The structure of vitamin B 12 - IV. The X-ray analysis of air-dried crystals of B 12

1962 ◽  
Vol 266 (1327) ◽  
pp. 475-493 ◽  
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Electron Density Distribution ◽  
Three Dimensional ◽  
Successive Approximations ◽  
Water Molecules ◽  
Vitamin B ◽  
Dimensional Electron ◽  
X Ray ◽  
Vitamin B 12

Measurements were made during 1948-9 of all the intensities of hkl reflexions observable with chromium Koc X-radiation from air-dried crystals of vitamin B 12 . Calculations parallel with those of J. G. White were carried out on these data. The positions of the cobalt atoms in the crystal structure were found from three-dimensional Patterson series and the positions of 90 atoms of the B 12 molecule and 7 water molecules were derived through three successive approximations to the three-dimensional electron density distribution. The choice of atomic positions was checked against superposition maps derived from the original Patterson series, and assisted by comparisons with other B 12 derivatives. Minor differences appear between the positions derived here and in III; some of these may be real differences due to the state of dryness of the crystals.

The structure of vitamin B 12 . II. The crystal structure of a hexacarboxylic acid obtained by the degradation of vitamin B 12

1959 ◽  
Vol 251 (1266) ◽  
pp. 306-352 ◽  
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Cobalt Atom ◽  
Side Chain ◽  
Vitamin B ◽  
X Ray ◽  
Structure Factors ◽  
Lactam Ring ◽  
Vitamin B 12 ◽  
Made In

A hexacarboxylic acid, obtained by the degradation of vitamin B 12 by Cannon, Johnson & Todd in 1953 has been examined by X-ray analytical methods. These lead to a solution of both the crystal and chemical structure of the acid. The crystals are orthorhombic, a = 24·58, b = 15·52, c = 13·32 Å, space group, P 2 1 2 1 2 1 , n = 4. The asymmetric unit is found to consist essentially of one molecule of hexacarboxylic acid, C 46 H 58 O 13 N 6 . CoCl, two molecules of water and one of acetone. The hexacarboxylic acid molecule has a central cobalt atom in approximately octahedral co-ordination attached to one cyanide group, one chlorine atom and four nitrogen atoms of the corrin nucleus. The nucleus itself is substituted by acetic and propionic acid groups, a lactam ring and a number of methyl groups. The position of the cobalt atom in the crystal structure was first found from Patterson projections and the remaining atomic positions then derived from a series of calculated approximations to the three-dimensional electron density distribution. For these calculations, phases were derived from structure factors calculated on gradually increasing numbers of selected atomic positions from the stage of ρ 1, where only the cobalt atom sites were known, to ρ 10 where 73 atoms, not counting hydrogen, had been placed. The process was not quite straightforward; particular difficulty was experienced in finding the positions of the atoms of one side-chain which may be affected by disorder. The parameters of the atoms have been refined by two cycles of least-squares calculations. A number of observations were made in the course of the analysis which bear on the further use of non-centrosymmetric Fourier syntheses in the study of complex structures. An appendix by A. Vos deals with intensity anomalies observed on the X-ray photographs of the hexacarboxylic acid which provide evidence of its absolute configuration. An appendix by K. N. Trueblood summarizes various aspects of the analysis of the hexacarboxylic acid, seen as a whole.

The structure of vitamin B 12 . VIII. The crystal structure of vitamin B 12 -5'-phosphate

1970 ◽  
Vol 318 (1533) ◽  
pp. 143-167 ◽  
Keyword(s):  
Crystal Structure ◽  
Phosphate Ester ◽  
Water Molecules ◽  
Vitamin B ◽  
X Ray Diffraction ◽  
Fourier Synthesis ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Vitamin B 12 ◽  
Difference Fourier

The crystal structure of vitamin B 12 -5' -phosphate, a biosynthetic precursor of vitamin B 12 , has been determined by X-ray diffraction methods. The air-dried crystals are orthorhombic, space group P 2 1 2 1 2 1 , with a = 23.72 Å, b = 21.74 Å and c = 16.07 Å. The observed density of 1.362 g cm -3 indicates four vitamin B 12 -5' -phosphate and about sixty water molecules in the unit cell. The X-ray diffraction data to 1.2 Å resolution were collected with a PAILRED linear diffractometer using Cu K α radiation from a silicon monochromator. The structure was solved by using Patterson methods in conjunction with the tangent formula and was refined by Fourier and least-squares methods. The final R value for the 2112 observed reflexions is 16.2 %. The structure is very similar to that found by Hodgkin and co-workers for air-dried vitamin B 12 crystals. The difference Fourier synthesis between this compound and vitamin B 12 shows that two water molecules move into phosphate oxygen positions when the phosphate in the precursor is removed, and one acetamide in contact with these water molecules in the vitamin is rotated out of the way in the phosphate. A second acetamide is also differently oriented in the two crystals. The α -glycosidic bond between the ribose and the dimethylbenzimidazole is 16° out of the plane of the base. The ribose conformation is C2'>- exo , and the phosphate ester conformations are similar to those found in other B 12 crystals.

A study on α-RuCl3 crystal structure by scanning tunneling microscopy

1989 ◽  
Vol 47 ◽  
pp. 30-31
Author(s):  
H.-J. Cantow ◽  
H. Hillebrecht ◽  
S. Magonov ◽  
H. W. Rotter ◽  
G. Thiele
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Scanning Tunneling Microscopy ◽  
Electron Density ◽  
Structure Determination ◽  
Electron Density Distribution ◽  
Scanning Tunneling ◽  
Monoclinic Space Group ◽  
Tunneling Microscopy ◽  
X Ray

From X-ray analysis, the conclusions are drawn from averaged molecular informations. Thus, limitations are caused when analyzing systems whose symmetry is reduced due to interatomic interactions. In contrast, scanning tunneling microscopy (STM) directly images atomic scale surface electron density distribution, with a resolution up to fractions of Angstrom units. The crucial point is the correlation between the electron density distribution and the localization of individual atoms, which is reasonable in many cases. Thus, the use of STM images for crystal structure determination may be permitted. We tried to apply RuCl3 - a layered material with semiconductive properties - for such STM studies. From the X-ray analysis it has been assumed that α-form of this compound crystallizes in the monoclinic space group C2/m (AICI3 type). The chlorine atoms form an almost undistorted cubic closed package while Ru occupies 2/3 of the octahedral holes in every second layer building up a plane hexagon net (graphite net). Idealizing the arrangement of the chlorines a hexagonal symmetry would be expected. X-ray structure determination of isotypic compounds e.g. IrBr3 leads only to averaged positions of the metal atoms as there exist extended stacking faults of the metal layers.

scholarly journals High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution

IUCrJ ◽  
2016 ◽  
Vol 3 (2) ◽  
pp. 115-126 ◽  
Author(s):  
E. I. Howard ◽  
B. Guillot ◽  
M. P. Blakeley ◽  
M. Haertlein ◽  
M. Moulin ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Fatty Acid ◽  
High Resolution ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Room Temperature ◽  
Water Molecules ◽  
X Ray

Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H...H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.

scholarly journals Building brain network in electron density map determined by micro-CT

2014 ◽  
Vol 70 (a1) ◽  
pp. C1752-C1752
Author(s):  
Rino Saiga ◽  
Susumu Takekoshi ◽  
Naoya Nakamura ◽  
Akihisa Takeuchi ◽  
Kentaro Uesugi ◽  
...  
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Model Building ◽  
Three Dimensional ◽  
Brain Network ◽  
X Ray ◽  
Density Maps ◽  
Density Map ◽  
Electron Density Map

In macromolecular crystallography, an electron density distribution is traced to build a model of the target molecule. We applied this method to model building for electron density maps of a brain network. Human cerebral tissue was stained with heavy atoms [1]. The sample was then analyzed at the BL20XU beamline of SPring-8 to obtain a three-dimensional map of X-ray attenuation coefficients representing the electron density distribution. Skeletonized wire models were built by placing and connecting nodes in the map [2], as shown in the figure below. The model-building procedures were similar to those reported for crystallographic analyses of macromolecular structures, while the neuronal network was automatically traced by using a Sobel filter. Neuronal circuits were then analytically resolved from the skeletonized models. We suggest that X-ray microtomography along with model building in the electron density map has potential as a method for understanding three-dimensional microstructures relevant to biological functions.

Crystal Structures and Thermal Behavior of Alkaline Earth Tricyanomethanides

2008 ◽  
Vol 63 (3) ◽  
pp. 285-288 ◽  
Author(s):  
Karl E. Bessler ◽  
Claudia C. Gatto ◽  
Lincoln L. Romualdo ◽  
Javier A. Ellena ◽  
Maria J. de A. Sales
Keyword(s):  
Crystal Structure ◽  
Coordination Polymer ◽  
Thermal Behavior ◽  
Crystal Structures ◽  
Alkaline Earth ◽  
Three Dimensional ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Interpenetrating Networks ◽  
X Ray

The alkaline earth tricyanomethanides Mg(tcm)2 · 2H2O, Ca(tcm)2, Sr(tcm)2 ・H2O and Ba(tcm)2 · 2H2O were prepared from aqueous solutions of the respective chlorides and silver tricyanomethanide. Their IR spectra and thermal behavior are described. The crystal structures of Ca(tcm)2 and Ba(tcm)2 · 2H2O were determined by single crystal X-ray diffraction. The structure of Ca(tcm)2 is of the type found for several transition metal tricyanomethanides [1], containing two independent interpenetrating networks. Ba(tcm)2 · 2H2O has a unique crystal structure corresponding to a three-dimensional coordination polymer with nine fold coordinated Ba atoms connected by water molecules and tricyanomethanide anions.

Notizen: Mapping Parts of the Electron Density Distribution from X-Ray Bragg Scattering Intensities (Lambda Technique)

1981 ◽  
Vol 36 (11) ◽  
pp. 1253-1254
Author(s):  
Karl F. Fischer
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Bragg Scattering ◽  
X Ray ◽  
Selection Of

By appropriate selection of two or three wavelengths, intensity differences can be used for obtaining directly the electron density distribution (i.e. the arrangement of atoms) for parts of a crystal structure. Application to macro­molecules and amorphous binary substances appear fea­sible.

scholarly journals A New 3D Coordination Polymer of Bismuth with Nicotinic AcidN-Oxide

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Farzin Marandi ◽  
Ingo Pantenburg ◽  
Gerd Meyer
Keyword(s):  
Crystal Structure ◽  
Thermal Stability ◽  
Coordination Polymer ◽  
Three Dimensional ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
H Nmr ◽  
Thermal Stability Of

The new three-dimensional coordination polymer {[Bi(NNO)2(NO3)]·1.5H2O}n(1, NNO−= nicotinateN-oxide) was synthesized and characterized by elemental analysis, IR and1H-NMR spectroscopy, as well as single-crystal X-ray diffraction analysis.1crystallizes in the monoclinic space group C2/c. The crystal structure consists of a rectangular-shaped grid constructed with NNO linkers. Cavities of a diameter of 7.9–8.3 Å2are filled with disordered water molecules. The thermal stability of the compound was evaluated by thermogravimetric analysis.

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