Cambridge Crystallographic Data Centre Research Articles

Design, Molecular Docking and Molecular Dynamic Simulation of New Heterocyclic Derivatives as Potential Anticancer Agents

Background: Despite significant progress in the development of anticancer medications, obstacles such as drug resistance, poor efficacy, and excessive toxicity have significantly impacted the daily lives of cancer patients. Consequently, the search for highly selective, effective, and non-toxic molecules remains a major challenge for cancer researchers. Objective: To utilize a computer program for evaluating new benzothiophene derivatives to investigate how they influence the estrogen-related receptor-gamma (ERRγ) active sites as anticancer agents. Methods: The molecular docking method used the Cambridge Crystallographic Data Centre's (CCDC) Genetic Optimization for Ligand Docking (GOLD) tool. We used the Desmond modules of the Schrodinger 2023 to perform MDS on the derivative with the highest docking score. The Swiss ADME server then assessed our drugs' pharmacokinetic profile, which included how well they crossed the blood-brain barrier (BBB), bound to P-gp, and were bioavailable. Results: The compounds were docked with the ERRγ crystal structure (2GPV) to assess their binding affinity to active sites. One of them earned a high score (102.62), and six compounds had a higher binding energy than the gold standard medication, tamoxifen. The molecular dynamic simulation analysis found that compound 1 closely matched the ERRγ based on RMSD and RMSF data. After examining the ADME study of practically active substances, they follow Lipinski's laws and other pharmacokinetic features. Conclusions: These chemicals have the potential to act as precursors in the development of new anticancer medicines.

Modified nanomagnetite silica core shell with new Cu (II) N,N‐ chelating complex as an efficient and reusable catalyst in the C‐N bond formation

In this article, initially, the TCTCl (DiPrAEA)2 ligand was synthesized and characterized by Fourier transform infrared (FT‐IR), X‐ray crystallography, 1H‐ and 13C‐NMR spectroscopy, and elemental analysis. The crystallographic structure data for the ligand has been deposited at the Cambridge Crystallographic Data Centre (CCDC No. 2282732). Then, using of this novel multidentate ligand, a novel and stable copper (II) nanocatalyst complex was synthesized by anchoring copper (II) acetate onto the core‐shell surface (Fe3O4@SiO2) via the novel multidentate ligand TCTCl (DiPrAEA)2. The successful synthesis of the Fe3O4@SiO2‐NH‐TCT (DiPrAEA)2‐Cu (II) nanocatalyst was confirmed by employing physicochemical techniques such as FT‐IR, X‐ray diffraction, ultraviolet‐visible, thermogravimetric analysis, X‐ray photoelectron spectroscopy, Brunauer–Emmett–Teller, energy‐dispersive X‐ray, dynamic light scattering, inductively coupled plasma, transmission electron microscopy, field emission scanning electron microscopy, and vibrating sample magnetometer. Subsequently, this novel copper (II) nanomagnetic complex was evaluated as an efficient, reusable, and novel catalyst for the formation of C‐N bonds via the Ullmann coupling reaction of aryl halides and nitrogen‐containing compounds. The influence of this novel TCTCl (DiPrAEA)2 ligand on the reactivity and stability of the nanomagnetic copper complex was visible in the Ullmann reaction, which resulted in rapid reaction times and excellent yields, and seven times reusability.

What has scripting ever done for us? The CSD Python application programming interface (API)

Since its first release in 2016, the Cambridge Structural Database Python application programming interface (CSD Python API) has seen steady uptake within the community that the Cambridge Crystallographic Data Centre serves. This article reviews the history of scripting interfaces, demonstrating the need, and then briefly outlines the technical structure of the API. It describes the reach of the CSD Python API, provides a selected review of its impact and gives some illustrative examples of what scientists can do with it. The article concludes with speculation as to how such endeavours will evolve over the next decade.

Study of 25R-NBOHs (R = Br, Cl, Et, I): Thermal stability investigation and presumptive identification by SCXRD and PXRD data

New psychoactive substances (NPS) are present in the drug market and can be used as legal substitutes, making enforcement difficult. One of the classes of NPSs is the phenylethylamines, among which 25R-NBOHs (with R being a halogen or an alkyl group) are included. These compounds degrade when subjected to gas chromatography-mass spectrometry (GC–MS), one of the techniques routinely used to identify illicit substances, thereby complicating their identification. This study conducted the identification of NBOH samples using FTIR, XRD, and GC–MS techniques, as well as thermal analysis to obtain information that may assist in the development of new methods for the analysis of these synthetic substances. ATR-FTIR spectra presented characteristic bands of 25R-NBOH compounds (R = Br, Cl, Et, I). The UV–Vis spectra of the 25R-NBOH (R = Br, Cl, I) and 25E-NBOH samples showed a different profile, which may serve as a means to differentiate these compounds. The crystalline structure of the compounds was confirmed by comparing the experimentally obtained diffractograms with the diffraction patterns calculated using data from the Cambridge Crystallographic Data Center (CCDC) database. Thermal analysis indicated that the samples were not pure, confirming the FTIR and XRD analyses, which revealed the presence of impurities and the onset of sample degradation.

Does Conformation Affect the Analytical Response? A Structural and Infrared Spectral Evaluation of Phenethylamines (2C-H, 25H-NBOH, and 25I-NBOMe) Using In Silico Methodology

The identification of new psychoactive substances (compounds that mimic the effects of outlawed substances) poses a significant challenge due to their rapid emergence and continuous modifications. This phenomenon results in these molecules escaping legal regulation, allowing them to circumvent legislation. The phenethylamine class has garnered attention because its molecules replicate the effects of LSD and are associated with numerous cases of intoxication. In this study, we focused on three phenethylamines—2C-H, 25H-NBOH, and 25I-NBOMe—with crystallographic structures available in the Cambridge Crystallographic Data Center (CCDC) database. We conducted a systematic conformational analysis and compared the structural information obtained. Subsequently, we compared the spectra derived from this analysis with experimental details from the ENFSI database. Structural comparisons were made based on the RMSDs between the lower energy conformations and experimental crystallographic structures. Additionally, structures obtained from direct optimization were compared. We then simulated the spectra based on the X-ray structures and compared them with those in the experimental database. Interpretation was carried out using heat maps and PCA in Pirouette software. Combining in silico methods with experimental approaches provides a more comprehensive understanding of the characterization process of new psychoactive substances (NPSs).

Accelerated Organic Crystal Structure Prediction with Genetic Algorithms and Machine Learning.

We present a high-throughput, end-to-end pipeline for organic crystal structure prediction (CSP)─the problem of identifying the stable crystal structures that will form from a given molecule based only on its molecular composition. Our tool uses neural network potentials to allow for efficient screening and structural relaxation of generated crystal candidates. Our pipeline consists of two distinct stages: random search, whereby crystal candidates are randomly generated and screened, and optimization, where a genetic algorithm (GA) optimizes this screened population. We assess the performance of each stage of our pipeline on 21 molecules taken from the Cambridge Crystallographic Data Centre's CSP blind tests. We show that random search alone yields matches for ≈50% of targets. We then validate the potential of our full pipeline, making use of the GA to optimize the root-mean-square deviation between crystal candidates and the experimentally derived structure. With this approach, we are able to find matches for ≈80% of candidates with 10-100 times smaller initial population sizes than when using random search. Lastly, we run our full pipeline with an ANI model that is trained on a small data set of molecules extracted from crystal structures in the Cambridge Structural Database, generating ≈60% of targets. By leveraging machine learning models trained to predict energies at the density functional theory level, our pipeline has the potential to approach the accuracy of ab initio methods and the efficiency of empirical force fields.

Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning.

Metalloproteins require metal ions as cofactors to catalyze specific reactions with remarkable efficiency and specificity. In various electron transfer reactions, metals in the active sites change their oxidation states to facilitate the biochemical reactions. Cryogenic electron microscopy, X-ray, and X-ray free electron laser (XFEL) crystallography are used to image metalloproteins to understand the reaction mechanisms. However, radiation damage in cryoEM and X-ray crystallography, and the challenge of generating homogeneous crystals and keeping the appropriate experimental conditions for all the crystals in XFEL crystallography, may alter the oxidation states. Here, we build machine learning models trained on a large data set from the Cambridge Crystallographic Data Center to evaluate the metal oxidation states. The models yield high accuracy scores (from 82% to 94%) for all metals in the small molecules. Then, they were used to predict the oxidation states of more than 30 000 metal clusters in metalloproteins with Fe, Mn, Co, and Cu in their active sites. We found that most of the metals exist in the lower oxidation states (Fe2+ 77%, Mn2+ 85%, Co2+ 65%, and Cu+ 64%), and these populations correlate with the standard reduction potentials of the metal ions. Furthermore, we found no clear correlation between these populations and the resolution of the structures, which suggests no significant dependence of these predictions on the resolution. Our models represent a valuable tool for evaluating the oxidation states of the metals in metalloproteins imaged with different techniques. The data files and the machine learning code are available in a public GitHub repository: https://github.com/mamin03/OxitationStatesMetalloprotein.git.

LANTHANIDE CONTRACTION IN CHELATES OF ETHYLENEDIAMINETETRAACETIC ACID BASED ON CRYSTALLOGRAPHIC DATA: A SHORT REVIEW

The lanthanide (Ln) series has been attracted so much attention not only for its physical properties but also for its applications in organic synthesis and biomedical engineering. In the lanthanide chemistry, lanthanide contraction is a crucial concept meaning the gradual decrease in ionic radii as the atomic number of the Ln series increases. As a prominent chelator, ethylenediaminetetraacetic acid (EDTA) has been well-known to give stable complexes with various metals including Ln ions, resulted in forming (EDTA−4H)4− anion by deprotonation; over 100 kinds of Ln-EDTA complexes have hitherto been synthesized and structurally characterized using X-ray crystallography. While the lanthanide contraction phenomenon has been extensively studied in certain complexes of Ln, systematization on the Ln-EDTA remains inadequate though the chelates of EDTA are commonly used. Thus, this study presents a comprehensive analysis based on the data from the Cambridge Crystallographic Data Centre (CCDC). In mononuclear EDTA complexes X[Ln(EDTA−4H)(H2O)m]·nH2O (X+ = NH4+and its analogues) systematic lanthanide contraction depending on their coordination number are presented except for a few cases. However, in the case of non-mononuclear complexes or coordination polymers, the compositions become more complicated, and a greater variation in atomic bond length occurs, which is unusual for the lanthanide contraction studies in previous research. These varieties are considered to be influenced by different types of counter-cations, inorganic anions, solvent molecules and bridging O atoms from another EDTA anions. This suggests the flexibility and versatility of EDTA as a ligand. Such findings in the Ln-EDTA complexes could potentially provide us further development of a novel function in the future.

Structure-based biological investigations on ruthenium complexes containing 2,2'-bipyridine ligands and their applications in photodynamic therapy as a potential photosensitizer.

Ruthenium complexes have been investigated for various biological applications by virtue of their radical scavenging, DNA binding, receptor binding, and cytotoxic abilities; especially the possible potential application of these complexes in photodynamic therapy (PDT). This study focuses on the synthesis, structural characterization and biological application (pertaining to its cytotoxicity and radical generation) of ruthenium complexed with salicylaldehyde fumaryl-dihydrazone (slfhH4 ), salicylaldehyde glutaryl-di-hydrazone (slfgH4 ) and 2,2'-bipyridine (bpy). During the synthesis, the anticipated complex was precipitated out but as serendipity, Ruthenium(II) tris (2,2'-bipyridyl) monochloride nonahydrate {[Ru(bpy)3 ]2+ .Cl.9H2 O} (RBMN) and Ruthenium(II) tris (2,2'-bipyridyl) monochloride septahydrate {[Ru(bpy)3 ]2+ .Cl.7H2 O}(RBMS) were crystallized from the filtrate. The crystal structure of complexes RBMN and RBMS were determined by a single-crystal X-ray diffraction methods and it showed that chlorine anion lies at the crystallographic axis and forms a halogen hydrogen-bonded organic framework (XHOF) to provide the stability. In comparison with similar structures in Cambridge Crystallographic Data Center (CCDC) revealed that the nature of the XHOF framework and the layered packing are conserved. The compounds showed excellent cytotoxic ability (against L6 cells) and the nitro blue tetrazolium (NBT) assay upon irradiation to light revealed its ability to produce reactive oxygen species (ROS). The presence of partially occupied water molecules in the layered organization within the crystal packing mimics the release of ROS resulting in cytotoxicity. The structural results together with the biological data make these complexes interesting candidates for potential photosensitizers for PDT applications.

Noncovalent Interactions, Structure Elucidation and Docking Studies of anti-Fungal Pyridine Carboxamide Derivatives of Co(II), Ni(II), Cu(II) & Zn(II)

Computational analysis of four antifungal transition metal complexes of Co(II), Ni(II), Cu(II) and Zn(II) with pyridine carboxamide derivates (methyl 2-amino-3- methylbenzoate isonicotinic acid amide (L1) and methyl 2-amino-3-methylbenzoate picolinic acid amide (L2)) as ligands is provided here within the DFT framework. Geometry optimization, binding energy, HOMO-LUMO energy gap, Density of States (DOS) plots, and MEP surfaces have been calculated to rationalize the molecular structure of these complexes. The effect of noncovalent interactions on the crystal structure of these complexes has been deciphered using CE-B3LYP model instigated into CrystalExplorer using experimental geometries accessed from Cambridge Crystallographic Data Center (CCDC). These complexes are docked against Enterococcus Faecalis using AutoDock Vina to quantify binding energy between the complexes and protein accessed from the protein data bank (PDB).

Ligand and Substituent Effect on Regium-π Bonding in Cu and Ag π-Conjugated Complexes: A Density Functional Study.

Density functional theory investigation of regium (Rg)-π bonding using the RgL-X model system, where Rg = Cu and Ag; L = CN, NO2, and OH; X = π-conjugated system (benzene, cyanobenzene, benzoic acid, pyridine, 2-methoxy aniline, 1,4-dimethoxy benzene, and cyclophane), has been performed. Conclusive evidence of the Rg-π bond has been provided by analysis of molecular electrostatic potential surfaces, Rg-π bond length, interaction energy (ΔE), second-order perturbation energy (E2), charge transfer (Δq), quantum theory of atom in molecules, and noncovalent interaction plots for 42 structural arrangements with varying ligands and the substituted aromatic ring. The Rg-π bond length in the optimized model systems varies from 2.03 to 2.12 Å in Cu complexes (1-21) and from 2.26 to 2.38 Å in Ag complexes (22-42) at the PBE0-D3 functional. While the ligand (L) attached to the Rg metal has a bargaining effect on the strength of the Rg-π bond (in the order of -OH > -CN = -NO2), the π-conjugated systems have a diminutive effect. Two X-ray crystal structures (CUCSOI and AHIDQU) having the Rg-π bond, accessed from Cambridge Crystallographic Data Centre (CCDC), are discussed here to signify the influence of Rg-π bonding on the crystal structure.

Benchmark Study of Density Functional Theory Methods in Geometry Optimization of Transition Metal-Dinitrogen Complexes.

The current benchmark study is focused on determining the most precise theoretical method for optimizing the geometry of transition metal-dinitrogen complexes. To accomplish this goal, seven density functional (DF) methods from five distinct classes of density functional theory (DFT) have been selected, including B3LYP-D3(BJ), BP86-D3(BJ), PBE0-D3(BJ), ωB97X-D, M06, M06-L, and TPSSh-D3(BJ). These DFs will be utilized with the Karlsruhe basis set (def2-SVP). To carry out this benchmark study, a total of forty-two structurally diverse transition metal-dinitrogen compounds with experimentally known X-ray data have been selected from the Cambridge Crystallographic Data Centre (CCDC). Based on a comparison of the theoretical data with experimental values (X-ray) of the selected transition metal-dinitrogen compounds, statistical parameters such as root-mean-square deviation (RMSD) and N-N and M-N bond lengths are obtained to evaluate the performance of the seven chosen DFs. According to the obtained results, among all DFT methods used in the study, Minnesota functionals (M06 and M06-L) and TPSSh-D3(BJ) show good performance, with lower RMSD values. This suggests that these three methods are the most reliable for optimizing the geometry of transition metal-dinitrogen complexes. Based on the absolute errors of the N-N and M-N bond lengths relative to the X-ray data, further analysis is conducted, and it is determined that M06-L is the best functional for optimizing the geometry of transition metal-dinitrogen compounds. Additionally, the influence of using a high-level basis set (def2-TZVP) compared to def2-SVP on the calculated RMSD among the seven chosen methods is found to be negligible.

Effect of the extra-nuclear cation on the cytotoxicity and mechanism of action of pyridine-2,6-dicarboxylate Ga(III) complexes

Two Ga(III) complexes (C1) and (C2) were prepared by the one-pot reaction of pyridine-2,6-dicarboxylic acid and aminopyridine derivatives with gallium(III) nitrate octahydrate. The compounds were characterized by single-crystal X-ray diffraction. The distorted octahedral geometry was confirmed by crystallographic data for both complexes. The study of the in vitro cytotoxicity of the compounds showed that the presence of different extra-nuclear cations can affect the cytotoxicity of the same anionic complexes. The most significant antiproliferative activity was observed for C1 (IC50 = 0.69 μM, MAE = 73.96%) and C2 (IC50 = 3.78 μM, MAE = 60.35%) (where MAE represents the maximal antiproliferative effect) against A431 cell line. The mechanistic study evidenced the same pathway for the death of A431 cells treated with the complexes, although the results for C2 were obtained at approximately five times the concentration of C1. According to the study, both complexes induced cell cycle arrest in G2/M phase in A431 cells by upregulating the levels of p21, p27, p-cdc25C, and p-cdc2 and downregulating the levels of cdc25C, cdc2, and cyclin B1. In addition, apoptosis via a caspase-dependent mitochondrial pathway was confirmed by a decrease in Bcl-2 family proteins and an increase in the expression of procaspase-9 and 3. Also, the complexes induced autophagic cell death by activating the RAGE /PI3KC3/Beclin 1 pathway in A431 cells. Data availabilityCCDC 874052 and 874055 contain the supplementary crystallographic data for C1 and C2, respectively. These data can be obtained free of charge via http://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:874052,874055&sid=CCDCManual, or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: (+44) 1223–336–033; or e-mail: deposit@ccdc.cam.ac.uk.

Completion of Crystallographic Data for the Series of 4-Halogenated-1H-pyrazoles: Crystal Structure Determination of 4-Iodo-1H-pyrazole and Spectroscopic Comparison

Prior to 2021, 4-bromo-1H-pyrazole (published in 1999) was the only structurally characterized 4-halogenated-1H-pyrazole in the Cambridge Crystallographic Data Center (CCDC). The structures of 4-chloro-1H-pyrazole and 4-fluoro-1H-pyrazole were published in 2021 and 2023, respectively. Herein, we report the crystal structure for 4-iodo-1H-pyrazole, completing the crystallographic data for the series of 4-halogenated-1H-pyrazoles. The bromo and chloro analogs are isostructural, forming trimeric H-bonding motifs, whereas the fluoro and iodo analogs form non-isostructural catemers. We also compare the experimental and theoretical (by DFT calculations) IR and 1H NMR spectroscopic data of the four halogenated 4-X-pzH compounds and unsubstituted pyrazole (pzH). An explanation is offered for some counterintuitive structural, infrared, and 1H-NMR spectroscopic data.

Molecular Docking Study of New Sorafenib Analogues as Platelet-Derived Growth Factor Receptor Inhibitors for the Treatment of Cancer.

Cancer is a disease triggered by an uncontrolled growth of a group of cells usually from a single cell. Chemotherapy is a common and systematic therapy that involves the use of anticancer drugs also known as chemotherapeutical agents to treat cancer. Tyrosine kinases are a subset of protein kinases that are a family of over 90 enzymes that selectively phosphorylate tyrosine residues in various substrates. Receptors with internal tyrosine kinase activity mediate the actions of several growth factors, differentiation factors, and hormones, resulting in the reproduction and differentiation of the affected cells. In the fight against cancer, the platelet-derived growth factor receptor has emerged as a novel target via inhibition of this receptor resulting in the inhibition of tyrosine kinase cascade. Docking investigations were conducted using the Genetic Optimization for Ligand Docking (GOLD) Suite (v. 5.7.1) from the Cambridge Crystallographic Data Center. A high-definition X-ray crystallography of the platelet-derived growth factor protein [Protein Data Bank (PDB) ID 6JOL] was downloaded from the website PDB with a resolution of 2 A. Compounds II, III, VII, and VIII have greater binding energies than the GOLD standard medication sorafenib, which gives Piecewise Linear Potential (PLP) fitness value (85.3). Other ligands exhibit good inhibitory action and docking scores comparable to that of the reference ligand sorafenib.

In silico Study of New Vascular Endothelial Growth Factor Receptor Inhibitors for The Treatment of Hepatocellular Carcinoma

Novel therapeutics are desperately needed for the difficult-to-treat and very lethal malignancy known as hepatocellular carcinoma (HCC). The first drug now authorized for the treatment of individuals with advanced HCC is sorafenib. To find novel Vascular Endothelial Growth Factor Receptor Inhibitors as prospective candidate therapeutics for HCC, an in-silico technique was used in this case. Docking investigations were conducted using the GOLD Suite (v. 5.7.1) from the Cambridge Crystallographic Data Centre (CCDC). The docking/scoring methods of CCDC were validated by reproducing the docking interactions and poses of Sorafenib. Based on their PLP fitness, compounds I–X and sorafenib were graded for their ability to inhibit VEGF. Compounds II, III and VIII among other ligands exhibit higher binding energies than the standard drug sorafenib that give PLP fitness value (80.4).

Antihypertensive effects of pentacyclic triterpenoid from Convolvulus pluricaulis and its plausible mechanism of action hypothesizing its selectivity targeting Mineralocorticoid receptor of RAAS.

BackgroundThe renin-angiotensin-aldosterone system (RAAS) is important in maintaining blood pressure and malfunction of this system leads to the main cause of hypertension. Though a variety of synthetic inhibitors have been used to treat hypertension and related disorders, chronic use of these inhibitors causes undesirable side effects. To eliminate this problem, several scientific studies have proved that plant based and food derived products could be used as an alternative strategy to treat high blood pressure. PurposeWe intend to isolate the major bioactive compound from the medicinal plant Convolvulus pluricaulis as it is reported to possess anti-hypertensive activity. We also aimed to address the mechanism of action of taraxerol and to hypothesize its selectivity targeting RAAS. Study designThe study was designed to isolate the phytoconstituent from C. pluricaulis and characterization by XRD, NMR, FT-IR, and UV–Vis. To further elucidate the activity of isolated molecules, we have designed a two-way approach using in-silico and in-vitro methodologies. MethodsThe roots of Convolvulus pluricaulis were dried, powdered and the extract was purified by repeated column chromatography. The purified compound was characterized by UV–Vis, IR, NMR, and single crystal X-ray diffraction. The high quality single crystal was grown from the mixture of hexane ethyl acetate. Molecular docking was done to identify the interaction pattern and binding efficacy of isolated compounds against various receptors of RAAS and the stability of the molecule was analyzed by molecular dynamic simulations. The cytotoxicity of the molecule was checked using the MTT assay and the IC50 value was also calculated against the AngII-induced cardiac hypertrophy in H9c2 cells. Tanimoto coefficient was calculated to check the similarity indices with the already reported antihypertensives from plants/herbs. ResultsThe crystal structure of taraxerol solved by crystallography has been deposited with the Cambridge Crystallographic Data Centre (CCDC: 2,180,265). Taraxerol had an IC50 at 20 μM concentration against AngII-induced cardiac hypertrophy in H9c2 cells, indicating that it suggestively increased the cell viability as compared to positive control. In-silico molecular docking analysis of taraxerol found that taraxerol binds to mineralocorticoid receptor with the binding energy of −11.03 kcal/mol. Molecular Dynamics (MD) simulations were further done to check the stability of MR-taraxerol complex to unravel the structure activity relationship of taraxerol. Furthermore, SAR studies show that taraxerol had the highest degree of molecular similarity (0.78% – 0.93%) with reported antihypertensive oleanane triterpenoids highlighting its efficacy. ConclusionOur findings corroborate taraxerol as a potential anti-hypertensive agent and leads to the hypothesis of its specificity towards Mineralocorticoid receptor than other receptors in RAAS.

Синтез и строение органосульфонатов тетраорганилфосфония [R4P][OSO2R’], R = Me, R’ = C6H3Cl2-2,5; R = Bu, R’ = C10H5(OH-1)(NO2)2-2,4; [Ph3PR][OSO2R’], R = CH2CH=CHCH2PPh3, R’ = OSO2C9H4N(OH-8)(I-7); R = C6H11-cyclo, R’ = C6H3(NO2)2-2,4; R = CH2CH=CHMe, R’ = C6H3Cl2-2,5

The interaction of equimolar amounts of tetraorganylphosphonium halides with 2,5-dichlorobenzenesulfonic, 2,4-dinitrobenzenesulfonic, 1-hydroxy-2,4-dinitro-7-naphthalenesulfonic and 8-hydroxy-7-iodo-5-quinolinesulfonic acids in water leads to the formation of ionic tetraorganylphosphonium organosulfonates [R4P][OSO2R’], R = Me, R’ = C6H3Cl2-2,5 (1); R = Bu, R’ = C10H5(OH-1)(NO2)2-2,4 (2); [Ph3PR][OSO2R’], R = CH2CH=CHCH2PPh3, R’ = C9H4N(OH-8)(I-7) (3); R = C6H11-cyclo, R’ = C6H3(NO2)2-2,4 (4); R = CH2CH=CHMe, R’ = C6H3Cl2-2,5 (5). The structures of complexes 1‒4 have been established by X-ray diffraction analysis. The X-ray structural analysis has been carried out on an automatic four-circle D8 Quest Bruker diffractometer (МоКα-radiation, λ = 0.71073 Å, graphite monochromator) at 293 K. Crystals 1 [C16H22O8PS2Cl4, M 579.23; monoclinic syngony, space group С2/с; сell parameters: a = 35.69(4), b = 7.454(9), c = 23.67(2) Å;  = 90.00, β = 129.16(3),  = 90.00 deg., V = 4883(9) Å3, Z = 8; calc = 1.576 g/cm3], 2 [C42H77N2O8P2S, M 832.06; orthorhombic syngony, space group Pbca; сell parameters: a = 14.712(9), b = 22.825(16), c = 29.475(16) Å;  = 90.00, β = 90.00,  = 90.00 deg., V = 9898(11) Å3, Z = 8; calc = 1.117 g/cm3], 3 [C29H27O6PSIN, M 675.45; triclinic syngony, space group P–1; сell parameters: a = 9.506(8), b = 11.323(12), c = 13.662(10) Å;  = 82.21(4), β = 89.26(2),  = 72.60(4) deg., V = 1390(2) Å3, Z = 2; calc = 1.614 g/cm3], and 4 [C30H29N2O7PS, M 592.58; triclinic syngony, space group P–1; сell parameters: a = 9.793(5), b = 11.214(5), c = 14.341(7) Å;  = 109.495(17), β = 99.55(3),  = 94.58(2) deg., V = 1448.5(12) Å3, Z = 2; calc = 1.359 g/cm3]. The coordination of the phosphorus atoms in cations 1‒5 is distorted tetrahedral; organosulfonate anions have the usual geometry with a tetrahedral sulfur atom. The Р−С bond lengths are 1.746(7)−1.841(19) Å, which is less than the sum of the covalent radii of the partner atoms (1.83 Å). The S−C distances are in the range of 1.759(5)−1.815(3) Å. The СРС valence angles vary in the range 85.2(8) −114.0(5) deg. The structural organization in crystals 1‒4 is due to weak intermolecular contacts of the O···Н type, 1.60–2.72 Å (the sum of the Van der Waals radii of the partner atoms is 2.62 Å). Complete tables of atomic coordinates, bond lengths and bond angles for structures have been deposited at the Cambridge Crystallographic Data Centre (No. 2153156 (1), No. 2157531 (2), No. 2160476 (3), No. 2157713 (4); deposit@ccdc.cam.ac.uk; https://www.ccdc.cam.ac.uk).

CSD Communications of the Cambridge Structural Database.

The Cambridge Structural Database (CSD) is a collection of over one million experimental three-dimensional structures obtained through crystallographic analyses. These structures are determined by crystallographers worldwide and undergo curation and enhancement by scientists at the Cambridge Crystallographic Data Centre (CCDC) prior to their addition to the database. Though the CSD is substantial and contains widespread chemical diversity across organic and metal-organic compounds, it is estimated that a significant proportion of crystal structures determined are not published or shared through the peer-reviewed journal mechanism. To help overcome this, scientists can publish structures directly through the database as CSD Communications and these structural datasets are made publicly available alongside structures associated with scientific articles. CSD Communications contribute to the collective crystallographic knowledge as nearly two thirds are novel structures that are not otherwise available in the scientific literature. The primary benefits of sharing data through CSD Communications include the long-term preservation of scientific data, the strengthening of a widely data-mined world repository (the CSD), and the opportunity for scientists to receive recognition for their work through a formal and citable data publication. All CSD Communications are assigned unique digital object identifiers (DOIs). Contributions as CSD Communications currently comprise about 3.89% of the total CSD entries. Each individual CSD Communication is free to view and retrieve from the CCDC website.

Реакции пентафенил- и пента(пара-толил)сурьмы с фумаровой кислотой

The interaction of pentaphenylantimony with fumaric acid in benzene (24 h, 24 С, molar ratio 4:3) gave a solvate with benzene Ph4SbOC(O)CH=CHC(O)OSbPh4 ∙ 2Ph4SbOC(O)CH=CHC(O)H ∙ 3PhH (1). At a molar ratio of the initial reagents of 2:1, the binuclear derivative of fumaric acid Ph4SbOC(O)CH=CHC(O)OSbPh4 (2) was formed. In similar reactions of penta(para-tolyl)antimony with fumaric acid, the adduct p-Tol4SbOC(O)CH=CHC(O)OSbTol4 ∙ HOC(O)CH=CHC(O)OH ∙ 4PhH (3) and the solvate of the binuclear derivative of fumaric acid with benzene p-Tol4SbOC(O)CH=СHC(O)OSbTol4 ∙ 3PhH (4) were formed, respectively. According to X-ray diffraction analysis performed at 293 K on a D8 Quest Bruker automatic four-circle diffractometer (two-coordinate CCD detector, Mo Kα radiation, λ = 0.71073 Å, graphite monochromator), the antimony atoms in crystals 1 [C63H53O6Sb2, M 1149.55; triclinic syngony, symmetry group P–1; cell parameters: a = 9.938(4), b = 14.999(8), c = 19.088(8) Å;  = 92.833(17), β = 102.148(16),  = 99.02(3) degrees; V = 2737(2) Å3; crystal size 0.3 × 0.17 × 0.05 mm; reflec-tion index intervals –13 ≤ h ≤ 13, –20 ≤ k ≤ 20, –25 ≤ l ≤ 25; total reflections 89119; independent reflections 14039; Rint = 0.0698; GOOF 1.070; R1 = 0.0442, wR2 = 0.0675; residual electron density 0.47/–0.80 e/Å3], 2 [C26H21O2Sb, M 487.18; monoclinic syngony, symmetry group С2/с; cell parameters: a = 28.35(3), b = 10.453(15), c = 17.49(2) Å; β = 93.01(5) degrees; V = 5176(12) Å3; crystal size 0.2×0.12×0.08 mm; reflection index intervals –26 ≤ h ≤ 30, –11 ≤ k ≤ 11, –19 ≤ l ≤ 13; total reflections 6329; independent reflections 3283; Rint = 0.1220; GOOF 1.318; R1 = 0.1253 wR2 = 0.3080; residual electron density 2.09–4.45 e/Å3], 3 [C88H86O8Sb2, M 1515.09; triclinic syngony, symmetry group P–1; cell parameters: a = 13.35(2), b = 13.50(2), c = 14.15(2) Å;  = 67.02(5), β = 62.29(6),  = 65.63(6) degrees; V = 1994(5) Å3; crystal size 0.55 × 0.33 × 0.28 mm; reflection index intervals –17 ≤ h ≤ 17, –17 ≤ k ≤ 17, –18 ≤ l ≤ 18; total reflections 54923; independent reflections 9183; Rint = 0.0604; GOOF 1.069; R1 = 0.0494, wR2 = 0.1159; residual electron density 1.83–1.68 e/Å3], 4 [C39H38O2Sb, M 660.44; triclinic syngony, symmetry group P-1; cell parameters: a = 11.328(6), b = 12.416(7), c = 12.997(6) Å;  = 82.24(2), β = 72.87(2),  = 75.50(3) degrees; V = 1687.5(15) Å3; crystal size 0.23×0.17×0.05 mm; reflection index in-tervals –14 ≤ h ≤ 14, –15 ≤ k ≤ 15, –16 ≤ l ≤ 16; total reflections 40178; independent reflections 7469; Rint 0.2589; GOOF 1.029; R1 = 0.0627, wR2 = 0.1275; residual electron density 0.95/–1.72 e/Å3], have a distorted trigonal-bipyramidal coordination with the carbon and oxygen atoms in axial positions (axial angles are 173.65(10), 175.74(11) for 1, 176.6(7)° for 2, 176.07(10)° for 3, 178.41(16)° for 4). The Sb–O distances are 2.253(2) and 2.240(2) Å for 1, 2.262(17) Å for 2, 2.302(3) Å for 3, and 2.234(4) Å for 4. The Sb–C bond lengths vary in a narrow range of values (2.110(3)–2.176(3) Å for 1, 2.114(2)–2.18(3) Å for 2, 2.109(5)–2.188(4) Å for 3, 2.113(5)–2.184(5) Å for 4). Structural organization in crystals is due to weak intermolecular contacts of the C=O•••H type (1.83–2.71 Å for 1, 1.81–2.71 Å for 3, 2.69 Å for 4). In crystals 1, 3, 4 the blocks of two dicarboxylic acids are linked to each other via the -C=O•••HOC(O)-chains (1.83, 1.83, 1.81 Å, respectively). Complete tables of atomic coordinates, bond lengths, and bond angles for the structures were deposited at the Cambridge Crystallographic Data Center (no. 2217281 for 1, (no. 2214920 for 2, no. 2220380 for 3, no. 2217063 for 4; deposit@ccdc.cam.ac.uk; https://www.ccdc.cam.ac.uk).