Simplify to understand: how to elucidate crystal structures?

Synthesis, crystal structure analysis, computational modelling and evaluation of anti-cervical cancer activity of novel 1,5-dicyclooctyl thiocarbohydrazone

Thiocarbazones are widely used as bioactive and pharmaceutical intermediates in medicinal chemistry and have been shown to exhibit diverse biological and pharmacological activities such as antimicrobial, anticancer, anti-viral, anti-convulsant and anti-inflammatory etc. In continuation of our interest in biologically active heterocycles and in an attempt to synthesize a spiro derivative, 1,2,4,5-tetraazaspiro[5.7]tridecane-3-thione, herein, the synthesis of 1,5-dicyclooctyl thiocarbohydrazone (3) has been reported via reaction of the cyclooctanone and thiocarbohydrazide. The structure was assigned on the basis of detailed spectral analysis and also confirmed by X-ray crystal studies. The Hirshfeld surface analysis indicates that the most significant interaction is S⋯H (12.7%). The presentation of mechanistic aspects regarding the plausible route of its formation has also been included. The first hyperpolarizability (β0) was found to be 10.22 × 10-30 esu, which indicates that the compound exhibits good non-linear optical properties. The density functional theory (DFT) method has been used to characterize the spectroscopic properties and vibrational analysis of 1,5-dicyclooctyl thiocarbohydrazone (3) theoretically. The compound and cisplatin (standard) were screened for their antiproliferative activity against the human cervical cancer cell line (SiHa) and they exhibited significant activity with IC50 values of 250 μM and 15 μM, respectively. The inhibitory nature of the title compound against viral oncoprotein E6 was confirmed by studies using molecular docking analysis. The results of biological activity and in silico analysis indicate that the synthesized molecule could act as a precursor for the synthesis of new heterocyclic derivatives of medicinal importance.

Diamondoid Ni(II) Coordination Polymer as an Electrocatalyst for Hydrogen and Oxygen Evolution Reactions and Overall Water Splitting

We have successfully synthesized a new Ni(II)-based coordination polymer (CP) [Ni2(cis-1,4-chdc)2(4,4'-bpy)3(H2O)2] (1); (cis-1,4- H2chdc=cis-1,4-cyclohexanedicarboxylic acid and 4,4'-bpy=4,4'-bipyridine) employing slow diffusion method in a single pot technique. The connectivity of Ni(II) ions and bridging cis-1,4-chdc ligand gives rise to a three-dimensional (3D) framework with 2-fold interpenetrated diamondoid topology. Interestingly, the synthesized CP acts as efficient catalyst for electrocatalytic water splitting. The water oxidation activity of compound 1 exhibits Tafel slope equivalent to 361.48 mV.dec-1 for hydrogen evolution reaction (HER) and 353.53 mV.dec-1 for oxygen evolution reaction (OER) in an alkaline medium while almost similar values of Tafel slope for HER and OER equivalent to 287.33 mV.dec-1 and 289.93 mV.dec-1 respectively in acidic medium. Thus, the compound 1 has excellent efficacy in catalyzing HER and OER in acidic as well as alkaline medium, which is ascribed to its distinctive 3D architecture.

A New Member of the Metal-Porphyrin Frameworks Family: Structure, Physicochemical Properties, Hydrogen and Carbon Dioxide Adsorption

A novel holmium-based porous metal-porphyrin framework, {(H3 O+ )[Ho(H2 TPPS)]-  ⋅ 4H2 O}n (denoted as UPJS-17), was synthesised by hydrothermal reaction. Structural analysis reveals, that UPJS-17 has a three-dimensional open framework. The framework is negatively charged and the negative charge is compensated by hydronium cation. The compound showed no N2 adsorption but the Ar, CO2 and H2 . From the argon adsorption, the surface area of ~150 m2  g-1 was determined. Carbon dioxide adsorption was measured at various temperatures (0, 10, 20, 30 and 40 °C) and the compound showed the highest adsorption capacity (at 0 °C) of 7.0 wt % of CO2 . From the carbon dioxide adsorption isotherms the isosteric heat of 56,5 kJ mol-1 was determined. Hydrogen adsorption was studied at -196 °C with hydrogen uptake of 2.1 wt % at 1 bar.

Hierarchical topological analysis of crystal structures: the skeletal net concept

Topological analysis of crystal structures faces the problem of the `correct' or the `best' assignment of bonds to atoms, which is often ambiguous. A hierarchical scheme is used where any crystal structure is described as a set of topological representations, each of which corresponds to a particular assignment of bonds encoded by a periodic net. In this set, two limiting nets are distinguished, complete and skeletal, which contain, respectively, all possible bonds and the minimal number of bonds required to keep the structure periodicity. Special attention is paid to the skeletal net since it describes the connectivity of a crystal structure in the simplest way, thus enabling one to find unobvious relations between crystalline substances of different composition and architecture. The tools for the automated hierarchical topological analysis have been implemented in the program package ToposPro. Examples, which illustrate the advantages of such analysis, are considered for a number of classes of crystalline substances: elements, intermetallics, ionic and coordination compounds, and molecular crystals. General provisions of the application of the skeletal net concept are also discussed.

Bifunctional Cu(II)-based 2D coordination polymer and its composite for high-performance photocatalysis and electrochemical energy storage

Coordination polymers (CPs) have been widely proven as sacrificial electrode materials for energy storage applications because of their high porosity, specific surface area and tunable structural topology. In this work, a new 2D Cu(II)-based CP, formulated as [Cu2(btc)(μ-Cl)2(H2O)4]n (CP-1) (H3btc = benzene-1,3,5-tricarboxylic acid), fabrication of copper oxide nanoparticles (CuO NPs) and its composite (CuO@CP-1) were successfully synthesized using solvothermal, precipitation and mechanochemical grinding approaches. Single-crystal X-ray analysis authenticated a two-dimensional (2D) layered network of CP-1. Further, CP-1, CuO NPs and composite were characterized by diffraction (Powder-XRD), spectroscopic (FTIR), microscopic (SEM), and thermal (TGA) techniques. The porosity and surface behavior of CP-1 and the composite were demonstrated using BET analyzer. Topological simplification of CP-1 shows a 3-c connected hcb periodic net. The photocatalytic behavior of CP-1 was examined over methyl red (MR) dye in the presence of sunlight and showed a promising degradation efficiency of 96.80%. The electrochemical energy storage properties of CP-1, CuO NPs and composite were investigated using cyclic voltammetry (CV) and galvanostatic charge-discharge (GCD) analysis under aqueous 1 M H2SO4 electrolyte. The electrochemical results show better charge storage performance of CP-1 with a specific capacitance of 602.25 F g-1 at 1 A g-1 current density by maintaining a retention of up to 84.51% after 5000 cycles at 10 A g-1 current density. Comparative electrochemical studies reveal that CP-1 is a promising electrode material for energy storage.

A topological approach to reconstructive solid-state transformations and its application for generation of new carbon allotropes

A novel approach is proposed for the description of possible reconstructive solid-state transformations, which is based on the analysis of topological properties of atomic periodic nets and relations between their subnets and supernets. The concept of a region of solid-state reaction that is the free space confined by a tile of the net tiling is introduced. These regions (tiles) form the reaction zone around a given atom A thus unambiguously determining the neighboring atoms that can interact with A during the transformation. The reaction zone is independent of the geometry of the crystal structure and is determined only by topological properties of the tiles. The proposed approach enables one to drastically decrease the number of trial structures when modeling phase transitions in solid state or generating new crystal substances. All crystal structures which are topologically similar to a given structure can be found by the analysis of its topological vicinity in the configuration space. Our approach predicts amorphization of the phase after the transition as well as possible single-crystal-to-single-crystal transformations. This approach is applied to generate 72 new carbon allotropes from the initial experimentally determined crystalline carbon structures and to reveal four allotropes, whose hardness is close to diamond. Using the tiling model it is shown that three of them are structurally similar to other superhard carbon allotropes, M-carbon and W-carbon.

Ratiometric luminescent sensing of a biomarker for sugar consumption in an aqueous medium using a Cu(II) coordination polymer

An innovative [Cu(Hadp)₂(Bimb)]_n (KA@CP-S3) coordination polymer expands its dimensionality from a 1D chain to a 2D network. The topological analysis reveals that KA@CP-S3 has 2-connected uninodal 2D 2C1 topology. KA@CP-S3 has capable luminescent sensing for volatile organic compounds (VOCs), nitroaromatics, heavy metal ions, anions, disposed antibiotics (nitrofurantoin and tetracycline) and biomarkers. Intriguingly, KA@CP-S3 exhibits outstanding selective quenching of about 90.7% and 90.5% for the 125 mg dl^-1 and 150 mg dl^-1 strengths of sucrose, respectively, in aqueous solution along with other ranges in between. The photocatalytic degradation efficiency of KA@CP-S3 for the potentially harmful organic dye Bromophenol Blue displays 95.4%, which is the highest among the 13 dyes that were evaluated.

Sr(II) and Ba(II) Alkaline Earth Metal-Organic Frameworks (AE-MOFs) for Selective Gas Adsorption, Energy Storage, and Environmental Application

Two new alkaline earth metal-organic frameworks (AE-MOFs) containing Sr(II) (UPJS-15) or Ba(II) (UPJS-16) cations and extended tetrahedral linker (MTA) were synthesized and characterized in detail (UPJS stands for University of Pavol Jozef Safarik). Single-crystal X-ray analysis (SC-XRD) revealed that the materials are isostructural and, in their frameworks, one-dimensional channels are present with the size of ~11 × 10 Å2. The activation process of the compounds was studied by the combination of in situ heating infrared spectroscopy (IR), thermal analysis (TA) and in situ high-energy powder X-ray diffraction (HE-PXRD), which confirmed the stability of compounds after desolvation. The prepared compounds were investigated as adsorbents of different gases (Ar, N2, CO2, and H2). Nitrogen and argon adsorption measurements showed that UPJS-15 has SBET area of 1321 m2 g-1 (Ar) / 1250 m2 g-1 (N2), and UPJS-16 does not adsorb mentioned gases. From the environmental application, the materials were studied as CO2 adsorbents, and both compounds adsorb CO2 with a maximum capacity of 22.4 wt.% @ 0 °C; 14.7 wt.% @ 20 °C and 101 kPa for UPJS-15 and 11.5 wt.% @ 0°C; 8.4 wt.% @ 20 °C and 101 kPa for UPJS-16. According to IAST calculations, UPJS-16 shows high selectivity (50 for CO2/N2 10:90 mixture and 455 for CO2/N2 50:50 mixture) and can be applied as CO2 adsorbent from the atmosphere even at low pressures. The increased affinity of materials for CO2 was also studied by DFT modelling, which revealed that the primary adsorption sites are coordinatively unsaturated sites on metal ions, azo bonds, and phenyl rings within the MTA linker. Regarding energy storage, the materials were studied as hydrogen adsorbents, but the materials showed low H2 adsorption properties: 0.19 wt.% for UPJS-15 and 0.04 wt.% for UPJS-16 @ -196 °C and 101 kPa. The enhanced CO2/H2 selectivity could be used to scavenge carbon dioxide from hydrogen in WGS and DSR reactions. The second method of applying samples in the area of energy storage was the use of UPJS-15 as an additive in a lithium-sulfur battery. Cyclic performance at a cycling rate of 0.2 C showed an initial discharge capacity of 337 mAh g-1, which decreased smoothly to 235 mAh g-1 after 100 charge/discharge cycles.

Crystal Structure, Topology, DFT and Hirshfeld Surface Analysis of a Novel Charge Transfer Complex (L3) of Anthraquinone and 4-{[(Anthracen-9-yl)meth­yl] Amino}­Benzoic Acid (L2) Exhibiting Photocatalytic Properties: An Experimental and Theoretical Approach

Here, we report a facile route to the synthesizing of a new donor–acceptor complex, L3, using 4-{[(anthracen-9-yl)meth-yl] amino}-benzoic acid, L2, as donor moiety with anthraquinone as an acceptor moiety. The formation of donor–acceptor complex L3 was facilitated via H-bonding and characterized by single-crystal X-ray diffraction. The X-ray diffraction results confirmed the synthesized donor–acceptor complex L3 crystal belongs to the triclinic system possessing the P-1 space group. The complex L3 was also characterized by other spectral techniques, viz., FTIR and UV absorption spectroscopy, which confirmed the formation of new bonds between donor L2 moiety and acceptor anthraquinone molecule. The crystallinity and thermal stability of the newly synthesized complex L3 was confirmed by powdered XRD and TGA analysis and theoretical studies; Hirshfeld surface analysis was performed to define the type of interactions occurring in the complex L3. Interestingly, theoretical results were successfully corroborated with experimental results of FTIR and UV absorption. The density functional theory (DFT) calculations were employed for HOMO to LUMO; the energy gap (∆E) was calculated to be 3.6463 eV. The complex L3 was employed as a photocatalyst for the degradation of MB dye and was found to be quite efficient. The results showed MB dye degraded about 90% in 200 min and followed the pseudo-first-order kinetic with rate constant k = 0.0111 min⁻¹ and R² = 0.9596. Additionally, molecular docking reveals that the lowest binding energy was −10.8 Kcal/mol which indicates that the L3 complex may be further studied for its biological applications.

The role of local heteropolyhedral substitutions in the stoichiometry, topological characteristics and ion-migration paths in the eudialyte-related structures: a quantitative analysis

Topological analysis of the heteropolyhedral MT framework (where M and T are octahedral and tetrahedral cations, respectively) in the eudialyte-type structure and its derivatives was performed based on a natural tiling analysis of the 3D cation. To analyze the migration paths of sodium cations in these structures, the Voronoi method was used. The parental eudialyte-type MT framework is formed by isolated ZO₆ octahedra, six-membered [M(1)₆O₂₄] rings of edge-sharing M(1)O₆ octahedra, and two kinds of rings of tetrahedra, [Si₃O₉] and [Si₉O₂₇]. Different occupancies of M(2), M(3) and M(4) sites with variable coordination numbers by the additional Q, T* and M* cations, respectively, result in 12 different types of the MT framework. Based on the results of natural tilings calculations as well as theoretical analysis of migration paths, it is found that Na⁺ ions can migrate through six- and seven-membered rings, while all other rings are too small for the migration. In eight types of MT frameworks, Na⁺-ion migration and diffusion is possible at ambient temperature and pressure, while in four other types cages are connected by narrow windows and, as a result, the Na⁺ diffusion in them is complicated at ambient conditions because of the window diameter, but may be possible either at higher temperatures or under mild geological conditions for long periods of time.

A new {Cu3-Gd2} cluster as two-in-one functional material with unique topology acting as a refrigerant as well as adsorbent for cationic dye

A new heterometallic cluster system, [Cu3Gd2(H3btp)2(OAc)6]3H2O {Cu3-Gd2} is designed by employing 1,3-Bis(tris(hydroxymethyl)methylamino)propane (H6btp) as a ligand. The cluster is characterized by FTIR, TGA, PXRD, SCXRD and topological analyses. The crystallography...

Topological transformations in metal–organic frameworks: a prospective design route?

We apply a topological approach based on the underlying net and transformation pattern concepts as well as on the ‘supernet–subnet’ formalism to uncover mechanisms of solid-state transformations in coordination polymers and metal–organic frameworks.