Ab Initio X-ray Powder Diffraction Research Articles

Solid-State Phase Transition of Agomelatine–Phosphoric Acid Molecular Complexes along the Salt–Cocrystal Continuum: Ab Initio Powder X-ray Diffraction Structure Determination and DFT-D2 Analysis

The solid-state phase transition of a multicomponent active pharmaceutical ingredient (M-APIs), composed of (1:1) agomelatine and phosphoric acid (AGL-P), is characterized using a set of complement...

Atomically Precise Structure Determination of Porous Organic Cage from Ab Initio PXRD Structure Analysis: Its Molecular Click Postfunctionalization and CO2 Capture Application.

A novel porous organic cage (POC) was prepared via condensation reaction between 1,3,5-triformylbenzene (TFB) and (1R,2R)-4-cyclohexene-1,2-diamine (CHEDA). This POC could pack in either an amorphous structure or a crystalline one. Atomically precise structure determination of POC was achieved through ab initio powder X-ray diffraction (PXRD) structure analysis in the chiral trigonal space group R3. The same atomically precise structure determination of POC from single-crystal X-ray diffraction (SXRD) structure analysis could be obtained independently with a slight difference in cell parameter, indicating that the refinement method through ab initio PXRD structure analysis is reliable and may serve as an essential method for atomically precise structure determination. The cage could adsorb up to 8 mmol/g CO2 at 298 K and 1 bar. Furthermore, 1-thioglycerol and 1-octadecanethiol were chosen to prove that postmodification of this POC was flexible. After post-synthetic modification (PSM) via highly efficient photoinitiated thiol-ene click reaction, the products still kept porous with relatively higher special surface area (337 m2/g of 5T and 156 m2/g of 5O) than mostly reported cages via the reduced-amine approach.

Thermal Reactivity in Metal Organic Materials (MOMs): From Single-Crystal-to-Single-Crystal Reactions and Beyond.

Thermal treatment is important in the solid-state chemistry of metal organic materials (MOMs) because it can create unexpected new structures with unique properties and applications that otherwise in the solution state are very difficult or impossible to achieve. Additionally, high-temperature solid-state reactivity provide insights to better understand chemical processes taking place in the solid-state. This review article describes relevant thermally induced solid-state reactions in metal organic materials, which include metal organic frameworks (MOFs)/coordination polymers (CPs), and second coordination sphere adducts (SSCs). High temperature solid-state reactivity can occur in a single-crystal-to-single crystal manner (SCSC) usually for cases where there is small atomic motion, allowing full structural characterization by single crystal X-ray diffraction (SC-XRD) analysis. However, for the cases in which the structural transformations are severe, often the crystallinity of the metal-organic material is damaged, and this happens in a crystal-to-polycrystalline manner. For such cases, in the absence of suitable single crystals, structural characterization has to be carried out using ab initio powder X-ray diffraction analysis or pair distribution function (PDF) analysis when the product is amorphous. In this article, relevant thermally induced SCSC reactions and crystal-to-polycrystalline reactions in MOMs that involve significant structural transformations as a result of the molecular/atomic motion are described. Thermal reactivity focusing on cleavage and formation of coordination and covalent bonds, crystalline-to-amorphous-to-crystalline transformations, host–guest behavior and dehydrochlorination reactions in MOFs and SSCs will be discussed.

Solid-Gas Phase Synthesis of Coordination Networks by Using Redox-Active Ligands and Elucidation of Their Oxidation Reaction.

Formation of coordination networks is a complex process affected by a multitude of factors. Many synthetic strategies have been developed that attempt to control these factors and direct the structure of the final product. Coordination bond formation and structural assembly processes, however, typically take place either in the solution or solid states. In comparison, gas-phase network synthesis remains largely unexplored. Herein, two new two-dimensional coordination networks are obtained from the solid-gas phase reaction between ZnX2 (X=I, Br) and the redox-active 2,5,8-tri(4-pyridyl)1,3-diazaphenalene (HTPDAP) ligand. Their structures were solved by ab initio powder X-ray diffraction analysis and feature a novel Zn halide trimeric cluster. This strategy is contrasted with a conventional solvothermal synthesis, which led to a one-dimensional coordination polymer instead. The intrinsic electroactive properties of these materials were probed by solid-state cyclic voltammetry measurements, which revealed the presence of HTPDAP and halide-based processes. Chemical oxidation of the two-dimensional networks by using NOPF6 agent, unexpectedly, led to the formation of a nitrated analog of HTPDAP, the PF6 - salt of diprotonated 4,6,7,9-tetranitro-2,5,8-tris(4-pyridyl)diazaphenalene cation (denoted N-TPDAP), which was isolated and characterized. These results provide deeper insights into the oxidation process of HTPDAP-containing networks and uncover unique redox-induced chemical transformations.

A silver(i) coordination polymer with sodium 3,5-dimethyl-4-sulfonate pyrazolate: a nice example of PXRD structure solution and time-driven crystallization

A silver(i) coordination polymer with the sodium salt of 3,5-dimethyl-4-sulfonate pyrazole (HLNa) has been prepared and structurally characterized by ab initio X-ray powder diffraction.

Conformational and characterization of benidipine hydrochloride polymorphs: Spectroscopic and computational modeling investigations

Polymorphism has attracted increasing attentions due to its particular importance in the field of pharmaceutical industry, especially the studies on the conformations of different crystal structures. In this work, the relationship between crystalline forms and conformations of benidipine hydrochloride was systematically investigated by spectroscopic analysis with theoretical simulation. The structures of two polymorphs for benidipine hydrochloride were characterized on the basis of detailed study of Infrared spectroscopy, powder X-ray diffraction and differential scanning calorimetry. A method which combining IR, theoretical study and potential energy distribution was utilized to identify the monomeric conformers of benidipine hydrochloride in polymorphs. Simulations for the dimeric forms were also carried out by molecular electrostatic potential and natural bond orbital to improve the assignment of the bands in solid state and to analyze the intermolecular interactions. The results of calculated IR spectra showed highly accordance with experimental data, thus the conformers were demonstrated to be presented in the polymorphs appropriately. Furthermore, ab initio powder X-ray diffraction patterns were further simulated to estimate the attribution of conformers in polymorphic forms. The chemical and thermodynamic stability of two polymorphs were evaluated by the frontier molecular orbitals analysis and differential scanning calorimetry analysis.

Supramolecular Nanostructures of Chiral Perylene Diimides with Amplified Chirality for High-Performance Chiroptical Sensing.

Chiral supramolecular nanostructures with optoelectronic functions are expected to play a central role in many scientific and technological fields but their practical use remains in its infancy. Here, this paper reports photoconductive chiral organic semiconductors (OSCs) based on perylene diimides with the highest electron mobility among the chiral OSCs and investigates the structure and optoelectronic properties of their homochiral and heterochiral supramolecular assemblies from bottom-up self-assembly. Owing to the well-ordered supramolecular packing, the homochiral nanomaterials exhibit superior charge transport with significantly higher photoresponsivity and dissymmetry factor compared with those of their thin film and monomeric equivalents, which enables highly selective detection of circularly polarized light, for the first time, in visible spectral range. Interestingly, the heterochiral nanostructures assembled from co-self-assembly of racemic mixtures show extraordinary chiral self-discrimination phenomenon, where opposite enantiomeric molecules are packed alternately into heterochiral architectures, leading to completely different optoelectrical performances. In addition, the crystal structures of homochiral and heterochiral nanostructures have first been studied by ab initio X-ray powder diffraction analysis. These findings give insights into the structure-chiroptical property relationships of chiral supramolecular self-assemblies and demonstrate the feasibility of supramolecular chirality for high-performance chiroptical sensing.

Difluprednate: More than meets the eye

Difluprednate, a FDA approved topical corticosteroid indicated for the treatment of inflammation and pain associated with ocular surgery, affords three polymorphic crystal forms (one hexagonal, sg. P65, and two distinct orthorhombic, both sg.’s P212121, phases), whose preparation, thermal stability ranges, crystal structures and stereochemical preferences are here reported. Using DSC, single-crystal structural analysis and less conventional ab-initio X-ray powder diffraction methods, the rich structural and thermal behavior of three difluprednate polymorphs have been clarified, and the validity of previous complex and sometimes contradicting literature reports has been challenged. Complementary solution state NMR provided 1H, 13C and 19F chemical shifts full assignment of the corresponding signals. These results allow us to precisely describe the selective isolation pathways toward three distinct crystal phases, and to define their structural and analytical data necessary for identification and easy and accurate quantification, by modern Rietveld analysis, of complex difluprednate polymorphic mixtures, often obtained as a result of poorly controlled (co)-precipitation methods.

Bending by Faulting: A Multiple Scale Study of Copper and Silver Nitropyrazolates

A multiscale approach, combining structural and microstructural characterizations, was applied to tackle an uncommon and so far unsolved structural problem occurring in group 11 nitropyrazolates. To this goal, the average structure of the [Ag(4-NO2-pz)]3 and [Cu(4-NO2-pz)]3 species was determined through ab initio X-ray powder diffraction techniques on high-resolution synchrotron data, and used to infer molecular models of randomly distributed defects within molecular stacks of trimeric molecules of D3h idealized symmetry. By cross-coupling the size and shape information on nanocrystalline coherent domains derived from tailored Debye function simulations with those obtained from scanning electron miscroscopy images on multidomain particles, the mechanism of structural disorder disrupting crystal periodicity is proposed. Such a model was further supported through the derivation of the pair distribution function, which affords local features to be sought independently from the presence of structural periodicity. Finally, the effects of stacking faults on the electrical properties of [Ag(4-NO2-pz)]3 have been experimentally evaluated.

ChemInform Abstract: Enclosing the Functional Properties of Pyrazolato‐Based Coordination Polymers within a Structural Frame: The Role of Laboratory X‐Ray Powder Diffraction

Ab initio X-ray powder diffraction structural analyses from laboratory data have been widely employed in the characterization of coordination polymers not affording single crystals of suitable quality to undergo conventional structural determinations. This is particularly true for coordination polymers built upon strong ligand-to-metal bonds, as those formed by anionic, nitrogen-based heterocycles - pyrazolates, imidazolates, pyrimidinolates and more complex moieties derived therefrom. More than one hundred species belonging to this class have been structurally characterized in the last three decades, affording key, otherwise inaccessible stereochemical and supramolecolar features. This contribution summarizes our most recent experience in the XRPD structural characterization of pyrazolato-based coordination polymers, devoting a special consideration to the methodologies and tricks which allowed us to juxtapose the structural description of these materials to their physico-chemical and, above all, functional properties.

細孔性ネットワーク錯体を用いたS<sub>3</sub>分子の単離と粉末X線回折による構造決定

In this review, we report isolation of unstable tri-sulfur, S3, in a porous coordination network which is used as a crystalline molecular flask. The ozone-like structure of S3 in a pore was determined by ab initio X-ray powder diffraction analysis. The S3 in the pore was interacted with iodine which faces to the pore of the network. The S3 in the network was quite stable unlike unstable gaseous S3 molecule because of the S-I interaction in the pore. Furthermore, the S3 in the network could be transformed to S6 by mechanical grinding or heating in the presence of NH4Cl. We will introduce new chemistry of small sulfur based on crystal structure.

Enclosing the functional properties of pyrazolato-based coordination polymers within a structural frame: the role of laboratory X-ray powder diffraction

Ab initio X-ray powder diffraction structural analyses from laboratory data have been widely employed in the characterization of coordination polymers not affording single crystals of suitable quality to undergo conventional structural determinations. This is particularly true for coordination polymers built upon strong ligand-to-metal bonds, as those formed by anionic, nitrogen-based heterocycles - pyrazolates, imidazolates, pyrimidinolates and more complex moieties derived therefrom. More than one hundred species belonging to this class have been structurally characterized in the last three decades, affording key, otherwise inaccessible stereochemical and supramolecolar features. This contribution summarizes our most recent experience in the XRPD structural characterization of pyrazolato-based coordination polymers, devoting a special consideration to the methodologies and tricks which allowed us to juxtapose the structural description of these materials to their physico-chemical and, above all, functional properties.

Selective Trapping of Labile S3 in a Porous Coordination Network and the Direct X-ray Observation

S3 is one of the basic allotropes of sulfur but is still a mysterious labile species. We selectively trapped S3 in a pore of a thermally stable coordination network and determined S3 structure by ab initio X-ray powder diffraction analysis. S3 in a pore has a C2v bent structure. The network containing trapped S3 is remarkably stable under ambient conditions and is inert to photoirradiation. S3 in the network could be transformed to S6 by mechanical grinding or heating in the presence of NH4X (X = Cl or Br). S6 could be reverse-transformed to S3 by photoirradiation. We also determined the structure of the network containing S6 by ab initio X-ray powder diffraction analysis.

Enlarging an Isoreticular Family: 3,3′,5,5′-Tetramethyl-4,4′-bipyrazolato-Based Porous Coordination Polymers

The solvothermal reaction between the rigid spacer 3,3′,5,5′-tetramethyl-4,4′-bipyrazole (H2Me4BPZ) and a number of transition metal salts promoted the formation of the coordination polymers [M(Me4BPZ)] (M = Zn, 1; Co, 2; Cd, 3; Cu, 4). Ab initio X-ray powder diffraction analyses revealed the main structural aspects of the four materials. 1 and 2 are representative examples of the so-called isoreticular strategy: isostructural to [M(BPZ)] and [M(BDP)] (H2BPZ = 4,4′-bipyrazole; H2BDP = 1,4-bis(1H-pyrazol-4-yl)benzene), they feature three-dimensional (3-D) porous networks containing square-shaped channels. In 3, tetrahedral Cd(II) ions are arranged within homochiral helices reciprocally linked by radial Me4BPZ spacers, overall creating a 3-D nonporous network. Finally, the 3-D porous framework of 4 comprises square Cu4 nodes linked to eight neighboring ones by the bridging spacers. Thermogravimetric analyses, coupled to variable-temperature X-ray powder diffraction, demonstrated the remarkable thermal robus...

Modulation of the Magnetic Properties of Two-Dimensional Compounds [NiX2(N–N)] by Tailoring Their Crystal Structure

A series of 2-D nickel compounds with the stoichiometry [NiCl2(N-N)] has been prepared, [N-N = pyrazine (1), 4,4'-bipyridine (2), trans-4,4'-azopyridine (3), trans-1,2-bis(4-pyridyl)ethylene (4), and 1,2-bis(4-pyridyl)ethane (5)]. The complex [NiBr2(4,4'-bpy)] (6) was also obtained for comparative reasons. Compound 2 is the β phase of the previously reported complex [NiCl2(4,4'-bpy)]. The syntheses of complexes 1-6 were carried out using solvothermal and microwave techniques. The compounds have been characterized by elemental analysis, infrared spectroscopy, thermogravimetry, and powder X-ray diffraction. The crystal structures of compounds 1, 4, and 5 have been solved using ab initio X-ray powder diffraction methods. Compounds 1-6 show the same arrangement, and their structures are described as layers formed by [NiX2] chains linked perpendicularly by N-N ligands. The magnetic properties of the compounds are explained as a balance between the ferromagnetic interactions along the [NiX2] chains and the antiferromagnetic interactions between chains from different layers. This work demonstrates that this balance can be tuned by the length of the N-N ligand.

Solid-State Hydration/Dehydration of Erythromycin A Investigated by ab Initio Powder X-ray Diffraction Analysis: Stoichiometric and Nonstoichiometric Dehydrated Hydrate

The stable dihydrate crystalline phase (DH) of erythromycin A loses water upon heating to give the anhydrous phase I (AI). Further heating then results in a polymorphic transformation via the amorphous state (melt) to give another anhydrous phase II (AII). The anhydrous phases of AI and AII undergo hydration when increasing the humidity. The crystals of AI showed stoichiometric hydration to give DH, whereas the crystals of AII showed nonstoichiometric hydration to give the humidity dependent nonstoichiometric hydrate phase (NSH). The crystal structures of AI and AII were directly determined from powder X-ray diffraction data using the direct space strategy for the structure solution followed by Rietveld refinement. From the structural properties of AI and AII, aspects of the mechanism of the solid-state transformations of DH and the hydration behavior of AI and AII have been determined, and the importance of the hydrophilicity of the voids has been revealed.

Solid–gas sorption behavior of a new polymorph of azacalix[5]arene pentamethyl ether as controlled by crystal architecture

Described are the crystal structure and solid–gas sorption behavior of a new polymorph of azacalix[5]arene 2. Single crystals of the benzene clathrate of 2 tolerated guest removal and furnished a solvent-free crystalline powder material 2PB that was in a polymorphic relationship with our previously studied crystalline powder 2PD. A newly prepared polymorph 2PB was nonporous to all of the examined gases, whereas 2PD exhibited the selective uptake of CO2 under ambient temperature and pressure conditions. Ab initio powder X-ray diffraction analysis and potential energy distribution analysis revealed that a difference in the crystal architecture of 2PB and 2PD played a critical role in defining the potential energy distribution in the crystals and hence controlling the solid–gas sorption behavior.

Kinetic Products in Coordination Networks: Ab Initio X-ray Powder Diffraction Analysis

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Mechanism of Dehydration–Hydration Processes of Lisinopril Dihydrate Investigated by ab Initio Powder X-ray Diffraction Analysis

Lisinopril is extensively used as an ethical anti-hypertensive drug in its dihydrate crystalline phase, where this phase undergoes dehydration to the metastable monohydrate and anhydrous phases upon being heated. The mechanistic aspects of this two-step dehydration process are successfully established from their crystal structures, determined for the first time by ab initio powder X-ray diffraction (PXRD) analysis. Furthermore, the hydration process of the anhydrous phase was investigated by humidity-controlled PXRD and dynamic vapor sorption. Although the dehydration process of the dihydrate phase proceeded in two steps via the metastable monohydrate phase, the hydration process from the anhydrous phase to the dihydrate phase proceeded in a single step. The mechanisms of these different pathways for the dehydration and hydration processes were also established from the crystal structures.

Pro-porous Coordination Polymers of the 1,4-Bis((3,5-dimethyl-1H-pyrazol-4-yl)-methyl)benzene Ligand with Late Transition Metals

Solvothermal reactions of the flexible, pyrazole-based 1,4-bis((3,5-dimethyl-1H-pyrazol-4-yl)methyl)benzene ligand (H(2)BDMPX) with late transition metal ions allowed the isolation of the four coordination compounds M(x)(BDMPX) (x = 1 for M = Zn, 1; Co, 2; Cd, 3; x = 2 for M = Cu, 4). The investigation of the thermal behavior assessed the high thermal robustness of these materials, which are stable in air at least up to 300 °C, with the Cd(II) derivative starting to decompose only around 500 °C. As retrieved by ab initio X-ray powder diffraction, the isomorphous compounds 1-3 possess a dense 3-D network featuring rhombic motifs hinged about rigid and parallel chains of tetrahedral MN(4) chromophores. As demonstrated by thermodiffractometric measurements, temperature increase triggers framework flexibility. The latter is at work also when N(2) adsorption is assayed at 77 K: 1 and 2 show permanent porosity, with BET and Langmuir specific surface areas of 515, 667 m(2)/g and 209, 384 m(2)/g, respectively. 1 and 2 thus represent an intriguing example of "porosity without pores", their pro-porous nature being explained in terms of the flexibility of the rhombic motifs, stimulated by the gas probe and facilitated by the nature of the ligand.