Effect of Te addition on the optical properties of As(2)S(3) thin film

Bilayer thin films of Te/As(2)S(3) were prepared from Te and As(2)S(3) by thermal technique under high vacuum. Optical constants were calculated by analysing the transmission spectrum in the spectral range 400-1100 nm. The optical band gap decreases with the addition of Te to As(2)S(3). The decrease of optical band gap has been explained on the basis of density of states and the increase in disorder in the system. We have irradiated the as-deposited films using a diode pumped solid state laser of 532 nm wavelength to study photo-diffusion of Te into As(2)S(3). The changes were characterised by Fourier Transform Infrared and X-ray Photoelectron Spectroscopy (XPS). The optical band gap is found to be decreased with the light irradiation which is proposed due to homopolar bond formation. The core level peaks in XPS spectra give information about different bond formation. (C) 2011 Elsevier B.V. All rights reserved.

A mostly-digital analog scan-out chain for low bandwidth voltage measurement for analog IP test

A method of precise measurement of on-chip analog voltages in a mostly-digital manner, with minimal overhead, is presented. A pair of clock signals is routed to the node of an analog voltage. This analog voltage controls the delay between this pair of clock signals, which is then measured in an all-digital manner using the technique of sub-sampling. This sub-sampling technique, having measurement time and accuracy trade-off, is well suited for low bandwidth signals. This concept is validated by designing delay cells, using current starved inverters in UMC 130nm CMOS process. Sub-mV accuracy is demonstrated for a measurement time of few seconds.

Characterisation of Landscape with Forest Fragmentation Dynamics

Land cover (LC) and land use (LU) dynamics induced by human and natural processes play a major role in global as well as regional patterns of landscapes influencing biodiversity, hydrology, ecology and climate. Changes in LC features resulting in forest fragmentations have posed direct threats to biodiversity, endangering the sustainability of ecological goods and services. Habitat fragmentation is of added concern as the residual spatial patterns mitigate or exacerbate edge effects. LU dynamics are obtained by classifying temporal remotely sensed satellite imagery of different spatial and spectral resolutions. This paper reviews five different image classification algorithms using spatio-temporal data of a temperate watershed in Himachal Pradesh, India. Gaussian Maximum Likelihood classifier was found to be apt for analysing spatial pattern at regional scale based on accuracy assessment through error matrix and ROC (receiver operating characteristic) curves. The LU information thus derived was then used to assess spatial changes from temporal data using principal component analysis and correspondence analysis based image differencing. The forest area dynamics was further studied by analysing the different types of fragmentation through forest fragmentation models. The computed forest fragmentation and landscape metrics show a decline of interior intact forests with a substantial increase in patch forest during 1972-2007.

Alkylation of toluene by methanol over alkali exchanged zeolite-X: side chain versus ring alkylation

The ring versus side-chain alkylation of toluene with methanol over alkali-exchanged zeolite-X of differing basicity has been investigated by in situ infrared spectroscopy and TPD measurements. Over the basic Cs-exchanged zeolite the product of alkylation is styrene/ethylbenzene while over the acidic Li-exchanged zeolite ring alkylation occurs to give mainly xylene as the product. FTIR and TPD investigations reveal that, the key difference in the two types of alkylation processes lies in the state of the adsorbed methanol present at higher temperatures in the zeolite. In basic zeolites, methanol decomposes to formaldehyde and formates. The former is the key ‘side-chain’ alkylating species that leads to the formation of styrene. In the acidic zeolites it is shown that methanol bound to the acid sites plays an active role in the ‘ring alkylation’ of toluene to xylene.

Barrier crossing by a flexible long chain molecule - The kink mechanism

The problem and related earlier work All the above problems involve the passage of a long chain molecule, through a region in space, where the free energy per segment is higher, thus effectively presenting a barrier for the motion of the molecule. This is what we refer to as the Kramers proble...

Combined Electron Transfer Dissociation-Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products

Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(center dot) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Delta m = 43 Da) or ethyl radicals (Delta m = 29 Da), through collisional activation of z(center dot) radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific e ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MSn) method has been successfully implemented in a liquid chromatography MSn platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.

Chain Length Effects on Helix-Hairpin Distribution in Short Peptides with Aib-(D)Ala and Aib-Aib Segments

The Aib-(D)Ala dipeptide segment has a tendency to form both type-I'/III' and type-I/III beta-turns. The occurrence of prime turns facilitates the formation of beta-hairpin conformations, while type-I/III turns can nucleate helix formation. The octapeptide Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (1) has been previously shown to form a beta-hairpin in the crystalline state and in solution. The effects of sequence truncation have been examined using the model peptides Boc-Phe-Val-Aib-Xxx-Leu-Phe-NHMe (2, 6), Boc-Val-Aib-Xxx-Leu-NHMe (3, 7), and Boc-Aib-Xxx-NHMe (4, 8), where Xxx = (D)Ala, Aib. For peptides with central Aib-Aib segments, Boc-Phe-Val-Aib-Aib-Leu-Phe-NHMe (6), Boc-Val-Aib-Aib-Leu-NHMe (7), and Boc-Aib-Aib-NHMe (8) helical conformations have been established by NMR studies in both hydrogen bonding (CD(3)OH) and non-hydrogen bonding (CDCl(3)) solvents. In contrast, the corresponding hexapeptide Boc-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-NHMe (2) favors helical conformations in CDCl(3) and beta-hairpin conformations in CD(3)OH. The beta-turn conformations (type-I'/III) stabilized by intramolecular 4 -> 1 hydrogen bonds are observed for the peptide Boc-Aib-(D)Ala-NHMe (4) and Boc-Aib-Aib-NIiMe (8) in crystals. The tetrapeptide Boc-Val-Aib-Aib-Leu-NHMe (7) adopts an incipient 3(10)-helical conformation stabilized by three 4 -> 1 hydrogen bonds. The peptide Boc-Val-Aib-(D)Ala-Leu-NHMe (3) adopts a novel et-turn conformation, stabilized by three intramolecular hydrogen bonds (two 4 -> 1 and one 5 -> 1). The Aib-L(D)Ala segment adopts a type-I' beta-turn conformation. The observation of an NOE between Val (1) NH <-> HNCH(3) (5) in CD(3)OH suggests, that the solid state conformation is maintained in methanol solutions. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 744-756, 2011.

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution = 1.5 angstrom). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (Cn, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C10 (COdi .NHi + 2), C13 (COdi .NHi + 3) and C17 (NdHi .COi - 4) structures. In contrast, Gln predominantly forms C16 (COei .NHi - 3), C12 (NeHi .COi - 2), C15 (NeHi .COi - 3) and C18 (NeHi .COi - 4) motifs, with only the C18motif being analogous to the Asn C17structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone beta-turns and a-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

Hypoxia-Mediated Impairment of the Mitochondrial Respiratory Chain Inhibits the Bactericidal Activity of Macrophages

In infected tissues oxygen tensions are low. As innate immune cells have to operate under these conditions, we analyzed the ability of macrophages (M phi) to kill Escherichia coli or Staphylococcus aureus in a hypoxic microenvironment. Oxygen restriction did not promote intracellular bacterial growth but did impair the bactericidal activity of the host cells against both pathogens. This correlated with a decreased production of reactive oxygen intermediates (ROI) and reactive nitrogen intermediates. Experiments with phagocyte NADPH oxidase (PHOX) and inducible NO synthase (NOS2) double-deficient M phi revealed that in E. coli- or S. aureus-infected cells the reduced antibacterial activity during hypoxia was either entirely or partially independent of the diminished PHOX and NOS2 activity. Hypoxia impaired the mitochondrial activity of infected M phi. Inhibition of the mitochondrial respiratory chain activity during normoxia (using rotenone or antimycin A) completely or partially mimicked the defective antibacterial activity observed in hypoxic E. coli-or S. aureus-infected wild-type M phi, respectively. Accordingly, inhibition of the respiratory chain of S. aureus-infected, normoxic PHOX-/- NOS2(-/-) M phi further raised the bacterial burden of the cells, which reached the level measured in hypoxic PHOX-/- NOS2(-/-) M phi cultures. Our data demonstrate that the reduced killing of S. aureus or E. coli during hypoxia is not simply due to a lack of PHOX and NOS2 activity but partially or completely results from an impaired mitochondrial antibacterial effector function. Since pharmacological inhibition of the respiratory chain raised the generation of ROI but nevertheless phenocopied the effect of hypoxia, ROI can be excluded as the mechanism underlying the antimicrobial activity of mitochondria.

Composites of Graphene and Other Nanocarbons with Organogelators Assembled through Supramolecular Interactions

Carbon nanomaterials (CNMs), such as exfoliated graphene (EG), long-chain functionalized EG, single-walled carbon nanotubes (SWNTs), and fullerene (C-60), have been investigated for their interaction with two structurally different gelators based on all-trans tri-p-phenylenevinylene bis-aldoxime (1) and n-lauroyl-L-alanine (2) both in solution and in supramolecular organogels. Gelation occurs in toluene through hydrogen bonding and van der Waals interactions for 1 and 2 in addition to pp stacking specifically in the case of 1. These nanocomposites provide a thorough understanding in terms of molecular-level interactions of dimensionally different CNMs with structurally different gelators. The presence of densely wrapped CNMs encapsulated fibrous network in the resulting composites is evident from various spectroscopic and microscopic studies, indicating the presence of supramolecular interactions. Concentration- and temperature-dependent UV/Vis and fluorescence spectra show that CNMs promote aggregation of the gelator molecules, leading to hypochromism and quenching of the fluorescence intensity. Thermotropic mesophases of 1 are altered by the inclusion of a small amount of CNMs. The gelCNM composites show increased electrical conductivity compared with that of the native organogel. Rheological studies of the composites demonstrate the formation of rigid and viscoelastic solidlike assembly due to reinforced aggregation of the gelators on CNMs. Synergistic behavior is observed in case of the composite gel of 1, containing a mixture of EG and SWNT, when compared with other mixtures of CNMs in all combinations with EG. This affords new nanocomposites with interesting optical, thermal, electrical, and mechanical properties.

Study of Low Temperature Magnetic Properties of a Single Chain Magnet with Alternate Isotropic and Non-collinear Anisotropic Units

Here we study thermodynamic properties of an important class of single-chain magnets (SCMs), where alternate units are isotropic and anisotropic with anisotropy axes being non-collinear. This class of SCMs shows slow relaxation at low temperatures which results from the interplay of two different relaxation mechanisms, namely dynamical and thermal. Here anisotropy is assumed to be large and negative, as a result, anisotropic units behave like canted spins at low temperatures; but even then simple Ising-type model does not capture the essential physics of the system due to quantum mechanical nature of the isotropic units. We here show how statistical behavior of this class of SCMs can be studied using a transfer matrix (TM) method. We also, for the first time, discuss in detail how weak inter-chain interactions can be treated by a TM method. The finite size effect is also discussed which becomes important for low temperature dynamics. At the end of this paper, we apply this technique to study a real helical chain magnet.

Influence of minor addition of boron on tensile and fatigue properties of wrought Ti-6Al-4V alloy

Addition of boron to cast Ti-6Al-4V alloy leads to significant refinement in grain size, which in turn improves processibilty as well as the mechanical properties of the as-cast alloy. Room temperature tensile and fatigue properties of Wrought Ti-6Al-4V-B alloys with B up to 0.09 wt.% are investigated. Thermo-mechanical processing at 950 degrees C caused kinking of alpha lamellae and alignment of TiB particles in the flow direction with a negligible change in prior beta grain and colony sizes, indicating the absence of dynamic recrystallisation during forging. Characterisation with the aid of X-ray and electron back scattered diffraction reveal a strong basal texture in B free alloy which gets randomised with the 0.09B addition in the forged condition. Marginal enhancement in tensile and fatigue properties upon forging is noted. B free wrought Ti-6Al-4V alloy exhibits better tensile strength as compared to B containing alloy, due to the operation of < c+a > slip on pyramidal planes with high value of CRSS as compared to < a > slip on basal and prismatic planes. Decrease in fatigue strength of Ti-6Al-4V-0.04B in as-cast and the wrought state is observed due to increase in the volume fraction of grain boundary a phase with B addition, which acts as a crack nucleation site. No significant effect of TiB particles on tensile and fatigue properties is observed. (C) 2012 Elsevier B.V. All rights reserved.

Catalytic enantioselective construction of quaternary stereocenters by direct vinylogous Michael addition of deconjugated butenolides to nitroolefins

A direct vinylogous Michael reaction of gamma-substituted deconjugated butenolides with nitroolefins has been developed with the help of a newly identified quinine-derived bifunctional catalyst, allowing the synthesis of densely functionalized products with contiguous quaternary and tertiary stereocenters in excellent yield with perfect diastereoselectivity (>20 : 1 dr) and high enantioselectivity (up to 99 : 1 er).

Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.