High Temperature Electron Diffraction on Organic Crystals: In Situ Crystal Structure Determination of Pigment Orange 34.

Small molecule structures and their applications rely on good knowledge of their atomic arrangements. However, the crystal structures of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis of submicrometer-sized organic materials. The reduction of electron beam damage is essential for successful structure determination and often prevents the analysis of organic materials at room temperature, not to mention high temperature studies. In this work, we apply advanced 3D ED methods at different temperatures enabling the accurate structure determination of two phases of Pigment Orange 34 (C34H28N8O2Cl2), a biphenyl pyrazolone pigment that has been industrially produced for more than 80 years and used for plastics application. The crystal structure of the high-temperature phase, which can be formed during plastic coloration, was determined at 220 °C. For the first time, we were able to observe a reversible phase transition in an industrial organic pigment in the solid state, even with atomic resolution, despite crystallites being submicrometer in size. By localizing hydrogen atoms, we were even able to detect the tautomeric state of the molecules at different temperatures. This demonstrates that precise, fast, and low-dose 3D ED measurements enable high-temperature studies the door for general in situ studies of nanocrystalline materials at the atomic level.

Leucopterin, the white pigment in butterfly wings: structural analysis by PDF fit, FIDEL fit, Rietveld refinement, solid-state NMR and DFT-D.

Leucopterin (C6H5N5O3) is the white pigment in the wings of Pieris brassicae butterflies, and other butterflies; it can also be found in wasps and other insects. Its crystal structure and its tautomeric form in the solid state were hitherto unknown. Leucopterin turned out to be a variable hydrate, with 0.5 to about 0.1 molecules of water per leucopterin molecule. Under ambient conditions, the preferred state is the hemihydrate. Initially, all attempts to grow single crystals suitable for X-ray diffraction were to no avail. Attempts to determine the crystal structure by powder diffraction using the direct-space method failed, because the trials did not include the correct, but rare, space group P2/c. Attempts were made to solve the crystal structure by a global fit to the pair distribution function (PDF-Global-Fit), as described by Prill and co-workers [Schlesinger et al. (2021). J. Appl. Cryst. 54, 776-786]. The approach worked well, but the correct structure was not found, because again the correct space group was not included. Finally, tiny single crystals of the hemihydrate could be obtained, which allowed at least the determination of the crystal symmetry and the positions of the C, N and O atoms. The tautomeric state of the hemihydrate was assessed by multinuclear solid-state NMR spectroscopy. 15N CPMAS spectra showed the presence of one NH2 and three NH groups, and one unprotonated N atom, which agreed with the 1H MAS and 13C CPMAS spectra. Independently, the tautomeric state was investigated by lattice-energy minimizations with dispersion-corrected density functional theory (DFT-D) on 17 different possible tautomers, which also included the prediction of the corresponding 1H, 13C and 15N chemical shifts in the solid. All methods showed the presence of the 2-amino-3,5,8-H tautomer. The DFT-D calculations also confirmed the crystal structure. Heating of the hemihydrate results in a slow release of water between 130 and 250 °C, as shown by differential thermal analysis and thermogravimetry (DTA-TG). Temperature-dependent powder X-ray diffraction (PXRD) showed an irreversible continuous shift of the reflections upon heating, which reveals that leucopterin is a variable hydrate. This observation was also confirmed by PXRD of samples obtained under various synthetic and drying conditions. The crystal structure of a sample with about 0.2 molecules of water per leucopterin was solved by a fit with deviating lattice parameters (FIDEL), as described by Habermehl et al. [Acta Cryst. (2022), B78, 195-213]. A local fit, starting from the structure of the hemihydrate, as well as a global fit, starting from random structures, were performed, followed by Rietveld refinements. Despite dehydration, the space group remains P2/c. In both structures (hemihydrate and variable hydrate), the leucopterin molecules are connected by 2-4 hydrogen bonds into chains, which are connected by further hydrogen bonds to neighbouring chains. The molecular packing is very efficient. The density of leucopterin hemihydrate is as high as 1.909 kg dm-3, which is one of the highest densities for organic compounds consisting of C, H, N and O only. The high density might explain the good light-scattering and opacity properties of the wings of Pieris brassicae and other butterflies.

Solid-State NMR-Driven Crystal Structure Prediction of Molecular Crystals: The Case of Mebendazole.

Among all possible NMR crystallography approaches for crystal-structure determination, crystal structure prediction - NMR crystallography (CSP-NMRX) has recently turned out to be a powerful method. In the latter, the original procedure exploited solid-state NMR (SSNMR) information during the final steps of the prediction. In particular, it used the comparison of computed and experimental chemical shifts for the selection of the correct crystal packing. Still, the prediction procedure, generally carried out with DFT methods, may require important computational resources and be quite time-consuming, especially if there are no available constraints to use at the initial stage. Herein, the successful application of this combined prediction method, which exploits NMR information also in the input step to reduce the search space of the predictive algorithm, is presented. Herein, this method was applied on mebendazole, which is characterized by desmotropism. The use of SSNMR data as constraints for the selection of the right tautomer and the determination of the number of independent molecules in the unit cell led to a considerably faster process, reducing the number of calculations to be performed. In this way, the crystal packing was successfully predicted for the three known phases of mebendazole. To evaluate the quality of the predicted structures, these were compared to the experimental ones. The crystal structure of phase B of mebendazole, in particular, was determined de novo by powder diffraction and is presented for the first time in this paper.

Sustained-release hot melt extrudates of the weak acid TMP-001: A case study using PBB modelling.

Over the last 30 years, hot melt extrusion has become a leading technology in the manufacture of amorphous drug delivery systems. Mostly applied as an 'enabling formulation' for poorly soluble compounds, application in the design of sustained-release formulations increasingly attracts the attention of the pharmaceutical industry. The drug candidate TMP-001 is currently under evaluation for the early treatment of Multiple Sclerosis. Although this weak acid falls into class II of the Biopharmaceutics Classification System, the compound exhibits high solubility in the upper intestine resulting in high peroral bioavailability. In the present studies, four different formulation prototypes varying in their sustained-release behavior were developed, using L-arginine as a pore-forming agent in concentrations ranging between 0 and 20%. Initially, biorelevant release testing was applied to assess the dissolution behavior of the prototypes. For these formulations, a total drug release of 44.7%, 64.6%, 75%, and 90.5% was achieved in FaSSIF-v2 after 24 h. Two candidates were selected for further characterization considering the crystal structure and the physical stability of the amorphous state of TMP-001 in the formulations together with the release behavior in Level II biorelevant media. Our findings indicate L-arginine as a valuable excipient in the formulation of hot melt extrudates, as its presence led to a considerable stabilization of the amorphous state and favorably impacted the milling process and release behavior of TMP-001. To properly evaluate the proposed formulations and the importance of colonic dissolution and absorption on the overall bioavailability, a physiologically-based biopharmaceutics model was used.

Building up Strain in One Step: Synthesis of an Edge-Fused Double Silacyclobutene from an Extensively Trichlorosilylated Butadiene Dianion.

The exhaustive trichlorosilylation of hexachloro-1,3-butadiene was achieved in one step by using a mixture of Si2 Cl6 and [nBu4 N]Cl (7:2 equiv) as the silylation reagent. The corresponding butadiene dianion salt [nBu4 N]2 [1] was isolated in 36 % yield after recrystallization. The negative charges of [1]2- are mainly delocalized across its two carbanionic (Cl3 Si)2 C termini (α-effect of silicon) such that the central bond possesses largely C=C double-bond character. Upon treatment with 4 equiv of HCl, [1]2- is converted into neutral 1,2,3,4-tetrakis(trichlorosilyl)but-2-ene, 3. The Cl- acceptor AlCl3 , induces a twofold ring-closure reaction of [1]2- to form a six-membered bicycle 4 in which two silacyclobutene rings are fused along a shared C=C double bond (84 %). Compound 4, which was structurally characterized by X-ray crystallography, undergoes partial ring opening to a monocyclic silacyclobutene 2 in the presence of HCl, but is thermally stable up to at least 180 °C.

A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data.

By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that of the low-temperature phase. The anisotropic displacement parameters calculated from the MD simulations readily identified libration as the driving force behind the phase transition. Both the predicted crystal structure and the phase-transition mechanism were verified experimentally using TLS (translation, libration, screw) refinement against X-ray powder diffraction data.

On the correlation between hydrogen bonding and melting points in the inositols.

Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006 ▶). CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect of molecular symmetry, and that the three lowest melting points may need to be revised. This prompted a full investigation, with additional experiments on six of the nine inositols. Thirteen new phases were discovered; for all of these their crystal structures were examined. The crystal structures of eight ordered phases could be determined, of which seven were obtained from laboratory X-ray powder diffraction data. Five additional phases turned out to be rotator phases and only their unit cells could be determined. Two previously unknown melting points were measured, as well as most enthalpies of melting. Several previously reported melting points were shown to be solid-to-solid phase transitions or decomposition points. Our experiments have revealed a complex picture of phases, rotator phases and phase transitions, in which a simple correlation between melting points and hydrogen-bonding patterns is not feasible.

Antidiarrhetic loperamide hydrochloride.

Single crystals of the anhydrous form of the title compound {systematic name: 1-[3-(dimethylcarbamoyl)-3,3-diphenylpropyl]-4-hydroxy-4-(4-chlorophenyl)piperidin-1-ium chloride}, C(29)H(34)ClN(2)O(2)(+)·Cl(-), were obtained by diffusion of acetone into a solution in 2-propanol. In the structure, N-H...Cl(-) and O-H...Cl(-) hydrogen bonds connect neighbouring molecules and chloride anions to form chains along the c-axis direction. Neighbouring chains along the b-axis direction are connected by intermolecular C-H...Cl(-) contacts, defining layers parallel to the (100) planes. The layers are connected by weak intermolecular C-H...Cl interactions only, which may account for the plate-like shape of the crystals.

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

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 kJmol(-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 (CH(3))(3)C-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 kJmol(-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.

Characterization of a new solvate of risedronate.

Three new forms of the osteoporosis drug sodium risedronate, sodium [1-hydroxy-2-(3-pyridinyl)ethylidene]bisphosphonate, were identified and designated as the J, K, and M phases. Form J is an acetic acid disolvate with the chemical composition Na(+) [C(7) H(10) NO(7) P(2)](-) · 2CH(3) COOH, as determined by single-crystal structure analysis. This novel solvate is easily formed by the recrystallization of sodium risedronate from acetic acid. Dissolution of the new disolvate was characterized in distilled water, a compendial buffer, simulated gastric fluid sine pepsin (pH 1.2), and a biorelevant buffer system FaSSIF-V2 (pH 6.8). It was demonstrated that solubility of the disolvate in physiological buffers differed significantly from that of the original molecule, with delayed dissolution under simulated esophageal and gastric conditions, but rapid and complete dissolution under simulated intestinal conditions. These studies suggest that through the generation of novel solvates, the biopharmaceutical properties of poorly soluble drug candidates can be improved.

Solvent-free mesityllithium: solid-state structure and its reactivity towards white phosphorus.

The donor-free mesityllithium was prepared from the reaction of MesBr with n-BuLi in diethyl ether at -78 degrees C. The solid-state structure of unsupported mesityllithium consists of C(2)Li(2)-rings composed of two LiMes units, which interact with adjacent dimers [LiMes](2), forming a polymeric infinite chain along the crystallographic c-axis (monoclinic space group, P2(1)/n). The structure of donor-free mesityllithium reveals short contacts between the C atoms of the mesityl rings and the lithium atoms of neighbouring [LiMes](2) units. The structure determination of LiMes was performed by X-ray powder diffraction. In addition we have investigated the reaction of LiMes with Me(3)SnCl and P(4) for our understanding of the reactivity of donor-free mesityllithium. The heterogeneous reaction of donor-free mesityllithium with Me(3)SnCl produces conveniently the stannylated mesitylene Me(3)SnMes (triclinic, space group P1). White phosphorus reacts with three equivalents of unsupported mesityllithium in benzene to give Li(3)P(4)Mes(3). In this context it should be noted that a tetraphosphide with an identical LiP-core as in Li(3)P(4)Mes(3) had been formed in the 1:3 reaction of P(4) with the silanide Li[SitBu(3)]. The tetraphosphide Li(3)P(4)Mes(3) was analyzed using X-ray crystallography (monoclinic, space group C2/c).

Ezetimibe anhydrate, determined from laboratory powder diffraction data.

Ezetimibe {systematic name: (3R,4S)-1-(4-fluorophenyl)-3-[(3S)-3-(4-fluorophenyl)-3-hydroxypropyl]-4-(4-hydroxyphenyl)azetidin-2-one}, C(24)H(21)F(2)NO(3), is used to lower cholesterol levels by inhibiting cholesterol resorption in the human intestine. The crystal structure of ezetimibe anhydrate was solved from laboratory powder diffraction data by means of real-space methods using the program DASH [David et al. (2006). J. Appl. Cryst. 39, 910-915]. Subsequent Rietveld refinement with TOPAS Academic [Coelho (2007). TOPAS Academic User Manual. Version 4.1. Coelho Software, Brisbane, Australia] led to a final R(wp) value of 8.19% at 1.75 A resolution. The compound crystallizes in the space group P2(1)2(1)2(1) with one molecule in the asymmetric unit. The molecules are closely packed and two intermolecular hydrogen bonds form an extended hydrogen-bond architecture.

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

No crystal structure at ambient pressure is known for tetramethylsilane, Si(CH(3))(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 (Pa3, 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 Pa3, Z = 8.

catena-Poly[[dipyridine-nickel(II)]-trans-di-µ-chlorido] from powder data.

The asymetric unit of the title compound, [NiCl(2)(C(5)H(5)N)(2)](n), contains two Ni(II) ions located on different twofold rotational axes, two chloride anions and two pyridine rings in general positions. Each Ni(II) ion is coordinated by two pyridine rings, which form dihedral angles of 33.0 (2) and 11.0 (2)° for the two centers, and four chloride anions in a distorted octa-hedral geometry. The chloride anions bridge Ni(II) ions related by translation along the short b axes into two crystallographically independent polymeric chains.

Electron diffraction, X-ray powder diffraction and pair-distribution-function analyses to determine the crystal structures of Pigment Yellow 213, C23H21N5O9.

The crystal structure of the nanocrystalline alpha phase of Pigment Yellow 213 (P.Y. 213) was solved by a combination of single-crystal electron diffraction and X-ray powder diffraction, despite the poor crystallinity of the material. The molecules form an efficient dense packing, which explains the observed insolubility and weather fastness of the pigment. The pair-distribution function (PDF) of the alpha phase is consistent with the determined crystal structure. The beta phase of P.Y. 213 shows even lower crystal quality, so extracting any structural information directly from the diffraction data is not possible. PDF analysis indicates the beta phase to have a columnar structure with a similar local structure as the alpha phase and a domain size in column direction of approximately 4 nm.

Structure determination of seven phases and solvates of Pigment Yellow 183 and Pigment Yellow 191 from X-ray powder and single-crystal data.

The crystal structures of two industrially produced laked yellow pigments, Pigment Yellow 183 [P.Y. 183, Ca(C16H10Cl2N4O7S2), alpha phase] and Pigment Yellow 191 [P.Y. 191, Ca(C17H13ClN4O7S2), alpha and beta phases], were determined from laboratory X-ray powder diffraction data. The coordinates of the molecular fragments of the crystal structures were found by means of real-space methods (simulated annealing) with the program DASH. The coordinates of the calcium ions and the water molecules were determined by combining real-space methods (DASH and MRIA) and repeated Rietveld refinements (TOPAS) of the partially finished crystal structures. TOPAS was also used for the final Rietveld refinements. The crystal structure of beta-P.Y. 183 was determined from single-crystal data. The alpha phases of the two pigments are isostructural, whereas the beta phases are not. All four phases exhibit a double-layer structure, built from nonpolar layers containing the C/N backbone and polar layers containing the calcium ions, sulfonate groups and water molecules. Furthermore, the crystal structures of an N,N-dimethylformamide solvate of P.Y. 183, and of P.Y. 191 solvates with N,N-dimethylformamide and N,N-dimethylacetamide were determined by single-crystal X-ray analysis.

Magnetic properties of two double-layer structures built from hydroxynaphthoic acids and manganese.

Double-layer structures consisting of alternating polar and non-polar layers have been prepared using Mn2+ ions and o-hydroxynaphthoic acids. The polar layers contain the Mn2+ ions, carboxylate groups, hydroxy groups and water molecules. The non-polar layers are built up from the naphthalene moieties. In catena-poly[[diaquamanganese(II)]bis(mu-3-hydroxy-2-naphthoato-kappa2O:O')] (also called manganese 3-hydroxy-2-naphthoate dihydrate), [Mn(C11H7O3)2(H2O)2]n, (I), the Mn2+ ions are connected by carboxylate groups to form two-dimensional networks. This compound shows distinct antiferromagnetic interactions and long-range ordering at low temperature. In contrast, tetraaquabis(1-hydroxy-2-naphthoato-kappaO)manganese(II), [Mn(C11H7O3)2(H2O)4], (II), which lacks a close linkage between the Mn2+ ions, reveals purely paramagnetic behaviour. In (II), the Mn2+ ion lies on an inversion centre.

Solvent-free methylthiomethyllithium [LiCH2SMe]infinity: solid state structure and thermal decomposition.

Solvent-free [LiCH2SMe]infinity forms a layer structure consisting of four- (Li2C2), five- (Li2CS2), and six-membered (Li2C2S2) rings in the solid state; the compound violently explodes upon heating to T=160+/-5 degrees C under an argon atmosphere.