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.

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.

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 The crystal structure of trandolapril, C24H34N2O5: an example of the utility of raw data deposition in the powder diffraction file

2016 ◽  
Vol 31 (3) ◽  
pp. 205-210 ◽  
Author(s):  
Joel W. Reid ◽  
James A. Kaduk ◽  
Martin Vickers
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Rietveld Refinement ◽  
Powder Diffraction ◽  
Software Package ◽  
Density Functional ◽  
Parallel Tempering ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
Functional Theory

The crystal structure of trandolapril has been solved by parallel tempering using the FOX software package with laboratory powder diffraction data submitted to and published in the Powder Diffraction File. Rietveld refinement was performed with the software package GSAS yielding orthorhombic lattice parameters of a = 19.7685(4), b = 15.0697(4), and c = 7.6704(2) Å (C24H34N2O5, Z = 4, space group P212121). The Rietveld refinement results were compared with density functional theory (DFT) calculations performed with CRYSTAL14. While the structures are similar, discrepancies are observed in the configuration of the octahydroindole ring between the Rietveld and DFT structures, suggesting the refined and calculated molecules are diastereomers.

Crystal structure of citalopram hydrobromide, C20H22FN2OBr

2016 ◽  
Vol 31 (3) ◽  
pp. 176-184
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
X Ray ◽  
Van Der Waals Attraction

The crystal structure of citalopram hydrobromide has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Citalopram hydrobromide crystallizes in space group P21/c (#14) with a = 10.766 45(6), b = 33.070 86(16), c = 10.892 85(5) Å, β = 90.8518(3)°, V = 3878.03(4) Å3, and Z = 8. N–H⋯Br hydrogen bonds are important to the structure, but the crystal energy is dominated by van der Waals attraction. The powder pattern was submitted to International Centre for Diffraction Data for inclusion in the Powder Diffraction File™.

scholarly journals Ab initio and DFT study on Cu (II) complex salicylate derivative

2014 ◽  
Vol 70 (a1) ◽  
pp. C1442-C1442
Author(s):  
Karthikeyan Natarajan ◽  
Sathya Duraisamy ◽  
Sivakumar Kandasamy
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray

X -ray diffraction becomes a routine process these decades for determining crystal structure of the materials. Most of the crystal structures solved nowadays is based on single crystal X-ray diffraction because it solves the crystal and molecular structures from small molecules to macro molecules without much human intervention. However it is difficult to grow single crystals of sufficient size and quality for conventional single-crystal X-ray diffraction studies. In such cases it becomes essential that structural information can be determined from powder diffraction data. With the recent developments in the direct-space approaches for structure solution, ab initio crystal structure analysis of molecular solids can be accomplished from X-ray powder diffraction data. It should be recalled that crystal structure determination from laboratory X-ray powder diffraction data is a far more difficult task than that of its single-crystal counterpart, particularly when the molecule possesses considerable flexibility or there are multiple molecules in the asymmetric unit. Salicylic acid and its derivatives used as an anti-inflammatory drug are known for its numerous medicinal applications. In our study, we synthesized mononuclear copper (II) complex of salicylate derivative. The structural characterization of the prepared compound was carried out using powder X-ray diffraction studies. Crystal structure of the compound has been solved by direct-space approach and refined by a combination of Rietveld method using TOPAS Academic V4.1. Density Functional Theory (DFT) calculations have to be carried in the solid state for the compound using GaussianW9.0 in the frame work of a generalized-gradient approximation (GGA). The geometry optimization was to be performed using B3LYP density functional theory. The atomic coordinates were taken from the final X-ray refinement cycle.

Rietveld refinement using synchrotron powder diffraction data for curcumin, C21H20O6, and comparison with density functional theory

2014 ◽  
Vol 30 (1) ◽  
pp. 67-75 ◽  
Author(s):  
Joel W. Reid ◽  
James A. Kaduk ◽  
Subrahmanyam V. Garimella ◽  
John S. Tse
Keyword(s):  
Density Functional Theory ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Software Package ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Powder Diffraction Data ◽  
Functional Theory ◽  
Synchrotron Powder Diffraction ◽  
Monoclinic Lattice

Synchrotron powder diffraction data from beamline 08B1-1 at the Canadian Light Source have been used to examine the structure of curcumin, a prime component of the Asian spice turmeric. Rigid body refinement, with the application of restraints on distances and angles, was performed with the Rietveld software package GSAS yielding monoclinic lattice parameters ofa= 12.6967(1) Å,b= 7.198 52(3) Å,c= 19.9533(2) Å, andβ= 95.1241(6)° (C21H20O6,Z= 4, and space groupP2/n). The refinement was compared with a recent single-crystal structure andab initioresults obtained with density functional theory calculations.

Powder X-ray diffraction of daclatasvir dihydrochloride Form N-2 (Daklinza®), C40H52N8O6Cl2

2021 ◽  
pp. 1-4
Author(s):  
Ryan L. Hodge ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
X Ray

The crystal structure of daclatasvir dihydrochloride Form N-2 (Daklinza®) has been refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Daclatasvir dihydrochloride, Form N-2, crystallizes in space group P1 (#1) with a = 7.54808 (15), b = 9.5566 (5), c = 16.2641 (11) Å, α = 74.0642 (24), β = 84.0026 (13), γ = 70.6322 (5)°, V = 1064.150(11) Å3, and Z = 1. The hydrogen bonds were identified and quantified. Strong N–H⋯Cl hydrogen bonds link the cations and anions in chains along the a-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Theoretical determination of the structures of CaSiO3 perovskites

2006 ◽  
Vol 62 (6) ◽  
pp. 1025-1030 ◽  
Author(s):  
Razvan Caracas ◽  
Renata M. Wentzcovitch
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Density Functional Theory ◽  
Density Functional ◽  
Theoretical Determination ◽  
Functional Theory ◽  
Starting Point ◽  
Atomic Coordinates ◽  
The Ideal

Density functional theory is used to determine the possible crystal structure of the CaSiO3 perovskites and their evolution under pressure. The ideal cubic perovskite is considered as a starting point for studying several possible lower-symmetry distorted structures. The theoretical lattice parameters and the atomic coordinates for all the structures are determined, and the results are discussed with respect to experimental data.

The crystal structure of Na(NH4)Mo3O10·H2O

2017 ◽  
Vol 32 (2) ◽  
pp. 140-147 ◽  
Author(s):  
Joel W. Reid ◽  
James A. Kaduk ◽  
Jeremy A. Olson
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Rietveld Refinement ◽  
Software Package ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Parallel Tempering ◽  
Powder Diffraction Data ◽  
Functional Theory ◽  
Synchrotron Powder Diffraction

The crystal structure of Na(NH4)Mo3O10·H2O has been solved by parallel tempering using the FOX software package with synchrotron powder diffraction data obtained from beamline 08B1-1 at the Canadian Light Source. Rietveld refinement, performed with the software package GSAS, yielded orthorhombic lattice parameters of a = 13.549 82(10), b = 7.618 50(6), and c = 9.302 74(7) Å (Z = 4, space group Pnma). The structure is composed of molybdate chains running parallel to the b-axis. The Rietveld refinement results were compared with density functional theory calculations performed with CRYSTAL14, and show excellent agreement with the calculated structure.

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