On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Photodissociation dynamics of CH2ICl at 222, 236, 266, 280, and-304 nm

Dynamics of I*(P-2(1/2)) formation from CH2ICl dissociation has-been investigated at five different ultraviolet excitation wavelengths, e.g., 222, 236, 266, 280, and similar to304 nm. The quantum yield of I*((2)p(1/2)) production, phi*, has been measured by monitoring nascent I(P-2(3/2)) and I* concentrations using a resonance enhanced multiphoton ionization detection scheme. The measured quantum yield as a function of excitation energy follows the same trend as that of methyl iodide except at 236 run. The photodissociation dynamics of CH2ICl also involves three upper states similar to methyl iodide, and a qualitative correlation diagram has been constructed to account for the observed quantum yield. From the difference in behavior at 236 nm, it appears that the crossing region between the two excited states ((3)Q(0) and (1)Q(1)) is located near the exit valley away from the Franck Condon excitation region. The B- and C-band transitions do not participate in the dynamics, and the perturbation of the methyl iodide states due to Cl-I interaction is relatively weak at the photolysis wavelengths employed in this investigation.

Reactivity ratios for the oxidative copolymerizations of indene with methyl methacrylate and methacrylonitrile

The copolyperoxides of indene with methyl methacrylate and methacrylonitrile have been synthesized by the free-radical-initiated oxidative copolymerization of indene and the monomers. The compositions of copolyperoxides, obtained from H-1 and C-13 NMR spectra, have been utilized to determine the reactivity ratios. The reactivity ratios indicate that the copolyperoxides contain a large proportion of the indene units in random placement. Thermal degradation studies of the copolyperoxides by differential scanning calorimetry and electron-impact mass spectroscopy support alternating peroxide units in the copolyperoxide chain. The energy of activation for thermal degradation suggests that the degradation is controlled by the dissociation of the peroxide (-O-O-) bonds in the copolyperoxide chain. The flexibility of copolyperoxide in terms of glass transition temperature (T-g) has also been examined. (C) 2002 Elsevier Science Ltd. All rights reserved.

Synthesis, properties, and comparative analyses on the chain flexibility of an ultrastable vinyl polyperoxide

The most stable vinyl polyperoxide, namely, poly(indene peroxide) (PINDP), an alternating copolymer of indene and oxygen, was synthesized by the oxidative polymerization of indene. It was characterized by H-1-NMR and C-13-NMR, Fourier transform infrared, differential scanning calorimetry, direct pyrolysis mass spectrometry, and gas chromatography mass spectrometry studies. The overall activation energy for the degradation and the glass-transition temperature of PINDP were 47 kcal/mol and 327 K respectively, which were very high compared to those of other vinyl polyperoxides. (C) 2002 Wiley Periodicals, Inc.

Almost quarter-pinched Kähler metrics and Chern numbers

Given n is an element of Z(+) and epsilon > 0, we prove that there exists delta = delta(epsilon, n) > 0 such that the following holds: If (M(n),g) is a compact Kahler n-manifold whose sectional curvatures K satisfy -1 -delta <= K <= -1/4 and c(I)(M), c(J)(M) are any two Chern numbers of M, then |c(I)(M)/c(J)(M) - c(I)(0)/c(J)(0)| < epsilon, where c(I)(0), c(J)(0) are the corresponding characteristic numbers of a complex hyperbolic space form. It follows that the Mostow-Siu surfaces and the threefolds of Deraux do not admit Kahler metrics with pinching close to 1/4.

Carbothermal reduction and nitridation reaction of SiOx and preoxidized SiOx: Formation of α-Si3N4 fibers

The chemical composition of amorphous SiOx has been analyzed by oxidation studies and is found to be SiO1.7. SiO1.7 appears to be a monophasic amorphous material on the basis of 29Si nuclear magnetic resonance, high resolution electron microscopy, and comparative behavior of a physical mixture of Si and SiO2. Carbothermal reduction and nitridation reactions have been carried out on amorphous SiO1.7 and on amorphous SiO2 obtained from oxidation of SiO1.7. At 1623 K reactions of SiO1.7 lead exclusively to the formation of Si2N2O, while those of SiO2 lead exclusively to the formation of Si3N4. Formation of copious fibers of α-Si3N4 was observed in the latter reaction. It is suggested that the partial pressure of SiO in equilibrium with reduced SiO1.7 and SiO2 during the reaction is the crucial factor that determines the chemistry of the products. The differences in the structures of SiO2 and SiO1.7 have been considered to be the origin of the differences in the SiO partial pressures of the reduction products formed prior to nitridation. The effect of the ratios, C:SiO1.7 and C:SiO2, in the reaction mixture as well as the effect of the temperature on the course of the reactions have also been investigated.

Universality of scaling laws in correlation between velocity and shear stress in turbulent boundary layers

In this study, we analyse simultaneous measurements (at 50 Hz) of velocity at several heights and shear stress at the surface made during the Utah field campaign for the presence of ranges of scales, where distinct scale-to-scale interactions between velocity and shear stress can be identified. We find that our results are similar to those obtained in a previous study [Venugopal et al., 2003] (contrary to the claim in V2003, that the scaling relations might be dependent on Reynolds number) where wind tunnel measurements of velocity and shear stress were analysed. We use a wavelet-based scale-to-scale cross-correlation to detect three ranges of scales of interaction between velocity and shear stress, namely, (a) inertial subrange, where the correlation is negligible; (b) energy production range, where the correlation follows a logarithmic law; and (c) for scales larger than the boundary layer height, the correlation reaches a plateau.

Structural, thermal, and electrical properties of CrSi2

Stoichiometric CrSi2 was prepared by arc melting and compacted by uniaxial hot pressing for property measurements. The crystal structure of CrSi2 was investigated using the powder x-ray diffraction method. From the Rietveld refinement, the lattice parameters were found to be a = 4.427 57 (7) and c = 6.368 04 (11) Å, respectively. The thermal expansion measurement revealed an anisotropic expansion in the temperature range from room temperature 800 K with αa = 14.58×10−6/K, αc = 7.51×10−6/K, and αV = 12.05×10−6/K. The volumetric thermal expansion coefficient shows an anomalous decrease in the temperature range of 450–600 K. The measured electrical resistivity ρ and thermoelectric power S have similar trends with a maxima around 550 K. Thermal conductivity measurements show a monotonic decrease with increasing temperature from a room temperature value of 10 W m−1 K−1. The ZT values increase with temperature and have a maximum value of 0.18 in the temperature range studied. An analysis of the electronic band structure is provided.

Synthesis, Reactivity Studies, Structural Aspects, and Solution Behavior of Half Sandwich Ruthenium(II) N,N `,N `'-Triarylguanidinate Complexes

[(eta(6)-C(10)H(14))RuCl(mu-Cl)](2) (eta(6)-C(10)H(14) = eta(6)-p-cymene) was subjected to a bridge-splitting reaction with N,N',N `'-triarylguanidines, (ArNH)(2)C=NAr, in toluene at ambient temperature to afford [(eta(6)-C(10)H(14))RuCl{kappa(2)(N,N')((ArN)(2)C-N(H)Ar)}] (Ar = C(6)H(4)Me-4 (1), C(6)H(4)(OMe)-2 (2), C(6)H(4)Me-2 (3), and C(6)H(3)Me(2)-2,4 (4)) in high yield with a view aimed at understanding the influence of substituent(s) on the aryl rings of the guanidine upon the solid-state structure, solution behavior, and reactivity pattern of the products. Complexes 1-3 upon reaction with NaN(3) in ethanol at ambient temperature afforded [(eta(6)-C(10)H(14))RuN(3){kappa(2)(N,N')((ArN)(2)C-N(H)Ar)}] (Ar = C(6)H(4)Me-4 (5), C(6)H(4)(OMe)-2 (6), and C(6)H(4)Me-2 (7)) in high yield. [3 + 2] cycloaddition reaction of 5-7 with RO(O)C-C C-C(O)OR (R = Et (DEAD) and Me (DMAD)) (diethylacetylenedicarboxylate, DEAD; dimethylacetylenedicarboxylate, DMAD) in CH(2)Cl(2) at ambient temperature afforded [(eta(6)-C(10)H(14))Ru{N(3)C(2)(C(O)OR)(2)}{kappa(2)(N,N')((ArN)(2) C-N(H)Ar)}center dot xH(2)O (x = 1, R = Et, Ar = C(6)H(4)Me-4 (8 center dot H(2)O); x = 0, R = Me, Ar = C(6)H(4)(OMe)-2 (9), and C(6)H(4)Me-2 (10)) in moderate yield. The molecular structures of 1-6, 8 center dot H(2)O, and 10 were determined by single crystal X-ray diffraction data. The ruthenium atom in the aforementioned complexes revealed pseudo octahedral ``three legged piano stool'' geometry. The guanidinate ligand in 2, 3, and 6 revealed syn-syn conformation and that in 4, and 10 revealed syn-anti conformation, and the conformational difference was rationalized on the basis of subtle differences in the stereochemistry of the coordinated nitrogen atoms caused by the aryl moiety in 3 and 4 or steric overload caused by the substituents around the ruthenium atom in 10. The bonding pattern of the CN(3) unit of the guanidinate ligand in the new complexes was explained by invoking n-pi conjugation involving the interaction of the NHAr/N(coord)Ar lone pair with C=N pi* orbital of the imine unit. Complexes 1, 2, 5, 6, 8 center dot H(2)O, and 9 were shown to exist as a single isomer in solution as revealed by NMR data, and this was ascribed to a fast C-N(H)Ar bond rotation caused by a less bulky aryl moiety in these complexes. In contrast, 3 and 10 were shown to exist as a mixture of three and five isomers in about 1:1:1 and 1.0:1.2:2:7:3.5:6.9 ratios, respectively in solution as revealed by a VT (1)H NMR, (1)H-(1)H COSY in conjunction with DEPT-90 (13)C NMR data measured at 233 K in the case of 3. The multiple number of isomers in solution was ascribed to the restricted C-N(H)(o-tolyl) bond rotation caused by the bulky o-tolyl substituent in 3 or the aforementioned restricted C-NH(o-tolyl) bond rotation as well as the restricted ruthenium-arene(centroid) bond rotation caused by the substituents around the ruthenium atom in 10.

Designed Cyclic Permutants of HIV-1 gp120: Implications for Envelope Trimer Structure and Immunogen Design

Most HIV-1 broadly neutralizing antibodies are directed against the gp120 subunit of the env surface protein. Native env consists of a trimer of gp120-gp41 heterodimers, and in contrast to monomeric gp120, preferentially binds CD4 binding site (CD4bs)-directed neutralizing antibodies over non-neutralizing ones. Some cryo-electron tomography studies have suggested that the V1V2 loop regions of gp120 are located close to the trimer interface. We have therefore designed cyclically permuted variants of gp120 with and without the h-CMP and SUMO2a trimerization domains inserted into the V1V2 loop. h-CMP-V1cyc is one such variant in which residues 153 and 142 are the N- and C-terminal residues, respectively, of cyclically permuted gp120 and h-CMP is fused to the N-terminus. This molecule forms a trimer under native conditions and binds CD4 and the neutralizing CD4bs antibodies b12 with significantly higher affinity than wild-type gp120. It binds non-neutralizing CD4bs antibody F105 with lower affinity than gp120. A similar derivative, h-CMP-V1cycl, bound the V1V2 loop-directed broadly neutralizing antibodies PG9 and PG16 with similar to 20-fold higher affinity than wild-type JRCSF gp120. These cyclic permutants of gp120 are properly folded and are potential immunogens. The data also support env models in which the V1V2 loops are proximal to the trimer interface.

Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.

Dynamic Internal Cavities of Dendrimers as Constrained Media. A Study of Photochemical Isomerizations of Stilbene and Azobenzene Using Poly(alkyl aryl ether) Dendrimers

Dendritic rnicroenvironments defined by dynamic internal cavities of a dendrimer were probed through geometric isomerization of stilbene and azobenzene. A third-generation poly(alkyl aryl ether) dendrimer with hydrophilic exterior and hydrophobic interior was used as a reaction cavity in aqueous medium. The dynamic inner cavity sizes were varied by utilizing alkyl linkers that connect the branch junctures from ethyl to n-pentyl moiety (C(2)G(3)-C(5)G(3)). Dendrimers constituted with n-pentyl linker were found to afford higher solubilities of stilbene and azobenzene. Direct irradiation of trans-stilbene showed that C(5)G(3) and C(4)G(3) dendrimers afforded considerable phenanthrene formation, in addition to cis-stilbene, whereas C(3)G(3) and C(2)G(3) gave only cis-stilbene. An electron-transfer sensitized trans-cis isomerization, using cresyl violet perchlorate as the sensitizer, also led to similar results. Thermal isomerization of cis-azobenzene to trans-azobenzene within dendritic microenvironments revealed that the activation energy of the cis- to trans-isomer was increasing in the series C(5)G(3) < C(4)G(3) < C(3)G(3)

Interdiffusion and Growth of the Phases in CoNi/Mo and CoNi/W Systems

Deleterious topological-closed-packed (tcp) phases grow in the interdiffusion zone in turbine blades mainly because of the addition of refractory elements such as Mo and W in the Ni- and Co-based superalloys. CoNi/Mo and CoNi/W diffusion couples are prepared to understand the growth mechanism of the phases in the interdiffusion zone. Instead of determining the main and cross-interdiffusion coefficients following the conventional method, we preferred to determine the average effective interdiffusion coefficients of two elements after fixing the composition of one element more or less the same in the interdiffusion zone. These parameters can be directly related to the growth kinetics of the phases and shed light on the atomic mechanism of diffusion. In both systems, the diffusion rate of elements and the phase layer thickness increased because of the addition of Ni in the solid solution phase, probably because of an increase in driving force. On the other hand, the growth rate of the mu phase and the diffusion coefficient of the species decreased because of the addition of Ni. This indicates the change in defect concentration, which assists diffusion. Further, we revisited the previously published Co-Ni-Mo and Co-Ni-W ternary phase diagrams and compared them with the composition range of the phases developed in the interdiffusion zone. Different composition ranges of the tcp phases are found, and corrected phase diagrams are shown. The outcome of this study will help to optimize the concentration of elements in superalloys to control the growth of the tcp phases.

Structural, vibrational and thermal studies of a new nonlinear optical material: L-Asparagine-L-tartaric acid

Crystals of a new nonlinear optical (NLO) material, viz., L-asparagine-L-tartaric acid (LALT)(1) were grown by slow evaporation of an aqueous solution containing equimolar concentrations of L-asparagine and t-tartaric acid. The structure of the title compound which crystallizes in the non-centrosymmetric monoclinic space group P2(1) consists of a molecule of L-asparagine and a molecule of free L-tartaric acid both of which are interlinked by three varieties of H-bonding interactions namely O-H center dot center dot center dot O, N-H center dot center dot center dot O and C-H center dot center dot center dot O. The UV-Vis-NIR spectrum of 1 reveals its transparent nature while the vibrational spectra confirm the presence of the functional groups in 1. The thermal stability and second harmonic generation (SHG) conversion efficiency of 1 were investigated. (C) 2012 Elsevier B.V. All rights reserved.

Synthesis and characterization of carbon-covered alumina (CCA) supported TiO2 nanocatalysts with enhanced visible light photodegradation of Rhodamine B

The anatase phase of titania (TiO2) nano-photocatalysts was prepared using a modified sol gel process and thereafter embedded on carbon-covered alumina supports. The carbon-covered alumina (CCA) supports were prepared via the adsorption of toluene 2,4-diisocyanate (TDI) on the surface of the alumina. TDI was used as the carbon source for the first time for the carbon-covered alumina support system. The adsorption of TDI on alumina is irreversible; hence, the resulting organic moiety can undergo pyrolysis at high temperatures resulting in the formation of a carbon coating on the surface of the alumina. The TiO2 catalysts were impregnated on the CCA supports. X-ray diffraction analysis indicated that the carbon deposited on the alumina was not crystalline and also showed the successful impregnation of TiO2 on the CCA supports. In the Raman spectra, it could be deduced that the carbon was rather a conjugated olefinic or polycyclic hydrocarbons which can be considered as molecular units of a graphitic plane. The Raman analysis of the catalysed CCAs showed the presence of both the anatase titania and D and G band associated with the carbon of the CCAs. The scanning electron microscope micrographs indicated that the alumina was coated by a carbon layer and the energy dispersive X-ray spectra showed the presence of Al, O and C in the CCA samples, with the addition of Ti for the catalyst impregnated supports. The Brunauer Emmet and Teller surface area analysis showed that the incorporating of carbon on the alumina surface resulted in an increase in surface area, while the impregnation with TiO2 resulted in a further increase in surface area. However, a decrease in the pore volume and diameter was observed. The photocatalytic activity of the nanocatalysts was studied for the degradation of Rhodamine B dye. The CCA-TiO2 nanocatalysts were found to be more photocatalytically active under both visible and UV light irradiation compared to the free TIO2 nanocatalysts.