Effect of constraints by threonine on proline containing αa-helix—A molecular dynamics approach

Proline plays an important role in the secondary structure of proteins. In the pursuit of understanding its structural role, Proline containing helices with constraints have been studied by employing molecular dynamics (MD) technique. In the present study, the constraint introduced is a threonine residue, whose sidechain has intramolecular hydrogen bond interaction with the backbone oxygen atom. The three systems that have been chosen for characterization are: (1) Ace-(Ala)12−Thr-Pro-(Ala)10−NHMe, (2) Ace-(Ala)13-Pro-Ala-Thr- (Ala)8-NHMe and (3) Ace-(Ala)13-Pro-(Ala)3-Thr-(Ala)6-NHMe. The equilibrium structures and structural transitions have been identified by monitoring the backbone dihedral angles, bend related parameters and the hydrogen bond interactions. The MD averages and root mean square (r.m.s.) fluctuations are compared and discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.

High Pressure NMR Study of Ammonium Thiocyanate

Wide-line proton NMR spectra of ammonium thiocyanate have been recorded at 77 K as a function of external hydrostatic pressure. Contrary to expectations the line-width and the second moment decrease with the increase of pressure. This, however, is in accordance with the anomalous behaviour observed in other magnetic resonance studies of this compound and can be understood in terms of the change of electron density around the nitrogen atom of the SCN- group.

Synthesis, characterization, and thermal degradation studies on group VIA derived weak-link polymers

Polymers containing group VIA derived weak links, viz. poly(styrene disulfide) (PSD), poly- (styrene tetrasulfide) (PST), and poly(styrene diselenide) (PSDSE), have been synthesized. The polymers PSD and PST were characterized by NMR, IR, UV, TGA, and fast atom bombardment m w spectrometric (FABMS) techniques. The presence of different configurational sequences in PSD and PST were identified by *3C NMR spectroscopy. PSDSE, being insoluble in common organic solvents, was characterized using solid-state lac NMR (CP-MAS) spectroscopy. Thermal degradation of polymers under direct pyrolysis-mass spectrometric (DP-MS) conditions revealed that all the polymers undergo degradation through the weaklink scission. A comparative study of the pyrolysis products of these polymers with that of poly(styrene peroxide) (PSP) revealed a smooth transformation down the group with no monomer (styrene or oxygen) formation in PSP to only styrene and selenium metal in PSDSE. This trend of group VIA is explained from the energetics of the C-X bond (X = 0, S, and Se) which also seems to be important in addition to the weak X-X bond cleavage. In PSP and PSD, the behavior is also explained from the energetics of the alkoxy and thiyl radicals. The unique exothermic degradation in PSP compared to endothermic degradation in PSD and PSDSE is explained from the nature of the producta of degradation.

Armchair or Zigzag? A tool for characterizing graphene edge

Electronic, magnetic, and structural properties of graphene flakes depend sensitively upon the type of edge atoms. We present a simple software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. Whether an edge atom is of armchair or zigzag type is decided by the unique pattern of its nearest neighbors. Particular attention is paid to the practical aspects of using the tool, as additional features such as extracting out the edges from the lattice could help in analyzing images from transmission microscopy or other experimental probes. Ultimately, the tool in combination with density-functional theory or tight-binding method can also be helpful in correlating the properties of graphene flakes with the different armchair-to-zigzag ratios. Program summary Program title: edgecount Catalogue identifier: AEIA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 66685 No. of bytes in distributed program, including test data, etc.: 485 381 Distribution format: tar.gz Programming language: FORTRAN 90/95 Computer: Most UNIX-based platforms Operating system: Linux, Mac OS Classification: 16.1, 7.8 Nature of problem: Detection and classification of edge atoms in a finite patch of honeycomb lattice. Solution method: Build nearest neighbor (NN) list; assign types to edge atoms on the basis of their NN pattern. Running time: Typically similar to second(s) for all examples. (C) 2010 Elsevier B.V. All rights reserved.

Nano structured carbon nitrides prepared by chemical vapour deposition

Nanostructured carbon nitride films were prepared by pyrolysis assisted chemical vapour deposition(CVD). A two zone furnace with a temperature profile having a uniform temperature over a length of 20 cm length has been designed and developed. The precursor Azabenzimidazole was taken in a quartz tube and evaporated at 400 degrees C. The dense vapours enter the pyrolysis zone kept at a desired temperature and deposit on the quartz substrates. The FTIR spectrum of the prepared samples shows peaks at 1272 cm(-1) (C-N stretching) and 1600 cm(-1) (C=N) confirms the bonding of nitrogen with carbon. Raman D and G peaks, are observed at 1360 cm(-1) and 1576 cm(-1) respectively. XPS core level spectra of C 1s and N 1s show the formation of pi bonding between carbon and nitrogen atoms. The size of the nano crystals estimated from the SEM images and XRD is similar to 100 nm. In some regions of the sample a maximum of 57 atom % of nitrogen has been observed.

Strong nonlocalization induced by small scale parameter on terahertz flexural wave dispersion characteristics of a monolayer graphene

This paper presents the strong nonlocal scale effect on the flexural wave propagation in a monolayer graphene sheet. The graphene is modeled as an isotropic plate of one atom thick. Nonlocal governing equation of motion is derived and wave propagation analysis is performed using spectral analysis. The present analysis shows that the flexural wave dispersion in graphene obtained by local and nonlocal elasticity theories is quite different. The nonlocal elasticity calculation shows that the wavenumber escapes to infinite at certain frequency and the corresponding wave velocity tends to zero at that frequency indicating localization and stationary behavior. This behavior is captured in the spectrum and dispersion curves. The cut-off frequency of flexural wave not only depend on the axial wavenumber but also on the nonlocal scaling parameter. The effect of axial wavenumber on the wave behavior in graphene is also discussed in the present manuscript. (C) 2010 Elsevier B.V. All rights reserved.

Anharmonic Effects in Germanium

A precise X-ray investigation is carried out to probe the lowest-order anharmonic contribution of the atomic potential of the germanium atom. A total number of 1052 reflections (h + k + l = 4n and 4n +/- 1) are precisely measured at room temperature using a spherical single crystal of germanium and using a Nonius CAD-4 X-ray diffractometer with crystal monochromatized MoKalpha radiation. A least-square refinement program is used to refine the harmonic and anharmonic thermal parameters of the crystal. The refinement gives beta(Ge) = (-0.749 +/- 1.79) x 10-(16) J nm-3 with B(Ge) = (0.528 +/- 0.004) x 10(-2) nm2. The reliability index (R) amounts to 1.71% for germanium.

The Zintl ion As-7](2-): an example of an electron-deficient As-x radical anion

K(2,2,2-crypt)](2)As-7]center dot THF, 1 (2,2,2-crypt = 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo8.8.8]hexacosane) is the first well characterized seven-atom radical anion of group 15. UV-Vis spectroscopy confirms the presence and electronic structure of As-7](2-). Cyclic voltammetry in DMF solution shows the As-7(3) /As-7(2) redox couple as a one-electron reversible process. Theoretical investigations explore the bonding and properties of compound 1.

Modification of the sugar specificity of a plant lectin: structural studies on a point mutant of Erythrina corallodendron lectin

A mutant of Erythrina corallodendron lectin was generated with the aim of enhancing its affinity for N-acetylgalactosamine. A tyrosine residue close to the binding site of the lectin was mutated to a glycine in order to facilitate stronger interactions between the acetamido group of the sugar and the lectin which were prevented by the side chain of the tyrosine in the wild-type lectin. The crystal structures of this Y106G mutant lectin in complex with galactose and N-acetylgalactosamine have been determined. A structural rationale has been provided for the differences in the relative binding affinities of the wild-type and mutant lectins towards the two sugars based on the structures. A hydrogen bond between the O6 atom of the sugars and the variable loop of the carbohydrate-binding site of the lectin is lost in the mutant complexes owing to a conformational change in the loop. This loss is compensated by an additional hydrogen bond that is formed between the acetamido group of the sugar and the mutant lectin in the complex with N-acetylgalactosamine, resulting in a higher affinity of the mutant lectin for N-acetylgalactosamine compared with that for galactose, in contrast to the almost equal affinity of the wild-type lectin for the two sugars. The structure of a complex of the mutant with a citrate ion bound at the carbohydrate-binding site that was obtained while attempting to crystallize the complexes with sugars is also presented.

A salt of a protonated (amino)spirocyclic cyclotriphosphazene

The title compound 4,4,6,6-tetrakis(dimethylamino)-2 lambda(5),4 lambda(5),6 lambda(5)-cyclotriphosphaza- 1,3,5-trien-1-ium-2-spiro-2'-(2'-phospha-1',3'-diazacyclohexane) tetrachloroplatinate, [HN3P3(NMe(2))(4)(NHCH2CH2CH2NH)](2)-[PtCl4], contains a cyclophosphazenium cation in which the hetero-substituted (amino)spirocyclic cyclotriphosphazene is protonated. The protonation has occurred on one of the P3N3 ring N atoms adjacent to the spiro P atom. The protonation results in lengthening of the ring P-N bonds and puckering of the phosphazene ring. In the crystal lattice, 2n cyclophosphazenium cations are connected by n [PtCl4](2-) anions mediated by N-H...Cl hydrogen bonds to form a linear polymeric structure.

Edge-sharing bioctahedral diruthenium(III) complexes containing methoxy and carboxylate bridges:x-ray structures, redox behavior, and core stability

Edge-sharing bioctahedral (ESBO) complexes [Ru-2(OMe)(O2CC6H4-p-X)3(1-MeIm)(4)](ClO4)2 (X = OMe (1a), Me (1b)) and [Ru-2(O2CC6H4-P-X)(4)(1-MeIm)(4)](ClO4)(2) (X = OMe (2a), Me (2b)) are prepared by reacting Ru2Cl(O(2)CR)(4) with 1-methylimidazole (1-MeIm) in methanol followed by treatment with NaClO4. Complex 2a and the PF6- salt (1a') of 1a have been structurally characterized. Crystal data for 1a.1.5MeCN. 0.5Et(2)O: triclinic, P (1) over bar, a = 13.125(2) Angstrom, b = 15.529(3) Angstrom, c 17.314(5) Angstrom, a; 67.03(2)degrees, beta 68.05(2)degrees, gamma = 81.38(1)degrees, V 3014(1) Angstrom(3), Z = 2. Crystal data for 2a: triclinic, P (1) over bar, a 8.950(1) Angstrom, b = 12.089(3) Angstrom, c = 13.735(3) Angstrom, alpha 81.09(2)degrees, beta = 72.27(1)degrees, gamma = 83.15(2)degrees, V = 1394(1) Angstrom(3), Z = 1. The complexes consist of a diruthenium(III) unit held by two monoatomic and two three-atom bridging ligands. The 1-MeIm ligands are at the terminal sites of the [Ru-2(mu-L)(eta(1):mu-O(2)CR)(eta(1):eta(1):mu-O(2)CR)(2)](2+) core having a Ru-Ru single bond (L = OMe or eta(1)-O(2)CR). The Ru-Ru distance and the Ru-O-Ru angle in the core of 1a' and 2a are 2.49 Angstrom and similar to 76 degrees. The complexes undergo one-electron oxidation and reduction processes in MeCN-0.1 M TBAP to form mixed-valence diruthenium species with Ru-Ru bonds of orders 1.5 and 0.5, respectively.

Orientational Order of Liquid-Crystalline 4-Alkyl-N-(p-cyanophenyl)piperidines by 2H and 13C NMR Spectroscopies

The orientational order of nematic 4-alkyl-N-(4-cyanophenyl) piperidines (I) has been determined from H-2 and C-13 NMR spectra. Molecular-order parameters are derived from the carbon-13 chemical shift of the cyano carbon atom in the nematic and the isotropic phases; the sign of the diamagnetic anisotropy is positive. Deuterium quadrupolar splittings from the partially deuterated piperidine ring of I are then related to various C-D bonds.

Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Chemical Synthesis of Metal Nanoparticles Using Amine-Boranes

The development of new synthetic strategies to obtain mono-disperse metal nanoparticles on large scales is an attractive prospect in the context of sustainability. Recently, amine-boranes, the classical Lewis acid-base adducts, have been employed as reducing agents for the synthesis of metal nanoparticles. They offer several advantages over the traditional reducing agents like the borohydrides; for example, a much better control of the rate of reduction and, hence, the particle size distribution of metal nanoparticles; diversity in their reducing abilities by varying the substituents on the nitrogen atom; and solubility in various protic and aprotic solvents. Amine-boranes have not only been used successfully as reducing agents in solution but also in solventless conditions, in which along with the reduction of the metal precursor, they undergo in situ transformation to afford the stabilizing agent for the generated metal nanoparticles, thereby bringing about atom economy as well. The use of amine boranes for the synthesis of metal nanoparticles has experienced an explosive growth in a very short period of time. In this Minireview, recent progress on the use of amine boranes for the synthesis of metal nanoparticles, with a focus towards the development of pathways for sustainability, is discussed.

Reactions of palladium chloride with amino spirocyclic cyclotriphosphazenes: Isolation and Crystal Structures of Novel Mono- and Bimetallic Complexes Formed by the Hydrolysis of a .lambda.5-Diazaphospholane Ring

The reaction of the amino spirocyclic cyclotriphosphazene N3P3(NMe2)4(NHCH2CH2CH2NH) (2) with palladium chloride gives the stable chelate complex [PdCl2.2] (4). An X-ray crystallographic study reveals that one of the nitrogen atoms of the diaminoalkane moiety and an adjacent phosphazene ring nitrogen atom are bonded to the metal. An analogous reaction with the phosphazene N3P3(NMe2)4(NHCH2CH2NH) (1) gives initially a similar complex which undergoes facile hydrolysis to give the novel monometallic and bimetallic complexes [PdCl2.HN3P3(O)(NMe2)4(NHCH2CH2NH2)] (5) and [PdCl{N3P3(NMe2)4(NCH2CH2NH2)}]2(O) (6), which have been structurally characterized; in the former, an (oxophosphazadienyl)ethylenediamine is chelated to the metal whereas, in the latter, an oxobridged bis(cyclotriphosphazene) acts as a hexadentate nitrogen donor ligand in its dianionic form. Crystal data for 4 : a = 14.137(1) angstrom, b = 8.3332(5) angstrom, c = 19.205(2) angstrom, beta = 96.108(7)degrees, P2(1)/c, Z = 4, R = 0.027 with 3090 reflections (F > 5sigma(F)). Crystal data for 5 : a = 8.368(2) angstrom, b = 16.841(4) A, c = 16.092(5) angstrom, beta = 98.31(2)degrees, P2(1)/n, Z = 4, R = 0.049 with 3519 reflections (F > 5sigma(F)). Crystal data for 6 : a = 22.455(6) angstrom, b = 14.882(3) angstrom, c = 13.026(5) angstrom, 6 = 98.55(2)degrees, C2/c, Z = 4, R = 0.038 with 3023 reflections (F > 5sigma(F)).