Crystalline conformation and structure of lichenan and barley β-glucan

1983 ◽  
Vol 61 (7) ◽  
pp. 1608-1616 ◽  
Author(s):  
I. Tvaroska ◽  
K. Ogawa ◽  
Y. Deslandes ◽  
R. H. Marchessault
Keyword(s):  
Cell Walls ◽  
Unit Cell ◽  
Group Symmetry ◽  
Fiber Axis ◽  
Dihedral Angles ◽  
X Ray ◽  
Naturally Occurring ◽  
C Fiber ◽  
Intramolecular Hydrogen ◽  
Helical Parameters

An investigation based on X-ray fiber diffraetion and conformational analysis methods has provided a proposed chain conformation and crystalline structure for lichenan, a poly β(1 → 3) cellotriose. The analysis of the fiber diagram of the hydrated form of lichenan led to a trigonal unit cell of dimension a = b = 9.92 Å and c (fiber axis) = 42.03 Å, with cellotriose as the asymmetric unit and six cellotriose residues per unit cell. A unit cell of the dry form is also trigonal with a = b = 9.36 Å and c = 42.03 Å. A right-handed threefold helix made up of three cellotriose residues was derived from a comparison of experimental helical parameters with isoenenergy conformational maps made by plotting dihedral angles ([Formula: see text], ψ) at the β(1 → 3) linkage. A virtual bond approach was also used to arrive at the proposed conformation which is stabilized by intramolecular hydrogen bonds between all carbohydrate units. The refinement of geometrical and packing parameters produced results consistent with an antiparallel arrangement of the two chains corresponding to a space group symmetry of P31. The naturally occurring copolysaccharides known as mixed (1 → 3) and (1 → 4) β-glucans from the cell walls of barley endosperm have been shown to crystallize in the same fashion as lichenan.

Hierarchial Structure and Physical Properties of Natural Cellulosic Fibers

1991 ◽  
Vol 255 ◽  
Author(s):  
Ludwig Rebenfeld
Keyword(s):  
Building Blocks ◽  
Decomposition Temperature ◽  
Fiber Axis ◽  
Hydroxyl Groups ◽  
Wood Fibers ◽  
Cellulosic Fibers ◽  
Naturally Occurring ◽  
Specific Source ◽  
Free Hydroxyl ◽  
Intramolecular Hydrogen

AbstractNatural cellulosic fibers have in common the fact that cellulose is the key polymeric component in the structure, although the chemical composition varies widely depending on the specific source of the fibers. Cellulose is a long-chain linear condensation polymer of β-D-glucose with three free hydroxyl groups on each monomeric unit, resulting in strong inter- and intramolecular hydrogen bonds. Because of the hydrogen bond network, and also due to restricted rotation around the polymeric 1,4- β-linkage, cellulose is a rigid and stiff chain with a Tg well above the chemical decomposition temperature.Despite the high Tg native cellulose is invariably highly crystalline as a result of the biosynthetic process. In naturally occurring cellulosic fibers, the cellulose crystallites are aggregated into fibrils which constitute the underlying building blocks of the fiber. In cotton, the fibrils are laid down during the development or growth of the fiber in the form of concentric layers. The fibrils are disposed at an angle of 23° with respect to the fiber axis and thus they describe a helical pattern. The sense of the helix reverses frequently along the length of the fiber. This morphology is unique to cotton; other cellulosic fibers such as ramie and jute have similar fibrillar structures, but fibrillar angles in the 5 to 10 degree range, with no reversals. Wood fibers, on the other hand, are structurally more heterogeneous and may be considered as composites.

Octahedral tilting in the tungsten bronzes

2015 ◽  
Vol 71 (3) ◽  
pp. 342-348 ◽  
Author(s):  
Thomas A. Whittle ◽  
Siegbert Schmid ◽  
Christopher J. Howard
Keyword(s):  
Group Theory ◽  
Computer Program ◽  
Unit Cell ◽  
Group Symmetry ◽  
Space Group Symmetry ◽  
Space Group ◽  
X Ray ◽  
Unit Cells ◽  
Octahedral Tilting ◽  
Special Points

Possibilities for `simple' octahedral tilting in the hexagonal and tetragonal tungsten bronzes (HTB and TTB) have been examined, making use of group theory as implemented in the computer programISOTROPY. For HTB, there is one obvious tilting pattern, leading to a structure in space groupP63/mmc. This differs from the space groupP63/mcmfrequently quoted from X-ray studies – these studies have in effect detected only displacements of the W cations from the centres of the WO6octahedra. The correct space group, taking account of both W ion displacement and the octahedral tilting, isP6322 – structures in this space group and matching this description have been reported. A second acceptable tilting pattern has been found, leading to a structure inP6/mmmbut on a larger `2 × 2 × 2' unit cell – however, no observations of this structure have been reported. For TTB, a search at the special points of the Brillouin zones revealed only one comparable tilting pattern, in a structure with space-group symmetryI4/mon a `21/2 × 21/2by 2' unit cell. Given several literature reports of larger unit cells for TTB, we conducted a limited search along the lines of symmetry and found structures with acceptable tilt patterns inBbmmon a `21/22 × 21/2 × 2' unit cell. A non-centrosymmetric version has been reported in niobates, inBbm2 on the same unit cell.

The structure and conformation of cis-2-phenylcyclobutanecarboxylic acid and cis-3-(p-fluorophenyl)cyclobutanecarboxylic acid

1983 ◽  
Vol 61 (7) ◽  
pp. 1422-1427 ◽  
Author(s):  
George M. Reisner ◽  
James D. Korp ◽  
Ivan Bernal ◽  
Richard Fuchs
Keyword(s):  
Unit Cell ◽  
The Other ◽  
Dihedral Angles ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Cyclobutanecarboxylic Acid ◽  
Cyclobutane Ring

The structure of cis-2-phenylcyclobutanecarboxylic acid (1) and cis-3-(p-fluorophenyl)cyclobutanecarboxylic acid (2) have been determined by X-ray diffraction methods. Crystals of 1 are monoclinic, space group C2/c with a = 15.420(8), b = 11.687(6), c = 11.226(5) Å, β = 112.45(4)°, and eight molecules in the unit cell. Crystals of 2 are monoclinic, space group P21/n, a = 8.038(5), b = 5.405(4), c = 22.69(1) Å, and β = 97.30(4)°, with four molecules in the unit cell. In both compounds the cyclobutane ring is puckered, with dihedral angles of 27° and 31°. The bond joining the substituted ring atoms in 1 is significantly longer (1.581(2) Å) than the other three (average 1.535(2) Å), due to crowding of substituents. In 2 both the carboxyl and phenyl substituents are close to the bisecting geometry, whereas in 1 both substituents deviate from this conformation, the carboxyl more than the phenyl.

Highly Polymeric Compounds. CLXIV. Unit Cell Diagrams and the Microstructure of “Single Crystals” of Rubber. Determination of the Lattice of Macromolecules of Rubber according to New X-Ray Methods

1939 ◽  
Vol 12 (4) ◽  
pp. 719-733
Author(s):  
Erwin Sauter
Keyword(s):  
Considerable Extent ◽  
Unit Cell ◽  
Fiber Axis ◽  
X Ray ◽  
Ordinary Temperature ◽  
Polymeric Compounds ◽  
Face Centered ◽  
Pass Through ◽  
Ray Methods

Abstract 1. The macromolecular lattice of rubber is rhombic and has the constants: a .......................12.60 ± 0.05 A.U. c ....................... 8.91 ± 0.05 A.U. b ....................... 8.20 ± 0.05 A.U. 2. The number of isoprene residues in the cell is computed to be 7.92, i.e., essentially 8; the density obtained roentgenographically is 0.974, which is in reasonable agreement with the value of 0.965 found experimentally. The discrepancies of earlier measurements are at the same time eliminated. (3) The four chains which pass through the unit cell in the direction of the fiber axis are probably columnar tub-like chains with a cis-arrangement at the double bonds which are assembled after the manner of a lattice face-centered on one side. (4) After being stretched to a considerable extent at ordinary temperature, eucolloidal “fused” rubber crystallizes with formation of microscopic crystalline regions of indefinitely great linear tension.

Die Kristallstrukturen von cis- und trans-Dichlorstilben

1984 ◽  
Vol 39 (4) ◽  
pp. 409-415 ◽  
Author(s):  
Evamarie Hey ◽  
Frank Weller ◽  
Kurt Dehnicke ◽  
Günther Maier
Keyword(s):  
Bond Length ◽  
Point Group ◽  
Unit Cell ◽  
Dihedral Angles ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Phenyl Rings ◽  
Cis And Trans

The crystal structures of cis- and trans-dichlorostilbene were determined from X-ray diffraction data, cw-dichlorostilbene crystallizes in the rhombohedral space group R3̄ with 18 formula units per unit cell (821 observed independent reflexions, R = 0.064) with the dimensions a = b = 3323, c = 601 pm, γ = 120°. The molecule corresponds to the point group C1 with a C = C bond length of 133 pm; the dihedral angles of the phenyl rings with the corresponding C = C-Cl plane are 48° and 72°, respectively. Trans-dichlorostilbene crystallizes in the monoclinic space group P21/n with two formula units per unit cell (1138 independent reflexions, R = 0.056) with the dimensions a = 572, b = 1733, c = 641 pm, β = 111°. The molecule is centrosymmetric (Ci) with a C = C bond length of 133 pm; the dihedral angle of the phenyl rings and the Cl - C = C plane is 71°. The stilbene molecules are disordered about the centre of symmetry in two orientations with the ratio 3:7.

scholarly journals Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2

2021 ◽  
Author(s):  
Aayatti Mallick Gupta ◽  
Sasthi Charan Mandal ◽  
Jaydeb Chakrabarti ◽  
Sukhendu Mandal
Keyword(s):  
Conformational Changes ◽  
Md Simulation ◽  
Immune Escape ◽  
Dihedral Angles ◽  
Radius Of Gyration ◽  
Simulation Studies ◽  
Epitope Region ◽  
Naturally Occurring ◽  
Intramolecular Hydrogen ◽  
Opening Up

SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein which may influence the pathogenesis of the concern SARS-CoV-2 through the development of antibody escape variants. We consider the effect of mutations in some of the epitope regions including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. P323L mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, the fluctuations in the dihedral angles in the epitope:paratope (IgG) interface increase which destabilize the interface. Such mutations may help in escaping antibody mediated immunity of the host.

Hétérocycles à fonction quinone. V. Réaction anormale de la butanedione avec la diamino-1,2 anthraquinone; structure cristalline de la naphto [2,3-f] quinoxalinedione-7,12 obtenue

1984 ◽  
Vol 62 (3) ◽  
pp. 526-530 ◽  
Author(s):  
Michel Baron ◽  
Sylviane Giorgi-Renault ◽  
Jean Renault ◽  
Patrick Mailliet ◽  
Daniel Carré ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Direct Method ◽  
Intramolecular Hydrogen Bonding ◽  
Unit Cell ◽  
Principal Characteristic ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
Intramolecular Hydrogen ◽  
Unit Cell Dimensions

Butanedione reacts on heating with 1,2-diaminoanthraquinone to give, not the expected 2,3-dimethyl-naphtho[2,3-f]quinoxaline-7,12-dione 3, but 2-(2-hydroxy-2-methyl-3-oxobutyl)-3-methylnaphtho[2,3-f]quinoxaline-7,12-dione 4a whose structure was established by X-ray diffraction. This compound crystallizes in the triclinic [Formula: see text] space group with unit cell dimensions of a = 9.091 (1), b = 16.966 (4), c = 12.375 (3) Å; α = 100.75 (2), β = 101.83 (2), γ = 100.29 (2)°, V = 1789 Å3, Z = 4. The structure was resolved by the direct method and refined to R = 0.039 for 3027 independent reflections. The overall conformation of the molecule is essentially planar. The principal characteristic is the presence of two cyclic arrangements caused by intramolecular hydrogen bonding. 2,3-Dimethylnaphtho[2,3-f]quinoxaline-7,12-dione is the intermediate in this reaction.

Cadmium complexes of thiones. Part II.1 A synthetic, solution, and solid-state MAS 111/113Cd NMR study of cadmium complexes of 1,3-thiazolidine-2-thione, and the structures of [tetrakis(1,3-thiazolidine-2-thione)cadmium] trifluoromethanesulfonate ([Cd(C3H5NS2)4](CF3SO3)2) and [tetrakis(1,3-thiazolidine-2-thione)cadmium][tetrakis(nitrato-O,O')cadmate] ([Cd(C3H5NS2)4][Cd(O2NO)4])

2001 ◽  
Vol 79 (9) ◽  
pp. 1330-1337
Author(s):  
Umarani Rajalingam ◽  
Philip AW Dean ◽  
Hilary A Jenkins ◽  
Michael Jennings ◽  
James M Hook
Keyword(s):  
Point Group ◽  
Mas Nmr ◽  
Unit Cell ◽  
Group Symmetry ◽  
Cadmium Complexes ◽  
Space Group ◽  
X Ray ◽  
Nmr Data ◽  
Group I ◽  
Cp Mas Nmr

Treatment of Cd(O3SCF3)2 with the stoichiometric quantity of 1,3-thiazolidine-2-thione (tztH) allows isolation of [Cd(tztH)4](O3SCF3)2 (1). When tztH:Cd [Formula: see text] 2 the reaction of Cd(NO3)2·4H2O with tztH leads to [Cd(tztH)4][Cd(O2NO)4] (2). The structures of both 1 and 2 have been determined by single crystal X-ray analysis. Colourless crystals of 1 are orthorhombic, space group Fdd2, with eight molecules per unit cell (Z = 8) of dimensions a = 20.139(3), b = 23.332(5), c = 14.214(3) Å. Those of 2 are tetragonal, space group I [Formula: see text], with four molecules per unit cell (Z = 4) of dimensions a = 13.8853(11), c = 8.077(2) Å. The discrete homoleptic cation [Cd(tztH)4]2+ is characterized for the first time in 1 and 2. The cations are of point group symmetry C2 and S4 in 1 and 2, respectively. In both cases the ligands are S-bound, and the CdS4 kernel is a squashed tetrahedron. In 2, the eight-coordinate anion [Cd(O2NO)4]2- is characterized for the second time. 113Cd CP MAS NMR data are reported for solid 1 and 2, and also for solids produced by fusing Cd(NO3)2·4H2O with different molar ratios amounts of tztH, and by fusing Cd(O3SCF3)2 with six mol equivalents of tztH. In the Cd(NO3)2·4H2O:tztH mixtures, species identified include unreacted cadmium salt 2 ([Cd(tztH)4](NO3)2) and possibly Cd(tztH)3(NO3)2. [Cd(tztH)4](NO3)2 becomes the major species only when a significant excess of tztH is used. In the mixtures with tztH:Cd > 4, neither Cd(NO3)2·4H2O nor Cd(O3SCF3)2 form complexes containing more than four tztH ligands. Reduced-temperature 111Cd NMR data are reported for Cd(ClO4)2·6H2O:tztH mixtures in MeOH. Species identified are Cd(tztH)w2+(solv) (w = 0–3).Key words: 1,3-thiazolidine-2-thione, cadmium complexes, X-ray analysis, 113Cd CP MAS NMR, solution 111Cd NMR, tetrakis(1,3-thiazolidine-2-thione)cadmium(2+) cation, tetrakis(nitrato-O,O')cadmate(2–) anion.

scholarly journals An X-ray study of horse methaemoglobin. I

1947 ◽  
Vol 191 (1024) ◽  
pp. 83-132 ◽  
Keyword(s):  
Internal Structure ◽  
Free Water ◽  
Unit Cell ◽  
Group Symmetry ◽  
Monoclinic Space Group ◽  
Average Height ◽  
X Ray Diffraction ◽  
Molecular Scattering ◽  
Space Group ◽  
X Ray

The paper describes a detailed study of horse methaemoglobin by single crystal X-ray diffraction methods. The results give information on the arrangement of the molecules in the crystal, their shape and dimensions, and certain features of their internal structure. Horse methaemoglobin crystallizes in the monoclinic space group C 2 with two molecules of weight 66, 700 per unit cell. In addition, the wet crystals contain liquid of crystallization which fills 52.4% of the unit cell volume. Deliberate variations in the amount and com­position of the liquid of crystallization, and the study of the effects of such variations on the X-ray diffraction pattern, form the basis of the entire analysis. The composition of the liquid of crystallization can be varied by allowing heavy ions to diffuse into the crystals. This increases the scattering contribution of the liquid relative to that of the protein molecules and renders it possible to distinguish the one from the other. The method is analogous to that of isomorphous replacement commonly used in X-ray analysis. It yielded valuable information on the shape and character of the haemoglobin molecules and also led to the determination of the phase angles of certain reflexions. The amount of liquid of crystallization was varied by swelling and shrinkage of the crystals. This involves stepwise, reversible transitions between different well-defined lattices, each being stable in a particular environment of the crystal. The lattice changes were utilized in two different ways: the first involved comparison of Patters on projections at different stages of swelling and shrinkage, and the second an attempt to trace the molecular scattering curve as a function of the diffraction angle. The results of the analysis can be summarized as follows. The methaemoglobin molecules resemble cylinders of an average height of 34 A and a diameter of 57 A. In the crystal these cylinders form close-packed layers which alternate with layers of liquid of crystallization. The layers of haemoglobin molecules themselves do not swell or shrink, either in thickness or in area, except on complete drying, and lattice changes merely involve a shearing of the haemoglobin layers relative to each other, combined with changes in the thickness of the liquid layer. Thus the molecules do not seem to be penetrated by the liquid of crystallization, and their structure is unaffected by swelling and shrinkage of the crystal. Space-group symmetry requires that each molecule consists of two chemically and struc­turally identical halves. Evidence concerning the internal structure of the molecules comes both from two-dimensional Patterson projections and one-dimensional Fourier projections. The former indicate that interatomic vectors of 9 to 11 A occur frequently in many directions, and the latter show four prominent concentrations of scattering matter just under 9 A apart along a line normal to the layers of haemoglobin molecules. No structural interpretation of these features is as yet attempted. The liquid of crystallization consists of two distinct components: water ‘bound’ to the protein and not available as solvent to diffusing ions, and ‘free’ water in dynamic equilibrium with the suspension medium. An estimate of the ‘frictional ratio’ based on the molecular shape and hydration found in this analysis is in good agreement with the frictional ratio calculated from the sedimentation constant.

The External Shape of Human γ GI Immunoglobulin from Crystal Sections

1971 ◽  
Vol 29 ◽  
pp. 428-429
Author(s):  
L. W. Labaw
Keyword(s):  
Molecular Weight ◽  
Sodium Phosphate ◽  
Osmium Tetroxide ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Large Molecular Weight ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystallographic Axes

Crystals of a human γGl immunoglobulin have the external morphology of diamond shaped prisms. X-ray studies have shown them to be monoclinic, space group C2, with 2 molecules per unit cell. The unit cell dimensions are a = 194.1, b = 91.7, c = 51.6Å, 8 = 102°. The relatively large molecular weight of 151,000 and these unit cell dimensions made this a promising crystal to study in the EM.Crystals similar to those used in the x-ray studies were fixed at 5°C for three weeks in a solution of mother liquor containing 5 x 10-5M sodium phosphate, pH 7.0, and 0.03% glutaraldehyde. They were postfixed with 1% osmium tetroxide for 15 min. and embedded in Maraglas the usual way. Sections were cut perpendicular to the three crystallographic axes. Such a section cut with its plane perpendicular to the z direction is shown in Fig. 1.This projection of the crystal in the z direction shows periodicities in at least four different directions but these are only seen clearly by sighting obliquely along the micrograph.

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