scholarly journals Hydrogen properties in an organic molecule revealed by XFEL and electron crystallography

2021 ◽  
Author(s):  
Kiyofumi Takaba ◽  
Saori Maki-Yonekura ◽  
Ichiro Inoue ◽  
Kensuke Tono ◽  
Tasuku Hamaguchi ◽  
...  
Keyword(s):  
Organic Molecule ◽  
Drug Efficacy ◽  
Theoretical Models ◽  
Electron Crystallography ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Small Crystals ◽  
Target Molecules ◽  
Material Sciences ◽  
Coulomb Potentials

Structure analysis of small crystals is important in synthetic organic chemistry, pharmaceutical and material sciences, and related areas, as the conformation of these molecules may differ in large and small crystals, thus affecting the interpretation of their functional properties and drug efficacy. From small crystals, X-ray and electron beams could furnish electron densities and Coulomb potentials of target molecules, respectively. The two beams provide distinctly different information, and this potential has not been fully explored. Here we present the detailed structure of an organic molecule, rhodamine-6g by X-ray free-electron laser (XFEL) and electron crystallography from the same sample batch of microcrystals. This is the first organic molecular structure determined using XFEL at subatomic resolution. Direct comparison between the electron-density and the Coulomb-potential maps together with theoretical models based on Poisson’s equation shows that the position of hydrogen atoms depends on bond type and charge distribution. The combined approach could lead to better insights into their chemical and/or binding properties for a broad range of organic molecules.

The crystal and molecular structure of 1, 2, 3, 4-tetrachloro-5, 6-diphenylcalicene

1970 ◽  
Vol 316 (1527) ◽  
pp. 551-573 ◽  
Keyword(s):  
Crystal And Molecular Structure ◽  
Theoretical Models ◽  
Hydrogen Atoms ◽  
Orthorhombic Space Group ◽  
Full Matrix ◽  
X Ray ◽  
Heavy Atoms ◽  
Atom Pairs ◽  
Anisotropic Temperature ◽  
Novel Method

X-ray structure analysis shows unequivocally that tetrachlorodiphenylcalicene is a polyolefin. The crystals are orthorhombic, space group P 2 1 2 1 2 1 , with a = 11.588, b = 21.158, c = 7.020Å, Z = 4. The structure has been refined by full-matrix least-squares analysis with anisotropic temperature parameters for the heavy atoms and isotropic parameters for the hydrogen atoms. Refinement converged at an R -value of 0.057 for the 1836 observed reflexions. A novel method was used to test theoretical models and compare them with the experi­mentally determined structure. The method is an extension of the constrained refinement technique suggested by Waser in which subsidiary conditions are treated as observations and the constraints are defined by specifying distances between atom pairs.

High Resolution Replication of Organoclay Surfaces

1982 ◽  
Vol 40 ◽  
pp. 576-577
Author(s):  
W. W. Barker ◽  
W. E. Rigsby ◽  
V. J. Hurst ◽  
W. J. Humphreys
Keyword(s):  
Clay Mineral ◽  
Organic Molecule ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Xrd Pattern ◽  
X Ray ◽  
Naturally Occurring ◽  
Silicate Layers ◽  
Mineral Identification

Experimental clay mineral-organic molecule complexes long have been known and some of them have been extensively studied by X-ray diffraction methods. The organic molecules are adsorbed onto the surfaces of the clay minerals, or intercalated between the silicate layers. Natural organo-clays also are widely recognized but generally have not been well characterized. Widely used techniques for clay mineral identification involve treatment of the sample with H2 O2 or other oxidant to destroy any associated organics. This generally simplifies and intensifies the XRD pattern of the clay residue, but helps little with the characterization of the original organoclay. Adequate techniques for the direct observation of synthetic and naturally occurring organoclays are yet to be developed.

Examination of Rabbit Fc Crystals

1968 ◽  
Vol 26 ◽  
pp. 140-141
Author(s):  
J. P. Robinson ◽  
P. G. Lenhert
Keyword(s):  
Molecular Weight ◽  
Flat Plate ◽  
Phosphate Buffer ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutral Ph ◽  
Small Crystals ◽  
Carbon Coated ◽  
Diffraction Patterns

Crystallographic studies of rabbit Fc using X-ray diffraction patterns were recently reported. The unit cell constants were reported to be a = 69. 2 A°, b = 73. 1 A°, c = 60. 6 A°, B = 104° 30', space group P21, monoclinic, volume of asymmetric unit V = 148, 000 A°3. The molecular weight of the fragment was determined to be 55, 000 ± 2000 which is in agreement with earlier determinations by other methods.Fc crystals were formed in water or dilute phosphate buffer at neutral pH. The resulting crystal was a flat plate as previously described. Preparations of small crystals were negatively stained by mixing the suspension with equal volumes of 2% silicotungstate at neutral pH. A drop of the mixture was placed on a carbon coated grid and allowed to stand for a few minutes. The excess liquid was removed and the grid was immediately put in the microscope.

Factors in Photographic Emulsions for Low Dose Electron Crystallography

1980 ◽  
Vol 38 ◽  
pp. 230-231
Author(s):  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
Radiation Damage ◽  
Low Dose ◽  
Damage Effect ◽  
Photographic Emulsion ◽  
Electron Crystallography ◽  
Electron Microscopic ◽  
X Ray ◽  
Signal Contrast ◽  
Diffraction Patterns ◽  
Photographic Emulsions

With the advances in preparing biological materials in a thin and highly ordered form, and in maintaining them hydrated under vacuum, electron crystallography has become an important tool for biological structure investigation at high resolution (1,2). However, the electron radiation damage would limit the capability of recording reflections with low intensities in an electron diffraction pattern. It has been demonstrated that the use of a low temperature stage can reduce the radiation damage effect and that one can expose the specimen with a higher dose in order to increase the signal contrast (3). A further improvement can be made by selecting a proper photographic emulsion. The primary factors in evaluating the suitability of photographic emulsion for recording low dose diffraction patterns are speed, fog level, electron response at low electron exposure, linearity, and usable range of exposure. We have compared these factors with three photographic emulsions including Kodak electron microscopic plate (EMP), Industrex AA x-ray film (AA x-ray) and Kodak nuclear track film (NTB3).

scholarly journals Brightest cluster galaxies: the centre can(not?) hold

2020 ◽  
Vol 500 (1) ◽  
pp. 310-318
Author(s):  
Roberto De Propris ◽  
Michael J West ◽  
Felipe Andrade-Santos ◽  
Cinthia Ragone-Figueroa ◽  
Elena Rasia ◽  
...  
Keyword(s):  
Dark Matter ◽  
Local Environment ◽  
Major Axis ◽  
Theoretical Models ◽  
Dark Matter Halo ◽  
Gas Distribution ◽  
X Ray ◽  
Cluster Galaxies ◽  
Peculiar Velocities ◽  
Brightest Cluster Galaxies

ABSTRACT We explore the persistence of the alignment of brightest cluster galaxies (BCGs) with their local environment. We find that a significant fraction of BCGs do not coincide with the centroid of the X-ray gas distribution and/or show peculiar velocities (they are not at rest with respect to the cluster mean). Despite this, we find that BCGs are generally aligned with the cluster mass distribution even when they have significant offsets from the X-ray centre and significant peculiar velocities. The large offsets are not consistent with simple theoretical models. To account for these observations BCGs must undergo mergers preferentially along their major axis, the main infall direction. Such BCGs may be oscillating within the cluster potential after having been displaced by mergers or collisions, or the dark matter halo itself may not yet be relaxed.

Macromolecular Structure Visualization Tools at NCMI

2000 ◽  
Vol 6 (S2) ◽  
pp. 282-283
Author(s):  
Matthew Dougherty ◽  
Wah Chiu
Keyword(s):  
Human Factors ◽  
3D Visualization ◽  
Three Dimensional ◽  
Theoretical Models ◽  
Biological Research ◽  
Macromolecular Structure ◽  
X Ray ◽  
Visualization Tools ◽  
Types Of Information ◽  
3D Em

Sophisticated tools are needed to examine the results of cyro-microscopy. As the size and resolution of three dimensional macromolecular structures steadily improve, and the speed at with which they can be generated increases, researchers are finding they are inundated with larger datasets and at the same time are compelled to expediently evaluate these structures in unforeseen ways. Integration of EM data with other types of information is becoming necessary and routine; for example X-ray data, 3D EM reconstructions, and theoretical models, must be evaluated in concert to discount or propose hypothesis. To create such tools, the developer must take into account not only the empirical and theoretical possibilities, but also they must master the human factors and computational limits. During the last five years, the National Center for Macromolecular Imaging (NCMI) has progressed from a remedial 3D visualization capability to a collection of visualization tools allowing researchers to focus on the discovery phase of biological research.

The first proof of protonated anion tetrahedra in the tsumcorite-type compounds

2004 ◽  
Vol 68 (5) ◽  
pp. 757-767 ◽  
Author(s):  
T. Mihajlović ◽  
H. Effenberger
Keyword(s):  
Crystal Structure ◽  
Hydrothermal Synthesis ◽  
Single Crystal ◽  
Diffraction Data ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Synthetic Compounds ◽  
X Ray

AbstractHydrothermal synthesis produced the new compound SrCo2(AsO4)(AsO3OH)(OH)(H2O). The compound belongs to the tsumcorite group (natural and synthetic compounds with the general formula M(1)M(2)2(XO4)2(H2O,OH)2; M(1)1+,2+,3+ = Na, K, Rb, Ag, NH4, Ca, Pb, Bi, Tl; M(2)2+,3+ = Al, Mn3+, Fe3+, Co, Ni, Cu, Zn; and X5+,6+ = P, As, V, S, Se, Mo). It represents (1) the first Sr member, (2) the until now unknown [7]-coordination for the M(1) position, (3) the first proof of (partially) protonated arsenate groups in this group of compounds, and (4) a new structure variant.The crystal structure of the title compound was determined using single-crystal X-ray diffraction data. The compound is monoclinic, space group P21/a, with a = 9.139(2), b = 12.829(3), c = 7.522(2) Å, β = 114.33(3)°, V = 803.6(3) Å3, Z = 4 [wR2 = 0.065 for 3530 unique reflections]. The hydrogen atoms were located experimentally.

scholarly journals Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

2013 ◽  
Vol 6 (1) ◽  
pp. 308 ◽  
Author(s):  
Mikael Elias ◽  
Dorothee Liebschner ◽  
Jurgen Koepke ◽  
Claude Lecomte ◽  
Benoit Guillot ◽  
...  
Keyword(s):  
High Resolution ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Diffraction Structure

Bestimmung von innermolekularen Torsionswinkeln aus Hyperfeinstruktur-Aufspaltungen und g-Faktoren

1965 ◽  
Vol 20 (9) ◽  
pp. 1117-1121 ◽  
Author(s):  
K. Möbius
Keyword(s):  
Electron Diffraction ◽  
Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbons ◽  
Small Amplitude ◽  
Membered Ring ◽  
Radical Ions ◽  
Hydrogen Atoms ◽  
Stereochemical Structure ◽  
X Ray ◽  
Phenyl Rings

The stereochemical structure of aromatic hydrocarbons in solution being overcrowded with hydrogen atoms is not known with certainty, because the conventional X-ray and electron diffraction methods are suitable only for samples in the crystalline and vapor phase. Using EPR spectroscopy for the aromatic hydrocarbon radicals biphenyl (—), phenanthrene (—) and pentaphenylcyclopentadienyl (PPCPD) innermolecular twist and bond angles could be determined by means of hfssplittings and g-factors. Stably solvated biphenyl radical ions are found to have twist angles of 38 ±2°; phenanthrene ions turn out to be planar but change their angles of hybridization at particular positions; in the PPCPD radical the phenyl rings oscillate with small amplitude around planes orthogonal to the five-membered ring.

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

2021 ◽  
Vol 19 ◽  
Author(s):  
Kikuko Iida ◽  
Toyokazu Muto ◽  
Miyuki Kobayashi ◽  
Hiroaki Iitsuka ◽  
Kun Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Molecular Conformation ◽  
Weak Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Molecular Surface ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Classical Hydrogen Bond

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

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