Collagen: the organic matrix of bone

1984 ◽  
Vol 304 (1121) ◽  
pp. 455-477 ◽  
Keyword(s):  
Self Assembly ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Organic Matrix ◽  
Calcium Hydroxyapatite ◽  
Collagen Molecule ◽  
Crystalline Region ◽  
X Ray ◽  
Molecular Arrangement ◽  
Diffraction Patterns

Collagen is the principal organic matrix in bone. The triple helical region of the molecule is 1014 amino acids long. In fibrils these molecules are staggered axially by integers of 234 residues or 68 nm ( D ). This axial shift occurs by self-assembly and can be understood in terms of a periodicity in the occurrence of apolar and polar residues in the amino acid sequence. Because the molecular length L = 4.47 D , there are gaps 1.5 x 36.5 nm regularly arrayed throughout the fibrils. The three-dimensional molecular arrangement is a quasi-hexagonal lattice with three distinct values for the principal interplanar spacings. Analysis of the intensity distribution in the medium-angle X -ray diffraction patterns from tendons has produced the following picture of the molecular arrangement in fibrils (Fraser et al . 1983). The molecular helices have a coherent length of 32 nm and are tilted parallel to a specific place within the lattice. A regular azimuthal interaction exists between these helices. This crystalline region could be the overlap region with a non-crystalline gap region. However, the gap is still regular axially and the molecular helices retain their structure; their lateral packing is perturbed although they retain a ‘gap’. Neutron and X -ray scattering experiments have shown that calcium hydroxyapatite crystals occur in the gap and are nucleated at a specific though unknown location within the gap. The c -axis of the apatite crystals is parallel to the fibril axis and its length c = 0.688 nm is close to the axial periodicity in a protein with an extended β-conformation. If the telopeptides at the end of a collagen molecule do have this conformation they would either have a highly heterogeneous conformation or exist in a folded manner because the overall length of the telopeptides is shorter than a regular collagen repeat of 0.029 nm would allow.

Solid State Ordering of Wholly Aromatic Copolyesters of Random Monomer Sequence

1993 ◽  
Vol 321 ◽  
Author(s):  
J. Blackwell ◽  
A.-I. Schneider ◽  
C. M. McCullagh
Keyword(s):  
Random Sequence ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Molecular Mechanics Calculations ◽  
Polymer Systems ◽  
X Ray ◽  
Monomer Sequence ◽  
Naphthoic Acid ◽  
Diffraction Patterns

ABSTRACTX-ray diffraction and computer molecular modeling Methods are being used to investigate the ordering of random sequence copolyesters when cooled for the nematic Melt. Data will be presented for the copolymers prepared from p-hydroxybenzoic acid (HBA) and 6-hydroxy-2-naphthoic acid. The non-periodic diffraction patterns arising from the random monomer sequences are also indicative of the presence of limited three dimensional order. For both polymer systems, we can generate the qualitative feature of the x-ray data using models in which short non-identical segments of 10–12 Monomers on adjacent chains are approximately in register at their center. Molecular Mechanics calculations show that mese non-identical sequences can be packed on the observed hexagonal lattice with only small energy differences when compared to analogous homopolymer structures. Data will also be presented showing how x-ray diffraction can be used to follow transesterification of copoly (HBA/HNA) in the nematic MelL

A new model for packing of type-I collagen molecules in the native fibril

1981 ◽  
Vol 1 (10) ◽  
pp. 801-810 ◽  
Author(s):  
Karl A. Piez ◽  
Benes L. Trus
Keyword(s):  
Type I Collagen ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Equatorial Region ◽  
Type I ◽  
X Ray Diffraction ◽  
X Ray ◽  
Left Handed ◽  
Crystal Model ◽  
Collagen Molecules

A specific fibril model is presented consisting of bundles of five-stranded microfibrils, which are usually disordered (except axially) but under lateral compression become ordered. The features are as follows (where D = 234 residues or 67 nm): (1) D-staggered collagen molecules 4.5 D long in the helical microfibril have a left-handed supercoil with a pitch of 400–700 residues, but microfibrils need not have helical symmetry. (2) Straight-tilted 0.5-D overlap regions on a near-hexagonal lattice contribute the discrete x-ray diffraction reflections arising from lateral order, while the gap regions remain disordered. (3) The overlap regions are equivalent, but are crystallographically distinguished by systematic displacements from the near-hexagonal lattice. (4) The unit cell is the same as in a recently proposed three-dimensional crystal model, and calculated intensities in the equatorial region of the x-ray diffraction pattern agree with observed values.

2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

2021 ◽  
pp. 096739112199822
Author(s):  
Ahmed I Abou-Kandil ◽  
Gerhard Goldbeck
Keyword(s):  
Crystalline Structure ◽  
Molecular Modelling ◽  
Three Dimensional ◽  
Uniaxial Stress ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Modelling Techniques ◽  
Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

Determining the C60 molecular arrangement in thin films by means of X-ray diffraction

2011 ◽  
Vol 44 (5) ◽  
pp. 983-990 ◽  
Author(s):  
Chris Elschner ◽  
Alexandr A. Levin ◽  
Lutz Wilde ◽  
Jörg Grenzer ◽  
Christian Schroer ◽  
...  
Keyword(s):  
Thin Films ◽  
Structural Information ◽  
Grazing Incidence ◽  
Test Material ◽  
C60 Fullerene ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Molecular Arrangement ◽  
Diffraction Patterns

The electrical and optical properties of molecular thin films are widely used, for instance in organic electronics, and depend strongly on the molecular arrangement of the organic layers. It is shown here how atomic structural information can be obtained from molecular films without further knowledge of the single-crystal structure. C60 fullerene was chosen as a representative test material. A 250 nm C60 film was investigated by grazing-incidence X-ray diffraction and the data compared with a Bragg–Brentano X-ray diffraction measurement of the corresponding C60 powder. The diffraction patterns of both powder and film were used to calculate the pair distribution function (PDF), which allowed an investigation of the short-range order of the structures. With the help of the PDF, a structure model for the C60 molecular arrangement was determined for both C60 powder and thin film. The results agree very well with a classical whole-pattern fitting approach for the C60 diffraction patterns.

scholarly journals Hard X-ray polarizer to enable simultaneous three-dimensional nanoscale imaging of magnetic structure and lattice strain

2016 ◽  
Vol 23 (5) ◽  
pp. 1210-1215 ◽  
Author(s):  
Jonathan Logan ◽  
Ross Harder ◽  
Luxi Li ◽  
Daniel Haskel ◽  
Pice Chen ◽  
...  
Keyword(s):  
Magnetic Circular Dichroism ◽  
Three Dimensional ◽  
Control Sample ◽  
Magnetic Ordering ◽  
X Rays ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
Diffraction Patterns ◽  
A New Technique

Recent progress in the development of dichroic Bragg coherent diffractive imaging, a new technique for simultaneous three-dimensional imaging of strain and magnetization at the nanoscale, is reported. This progress includes the installation of a diamond X-ray phase retarder at beamline 34-ID-C of the Advanced Photon Source. The performance of the phase retarder for tuning X-ray polarization is demonstrated with temperature-dependent X-ray magnetic circular dichroism measurements on a gadolinium foil in transmission and on a Gd5Si2Ge2crystal in diffraction geometry with a partially coherent, focused X-ray beam. Feasibility tests for dichroic Bragg coherent diffractive imaging are presented. These tests include (1) using conventional Bragg coherent diffractive imaging to determine whether the phase retarder introduces aberrations using a nonmagnetic gold nanocrystal as a control sample, and (2) collecting coherent diffraction patterns of a magnetic Gd5Si2Ge2nanocrystal with left- and right-circularly polarized X-rays. Future applications of dichroic Bragg coherent diffractive imaging for the correlation of strain and lattice defects with magnetic ordering and inhomogeneities are considered.

Construction of a three-dimensional supramolecular framework based on an anionic cadmium(II) coordination network and protonated dipyridine organic cations

2018 ◽  
Vol 74 (8) ◽  
pp. 889-893
Author(s):  
Qian-Kun Zhou ◽  
Lin Wang ◽  
Dong Liu
Keyword(s):  
Hydrogen Bonding ◽  
Self Assembly ◽  
Title Compound ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Coordination Network ◽  
Hydrogen Bonding Interactions ◽  
Point Symbol

As a class of multifunctional materials, crystalline supramolecular complexes have attracted much attention because of their unique architectures, intriguing topologies and potential applications. In this article, a new supramolecular compound, namely catena-poly[4,4′-(buta-1,3-diene-1,4-diyl)dipyridin-1-ium [(μ4-benzene-1,2,4,5-tetracarboxylato-κ6 O 1,O 1′:O 2:O 4,O 4′:O 5)cadmium(II)]], {(C14H14N2)[Cd(C10H2O8)]} n or {(1,4-H2bpbd)[Cd(1,2,4,5-btc)]} n , has been prepared by the self-assembly of Cd(NO3)2·4H2O, benzene-1,2,4,5-tetracarboxylic acid (1,2,4,5-H4btc) and 1,4-bis(pyridin-4-yl)buta-1,3-diene (1,4-bpbd) under hydrothermal conditions. The title compound has been structurally characterized by IR spectroscopy, elemental analysis, powder X-ray diffraction and single-crystal X-ray diffraction analysis. Each CdII centre is coordinated by six O atoms from four different (1,2,4,5-btc)4− tetraanions. Each CdII cation, located on a site of twofold symmetry, binds to four carboxylate groups belonging to four separate (1,2,4,5-btc)4− ligands. Each (1,2,4,5-btc)4− anion, situated on a position of \overline{1} symmetry, binds to four crystallographically equivalent CdII centres. Neighbouring CdII cations interconnect bridging (1,2,4,5-btc)4− anions to form a three-dimensional {[Cd(1,2,4,5-btc)]2−} n anionic coordination network with infinite tubular channels. The channels are visible in both the [1\overline{1}0] and the [001] direction. Such a coordination network can be simplified as a (4,4)-connected framework with the point symbol (4284)(4284). To balance the negative charge of the metal–carboxylate coordination network, the cavities of the network are occupied by protonated (1,4-H2bpbd)2+ cations that are located on sites of twofold symmetry. In the crystal, there are strong hydrogen-bonding interactions between the anionic coordination network and the (1,4-H2bpbd)2+ cations. Considering the hydrogen-bonding interactions, the structure can be further regarded as a three-dimensional (4,6)-connected supramolecular architecture with the point symbol (4264)(42687·84). The thermal stability and photoluminescence properties of the title compound have been investigated.

The Atomic Order in Guinier-Preston Zones of Aluminum-Silver Alloys

1963 ◽  
Vol 7 ◽  
pp. 1-13 ◽  
Author(s):  
Volkmar Gerold ◽  
Heinz Auer ◽  
Winfried Merz
Keyword(s):  
Room Temperature ◽  
Three Dimensional ◽  
Miscibility Gap ◽  
X Rays ◽  
Atomic Order ◽  
Zone Size ◽  
X Ray ◽  
Angle Scattering ◽  
Diffraction Patterns ◽  
Step Quenching

AbstractThe formation of the spherical Guinier—Preston zones in an aluminum-silver alloy is governed by a metastable miscibility gap, which consists of two different sections. The lower section occurs below 170°C (η state), the higher section up to 420°C (∊ state). The zones in the two sections differ in their silver concentration and in their atomic order. To prove the change in order, a combination of X-ray small-angle scattering and electric resistivity measurements was used. As the resistivity depends on the zone size and the atomic order, the change in order can be found when the zone size is known. This size was measured by the X-ray technique. To complete the results, X-rays ingle-crystal diffraction patterns with monochromatic radiation were taken at different stages. According to these patterns, three different states must be distinguished.The η′ state exists at room temperature after quenching from 550°C. The silver atoms prefer a layered arrangement in the zones, which is not very stable. It is destroyed after short annealings above 100°C. The η state is developed during annealing below 170°C. A three-dimensional atomic order is built up with increasing zone size, which results in a marked decrease in the resistivity. For the ∊ state (above 170°C), a nearly random atomic distribution exists. Step-quenching experiments prove that the ordered η state can also be developed at room temperature.

Algorithms for the calculation of X-ray diffraction patterns from finite element data

2010 ◽  
Vol 43 (6) ◽  
pp. 1287-1299 ◽  
Author(s):  
E. Wintersberger ◽  
D. Kriegner ◽  
N. Hrauda ◽  
J. Stangl ◽  
G. Bauer
Keyword(s):  
Finite Element ◽  
Three Dimensional ◽  
Point Of View ◽  
X Ray Diffraction ◽  
Displacement Fields ◽  
X Ray ◽  
Si Substrates ◽  
Diffraction Patterns ◽  
Simulation Point ◽  
Ccd Detectors

A set of algorithms is presented for the calculation of X-ray diffraction patterns from strained nanostructures. Their development was triggered by novel developments in the recording of scattered intensity distributions as well as in simulation practice. The increasing use of two-dimensional CCD detectors in X-ray diffraction experiments, with which three-dimensional reciprocal-space maps can be recorded in a reasonably short time, requires efficient simulation programs to compute one-, two- and three-dimensional intensity distributions. From the simulation point of view, the finite element method (FEM) has become the standard tool for calculation of the strain and displacement fields in nanostructures. Therefore, X-ray diffraction simulation programs must be able to handle FEM data properly. The algorithms presented here make use of the deformation fields calculated on a mesh, which are directly imported into the calculation of diffraction patterns. To demonstrate the application of the developed algorithms, they were applied to several examples such as diffraction data from a dislocated quantum dot, from a periodic array of dislocations in a PbSe epilayer grown on a PbTe pseudosubstrate, and from ripple structures at the surface of SiGe layers deposited on miscut Si substrates.

scholarly journals X-ray studies of the structure of hair, wool, and related fibres - III—The configuration of the keratin molecule and its orientation in the biological cell

1935 ◽  
Vol 150 (871) ◽  
pp. 533-551 ◽  
Keyword(s):  
Average Distance ◽  
Three Dimensional ◽  
Side Chains ◽  
X Ray ◽  
Molecular Arrangement ◽  
Proposed Model ◽  
Basic Features ◽  
Geometrical Argument ◽  
Diffraction Effects ◽  
Physical And Chemical

One of the difficulties associated with the X-ray study of biological structures arises from the fact that such structures, while not in general unorganized “powders,” are nevertheless usually built up of numerous submicroscopic individuals of continuously varying orientation: in the typical biological “fibre,” for example, the imperfectly crystalline mole­cular aggregates all lie with one and the same crystallographic direction either approximately parallel to the fibre-axis or spirally inclined at some approximately constant angle to it; but subject to this limitation there may be present within the compass of the X-ray beam all orientations up to the maximum possible consistent with axial symmetry. This means that though we may not be condemned to work in the least profitable field of X-ray technique, that of the completely random “powder photograph,” yet we are debarred from the full geometrical advantages to be derived from operating with a single macroscopic crystal. Speaking briefly, the main trouble lies in the difficulty or impossibility of measuring sufficient inter-directional angles to define the molecular arrangement without ambiguity. Sometimes it is possible to draw very plausible conclusions, or even conclusions almost certainly correct; but in others the diffraction effects are so ill-defined as to preclude altogether the use of direct geometrical argument, and compel us to fall back on indirect reasoning based on evidence from various sources, including comparative photographs of related structures. The X-ray investigation of proteins in particular is a many-sided enquiry of this nature, for the diffraction effects are susceptible of interpretation only in relation to other physical and chemical data. The X-ray photographs then serve to give form, so to speak, to such data—to provide the three-dimensional framework necessary to build them into a coherent whole. Papers I and II in this series show how, working along these lines, it has been found possible to derive the basic features of the keratin molecule or complex, both in its unextended form (α) and in its extended form ((β), and to apply the proposed model to the interpretation of the long-range elasticity and other characteristic properties of mammalian hairs. The structure of β-keratin may be described most simply as that of a flat “polypeptide grid,” in which a succession of fully extended main-chains are bound side by side through linkages, both electrostatic and co-valent, between certain of their side-chains; while that of α-keratin (the normal equilibrium form) may be thought of as derived from (β-keratin by a regular folding of the main-chains in planes transverse to the side-chains. By this means the length of the molecule in the direction of the main-chains is reduced to approximately one-half (the average distance apart of the side-chains is decreased from rather less than 3·4 A to about 1·7 A), while the average separation of the main-chains in the plane of the side-chains (the plane of the “grid”) remains roughly constant (9·8 A). In the β-keratin crystallites the grids are piled one on top of another with the main-chains parallel and separated by a distance of 4·65 A.

Incorporating particle symmetry into orientation determination in single-particle imaging

2018 ◽  
Vol 74 (5) ◽  
pp. 512-517
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Three Dimensional ◽  
Symmetric Case ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
Orientation Determination

In coherent-diffraction-imaging experiments X-ray diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. If the particle has symmetry, finding the orientation of a pattern can be ambiguous. With some modifications, the correlation-maximization method can find the relative orientations of the diffraction patterns for the case of symmetric particles as well. After convergence, the correlation maps show the symmetry of the particle and can be used to determine the symmetry elements and their orientations. The C factor, slightly modified for the symmetric case, can indicate the consistency of the assembled three-dimensional intensity distribution.

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