C-H…O hydrogen bond mediated chain reversal in a peptide containing g-amino acid residue, determined directly from powder X-ray diffraction data

The finding that peptides containing -amino acid residues give rise to folding patterns hitherto unobserved in -amino acid peptides[1] has stimulated considerable interest in the conformational properties of peptides built from , and residues,[2] as the introduction of additional methylene (CH2) units into peptide chains provides further degrees of conformational freedom.

A C-H…O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins.

The serendipitous observation of a C–Hcdots, three dots, centeredO hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C–Hcdots, three dots, centeredO interaction between the T−4 CαH and T+1 C=O group (Ccdots, three dots, centeredO≤3.5 Å) becomes possible only when the T+1 residue adopts an extended β conformation (T is defined as the helix terminating residue adopting an αL conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational preferences at positions T−4, T, and T+1 determined. A marked preference for residues like Ser, Glu and Gln is observed at T−4 position with the motif being further stabilized by the formation of a side-chain–backbone Ocdots, three dots, centeredH–N hydrogen bond involving the side-chain of residue T−4 and the N–H group of residue T+3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in β conformation. In a majority of these cases, the succeeding β strand lies approximately antiparallel with the helix, suggesting that the backbone C–Hcdots, three dots, centeredO interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C–Hcdots, three dots, centeredO hydrogen bonds between (T−4) CαHcdots, three dots, centeredC=O (T+1) and (T−8) CαHcdots, three dots, centeredC=O (T+3).

Reactivity with hydrogen of pure iron oxide and of iron oxides doped with oxides of Mn, Co, Ni and Cu

Using dynamic TG in H2, X-ray powder diffraction and Mössbauer Spectroscopy the reactivities fot hydrogen reduction of Fe2O3 prepared at different temperatures, Fe2O3 doped with oxides of Mn, Co, Ni and Cu prepared at 300DaggerC from nitrate precursors and intermediate spinels derived from above samples during reduction have been explored. The reactivity is higher for finely divided Fe2O3 prepared at 250DaggerC. The reduction is retarded by Mn, marginally affected by Co and accelerated by Ni and Cu, especially at higher (5 at.%) dopant concentration. These reactivities confirmed also by isothermal experiments, are ascribed to the nature of disorder in the metastable intermediate spinels and to hydrogen rsquospill overrsquo effects.

Oxidation of aromatic substrates with hydrogen peroxide and hydrochloric acid

Chloroquinones are prepared conveniently from phenol, naphthols and aromatic amines.

The Mechanism Of The Hydrogen Abstraction Process By Photo-Excited Ketones

Qualitative potential energy surfaces for hydrogen abstraction from alkanes containing primary, secondary and tertiary C-H bonds by a photo-excited ketone have been reported, The results suggest that the activation barriers for these processes decrease in the order primary > secondary > tertiary in agreement with the observed trend in the rate constants. The analysis of the electronic structure of the transition-state reveal that electron-transfer from hydrocarbon to ketone and formation of a new bond are almost synchronous in the hydrogen transfer process. The tunneling of hydrogen is not important in the normal temperature region even though the barriers are small.

Catalytic hydrogen combustion for treatment of combustible gases from fuel cell processors

Catalytic combustion of H-2 was carried out over combustion synthesized noble metal (Pd or Pt) ion-substituted CeO2 based catalysts using a feed stream that simulated exhaust gases from a fuel cell processor The catalysts showed a high activity for H-2-combustion and complete conversion was achieved below 200 C over all the catalysts when O-2 was used in a stoichiometric amount With higher amounts of O-2 the reaction rates Increased and complete conversions were possible below 100 C The reaction was also carried out over Pd-impregnated CeO2 The conversions of H-2 with stoichiometric amount of O-2 were found to be higher over Pd-substituted compound The mechanism of the reaction over noble metal-substituted compounds was proposed on the basis of X-ray photoelectron spectroscopy studies The redox couples between Ce and metal ions were established and a dual site redox mechanism was pi posed for the reaction (C) 2010 Elsevier B V All rights reserved

Stereochemical studies on cyclic peptides. Part XI. Conformation of cyclic pentapeptides having intramolecular 3 leads to 1 hydrogen bonds.

Conformational analysis of cyclic pentapeptides having two intra-ring 3 leads to 1 hydrogen bonds has been carried out. It is found that the structure can easily be formed with trans planar peptide units without causing significant angular strain at the alpha-carbon atoms. Four different types of conformations designated Types I--IV are possible for the backbone structure. Details of these four types of conformations and also the accommodating possibility of these types for allglycyl and all-alanyl residues are presented. Three of the four types have relatively low energies for glycyl residues whereas the other one has a slightly higher energy. When alanyl residues are introduced at the five alpha-carbon atoms, the types that are energetically favourable depend upon the sequence of isomers. Energy calculations have also been carried out for the combinations of glycyl, L- and D-alanyl residues. The theoretical results are compared with available experimental observations both from solution and solid state studies.

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a tripler comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such tripler structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Reinstate hydrogen peroxide as the product of alternative oxidase of plant mitochondria

Chill treatment of potato tubers for 8 days induced mitochondrial O-2 consumption by cyanide-insensitive alternative oxidase (AOX). About half of the total O-2 consumption in such mitochondria was found to be sensitive to salicylhydroxamate (SHAM), a known inhibitor of AOX activity. Addition of catalase to the reaction mixture of AOX during the reaction decreased the rate of SHAM-sensitive O-2 consumption by nearly half, and addition at the end of the reaction released half of the O-2 consumed by AOX, both typical of catalase action on H2O2. This reaffirmed that the product of reduction of O-2 by plant AOX was H2O2 as found earlier and not H2O as reported in some recent reviews.

Noble metal ionic sites for catalytic hydrogen combustion: spectroscopic insights

A catalytic hydrogen combustion reaction was carried out over noble metal catalysts substituted in ZrO2 and TiO2 in ionic form. The catalysts were synthesized by the solution combustion technique. The compounds showed high activity and CO tolerance for the reaction. The activity of Pd and Pt ion substituted TiO2 was comparable and was higher than Pd and Pt ion substituted ZrO2. The mechanisms of the reaction over the two supports were proposed by making use of the X-ray photoelectron spectroscopy and FT infrared spectroscopic observations. The reaction over ZrO2 supported catalysts was proposed to take place by the utilization of the surface hydroxyl groups while the reaction over TiO2 supported catalysts was hypothesized to be a hybrid mechanism utilizing surface hydroxyl groups and the lattice oxygen.