Coordination-Driven Self-Assembly of 2D-Metallamacrocycles Using a New Carbazole-Based Dipyridyl Donor: Synthesis, Characterization, and C-60 Binding Study

A new carbazole-based 90 degrees dipyridyl donor 3,6-di(4-pyridylethynyl)carbazole (L) containing carbazole-ethynyl functionality is synthesized in reasonable yield using the Sonagashira coupling reaction. Multinuclear NMR, electrospray ionization-mass spectrometry (ESI-MS), including single crystal X-ray diffraction analysis characterized this 90 degrees building unit. The stoichiometry combination of L with several Pd(II)/Pt(II)-based 90 degrees acceptors (1a-1d) yielded 2 + 2] self-assembled metallacycles (2a-2d) under mild conditions in quantitative yields 1a = cis-(dppf)Pd(OTf)(2); 1b = cis-(dppf)Pt(OTf)(2); 1c = cis-(tmen)Pd(NO3)(2); 1d = 3,6-bis{trans-Pt(C C) (PEt3)(2)(NO3))carbazole]. All these macrocycles were characterized by various spectroscopic techniques, and the molecular structure of 2a was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of ethynyl functionality to the carbazole backbone causes the resulted macrocycles (2a-2d) to be pi-electron rich and thereby exhibit strong emission characteristics. The macrocycle 2a has a large internal concave aromatic surface. The fluorescence quenching study suggests that 2a forms a similar to 1:1 complex with C-60 with a high association constant of K-sv = 1.0 X 10(5) M-1.

Sesbania Mosaic Virus (SeMV) Infectious Clone: Possible Mechanism of 3 ` and 5 ` End Repair and Role of Polyprotein Processing in Viral Replication

Sesbania mosaic virus (SeMV) is a positive stranded RNA virus belonging to the genus Sobemovirus. Construction of an infectious clone is an essential step for deciphering the virus gene functions in vivo. Using Agrobacterium based transient expression system we show that SeMV icDNA is infectious on Sesbania grandiflora and Cyamopsis tetragonoloba plants. The efficiency of icDNA infection was found to be significantly high on Cyamopsis plants when compared to that on Sesbania grandiflora. The coat protein could be detected within 6 days post infiltration in the infiltrated leaves. Different species of viral RNA (double stranded and single stranded genomic and subgenomic RNA) could be detected upon northern analysis, suggesting that complete replication had taken place. Based on the analysis of the sequences at the genomic termini of progeny RNA from SeMV icDNA infiltrated leaves and those of its 3' and 5' terminal deletion mutants, we propose a possible mechanism for 3' and 5' end repair in vivo. Mutation of the cleavage sites in the polyproteins encoded by ORF 2 resulted in complete loss of infection by the icDNA, suggesting the importance of correct polyprotein processing at all the four cleavage sites for viral replication. Complementation analysis suggested that ORF 2 gene products can act in trans. However, the trans acting ability of ORF 2 gene products was abolished upon deletion of the N-terminal hydrophobic domain of polyprotein 2a and 2ab, suggesting that these products necessarily function at the replication site, where they are anchored to membranes.

Regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C through the transcriptional repression of upstream activating sequence inositol containing genes

The regulation of phospholipid biosynthesis in Saccharomyces cerevisiae through cis-acting upstream activating sequence inositol (UAS(ino)) and trans-acting elements, such as the INO2-INO4 complex and OPI1 by inositol supplementation in growth is thoroughly studied. In this study, we provide evidence for the regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C (PLC) through UAS(ino) and the trans-acting elements. Gene expression analysis and radiolabelling experiments demonstrated that the overexpression of rice PLC in yeast cells altered phospholipid biosynthesis at the levels of transcriptional and enzyme activity. This is the first report implicating PLC in the direct regulation of lipid biosynthesis. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Sm(III)nitrate-catalyzed one-pot synthesis of furano3,2c]-1,2,3,4-tetrahydroquinolines and DNA photocleavage studies

The synthesis and DNA photocleavage studies of furano3,2-c]-1,2,3,4-tetrahydroquinolines have been reported. Sm(III)nitrate was found to be an efficient for the Diels-Alder reaction of aryl amines with 2,3-dihydrofuran to offer the corresponding furano3,2-c]-1,2,3,4-tetrahydroquinolines derivatives as a mixture of cis/trans stereoisomers in moderate yields. The aqueous solubility of acid catalyst can be recycled without significant loss of activity. The DNA photocleavage studies shows that, the cis/trans stereoisomers are good DNA cleavage mimic in terms of molecular structure. (C) 2012 Elsevier B.V. All rights reserved.

Sliding-Mode Guidance and Control for All-Aspect Interceptors with Terminal Angle Constraints

In this paper, sliding-mode-control-based guidance laws to intercept stationary, constant-velocity, and maneuvering targets at a desired impact angle are proposed. The desired impact angle, which is defined in terms of a desired line-of-sight angle, is achieved in finite time by selecting the missile's lateral acceleration to enforce terminal sliding mode on a switching surface designed using nonlinear engagement dynamics. The conditions for capturability are also presented. In addition, by considering a three-degree-of-freedom linear-interceptor dynamic model and by following the procedure used to design a dynamic sliding-mode controller, the interceptor autopilot is designed as a simple static controller to track the lateral acceleration generated by the guidance law. Numerical simulation results are presented to validate the proposed guidance laws and the autopilot design for different initial engagement geometries and impact angles.

Cis-trans peptide variations in structurally similar proteins

The presence of energetically less favourable cis peptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between the cis and trans conformations also has an important role in the folding process. In this study, we analyse the extent of conservation of cis peptides among similar folds. We look at both the amino acid preferences and local structural changes associated with such variations. Nearly 34% of the Xaa-Proline cis bonds are not conserved in structural relatives; Proline also has a high tendency to get replaced by another amino acid in the trans conformer. At both positions bounding the peptide bond, Glycine has a higher tendency to lose the cis conformation. The cis conformation of more than 30% of beta turns of type VIb and IV are not found to be conserved in similar structures. A different view using Protein Block-based description of backbone conformation, suggests that many of the local conformational changes are highly different from the general local structural variations observed among structurally similar proteins. Changes between cis and trans conformations are found to be associated with the evolution of new functions facilitated by local structural changes. This is most frequent in enzymes where new catalytic activity emerges with local changes in the active site. Cis-trans changes are also seen to facilitate inter-domain and inter-protein interactions. As in the case of folding, cis-trans conversions have been used as an important driving factor in evolution.

A method for stabilizing the cis prolyl peptide bond: influence of an unusual n -> pi* interaction in 1,3-oxazine and 1,3-thiazine containing peptidomimetics

The cis/trans isomer ratios of the Xaa-Pyr (Pyr = pyrrolidine) 3 degrees amide bonds are significantly high (similar to 90% cis) in the novel peptidomimetics where Pyr contains 1,3-oxazine (Oxa) or 1,3-thiazine (Thi) at its 2 position. We find that an unusual n -> pi(i-1)* interaction, selectively stabilizes the cis conformer and the n X n repulsion destabilizes the trans conformer of these molecules. Both these electronic effects oppose the steric effects in the 3 degrees amide bond. The structural requirements for manifestation of these electronic effects are determined. (c) 2012 Elsevier Ltd. All rights reserved.

Diffusion mechanism in the mu phase in Nb-X (X = Ni, Co, Fe) systems

Nb is one of the common refractory elements added in Ni, Co and Fe based superalloys. This lead to the formation of brittle topological close packed (tcp) mu phase, which is deleterious to the structure. It mainly grows by interdiffusion and in the present article, the interdiffusion process in different Nb-X (X=Ni, Co, Fe) systems is discussed. The activation energy for interdiffusion is lower in the Co-Nb system (173 kJ/mol) than Fe-Nb system (233 kJ/mol), which is again lower than the value found in the Ni-Nb system (319.7 kJ/mol). The mole fraction of Nb in this phase is less than Fe or Co at stoichiometric compositions in the Nb-Fe (that is Fe7Nb6) and Nb-Co (that is Co7Nb6) systems. On the other hand, the mole fraction of Nb is higher than Ni in the same phase (Ni6Nb2) in Ni-Nb system. However, in all the phases, Nb has lower diffusion rate. Possible diffusion mechanism in this phase is discussed with respect to the crystal structure.

Deformation behaviour of Titanium in torsion

The evolution of microstructure and texture in Hexagonal Close Pack commercially pure titanium has been studied in torsion in a strain rate regime of 0.001 to 1 s(-1). Free end torsion tests carried out on titanium rods indicated higher stress levels at higher strain rate but negligible change in the strain-hardening behaviour. There was a decrease in the intra-granular misorientation while a negligible change in the amount of contraction and extension twins was observed with increase in strain rate. The deformed samples showed a C-1 fibre (c-axis is first rotated 90 degrees in shear direction and then +30 degrees in shear plane direction) at all the strain rates. With the increase in strain rate, there was an increase in the intensity of the C-1 fibre and it became more heterogeneous with a strong {11(2)over-bar6}< 2(8)over-bar)63 > component. In the absence of extensive twinning, pyramidal < c+a > slip system is attributed for the observed deformation texture. The present investigation, therefore, substantiates the theoretical prediction of increase in strength of texture with strain rate in torsion.

All flavours of El Nino have similar early subsurface origins

The El Nino/Southern Oscillation phenomenon, characterized by anomalous sea surface temperatures and winds in the tropical Pacific, affects climate across the globe(1). El Ninos occur every 2-7 years, whereas the El Nino/Southern Oscillation itself varies on decadal timescales in frequency and amplitude, with a different spatial pattern of surface anomalies(2) each time the tropical Pacific undergoes a regime shift. Recent work has shown that Bjerknes feedback(3,4) (coupling of the atmosphere and the ocean through changes in equatorial winds driven by changes in sea surface temperature owing to suppression of equatorial upwelling in the east Pacific) is not necessary(5) for the development of an El Nino. Thus it is unclear what remains constant through regimes and is crucial for producing the anomalies recognized as El Nino. Here we show that the subsurface process of discharging warm waters always begins in the boreal summer/autumn of the year before the event (up to 18 months before the peak) independent of regimes, identifying the discharge process as fundamental to the El Nino onset. It is therefore imperative that models capture this process accurately to further our theoretical understanding, improve forecasts and predict how the El Nino/Southern Oscillation may respond to climate change.

Cyclodextrin and its complexation for resolution of isomers using diffusion ordered spectroscopy

Diffusion ordered spectroscopy (DOSY) generally fails to separate the peaks pertaining to isomeric species possessing identical molecular weights and similar hydrodynamic radii. The present study demonstrates the resolution of isomers using alpha/beta-cyclodextrin as a co-solute by Matrix Assisted Diffusion Ordered Spectroscopy. The resolution of isomers has been achieved by measuring the significant differences in the diffusion rates between the positional isomers of aminobenzoic acids, benzenedicarboxylic acids and between the cis, trans isomers, fumaric acid and maleic acid. (C) 2012 Elsevier B.V. All rights reserved.

An algorithm to find all palindromic sequences in proteins

A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.

Steric and Electronic Interactions Controlling the cis/trans Isomer Equilibrium at X-Pro Tertiary Amide Motifs in Solution

A systematic understanding of the noncovalent interactions that influence the structures of the cis conformers and the equilibrium between the cis and the trans conformers, of the X-Pro tertiary amide motifs, is presented based on analyses of H-1-, C-13-NMR and FTIR absorption spectra of two sets of homologous peptides, X-Pro-Aib-OMe and X-Pro-NH-Me (where X is acetyl, propionyl, isobutyryl and pivaloyl), in solvents of varying polarities. First, this work shows that the cis conformers of any X-Pro tertiary amide motif, including Piv-Pro, are accessible in the new motifs X-Pro-Aib-OMe, in solution. These conformers are uniquely observable by FTIR spectroscopy at ambient temperatures and by NMR spectroscopy from temperatures as high as 273 K. This is made possible by the persistent presence of n(i-1i)* interactions at Aib, which also influence the disappearance of steric effects at these cis X-Pro rotamers. Second, contrary to conventional understanding, the energy contribution of steric effects to the cis/trans equilibrium at the X-Pro motifs is found to be nonvariant (0.54 +/- 0.02 kcal/mol) with increase in steric bulk on the X group. Third, the current studies provide direct evidence for the weak intramolecular interactions namely the n(i-1i)*, the N-Pro center dot center dot center dot Hi+1 (C(5)a), and the C-7 hydrogen bond that operate and influence the structures, stabilities, and dynamics between different conformational states of X-Pro tertiary amide motifs. NMR and IR spectral data suggest that the cis conformers of X-Pro motifs are ensembles of short-lived rotamers about the C-X-N-Pro bond. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 66-77, 2014.

P3F92-: An All-Pseudo-pi* 2 pi-Aromatic

A qualitative MO analysis suggests (PH3)(3)(2-) as a candidate for an all-pseudo-pi* 2 pi-aromatic; however computational studies rule out its existence. Fluorine substitution which increases the contribution of p orbitals on P in the pseudo-pi* MO makes (PF3)(3)(2-) a minimum and an aromatic. The 2 pi aromaticity arising from the bonding combination of the three pseudo-pi* fragment MOs is comparable to that in C3O32- and is another example for the analogy between CO and PF3. The dianion (PF3)(3)(2-) forms the first example of a three-membered ring with all the vertices constituted by pentacoordinate phosphorus. The ability of PF3 to form the all-pseudo-pi* 2 pi-aromatic system is not shared by the heavier analogues, AsF3 and SbF3.

Conformational Diversity in Contryphans from Conus Venom: cis-trans Isomerisation and Aromatic/Proline Interactions in the 23-Membered Ring of a 7-Residue Peptide Disulfide Loop

Conformational diversity or shapeshifting in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCV(D)LYPWC* (In936) and Conus loroisii, GCP(D)WDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds.