(Dimethylamino)borylene and Related Complexes of Electron-Rich Metal Fragments: Generation of Nucleophile-Resistant Cations by Spontaneous Halide Ejection

Spontaneous halide ejection from a three-coordinate Lewis acid has been shown to offer a remarkable new route to cationic metal complexes featuring a linear, multiply bonded boron-donor Ligand. The exploitation of electron-rich [CpM(PR3)(2)] fragments within boryl systems of the type LnMB(hal)NR2 leads to the spontaneous formation in polar solvents of chemically robust borylene complexes, [LnM(BNR2)](+), with exceptionally low electrophilicity and short M-B bonds. This is reflected by M-B distances (ca. 1.80 angstrom for FeB systems) which are more akin to alkyl-/aryl-substituted borylene complexes and, perhaps most strikingly, by the very low exothermicity associated with the binding of pyridine to the two-coordinate boron center (Delta H = -7.4 kcal mol(-1), cf. -40.7 kcal mol(-1) for BCl3). Despite the strong pi electron release from the metal fragment implied by this suppressed reactivity and by such short M-B bonds, the barrier to rotation about the Fe=B bond in the unsymmetrical variant [CpFe(dmpe)(BN{C6H4OMe-4}Me)](+) is found to be very small (ca. 2.9 kcal mol(-1)). This apparent contradiction is rationalized by the orthogonal orientations of the HOMO and HOMO-2 orbitals of the [CpML2](+) fragment, which mean that the M-B pi interaction does not fall to zero even in the highest energy conformation.

Fragment Finder 2.0: a computing server to identify structurally similar fragments

Fragment Finder 2.0 is a web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally similar fragments using the protein backbone C alpha angles. In addition, the identified fragments can be superimposed using either of the two structural superposition programs, STAMP and PROFIT, provided in the server. The freely available Java plug-in Jmol has been interfaced with the server for the visualization of the query and superposed fragments. The server is the updated version of a previously developed search engine and employs an in-house-developed fast pattern matching algorithm. This server can be accessed freely over the World Wide Web through the URL http://cluster.physics.iisc.ernet.in/ff/.

Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.

Does aluminium bind to histidine? an NMR investigation of Amyloid beta 12 and Amyloid beta 16 fragments

Aluminium and zinc are known to be the major triggering agents for aggregation of amyloid peptides leading to plaque formation in Alzheimer's disease. While zinc binding to histidine in A (amyloid ) fragments has been implicated as responsible for aggregation, not much information is available on the interaction of aluminium with histidine. In the NMR study of the N-terminal A fragments, DAEFRHDSGYEV (A12) and DAEFRHDSGYEVHHQK (A16) presented here, the interactions of the fragments with aluminium have been investigated. Significant chemical shifts were observed for few residues near the C-terminus when aluminium chloride was titrated with A12 and A16 peptides. Surprisingly, it is nonhistidine residues which seem to be involved in aluminium binding. Based on NMR constrained structure obtained by molecular modelling, aluminium-binding pockets in A12 were around charged residues such as Asp, Glu. The results are discussed in terms of native structure propagation, and the relevance of histidine residues in the sequences for metal-binding interactions. We expect that the study of such short amyloid peptide fragments will not only provide clues for plaque formation in aggregated conditions but also facilitate design of potential drugs for these targets.

Stabilization of diborane(4) by transition metal fragments and a novel metal to pi Dewar-Chatt-Duncanson model of back donation

The feasibility of using transition metal fragments to stabilize B2H4 in planar configuration by donating 2 electrons to the boron moiety is investigated. Building upon the existing theoretical and experimental data and aided by the isolobal analogy, the model transition metal complexes Cr(CO)(4)B2H4 (6), Mn(CO)-CpB2H4 (7), Fe(CO)(3)B2H4 (8) and CoCpB2H4 (9) are chosen to illustrate this unique bonding feature bond strengthening with pi-back donation. Other possible types of complexes with B2H4 and the metal fragment are also explored and the energies are compared. One of the low energy isomers wherein the planar B2H4 interacts with the metal fragment in an in-plane fashion represents a unique case study for the Dewar-Chatt-Duncanson model. In this complex the back-donation from the metal fills the p bonding orbital between the two boron atoms thus forming a B=B double bond.

Eigen-profiles of spatio-temporal fragments for adaptive region-based tracking

We propose a novel space-time descriptor for region-based tracking which is very concise and efficient. The regions represented by covariance matrices within a temporal fragment, are used to estimate this space-time descriptor which we call the Eigenprofiles(EP). EP so obtained is used in estimating the Covariance Matrix of features over spatio-temporal fragments. The Second Order Statistics of spatio-temporal fragments form our target model which can be adapted for variations across the video. The model being concise also allows the use of multiple spatially overlapping fragments to represent the target. We demonstrate good tracking results on very challenging datasets, shot under insufficient illumination conditions.

Organic fragments from graphene oxide: Isolation, characterization and solvent effects

As-prepared graphene oxide (GO) contains oxidative debris which can be washed using basic solutions. We present the isolation and characterization of these debris. Dynamic light scattering (DLS) is used to monitor the separation of the debris in various solvents in the presence of different protic and aprotic alkylamino bases. The study reveals that the debris are rich in carbonyl functional groups and water is an essential component for separation and removal of the debris from GO under oxidative reaction conditions.

Hydrological importance of sacred forest fragments in Central Western Ghats of India

Sacred groves are patches of forests of special spiritual significance to humans, offering also a diverse range of ecological and environmental services. We have attempted here to understand the local hydrological dynamics of a sacred forest, in terms of the benefits the village community derive, in central Western Ghats region of India. A comparative assessment has been made between two small watersheds in terms of their landscape structure (woody species composition) with soil water properties and availability of water in the respective downstream villages. The result shows that, sacred site with more primeval vegetation has close association with soil moisture in comparison to non-sacred site during dry spell of the year. The higher soil moisture ensures year long availability of water in the downstream village of the sacred site which facilitates farming of commercial crops with higher economic returns to the farmers, unlike the farmers in the other village where they face water crisis during the lean season. The study emphasizes the need for conservation endeavour on sacred groves highlighting its potential for water conservation at local and regional levels.