Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Anaerobic ammonium oxidation (anammox) in sediments of the Gulf of Finland

Anaerobic ammonium oxidation (anammox) and denitrification were measured in the open sea and coastal accumulation basins of the Gulf of Finland. The different methods used gave conflicting results on the importance of the anammox process in the sediments. Anammox generally contributed less than 20 % to the total N-2 production, and no anammox was found in a shallow inner estuary basin. However, the discovery of the anammox process in the open sea sediments challenges the denitrification measurements made in the area, as the coexistence of anammox and denitrification compromises the central assumptions behind the method used in denitrification measurements and causes overestimates of the N-2 production. The high (NO3-)-N-15 incubation concentration used in Baltic Sea denitrification measurements exacerbates this overestimation, which is likely to have been substantial.

Electrochemical preparation of few layer-graphene nanosheets via reduction of oriented exfoliated graphene oxide thin films in acetamide-urea-ammonium nitrate melt under ambient conditions

Electrochemical reduction of exfoliated graphene oxide, prepared from pre-exfoliated graphite, in acetamide-urea-ammonium nitrate ternary eutectic melt results in few layer-graphene thin films. Negatively charged exfoliated graphene oxide is attached to positively charged cystamine monolyer self-assembled on a gold surface. Electrochemical reduction of the oriented graphene oxide film is carried out in a room temperature, ternary molten electrolyte. The reduced film is characterized by atomic force microscopy (AFM), conductive AFM, Fourier-transform infrared spectroscopy and Raman spectroscopy. Ternary eutectic melt is found to be a suitable medium for the regulated reduction of graphene oxide to reduced graphene oxide-based sheets on conducting surfaces. (C) 2010 Elsevier B.V. All rights reserved.

Phase modification of ammonium nitrate by potassium salts

Modification of the room temperature phase (IV-III) of ammonium nitrate (AN) has been attempted using a variety of potassium salts namely, KF, KCl, KI, KNO3, K2CO3, K2SO4, KSCN and K2Cr2O7. No phase transition was observed when AN containing 1-2% by mass of these potassium salts is heated from room temperature (25 degrees C) onwards in DTA and DSC scans, but the linear expansion due to phase transition was still observable in TMA measurements. Complete arrest of the linear expansion occurs only when a higher concentration of the additive is used. Similarly, in thermal cycling experiments, complete phase modification in the temperature range -80 to 100 degrees C occurs only with a higher percentage of the potassium salt. The extent of modification, however, is found to be dependent both on the concentration, and the type of the anion. Potassium dichromate when used as an additive modifies the phase as well as the decomposition pattern of AN.

Michael addition of masked thiolates to conjugated systems in aqueous media promoted by ammonium tetrathiomolybdate

Thiolates generated in situ by the action of ammonium tetrathiomolybdate on alkyl halides, thiocyanates and disulfides undergo Michael addition to alpha,beta-unsaturated esters, nitriles :and ketones in water under neutral conditions.

Charge Density Analysis of a Pentaborate Ion in an Ammonium Borate: Toward the Understanding of Topological Features in Borate Minerals

Structural and charge density distribution studies have been carried out on a single crystal data of an ammonium borate, [C(10)H(26)N(4)][B(5)O(6)(OH)(4)](2), synthesized by solvothermal method. Further, the experimentally observed geometry is used for the theoretical charge density calculations using the B3LYP/6-31G** level of theory, and the results are compared with the experimental values. Topological analysis of charge density based on the Atoms in Molecules approach for B-O bonds exhibit mixed covalent/ionic character. Detailed analysis of the hydrogen bonds in the crystal structure in the ammonium borate provides insights into the understanding of the reaction pathways that net atomic charges and electrostatic potential isosurfaces also give additional such systems. could result in the formation of borate minerals. The input to evaluate chemical and physical properties in such systems.

Preparation of a thermally sensitive ammonium perchlorate

The effect of ultrasound on the thermal decomposition behaviour of ammonium perchlorate (AP) has been investigated. It was observed that significant changes in the thermal behaviour of A-P, followed using differential thermal analysis and thermogravimetry, was observed when AP was subjected to power ultrasound in water saturated with oxygen-nitrogen mixture. The decomposition temperature of AP was found to have been lowered by nearly 25degreesC. A similar thermal sensitization was observed in AP when subjected to sonication in the presence of transition metal oxides. Kinetic parameters were calculated for AP, modified AP and catalyzed AP decomposition using non-isothermal kinetics. The activation energy for the decomposition of the sonicated AP samples were found to be lower than normal AP.

In-situ measurements of concentration and temperature during transient solidification of aqueous solution of ammonium chloride using laser interferometry

The variation in temperature and concentration plays a crucial role in predicting the final microstructure during solidification of a binary alloy. Most of the experimental techniques used to measure concentration and temperature are intrusive in nature and affect the flow field. In this paper, the main focus is laid on in-situ, non-intrusive, transient measurement of concentration and temperature during the solidification of a binary mixture of aqueous ammonium chloride solution (a metal-analog system) in a top cooled cavity using laser based Mach-Zehnder Interferometric technique. It was found from the interferogram, that the angular deviation of fringe pattern and the total number of fringes exhibit significant sensitivity to refractive index and hence are functions of the local temperature and concentration of the NH4Cl solution inside the cavity. Using the fringe characteristics, calibration curves were established for the range of temperature and concentration levels expected during the solidification process. In the actual solidification experiment, two hypoeutectic solutions (5% and 15% NH4Cl) were chosen. The calibration curves were used to determine the temperature and concentration of the solution inside the cavity during solidification of 5% and 15% NH4Cl solution at different instants of time. The measurement was carried out at a fixed point in the cavity, and the concentration variation with time was recorded as the solid-liquid interface approached the measurement point. The measurement exhibited distinct zones of concentration distribution caused by solute rejection and Rayleigh Benard convection. Further studies involving flow visualization with laser scattering confirmed the Rayleigh Benard convection. Computational modeling was also performed, which corroborated the experimental findings. (C) 2011 Elsevier Ltd. All rights reserved.

Exceptional activity of mesoporous beta-MnO2 in the catalytic thermal sensitization of ammonium perchlorate

Mesoporous beta-MnO2 has been prepared, characterized and demonstrated to possess excellent catalytic activity in the thermal decomposition of ammonium perchlorate. The observed unprecedentedly low decomposition temperatures, fast reaction rates and enhanced heat releases in the catalysed formulations make mesoporous beta-MnO2 promising as a high-performing ballistic modifier in AP-based composite solid rocket propellants.

Surfactant solubility and micellization in ternary eutectic melt (acetamide plus urea plus ammonium nitrate)

Cationic surfactants such as dodecyltrimethylammonium bromide (DTAB), tetradecyltrimehtylammonium bromide (TTAB) and hexadecyltrimethylammonium bromide (HTAB); and anionic surfactants such as sodium decyl sulphate (SDeS), sodium dodecyl sulphate (SDS) and sodium tetradecyl sulphate (STDS) have been used to determine their solubility and micellization in ternary eutectic melt (acetamide + urea + ammonium nitrate) at 50 degrees C. We employed the electrical conductivity and the surface tension measurement techniques to determine the critical micelle concentration (CMC). The deviation in the slope of the specific conductance/surface tension against surfactant concentration plots indicated the aggregations of surfactants and hence, their CMC. CMC decreases with increase of alkyl chain length due to the increased van der Waals forces. The calculated increment in Gibb's energy per methylene group for cationic and anionic surfactants is about -6 kJ mol(-1) and -4 kJ mol(-1) respectively. It is found that, the CMCs of the surfactants in the ternary melt are higher than the CMCs of same surfactants in water (similar to 25 degrees C). (C) 2012 Elsevier B.V. All rights reserved.

Small-Angle Neutron-Scattering Studies of Mixed Micellar Structures Made of Dimeric Surfactants Having Imidazolium and Ammonium Headgroups

Planar imidazolium cation based gemini surfactants 16-Im-n-Im-16], 2Br(-) (where n = 2, 3, 4, 5, 6, 8, 10, and 12), exhibit different morphologies and internal packing arrangements by adopting different supramolecular assemblies in aqueous media depending on their number of spacer methylene units (CH2)(n). Detailed measurements of the small-angle neutron-scattering (SANS) cross sections from different imidazolium-based surfactant micelles in aqueous media (D2O) are reported. The SANS data, containing the information of aggregation behavior of such surfactants in the molecular level, have been analyzed on the basis of the Hayter and Penfold model for the macro ion solution to compute the interparticle structure factor S(Q) taking into account the screened Coulomb interactions between the dimeric surfactant micelles. The characteristic changes in the SANS spectra of the dimeric surfactant with n = 4 due to variation of temperature have also been investigated. These data are then compared with the SANS characterization data of the corresponding gemini micelles containing tetrahedral ammonium ion based polar headgroups. The critical micellar concentration of each surfactant micelle (cmc) has been determined using pyrene as an extrinsic fluorescence probe. The variation of cmc as a function of spacer chain length has been explained in terms of conformational variation and progressive looping of the spacer into the micellar interior upon increasing the n values. Small-angle neutron-scattering (SANS) cross sections from different mixed micelles composed of surfactants with ammonium headgroups, 16-A(0), 16-Am-n-Am-16], 2Br(-) (where n = 4), 16-I-0, and 16-Im-n-Im-16], 2Br(-) (where n = 4), in aqueous media (D2O) have also been analyzed. The aggregate composition matches with that predicted from the ideal mixing model.