Arene ruthenium complexes of N,N′- and N,O-donor schiff base ligands: an X-ray structure of [(η6-p-cymene) RuCl(C5,H4N-2-CH=NC6H4-p-Me)Cl·C6H6·H2O

Arene ruthenium(II) Schiff base complexes of formulations [(η -p-cymene)RuCl(C5H4N-2-CH=NC6H4-p-X)](ClO4) (1) and [(η6-p-cymene)RuCl(O-o-C6H4CH=NC6H4-p-X)] (2) (X = H, Me, OMe, NO2, Cl) were prepared by reacting [(η6-p-cymene)RuCl2]2 with corresponding pyridine-2-carboxaldimines and sodium salts of salicylaldimines in dry THF, respectively. Complex 1 is isolated as a perchlorate salt. The molecular structure of [(η6-p-cymene)RuCl(C5H4 N-2-CH=NC6H4-p-Me)]Cl·C6H6·H2O has been determined by X-ray crystallography. The complex contains an η6-p-cymene group, a chloride and a bidentate chelating Schiff base ligand.

Electrobioleaching of base metal sulfides

Bioleaching of base metal sulfides, such as pyrite, chalcopyrite, and sphalerite, under the influence of applied direct current (DC) potentials is discussed. Contributions toward mineral dissolution from three effects, namely, galvanic, applied potential, and microbiological, are analyzed and compared. Sphalerite could be selectively bioleached in the presence of Thiobacillus ferrooxidans under an applied potential of -500 mV (SCE) from mixed sulfides containing sphalerite, pyrite, and chalcopyrite. Bacterial activity and growth were found to be promoted under electrobioleaching conditions. Probable mechanisms involved in the bioleaching of different sulfides under positive and negative applied potentials are discussed.

CA/TG sequence at the 5' end of oligo(A)-tracts strongly modulates DNA curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

Conformational Polymorphism in G-tetraplex Structures: Strand Reversal by Base Flipover or Sugar Flipover

Guanine rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosidic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanine tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanines along a strand and different possible orientations of guanine strands in a G-tetraplex structure. It is found that for an oligo G stretch per se, a parallel four stranded structure with all guanines in anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanines along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosidic conformation and the inverted stacking arrangement arising from base flipover, in antiparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Two forms of Pf1 Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit

Inovirus is a helical array of alpha-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover

Guanlne rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosldic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanlne tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanlnes along a strand and different possible orientations of guanlne strands In a G-tetraplex structure. It is found that for an ollgo G stretch per se, a parallel four stranded structure with all guanines In anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanlnes along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosldic conformation and the inverted stacking arrangement arising from base filpover, In antlparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

CA\TG Sequence at the 5'end of Oligo(A)-tracts Strongly Modulates DNA Curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

Two forms of PF1 INOVIRUS: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the assymetric unit

Inovirus is a helical array of agr-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Structure and conformation of the calcium complex of cyclo(Ala-Leu-Pro-Gly)2 in two crystal forms

Crystal structures of two different forms of the calcium perchlorate complex of cyclo(Ala-Leu-Pro-Gly)2 have been determined and refined using X-ray crystallographic techniques. Orthorhombic form: C32H52N8O8.Ca(ClO4)2.7H2O.2CH3OH, space group C222(1), a = 14.366, b = 18.653, c = 19.824 A, Z = 4, R = 0.068 for 2208 observed reflections. Monoclinic form: C32H52N8O8.Ca(ClO4)2.4H2O, space group C2, a = 21.096, b = 10.182, c = 11.256 A, beta = 103.33 degrees, Z = 2, R = 0.075 for 2165 observed reflections. The cyclic peptide molecule in both the structures has the form of a twofold symmetric, slightly elongated bowl. Type II' beta-turns, involving Gly and Ala at the corners, exist at the two ends of the molecule. The interior of the molecule is substantially hydrophilic, and the external surface of the bowl is largely hydrophobic. The calcium ion is located at the centre of the mouth of the bowl-like molecule. In both crystal forms, four peptide carbonyl oxygens from the cyclic peptide and two solvent oxygens coordinate to the metal ion. The mode of complexation may be described as incomplete encapsulation as, for example, in the case of metal complexes of antamanide. In the crystal structures the complex ions are held together by hydrogen bonds involving perchlorate ions and water molecules. The molecular structure observed in the crystals is entirely consistent with the results of solution studies, which also indicate the conformation of the cyclic peptide in the complex to be similar to that of the uncomplexed molecule.

Mobile Base Stations Placement and Energy Aware Routing in Wireless Sensor Networks

Increasing network lifetime is important in wireless sensor/ad-hoc networks. In this paper, we are concerned with algorithms to increase network lifetime and amount of data delivered during the lifetime by deploying multiple mobile base stations in the sensor network field. Specifically, we allow multiple mobile base stations to be deployed along the periphery of the sensor network field and develop algorithms to dynamically choose the locations of these base stations so as to improve network lifetime. We propose energy efficient low-complexity algorithms to determine the locations of the base stations; they include i) Top-K-max algorithm, ii) maximizing the minimum residual energy (Max-Min-RE) algorithm, and iii) minimizing the residual energy difference (MinDiff-RE) algorithm. We show that the proposed base stations placement algorithms provide increased network lifetimes and amount of data delivered during the network lifetime compared to single base station scenario as well as multiple static base stations scenario, and close to those obtained by solving an integer linear program (ILP) to determine the locations of the mobile base stations. We also investigate the lifetime gain when an energy aware routing protocol is employed along with multiple base stations.

Transformation formula for exponential sums involving fourier coefficients of modular forms

In 1984 Jutila [5] obtained a transformation formula for certain exponential sums involving the Fourier coefficients of a holomorphic cusp form for the full modular group SL(2, Z). With the help of the transformation formula he obtained good estimates for the distance between consecutive zeros on the critical line of the Dirichlet series associated with the cusp form and for the order of the Dirichlet series on the critical line, [7]. In this paper we follow Jutila to obtain a transformation formula for exponential sums involving the Fourier coefficients of either holomorphic cusp forms or certain Maass forms for congruence subgroups of SL(2, Z) and prove similar estimates for the corresponding Dirichlet series.

CAITG sequence at the 5' end of Oligo(A)-tracts strongly modulates DNA curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

The Reaction of a Nitro-Capped Cobalt(III) Cage Complex With Base: the Crystal Structure of a Contracted Cage Complex, and the Mechanism of Its Formation

The synthesis, properties and crystal structure of the cage complex (1-hydroxy-8-methyl-3,6,10,13,15,18-hexaazabicyclo[6.6.5]nonadecane)cobalt(III) chloride hydrate ([Co(Me,OH-absar)] C13.H2O) are reported. The mechanism of the formation of this contracted cavity cage from a nitro-capped hexaazabicycloicosane type cage has been investigated. Treatment of (1-methyl-8-nitro-3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane)cobalt(III) chloride ([Co(Me,NO2-sar)] 3+) with excess base in aqueous solution leads initially to rapid (t1/2 < 1 ms) and reversible deprotonation of one coordinated secondary amine. This species undergoes a retro-Mannich type reaction and imine hydrolysis (t1/2 almost-equal-to 90 s). Quenching the reaction with acid gives rise to a pair of isomeric intermediate species which have been isolated and characterized. They have a pendant arm macrocyclic structure, resulting from the loss of a methylene unit from one of the arms of the cap. Heating either isomer in aqueous solution gives the new cage compound with the contracted cap. It is postulated that this occurs through a Nef reaction, resulting in the formation of a ketone which then condenses with the coordinated primary amine. A comparison with the corresponding bicycloicosane analogue indicates a reduced chromophoric cavity size for the contracted cage. The reduction potential of the cobalt(III)/cobalt(II) couple is 170 mV more negative for the smaller cage, and, in the electronic spectrum of the cobalt(III) complex, the d-d transitions are both shifted to higher energy, corresponding to a stronger ligand field.

Asymmetric synthesis of steroidal Tröger's base analogues. X-Ray molecular structure of methyl 3?,12?-{6H,12H-5,11-methanodibenzo[b,f][1,5]diazocine-2,8-bisacetoxy}-5?-cholan-24-oate

Cyclization of compound 5c in trifluoroacetic acid/hexamethylenetetramine produces Tröger's base analogue 6c in 75% yield with 70% diastereoselectivity.