Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory

2017 ◽  
Vol 73 (4) ◽  
pp. 756-766 ◽  
Author(s):  
Daniela Hempler ◽  
Martin U. Schmidt ◽  
Jacco van de Streek
Keyword(s):  
Density Functional Theory ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Energy Minimization ◽  
Molecular Crystal ◽  
Density Functional ◽  
Group Symmetry ◽  
Functional Theory ◽  
Space Group Symmetry ◽  
Space Group

More than 600 molecular crystal structures with correct, incorrect and uncertain space-group symmetry were energy-minimized with dispersion-corrected density functional theory (DFT-D, PBE-D3). For the purpose of determining the correct space-group symmetry the required tolerance on the atomic coordinates of all non-H atoms is established to be 0.2 Å. For 98.5% of 200 molecular crystal structures published with missed symmetry, the correct space group is identified; there are no false positives. Very small, very symmetrical molecules can end up in artificially high space groups upon energy minimization, although this is easily detected through visual inspection. If the space group of a crystal structure determined from powder diffraction data is ambiguous, energy minimization with DFT-D provides a fast and reliable method to select the correct space group.

scholarly journals Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

2014 ◽  
Vol 70 (6) ◽  
pp. 1020-1032 ◽  
Author(s):  
Jacco van de Streek ◽  
Marcus A. Neumann
Keyword(s):  
Density Functional Theory ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Energy Minimization ◽  
Molecular Crystal ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
High Quality ◽  
Functional Theory ◽  
Atomic Coordinates

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Accurate modeling of molecular crystal through dispersion-corrected density functional theory (DFT-D) method

2011 ◽  
Vol 1301 ◽  
Author(s):  
Bohdan Schatschneider ◽  
Jian-jie Liang
Keyword(s):  
Density Functional Theory ◽  
Phase Transformation ◽  
Density Functional ◽  
Pressure Response ◽  
Van Der Waals Interactions ◽  
Group Symmetry ◽  
Functional Theory ◽  
Space Group Symmetry ◽  
Space Group ◽  
Structural Details

ABSTRACTCrystal structure, pressure response, and polymorph transformation were investigated for crystalline indole through dispersion-corrected density functional theory (DFT-D) method. An accurate, nonempirical method (as in the latest implementations of CASTEP) is used to correct for the general DFT scheme to include van der Waals interactions important in molecular crystals. Ambient structural details, including space group symmetry, density, and fine structural details, such as bicyclic angles, have been reproduced to within experimental accuracy. Pressure response of the structure was obtained to isostatic pressure up to 25 GPa, in increments of 1 GPa. Evolution of space group symmetry and the bicyclic angle were mapped as a function of pressure. A previously unknown phase transformation has been identified around 14 GPa of isostatic pressure. Total energies of the phases before and after phase transformation are nearly identical, with a phase transformation barrier of 0.9 eV. The study opens up the door to reliable DFT investigations of chemical reactions of crystalline aromatic systems under high pressure (e.g. formation of amorphous sp3 hybridized phases).

Crystal structure of donepezil hydrochloride form III, C24H29NO3⋅HCl

2021 ◽  
pp. 1-8
Author(s):  
Joel W. Reid ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Powder Diffraction ◽  
Density Functional ◽  
Chloride Anion ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
Monoclinic Lattice ◽  
Donepezil Hydrochloride

The crystal structure of donepezil hydrochloride, form III, has been solved with FOX using laboratory powder diffraction data previously submitted to and published in the Powder Diffraction File. Rietveld refinement with GSAS yielded monoclinic lattice parameters of a = 14.3662(9) Å, b = 11.8384(6) Å, c = 13.5572(7) Å, and β = 107.7560(26)° (C24H30ClNO3, Z = 4, space group P21/c). The Rietveld-refined structure was compared to a density functional theory (DFT)-optimized structure, and the structures exhibit excellent agreement. Layers of donepezil molecules parallel to the (101) planes are maintained by columns of chloride anions along the b-axis, where each chloride anion hydrogen bonds to three donepezil molecules each.

scholarly journals Ab initio study of elastic anisotropies and thermal conductivities of rhenium diborides in different crystal structures

RSC Advances ◽  
2020 ◽  
Vol 10 (61) ◽  
pp. 37142-37152
Author(s):  
Yi X. Wang ◽  
Ying Y. Liu ◽  
Zheng X. Yan ◽  
W. Liu ◽  
Jian B. Gu
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Crystal Structures ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Ab Initio Study ◽  
Ambient Conditions ◽  
Functional Theory ◽  
Thermal Conductivities

The phase stabilities, elastic anisotropies, and thermal conductivities of ReB2 diborides under ambient conditions have been investigated by using density functional theory calculations.

scholarly journals Synthesis, Characterization, and Crystal Structure Determination of a New Lithium Zinc Iodate Polymorph LiZn(IO3)3

Crystals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 464 ◽  
Author(s):  
Hebboul ◽  
Galez ◽  
Benbertal ◽  
Beauquis ◽  
Mugnier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Density Functional ◽  
Second Harmonic ◽  
Infrared Absorption Spectrum ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Synthesis and characterization of anhydrous LiZn(IO3)3 powders prepared from an aqueous solution are reported. Morphological and compositional analyses were carried out by using scanning electron microscopy and energy-dispersive X-ray measurements. The synthesized powders exhibited a needle-like morphology after annealing at 400 °C. A crystal structure for the synthesized compound was proposed from powder X-ray diffraction and density-functional theory calculations. Rietveld refinements led to a monoclinic structure, which can be described with space group P21, number 4, and unit-cell parameters a = 21.874(9) Å, b = 5.171(2) Å, c = 5.433(2) Å, and  = 120.93(4)°. Density-functional theory calculations supported the same crystal structure. Infrared spectra were also collected, and the vibrations associated with the different modes were discussed. The non-centrosymmetric space group determined for this new polymorph of LiZn(IO3)3, the characteristics of its infrared absorption spectrum, and the observed second-harmonic generation suggest it is a promising infrared non-linear optical material.

scholarly journals Structure and Symmetrization of Hydrogen Bonding in Ices VIII and X at High Pressure: A Density Functional Theory Approach

2015 ◽  
Vol 19 (2) ◽  
pp. 14-18
Author(s):  
Nurapati Pantha ◽  
Narayan Prasad Adhikari
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Science And Technology ◽  
Group Symmetry ◽  
Initial Structure ◽  
Theory Approach ◽  
Functional Theory ◽  
Cell Parameters ◽  
Transition Pressure ◽  
Experimental Values

We study the change in structural properties of ice by taking initial structure of “ice VIII”, with space group symmetry I41/amd, as a function of elevating pressure up to 120 GPa in density-functional theory (DFT) level of calculations implemented by Quantum ESPRESSO package. Consistent with the standard laws of thermodynamics, our calculations show that the physical size (volume and cell parameters) of the unit cell compresses monotonically on increasing pressure. We also compare our DFT results of these parameters with the available experimental values performed at finite temperature. The comparison shows good agreement between the quantities, within 5%, with slightly higher experimental values. At 100 GPa of pressure, hydrogen atom comes exactly at the midpoint of two boneded oxygens, called hydrogen-bonded symmetrization, which at low pressure remains nearby one of the oxygens. This symmmetrized structure is characterized by a new phase of the system known as “ice X” and the boundary pressure, 100 GPa, defines the transition pressure (P0) for changing phase from “ice VIII” to “ice X”. The transition pressure (P0) of the present work agrees well within 2% of previously reported results.Journal of Institute of Science and Technology, 2014, 19(2): 14-19Journal of Institute of Science and Technology, 2014, 19(2): 14-18

scholarly journals Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

2010 ◽  
Vol 66 (5) ◽  
pp. 544-558 ◽  
Author(s):  
Jacco van de Streek ◽  
Marcus A. Neumann
Keyword(s):  
Density Functional Theory ◽  
Crystal Structures ◽  
Density Functional ◽  
Unit Cell ◽  
Organic Crystal ◽  
Large Temperature ◽  
Unit Cell Parameters ◽  
Functional Theory ◽  
Cell Parameters ◽  
Experimental Crystal

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Study of the magnetic and electronic properties of nanocrystalline PrCo3by neutron powder diffraction and density functional theory

2013 ◽  
Vol 25 (11) ◽  
pp. 116001 ◽  
Author(s):  
Khedidja Younsi ◽  
Jean-Claude Crivello ◽  
Valérie Paul-Boncour ◽  
Lotfi Bessais ◽  
Florence Porcher ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
Powder Diffraction ◽  
Density Functional ◽  
Neutron Powder Diffraction ◽  
Functional Theory
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