UVPES and ab initio molecular orbital studies on the electron donor-acceptor complexes of bromine with methylamines

The He I photoelectron spectra of bromine, methylamine, and their complex have been obtained, and the spectra show that lone-pair orbital energy of nitrogen in methylamine is stabilized by 1.8 eV and the bromine orbital energies are destabilized by about 0.5 eV due to complexation. Ab initio calculations have been performed on the charge-transfer complexes of Br-2 with ammonia and methyl-, dimethyl-, and trimethylamines at the 3-21G*, 6-311G, and 6-311G* levels and also with effective core potentials. Calculations predict donor and acceptor orbital energy shifts upon complexation, and there is a reasonable agreement between the calculated and experimental results. Complexation energies have been corrected for BSSE. Frequency analysis has confirmed that ammonia and trimethylamine form complexes with C-3v symmetry and methylamine and dimethylamine with C-s symmetry. Calculations reveal that the lone-pair orbital of nitrogen in amine and the sigma* orbital of Br-2 are involved in the charge-transfer interaction. LANL1DZ basis seems to be consistent and give a reliable estimate of the complexation energy. The computed complexation energies, orbital energy shifts, and natural bond orbital analysis show that the strength of the complex gradually increases from ammonia to trimethylamine.

The design and synthesis of redox core-alpha amino acid composites based on thiol-disulfide exchange mechanism and a comparative study of their zinc abstraction potential from [CCXX] boxes in proteins

The design and synthesis of agents that can abstract zinc from their [CCXX] (C=cysteine; X=cysteine/histidine) boxes by thioldisulfide exchange-having as control, the redox parities of the core sulfur ligands of the reagent and the enzyme, has been illustrated, and their efficiency demonstrated by monitoring the inhibition of the transcription of calf thymus DNA by E. coli RNA polymerase, which harbors two zinc atoms in their [CCXX] boxes of which one is exchangeable. Maximum inhibition possible with removal of the exchangeable zinc was seen with redox-sulfanilamide-glutamate composite. In sharp contrast, normal chelating agents (EDTA, phenanthroline) even in a thousand fold excess showed only marginal inhibition, thus supporting an exchange mechanism for the metal removal. (C) 2002 Elsevier Science Ltd. All rights reserved.

Biochemistry of water-logged soils. Part IV. Carbon and nitrogen transformations

1. During the fermentation of water-logged soil containing added substances with different carbon-nitrogen ratios, the reaction first turns slightly acid, but soon returns to the original hydrogen-ion concentration (pH 7·6). 2. The quantities of ammonia present in the medium increase up to a point, after which there is steady decrease. 3. There is nitrification only in the case of substances with narrow C/N ratios. The production of nitrate generally commences only after about a month, when the vigour of the initial fermentation has subsided and fairly large quantities of ammonia have accumulated in the medium. 4. The extent of mineralisation of nitrogen is determined chiefly by the C/N ratio, though in the cases of substances like mahua and lantana the presence of other constituents may also influence the processes. The quantities of mineralised nitrogen present in the soil system generally tend to decrease after about two months.

Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

Dicopper(II) complexes showing DNA hydrolase activity and monomeric adduct formation with bis(4-nitrophenyl)phosphate

Ferromagnetic dicopper(II) complexes [Cu(2)(mu-O(2)CCH(3))(mu-OH)(L)(2)(mu-L(1))](PF(6))(2), where L = 1,10-phenanthroline (phen), L(1) = H(2)O in 1 and L = dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), L(1) = CH(3)CN in 2, are prepared and structurally characterized. Crystals of 1 and 2 belong to the monoclinic space group of P2(1)/n and P2(1)/m, respectively. The copper(II) centers display distorted square-pyramidal geometry having a phenanthroline base and two oxygen atoms of the bridging hydroxo and acetate group in the basal plane. The fifth coordination site has weak axially bound bridging solvent molecule H(2)O in 1 and CH(3)CN in 2. The Cu center dot center dot center dot Cu distances are 3.034 and 3.046 angstrom in 1 and 2, respectively. The complexes show efficient hydrolytic cleavage of supercoiled pUC19 DNA as evidenced from the mechanistic studies that include T4 DNA ligase experiments. The binuclear complexes form monomeric copper(II) adducts [Cu(L)(2)(BNPP)](PF(6)) (L = phen, 3; dpq, 4) with bis(4-nitrophenyl)phosphate (BNPP) as a model phosphodiester. The crystal structures of 3 and 4 reveal distorted trigonal bipyramidal geometry in which BNPP binds through the oxygen atom of the phosphate. The kinetic data of the DNA cleavage reactions of the binuclear complexes under pseudo- and true-Michaelis-Menten conditions indicate remarkable enhancement in the DNA hydrolysis rate in comparison to the control data. (C) 2011 Elsevier B.V. All rights reserved.

Biomonitoring of Lotic habitats through Diatoms

Freshwater ecosystems vary in size and composition and contain a wide range of organisms which interact with each other and with the environment. These interactions are between organisms and the environment as nutrient cycling, biomass formation and transfer, maintenance of internal environment and interactions with the external environment. The range of organisms present in aquatic communities decides the generation and transfer function of biomass, which defines and characterises the system. These organisms have distinct roles as they occupy particular trophic levels, forming an interconnected system in a food chain. Availability of resources and competition would primarily determine the balance of individual species within the food web, which in turn influences the variety and proportions of the different organisms, with important implications for the overall functioning of the system. This dynamic and diverse relationship decides the physical, chemical and biological elements across spatial and temporal scales in the aquatic ecosystem, which can be recorded by regular inventorying and monitoring to maintain the integrity and conserve the ecosystem. Regular environmental monitoring, particularly water quality monitoring allows us to detect, assess and manage the overall impacts on the rivers. The appreciation of water quality is in constant flux. Water quality assessments derived through the biotic indices, i.e. assessments based on observations of the resident floral and faunal communities has gained importance in recent years. Biological evaluations provide a description of the water quality that is often not achievable from elemental analyses alone. A biological indicator (or bioindicator) is a taxon or taxa selected based on its sensitivity to a particular attribute, and then assessed to make inferences about that attribute. In other words, they are a substitute for directly measuring abiotic features or other biota. Bioindicators are evaluated through presence or absence, condition, relative abundance, reproductive success, community structure (i.e. composition and diversity), community function (i.e. trophic structure), or any combination thereof.Biological communities reflect the overall ecological integrity by integrating various stresses, thus providing a broad measure of their synergistic impacts. Aquatic communities, both plants and animals, integrate and reflect the effects of chemical and physical disturbances that occur over extended periods of time. Monitoring procedures based on the biota measure the health of a river and the ability of aquatic ecosystems to support life as opposed to simply characterising the chemical and physical components of a particular system. This is the central purpose of assessing the biological condition of aquatic communities of a river.Diatoms (Bacillariophyceae), blue green algae (Cyanophyceae), green algae (Chlorophyceae), and red algae (Rhodphyceae) are the main groups of algae in flowing water. These organisms are widely used as biological indicators of environmental health in the aquatic ecosystem because algae occupy the most basic level in the transfer of energy through natural aquatic systems. The distribution of algae in an aquatic ecosystem is directly related to the fundamental factors such as physical, chemical and biological constituents. Soft algae (all the algal groups except diatoms) have also been used as indicators of biological integrity, but they may have less efficiency than diatoms in this respect due to their highly variable morphology. The diatoms (Bacillariophyceae) comprise a ubiquitous, highly successful and distinctive group of unicellular algae with the most obvious distinguishing characteristic feature being siliceous cell walls (frustules). The photosynthetic organisms living within its photic zone are responsible for about one-half of global primary productivity. The most successful organisms are thought to be photosynthetic prokaryotes (cyanobacteria and prochlorophytes) and a class of eukaryotic unicellular algae known as diatoms. Diatoms are likely to have arisen around 240 million years ago following an endosymbiotic event between a red eukaryotic alga and a heterotrophic flagellate related to the Oomycetes.The importance of algae to riverine ecology is easily appreciated when one considers that they are primary producers that convert inorganic nutrients into biologically active organic compounds while providing physical habitat for other organisms. As primary producers, algae transform solar energy into food from which many invertebrates obtain their energy. Algae also transform inorganic nutrients, such as atmospheric nitrogen into organic forms such as ammonia and amino acids that can be used by other organisms. Algae stabilises the substrate and creates mats that form structural habitats for fish and invertebrates. Algae are a source of organic matter and provide habitat for other organisms such as non-photosynthetic bacteria, protists, invertebrates, and fish. Algae's crucial role in stream ecosystems and their excellent indicator properties make them an important component of environmental studies to assess the effects of human activities on stream health. Diatoms are used as biological indicators for a number of reasons: 1. They occur in all types of aquatic ecosystems. 2. They collectively show a broad range of tolerance along a gradient of aquatic productivity, individual species have specific water chemistry requirements. 3. They have one of the shortest generation times of all biological indicators (~2 weeks). They reproduce and respond rapidly to environmental change and provide early measures of both pollution impacts and habitat restoration. 4. It takes two to three weeks before changes are reflected to a measurable extent in the assemblage composition.

Electrochemical oxidation of boron containing compounds on titanium carbide and its implications to direct fuel cells

Electrochemical oxidation of sodium borohydride (NaBH(4)) and ammonia borane (NH(3)BH(3)) (AB) have been studied on titanium carbide electrode. The oxidation is followed by using cyclic voltammetry, chronoamperometry and polarization measurements. A fuel cell with TiC as anode and 40 wt% Pt/C as cathode is constructed and the polarization behaviour is studied with NaBH(4) as anodic fuel and hydrogen peroxide as catholyte. A maximum power density of 65 mW cm(-2) at a load current density of 83 mA cm(-2) is obtained at 343 K in the case of borhydride-based fuel cell and a value of 85 mW cm(-2) at 105 mA cm(-2) is obtained in the case of AB-based fuel cell at 353 K. (C) 2011 Elsevier Ltd. All rights reserved.

Hydrogen generation fromammonia borane using nanocatalysts

The rapidly depleting petroleum feed stocks and increasing green house gas emissions around the world has necessitated a search for alternative renewable energy sources. Hydrogen with molecular weight of 2.016 g/mol and high chemical energy per mass equal to 142 MJ/kg has clearly emerged as an alternative to hydrocarbon fuels. Means for safe and cost effective storage are needed for widespread usage of hydrogen as a fuel.Chemical storage is the one of the safer ways to store hydrogen compared to compressed and liquefied hydrogen. It involves storing hydrogen in chemical bonds in molecules and materials where an on-board reaction is used to release hydrogen. Ammonia–borane, (AB,H3N·BH3) with a potential capacity of 19.6 wt% is considered a very promising solid state hydrogen storage material. It is thermally stable at ambient temperatures. There are two major routes for the generation of H2 from AB: catalytic hydrolysis/alcoholysis and catalytic thermal decomposition. There has been a flurry of research activity on the generation of H2 from AB recently. The present review deals with an overview of our efforts in developing cost-effective nanocatalysts for hydrogen generation from ammonia borane in protic solvents.

Oneand twodimensional single quantumand multiplequantumNMR methodologies: tools for chiral analyses

It is well known that enantiomers cannot be distinguished by NMR spectroscopy unless diastereomorphic interactions are imposed. Several chiral aligning media have therefore been reported for their visualization, although extensive studies are carried out using the liquid crystal made of polypeptide poly-γ-benzyl-L-glutamate (PBLG) in organic solvent. In PBLG medium the spin systems are weakly coupled and the first order analyses of the spectra are generally possible. But due to large number of pair wise interactions of nuclear spins resulting in many degenerate transitions the 1H NMR spectra are not only complex but also broad and featureless, in addition to an indistinguishable overlap of the spectra of enantiomers. This enormous loss of resolution severely hinders the analyses of proton spectra, even for spin systems with 5–6 interacting protons, thereby restricting itsroutine application. In this review we discuss our recently developed several one and multidimensional NMR experiments to circumvent these difficulties taking specific examples of the molecules containing a single chiral centre.

Towards sustainability: a new, solid-state synthetic route for supported metal nanocatalysts

Noble metal ions like Pt(IV) and Pd(II) were impregnated on gamma-alumina and aerosol 300 silica surfaces. Reduction of these ions using ammonia borane in the solid state resulted in the formation of the respective metal nanoparticles embedded in BNHx polymer which is dispersed on the oxide support. Removal of the BNH polymer was accomplished by washing the samples repeatedly with methanol. In this process the polymer undergoes solvolysis to release H-2 accompanied by the formation of ammonium methoxy borate salt, which has been removed by repeated methanol washings. As a result, metal nanoparticles well dispersed on gamma-alumina and aerosol 300 silica were obtained. These samples have been characterized by a combination of techniques, including electron microscopy, powder X-ray diffraction, NMR spectroscopy and surface area analyser.

Catalyst-Packed Non-Thermal Plasma Reactor for Removal of Nitrogen Oxides

A single-stage plasma-catalytic reactor in which catalytic materials were packed was used to remove nitrogen oxides. The packing material was scoria being made of various metal oxides including Al2O3, MgO, TiO2, etc. Scoria was able to act not only as dielectric pellets but also as a catalyst in the presence of reducing agent such as ethylene and ammonia. Without plasma discharge, scoria did not work well as a catalyst in the temperature range of 100 °C to 200 °C, showing less than 10% of NOx removal efficiency. When plasma is produced inside the reactor, the NOx removal efficiency could be increased to 60% in this temperature range.

DeNOx Study in Diesel Engine Exhaust Using Barrier Discharge Corona Assisted by V2O5/TiO2 Catalyst

A plasma-assisted catalytic reactor was used to remove nitrogen oxides (NOx) from diesel engine exhaust operated under different load conditions. Initial studies were focused on plasma reactor (a dielectric barrier discharge reactor) treatment of diesel exhaust at various temperatures. The nitric oxide (NO) removal efficiency was lowered when high temperature exhaust was treated using plasma reactor. Also, NO removal efficiency decreased when 45% load exhaust was treated. Studies were then made with plasma reactor combined with a catalytic reactor consisting of a selective catalytic reduction (SCR) catalyst, V2O5/TiO2. Ammonia was used as a reducing agent for SCR process in a ratio of 1:1 to NOx. The studies were focused on temperatures of the SCR catalytic reactor below 200°C. The plasma-assisted catalytic reactor was operated well to remove NOx under no-load and load conditions. For an energy input of 96 J/l, the NOx removal efficiencies obtained under no-load and load conditions were 90% and 72% respectively at an exhaust temperature of 100°C.

Nonthermal-Plasma-Promoted Catalysis for the Removal of NOx From a Stationary Diesel-Engine Exhaust

A detailed study on the removal of oxides of nitrogen (NOx) from the exhaust of a stationary diesel engine was carried out using nonthermal-plasma (pulsed electrical-discharge plasma)-promoted catalytic process. In this paper, the filtered exhaust from the diesel engine is made to pass through a combination of nonthermal plasma reactor and a catalytic reactor connected in series. This combination is referred to as cascade. Two types of cascaded systems were studied. In one type, the plasma treating filtered exhaust was cascaded with a reduction catalyst V2O5/TiO2 using ammonia as reducing agent, and in the other type, the plasma treating filtered exhaust was cascaded with activated-alumina catalyst without any additive. Improved NOx-removal performance of both the cascaded processes and the role of nonthermal plasma in promoting catalysis are explained. Along with the NOx, total hydrocarbon and aldehydes were also removed. Furthermore, experiments were conducted at different temperatures and engine-loading conditions.

Time-Dependent Predominance of Nonhomologous DNA End-Joining Pathways during Embryonic Development in Mice

Repair of DNA double-strand breaks (DSBs) is crucial for maintaining genomic integrity during the successful development of a fertilized egg into a whole organism. To date, the mechanism of DSB repair in postimplantation embryos has been largely unknown. In the present study, using a cell-free repair system derived from the different embryonic stages of mice, we find that canonical nonhomologous end joining (NHEJ), one of the major DSB repair pathways in mammals, is predominant at 14.5 day of embryonic development. Interestingly, all four types of DSBs tested were repaired by ligase IV/XRCC4 and Ku-dependent classical NHEJ. Characterization of end-joined junctions and expression studies further showed evidences for canonical NHEJ. Strikingly, in contrast to the above, we observed noncanonical end joining accompanied by DSB resection, dependent on microhomology and ligase III in 18.5-day embryos. Interestingly, we observed an elevated expression of CtIP, MRE11, and NBS1 at this stage, suggesting that it could act as a switch between classical end joining and microhomology-mediated end joining at later stages of embryonic development. Thus, our results establish for the first time the existence of both canonical and alternative NHEJ pathways during the postimplantation stages of mammalian embryonic development. (C) 2012 Elsevier Ltd. All rights reserved.

Evaporation Heat Transfer Coefficient in a Capillary Pumped Loop and Loop Heat Pipe for Different Working Fluids

Capillary pumped loop (CPL) and loop heat pipe (LHP) are passive two-phase heat transport devices. They have been gaining importance as a part of the thermal control system of spacecraft. The evaporation heat transfer coefficient at the tooth-wick interface of an LHP or CPL has a significant impact on the evaporator temperature. It is also the main parameter in sizing of a CPL or LHP. Experimentally determined evaporation heat transfer coefficients from a three-port CPL with tubular axially grooved (TAG) evaporator and a TAG LHP with acetone, R-134A, and ammonia as working fluids are presented in this paper. The influences of working fluid, hydrodynamic blocks in the core, evaporator configuration (LHP or CPL), and adverse elevation (evaporator above condenser) on the heat transfer coefficient are presented.