Reactivity of Bispropargyl Sulfones under Basic Conditions: Interplay Between Garratt-Braverman and Schmittel/Myers-Saito Cyclization Pathway

The preference for GarrattBraverman (GB) over MyersSaito (MS) and Schmittel (SCM) cyclizations has recently been demonstrated in sulfones capable of undergoing all three of the processes. As the GB cyclization is a self-quenching process, there is a need to change the selectivity to the non-self-quenching MS or SCM pathway so as to enhance the DNA-cleaving efficiency that operates through the radical-mediated process. Herein we report a conformational constraint-based strategy developed by using computations (M06-2X/6-31+G*) to switch the selectivity from GB to MS/SCM pathway which also results in greater DNA-cleavage activity. The preference for GB could be brought back by easing the constraint with the help of spacers.

Automatic compilation of MATLAB programs for synergistic execution on heterogeneous processors

MATLAB is an array language, initially popular for rapid prototyping, but is now being increasingly used to develop production code for numerical and scientific applications. Typical MATLAB programs have abundant data parallelism. These programs also have control flow dominated scalar regions that have an impact on the program's execution time. Today's computer systems have tremendous computing power in the form of traditional CPU cores and throughput oriented accelerators such as graphics processing units(GPUs). Thus, an approach that maps the control flow dominated regions to the CPU and the data parallel regions to the GPU can significantly improve program performance. In this paper, we present the design and implementation of MEGHA, a compiler that automatically compiles MATLAB programs to enable synergistic execution on heterogeneous processors. Our solution is fully automated and does not require programmer input for identifying data parallel regions. We propose a set of compiler optimizations tailored for MATLAB. Our compiler identifies data parallel regions of the program and composes them into kernels. The problem of combining statements into kernels is formulated as a constrained graph clustering problem. Heuristics are presented to map identified kernels to either the CPU or GPU so that kernel execution on the CPU and the GPU happens synergistically and the amount of data transfer needed is minimized. In order to ensure required data movement for dependencies across basic blocks, we propose a data flow analysis and edge splitting strategy. Thus our compiler automatically handles composition of kernels, mapping of kernels to CPU and GPU, scheduling and insertion of required data transfer. The proposed compiler was implemented and experimental evaluation using a set of MATLAB benchmarks shows that our approach achieves a geometric mean speedup of 19.8X for data parallel benchmarks over native execution of MATLAB.

Basic features of current induced/shared by cables mounted on down conductors/towers during stroke interception

The telecommunication, broadcasting and other instrumented towers carry power and/or signal cables from their ground end to their upper regions. During a direct hit to the tower, significant induction can occur to these mounted cables. In order to provide adequate protection to the equipments connected to them, protection schemes have been evolved in the literature. Development of more effective protection schemes requires a quantitative knowledge on various parameters. However, such quantitative knowledge is difficult to find at present. Amongst several of these aspects, the present work aims to investigate on the two important aspects: (i) what would be the nature of the induced currents and (ii) what will be the current sharing if as per the practice, the sheath of the cable is connected to the down conductor/tower. These aspects will be useful in design of protection schemes and also in analyzing the field structure around instrumented towers.

Effect of fault resistance and grid short circuit MVA on impedance seen by distance relays on lines fed from wind turbine generating units (WTGU)

This paper deals with line protection challenges experienced in system having substantial wind generation penetration. Two types of WTGU: Doubly Fed (DFIG) and Squirrel Cage (SCIG) Induction Generators are simulated and connected to grid with single circuit transmission line. The paper summarizes analytical investigations carried out on the impedance seen by distance relays by varying fault resistances and grid short circuit MVA, for the protection of such transmission lines during faults. The results are also compared with systems having conventional synchronous machine connected to the grid.

Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage

Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn2+ fingers from the mycobacterial topoI could be associated with Zn2+ export and homeostasis.

Versatility of azide in serendipitous assembly of Copper(II) Magnetic Polyclusters

Engineering at the molecular level is one of the most exciting new developments for the generation of functional materials. However, the concept of designing polynuclear extended structures from bottom up is still not mature. Although progress has been made with secondary building units (SBUs) in metal organic frameworks (MOFs), the control seems to be just an illusion when it comes to bridging ligands such as the azide ion. When we say that the azido ligand is versatile in its bridging capabilities, what we mean is that it would be difficult to predict or control its bridging properties. However, this kind of serendipity is not always bad news. For example, scientists have shown that the azido ligand can mediate magnetic exchanges between paramagnetic metals in a predictable fashion (usually depending upon the bonding geometries). Therefore, it is a well-respected ligand in polynuclear assemblies. Serendipitous assemblies offer new magnetic structures that we may not otherwise even think about synthesizing. The azido ligand forms a variety of complexes with copper(II) using different blocking amines or pyridine based ligands. Its structural nature changes upon changing the substitution on amine, as well as the amount of blocking ligand. In principle, if we take any of these complexes and provide more coordination sites to the bridging azido ligands by removing a fraction of the blocking ligands, we can get new complexes with intricate structural networks and therefore different magnetic properties with the same components as used for the parent complex. In this Account, we mainly discuss the development of a number of new topological and magnetic exchange systems synthesized using this concept. Not all of these new complexes can be grouped according to their basic building structures or even by the ratio of the metal to blocking ligand. Therefore, we divided the discussion by the nuclearity of the basic building structures. Some of the complexes with the same nuclearities have very similar or even almost identical basic structures. However, the way these building units are joined together (by the azido bridges) to form the overall extended structures differ almost in every case. The complexes having the Cu-6 core are particularly interesting from a structural point of view. Although they have almost identical basic structures, some of them are extended in three dimensions, but two of them are extended in two dimensions by two different bridging networks. In the complexes having linear Cu-4 basic units, we find that using similar ligands does not always give the same bridging networks even within the basic building structures. These complexes have also enriched the field of molecular magnetism. One of the complexes with a Cu-3 building unit has provided us with the opportunity to study the competing behavior of two different kinds of magnetic exchange mechanism (ferromagnetic and antiferromagnetic) acting simultaneously between two metal ions. Through density functional theory calculations, we showed how they work independently and their additive nature to produce the overall effect. The exciting methodology for the generation of copper(II) polyclusters presented in this Account will provide the opportunity to explore analogous serendipitous assembly of diverse structures with interesting magnetic behavior using other transition metal ions having more than one unpaired electrons.

Role of dicarboxylate linkers in Mn-III-salicylaldoximate based extended structures: synthesis, structures, and magnetic behavior

Four new oxo-centered Mn-III-salicylaldoximate triangle-based extended complexes (Mn6O2)-O-III(salox)(6)(EtOH)(4)(phda)](n)(saloxH(2))(n)(2H(2)O)(n) (1), (Mn6O2)-O-III(salox)(6)(MeOH)(5)(5-I-isoph)](n)(3MeOH)(n) (2), (Mn6O2)-O-III(salox)(6)(MeOH)(4)(H2O) (5-N-3-isoph)](n)(4MeOH)(n) (3) and (Mn3NaO)-Na-III(salox)(3)(MeOH)(4)(5-NO2-isoph)](n)(MeOH)(n) (H2O)(n) (4) salox=salicylaldoximate, phda=1,3-phenylenediacetate, isoph=isophthalate] have been synthesized under similar reaction conditions. Single crystal X-ray structures show that in 1, only one type of Mn-6 cluster is arranged in 1D, whereas in 2 and 3 there are two types of clusters, differing in the way the triangle units are joined and assembled. In complex4, however, the basic building structure is heteronuclear and based on Mn-3 units extended in 2D. Susceptibility measurements (dc and ac) over a wide range of temperatures and fields show that the complexes1, 2, and 3 behave as single molecule magnets (SMMs) with S=4ground state, while 4 is dominantly antiferromagnetic with a ground spin state S=2. Density functional theory calculations have been performed on model complexes to provide a qualitative theoretical interpretation for their overall magnetic behavior.

Self-assembly of discrete metallamacrocycles employing half-sandwich octahedral diruthenium(II) building units and imidazole-based ligands

Equimolar combination of a series of binuclear half-sandwich p-cymene ruthenium(II) building units Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](OTf)(2) 1a](OTf)(2), Ru-2(mu-eta(4)-N,N'-diphenyloxamidato)( MeOH)(2)(eta(6)-p-cymene)(2)](OTf)(2) 1b](OTf)(2) and Ru-2(mu-eta(4)-C6H2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](OTf)(2) 1c](OTf)(2) separately with imidazole-based ditopic ligands (L-1-L-2) in methanol yielded a series of tetranuclear metallamacrocycles 2-7](OTf)(4), respectively L-1 = 1,4-bis(imidazole-1-yl)benzene; L-2 = 4,4'-bis(imidazole-1-yl)biphenyl; OTf- = O3SCF3-]. Similarly, the reaction of Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)2](OTf)(2) 1a](OTf)(2) with a triazine-based tritopic ligand 1,3,5-tris(imidazole-1-yl) triazine (L3) in 3: 2 M ratio afforded an unexpected tetranuclear macrocycle 8](OTf)(4) instead of an expected trigonal prismatic cage 8a](OTf)(6). All the self-assembled macrocycles 2-8](OTf)(4) were isolated in moderate to high yields and were fully characterized by multinuclear H-1, F-19] NMR, IR and electrospray ionization mass spectrometry (ESI-MS). In addition, X-ray diffraction study on the single crystals of 3](OTf)(4) and 8](OTf)(4) also indicated the formation 2 + 2] self-assembled macrocycles. Despite the possibility of formation of different conformational isomeric macrocycles (syn-and anti) and polymeric product due to free rotation of ligand sites of imidazole linkers, the selective formation of single conformational isomer (anti) as the only product is quite interesting. Furthermore, the photo-and electrochemical properties of these assemblies have been studied using UV/Vis absorption and cyclic voltammetry analysis. (c) 2013 Elsevier B.V. All rights reserved.

Basic studies on the role of components of Bacillus megaterium as flotation biocollectors in sulphide mineral separation

Studies were carried out to assess the utility of the cellular and extracellular constituents of Bacillus megaterium for the flotation of sphalerite and galena minerals. Based on the flotation results on the individual minerals, it was observed that sphalerite was preferentially floated compared to galena. A maximum selectivity index (SI) value of 11.7 was achieved in the presence of the soluble fraction of the thermolysed cells, which was higher than that obtained with the intact cells (SI of 6.5) and the insoluble fraction of the thermolysed cells (SI of 9.6). The results of the various enzymatic treatment tests revealed that extracellular DNA played a vital role in the selective flotation of sphalerite. A noteworthy finding was that the single-stranded DNA (ssDNA) had a higher biocollector capacity vis-A -vis the double-stranded DNA (dsDNA), leading to better flotation efficiency. About 95 % recovery of sphalerite could be achieved from the mineral mixture by the combined addition of the ssDNA with the non-DNA components of the bacterial cells, resulting in a maximum SI of 19.1. Calcium and phosphate components of the nutrient media were found to be essential for better selectivity of separation of sphalerite. The mechanisms of microbe-mineral interaction are discussed.

Microscopic description of the evolution of the local structure and an evaluation of the chemical pressure concept in a solid solution

Extended x-ray absorption fine-structure studies have been performed at the Zn K and Cd K edges for a series of solid solutions of wurtzite Zn1-xCdxS samples with x = 0.0, 0.1, 0.25, 0.5, 0.75, and 1.0, where the lattice parameter as a function of x evolves according to the well-known Vegard's law. In conjunction with extensive, large-scale first-principles electronic structure calculations with full geometry optimizations, these results establish that the percentage variation in the nearest-neighbor bond distances are lower by nearly an order of magnitude compared to what would be expected on the basis of lattice parameter variation, seriously undermining the chemical pressure concept. With experimental results that allow us to probe up to the third coordination shell distances, we provide a direct description of how the local structure, apparently inconsistent with the global structure, evolves very rapidly with interatomic distances to become consistent with it. We show that the basic features of this structural evolution with the composition can be visualized with nearly invariant Zn-S-4 and Cd-S-4 tetrahedral units retaining their structural integrity, while the tilts between these tetrahedral building blocks change with composition to conform to the changing lattice parameters according to the Vegard's law within a relatively short length scale. These results underline the limits of applicability of the chemical pressure concept that has been a favored tool of experimentalists to control physical properties of a large variety of condensed matter systems.

Cu-II-Azide Polynuclear Complexes of Three Different Building Clusters with the Same Schiff-Base Ligand: Synthesis, Structures, Magnetic Behavior, and Density Functional Theory Studies

Three copper-azido complexes Cu-4(N-3)(8)(L-1)(2)(MeOH)(2)](n) (1), Cu-4(N-3)(8)(L-1)(2)] (2), and Cu-5(N-3)(10)(L-1)(2)](n) (3) L-1 is the imine resulting from the condensation of pyridine-2-carboxaldehyde with 2-(2-pyridyl)ethylamine] have been synthesized using lower molar equivalents of the Schiff base ligand with Cu(NO3)(2)center dot 3H(2)O and an excess of NaN3. Single crystal X-ray structures show that the basic unit of the complexes 1 and 2 contains Cu-4(II) building blocks; however, they have distinct basic and overall structures due to a small change in the bridging mode of the peripheral pair of copper atoms in the linear tetranudear structures. Interestingly, these changes are the result of changing the solvent system (MeOH/H2O to EtOH/H2O) used for the synthesis, without changing the proportions of the components (metal to ligand ratio 2:1). Using even lower proportions of the ligand, another unique complex was isolated with Cu-5(II) building units, forming a two-dimensional complex (3). Magnetic susceptibility measurements over a wide range of temperature exhibit the presence of both antiferromagnetic (very weak) and ferromagnetic exchanges within the tetranuclear unit structures. Density functional theory calculations (using B3LYP functional, and two different basis sets) have been performed on the complexes 1 and 2 to provide a qualitative theoretical interpretation of their overall magnetic behavior.

Adsorption study of silica gel particle for improvement in design of adsorption beds used in solar driven cooling units

Simulations using Ansys Fluent 6.3.26 have been performed to look into the adsorption characteristics of a single silica gel particle exposed to saturated humid air streams at Re=108 & 216 and temperature of 300K. The adsorption of the particle has been modeled as a source term in the species and the energy equations using a Linear Driving Force (LDF) equation. The interdependence of the thermal and the water vapor concentration field has been analysed. This work is intended to aid in understanding the adsorption effects in silica gel beds and in their efficient design. (C) 2013 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

The interaction of N-trifluoroacetylgalactosamine and its derivatives with winged bean (Psophocarpus tetragonolobus) basic agglutinin reveals differential mechanism of their recognition: a fluorine-19 nuclear magnetic resonance study

Here, we show the binding results of a leguminosae lectin, winged bean basic agglutinin (WBA I) to N-trifluoroacetylgalactosamine (NTFAGalN), methyl-alpha-N-trifluoroacetylgalactosamine (Me alpha NTFAGalN) and methyl-beta-tifluoroacetylgalactosamine (Me beta NTFAGalN) using (19) F NMR spectroscopy. No chemical shift difference between the free and bound states for NTFAGalN and Me beta NTFAGalN, and 0.01-ppm chemical shift change for Me alpha NTFAGalN, demonstrate that the Me alpha NTFAGalN has a sufficiently long residence time on the protein binding site as compared to Me beta NTFAGalN and the free anomers of NTFAGalN. The sugar anomers were found in slow exchange with the binding site of agglutinin. Consequently, we obtained their binding parameters to the protein using line shape analyses. Aforementioned analyses of the activation parameters for the interactions of these saccharides indicate that the binding of alpha and beta anomers of NTFAGalN and Me alpha NTFAGalN is controlled enthalpically, while that of Me beta NTFAGalN is controlled entropically. This asserts the sterically constrained nature of the interaction of the Me beta NTFAGalN with WBA I. These studies thus highlight a significant role of the conformation of the monosaccharide ligands for their recognition by WBA I.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.