An Assessment of Lattice Energy Minimization for the Prediction of Molecular Organic Crystal Structures

2004 ◽  
Vol 4 (6) ◽  
pp. 1327-1340 ◽  
Author(s):  
Graeme M. Day ◽  
James Chisholm ◽  
Ning Shan ◽  
W. D. Sam Motherwell ◽  
William Jones
Keyword(s):  
Crystal Structures ◽  
Energy Minimization ◽  
Lattice Energy ◽  
Organic Crystal

Which organic crystal structures are predictable by lattice energy minimisation?

CrystEngComm ◽  
2001 ◽  
Vol 3 (44) ◽  
pp. 178-212 ◽  
Author(s):  
Theresa Beyer ◽  
Thomas Lewis ◽  
Sarah L. Price
Keyword(s):  
Crystal Structures ◽  
Lattice Energy ◽  
Organic Crystal ◽  
Energy Minimisation

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.

Use of Atom-Atom Potentials in the Determination of Organic Crystal Structures

1979 ◽  
Vol 50 (1) ◽  
pp. 175-178 ◽  
Author(s):  
S. Ramdas
Keyword(s):  
Crystal Structures ◽  
Organic Crystal

scholarly journals Crystal structures and Hirshfeld surface analyses of (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide and the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide: lattice energy and intermolecular interaction energy calculations for the former. Corrigendum

2019 ◽  
Vol 75 (12) ◽  
pp. 1952-1952
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
James L. Wardell ◽  
Camila Capelini ◽  
José Daniel Figueroa Villar ◽  
...  
Keyword(s):  
Interaction Energy ◽  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Lattice Energy ◽  
Hirshfeld Surface ◽  
Intermolecular Interaction Energy ◽  
Acta Cryst ◽  
Energy Calculations

In the paper by Gomes et al. [Acta Cryst. (2019), E75, 1403–1410], there was an error and omission in the author and affiliation list.

scholarly journals FIDEL: A new method for SDPD of nanocrystalline organic compounds

2014 ◽  
Vol 70 (a1) ◽  
pp. C134-C134
Author(s):  
Martin Schmidt ◽  
Stefan Habermehl ◽  
Philipp Moerschel ◽  
Pierre Eisenbrandt
Keyword(s):  
Crystal Structures ◽  
Rietveld Refinement ◽  
Organic Compounds ◽  
Structure Data ◽  
Structural Model ◽  
Lattice Energy ◽  
Lattice Parameters ◽  
Low Energy ◽  
Powder Pattern ◽  
Field Methods

Rietveld refinements generally fail, if the lattice parameters of the structural model differ more than slightly from the correct lattice parameters and the simulated reflections do not overlap with the experimental ones. For molecular crystals, we have developed a more robust fitting algorithm, which uses the cross-correlation function of calculated and experimental powder patterns, and allows a FIt with DEviating Lattice parameters (FIDEL). The method is also successful for nanocrystalline organic compounds showing only 10-20 peaks in their powder diagrams. The FIDEL method has proven to be useful for various applications, including refinements starting from (1) structure data of an isostructural chemical derivative; (2) structure data of an isostructural hydrate or solvate; (3) structure data from measurements at another temperature (e.g. for fitting a room-temperature powder diagram starting with a structure determined from a single-crystal measurement at 100K). FIDEL is also used for determining crystal structures from non-indexed powder diagrams of nanocrystalline organic compounds. Three steps are performed: (1) Prediction of possible crystal structures in various space groups using global lattice-energy minimizations by force-field methods. (2) FIDEL fit of 100 to 600 low-energy structures to the experimental powder pattern. The structure candidate leading to the correct structure results in a significantly better fit than all other structures. (3) Rietveld refinement. The FIDEL method was used to determine the hitherto unknown crystal structure of the nanocrystalline alpha-phase of 2,9-dichloroquinacridone (C20H10Cl2N2O2). The upper part of the figure shows the experimental powder pattern and the simulated powder diagram of one of the predicted low-energy structures before any fitting. The lower part displays the result of the FIDEL fit, before the Rietveld refinement.

The lines-of-force landscape of interactions between molecules in crystals; cohesive versus tolerant and `collateral damage' contact

2010 ◽  
Vol 66 (3) ◽  
pp. 396-406 ◽  
Author(s):  
Angelo Gavezzotti
Keyword(s):  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Minimum Energy ◽  
Lattice Energy ◽  
Interaction Force ◽  
Coordination Shell ◽  
Geometrical Parameters ◽  
Interaction Energies ◽  
Organic Salts

A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule–molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in ∼ 9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO2, SO2). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom–atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care.

Simulating and predicting crystal structures

1993 ◽  
Vol 442 (1914) ◽  
pp. 85-96 ◽  
Keyword(s):  
Simulated Annealing ◽  
Crystal Structures ◽  
Energy Minimization ◽  
Computational Techniques

We summarize the computational techniques used in modelling crystal structures. Special attention is paid to energy minimization methodologies and more sophisticated simulated annealing techniques. We describe recent applications to the refinement of the structures of novel microporous catalysts and to the generation of the structures of the polymorphs of TiO 2 .

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.

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