Experimental determination of electrostatic properties of Na–X zeolite from high resolution X-ray diffraction

2014 ◽  
Vol 16 (24) ◽  
pp. 12228-12236 ◽  
Author(s):  
F. F. Porcher ◽  
M. Souhassou ◽  
C. E. P. Lecomte
Keyword(s):  
High Resolution ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Cation Site ◽  
X Ray ◽  
X Zeolite ◽  
Adsorption Of Water ◽  
Zeolite P ◽  
Resolution Single

High resolution single crystal X-ray diffraction is used to obtain the electron density and atomic charges in Na–X zeolite. The Coulomb potential and interaction energies are calculated for a given Na+ distribution and are discussed in connection with cation site affinities and adsorption of water molecules in the zeolite.

Etude structurale par diffraction des RX et spectroscopie IR des hydrates 10 et 8.4 Å de kaolinite

1999 ◽  
Vol 32 (5) ◽  
pp. 968-976 ◽  
Author(s):  
S. Jemai ◽  
A. Ben Haj Amara ◽  
J. Ben Brahim ◽  
A. Plançon
Keyword(s):  
Water Molecule ◽  
Octahedral Site ◽  
Ammonium Fluoride ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Tetrahedral Sheet ◽  
X Ray ◽  
Octahedral Sites ◽  
Sheet Structure

Two hydrated kaolinites, characterized by 10 and 8.4 Å basal distances, were synthesized by treating the kaolinite KGa-1 with dimethyl sulfoxide (DMSO) and ammonium fluoride (NH4F). The X-ray diffraction study was based on a comparison between the experimental and calculated profiles. This study was conducted in two steps: firstly, the study of the 00lreflections enabled the determination of the stacking mode alongc*, the number of water molecules and their positions along the normal to the plane of the sheet structure; secondly, the study of thehkbands, withhand/ork≠ 0, enabled the determination of the stacking mode and the positions of the water molecules in the (a,b) plane. The 10 Å hydrated kaolinite is characterized by two water molecules per Al2Si2O5(OH)4unit, situated at 3 and 3.4 Å from the hydroxyl surface, over the octahedral sites. Two adjacent layers are translated with respect to each other, withT11= −0.38a− 0.37b+ 10n. The 8.4 Å hydrated kaolinite is characterized by one water molecule per Al2Si2O5(OH)4unit, situated at 2.4 Å from the hydroxyl surface and inserted between the vacant octahedral site and the ditrigonal cavity of the tetrahedral sheet. The corresponding interlayer shift isT11= −0.355a+ 0.35b+ 8.4n.

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.

Determination of twist angle of in-plane mosaic spread of GaN films by high-resolution X-ray diffraction

2003 ◽  
Vol 255 (1-2) ◽  
pp. 63-67 ◽  
Author(s):  
X.H. Zheng ◽  
H. Chen ◽  
Z.B. Yan ◽  
Y.J. Han ◽  
H.B. Yu ◽  
...  
Keyword(s):  
High Resolution ◽  
Twist Angle ◽  
X Ray Diffraction ◽  
X Ray ◽  
Mosaic Spread

scholarly journals High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging

2013 ◽  
Vol 20 (6) ◽  
pp. 899-904 ◽  
Author(s):  
Atsushi Tokuhisa ◽  
Junya Arai ◽  
Yasumasa Joti ◽  
Yoshiyuki Ohno ◽  
Toyohisa Kameyama ◽  
...  
Keyword(s):  
High Resolution ◽  
High Speed ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Resolution Single

Composition determination of β-(AlxGa1−x)2O3layers coherently grown on (010) β-Ga2O3substrates by high-resolution X-ray diffraction

2016 ◽  
Vol 9 (6) ◽  
pp. 061102 ◽  
Author(s):  
Yuichi Oshima ◽  
Elaheh Ahmadi ◽  
Stefan C. Badescu ◽  
Feng Wu ◽  
James S. Speck
Keyword(s):  
High Resolution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Composition Determination

Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data

2020 ◽  
Author(s):  
Jan Zaucha ◽  
Charlotte A. Softley ◽  
Michael Sattler ◽  
Grzegorz M. Popowicz
Keyword(s):  
Deep Learning ◽  
High Resolution ◽  
Electron Density ◽  
Binding Sites ◽  
Hot Spots ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Water Binding ◽  
X Ray ◽  
Deep Learning Model

ABSTRACTThe surfaces of proteins are generally hydrophilic but there have been reports of sites that exhibit an exceptionally high affinity for individual water molecules. Not only do such molecules often fulfil critical biological functions, but also, they may alter the binding of newly designed drugs. In crystal structures, sites consistently occupied in each unit cell yield electron density clouds that represent water molecule presence. These are recorded in virtually all high-resolution structures obtained through X-ray diffraction. In this work, we utilized the wealth of data from the RCSB Protein Data Bank to train a residual deep learning model named ‘hotWater’ to identify sites on the surface of proteins that are most likely to bind water, the so-called water hot spots. The model can be used to score existing water molecules from a PDB file to provide their ranking according to the predicted binding strength or to scan the surface of a protein to determine the most likely water hot-spots de novo. This is computationally much more efficient than currently used molecular dynamics simulations. Based on testing the model on three example proteins, which have been resolved using both high-resolution X-ray crystallography (providing accurate positions of trapped waters) as well as low-resolution X-ray diffraction, NMR or CryoEM (where structure refinement does not yield water positions), we were able to show that the hotWater method is able to recover in the “water-free” structures many water binding sites known from the high-resolution structures. A blind test on a newly solved protein structure with waters removed from the PDB also showed good prediction of the crystal water positions. This was compared to two known algorithms that use electron density and was shown to have higher recall at resolutions >2.6 Å. We also show that the algorithm can be applied to novel proteins such as the RNA polymerase complex from SARS-CoV-2, which could be of use in drug discovery. The hotWater model is freely available at (https://pypi.org/project/hotWater/).

Charge-density analysis in polymorphs of urea–barbituric acid co-crystals

2011 ◽  
Vol 67 (2) ◽  
pp. 144-154 ◽  
Author(s):  
Marlena Gryl ◽  
Anna Krawczuk-Pantula ◽  
Katarzyna Stadnicka
Keyword(s):  
Hydrogen Bond ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Charge Density ◽  
Barbituric Acid ◽  
Van Der Waals Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Analysis ◽  
Resolution Single

High-resolution single-crystal X-ray diffraction measurements at 100 K were performed for the two polymorphs of urea–barbituric acid co-crystals: (I) P21/c and (II) Cc. Experimental and theoretical charge density and its properties were analysed for (I) and (II) in order to confirm the previous observation that in the polymorphs studied the barbituric acid molecules adopt different mesomeric forms, leading to different hydrogen-bond systems. Koch and Popelier criteria were applied to distinguish between hydrogen bonds and van der Waals interactions in the structures presented.

Determination of the Twist Angle of GaN Film by High Resolution X-ray Diffraction

2008 ◽  
Vol 1 ◽  
pp. 045004 ◽  
Author(s):  
Hongtao Li ◽  
Yi Luo ◽  
Lai Wang ◽  
Guangyi Xi ◽  
Yang Jiang ◽  
...  
Keyword(s):  
High Resolution ◽  
Twist Angle ◽  
X Ray Diffraction ◽  
X Ray ◽  
Gan Film
Sign in / Sign up

Export Citation Format

Share Document