Predicted and experimental crystal structures of ethyl-tert-butyl ether

2011 ◽  
Vol 67 (2) ◽  
pp. 155-162 ◽  
Author(s):  
Sonja M. Hammer ◽  
Edith Alig ◽  
Lothar Fink ◽  
Martin U. Schmidt
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Global Minimum ◽  
Lattice Energy ◽  
Real Space ◽  
Energy Structure ◽  
Butyl Ether ◽  
Crystallization Experiments ◽  
Rank 2 ◽  
Experimental Crystal

Possible crystal structures of ethyl-tert-butyl ether (ETBE) were predicted by global lattice-energy minimizations using the force-field approach. 33 structures were found within an energy range of 2 kJ mol−1 above the global minimum. Low-temperature crystallization experiments were carried out at 80–160 K. The crystal structure was determined from X-ray powder data. ETBE crystallizes in C2/m, Z = 4, with molecules on mirror planes. The ETBE molecule adopts a trans conformation with a (CH3)3C—O—C—C torsion angle of 180°. The experimental structure corresponds with high accuracy to the predicted structure with energy rank 2, which has an energy of 0.54 kJ mol−1 above the global minimum and is the most dense low-energy structure. In some crystallization experiments a second polymorph was observed, but the quality of the powder data did not allow the determination of the crystal structure. Possibilities and limitations are discussed for solving crystal structures from powder diffraction data by real-space methods and lattice-energy minimizations.

Predicted crystal structures of tetramethylsilane and tetramethylgermane and an experimental low-temperature structure of tetramethylsilane

2010 ◽  
Vol 66 (2) ◽  
pp. 229-236 ◽  
Author(s):  
Alexandra K. Wolf ◽  
Jürgen Glinnemann ◽  
Lothar Fink ◽  
Edith Alig ◽  
Michael Bolte ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Crystal Structures ◽  
Ambient Pressure ◽  
Lattice Energy ◽  
Energy Structure ◽  
Temperature Phase ◽  
Temperature Structure ◽  
Field Methods ◽  
Experimental Crystal

No crystal structure at ambient pressure is known for tetramethylsilane, Si(CH3)4, which is used as a standard in NMR spectroscopy. Possible crystal structures were predicted by global lattice-energy minimizations using force-field methods. The lowest-energy structure corresponds to the high-pressure room-temperature phase (Pa\overline{3}, Z = 8). Low-temperature crystallization at 100 K resulted in a single crystal, and its crystal structure has been determined. The structure corresponds to the predicted structure with the second lowest energy rank. In X-ray powder analyses this is the only observed phase between 80 and 159 K. For tetramethylgermane, Ge(CH_3)_4, no experimental crystal structure is known. Global lattice-energy minimizations resulted in 47 possible crystal structures within an energy range of 5 kJ mol−1. The lowest-energy structure was found in Pa\overline{3}, Z = 8.

SiBr4 – prediction and determination of crystal structures

2009 ◽  
Vol 65 (3) ◽  
pp. 342-349 ◽  
Author(s):  
Alexandra K. Wolf ◽  
Jürgen Glinnemann ◽  
Martin U. Schmidt ◽  
Jianwei Tong ◽  
Robert E. Dinnebier ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Powder Diffraction ◽  
Global Minimum ◽  
Lattice Energy ◽  
Field Methods ◽  
X Ray ◽  
Β Phase ◽  
Α Phase ◽  
Synchrotron Powder Diffraction

For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol−1 above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature β phase crystallizes in P21/c, the high-temperature α phase in Pa\overline{3}. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

scholarly journals Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Nicholas Francia ◽  
Louise Price ◽  
Matteo Salvalaglio
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Large Scale ◽  
Lattice Energy ◽  
Racemic Mixture ◽  
Dynamics Simulations

<p>The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy calculations, which are known to significantly over-predict the number of plausible crystal structures. A valuable tool to reduce overprediction is to employ physics-based, dynamic simulations to coalesce lattice energy minima separated by small barriers into a smaller number of more stable geometries once thermal effects are introduced. Molecular dynamics simulations and enhanced sampling methods can be employed in this context to simulate crystal structures at finite temperature and pressure. </p><p>Here we demonstrate the applicability of approaches based on molecular dynamics to systematically process realistic CSP datasets containing several hundreds of crystal structures. The system investigated is ibuprofen, a conformationally flexible active pharmaceutical ingredient that crystallises both in enantiopure forms and as a racemic mixture. By introducing a hierarchical approach in the analysis of finite-temperature supercell configurations, we can post-process a dataset of 555 crystal structures, identifying 65% of the initial structures as labile, while maintaining all the experimentally known crystal structures in the final, reduced set. Moreover, the extensive nature of the initial dataset allows one to gain quantitative insight into the persistence and the propensity to transform of crystal structures containing common hydrogen-bonded intermolecular interaction motifs.</p>

scholarly journals Theoretical Prediction of Crystal Polymorphs for Organic Molecules

2014 ◽  
Vol 70 (a1) ◽  
pp. C1626-C1626
Author(s):  
Shigeaki Obata ◽  
Mitsuaki Sato ◽  
Hitoshi Goto
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
High Speed ◽  
Prediction Method ◽  
Energy Calculation ◽  
Crystal Polymorphism ◽  
Energy Evaluation ◽  
Target Molecules ◽  
Experimental Crystal

Crystal structure prediction is one of the useful theoretical tools for designing and synthesizing new materials in pharmaceutical therapeutics and industrial electronics. Furthermore, the prediction can provide immense valuable scientific knowledge on a crystal growth, polymorphism and many properties of organic molecular crystals. Therefore, we have started the development of high-speed and high-accurate prediction method for organic molecular crystal structures [1,2]. In this work, we demonstrate the theoretical predictions of crystal structures of fourteen target molecules that were used in the international competitions known as CSP blind tests hosted by CCDC [3]. All strategies required for crystal lattice construction expanded to a given effective crystal radius, crystal energy calculation with the reliable molecular force field (MMFF94s) and exhaustive geometry search included a variety of crystal polymorphism are implemented into CONFLEX program [1]. As the results of the applications, we confirmed in all cases of target molecules that, at least, one calculated crystal structure in agreement with the corresponding observed ones can be found. Essential ability required for the prediction method to survive the CSP competitions is that the experimental crystal structure can computationally reproduce within top 3 of most stable structures in crystal energy evaluation. In these tests, only three applications to the target I (Orth. polymorph), II and VIII can successfully satisfy the demand. Details will be discussed in this conference.

Determination of the structure of the violet pigment C22H12Cl2N6O4 from a non-indexed X-ray powder diagram

2005 ◽  
Vol 61 (1) ◽  
pp. 37-45 ◽  
Author(s):  
Martin U. Schmidt ◽  
Martin Ermrich ◽  
Robert E. Dinnebier
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Lattice Energy ◽  
Frankfurt Am Main ◽  
Rietveld Refinements ◽  
X Ray ◽  
Space Groups ◽  
Violet Pigment

The violet pigment methylbenzimidazolonodioxazine, C22H12Cl2N6O4 (systematic name: 6,14-dichloro-3,11-dimethyl-1,3,9,11-tetrahydro-5,13-dioxa-7,15-diazadiimidazo-[4,5-b:4′,5′-m]pentacene-2,10-dione), shows an X-ray powder diagram consisting of only ca 12 broad peaks. Indexing was not possible. The structure was solved by global lattice energy minimizations. The program CRYSCA [Schmidt & Kalkhof (1999), CRYSCA. Clariant GmbH, Pigments Research, Frankfurt am Main, Germany] was used to predict the possible crystal structures in different space groups. By comparing simulated and experimental powder diagrams, the correct structure was identified among the predicted structures. Owing to the low quality of the experimental powder diagram the Rietveld refinements gave no distinctive results and it was difficult to prove the correctness of the crystal structure. Finally, the structure was confirmed to be correct by refining the crystal structure of an isostructural mixed crystal having a better X-ray powder diagram. The compound crystallizes in P\bar 1, Z = 1. The crystal structure consists of a very dense packing of molecules, which are connected by hydrogen bridges of the type N—H...O=C. This packing explains the observed insolubility. The work shows that crystal structures of molecular compounds may be solved by lattice energy minimization from diffraction data of limited quality, even when indexing is not possible.

Effects of terminal alkyl substituents on the low-dimensional arrangement of π-stacked molecules in the crystal structures of bisazomethine dyes

2016 ◽  
Vol 231 (8) ◽  
Author(s):  
Takumi Jindo ◽  
Byung-Soon Kim ◽  
Yoko Akune ◽  
Emi Horiguchi-Babamoto ◽  
Kyun-Phyo Lee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Lattice Energy ◽  
Structural Features ◽  
Substitution Effects ◽  
Amino Groups ◽  
One Dimensional ◽  
Alkyl Chains ◽  
Terminal Amino ◽  
Low Dimensional

AbstractCrystal structures of three bisazomethine dyes with dipropyl, dibutyl, and dihexyl substituents on their terminal amino groups are reported. To systematically interpret the effects of the terminal dialkyl substituents on the low-dimensional arrangements of the π–π stacked molecules, the structural features of the molecular geometries and the low-dimensional arrangements were compared with those in the reported crystal structure of two bisazomethine dyes, i.e. with terminal dimethylamino and diethylamino groups. Lattice energy calculations were also carried out to interpret the substitution effects from an energetic perspective. In the crystal structures of all five dyes, one-dimensional arrangements of the π–π stacked molecules were found. The slip angles between the π–π stacked molecules constituting the characteristic one-dimensional arrangements of the five bisazomethine dyes were distributed in the range of 24.66(4)–79.34(7)°. The lengths of the alkyl chains and projections of the terminal dialkyl substituents from the molecular planes in the five bisazomethine dyes were found to play significant roles in determining the slip angles between the π–π stacked molecules and the distances between the molecules aligned along the long molecular axes.

scholarly journals Predicting Porous Molecular Crystals and Clathrates

2014 ◽  
Vol 70 (a1) ◽  
pp. C1625-C1625
Author(s):  
Jonas Nyman ◽  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Molecular Crystals ◽  
Volume Ratio ◽  
Lattice Energy ◽  
Computer Algorithms ◽  
Crystal Structure Prediction ◽  
Powerful Method ◽  
Simple Molecules

The last decade has seen dramatic improvements in the theories and computer algorithms underlying computational Crystal Structure Predictions [1]. It is now possible to reliably obtain the most likely crystal structures of at least simple molecules starting from nothing more than a drawing of the molecule. We can now go even further and look for rare and exotic kinds of crystals such as porous molecular crystals, clathrates and inclusion compounds among our predictions and calculate their physical properties [2], paving the way for the "science of hypothetical materials". In our poster, we present results on the prediction of fluorophenol xenon clathrates. We have performed crystal structure predictions by global lattice energy searches on o- and m-fluorophenol. The predicted structures have then been analyzed for porosity and their likelihood of being clathrates. From the several thousands of predicted structures, we select a few likely candidates according to an empirical rule based on the guest to host volume ratio [3]. Results from solid state xenon-129 NMR indicate that we have successfully determined the crystal structures of both o- and m-fluorophenol xenon clathrates and we suggest that Crystal Structure Prediction in combination with xenon-129 NMR is a powerful method for determining the structures of clathrates in general.

Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts

2016 ◽  
Vol 72 (4) ◽  
pp. 551-561 ◽  
Author(s):  
Sharmarke Mohamed ◽  
Durga Prasad Karothu ◽  
Panče Naumov
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Energy Landscape ◽  
Lattice Energy ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Hydrochloride Salt ◽  
Salt Structure ◽  
A Chain ◽  
Experimental Crystal

The crystal energy landscapes of the salts of two rigid pharmaceutically active molecules reveal that the experimental structure of amantadine hydrochloride is the most stable structure with the majority of low-energy structures adopting a chain hydrogen-bond motif and packings that do not have solvent accessible voids. By contrast, memantine hydrochloride which differs in the substitution of two methyl groups on the adamantane ring has a crystal energy landscape where all structures within 10 kJ mol−1of the global minimum have solvent-accessible voids ranging from 3 to 14% of the unit-cell volume including the lattice energy minimum that was calculated after removing water from the hydrated memantine hydrochloride salt structure. The success in using crystal structure prediction (CSP) to rationalize the different hydration propensities of these substituted adamantane hydrochloride salts allowed us to extend the model to predict under blind test conditions the experimental crystal structures of the previously uncharacterized 1-(methylamino)adamantane base and its corresponding hydrochloride salt. Although the crystal structure of 1-(methylamino)adamantane was correctly predicted as the second ranked structure on the static lattice energy landscape, the crystallization of aZ′ = 3 structure of 1-(methylamino)adamantane hydrochloride reveals the limits of applying CSP when the contents of the crystallographic asymmetric unit are unknown.

Experimental and predicted crystal structures of Pigment Red 168 and other dihalogenated anthanthrones

2010 ◽  
Vol 66 (5) ◽  
pp. 515-526 ◽  
Author(s):  
Martin U. Schmidt ◽  
Erich F. Paulus ◽  
Nadine Rademacher ◽  
Graeme M. Day
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Lattice Energy ◽  
Molecular Structures ◽  
Actual Structure ◽  
Compound A ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
Experimental Diagram

The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize in P21/c, Z = 2, the dichloro derivative in P\bar 1, Z = 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another nor to the unsubstituted anthanthrone, which crystallizes in P21/c, Z = 8. In order to explain why the four anthanthrone derivatives have four different crystal structures, lattice-energy minimizations were performed using anisotropic atom–atom model potentials as well as using the semi-classical density sums (SCDS-Pixel) approach. The calculations showed the crystal structures of the dichloro and the diiodo derivatives to be the most stable ones for the corresponding compound; whereas for dibromo-anthanthrone the calculations suggest that the dichloro and diiodo structure types should be more stable than the experimentally observed structure. An experimental search for new polymorphs of dibromo-anthanthrone was carried out, but the experiments were hampered by the remarkable insolubility of the compound. A metastable nanocrystalline second polymorph of the dibromo derivative does exist, but it is not isostructural to the dichloro or diiodo compound. In order to determine the crystal structure of this phase, crystal structure predictions were performed in various space groups, using anisotropic atom–atom potentials. For all low-energy structures, X-ray powder patterns were calculated and compared with the experimental diagram, which consisted of a few broad lines only. It turned out that the crystallinity of this phase was not sufficient to determine which of the calculated structures corresponds to the actual structure of this nanocrystalline polymorph.

Sign in / Sign up

Export Citation Format

Share Document