Laboratory X-ray Powder Diffraction Data Research Articles

Mix and measure - Combining in situ X-ray powder diffraction and microtomography for accurate hydrating cement studies

It is reported an innovative methodology based on in situ MoKα1 laboratory X-ray powder diffraction (LXRPD) and microtomography (μCT) avoiding any sample conditioning. The pastes are injected in 2.0 mm capillaries and the extremes are just sealed. The measurements take place in the same region of the hydrating paste. Thick capillaries are key to avoiding self-desiccation, which dictates the need of high-energy X-ray radiation for the diffraction study. This approach has been tested with a PC 42.5 R paste having w/c = 0.50. μCT data were collected at 12 h and 1, 3, 7 and 79 days. LXRPD data were acquired at 1, 3, 7 and 77 days. In this proof-of-principle research, the same paste was also cured ex situ. Portlandite contents obtained by thermal analysis, ex situ powder diffraction, in situ mass balance calculation and in situ powder diffraction were 13.8, 13.1, 13.1 and 12.5 wt%, respectively. From the μCT study, the grey value histogram evolution with time showed a crossing point which allowed us to distinguish (appearing) hydrated products from (dissolving) unhydrated cement particles. Segmentations were carried out by global thresholding and the random forest approach (one type of supervised Machine Learning). The comparison of the segmented results for the unhydrated cement fraction and the Rietveld quantitative phase analysis outputs gave an agreement of 2 %. The potential of this methodology to deal with more complex binders is also presented.

Hydrogen bonding patterns and C-H...π interactions in the structure of the antiparkinsonian drug (R)-rasagiline mesylate determined using laboratory and synchrotron X-ray powder diffraction data.

The structure of (R)-rasagiline mesylate [(R)-RasH+·Mes-], an active pharmaceutical ingredient used to treat Parkinson's disease, is presented. The structure was determined from laboratory and synchrotron powder diffraction data, refined using the Rietveld method, and validated and optimized using dispersion-corrected DFT calculations. The unit-cell parameters obtained in both experiments are in good agreement and the refinement with both datasets converged to good agreement factors. The final parameters obtained from laboratory data were a = 5.4905 (8), b = 6.536 (2), c = 38.953 (3) Å, V = 1398.0 (4) Å3 and from synchrotron powder data were a = 5.487530 (10) Å, b = 6.528939 (12) Å, c = 38.94313 (9) Å, V = 1395.245 (5) Å3 with Z = 4 and space group P212121. Preferred orientation was properly accounted for using the synchrotron radiation data, leading to a March-Dollase parameter of 1.140 (1) instead of the 0.642 (1) value obtained from laboratory data. In the structure, (R)-RasH+ moieties form layers parallel to the ab plane connected by mesylate ions through N-H...O and C-H...O hydrogen bonds. These layers stack along the c axis and are further connected by C-H...π interactions. Hirshfeld surface analysis and fingerprint plot calculations indicate that the main interactions are: H...H (50.9%), H...C/C...H (27.1%) and H...O/O...H (21.1%).

Crystal structure of 2,5-di-hydroxy-terephthalic acid from powder diffraction data.

The crystal structure of anhydrous 2,5-dhy-droxy-terephthalic acid, C8H6O6, was solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The published structure of 2,5-di-hydroxy-terephthalic acid dihydrate was also optimized. The carb-oxy-lic acid groups form strong hydrogen bonds, which form centrosymmetric rings with graph set R 2 2(8). These hydrogen bonds link the mol-ecules into chains along [011]. There is an intra-molecular O-H⋯O hydrogen bond between the hydroxyl group and the carbonyl group of the carb-oxy-lic acid. The hydrogen bonding in the dihydrate is very different. Although the intra-molecular hy-droxy/carb-oxy-lic acid hydrogen bond is present, the water mol-ecule acts as an acceptor to the carb-oxy-lic acid and a donor to two other oxygen atoms. The carb-oxy-lic acid groups do not inter-act with each other directly.

Structures of dicobalt and dinickel 4,4'-bi-phenyldi-carboxyl-ate di-hydroxide, M 2(O2CC6H4C6H4CO2)(OH)2, M = Co and Ni, and di-ammonium 4,4'-bi-phenyldi-carboxyl-ate from powder diffraction data.

The triclinic structures of poly[(μ4-4,4'-bi-phenyldi-carboxyl-ato)di-μ-hydroxido-dicobalt], [Co2(C14H8O4)(OH)2] n , and poly[(μ4-4,4'-bi-phenyldi-carboxyl-ato)di-μ-hydroxido-dinickel], [Ni2(C14H8O4)(OH)2] n , were established using laboratory X-ray powder diffraction data. These structures, as well as that of poly[(μ4-4,4'-bi-phenyldi-carboxyl-ato)di-μ-hydroxido-dimanganese], [Mn2(C14H8O4)(OH)2] n , were optimized using density functional techniques. The structure of di-ammonium 4,4'-bi-phenyldi-carboxyl-ate, 2NH4 +·C14H8O4 2-, was also solved using laboratory powder data. The Mn and Co compounds are isostructural: the octa-hedral MO6 groups share edges to form chains running parallel to the c-axis. These chains share corners (OH groups) to link into layers lying parallel to the bc plane. The hydroxyl groups do not participate in hydrogen bonds. The structure of (NH4)2BPDC consists of alternating layers of BPDC and ammonium ions lying parallel to the ab plane. Each hydrogen atom of the ammonium ions in (NH4)2BPDC participates in a strong N-H⋯O hydrogen bond.

Crystal structure from laboratory X-ray powder diffraction data, DFT-D calculations, and Hirshfeld surface analysis of (S)-dapoxetine hydrochloride

The previously unreported crystal structure of (S)-Dapoxetine hydrochloride (DAPHCl), the only active pharmaceutical ingredient specially developed for the treatment of premature ejaculation in men, has been determined from laboratory X-ray powder diffraction data with DASH and refined by the Rietveld method with TOPAS-Academic. The structure was evaluated and optimized by dispersion-corrected DFT calculations. This compound crystallizes in an orthorhombic cell, space group P212121, with unit-cell parameters a= 6.3208(3) Å, b = 10.6681(5) Å, c = 28.1754(10) Å, V = 1899.89(14) Å3, Z = 4. The refinement converged to Rp= 0.0442, Rwp= 0.0577, and GoF = 2.440. The crystal structure is a complex 3D arrangement of DAPHCl moieties held together by hydrogen bonds, π⋯π, and C–H⋯π interactions. The chloride ions form layers parallel to the ab plane and are connected by dapoxetinium moieties through N–H⋯Cl and C–H⋯Cl hydrogen bonds. These layers stack along the c-axis, which are connected by C–H⋯π interactions. Hirshfeld surface analysis and fingerprint plot calculations have been performed.

Crystal structure of alfuzosin hydrochloride, C19H28N5O4Cl

The crystal structure of anhydrous alfuzosin hydrochloride has been solved and refined using laboratory X-ray powder diffraction data and optimized using density functional theory techniques. Anhydrous alfuzosin hydrochloride crystallizes in space groupP-1 witha= 9.3214(16),b= 9.3997(29),c= 12.6172(64) Å,α= 107.993(11),β= 100.386(9),γ= 90.229(6)°,V= 1032.1(10) Å3, andZ= 2 at ambient conditions. Thermal expansion is anisotropic, being 8× larger in thec-direction than in the other two. The crystal structure is characterized by a stack of planar fused rings along theb-axis, and layers of the more-corrugated portion of the molecule parallel to theab-plane. There are two strong N–H⋯Cl hydrogen bonds, as well as seven C-H⋯Cl hydrogen bonds. The powder patterns have been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

C-S-H seeding activation of Portland and Belite cements: An enlightening in situ synchrotron powder diffraction study

C-S-H seeding in Portland cements is well known from basic scientific works and field applications. Moreover, this activation approach could be beneficial for low-CO2 cements under development where a general drawback is poor mechanical strengths during the first week of hydration. However, a mechanistic understanding of the different processes taking place when seeding is still not developed. Here, we contribute to this knowledge gap by studying one commercial Portland cement and two industrial-trial belite cements. Three different admixtures are employed, viz. two types of commercial C-S-H seeding and triisopropanolamine as a typical alkanolamine. A multitechnique approach is employed including calorimetry, ultrasonic pulse velocity, thermal analysis and Rietveld analysis of laboratory X-ray powder diffraction data. Chiefly, an in situ X-ray synchrotron diffraction study has allowed mapping out the evolution of every crystalline phase. Furthermore, the use of an internal standard permitted to measure the changes in the overall amorphous content. In a nutshell, alite and belite (phases) hydrations are not significantly accelerated by C-S-H seeding for the three studied cements. Conversely, sulphate and aluminate phase dissolutions are enhanced. Faster ettringite crystallisation contributes to the observed improved mechanical properties at early ages. Moreover, a synergistic effect between C-S-H seeding and alkanolamine addition is proved. The importance of these findings for the possible acceleration of low-CO2 cement hydration is discussed.

Structural elucidation of phenoxybenzaldehyde derivatives from laboratory powder X-ray diffraction: A combined experimental and theoretical quantum mechanical study

Crystal structure of two new phenoxybenzaldehyde derivatives, 4-(4-bromophenoxy)benzaldehyde (1) and 4-(4-nitrophenoxy)benzaldehyde (2), have been determined from laboratory X-ray powder diffraction data. The synergies of intermolecular C–H···O hydrogen bond, π···π, anion···π and lone-pair(l.p)···π interactions assemble the molecules into supramolecular frameworks. The quantum chemical calculation has been performed to analyze and characterize weak noncovalent interactions in the molecules. Analysis of Hirshfeld surfaces of the compounds showed that the crystal structures are primarily characterized by H···H, H···C and H···O contacts. Bader's theory of ‘atoms-in-molecules’ (AIM) is applied to describe the noncovalent interactions for (1) and (2). The supramolecular frameworks are further characterized by theoretical ‘Noncovalent Interaction’ (NCI) plot index.

Powder X-ray diffraction as a powerful tool to exploit in organic electronics: shedding light on the first N,N',N''-trialkyldiindolocarbazole.

The first crystal structure of a fully N-alkylated diindolocarbazole derivative, namely, 5,8,14-tributyldiindolo[3,2-b;2',3'-h]carbazole (1, C36H39N3), has been determined from laboratory powder X-ray diffraction (PXRD) data. A complex trigonal structure with a high-volume unit cell of 12987 Å3 was found, with a very long a(=b) [52.8790 (14) Å] and a very short c [5.36308 (13) Å] unit-cell parameter (hexagonal setting). The detailed analysis of the intermolecular interactions observed in the crystal structure of 1 highlights its potential towards the implementation of this core as a semiconductor in organic thin-film transistor (OTFT) devices. Since the molecule has a flat configuration reflecting its π-conjugated system, neighbouring molecules are found to stack atop each other in a slipped parallel fashion via π-π stacking interactions between planes of ca 3.30 Å, with a centroid-centroid distance between the aromatic rings corresponding to the shortest axis of the unit cell (i.e. c). The alkylation of the three N atoms proves to be a decisive feature since it favours the presence of C-H...π interactions in all directions, which strengthens the crystal packing. As a whole, PXRD proves to be a valuable option for the resolution of otherwise inaccessible organic crystal structures of interest in different areas.

Crystal structures of lanthanide terephthalate tetrahydrate, R2(C8H4O4)3(H2O)4, R = La–Er

The crystal structures of 11 lanthanide terephthalate tetrahydrates have been refined using laboratory X-ray powder diffraction data and optimized using density functional techniques. The lattice parameters and R–O bonds exhibit expected trends based on the cation size. The R–O bond distances in the Rietveld-refined structures are similar. However, in the density functional theory (DFT)-optimized structures, the bond distances break into two distinct groups, longer and shorter R–O bonds. This indicates that the bond distance restraints imposed upon the refined structures may have a greater impact than is expected from their weights. The aromatic carboxyl groups were not completely planar, but it is known that the carboxyl groups can rotate to accommodate hydrogen bonding and coordination to the metal. Both water molecules coordinated to the lanthanides act as hydrogen bond donors, but only one of the three unique carboxyl groups acts as an acceptor.

Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of (RS)-trichlorme-thia-zide.

The structure of racemic (RS)-trichlorme-thia-zide [systematic name: (RS)-6-chloro-3-(di-chloro-meth-yl)-1,1-dioxo-3,4-di-hydro-2H-1λ6,2,4-benzo-thia-di-azine-7-sulfonamide], C8H8Cl3N3O4S2 (RS-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using DASH [David et al. (2006 ▸). J. Appl. Cryst. 39, 910-915.], refined by the Rietveld method with TOPAS-Academic [Coelho (2018 ▸). J. Appl. Cryst. 51, 210-218], and optimized using DFT-D calculations. The extended structure consists of head-to-tail dimers connected by π-π inter-actions which, in turn, are connected by C-Cl⋯π inter-actions. They form chains propagating along [101], further connected by N-H⋯O hydrogen bonds to produce layers parallel to the ac plane that stack along the b-axis direction, connected by additional N-H⋯O hydrogen bonds. The Hirshfeld surface analysis indicates a major contribution of H⋯O and H⋯Cl inter-actions (32.2 and 21.7%, respectively). Energy framework calculations confirm the major contribution of electrostatic inter-actions (E elec) to the total energy (E tot). A comparison with the structure of S-TCMZ is also presented.

Crystal structure determination of orthorhombic variscite2Oand its derivative AlPO4 structure at high temperature

AbstractVariscite [Al(PO4)·2H2O] is an uncommon secondary phosphate mineral but is important in a variety of environmental and technological applications. It exists in at least one monoclinic (metavariscite) and two orthorhombic polymorphs (“Lucin-type” and “Messbach-type”), but the fine-grained nature of the “Messbach-type” variscite has hampered the determination of its crystal structure. The crystal structure of the latter from Tooele County, Utah, was solved and refined using laboratory powder X-ray diffraction (XRD) data, charge-flipping, and the Rietveld method. Both variscite modifications belong to the family of framework 3D MT structures in which octahedra (M) and tetrahedra (T) are linked by bridging O atoms. Topological analysis reveals that the two structures are polytypes. Based on our results and our structural interpretations, we refer to “Lucin-type” variscite as variscite1O and the “Messbach-type” as variscite2O, to be consistent with modern polytype terminology. The similarity of these two structures suggests that 1O-2O interstratifications may exist in nature, which is consistent with observed broadening of diffraction peaks of the Tooele material. 31P and 27Al MAS/NMR measurements are consistent with the XRD-determined crystal structure, and they show distinct signals for each of the two independent P and Al positions in variscite2O.High-temperature XRD, thermal analyses, and NMR measurements were applied to study the nature of the transformation of variscite2O to a derivative AlPO4 structure above 473 K. Charge-flipping analysis showed that the crystal structure of the new anhydrous AlPO4 phase (AlPO4-var2O in analogy to its parent structure) can be described as a 3D framework of alternating AlO4 and PO4 tetrahedra linked by bridging O atoms. Thermogravimetric analyses revealed almost complete dehydration above ~450 K, and NMR results were consistent with tetrahedral Al and P atoms.

Crystal structure from laboratory X-ray powder diffraction data, DFT-D calculations, Hirshfeld surface analysis, and energy frameworks of a new polymorph of 1-benzothiophene-2-carboxylic acid — ERRATUM

Crystal structure from laboratory X-ray powder diffraction data, DFT-D calculations, Hirshfeld surface analysis, and energy frameworks of a new polymorph of 1-benzothiophene-2-carboxylic acid — ERRATUM - Volume 36 Issue 3

Crystal structure of the anticancer drug carmustine determined by X-ray powder diffraction

The structure of the anticancer drug carmustine (1,3-bis(2-chloroethyl)-1-nitrosourea, C5H9Cl2N3O2) was successfully determined from laboratory X-ray powder diffraction data recorded at 278 K and at 153 K. Carmustine crystallizes in the orthorhombic space groupP212121withZ= 4. The lattice parameters area= 19.6935(2) Å,b= 9.8338(14) Å,c= 4.63542(6) Å,V= 897.71(2) ų at 153 K, anda= 19.8522(2) Å,b= 9.8843(15) Å,c= 4.69793(6) Å,V= 921.85(2) ų at 278 K. The Rietveld fits are very good, with lowR-values and smooth difference curves of calculated and experimental powder data. The molecules form a one-dimensional hydrogen bond pattern. At room temperature, the investigated commercial sample of carmustine was amorphous.

Crystal structure refinement of magnesium zinc divanadate, MgZnV2O7, from powder X-ray diffraction data.

The crystal structure of magnesium zinc divanadate, MgZnV2O7, was determined and refined from laboratory X-ray powder diffraction data. The title compound was synthesized by a solid-state reaction at 1023 K in air. The crystal structure is isotypic with Mn0.6Zn1.4V2O7 (C2/m; Z = 6) and is related to the crystal structure of thortveitite. The asymmetric unit contains two metal sites with statistically distributed magnesium and zinc atoms with the atomic ratio close to 1:1. One (Mg/Zn) metal site (M1) is located on Wyckoff position 8j and the other (M2) on 4h. Three V sites (all on 4i), and eight O (three 8j, four 4i, and one 2b) sites complete the asymmetric unit. The structure is an alternate stacking of V2O7 layers and (Mg/Zn) atom layers along [20]. It is distinct from other related structures in that each V2O7 layer consists of two groups: a V2O7 dimer and a V4O14 tetra-mer. Mixed-occupied M1 and M2 are coordinated by oxygen atoms in distorted trigonal bipyramidal and octa-hedral sites, respectively.

Lithium dipotassium citrate monohydrate, LiK2C6H5O7(H2O).

The crystal structure of dilithium potassium citrate monohydrate, Li+·2K+·C6H5O7 3-·H2O or LiK2C6H5O7·H2O, has been solved by direct methods and refined against laboratory X-ray powder diffraction data, and optimized using density functional techniques. The complete citrate trianion is generated by a crystallographic mirror plane, with two C and three O atoms lying on the reflecting plane, and chelates to three different K cations. The KO8 and LiO4 coordination polyhedra share edges and corners to form layers lying parallel to the ac plane. An intra-molecular O-H⋯O hydrogen bond occurs between the hydroxyl group and the central carboxyl-ate group of the citrate anion as well as a charge-assisted inter-molecular O-H⋯O link between the water mol-ecule and the terminal carboxyl-ate group. There is also a weak C-H⋯O hydrogen bond.

Crystal structure of strontium hydrogen citrate monohydrate, Sr(HC6H5O7)(H2O)

The crystal structure of strontium hydrogen citrate monohydrate has been solved using laboratory X-ray powder diffraction data, refined using both laboratory and synchrotron data, and optimized using density functional techniques. Strontium hydrogen citrate monohydrate crystallizes in space groupC2/c(#15) witha= 25.15601(17),b= 10.90724(6),c= 6.37341(4) Å,β= 91.9846(6)°,V= 1747.704(12) Å3, andZ= 8. The Sr coordination and the hydrogen bonding result in a layered structure. The SrO8coordination polyhedra share edges to form corrugated layers parallel to thebc-plane. Hydrogen bonds between the carboxylic acid groups and water molecules link the layers. Intermolecular hydroxyl–carboxyl hydrogen bonds also link the layers in a ring pattern with a graph set symbolR2,2(12). After storage for 2 years, partial re-crystallization occurred, to an as-yet unknown compound with a triclinic unit cell.

Crystal structure from laboratory X-ray powder diffraction data, DFT-D calculations, Hirshfeld surface analysis, and energy frameworks of a new polymorph of 1-benzothiophene-2-carboxylic acid

Several benzothiophene-based compounds, including 1-benzothiophene-2-carboxylic acid, exhibit a wide variety of pharmacological activities. They have been extensively used to treat various types of diseases with high therapeutic effectiveness. In this contribution, the crystal structure of a new polymorph of 1-benzothiophene-2-carboxylic acid (BTCA) was determined from laboratory X-ray powder diffraction data with DASH, refined by the Rietveld method with TOPAS-Academic, and optimized using DFT-D calculations. The new form of 1-benzothiophene-2-carboxylic acid crystallizes in space group C2/c (No. 15) with a = 14.635(4), b = 5.8543(9), c = 19.347(3) Å, β = 103.95(1)°, V = 1608.8(6) Å3, and Z = 8. The structure is a complex 3D arrangement which can be described in terms of hydrogen-bonded dimers of BTCA molecules, joined by the acid–acid homosynthon, which interact through C–H⋯O hydrogen bonds to produce tapes further connected through head-to-tail π⋯π and edge-to-face C–H⋯π interactions. A comparison with a previously reported triclinic polymorph and with the related 1-benzofuran-2-carboxylic acid (BFCA) is also presented.

Redetermination of K2Mg3(OH)2(SO4)3(H2O)2 from single-crystal X-ray data revealing the correct hydrogen-atom positions.

In comparison with the previous structure determination of K2Mg3(OH)2(SO4)3(H2O)2, dipotassium trimagnesium di-hydroxide tris-(sulfate) dihydrate, from laboratory powder X-ray diffraction data [Kubel & Cabaret-Lampin (2013 ▸). Z. Anorg. Allg. Chem. 639, 1782-1786], the present redetermination against CCD single-crystal data has allowed for the modelling of all non-H atoms with anisotropic displacement parameters. As well as higher accuracy and precision in terms of bond lengths and angles, the clear localization of the H-atom positions leads also to a reasonable hydrogen-bonding scheme for this hy-droxy hydrate. The structure consists of (100) sheets composed of corner- and edge-sharing [MgO6] octa-hedra and sulfate tetra-hedra. Adjacent sheets are linked by the potassium cations and a hydrogen bond of medium strength involving the water mol-ecule. The title compound is isotypic with its CoII and MnII analogues: the three K2 M 3(OH)2(SO4)3(H2O)2 (M = Mg, Co, Mn) structures are qu-anti-tatively compared.

Crystal structure and thermal behavior of Bi$$_6$$Te$$_2$$O$$_{15}$$: investigation of synthetic and natural pingguite

The previously unknown crystal structure of pingguite was determined and refined from laboratory X-ray powder diffraction data using a synthetic sample. Additional single crystal diffraction of natural pingguite confirms that the crystal structure of the synthetic sample is identical to the natural mineral. This new crystal structure calls for a revised chemistry of the rare mineral pingguite to Bi $$_6$$ Te $$_2$$ O $$_{15}$$ instead of the previously reported formula Bi $$_6$$ Te $$_2$$ O $$_{13}$$ . Pingguite contains Te $$^\mathrm{VI}$$ only and not Te $$^\mathrm{IV}$$ as previously reported. Pingguite undergoes an irreversible phase transition around 840 $$^{\circ }$$ C which is characterized by a loss of oxygen and a reduction from Te $$^\mathrm{VI}$$ to Te $$^\mathrm{IV}$$ resulting in a $$\delta $$ -Bi $$_2$$ O $$_3$$ like type structure. In addition, we report the Raman spectroscopic data on the natural pingguite.