Rows Of Molecules Research Articles

5,6-Di-hydro-1,4-dithiine-2,3-di-carb-oxy-lic anhydride.

In the title com-pound (systematic name: 2,3-di-hydro-1,4-dithiino[2,3-c]furan-5,7-dione), C6H4O3S2, the observed geometry agrees well with those of its phthalamide, thieno and hy-droxy analogs, and with a calculated geometry obtained by density functional theory (DFT) calculations. Specific structural features are an S-C-C-S torsion angle of -70.39 (17)° and S-C bonds to sp 2-hybridized C atoms approximately 0.1 Å shorter than those to sp 3-hybridized C atoms. Unlike the extended structures of the analogs, there are no directed inter-molecular inter-actions and the head-to-tail rows of mol-ecules that are a prominent structural motif of the packing can be rationalized in terms of optimized dipole-dipole inter-actions.

Structural Investigations of the (5×√3) Striped Phase of Annealed 11-Phenoxy Undecanethiol Self-Assembled Monolayers on Au(111)

Self-assembled monolayers (SAMs) of 11-phenoxyundecanethiol on Au(111) were studied using scanning tunneling microscopy (STM), reflection absorption infrared spectroscopy (RAIRS), ellipsometry, and contact angle measurements before and after annealing in vacuum. The unannealed phenoxy SAM appeared to be disordered under the STM while RAIRS showed that the SAM has relatively significant organization, indicating there is local disordering of the phenoxy groups at the film surface. After annealing, the SAM formed striped domains with a (5×√3) rectangular structure with respect to the gold substrate. Molecularly resolved STM images of the stripes were obtained, and we were able to see that each stripe consists of two rows of molecules. On the basis of the results from all of the characterization techniques used here, we present a structure for the stripes that involve gauche conformations and the phenyl rings interacting in a favorable edge-to-face configuration. This study shows that mild annealing of aromat...

Molecular structure of extended defects in monolayer-scale pentacene thin films

The growth of pentacene thin films for applications in thin-film transistors and other organic electronic devices results in a variety of extended structural defects including dislocations, grain boundaries, and stacking faults. We have used scanning tunneling microscopy (STM) to probe the molecular-scale structure of grain boundaries and stacking faults in a pentacene thin film on a Si (001) surface modified with styrene. Styrene/Si (001) substrates produce pentacene films that are structurally similar to those grown on insulating substrates, but which are sufficiently smooth and conductive for STM studies. STM images show two types of grain boundaries: in-plane high-angle tilt grain boundaries at the junctions between pentacene islands, and twist boundaries between molecular layers. Segments of the tilt grain boundaries are faceted along low-energy crystallographic directions. Stacking faults are found in the plane of individual pentacene grains. Two rows of molecules near the stacking fault are shifted along the surface normal by 60 pm. Electronically relevant trap states may thus be associated with stacking faults in pentacene thin films.

Complexes of 1-hydroxopyridine-2-thione (LH) with Rh(III), Pd(II), Cd(II) and Hg(II): crystal structure of Pd(L)2 · CHCl3

The interactions of 1-hydroxopyridine-2-thione or 2-mercaptopyridine N-oxide (LH) with transition and d10 metal ions have been investigated. The complexes [RhL3] and [ML2] (M = Pd, Cd and Hg) were characterized by physicochemical and spectroscopic methods. The bis(1-oxopyridine-2-thionato)palladium(II) chloroform solvate crystallizes in space group Pna21 with a = 9.1569(15), b = 21.306(3), c = 8.4618(14) Â, Z = 4. The structure can be described in terms of rows of bis(2-mercaptopyridine N-oxide) palladium(II) molecules which alternate with another row of molecules at an angle of approximately 24.9°. The coordination geometry about palladium(II) is nearly square-planar.

Catena-Poly[[chloro(pyridinium-3-carboxylato-κO)zinc(II)]-μ-nicotinato-κ2O:N

The title bis-nicotinate zinc chloride, [Zn(C 6 H 4 NO 2 )Cl(C 6 H 5 NO 2 )] n , has an infinite head-to-tail one-dimensional chain structure. The compound was synthesized under mild hydrothermal conditions. The Zn II atom exhibits a distorted tetrahedral coordination geometry. The structure is statistically disordered, with 0.5 site occupancy for the Zn atom and the H atom located on the pyridine N atom. As a result, Zn positions in the crystal structure alternate between two sites related by a crystallographic twofold axis and rows of molecules are formed, supported by strong N-H...O hydrogen bonds.

Structures Formed by the Chiral Assembly of Racemic Mixtures of Enantiomers: Iodination Products of Elaidic and Oleic Acids

The self-assembled monolayer structure of the products of elaidic acid iodination (the racemic mixture of 9,10-(9S,10R)-diiodooctadecanoic acid and 9,10-(9R,10S)-diiodooctadecanoic acid) and the products of oleic acid iodination (the racemic mixture of 9,10-(9R,10R)-diiodooctadecanoic acid and 9,10-(9S,10S)-diiodooctadecanoic acid) are studied by high-resolution scanning tunneling microscopy. For the iodination products of elaidic acid, the separation of enantiomers into distinct chiral domains during the formation of the 2-D crystal on the highly ordered pyrolytic graphite (HOPG) surface is not observed. Instead, within the diiodooctadecanoic acid SAM, each row of molecules is composed of opposite racemates. The two opposite racemates pack alternately inside a row, using different faces to adsorb on the surface. The unit cell is composed of a pair of opposite racemates, forming a heterochiral structure. For the iodination products of oleic acid, the racemic mixture is observed to exhibit quasi-phase separation during the formation of the 2-D crystal on the HOPG surface. Each row is composed of homochiral acid molecules, either the 9,10-(9R,10R)-diiodooctadecanoic acid (R) or the 9,10-(9S,10S)-diiodooctadecanoic acid (S). The R row and the S row pack alternately, with a unit cell composed of four molecules. Two of the molecules in the unit cell are the 9,10-(9R,10R)-diiodooctadecanoic acid (R) molecules; two are the 9,10-(9S,10S)-diiodooctadecanoic acid (S) molecules. In the unit cell, the two molecules that have the same chirality pack antiparallel inside the homochiral row, using different faces to adsorb on the surface. These results suggest that several different types of chiral assembly are possible. Enantiomers with opposite chirality exhibit many chiral assembly patterns, forming heterochiral structures on the surface in addition to separation to form macroscopic chiral domains. By using different conformations, similar enantiomers with opposite chirality will display many chiral assembly patterns to form heterochiral structures on the surface.

Organic Adsorbate Induced Surface Reconstruction: p-Aminobenzoic Acid on Cu{110}

Large-scale facets, induced by annealing p-aminobenzoate on a Cu{110} surface, are observed in STM. The bunching of {110} steps aligned along the 〈112〉 directions with a separation of 12.75 Å forms the {11 13 1} facets. STM images show that there are two rows of molecules on each {110} terrace of the facet. The faceting mechanism and the relationship to the adsorbate structure are discussed. This large-scale modification of the surface morphology confirms that the adsorption of organic molecules on metal surfaces may cause a significant amount of mass transport in the process of two-dimensional adsorbate crystallization.

Transmission electron microscopy study on microstructure in Langmuir-Blodgett films of fullerene derivatives

Surface pressure-area isotherms of two C60 derivatives, ethoxycarbonyldecylentfullerene and bis(ethoxycarbonyldecylene) fullerene, have been investigated. The molecular aggregation at the air-water interface was reduced and the transfer behavior to various substrates was enhanced as compared with those of pure C60. Structural characterization of the LB films was carried out using high resolution transmission electron microscopy (HRTEM). The HRTEM images revealed regular stacking of the densest packed rows of molecules in the LB films.

Electron Microscopy of Human Erythrocyte Catalase: New Two-Dimensional Crystal Forms

Using the mica-spreading "negative staining-carbon film" procedure, human erythrocyte catalase has been shown to create a number of different periodic or crystalline two-dimensional (2-D) arrays which differ in the arrangement of molecules in the repeating units and the lattice type. Digital image processing has been performed with a 2-D array which contains regularly arranged "undulating" rows of molecules and also with a 2-D crystal form, exhibiting pgg (p22121) symmetry and lattice parameters of a = 12.7 nm, b = 44 nm, and γ= 92°. The data are compared with our previous analysis of a different human erythrocyte catalase 2-D crystal, and the effect of partial-depth negative staining occurring in all the various 2-D forms is discussed.

The organization of cross-linking in collagen fibrils.

The cross-linked peptides in cyanogen bromide digests from rabbit and calf fibrils of type I collagen have been compared by gel filtration and electrophoresis. Fibrils were prepared in vitro from acid-soluble collagen, or tendons were used; both were reduced with borohydride to stabilize cross-linking adducts. The cross-linked peptides were isolated and hydrolyzed, and the reducible cross-links were analyzed. We propose that a prominent pattern of cross-linking involves in-register palisades of molecules overlapping by 27 nm and joined through the condensation of amino-terminal aldol adducts on the carboxy-terminal helical regions of overlapping molecules. Lateral association probably occurs through the carboxy-terminal aldehydes from two molecules forming tri- or quadrivalent adducts with residues in the overlapped molecule. This model favors the recently proposed quasi-hexagonal organization of molecules in fibrils in which rows of molecules occur in lateral register.

Arrangement of cytochrome oxidase molecules in two-dimensional vesicle crystals

The structure of two-dimensional crystals of cytochrome oxidase (Vanderkooi et al. , 1972) has been investigated. By analysing about 30 electron micrographs, taken at different tilt-angles, from crystals stained with uranyl acetate, the crystallographic space group ( P 2 1 2 1 2), three-dimensional packing and rough shape of the cytochrome oxidase molecules have been obtained. The crystalline arrays are composed of two membrane layers which form the top and bottom of a collapsed vesicle. The protein molecules from the two membranes interlock on the inside of the vesicle, an interaction which is essential for the formation of the lattice. Within each membrane, the rows of molecules probably do not touch, being separated by lipid bilayer areas. Each cytochrome oxidase molecule sticks far out into solution on the inside surface of the vesicle, but probably less than half as far on the outside surface. Pairs of molecules are related by a crystallographic 2-fold axis perpendicular to the plane of the membrane, suggesting the possible occurrence of dimers in the natural state. It is not known whether the inside surface of the vesicles corresponds to the inside surface of the mitochondrial inner membrane. The nominal resolution of the analysis of stained material was 30 A. The projected structure of unstained crystals in glucose has also been determinded at a resolution of about 12 A. This projection is completely different from that of stained material and suggests that a more interpretable structure will be obtained from a three-dimensional analysis of unstained material.

The structure of Bacillus Thuringiensis berliner crystals

The structure of the protein crystals formed by Bacillus thuringiensis Berliner, determined from electron micrographs of shadowed carbon replicas of dry crystals, can be described by a tetramolecular face-centered-cubic unit cell 123 A on an edge. The protein molecules appear to be spherical, with a diameter D = 87 A. The bipyramidal shape of these crystals results from their being bounded by eight similar (221) faces on which the rows of molecules are separated by 3 D. Membrane fragments made up of hexagonal arrays of spheres or ellipsoids whose average center-to-center separation is 68 A were common in the preparations examined and were believed to be a component of the cell walls.

The structure of haemoglobin - VI. Fourier projections on the 010 plane

In the preceding papers the molecular Fourier transform was measured as a continuous function of c * along nine lines of constant h in the plane of k = 0. Fourier inversion of this transform gives an electron density map of a single row of molecules in projection on the 010 plane. This map shows molecules of irregular outline and complex internal structure. Because of lack of resolution and the great depth of material projected neither polypeptide chains nor haem groups can as yet be recognized. Along the c * direction the molecular dimensions can be measured with accuracy; along the a direction this is not yet possible, owing to overlap of neighbouring molecules in projection. Indications of the length of the molecules in that direction are obtained from the Fourier projection of a lattice slightly shrunk along a . At low resolution the molecular dimensions can be estimated from a Fourier projection derived by inversion of the ‘salt-water’.transform described in part III, which corresponds to the diffraction by a row of ̒ghost ̓ molecules having the same shape as haemoglobin, but a uniform density throughout. The tilted spheroid of 71 x 54 Å, proposed by us in part II, is a good approximation to the outline of the molecule shown on this projection. Its only unexpected feature is a hollow at the central dyad where the thickness of the molecule is apparently reduced to 32 Å. It is not yet clear what this hollow represents.