C-11/C-9 Helices in Crystals of alpha beta Hybrid Peptides and Switching Structures between Helix Types by Variation in the alpha-Residue

Close-packed helices with mixed hydrogen bond directionality are unprecedented in the structural chemistry of alpha-polypeptides. While NMR studies in solution state provide strong evidence for the occurrence of mixed helices in (beta beta)(n) and (alpha beta)(n) sequences, limited information is currently available in crystals. The peptide structures presented show the occurrence of C-11/C-9 helices in (alpha beta)(n) peptides. Transitions between C-11 and C-11/C-9 helices are observed upon varying the alpha-amino acid residue.

sigma-Ferrier rearrangement of carbohydrate derived vinylcyclopropanes: a facile approach to oxepane analogs

This article presents our work on the sigma-Ferrier ring-expansion of carbohydrate derived vinylcyclopropanes (VCPs) under electrophilic conditions mediated by chloramine-T and a phase-transfer catalyst. The present work serves as the first example on the studies of the reactivity of carbohydrate VCPs towards the synthesis of densely functionalized oxepane analogues. The work elaborates on a reasonable mechanism for the product formation and our observations on the diastereoselectivity based on control experiments and gas-phase calculations. (C) 2014 Elsevier Ltd. All rights reserved.

Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

MicroRNA-125a Reduces Proliferation and Invasion of Oral Squamous Cell Carcinoma Cells by Targeting Estrogen-related Receptor alpha IMPLICATIONS FOR CANCER THERAPEUTICS

Estrogen-related receptor (ESRRA) functions as a transcription factor and regulates the expression of several genes, such as WNT11 and OPN. Up-regulation of ESRRA has been reported in several cancers. However, the mechanism underlying its up-regulation is unclear. Furthermore, the reports regarding the role and regulation of ESRRA in oral squamous cell carcinoma (OSCC) are completely lacking. Here, we show that tumor suppressor miR-125a directly binds to the 3UTR of ESRRA and represses its expression. Overexpression of miR-125a in OSCC cells drastically reduced the level of ESRRA, decreased cell proliferation, and increased apoptosis. Conversely, the delivery of an miR-125a inhibitor to these cells drastically increased the level of ESRRA, increased cell proliferation, and decreased apoptosis. miR-125a-mediated down-regulation of ESRRA impaired anchorage-independent colony formation and invasion of OSCC cells. Reduced cell proliferation and increased apoptosis of OSCC cells were dependent on the presence of the 3UTR in ESRRA. The delivery of an miR-125a mimic to OSCC cells resulted in marked regression of xenografts in nude mice, whereas the delivery of an miR-125a inhibitor to OSCC cells resulted in a significant increase of xenografts and abrogated the tumor suppressor function of miR-125a. We observed an inverse correlation between the expression levels of miR-125a and ESRRA in OSCC samples. In summary, up-regulation of ESRRA due to down-regulation of miR-125a is not only a novel mechanism for its up-regulation in OSCC, but decreasing the level of ESRRA by using a synthetic miR-125a mimic may have an important role in therapeutic intervention of OSCC and other cancers.

Mixture of Fuels Approach for the Synthesis of SrFeO3-delta Nanocatalyst and Its Impact on the Catalytic Reduction of Nitrobenzene

A modified solution combustion approach was applied in the synthesis of nanosize SrFeO3-delta (SFO) using single as well as mixture of citric acid, oxalic acid, and glycine as fuels with corresponding metal nitrates as precursors. The synthesized and calcined powders were characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), thermogravimetric analysis and derivative thermogravimetric analysis (TG-DTG), scanning electron microscopy, transmission electron microscopy, N-2 physisorption methods, and acidic strength by n-butyl amine titration methods. The FT-IR spectra show the lower-frequency band at 599 cm(-1) corresponds to metal-oxygen bond (possible Fe-O stretching frequencies) vibrations for the perovskite-structure compound. TG-DTG confirms the formation temperature of SFO ranging between 850-900 degrees C. XRD results reveal that the use of mixture of fuels in the preparation has effect on the crystallite size of the resultant compound. The average particle size of the samples prepared from single fuels as determined from XRD was similar to 50-35 nm, whereas for samples obtained from mixture of fuels, particles with a size of 30-25 nm were obtained. Specifically, the combination of mixture of fuels for the synthesis of SFO catalysts prevents agglomeration of the particles, which in turn leads to decrease in crystallite size and increase in the surface area of the catalysts. It was also observed that the present approach also impacted the catalytic activity of the SFO in the catalytic reduction of nitrobenzene to azoxybenzene.

Observation of a reversible isomorphous phase transition and an interplay of ``sigma-holes'' and ``pi-holes'' in Fmoc-Leu-psiCH2-NCS]

Fmoc-Leu-psiCH2NCS] undergoes a reversible isomorphous phase transition upon cooling. The crystal structure at 100 K displays a short N=C=S center dot center dot center dot N=C=S intermolecular interaction, which has been characterized based on experimental charge density analysis, as a stabilizing interaction with both sigma-holes and pi-holes acting cooperatively.

Photoluminescence, photocatalysis and Judd-Ofelt analysis of Eu3+-activated layered BiOCl phosphors

Eu3+-activated layered BiOCl phosphors were synthesized by the conventional solid-state method at relatively low temperature and shorter duration (400 degrees C for 1 h). All the samples were crystallized in the tetragonal structure with the space group P4/nmm (no. 129). Field emission scanning electron microscopy (FE-SEM) studies confirmed the plate-like morphology. Photoluminescence spectra exhibit characteristic luminescent D-5(0) -> F-7(J) (J = 0-4) intra-4f shell Eu3+ ion transitions. The electric dipole transition located at 620 nm (D-5(0) -> F-7(2)) was stronger than the magnetic dipole transition located at 594 nm (D-5(0) -> F-7(1)). The evaluated Commission International de l'Eclairage (CIE) color coordinates of Eu3+-activated BiOCl phosphors were close to the commercial Y2O3:Eu3+ and Y2O2S:Eu3+ red phosphors. Intensity parameters (Omega(2), Omega(4)) and various radiative properties such as transition probability (A(tot)), radiative lifetime (tau(rad)), stimulated emission cross-section (sigma(e)), gain bandwidth (sigma(e) x Delta lambda(eff)) and optical gain (sigma(e) x tau(rad)) were calculated using the Judd-Ofelt theory. The experimental decay curves of the D-5(0) level in Eu3+-activated BiOCl have a single exponential profile. In comparison with other Eu3+ doped materials, Eu3+-activated BiOCl phosphors have a long lifetime (tau(exp)), low non-radiative relaxation rate (W-NR), high quantum efficiency (eta) and better optical gain (sigma(e) x tau(rad)). The determined radiative properties revealed the usefulness of Eu3+-activated BiOCl in developing red lasers as well as optical display devices. Further, these samples showed efficient photocatalytic activity for the degradation of rhodamine B (RhB) dye under visible light irradiation. These photocatalysts are useful for the removal of toxic and non-biodegradable organic pollutants in water.

Oxygen potentials and phase equilibria in the system Ca-Co-O and thermodynamic properties of Ca3Co2O6 and Ca3Co4O9.163

Oxygen potentials established by the equilibrium between three condensed phases, CaOss+CoOss+ Ca3Co2O6 and CoOss+Ca3Co2O6+Ca3CO3.93+O-alpha(9.36-delta), are measured as a function of temperature using solid-state electrochemical cells incorporating yttria-stabilized zirconia as the electrolyte and pure oxygen as the reference electrode. Cation non-stoichiometry and oxygen non-stoichiometry in Ca3Co3.93+alpha O9.36-delta are determined using different techniques under defined conditions. Decomposition temperatures and thermodynamic properties of Ca3Co2O6 and Ca3Co4O9.163 are calculated from the results. The standard entropy and enthalpy of formation of Ca3Co2O6 at 298.15 K are evaluated. Using thermodynamic data from this study and auxiliary information from the literature, phase diagram for the ternary system Ca-Co-O is computed. Isothermal sections at representative temperatures are displayed to demonstrate the evolution of phase relations with temperature. (C) 2014 Elsevier Inc. All rights reserved.

Limiting two-Higgs-doublet models

We update the constraints on two-Higgs-doublet models (2HDMs) focusing on the parameter space relevant to explain the present muon g - 2 anomaly, Delta alpha(mu), in four different types of models, type I, II, ``lepton specific'' (or X) and ``flipped'' (or Y). We show that the strong constraints provided by the electroweak precision data on the mass of the pseudoscalar Higgs, whose contribution may account for Delta alpha(mu), are evaded in regions where the charged scalar is degenerate with the heavy neutral one and the mixing angles alpha and beta satisfy the Standard Model limit beta - alpha approximate to pi/2. We combine theoretical constraints from vacuum stability and perturbativity with direct and indirect bounds arising from collider and B physics. Possible future constraints from the electron g - 2 are also considered. If the 126 GeV resonance discovered at the LHC is interpreted as the light CP-even Higgs boson of the 2HDM, we find that only models of type X can satisfy all the considered theoretical and experimental constraints.

An encaged sigma* orbital in 3-methoxy-2,4,10-trioxaadamantane. Preferred exo-anomeric effect as revealed by the crystal structure

In the titled tricyclic orthocarbonate derivative, the three endocyclic C-O bonds are longer than the exo-cyclic C-O bond (similar to 4.40 angstrom vs. similar to 1.37 angstrom). This indicates an anomeric-type interaction between the two electron lone pairs on the exocyclic oxygen atom and the antibonding orbitals of the two antiperiplanar endocyclic C-O bonds. The remaining endocyclic C-O bond - marginally shorter than the other two apparently adds to this effect. Intriguingly, the antibonding orbital of the exocyclic C-O bond extends into the interior of the adamantyl cage, and is stereoelectronically prevented from overlapping with any of the six adjacent lone pairs. The results also seem to indicate a preference for interaction between a single donor oxygen atom and multiple acceptor antibonding orbitals rather than vice versa. The results add insightfully to the substantial body of evidence favouring the antiperiplanar lone pair hypothesis (ALPH). (C) 2014 Elsevier B.V. All rights reserved.

Diurnal and seasonal variation of mixing ratio and delta C-13 of air CO2 observed at an urban station Bangalore, India

We present here observations on diurnal and seasonal variation of mixing ratio and delta C-13 of air CO2, from an urban station-Bangalore (BLR), India, monitored between October 2008 and December 2011. On a diurnal scale, higher mixing ratio with depleted delta C-13 of air CO2 was found for the samples collected during early morning compared to the samples collected during late afternoon. On a seasonal scale, mixing ratio was found to be higher for dry summer months (April-May) and lower for southwest monsoon months (June-July). The maximum enrichment in delta C-13 of air CO2 (-8.04 +/- 0.02aEuro degrees) was seen in October, then delta C-13 started depleting and maximum depletion (-9.31 +/- 0.07aEuro degrees) was observed during dry summer months. Immediately after that an increasing trend in delta C-13 was monitored coincidental with the advancement of southwest monsoon months and maximum enrichment was seen again in October. Although a similar pattern in seasonal variation was observed for the three consecutive years, the dry summer months of 2011 captured distinctly lower amplitude in both the mixing ratio and delta C-13 of air CO2 compared to the dry summer months of 2009 and 2010. This was explained with reduced biomass burning and increased productivity associated with prominent La Nina condition. While compared with the observations from the nearest coastal and open ocean stations-Cabo de Rama (CRI) and Seychelles (SEY), BLR being located within an urban region captured higher amplitude of seasonal variation. The average delta C-13 value of the end member source CO2 was identified based on both diurnal and seasonal scale variation. The delta C-13 value of source CO2 (-24.9 +/- 3aEuro degrees) determined based on diurnal variation was found to differ drastically from the source value (-14.6 +/- 0.7aEuro degrees) identified based on seasonal scale variation. The source CO2 identified based on diurnal variation incorporated both early morning and late afternoon sample; whereas, the source CO2 identified based on seasonal variation included only afternoon samples. Thus, it is evident from the study that sampling timing is one of the important factors while characterizing the composition of end member source CO2 for a particular station. The difference in delta C-13 value of source CO2 obtained based on both diurnal and seasonal variation might be due to possible contribution from cement industry along with fossil fuel / biomass burning as predominant sources for the station along with differential meteorological conditions prevailed.

Synthesis of Eu3+-activated BiOF and BiOBr phosphors: photoluminescence, Judd-Ofelt analysis and photocatalytic properties

A series of Bi1-xEuxOX (X = F and Br; x = 0, 0.01, 0.03 and 0.05) phosphors were synthesized at relatively low temperature and short duration (500 degrees C, 1 h). Rietveld refinement results verified that all the compounds were crystallized in the tetragonal structure with space group P4/nmm (no. 129). Photoluminescence spectra exhibit characteristic luminescence D-5(0) -> F-7(J) (J = 0-4) intra-4f shell Eu3+ ion transitions. The magnetic dipole (D-5(0) -> F-7(1)) transition dominates the emission of BiOF:Eu3+, while the electric dipole (D-5(0) -> F-7(2)) peak was stronger in BiOBr:Eu3+ phosphors. The evaluated CIE color coordinates for Bi0.95Eu0.05OBr (0.632, 0.358) are close to the commercial Y2O3:Eu3+ (0.645, 0.347) and Y2O2S:Eu3+ (0.647, 0.343) red phosphors. Intensity parameters (Omega(2), Omega(4)) and various radiative properties such as transition rates (A), branching ratios (beta), stimulated emission cross-section (sigma(e)), gain bandwidth (sigma(e) x Delta lambda(eff)) and optical gain (sigma(e) x tau) were calculated using the Judd-Ofelt theory. It was observed that BiOBr:Eu3+ phosphors have a long lifetime (tau) and better optical gain (sigma(e) x tau) as compared to reported Eu3+ doped materials. Furthermore, these compounds exhibit excellent photocatalytic activity for the degradation of rhodamine B dye under visible light irradiation. The determined radiative properties and photocatalytic results revealed that BiOBr:Eu3+ phosphors have potential applications in energy and environmental remedies, such as to develop red phosphors for white light-emitting diodes, red lasers and to remove toxic organic industrial effluents.

alpha-Tocopherol derived lipid dimers as efficient gene transfection agents. Mechanistic insights into lipoplex internalization and therapeutic induction of apoptotic activity

In this report, we present cationic dimeric (gemini) lipids for significant plasmid DNA (pDNA) delivery to different cell lines without any marked toxicity in the presence of serum. Six gemini lipids based on alpha-tocopherol were synthesized, which differed in their spacer chain lengths. Each of these gemini lipids mixed with a helper lipid, 1,2-dioleoyl phosphatidyl ethanolamine (DOPE), was capable of forming stable aqueous suspensions. These co-liposomal systems were examined for their potential to transfect pEGFP-C3 plasmid DNA into nine cell lines of different origins. The transfection efficacies noticed in terms of EGFP expression levels using flow cytometry were well corroborated using independent fluorescence microscopy studies. Significant EGFP expression levels were reported using the gemini co-liposomes, which counted significantly better than one well known commercial formulation, Lipofectamine 2000 (L2 K). Transfection efficacies were also analyzed in terms of the degree of intracellular delivery of labeled plasmid DNA (pDNA) using confocal microscopy, which revealed an efficient internalization in the presence of serum. The cell viability assays performed using optimized formulations demonstrated no significant toxicity towards any of the cell lines used in the study. We also had a look at the lipoplex internalization pathway to profile the uptake characteristics. A caveolae/lipid raft route was attributed to their excellent gene transfection capabilities. The study was further advanced by using a therapeutic p53-EGFP-C3 plasmid and the apoptotic activity was observed using FACS and growth inhibition assay.

Implication of a sigma-Methane Complex en Route to Elimination of Methane from a Ruthenium Complex: An Experimental and Theoretical Investigation

The five-coordinated 16-electron complex Ru(Me)(dppe)(2)]OTf] (3) undergoes methane elimination at room temperature to afford the ortho-metalated species (dppe){(C6H5)(C6H4)PCH2CH2P(C6H5)(2)}Ru]OTf] (7). Methane elimination, monitored using NMR spectroscopy, revealed no intermediate throughout the reaction. The NOE between Ru-Me protons and ortho phenyl protons and an agostic interaction trans to the methyl group were found in complex 3 by NMR spectroscopy, which form the basis for three plausible pathways for methane elimination and ortho metalation: pathway I (through spatial interaction), pathway II (through oxidative addition and reductive elimination), and pathway III (through agostic interaction). Methane elimination from complex 3 via pathway I was discounted, since it involves interactions through space and not through bonds. Moreover, the calculated energy barrier for the pathway I transition state was quite high (71.3 kcal/mol), which also indicates that this pathway is very unlikely. Furthermore, no spectroscopic evidence for oxidatively added seven-coordinated Ru(IV) species was found and the computed energy barrier of the transition state for pathway II was moderately high (41.1 kcal/mol), which suggests that this cannot be the right pathway for methane elimination and ortho-metalation of complex 3. On the other hand, indirect evidence in the form of chemical reactions point to the most plausible pathway for methane elimination, pathway III, via the intermediacy of a sigma-CH4 complex that could not be found spectroscopically. DFT calculations at several levels on this pathway showed an initial low-barrier rearrangement through TS1 to a square-pyramidal intermediate wherein methyl and agostic C-H are cis to each other. Migration of hydrogen from agostic C-H and elimination of methane proceed through the transition state TS2, which retains a weak metal-H bonding through most parts of the reaction coordinate. Upon comparison of all three pathways, pathway III was found to be the most likely for methane elimination and ortho-metalation of complex 3.

The Self-Association of Graphane Is Driven by London Dispersion and Enhanced Orbital Interactions

We investigated the nature of the cohesive energy between graphane sheets via multiple CH center dot center dot center dot HC interactions, using density functional theory (DFT) including dispersion correction (Grimmes D3 approach) computations of n]graphane sigma dimers (n = 6-73). For comparison, we also evaluated the binding between graphene sheets that display prototypical pi/pi interactions. The results were analyzed using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory. BLW interprets the intermolecular interactions in terms of frozen interaction energy (Delta E-F) composed of electrostatic and Pauli repulsion interactions, polarization (Delta E-pol), charge-transfer interaction (Delta E-CT), and dispersion effects (Delta E-disp). The BLW analysis reveals that the cohesive energy between graphane sheets is dominated by two stabilizing effects, namely intermolecular London dispersion and two-way charge transfer energy due to the sigma CH -> sigma*(HC) interactions. The shift of the electron density around the nonpolar covalent C-H bonds involved in the intermolecular interaction decreases the C-H bond lengths uniformly by 0.001 angstrom. The Delta E-CT term, which accounts for similar to 15% of the total binding energy, results in the accumulation of electron density in the interface area between two layers. This accumulated electron density thus acts as an electronic glue for the graphane layers and constitutes an important driving force in the self-association and stability of graphane under ambient conditions. Similarly, the double faced adhesive tape style of charge transfer interactions was also observed among graphene sheets in which it accounts for similar to 18% of the total binding energy. The binding energy between graphane sheets is additive and can be expressed as a sum of CH center dot center dot center dot HC interactions, or as a function of the number of C-H bonds.