Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.

Characterization Of Crystal Structure In Binary Mixtures Of Latex Globules

Colloidal crystals formed by two types of polystyrene particles of different sizes (94 and 141 nm) at various number ratios (94:141 nm) are studied. Experiments showed that the formation time of crystals lengthens as the number ratio of the two components approaches 1:1. The dependence of the mean interparticle distance (D-0), crystal structure and alloy structure on the number ratio of the two types of particles was Studied by means of Kossel diffraction technique and reflection spectra. The results showed that as the number ratio decreased, the mean interparticle distance (D-0) became larger. And the colloidal crystal in binary mixtures is more preferably to form the bcc structure. This study found that binary systems form the substitutional solid solution (sss)-type alloy structure in all cases except when the number ratio of two types of particles is 5:1, which results instead in the superlattice structure. (C) 2008 Elsevier Inc. All rights reserved.

Crystal structure and phase transition studies in perovskite-type oxides using powder-diffraction techniques and symmetry-mode analysis : SrLnMRuO6 (Ln=La,Pr,Nd; M=Zn,Co,Mg,Ni,Fe) and ALn2CuTi2O9 (A=Ca,Ba; Ln=La,Pr,Nd,Sm)

La tesis se ha centrado en la síntesis y caracterización estructural de materiales tipo perovskita: SrLnMRuO6 (Ln=La,Pr,Nd; M=Zn,Co,Mg,Ni,Fe) y ALn2CuTi2O9 (A=Ca,Ba; Ln=La,Pr,Nd,Sm). El estudio de las estructuras de los materiales se ha realizado mediante el análisis de los patrones de difracción en polvo de rayos-X, sincrotrón y/o neutrones. En el refinamiento por el método de Rietveld de las estructuras se han sustituido las coordenadas atómicas (el método más común), por coordenadas colectivas: las amplitudes de los modos que describen la distorsión de la fase prototipo. Los resultados generales para la serie SrLnMRuO6 (Ln=La,Pr,Nd; M=Zn,Co,Mg,Ni) a temperatura ambiente se ha recogido en un diagrama en el que se han indicado las amplitudes de los modos que transforman de acuerdo a las irreps en función del factor de tolerancia, ya que todos ellos cristalizan en la misma fase monoclínica (P21/n); y a temperaturas altas se ha construido un diagrama de fase. Los materiales SrLnFeRuO6 ( Ln=La,Pr,Nd) y CaLn2CuTi2O9 cristalizan en la fase ortorrómbica Pbnm a temperatura ambiente; mientras que BaLn2CuTi2O9 tienen una estructura más simétrica, I4/mcm. A altas temperaturas se han identificado las transiciones de fase inducidas por el cambio de temperatura.A temperaturas bajas se han analizado las estructuras magnéticas de algunos de los compuestos mediante difracción de neutrones.

I. The crystal structure of a new dimer of triphenylfluorocyclobutadiene. II. A low temperature refinement of the cyanuric triazide structure

I. THE CRYSTAL STRUCTURE OF A NEW DIMER OF TRIPHENYLFLUOROCYCLOBUTADIENE

The crystal structure of thermal isomer of the “head-to-head” dimer of triphenylfluorocyclobutadiene was determined by the direct method. The Σ₂ relationship involving the low angle reflections with the largest E’s were found and solved for the signs by the symbolic method of Zachariasen. The structure was seen in the electron density map and the E-map, and was refined antisotropically by the method of least squares. The residual R was 0.065.

The structure is a gem-difluorohexaphenyldihydropentalene. All of the phenyl groups are planar as it is the cyclopentadiene ring of the dihydropentalene skeleton. Overcrowding at the position of the flourines causes some deviations from the normal bond angles in the cyclopentene ring.

The list of observed and calculated structure factors on pages 32-34 will not be legible on the microfilm. Photographic copies may be obtained from the California Institute of Technology.

II. A LOW TEMPERATURE REFINEMENT OF THE CYANURIC TRIAZIDE STRUCTURE

The structure of cyanuric triazide was refined anisotropically by the method of least squares. Three-dimensional intensity data, which has been collected photographically with MoK_α radiation at -110˚C, were used in the refinement. The residual R was reduced to 0.081.

The structure is completely planar, and there is no significant bond alternation in the cyanuric ring. The packing of the molecules causes the azide groups to deviate from linearity by 8 degrees.

I. The crystal structure of potassium bis(tricyanovinyl)amine. II. Nuclear magnetic resonance studies of alkali halide solutions. III. Elucidation of the intramolecular hydrogen bond in acetylacetone by the deuterium isotope effect on the chemical shift of the bridge hydrogen

Part I

Potassium bis-(tricyanovinyl) amine, K⁺N[C(CN)=C(CN)₂]₂^-, crystallizes in the monoclinic system with the space group Cc and lattice constants, a = 13.346 ± 0.003 Å, c = 8.992 ± 0.003 Å, B = 114.42 ± 0.02°, and Z = 4. Three dimensional intensity data were collected by layers perpendicular to b* and c* axes. The crystal structure was refined by the least squares method with anisotropic temperature factor to an R value of 0.064.

The average carbon-carbon and carbon-nitrogen bond distances in –C-CΞN are 1.441 ± 0.016 Å and 1.146 ± 0.014 Å respectively. The bis-(tricyanovinyl) amine anion is approximately planar. The coordination number of the potassium ion is eight with bond distances from 2.890 Å to 3.408 Å. The bond angle C-N-C of the amine nitrogen is 132.4 ± 1.9°. Among six cyano groups in the molecule, two of them are bent by what appear to be significant amounts (5.0° and 7.2°). The remaining four are linear within the experimental error. The bending can probably be explained by molecular packing forces in the crystals.

Part II

The nuclear magnetic resonance of ⁸¹Br and ¹²⁷I in aqueous solutions were studied. The cation-halide ion interactions were studied by studying the effect of the Li⁺, Na⁺, K⁺, Mg⁺⁺, Cs⁺ upon the line width of the halide ions. The solvent-halide ion interactions were studied by studying the effects of methanol, acetonitrile, and acetone upon the line width of ⁸¹Br and ¹²⁷I in the aqueous solutions. It was found that the viscosity plays a very important role upon the halide ions line width. There is no specific cation-halide ion interaction for those ions such as Mg⁺⁺, Di⁺, Na⁺, and K⁺, whereas the Cs⁺ - halide ion interaction is strong. The effect of organic solvents upon the halide ion line width in aqueous solutions is in the order acetone ˃ acetonitrile ˃ methanol. It is suggested that halide ions do form some stable complex with the solvent molecules and the reason Cs⁺ can replace one of the ligands in the solvent-halide ion complex.

Part III

An unusually large isotope effect on the bridge hydrogen chemical shift of the enol form of pentanedione-2, 4(acetylacetone) and 3-methylpentanedione-2, 4 has been observed. An attempt has been made to interpret this effect. It is suggested from the deuterium isotope effect studies, temperature dependence of the bridge hydrogen chemical shift studies, IR studies in the OH, OD, and C=O stretch regions, and the HMO calculations, that there may probably be two structures for the enol form of acetylacetone. The difference between these two structures arises mainly from the electronic structure of the π-system. The relative population of these two structures at various temperatures for normal acetylacetone and at room temperature for the deuterated acetylacetone were calculated.

I. The 3.7 Å crystal structure of horse heart ferricytochrome C. II. The application of the Karle-Hauptman tangent formula to protein phasing

I. The 3.7 Å Crystal Structure of Horse Heart Ferricytochrome C.

The crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 Å using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.

Although it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 Å electron density map. Among these was the fact that cytochrome c contains little or no α-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.

The heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.

The high resolution analysis of cytochrome c is now in progress and should be completed within the next year.

II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.

The Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.

The tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.

Pages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.

I. Anisotropy and crystal structure of ferromagnetic thin films. II. Investigations into magnetic microstructure by Lorentz microscopy

The induced magnetic uniaxial anisotropy of Ni-Fe alloy films has been shown to be related to the crystal structure of the film. By use of electron diffraction, the crystal structure or vacuum-deposited films was determined over the composition range 5% to 85% Ni, with substrate temperature during deposition at various temperatures in the range 25° to 500° C. The phase diagram determined in this way has boundaries which are in fair agreement with the equilibrium boundaries for bulk material above 400°C. The (α+ ɤ) mixture phase disappears below 100°C.

The measurement of uniaxial anisotropy field for 25% Ni-Fe alloy films deposited at temperatures in the range -80°C to 375°C has been carried out. Comparison of the crystal structure phase diagram with the present data and those published by Wilts indicates that the anisotropy is strongly sensitive to crystal structure. Others have proposed pair ordering as an important source of anisotropy because of an apparent peak in the anisotropy energy at about 50% Ni composition. The present work shows no such peak, and leads to the conclusion that pair ordering cannot be a dominant contributor.

Width of the 180° domain wall in 76% Ni-Fe alloy films as a function of film thickness up to 1800 Å was measured using the defocused mode of Lorentz microscopy. For the thinner films, the measured wall widths are in good agreement with earlier data obtained by Fuchs. For films thicker than 800 Å, the wall width increases with film thickness to about 9000 Å at 1800 Å film thickness. Similar measurements for polycrystalline Co films with thickness from 200 to 1500 Å have been made. The wall width increases from 3000 Å at 400 Å film thickness to about 6000 Å at 1500 Å film thickness. The wall widths for Ni-Fe and Co films are much greater than predicted by present theories. The validity of the classical determination of wall width is discussed, and the comparison of the present data with theoretical results is given.

Finally, an experimental study of ripple by Lorentz microscopy in Ni-Fe alloy films has been carried out. The following should be noted: (1) the only practical way to determine experimentally a meaningful wavelength is to find a well-defined ripple periodicity by visual inspection of a photomicrograph. (2) The average wavelength is of the order of 1µ. This value is in reasonable agreement with the main wavelength predicted by the theories developed by others. The dependence of wavelength on substrate deposition temperature, alloy composition and the external magnetic field has been also studied and the results are compared with theoretical predictions. (3) The experimental fact that the ripple structure could not be observed in completely epitaxial films gives confirmation that the ripple results from the randomness of crystallite orientation. Furthermore, the experimental observation that the ripple disappeared in the range 71 and 75% Ni supports the theory that the ripple amplitude is directly dependent on the crystalline anisotropy. An attempt to experimentally determine the order of magnitude of the ripple angle was carried out. The measured angle was about 0.02 rad. The discrepancy between the experimental data and the theoretical prediction is serious. The accurate experimental determination of ripple angle is an unsolved problem.

Crystal structure and characterization of a new μ-oxo bridged iron porphyrin

Comunicacion a congreso: Póster presentado en VIII Reunión Científica de Bioinorgánica – Bioburgos 2013 (Burgos, 7 al 10 de julio de 2013)

Mild Hydrothermal Synthesis, Crystal Structure, Thermal Behavior, Spectroscopic and Magnetic Properties of (NH4)0.80Li0.20[Fe(AsO4)F]

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Growth temperature and V/III ratio effects on the morphology and crystal structure of InP nanowires

The effects of growth temperature and V/III ratio on the morphology and crystallographic phases of InP nanowires that are grown by metal organic chemical vapour deposition have been studied. We show that higher growth temperatures or higher V/III ratios promote the formation of wurtzite nanowires while zinc-blende nanowires are favourableat lower growth temperatures and lower V/III ratios. A schematic map of distribution of zinc-blende and wurtzite structures has been developed in the range of growth temperatures (400-510 °C) and V/III ratios (44 to 700) investigated in this study. © 2010 IOP Publishing Ltd.

Light extraction of GaN LEDs with 2-D photonic crystal structure

Ultraviolet photo-lithography is employed to introduce two-dimensional (2D) photonic crystal (PC) structure on the top surface of GaN-based light emitting diode (LED). PC patterns are transferred to 460-nm-thick transparent indium tin oxide (ITO) electrode by inductively coupled plasma (ICP) etching. Light intensity of PC-LED can be enhanced by 38% comparing with the one without PC structure. Rigorous coupled wave analysis method is performed to calculate the light transmission spectrum of PC slab. Simulation results indicate that total internal reflect angle which modulated by PC structure has been increased by 7 degrees, which means that the light extraction efficiency is enhanced outstandingly.

Effects of the crystal structure on electrical and optical properties of pyrite FeS2 films prepared by thermally sulfurizing iron films

Based on experimental results and theoretical analysis effects of the crystal structure on the optical and electrical properties of pyrite FeS2 films produced by thermally sulfurizing iron films at various temperatures have been systematically studied. The results indicate that the crystal structure and some related factors, such as the crystallization and the stoichiometry, remarkably influence the optical and electrical performances of the pyrite films. It is also shown that the preferred orientation of the crystal grain plays a major role in determining the crystal structure and the optical and electrical properties of the pyrite FeS2 films. Also we find that it is the crystal grains, rather than the particles that exercise a decisive influence on the electrical performance of pyrite films. (C) 2003 Elsevier Science B.V. All rights reserved.