A C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins

The serendipitous observation of a C-H...O 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-H...O interaction between the T - 4 (CH)-H-alpha and T + 1 C=O group (C...O 3.5 Angstrom) becomes possible only when the T + 1 residue adopts an extended beta conformation (T is defined as the helix terminating residue adopting an alpha(L) 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 Set, Glu and Gln is observed at T - 4 position with the motif being further stabilized by the formation of a side-chain-backbone O...H-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 beta conformation. In a majority of these cases, the succeeding beta strand lies approximately antiparallel with the helix, suggesting that the backbone C-H...O 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-H...O hydrogen bonds between (T - 4) (CH)-H-alpha...C=O (T + 1) and (T - 8) (CH)-H-alpha...C=O (T + 3). 0 2002 Published by Elsevier Science Ltd.

Characterization of alkyl chain conformation in an intercalated cationic lipid bilayer by IR spectroscopy

A structural analysis of alkyl chain conformation of an intercalated cationic lipid bilayer is described. Dialkyl dimethylammonium ions (di-C(n)DA) were ion exchanged into the galleries of layered cadmium thiophosphate to give Cd0.83PS3(di-C(n)DA)(0.34). The grafting density and interlayer expansions were identical to those for the intercalated single chain alkyl trimethylammonium (C(n)TA) bilayers. The increased methylene chain density in the galleries, however, forces the intercalated lipid to adopt a more trans ordered structure. Progression bands arising from the coupling of vibrational modes of trans methylene units are used to establish the extent of trans registry. Two types of ordered structures of the intercalated cationic lipid may be distinguished. One in which both alkyl chains adopt an all-trans geometry, and one in which the methylene bond adjacent to the headgroup on one of the alkyl chains is gauche. The latter structure is typically found in the crystalline state of these cationic lipids. The concentrations of the two structures were determined from the ratio of the intensities of the progression bands and were found to remain unchanged with temperature.

Ramachandran plot on the web

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.

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.

One-dimensional zinc phosphates with linear chain structure

Three one-dimensional zinc phosphates, [C5N2H14][Zn(HPO4)2], I, [C10N4H26][Zn(HPO4)2].2H2O II, and [C4N2H6]2[Zn(HPO4)], III, have been prepared employing hydro/solvothermal methods in the presence of organic amines. While I and II consist of linear chains of corner-shared four-membered rings, III is a polymeric wire where the amine molecule is directly bonded to the metal center. The wire, as well as the chain in these structures, are held together by hydrogen bond interactions involving the amine and the framework oxygens. The polymeric zinc phosphate with wire-like architecture, III, is only the second example of such architecture. Crystal data: I, monoclinic, P21/c (no. 14), a=8.603(2), b=13.529(2), c=10.880(1) Å, β=94.9(1)°, V=1261.6(1) Å3, Z=4, ρcalc.=1.893 gcm−3, μ(MoKα)=2.234 mm−1, R1=0.032, wR2=0.086, [1532 observed reflections with I>2σ(I)], II, orthorhombic, Pbca (no. 61), a=8.393(1), b=15.286(1), c=22.659(1) Å, V=2906.9(2) Å3, Z=8, ρcalc.=1.794 gcm−3, μ(MoKα)=1.957 mm−1, R1=0.055, wR2=0.11, [1565 observed reflections with I>2σ(I) and III, monoclinic, P21/c (no. 14), a=8.241(1), b=13.750(2), c=10.572(1) Å, β=90.9(1)°, V=1197.7(2) Å3, Z=4, ρcalc.=1.805 gcm−3, μ(MoKα)=2.197 mm−1, R1=0.036, wR2=0.10, [1423 observed reflections with I>2σ(I)].

Synthesis and Properties of a Novel (Main-Chain)– (Side-Chain) Polymeric Peroxide

A novel (main-chain)-(side-chain) vinyl polyperoxide, poly(dipentene peroxide)(PDP), an alternating copolymer of dipentene (DP) and oxygen, has been synthesized by thermal oxidative polymerization of DP. The PDP was characterized by 1H NMR, 13C NMR, FTIR, DSC, TGA, and EI-MS studies. The overall activation energies of the degradation from Kissinger’s method were 28 and 33 kcal/mol, respectively, for the endocyclic and acyclic peroxide units. The side-chain peroxy groups were found to be thermally more stable than the main chain. Above 45°C the rate of polymerization increases sharply at a particular instant showing an “autoacceleration” with the formation of knee point. The kinetics of autoacceleration has been studied at various temperatures (45–70°C) and pressures (50–250 psi). © 2000 John Wiley&Sons, Inc. J Appl Polym Sci 79: 1549–1555, 2001

Synthesis, structural characterization, thermal studies and chain dynamics of poly(methacrylonitrile peroxide) by NMR spectroscopy

Poly(methacrylonitrile peroxide) (PMNP) has been synthesized from methacrylonitrile by free radical initiated oxidative polymerization and characterized by different spectroscopic methods. NMR spectroscopy confirmed the alternating copolymer structure with labile peroxy bonds in the main chain. The extreme instability of PMNP was noted from FTIR spectroscopy. Thermal degradation studies by using differential scanning calorimetry and thermogravimetry have revealed that PMNP degrades highly exothermically and the heat of degradation, 42.5 kcal mol−1, is of the same order as that reported for other vinyl polyperoxides. Mass spectral fragmentation pattern under electron impact (EI) condition has also been investigated. The mechanism of the primary exothermic degradation has been substantiated by thermochemical calculations. The chain dynamics of the polyperoxide chain has been studied by means of 13C spin–lattice relaxation times (T1) of the main chain as well as the side chain carbons. The temperature dependence of the spin–lattice relaxation times shows that the PMNP is more flexible compared to the analogous poly(styrene peroxide).

Phase transitions in the anchored organic bilayers of long-chain alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4; n=12, 16, 18

The single perovskite slab alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4, n = 12, 16, 18, display two phase transitions, just above room temperature, associated with changes in the alkylammonium chains. We have followed these two phase transitions using scanning calorimetry, X-ray powder diffraction, and IR and Raman spectroscopies. We find the first phase transition to be associated with symmetry changes arising from a dynamic rotational disordering of the ammonium headgroup of the chain whereas the second transition, the melting of the chains in two dimensions, is characterized by an increased conformational disorder of the methylene units of the alkyl chains. We examine these phase transitions in light of the interesting optical properties of these materials, as well as the relevance of these systems as models for phase transitions in lipid bilayers.

Beta-structure of polypeptides in non-aqueous solutions. II. Side-chain orientation

The specific side-chain orientations of the phenyl group in the polypeptides poly-S-benzyl-L-cysteine, poly-S-carbobenzoxy-L-cysteine and poly-O-carbobenzoxy-L-serine in the beta-structure have been studied by spectral measurements in solutions. All the three polypeptides exhibit aromatic CD bands, indicating the asymmetric placement of the side-chain phenyl rings when the polypeptide backbone takes up the antiparallel beta-structure. Supporting evidence for this is derived from n.m.r. spectra of the polypeptides, which show upfield shift of the phenyl protons due to the stacking of the aromatic rings. Molecular model building studies reveal the stacking of alternate phenyl groups along the polypeptide chain.

Conformational studies of the phosphazenyl side chain in cyclophosphazenes. Part 3. Crystal and molecular structure of N3P3Cl4(NEt2)(NPPh3)

The crystal structure of N3P3Cl4(NEt2)(NPPh3) has been determined. The crystals are orthorhombic, space group Pbca, with a= 8.208(1), b= 21.890(1), c= 31.722(2)Å, Z= 8, and m.p. = 146.5 °C. The structure was solved by direct methods and refined to a final R value of 0.045 for 2 025 independent reflections. The analysis reveals significant variations in the ring P–N bond lengths. The two nitrogenous substituents, NPPh3 and NEt2, reside on the same phosphorus atom. The latter, NEt2, has an almost exact type II conformation (the plane NC2 almost perpendicular to the local NPN plane)(the first observed for a dialkylamino-group in cyclophosphazenes), the former, NPPh3, deviates from type II towards type III (in type III the plane Pring–N–Pexo makes an angle of ca. 45° with the local N–P–N ring plane). The present structure is compared with others of triphenylphosphazenyl-cyclophosphazenes and the conformation of the NPPh3 substituent and its electron supply in the ground and perturbed states are discussed.

Faster algorithms for all-pairs small stretch distances in weighted graphs

Abstract. Let G = (V,E) be a weighted undirected graph, with non-negative edge weights. We consider the problem of efficiently computing approximate distances between all pairs of vertices in G. While many efficient algorithms are known for this problem in unweighted graphs, not many results are known for this problem in weighted graphs. Zwick [14] showed that for any fixed ε> 0, stretch 1 1 + ε distances between all pairs of vertices in a weighted directed graph on n vertices can be computed in Õ(n ω) time, where ω < 2.376 is the exponent of matrix multiplication and n is the number of vertices. It is known that finding distances of stretch less than 2 between all pairs of vertices in G is at least as hard as Boolean matrix multiplication of two n×n matrices. It is also known that all-pairs stretch 3 distances can be computed in Õ(n 2) time and all-pairs stretch 7/3 distances can be computed in Õ(n 7/3) time. Here we consider efficient algorithms for the problem of computing all-pairs stretch (2+ε) distances in G, for any 0 < ε < 1. We show that all pairs stretch (2 + ε) distances for any fixed ε> 0 in G can be computed in expected time O(n 9/4 logn). This algorithm uses a fast rectangular matrix multiplication subroutine. We also present a combinatorial algorithm (that is, it does not use fast matrix multiplication) with expected running time O(n 9/4) for computing all-pairs stretch 5/2 distances in G. 1

A mostly-digital analog scan-out chain for low bandwidth voltage measurement for analog IP test

A method of precise measurement of on-chip analog voltages in a mostly-digital manner, with minimal overhead, is presented. A pair of clock signals is routed to the node of an analog voltage. This analog voltage controls the delay between this pair of clock signals, which is then measured in an all-digital manner using the technique of sub-sampling. This sub-sampling technique, having measurement time and accuracy trade-off, is well suited for low bandwidth signals. This concept is validated by designing delay cells, using current starved inverters in UMC 130nm CMOS process. Sub-mV accuracy is demonstrated for a measurement time of few seconds.

Alkylation of toluene by methanol over alkali exchanged zeolite-X: side chain versus ring alkylation

The ring versus side-chain alkylation of toluene with methanol over alkali-exchanged zeolite-X of differing basicity has been investigated by in situ infrared spectroscopy and TPD measurements. Over the basic Cs-exchanged zeolite the product of alkylation is styrene/ethylbenzene while over the acidic Li-exchanged zeolite ring alkylation occurs to give mainly xylene as the product. FTIR and TPD investigations reveal that, the key difference in the two types of alkylation processes lies in the state of the adsorbed methanol present at higher temperatures in the zeolite. In basic zeolites, methanol decomposes to formaldehyde and formates. The former is the key ‘side-chain’ alkylating species that leads to the formation of styrene. In the acidic zeolites it is shown that methanol bound to the acid sites plays an active role in the ‘ring alkylation’ of toluene to xylene.