Molecular packing groups and ab initio crystal-structure prediction

1999 ◽  
Vol 55 (4) ◽  
pp. 621-627 ◽  
Author(s):  
Daquan Gao ◽  
Donald E. Williams
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Energy Minimization ◽  
Structure Prediction ◽  
Group Symmetry ◽  
Crystal Structure Prediction ◽  
Asymmetric Unit ◽  
Efficient Procedure ◽  
Space Groups ◽  
Independent Molecules

Ab initio crystal structure prediction can proceed by minimization of the packing energy of Z independent molecules per cell, or alternatively by energy minimization taking one molecule as independent and Z-1 molecules as related by assumed space-group symmetry. In the former method, a large number of positional variables must be considered. In the latter method, a large number of space groups must be considered. An alternative, more efficient, procedure is proposed, where it is recognized that values of Z and the number of molecules in the asymmetric unit, Z′, impose restrictions on possible space groups. Examples of application of this method to crystal structure prediction are given.

scholarly journals New high-pressure phases of Fe7N3 and Fe7C3 stable at Earth's core conditions: evidences for carbon–nitrogen isomorphism in Fe-compounds

RSC Advances ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 3577-3581 ◽  
Author(s):  
Nursultan Sagatov ◽  
Pavel N. Gavryushkin ◽  
Talgat M. Inerbaev ◽  
Konstantin D. Litasov
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Ab Initio ◽  
Structure Prediction ◽  
Harmonic Approximation ◽  
Crystal Structure Prediction ◽  
Earth’S Core ◽  
Earth's Core ◽  
Core Conditions

We carried out ab initio calculations on the crystal structure prediction and determination of P–T diagrams within the quasi-harmonic approximation for Fe7N3 and Fe7C3.

scholarly journals Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography

2020 ◽  
Vol 76 (3) ◽  
pp. 322-335 ◽  
Author(s):  
Marta K. Dudek ◽  
Piotr Paluch ◽  
Edyta Pindelska
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Features ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
Crystal Forms ◽  
Space Groups ◽  
Nmr Crystallography

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z′ = 1 polymorph (form II), crystallize in P21/c and P 1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z′ = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Crystal structure prediction of LiBeH3 using ab initio total-energy calculations and evolutionary simulations

2008 ◽  
Vol 129 (23) ◽  
pp. 234105 ◽  
Author(s):  
Chao-Hao Hu ◽  
A. R. Oganov ◽  
Y. M. Wang ◽  
H. Y. Zhou ◽  
A. Lyakhov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Total Energy ◽  
Ab Initio ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Energy Calculations ◽  
Evolutionary Simulations

scholarly journals Crystal structure prediction of organic pigments: quinacridone as an example

2007 ◽  
Vol 40 (1) ◽  
pp. 105-114 ◽  
Author(s):  
N. Panina ◽  
F. J. J. Leusen ◽  
F. F. B. J. Janssen ◽  
P. Verwer ◽  
H. Meekes ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Energy Minimization ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Organic Pigments ◽  
Structural Database ◽  
Diffraction Patterns ◽  
Experimental Structure

The structures of the α, β and γ polymorphs of quinacridone (Pigment Violet 19) were predicted usingPolymorph Predictorsoftware in combination with X-ray powder diffraction patterns of limited quality. After generation and energy minimization of the possible structures, their powder patterns were compared with the experimental ones. On this basis, candidate structures for the polymorphs were chosen from the list of all structures. Rietveld refinement was used to validate the choice of structures. The predicted structure of the γ polymorph is in accordance with the experimental structure published previously. Three possible structures for the β polymorph are proposed on the basis of X-ray powder patterns comparison. It is shown that the α structure in the Cambridge Structural Database is likely to be in error, and a new α structure is proposed. The present work demonstrates a method to obtain crystal structures of industrially important pigments when only a low-quality X-ray powder diffraction pattern is available.

Ab initio crystal structure prediction?I. Rigid molecules

2004 ◽  
Vol 26 (3) ◽  
pp. 304-324 ◽  
Author(s):  
Panagiotis G. Karamertzanis ◽  
Constantinos C. Pantelides
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Structure Prediction ◽  
Crystal Structure Prediction

Synthesis and crystal structures of two structurally related kryptoracemates

2017 ◽  
Vol 73 (7) ◽  
pp. 575-581 ◽  
Author(s):  
Philipp Kramer ◽  
Michael Bolte
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Symmetry Element ◽  
Inversion Symmetry ◽  
Asymmetric Unit ◽  
Chiral Molecules ◽  
Space Groups ◽  
Independent Molecules

Kryptoracemates are racemic compounds (pairs of enantiomers) that crystallize in Sohnke space groups (space groups that contain neither inversion centres nor mirror or glide planes nor rotoinversion axes). Thus, the two symmetry-independent molecules cannot be transformed into one another by any symmetry element present in the crystal structure. Usually, the conformation of the two enantiomers is rather similar if not identical. Sometimes, the two enantiomers are related by a pseudosymmetry element, which is often a pseudocentre of inversion, because inversion symmetry is thought to be favourable for crystal packing. We obtained crystals of two kryptoracemates of two very similar compounds differing in just one residue, namely rac-N-[(1S,2R,3S)-2-methyl-3-(5-methylfuran-2-yl)-1-phenyl-3-(pivalamido)propyl]benzamide, C27H32N2O3, (I), and rac-N-[(1S,2S,3R)-2-methyl-3-(5-methylfuran-2-yl)-1-phenyl-3-(propionamido)propyl]benzamide dichloromethane hemisolvate, C25H28N2O3·0.5CH2Cl2, (II). The crystals of both compounds contain both enantiomers of these chiral molecules. However, since the space groups [P212121 for (I) and P1 for (II)] contain neither inversion centres nor mirror or glide planes nor rotoinversion axes, there are both enantiomers in the asymmetric unit, which is a rather uncommon phenomenon. In addition, it is remarkable that (II) contains two pairs of enantiomers in the asymmetric unit. In the crystal, molecules are connected by intermolecular N—H...O hydrogen bonds to form chains or layered structures.

Sign in / Sign up

Export Citation Format

Share Document