Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

Benzene carboxylic acids and Benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by H-1, C-13 and N-15 NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations. (C) 2012 Elsevier B.V. All rights reserved.

Repertoire of Protein Kinases Encoded in the Genome of Takifugu rubripes

Takifugu rubripes is teleost fish widely used in comparative genomics to understand the human system better due to its similarities both in number of genes and structure of genes. In this work we survey the fugu genome, and, using sensitive computational approaches, we identify the repertoire of putative protein kinases and classify them into groups and subfamilies. The fugu genome encodes 519 protein kinase-like sequences and this number of putative protein kinases is comparable closely to that of human. However, in spite of its similarities to human kinases at the group level, there are differences at the subfamily level as noted in the case of KIS and DYRK subfamilies which contribute to differences which are specific to the adaptation of the organism. Also, certain unique domain combination of galectin domain and YkA domain suggests alternate mechanisms for immune response and binding to lipoproteins. Lastly, an overall similarity with the MAPK pathway of humans suggests its importance to understand signaling mechanisms in humans. Overall the fugu serves as a good model organism to understand roles of human kinases as far as kinases such as LRRK and IRAK and their associated pathways are concerned.

Non-monotonic, distance-dependent relaxation of water in reverse micelles: Propagation of surface induced frustration along hydrogen bond networks

Layer-wise, distance-dependent orientational relaxation of water confined in reverse micelles (RM) is studied using theoretical and computational tools. We use both a newly constructed ``spins on a ring'' (SOR) Ising-type model (with Shore-Zwanzig rotational dynamics) and atomistic simulations with explicit water. Our study explores the effect of reverse micelle size and role of intermolecular correlations, compromised by the presence of a highly polar surface, on the distance (from the interface) dependence of water relaxation. The ``spins on a ring'' model can capture some aspects of distance dependence of relaxation, such as acceleration of orientational relaxation at intermediate layers. In atomistic simulations, layer-wise decomposition of hydrogen bond formation pattern clearly reveals that hydrogen bond arrangement of water at a certain distance away from the surface can remain frustrated due to the interaction with the polar surface head groups. This layer-wise analysis also reveals the presence of a non-monotonic slow relaxation component which can be attributed to this frustration effect and which is accentuated in small to intermediate size RMs. For large size RMs, the long time component decreases monotonically from the interface to the interior of the RMs with slowest relaxation observed at the interface. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4732095]

Kinetics of adsorption of methylene blue and rhodamine 6G on acrylic acid-based superabsorbents

Superabsorbent polymers (SAPs) of acrylic acid, sodium acrylate, and acrylamide (AM), crosslinked with ethylene glycol dimethacrylate, were synthesized by inverse suspension polymerization. The equilibrium swelling capacities of the SAPs were determined and these decreased with increasing AM content. The adsorption of the two cationic dyes, methylene blue and rhodamine 6G, on the dry as well as equilibrium swollen SAPs was investigated. The amount of the dye adsorbed at equilibrium per unit weight of the SAPs and the rate constants of adsorption were determined. The amount of the dye adsorbed at equilibrium by the SAPs decreased with increasing mol % of AM in the SAPs. The amount of the dye adsorbed at equilibrium was almost equal for the dry and equilibrium swollen SAPs. However, the equilibrium swollen SAPs adsorbed dyes at a higher rate than the dry SAPs. The higher rate of adsorption was attributed to the availability of all the anionic groups present in the fully elongated conformation of the SAPs in the equilibrium swollen state. The effect of initial dye concentration on the adsorption was also investigated and the adsorption was described by Langmuir adsorption isotherms. (C) 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012

Simultaneous refolding and purification of recombinant proteins by macro-(affinity ligand) facilitated three-phase partitioning

A strategy called macro-(affinity ligand) facilitated three-phase partitioning (MLFTPP) is described for refolding of a diverse set of recombinant proteins starting from the solubilized inclusion bodies. It essentially consists of: (i) binding of the protein with a suitable smart polymer and (ii) precipitating the polymer-protein complex as an interfacial layer by mixing in a suitable amount of ammonium sulfate and t-butanol. Smart polymers are stimuli-responsive polymers that become insoluble on the application of a suitable stimulus (e.g., a change in the temperature, pH, or concentration of a chemical species such as Ca 2+ or K +). The MLFTPP process required approximately 10min, and the refolded proteins were found to be homogeneous on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The folded proteins were characterized by fluorescence emission spectroscopy, circular dichroism spectroscopy, biological activity, melting temperature, and surface hydrophobicity measurements by 8-anilino-1-naphthalenesulfonate fluorescence. Two refolded antibody fragments were also characterized by measuring K D by Biacore by using immobilized HIV-1 gp120. The data demonstrate that MLFTPP is a rapid and convenient procedure for refolding a variety of proteins from inclusion bodies at high concentration. Although establishing the generic nature of the approach would require wider trials by different groups, its success with the diverse kinds of proteins tried so far appears to be promising.

High resolution methyl selective C-13-NMR of proteins in solution and solid state

New C-13-detected NMR experiments have been devised for molecules in solution and solid state, which provide chemical shift correlations of methyl groups with high resolution, selectivity and sensitivity. The experiments achieve selective methyl detection by exploiting the one bond J-coupling between the C-13-methyl nucleus and its directly attached C-13 spin in a molecule. In proteins such correlations edit the C-13-resonances of different methyl containing residues into distinct spectral regions yielding a high resolution spectrum. This has a range of applications as exemplified for different systems such as large proteins, intrinsically disordered polypeptides and proteins with a paramagnetic centre.

Approaches to alpha-amino acids via rearrangement to electron-deficient nitrogen: Beckmann and Hofmann rearrangements of appropriate carboxyl-protected substrates

The titled approaches were effected with various 2-substituted benzoylacetic acid oximes 3 (Beckmann) and 2-substituted malonamic acids 9 (Hofmann), their carboxyl groups being masked as a 2,4,10-trioxaadamantane unit (an orthoacetate). The oxime mesylates have been rearranged with basic Al2O3 in refluxing CHCl3, and the malonamic acids with phenyliodoso acetate and KOH/MeOH. Both routes are characterized by excellent overall yields. Structure confirmation of final products was conducted with X-ray diffraction in selected cases. The final N-benzoyl and N-(methoxycarbonyl) products are alpha-amino acids with both carboxyl and amino protection; hence, they are of great interest in peptide synthesis.

Retrobiosynthetic Approach Delineates the Biosynthetic Pathway and the Structure of the Acyl Chain of Mycobacterial Glycopeptidolipids

Glycopeptidolipids (GPLs) are dominant cell surface molecules present in several non-tuberculous and opportunistic mycobacterial species. GPLs from Mycobacterium smegmatis are composed of a lipopeptide core unit consisting of a modified C-26-C-34 fatty acyl chain that is linked to a tetrapeptide (Phe-Thr-Ala-alaninol). The hydroxyl groups of threonine and terminal alaninol are further modified by glycosylations. Although chemical structures have been reported for 16 GPLs from diverse mycobacteria, there is still ambiguity in identifying the exact position of the hydroxyl group on the fatty acyl chain. Moreover, the enzymes involved in the biosynthesis of the fatty acyl component are unknown. In this study we show that a bimodular polyketide synthase in conjunction with a fatty acyl-AMP ligase dictates the synthesis of fatty acyl chain of GPL. Based on genetic, biochemical, and structural investigations, we determine that the hydroxyl group is present at the C-5 position of the fatty acyl component. Our retrobiosynthetic approach has provided a means to understand the biosynthesis of GPLs and also resolve the long-standing debate on the accurate structure of mycobacterial GPLs.

A versatile resolving agent for diffusion edited separation of enantiomers, complex mixtures and constitutional isomers

The study is the first report of the utilization of a crown ether as a new and versatile resolving agent for the diffusion edited separation of enantiomers, complex mixtures and constitutional isomers. As a consequence of different binding affinities of enantiomers of a chiral molecule and individual components of the complex mixtures with the crown ether, the molecules diffuse at different rates. The enhanced separation achieved due to matrix assisted diffusion permitted their separation in the diffusion dimension. The generality and wide utility of the new resolving agent and the methodology are demonstrated on diverse examples, such as an organic chiral molecule, constitutional isomers and complex mixture of molecules possessing different functional groups that possess nearly identical molecular weights.

Meso-Structured Silica-Nafion Hybrid Membranes for Direct Methanol Fuel Cells

A series of novel organic-inorganic hybrid membranes have been prepared employing Nafion and acid-functionalized meso-structured molecular sieves (MMS) with varying structures and surface area. Acid-functionalized silica nanopowder of surface area 60 m(2)/g, silica meso-structured cellular foam (MSU-F) of surface area 470 m(2)/g and silica meso-structured hexagonal frame network (MCM-41) of surface area 900 m(2)/g have been employed as potential filler materials to form hybrid membranes with Nafion framework. The structural behavior, water uptake, proton conductivity and methanol permeability of these hybrid membranes have been investigated. DMFCs employing Nafion-silica MSU-F and Nafion-silica MCM-41 hybrid membranes deliver peak-power densities of 127 mW/cm(2) and 100 mW/cm(2), respectively; while a peak-power density of only 48 mW/cm(2) is obtained with the DMFC employing pristine recast Nafion membrane under identical operating conditions. The aforesaid characteristics of the hybrid membranes could be exclusively attributed to the presence of pendant sulfonic acid groups in the filler, which provide fairly continuous proton-conducting pathways between filler and matrix in the hybrid membranes facilitating proton transport without any trade-off between its proton conductivity and methanol crossover. (C) 2012 The Electrochemical Society. DOI: 10.1149/2.036211jes] All rights reserved.

3-MANIFOLD GROUPS, KÄHLER GROUPS AND COMPLEX SURFACES

Let G be a Kahler group admitting a short exact sequence 1 -> N -> G -> Q -> 1 where N is finitely generated. (i) Then Q cannot be non-nilpotent solvable. (ii) Suppose in addition that Q satisfies one of the following: (a) Q admits a discrete faithful non-elementary action on H-n for some n >= 2. (b) Q admits a discrete faithful non-elementary minimal action on a simplicial tree with more than two ends. (c) Q admits a (strong-stable) cut R such that the intersection of all conjugates of R is trivial. Then G is virtually a surface group. It follows that if Q is infinite, not virtually cyclic, and is the fundamental group of some closed 3-manifold, then Q contains as a finite index subgroup either a finite index subgroup of the three-dimensional Heisenberg group or the fundamental group of the Cartesian product of a closed oriented surface of positive genus and the circle. As a corollary, we obtain a new proof of a theorem of Dimca and Suciu in Which 3-manifold groups are Kahler groups? J. Eur. Math. Soc. 11 (2009) 521-528] by taking N to be the trivial group. If instead, G is the fundamental group of a compact complex surface, and N is finitely presented, then we show that Q must contain the fundamental group of a Seifert-fibered 3-manifold as a finite index subgroup, and G contains as a finite index subgroup the fundamental group of an elliptic fibration. We also give an example showing that the relation of quasi-isometry does not preserve Kahler groups. This gives a negative answer to a question of Gromov which asks whether Kahler groups can be characterized by their asymptotic geometry.

Adsorption on Edge-Functionalized Bilayer Graphene Nanoribbons: Assessing the Role of Functional Groups in Methane Uptake

A combination of ab initio and classical Monte Carlo simulations is used to investigate the effects of functional groups on methane binding. Using Moller-Plesset (MP2) calculations, we obtain the binding energies for benzene functionalized with NH2, OH, CH3, COOH, and H2PO3 and identify the methane binding sites. In all cases, the preferred binding sites are located above the benzene plane in the vicinity of the benzene carbon atom attached to the functional group. Functional groups enhance methane binding relative to benzene (-6.39 kJ/mol), with the largest enhancement observed for H2PO3 (-8.37 kJ/mol) followed by COOH and CH3 (-7.77 kJ/mol). Adsorption isotherms are obtained for edge-functionalized bilayer graphene nanoribbons using grand canonical Monte Carlo simulations with a five-site methane model. Adsorbed excess and heats of adsorption for pressures up to 40 bar and 298 K are obtained with functional group concentrations ranging from 3.125 to 6.25 mol 96 for graphene edges functionalized with OH, NH2, and COOH. The functional groups are found to act as preferred adsorption sites, and in the case of COOH the local methane density in the vicinity of the functional group is found to exceed that of bare graphene. The largest enhancement of 44.5% in the methane excess adsorbed is observed for COOH-functionalized nanoribbons when compared to H terminated ribbons. The corresponding enhancements for OH- and NH2-functionalized ribbons are 10.5% and 3.7%, respectively. The excess adsorption across functional groups reflects the trends observed in the binding energies from MP2 calculations. Our study reveals that specific site functionalization can have a significant effect on the local adsorption characteristics and can be used as a design strategy to tailor materials with enhanced methane storage capacity.

Orthogonal biofunctionalization of magnetic nanoparticles via ``clickable'' poly(ethylene glycol) silanes: a ``universal ligand'' strategy to design stealth and target-specific nanocarriers

The present work demonstrates a novel strategy to synthesize orthogonally bio-engineered magnetonanohybrids (MNPs) through the design of versatile, biocompatible linkers whose structure includes: (i) a robust anchor to bind with metal-oxide surfaces; (ii) tailored surface groups to act as spacers and (iii) a general method to implement orthogonal functionalizations of the substrate via ``click chemistry''. Ligands that possess the synthetic generality of features (i)-(iii) are categorized as ``universal ligands''. Herein, we report the synthesis of a novel, azido-terminated poly(ethylene glycol) (PEG) silane that can easily self-assemble on MNPs through hetero-condensation between surface hydroxyl groups and the silane end of the ligand, and simultaneously provide multiple clickable sites for high density, chemoselective bio-conjugation. To establish the universal-ligand-strategy, we clicked alkyl-functionalized folate onto the surface of PEGylated MNPs. By further integrating a near-infrared fluorescent (NIRF) marker (Alexa-Fluor 647) with MNPs, we demonstrated their folate-receptor mediated internalization inside cancer cells and subsequent translocation into lysosomes and mitochondria. Ex vivo NIRF imaging established that the azido-PEG-silane developed in course of the study can effectively reduce the sequestration of MNPs by macrophage organs (viz. liver and spleen). These folate-PEG-MNPs were not only stealth and noncytotoxic but their dual optical and magnetic properties aided in tracking their whereabouts through combined magnetic resonance and optical imaging. Together, these results provided a strong motivation for the future use of the ``universal ligand'' strategy towards development of ``smart'' nanohybrids for theragnostic applications.

Revisiting Riesz transforms on Heisenberg groups

We characterise higher order Riesz transforms on the Heisenberg group and also show that they satisfy dimension-free bounds under some assumptions on the multipliers. Using transference theorems, we deduce boundedness theorems for Riesz transforms on the reduced Heisenberg group and hence also for the Riesz transforms associated to multiple Hermite and Laguerre expansions.

NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded beta-Sheet Peptide

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel beta-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-(LFVPPLFV)-P-D-P-L-OMe (peptide 1) favors the beta-hairpin conformation nucleated by the type II' beta-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded beta-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C-alpha-C-beta(chi(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.