Molecular Dynamics Applied to X-ray Structure Refinement

2002 ◽  
Vol 35 (6) ◽  
pp. 404-412 ◽  
Author(s):  
Axel T. Brunger ◽  
Paul D. Adams
Keyword(s):  
Molecular Dynamics ◽  
Structure Refinement ◽  
X Ray

ChemInform Abstract: Molecular Dynamics Applied to X-Ray Structure Refinement

ChemInform ◽  
2010 ◽  
Vol 33 (36) ◽  
pp. no-no
Author(s):  
Axel T. Brunger ◽  
Paul D. Adams
Keyword(s):  
Molecular Dynamics ◽  
Structure Refinement ◽  
X Ray

X-ray Structure Refinement and Vibrational Spectroscopy of Ca8Gd2 (PO4)6 O2

2013 ◽  
Vol 12 (10) ◽  
pp. 719-726
Author(s):  
R. Ayadi ◽  
Mohamed Boujelbene ◽  
T. Mhiri
Keyword(s):  
Solid State ◽  
General Formula ◽  
Vibrational Spectroscopy ◽  
Powder Diffraction ◽  
Infrared Spectra ◽  
Solid State Reaction ◽  
Structure Refinement ◽  
Unit Cell ◽  
Cell Group ◽  
X Ray

The present paper is interested in the study of compounds from the apatite family with the general formula Ca10 (PO4)6A2. It particularly brings to light the exploitation of the distinctive stereochemistries of two Ca positions in apatite. In fact, Gd-Bearing oxyapatiteCa8 Gd2 (PO4)6O2 has been synthesized by solid state reaction and characterized by X-ray powder diffraction. The site occupancies of substituents is0.3333 in Gd and 0.3333 for Ca in the Ca(1) position and 0. 5 for Gd in the Ca (2) position.  Besides, the observed frequencies in the Raman and infrared spectra were explained and discussed on the basis of unit-cell group analyses.

Real-Space X-Ray Pair Distribution Function Analysis and Molecular-Dynamics Modelling of Diflunisal Channel Hydrates

2020 ◽  
Author(s):  
Anuradha Pallipurath ◽  
Francesco Civati ◽  
Jonathan Skelton ◽  
Dean Keeble ◽  
Clare Crowley ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Structural Dynamics ◽  
First Principles ◽  
Pair Distribution Function ◽  
Function Analysis ◽  
Real Space ◽  
X Ray ◽  
Dynamics Modelling ◽  
Dynamics Simulations

X-ray pair distribution function analysis is used with first-principles molecular dynamics simulations to study the co-operative H<sub>2</sub>O binding, structural dynamics and host-guest interactions in the channel hydrate of diflunisal.

Structure Investigations of Agonists of the Natural Neurotransmitter Acetylcholine, IV [1]. X-Ray Structure Analyses of Trimethylpentylammonium-chloride and (4-Acetoxybutyl) trimethylammonium-iodide

1986 ◽  
Vol 41 (5-6) ◽  
pp. 618-626
Author(s):  
Alfred Gieren ◽  
Michail Kokkinidis
Keyword(s):  
Structure Refinement ◽  
Pharmacological Action ◽  
Ammonium Nitrogen ◽  
Carbonyl Oxygen ◽  
Type B ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
X Ray ◽  
Structure Investigations ◽  
Automatic Diffractometer

The crystal structures of the title compounds which display cholinergic activity at the ganglionic receptor have been determined by X-ray structure analysis. [(CH3)3N+C5H11]Cl- (1) crystallizes in the orthorhombic space group Pbnm with half a formula unit per asymmetric unit, a = 11.381(14). b = 12.871(17), c = 7.316(4) Å. The intensities of 1106 independent reflections were collected with an automatic diffractometer. The structure refinement converged at R = 0.133 for the 355 observed reflections. The cation of 1 is disordered. [(CH3)3N + (CH2)4-O-C(O)-CH3]I- (2) crystallizes in the orthorhombic space group P212121 with four formula units per unit cell, a = 16.783(8), b = 10.276(6), c = 7.427(10) Å. The intensities of 1469 independent reflections were collected. The structure refinement converged at R = 0.071 for 1383 observed reflections. In both compounds the trimethylammonio methyl groups are coordinated nearly tetrahedrally by four anions in the first coordination sphere. Anions which occupy a special face type (B) of the tetrahedron of the (CH3)3N+ -CH2-group may be treated as a “model binding site” of the receptor. In the crystal structure of 2 the anions occupying B-type faces form together with the ammonium nitrogen and the carbonyl oxygen so called “Activity triangles”. The almost equal geometries of these activity triangles are correlated with the mode of pharmacological action.

Towards a revisitation of vesuvianite-group nomenclature: the crystal structure of Ti-rich vesuvianite from Alchuri, Shigar Valley

2016 ◽  
Vol 72 (5) ◽  
pp. 744-752 ◽  
Author(s):  
Sergey M. Aksenov ◽  
Nikita V. Chukanov ◽  
Vyacheslav S. Rusakov ◽  
Taras L. Panikorovskii ◽  
Ramiza K. Rastsvetaeva ◽  
...  
Keyword(s):  
Octahedral Site ◽  
Structure Refinement ◽  
Optical Measurements ◽  
Transition Elements ◽  
X Ray ◽  
Cell Parameters ◽  
Tetragonal Unit Cell ◽  
Northern Areas ◽  
Shigar Valley

Vesuvianite containing 5.85 wt% TiO2from an Alpine-cleft-type assemblage outcropped near Alchuri, Shigar Valley, Northern Areas, has been investigated by means of electron microprobe analyses, gas-chromatographic analysis of H2O, X-ray powder diffraction, single-crystal X-ray structure refinement,27Al NMR,57Fe Mössbauer spectroscopy, IR spectroscopy and optical measurements. Tetragonal unit-cell parameters are:a= 15.5326 (2),c= 11.8040 (2) Å, space groupP4/nnc. The structure was refined to finalR1= 0.031,wR2= 0.057 for 11247I> 2σ(I). A general crystal-chemical formula of studied sample can be written as follows (Z= 2):[8–9](Ca17.1Na0.9)[8]Ca1.0[5](Fe2+0.44Fe3+0.34Mg0.22)[6](Al3.59Mg0.41)[6](Al4.03Ti2.20Fe3+1.37Fe2+0.40) (Si18O68) [(OH)5.84O2.83F1.33]. The octahedral siteY2 is Al-dominant and does not contain transition elements. Another octahedral siteY3 is also Al-dominant and contains Fe2+, Fe3+and Ti. The siteY1 is split intoY1aandY1bpredominantly occupied by Fe2+and Fe3+, respectively. The role of theY1 site in the diversity of vesuvianite-group minerals is discussed.

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