performed kinetic studies of the oxidation of anthracene with nonheme iron(IV)-oxo complexes generated in situ, thereby determining kinetic and thermodynamic parameters, a Hammett rho value, and a kinetic isotope effect (KIE) value. A large negative Hammett rho value of -3.9 and an inverse KIE value of 0.9 indicate that the iron-oxo group attacks the aromatic ring via an electrophilic pathway. By carrying out isotope labeling experiments, the oxygen in oxygenated products was found to derive from the nonheme iron(IV)-oxo species. In the theoretical work, we have conducted density functional theory (DFT) calculations on the hydroxylation of benzene by [FeIV(N4Py)(O)]2+. The calculations show that the reaction proceeds via two-state reactivity patterns on competing triplet and quintet spin states via an initial rate determining electrophilic substitution step. In analogy to heme iron(IV)-oxo catalysts, the ligand is noninnocent and actively participates in the reaction mechanism by reshuttling a proton from the ipso position to the oxo group. Calculated kinetic isotope effects of C6H6 versus C6D6 confirm an inverse isotope effect for the electrophilic substitution pathway. Based on the experimental and theoretical results, we have concluded that the aromatic ring oxidation by mononuclear nonheme iron(IV)-oxo complexes does not occur via a hydrogen atom abstraction mechanism but involves an initial electrophilic attack on the pi-system of the aromatic ring to produce a tetrahedral radical or cationic sigma-complex.     

Use of in-tube sorptive extraction techniques for determination of benzene, toluene, ethylbenzene and xylenes in soft drinks

A comparison is made between static headspace analysis and headspace solid-phase dynamic extraction (HS-SPDE) for the quantitative determination of trace level BTEX solvents (benzene, toluene, ethylbenzene and o-, m-, and p-xylene) in soft drinks. Two non-polar extraction phases were investigated for SPDE using an automated sampler with a gas-tight syringe equipped with a special needle coated on the inside with the extraction phase. Following adsorption onto the phase, the analytes were thermally desorbed directly into a GC-MS. The techniques were optimised and evaluated by analysis of spiked soft drink samples. The use of the SPDE device gave comparable results to the static headspace method, with lower detection limits for some compounds, and also offers advantages for applications where lower temperatures are preferred.     

Large-volume sample stacking with polarity switching for the analysis of bacteria by capillary electrophoresis with laser-induced fluorescence detection

Capillary electrophoresis has been utilized for the rapid analysis of bacteria under specific experimental conditions. In this work, a method of large-volume sample stacking with polarity switching was evaluated for the analysis of bacteria by capillary electrophoresis with laser-induced fluorescence detection in order to enhance the detection sensitivity. The results indicated that the proposed method is not only effective for the focusing of bacterial cells, but also for the separation of mixtures of bacteria. With the optimized conditions, an enhancement factor of around 60-fold was obtained when long sample plug (up to 39.6% of capillary volume) was injected. Moreover, with the help of such stacking method, single, sharp, intense peak with high efficiency was observed without multiple peaks attributable to irregular clusters and aggregates of bacterial cells. This simple stacking approach appears to be promising as a rapid sterility test in various fields of applications.     

Single-molecule elasticity measurements of the onset of excluded volume in poly(ethylene glycol)

A polymer must reach a certain size to exhibit significant excluded-volume interactions and adopt a swollen random-walk configuration. We show that single-molecule measurements can sense the onset of swelling by modulating the effective chain size with force: as the force is reduced from a large value, the polymer is first highly aligned, then a Gaussian coil, then finally a swollen chain, with each regime exhibiting a distinct elasticity. We use this approach to quantify the structural parameters of poly(ethylene glycol) and show that they vary in the expected manner with changes in solvent.     

Quenching of surface traps in Mn doped ZnO thin films for enhanced optical transparency

The structural and photoluminescence analyses were performed on un-doped and Mn doped ZnO thin films grown on Si (1 0 0) substrate by pulsed laser deposition (PLD) and annealed at different post-deposition temperatures (500-800 °C). X-ray diffraction (XRD), employed to study the structural properties, showed an improved crystallinity at elevated temperatures with a consistent decrease in the lattice parameter ‘c’. The peak broadening in XRD spectra and the presence of Mn 2p3/2 peak at ∼640 eV in X-ray Photoelectron Spectroscopic (XPS) spectra of the doped thin films confirmed the successful incorporation of Mn in ZnO host matrix. Extended near band edge emission (NBE) spectra indicated the reduction in the concentration of the intrinsic surface traps in comparison to the doped ones resulting in improved optical transparency. Reduced deep level emission (DLE) spectra in doped thin films with declined PL ratio validated the quenching of the intrinsic surface traps thereby improving the optical transparency and the band gap, essential for optoelectronic and spintronic applications. Furthermore, the formation and uniform distribution of nano-sized grains with improved surface features of Mn-doped ZnO thin films were observed in Field Emission Scanning Electron Microscopy (FESEM) images.