Modelling the crystal structure of the 2-hydronitronylnitroxide radical (HNN): observed and computer-generated polymorphs

1999 ◽  
Vol 55 (4) ◽  
pp. 543-553 ◽  
Author(s):  
G. Filippini ◽  
A. Gavezzotti ◽  
J. J. Novoa
Keyword(s):  
Crystal Structure ◽  
Force Field ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Narrow Energy Range ◽  
Coulomb Type ◽  
Atomic Coordinates ◽  
Hydrogen Bonded

The crystal structures of two polymorphs of 4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-oxide (the 2-hydronitronylnitroxide radical, HNN) are analyzed by packing energy criteria. Other unobserved polymorphic crystal structures are generated using a polymorph predictor package and three different force fields, one of which is without explicit Coulomb-type terms. The relative importance of several structural motifs (hydrogen-bonded dimers, shape-interlocking dimers or extended hydrogen-bonded chains) is discussed. As usual, many crystal structures within a narrow energy range are generated by the polymorph predictor, confirming that ab initio crystal-structure prediction is still problematic. Comparisons of powder patterns generated from the atomic coordinates of the X-ray structure and from computational crystal structures confirm that although the energy ranking depends on the force field used, the X-ray structure of the \alpha polymorph was found to be among the most stable ones produced by the polymorph predictor, even using the chargeless force field.

scholarly journals Computational Pharmaceutical Materials Science: Beyond Static Structures.

2014 ◽  
Vol 70 (a1) ◽  
pp. C1541-C1541
Author(s):  
Jacco van de Streek ◽  
Kristoffer Johansson ◽  
Xiaozhou Li
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Force Field ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Force Fields ◽  
Individual Compound ◽  
Crystal Structure Prediction ◽  
Temperature Dependent ◽  
Mechanical Methods

The five Crystal-Structure Prediction (CSP) Blind Tests have shown that molecular-mechanics force fields are not accurate enough for crystal structure prediction[1]. The first--and only--method to successfully predict all four target crystal structures of one of the CSP Blind Tests was dispersion-corrected Density Functional Theory (DFT-D), and this is what we use for our work. However, quantum-mechanical methods (such as DFT-D), are too slow to allow simulations that include the effects of time and temperature, certainly for the size of molecules that are common in pharmaceutical industry. Including the effects of time and temperature therefore still requires molecular dynamics (MD) with less accurate force fields. In order to combine the accuracy of the successful DFT-D method with the speed of a force field to enable molecular dynamics, our group uses Tailor-Made Force Fields (TMFFs) as described by Neumann[2]. In Neumann's TMFF approach, the force field for each chemical compound of interest is parameterised from scratch against reference data from DFT-D calculations; in other words, the TMFF is fitted to mimic the DFT-D energy potential. Parameterising a dedicated force field for each individual compound requires an investment of several weeks, but has the advantage that the resulting force field is more accurate than a transferable force field. Combining crystal-structure prediction with DFT-D followed by molecular dynamics with a tailor-made force field allows us to calculate e.g. the temperature-dependent unit-cell expansion of each predicted polymorph, as well as possible temperature-dependent disorder. This is relevant for example when comparing the calculated X-ray powder diffraction patterns of the predicted crystal structures against experimental data.

scholarly journals Crystal structure prediction of indomethacin

2014 ◽  
Vol 70 (a1) ◽  
pp. C1540-C1540
Author(s):  
Xiaozhou Li ◽  
Kristoffer Johansson ◽  
Andrew Bond ◽  
Jacco van de Streek
Keyword(s):  
Crystal Structure ◽  
Force Field ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Molecular Crystal ◽  
Density Functional ◽  
Computational Cost ◽  
Stable Form ◽  
Crystal Structure Prediction ◽  
Blind Test

Indomethacin is a non-steroidal anti-inflammatory and antipyretic agent. Because different packing arrangements of the same drug can greatly affect drug properties such as colours, solubility, stability, melting point, dissolution rate and so forth, it is important to predict its polymorphs. The computational prediction of the stable form will reduce undesirable risks in both clinical trials and manufacturing. Reported polymorphs of indomethacin include α, β, γ, δ, ε, η and ζ [1], of which only the thermodynamically stable form γ and the metastable form α are determined. Density functional theory with dispersion-correction (DFT-D) has been used extensively to study molecular crystal structures[2]. It gives better results with a compromise between the computational cost and accuracy towards the reproduction of molecular crystal structures. In the fourth blind test of crystal structure prediction in 2007, the DFT-D method gave a very successful result that predicted all four structures correctly. Rather than using transferable force fields, a dedicated tailor-made force field (TMFF) parameterised by DFT-D calculations[3] is used for every chemical compound. The force field is used to generate a set of crystal structures and delimit a candidate window for energy ranking. The powder diffraction patterns of predicted polymorphs are calculated to compare with experimental data.

New similarity index for crystal structure determination from X-ray powder diagrams

2005 ◽  
Vol 38 (6) ◽  
pp. 861-866 ◽  
Author(s):  
Detlef Walter Maria Hofmann ◽  
Ludmila Kuleshova
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Similarity Index ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Organic Pigments ◽  
Structure Solution ◽  
Similarity Indices

A new similarity index for automated comparison of powder diagrams is proposed. In contrast to traditionally used similarity indices, the proposed method is valid in cases of large deviations in the cell constants. The refinement according to this index closes the gap between crystal structure prediction and automated crystal structure determination. The opportunities of the new procedure have been demonstrated by crystal structure solution of un-indexed powder diagrams of some organic pigments (PY111, PR181 and Me-PR170).

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.

scholarly journals Comparing hypothetical structures generated in the third Cambridge blind test of crystal structure prediction

2005 ◽  
Vol 61 (5) ◽  
pp. 528-535 ◽  
Author(s):  
Bouke P. van Eijck
Keyword(s):  
Crystal Structure ◽  
Force Field ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Good Correspondence ◽  
The Third ◽  
New Energy ◽  
Order Of Magnitude ◽  
True Energy

In the third Cambridge blind test of crystal structure prediction, participants submitted extended lists of up to 100 hypothetical structures. In this paper these lists are analyzed for the two small semi-rigid molecules, hydantoin and azetidine, by performing a new energy minimization using an accurate force field, and grouping these newly minimized structures into clusters of equivalent structures. Many participants found the same low-energy structures, but no list appeared to be complete even for the structures with one independent molecule in the asymmetric unit. This may well be due to the fact that a cutoff at even 100 structures cannot ensure the presence of a structure that has a relatively high ranking in another force field. Moreover, some structures should have possibly been discarded because they correspond to transition states rather than true energy minima. The r.m.s. deviation between energies in corresponding clusters was calculated to compare the reported relative crystal energies for each pair of participants. Some groups of force fields show a reasonably good correspondence, yet the order of magnitude of their discrepancies is comparable to the energy differences between, say, the first ten structures of lowest energy. Therefore, even if we assume that energy is a sufficient criterion, it is not surprising that crystal structure predictions are still inconsistent and unreliable.

Characterization of Complicated New Polymorphs of Chlorothalonil by X-ray Diffraction and Computer Crystal Structure Prediction

2004 ◽  
Vol 126 (22) ◽  
pp. 7071-7081 ◽  
Author(s):  
Maryjane Tremayne ◽  
Leanne Grice ◽  
James C. Pyatt ◽  
Colin C. Seaton ◽  
Benson M. Kariuki ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
X Ray Diffraction ◽  
X Ray

scholarly journals Machine Learning-based Crystal Structure Prediction for X-Ray Microdiffraction

2018 ◽  
Vol 24 (S2) ◽  
pp. 144-145 ◽  
Author(s):  
Yuta Suzuki ◽  
Hideitsu Hino ◽  
Yasuo Takeichi ◽  
Takafumi Hawai ◽  
Masato Kotsugi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Machine Learning ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
X Ray

scholarly journals ROY revisited, again: the eighth solved structure

2018 ◽  
Vol 211 ◽  
pp. 477-491 ◽  
Author(s):  
Melissa Tan ◽  
Alexander G. Shtukenberg ◽  
Shengcai Zhu ◽  
Wenqian Xu ◽  
Eric Dooryhee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Prediction Algorithms

X-ray powder diffraction and crystal structure prediction algorithms are used in synergy to establish the crystal structure of the eighth polymorph of ROY, form R05.

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.

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