New La2CuO4 derivatives La(2-2x)Sr(2x)Cu(1-x)M(x)O(4) (M=Ti, Mn, Fe, or Ru): A study of linear Cu-O-M electronic interaction in two dimensions

Oxides of the general formula La2-2xSr2xCu1-xII,M(x)(IV)O(4) (M = Ti, Mn, Fe, or Ru), crystallizing in the tetragonal K,NIF, structure, have been synthesized. For M=Ti, only the x=0,5 member could be prepared, while for M=Mn and Fe, the composition range is 0 Cu(III)-O-Fe(III) valence degeneracy. Increasing the strontium content at the expense of lanthanum in La2-2xSr2xCu1-xFexO4 for x less than or equal to 0.20 renders the samples metallic but not superconducting. (C) 1997 Academic Press.

Structure of 2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9-hexadecafluorodecyl 1,10-ditosylate by X-ray crystallography and F-19-NMR spectroscopy

2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9-hexadecafluorodecyl 1,10-ditosylate and its precursors were synthesized and characterized by H-1- and F-19-NMR spectroscopic methods and X-ray crystallography. These compounds are building blocks for the syntheses of the surfactants containing polyperfluoromethylene spacer. The molecule has extended all-trans conformation with molecular symmetry (1) over bar (C-i). There is a reasonably strong C-H ... O interaction in the crystal and there are two F ... F intermolecular contact distances less than the sum of van der Waals radii. (C) 1999 Elsevier Science B.V. All rights reserved.

Grain size effects on charge-ordering, phase segregation and related properties of rare-earth manganates, Nd(0.5)A(0.5)MnO(3) (A = Ca or Sr)

Grain size has marked effects on charge-ordering and other properties of Nd(0.5)A(0.5)MnO(3) (A=Ca or Sr). Thus, the anti-ferromagnetic (AFM) transition in Nd0.5Ca0.5MnO3 is observed distinctly only in samples sintered at 1273 K or higher. The sample with a small grain size (sintered at 1173 K) shows evidence for greater ferromagnetic (FM) interaction at low temperatures, probably due to phase segregation. The FM transition as well as the charge-ordering transition in Nd0.5Sr0.5MnO3 becomes sharper in samples sintered at 1273 K or higher. The sample sintered at 1173 K does not show the AFM-CO transition around 150 K and is FM down to low temperatures; the apparent T-c-T-co gap decreases with the increase in the grain size. The samples sintered at lower temperatures (<1673 K) show evidence for greater segregation of the AFM and FM domains. (C) 2002 Elsevier Science Ltd. All rights reserved.

Synthesis, biological studies of linear and branched arabinofuranoside-containing glycolipids and their interaction with surfactant protein A

Oligoarabinofuranoside-containing glycolipids relevant to mycobacterial cell wall components were synthesized in order to understand the functional roles of such glycolipids. A series of linear tetra-, hexa-, octa-and a branched heptasaccharide oligoarabinofuranosides, with 1 -> 2 and 1 -> 5 a-linkages between the furanoside residues, were synthesized by chemical methods from readily available monomer building blocks. Upon the synthesis of glycolipids, constituted with a double alkyl chain-substituted sn-glycerol core and oligosaccharide fragments, biological studies were performed to identify the effect of synthetic glycolipids on the biofilm formation and sliding motilities of Mycobacterium smegmatis. Synthetic glycolipids and arabinofuranosides displayed an inhibitory effect on the growth profile, but mostly on the biofilm formation and maturation. Similarly, synthetic compounds also influenced the sliding motility of the bacteria. Further, biophysical studies were undertaken, so as to identify the interactions of the glycolipids with a pulmonary surfactant protein, namely surfactant protein A (SP-A), with the aid of the surface plasmon resonance technique. Specificities of each glycolipid interacting with SP-A were thus evaluated. From this study, glycolipids were found to exhibit higher apparent association constants than the corresponding oligosaccharide portion alone, without the double alkyl group-substituted glycerol core.

Synthesis and DNA binding studies of Ni(II), Co(II), Cu(II) and Zn(II) metal complexes of N(1),N(5)-bis[pyridine-2-methylene]-thiocarbohydrazone Schiff-base ligand

The thiocarbohydrazone Schiff-base ligand with a nitrogen and sulphur donor was synthesized through condensation of pyridine-2-carbaldehyde and thiocarbohydrazide. Schiff-base ligands have the ability to conjugate with metal salts. A series of metal complexes with a general formula [MCl(2)(H(2)L)]center dot nH(2)O (M=Ni, Co, Cu and Zn) were synthesized by forming complexes of the N(1),N5-bis[pyridine-2-methylene]thiocarbohydrazone (H2L) Schiff-base ligand. These metal complexes and ligand were characterized by using ultraviolet-visible (UV-Vis), Fourier Transform Infrared (FT-IR), (1)H and (13)C NMR spectroscopy and mass spectroscopy, physicochemical characterization, CHNS and conductivity. The biological activity of the synthesized ligand was investigated by using Escherichia coli DNA as target. The DNA interaction of the synthesized ligand and complexes on E. coli plasmid DNA was investigated in the aqueous medium by UV-Vis spectroscopy and the binding constant (K(b)) was calculated. The DNA binding studies showed that the metal complexes had an improved interaction due to trans-geometrical isomers of the complexes than ligand isomers in cis-positions. (C) 2011 Elsevier B.V. All rights reserved.

Halogen Bonding and Structural Modularity in 2,3,4-and 3,4,5-Trichlorophenol

The crystal structure of 3,4,5-trichlorophenol contains hydrogen bonded domains that occur respectively in the structures of 4-chlorophenol and 3,5-dichlorophenol. Such modularity is also seen in 2,3,4-trichlorophenol. These structures, and those of the six isomeric dichlorophenols, illustrate the importance of halogen bonding as a structure determining interaction.

3-Ethyl-4-methyl-1H-pyrazol-2-ium-5-olate

The title compound, C(6)H(10)N(2)O, is a zwitterionic pyrazole derivative. The crystal packing is predominantly governed by a three-center iminium-amine N(+)-H center dot center dot center dot O(-)center dot center dot center dot H-N interaction, leading to an undulating sheet-like structure lying parallel to (100).

Issues in Achievement of Haptic Realism

This paper deals with haptic realism related to Kinematic capabilities of the devices used in manipulation of virtual objects in virtual assembly environments and its effect on achieving haptic realism. Haptic realism implies realistic touch sensation. In virtual world all the operations are to be performed in the same way and with same level of accuracy as in the real world .In order to achieve realism there should be a complete mapping of real and virtual world dimensions. Experiments are conducted to know the kinematic capabilities of the device by comparing the dimensions of the object in the real and virtual world. Registered dimensions in the virtual world are found to be approximately 1.5 times that of the real world. Dimensional variations observed were discrepancy due to exoskeleton and discrepancy due to real and virtual hands. Experiments are conducted to know the discrepancy due to exoskeleton and this discrepancy can be taken care of by either at the hardware or software level. A Mathematical model is proposed to know the discrepancy between real and virtual hands. This could not give a fixed value and can not be taken care of by calibration. Experiments are conducted to figure out how much compensation can be given to achieve haptic realism.

Ethyl 6-methyl-2-sulfanylidene-4-[4(trifluoromethyl)phenyl]-1,2,3,4-tetrahyd ropyrimidine-5-carboxylate

The title compound, C(15)H(15)F(3)N(2)O(2)S, adopts a conformation with an intramolecular C-H center dot center dot center dot pi interaction. The dihedral angles between the planes of the 4-(trifluoromethyl) phenyl and ester groups with the plane of the six-membered tetrahydropyrimidine ring are 81.8 (1) and 16.0 (1)degrees, respectively. In the crystal structure, intermolecular N-H center dot center dot center dot S hydrogen bonds link pairs of molecules into dimers and N-H center dot center dot center dot O interactions generate hydrogen-bonded molecular chains along the crystallographic a axis.

Interaction between oxygen and silver dissolved in liquid copper

The effect of silver on the activity of oxygen in solution in liquid copper has been measured at 1373 K. The results are compared with those of other authors who have studied the system; it is found that the results are in good agreement with Alcock and Richardson's quasichemical model when a coordination number of 2 is assigned to all atoms in the ternary solution.

Ribosome-RNA interaction: a potential target for developing antiviral against hepatitis C virus

Hepatitis C virus (HCV), a member of Flaviviridae, encoding a positive-sense single-stranded RNA translates by cap-independent mechanism using the internal ribosome entry site (IRES) present in the 5' UTR of the virus. The IRES has complex stem loop structures and is capable of recruiting the 40S ribosomal subunit in a factor-independent fashion. As the IRES sequence is highly conserved throughout the HCV genotypes and the translation is the first obligatory step of the HCV life cycle, the IRE'S-mediated translation, or more specifically, the ribosome HCV RNA interaction is an attractive target to design effective antivirals. This article will focus on the mechanism of the HCV IRES translation and the various ways in which the interaction of ribosome and IRES has been targeted.

Dynamics of end-to-end loop formation: A flexible chain in the presence of hydrodynamic interaction

Based on the Wilemski-Fixman approach G. Wilemski, M. Fixman, J. Chem. Phys. 60 (1974) 866], we show that, for a flexible chain in theta solvent, hydrodynamic interaction treated with a pre-averaging approximation makes ring closing faster if the chain is not very short. We also show that the ring closing time for a long chain with hydrodynamic interaction in theta solvent scales with the chain length (N) as N-1.5, in agreement with the previous renormalization group calculation based prediction by Freidman and O'Shaughnessy B. Friedman, B. O'Shaughnessy, Phys. Rev. A 40 (1989) 5950]. (C) 2012 Elsevier B.V. All rights reserved.

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Development of a New Generation of Vectors for Gene Expression, Gene Replacement, and Protein-Protein Interaction Studies in Mycobacteria

Escherichia coli-mycobacterium shuttle vectors are important tools for gene expression and gene replacement in mycobacteria. However, most of the currently available vectors are limited in their use because of the lack of extended multiple cloning sites (MCSs) and convenience of appending an epitope tag(s) to the cloned open reading frames (ORFs). Here we report a new series of vectors that allow for the constitutive and regulatable expression of proteins, appended with peptide tag sequences at their N and C termini, respectively. The applicability of these vectors is demonstrated by the constitutive and induced expression of the Mycobacterium tuberculosis pknK gene, coding for protein kinase K, a serine-threonine protein kinase. Furthermore, a suicide plasmid with expanded MCS for creating gene replacements, a plasmid for chromosomal integrations at the commonly used L5 attB site, and a hypoxia-responsive vector, for expression of a gene(s) under hypoxic conditions that mimic latency, have also been created. Additionally, we have created a vector for the coexpression of two proteins controlled by two independent promoters, with each protein being in fusion with a different tag. The shuttle vectors developed in the present study are excellent tools for the analysis of gene function in mycobacteria and are a valuable addition to the existing repertoire of vectors for mycobacterial research.

Fe as Hydrogen/Halogen Bond Acceptor in Square Pyramidal Fe(CO)(5)

Hydrogen bonded complexes formed between the square pyramidal Fe(CO)(5) with HX (X = F, Cl, Br), showing X-H center dot center dot center dot Fe interactions, have been investigated theoretically using density functional theory (DFT) including dispersion correction. Geometry, interaction energy, and large red shift of about 400 cm(-1) in the FIX stretching frequency confirm X-H center dot center dot center dot Fe hydrogen bond formation. In the (CO)(5)Fe center dot center dot center dot HBr complex, following the significant red shift, the HBr stretching mode is coupled with the carbonyl stretching modes. This clearly affects the correlation between frequency shift and binding energy, which is a hallmark of hydrogen bonds. Atoms in Molecule (AIM) theoretical analyses show the presence of a bond critical point between the iron and the hydrogen of FIX and significant mutual penetration. These X-H center dot center dot center dot Fe hydrogen bonds follow most but not all of the eight criteria proposed by Koch and Popelier (J. Phys. Chem. 1995, 99, 9747) based on their investigations on C-H center dot center dot center dot O hydrogen bonds. Natural bond orbital (NBO) analysis indicates charge transfer from the organometallic system to the hydrogen bond donor. However, there is no correlation between the extent of charge transfer and interaction,energy, contrary to what is proposed in the recent IUPAC recommendation (Pure Appl.. Chem. 2011, 83, 1637). The ``hydrogen bond radius'' for iron has been determined to be 1.60 +/- 0.02 angstrom, and not surprisingly it is between the covalent (127 angstrom) and van der Waals (2.0) radii of Fe. DFT and AIM theoretical studies reveal that Fe in square pyramidal Fe(CO)(5) can also form halogen bond with CIF and ClH as ``halogen bond donor''. Both these complexes show mutual penetration as well, though the Fe center dot center dot center dot Cl distance is closer to the sum of van der Waals radii of Fe and Cl in (CO)5Fe center dot center dot center dot ClH, and it is about 1 angstrom less in (CO)(5)Fe center dot center dot center dot ClF.