Cambridge Crystallographic Data Centre Research Articles

Исследование строения дикарбоксилатов трис(4-фторфенил)сурьмы (4-FC6H4)3Sb[OC(O)R]2 (R = C6H3F2-2,3, C6H3(NO2)2-3,5, C6H4OMe-2, CF2Br, CH=CHPh, CH3, C≡CH)

The interaction of tris(4-fluorophenyl)antimony with 2,3-difluorobenzoic acid, as well as with 3,5-dinitrobenzoic, 2-methoxybenzoic, bromodifluoroacetic, cinnamic, formic, and propionic acids in the presence of tert-butyl hydroperoxide (1:2:1 mol.) in ether at ambient temperature has given tris(4-fluorophenyl)antimony dicarboxylates (4-FC6H4)3Sb[OC(O)R]2, where R = C6H3F2-2,3 (1), C6H3(NO2)2-3,5 (2), C6H4OMe-2 (3), CF2Br (4), CH=CHPh (5), CH3 (6), и C≡CH (7). The IR spectra of compounds 17, recorded on a Shimadzu IRAffinity-1S Fourier transform IR spectrometer, in a KBr pellet within the 4000–400 cm–1 interval, contain absorption bands of carbonyl groups, which are shifted to the low-frequency vibration region in comparison with the IR spectra of the initial acids. According to the X-ray diffraction data obtained on a Bruker D8 QUEST diffractometer, compound 1 has the following crystallographic parameters of the unit cell: space group P-1, a = 9.034(4), b = 11.351(8), c = 14.814(9) Å, α = 70.11(3)°, β = 88.60(2)°, γ = 87.03(2)°, V = 1426(15) Å3, ρcalc = 1.679 g/cm3, Z = 2. The antimony atom in 1 has a distorted trigonal-bipyramidal coordination with carboxylate ligands in axial positions. The OSbO axial angle is 176.95 (6)°. The lengths of the Sb−O and Sb−C bonds are equal to 2.135(2), 2.121(2) and 2.113(3)–2.116 (3) Å. The Sb•••O=C distances are 3.040(2), 2.861 (3) Å, that is, less than the sum of the van der Waals radii of antimony and oxygen (3.70 Å). The antimony atom departs from the equatorial plane [C3] by 0.038 Å. Complete tables of atom coordinates, bond lengths and valence angles are deposited at the Cambridge Crystallographic Data Center (№ 2051716; deposit@ccdc.cam.ac.uk or http://www.ccdc.cam.ac.uk/data_request/cif).

Rational Preparation of Atomically Precise Non-Alkyl Tin-Oxo Clusters with Theoretical to Experimental Insights into Electrocatalytic CO 2 Reduction Applications

Tin oxides (SnO2) have been widely utilized in electronics, nanolithography, and catalysis. As the atomically precise models of SnO2, tin-oxo clusters (TOCs) not only provide opportunities for mech...

Multiple Hydrogen Bond-Induced Structural Distortion for Broadband White-Light Emission in Two-Dimensional Perovskites

Low-dimensional hybrid lead-halide perovskites with broadband white-light emission upon near-UV excitation have attracted immense scientific interest due to their potential application for the next...

Benchmark of Generic Shapes for Macrocycles.

Macrocycles target proteins that are otherwise considered undruggable because of a lack of hydrophobic cavities and the presence of extended featureless surfaces. Increasing efforts by computational chemists have developed effective software to overcome the restrictions of torsional and conformational freedom that arise as a consequence of macrocyclization. Moloc is an efficient algorithm, with an emphasis on high interactivity, and has been constantly updated since 1986 by drug designers and crystallographers of the Roche biostructural community. In this work, we have benchmarked the shape-guided algorithm using a dataset of 208 macrocycles, carefully selected on the basis of structural complexity. We have quantified the accuracy, diversity, speed, exhaustiveness, and sampling efficiency in an automated fashion and we compared them with four commercial (Prime, MacroModel, molecular operating environment, and molecular dynamics) and four open-access (experimental-torsion distance geometry with additional “basic knowledge” alone and with Merck molecular force field minimization or universal force field minimization, Cambridge Crystallographic Data Centre conformer generator, and conformator) packages. With three-quarters of the database processed below the threshold of high ring accuracy, Moloc was identified as having the highest sampling efficiency and exhaustiveness without producing thousands of conformations, random ring splitting into two half-loops, and possibility to interactively produce globular or flat conformations with diversity similar to Prime, MacroModel, and molecular dynamics. The algorithm and the Python scripts for full automatization of these parameters are freely available for academic use.

Secondary Metal Coordination Using a Tetranuclear Complex as Ligand Leading to Hexanuclear Complexes with Enhanced Thermal Barriers for Electron Transfer

Postsynthesis of the paramagnetic square-shaped complex {[(Tp*Me)Fe(μ-CN)2(CN)][Co(dmbpy)2]}2(BPh4)2·6MeCN·H2O [1, Tp*Me = tris(3,4,5-trimethylpyrazole)-borate; dmbpy = 4,4′-dimethyl-2,2′-bipyridin...

Acidity-Driven Bidirectional Room-Temperature Spin-State Switch and Fluorescence Modulation of a Mononuclear Fe(II) Complex

Room-temperature switchable materials showing multiple responses toward external stimuli are highly desired. Herein, we report bidirectional spin-state switch and fluorescence modulation of an Fe(I...

Positive/Negative Phototropism: Controllable Molecular Actuators with Different Bending Behavior

Herein, a series of molecular actuators based on the crystals of (E)-2-(4-fluorostyryl)benzo[d]oxazole (BOAF4), (E)-2-(2,4-difluorostyryl)benzo[d]oxazole (BOAF24), (E)-2-(4-fluorostyryl)benzo[d]thi...

Chiral Cobalt(II) Complex Catalyzed Asymmetric [2,3]-Sigmatropic Rearrangement of Allylic Selenides with α-Diazo Pyrazoleamides

Organoselenium compounds, due to their high structural diversity, special function, and biological activities, have drawn attention in synthetic chemistry. Herein, a novel example of chiral N,N′-di...

Facile Synthesis of Aryl-Substituted Cycloarenes via Bismuth(III) Triflate-Catalyzed Cyclization of Vinyl Ethers

Cycloarenes are an essential class of polycyclic aromatic hydrocarbons with unique electronic structure, but their synthesis is very challenging. Herein, we report a facile synthetic strategy prima...

High-Efficiency Narrow-Band Electro-Fluorescent Devices with Thermally Activated Delayed Fluorescence Sensitizers Combined Through-Bond and Through-Space Charge Transfers

Organic light-emitting diodes utilizing thermally activated delayed fluorescence sensitizers and multiple-resonance (MR) dopants may simultaneously offer high efficiencies and narrow-band emissions...

Crystalline Sponges as a Sensitive and Fast Method for Metabolite Identification: Application to Gemfibrozil and its Phase I and II Metabolites.

Understanding the metabolism of new drug candidates is important during drug discovery and development, as circulating metabolites may contribute to efficacy or cause safety issues. In the early phase of drug discovery, human in vitro systems are used to investigate human relevant metabolism. Though conventional techniques are limited in their ability to provide complete molecular structures of metabolites (liquid chromatography mass spectrometry) or require a larger amount of material not available from in vitro incubation (nuclear magnetic resonance), we here report for the first time the use of the crystalline sponge method to identify phase I and phase II metabolites generated from in vitro liver microsomes or S9 fractions. Gemfibrozil was used as a test compound. Metabolites generated from incubation with microsomes or S9 fractions, were fractionated using online fraction collection. After chromatographic purification and fractionation of the generated metabolites, single crystal X-ray diffraction of crystalline sponges was used to identify the structure of gemfibrozil metabolites. This technique allowed for complete structure elucidation of 5'-CH2OH gemfibrozil (M1), 4'-OH gemfibrozil (M2), 5'-COOH gemfibrozil (M3), and the acyl glucuronide of gemfibrozil, 1-O-β-glucuronide (M4), the first acyl glucuronide available in the Cambridge Crystallographic Data Centre. Our study shows that when optimal soaking is possible, crystalline sponges technology is a sensitive (nanogram amount) and fast (few days) method that can be applied early in drug discovery to identify the structure of pure metabolites from in vitro incubations. SIGNIFICANCE STATEMENT: Complete structure elucidation of human metabolites plays a critical role in early drug discovery. Low amounts of material (nanogram) are only available at this stage and insufficient for nuclear magnetic resonance analysis. The crystalline sponge method has the potential to close this gap, as demonstrated in this study.

Investigating discrepancies between experimental solid-state NMR and GIPAW calculation: N[dbnd]C–N 13C and OH⋯O 1H chemical shifts in pyridinium fumarates and their cocrystals

An NMR crystallography analysis is presented for four solid-state structures of pyridine fumarates and their cocrystals, using crystal structures deposited in the Cambridge Crystallographic Data Centre, CCDC. Experimental one-dimensional one-pulse 1H and 13C cross-polarisation (CP) magic-angle spinning (MAS) nuclear magnetic resonance (NMR) and two-dimensional 14N–1H heteronuclear multiple-quantum coherence MAS NMR spectra are compared with gauge-including projector augmented wave (GIPAW) calculations of the 1H and 13C chemical shifts and the 14N shifts that additionally depend on the quadrupolar interaction. Considering the high ppm (>10 ​ppm) 1H resonances, while there is good agreement (within 0.4 ​ppm) between experiment and GIPAW calculation for the hydrogen-bonded NH moieties, the hydrogen-bonded fumaric acid OH resonances are 1.2–1.9 ​ppm higher in GIPAW calculation as compared to experiment. For the cocrystals of a salt and a salt formed by 2-amino-5-methylpyridinium and 2-amino-6-methylpyridinium ions, a large discrepancy of 4.2 and 5.9 ​ppm between experiment and GIPAW calculation is observed for the quaternary ring carbon 13C resonance that is directly bonded to two nitrogens (in the ring and in the amino group). By comparison, there is excellent agreement (within 0.2 ​ppm) for the quaternary ring carbon 13C resonance directly bonded to the ring nitrogen for the salt and cocrystal of a salt formed by 2,6-lutidinium and 2,5-lutidinium, respectively.

SYNTHESIS AND STRUCTURE OF METHYLTRIPHENYLPHOSPHONIUM DICYANODIBROMOAURATE [Ph3PCH3] [Au(CN)2Br2

Methyltriphenylphosphonium dicyanodibromoaurate (1) [Ph3PMe]+[Au(CN)2Br2]– was synthesized by the reaction of potassium dicyanodibromoaurate with methyltriphenylphosphonium bromide in an aqueous solution and was structurally characterized. The complex is a yellow-colored, air-resistant crystalline substance with a clear melting point. The structure of the compound was established by IR spectroscopy, NMR spectroscopy and X-ray diffraction analysis. An intense absorption band was observed in the IR spectrum of compound at 2220 cm−1, corresponding to the stretching vibrations of cyano groups. The absorption band of the deformation vibrations of the P – СPh bonds in the IR spectrum is at 1438 cm−1. In the recorded 1Н, 13С, and 31Р NMR spectra, signals are observed for the number, value of chemical shifts and integral intensity that do not contradict the proposed complex structure. The X-ray diffraction analysis of crystal 1 was carried out on a Bruker D8 QUEST diffractometer (MoKα radiation, λ = 0.71073 Å, graphite monochromator). [C21H18AuBr2N2P, M = 686.13, crystal system triclinic, space group P-1, a = 8.802(5), b = 8.989(5), c = 15.233(11) Å, V = 1143.8(13) Å3, Z = 2, µ = 10.002 mm-1, F(000) = 644, crystal size 0.41×0.30×0.22 mm]. According to the X-ray diffraction analysis (XRDA) data there are two types of centrosymmetric crystallographically independent monomeric dicyanodibromoaurate anions and methyltriphenylphosphonium cations in the crystal of compound MFDDA. The cations have a distorted tetrahedral configuration: the CPC angles equal 108.8(2)°−110.0(2)°, the P−С distances are 1.791(5)−1.800(5) Å. All СAuC and BrAuBr trans-angles are 180.0° in the [Au(CN)2Br2]− anions. The Au−C distances in anions differ from each other and equal 2.040(7), 2.024(1), 1.991(2) Å. These values are close to the sum of the covalent radii of atoms (2.03 Å). The Au-Br bond lengths are equal to 2.4162(14), 2.4591, 2.474(5) Å in dicyanodibromoaurate anions. Formation of the crystal structure occurs due to formation of weak N···Н−С hydrogen bonds between cations and anions (2.68, 2.59, 2.38 Å) and Br···Н−С (3.03, 3.02 Å). Complete tables of coordinates of atoms, bond lengths and valence angles are deposited at the Cambridge Crystallographic Data Centre.

Mercury 4.0: from visualization to analysis, design and prediction.

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

Синтез и особенности строения 2,3-дифтор- и 2,3,4,5,6-пентафторбензоата тетрафенилсурьмы

Tetraphenylantimony 2,3-difluorobenzoate (1) and tetraphenylantimony 2,3,4,5,6-pentafluorobenzoate (2) was obtained by the interaction of pentaphenylantimony with 2,3-difluorobenzoic and 2,3,4,5,6-pentafluorobenzoic acids in benzene with a yield of up to 98 %. The compounds were also synthesized by the ligand redistribution reaction between pentaphenylantimony and triphenylantimony dicarboxylates. The compounds have been identified by IR spectroscopy and X-ray diffraction analysis. According to the X-ray diffraction data, the antimony atoms in compounds 1 and 2 have a distorted trigonal-bipyramidal coordination with the oxygen atom in axial positions. X-ray diffraction analysis was performed on a D8 QUEST diffractometer (Bruker). The crystallographic parameters of the unit cell of the compounds: 1 space group Р1 ̅, а = 9.857(5), b = 10.154(7), c = 14.362(11) Å, α = 83.74(4)°, β = 82.59(3), γ = 68.34(2)°, V = 1321.9(16) Å3, ρcalc = 1.475 g/cm3, Z = 2; 2 space group Р21/с, а = 16.186(9), b = 8.771(6), c = 20.413(13) Å, α = 90.00°, β = 113.073(17), γ = 90.00°, V = 2666(3) Å3, ρcalc = 1.597 g/cm3, Z = 4. The OSbO axial angles are slightly different and amount to 177.90(5)º in 1 and 179.00(5)º in 2. The sums of the CSbC equatorial angles are 356.89(9)º (1), 355.85(7)º (2). The Sb–Ceq distances in compounds 1 and 2 are 2.116(2), 2.119(2), 2.118(2) and 2.1073(17), 2.1158(18), 2.1152(19) Å respectively, which are significantly shorter than the Sb–Сax bond lengths (2.169(2) and 2.1617(19) Å). The organization of molecules in the crystals of compounds is due to hydrogen bonds and CHπ-interactions of the aryl and carboxyl ligands. The main difference between structures 1 and 2 is the different Sb–O bond lengths (2.2864(18) and 2.3168(18) Å), which is due to an increase in the electronegativity of the carboxyl ligand in 2, caused by the presence of five electronegative fluorine atoms in the benzoate substituent. Complete tables of atom coordinates, bond lengths and valence angles are deposited at the Cambridge Crystallographic Data Center (No. 1980908 (1); 1977189 (2); deposit@ccdc.cam.ac.uk; http://www.ccdc.cam.ac.uk/data_request/cif).

µ2-Oxo-Bis[(2,5-Dinitrophenoxo)triarylantimony]: Syntheses, Structures, and Reactions with Pentaarylantimony

Antimony aroxides [Ph3SbOC6H3(NO2)2-2,5]2O (I) and [(4-MeC6H4)3SbOC6H3(NO2)2-2,5]2O (II) were synthesized by the oxidation of triarylantimony with tert-butyl hydroperoxide in the presence of 2,5-dinitrophenol. The SbOSb fragments in compounds I and II are bent (the corresponding angles are 139.70(10)° and 142.32(12)°). The Sb−Оbr bonds (1.973(3), 1.980(3) A in I; 1.975(2), 1.977(2) A in II) are substantially shorter than Sb−Ot (2.211(3), 2.213(3) and 2.191(2), 2.191(2) A in I and II, respectively). Aroxides Ar4SbOC6H3(NO2)2-2,5 (Ar = Ph (III) and 4-MeC6H4 (IV)) and carbonates (Ar4Sb)2CO3 (Ar = Ph (V) and 4-MeC6H4 (VI)) are formed from Ar5Sb and compounds I and II in the presence of oxygen and carbon dioxide, respectively. In the trigonal bipyramidal molecules of compounds III and IV, the СSbO axial angles are 175.80(7)° and 176.86(10)° (Sb−O 2.290(2) and 2.342(2) A, respectively). One of the antimony atoms in compound V and in crystallographically independent molecules of two types of compound VI is pentacoordinated (the Sb−Oax bond is 2.245(6) A in V and is 2.263(3) and 2.263(3) A in VIа and VIb, respectively), whereas the second antimony atom is hexacoordinated (Sb−O 2.249(6) and 2.273(5) A in V; 2.216(2), 2.251(2) A and 2.217(2), 2.251(2) A in VIа and VIb). The crystallographic data are deposited with the Cambridge Crystallographic Data Centre (СIF files ССDС nos. 1890704 (I), 1890706 (II), 1890713 (III), 1890714 (IV), 994519 (V), and 994177 (VI)).

In Silico Design, Synthesis, and Characterization of Ibuprofen Derivative as Potential Antitumor Agent.

Background: Numerous animal studies and clinical trials in cancer have shown that ibuprofen reduces the incidence of and mortality from cancer. Synthesis of novel conjugate of ibuprofen with the 2-phenyl amino pyrimidine derivative (to mimic small molecules kinase inhibitor anticancers) exhibits significant increase, as compared to free ibuprofen, potential to inhibit proliferation of cancer cells. Methods: The docking study was performed with GOLD software supplied by the Cambridge Crystallographic Data Centre. Thereafter, the chemical synthesis was established. The chemical structures of this study was confirmed by spectral instrumentation; infrared, differential scanning calorimeter thermal analyzer, proton and carbon-13 nuclear magnetic resonance. Results and Discussions: The docking process was successfully conducted and the chemical synthesis yielded a good per cent. The spectral interpretations show characteristic identification of the target chemical compound.

Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge

Intermolecular interactions of organic, inorganic, and organometallic compounds are the key to many composition–structure and structure–property networks. In this review, some of these relations and the tools developed by the Cambridge Crystallographic Data Center (CCDC) to analyze them and design solid forms with desired properties are described. The potential of studies supported by the Cambridge Structural Database (CSD)-Materials tools for investigation of dynamic processes in crystals, for analysis of biologically active, high energy, optical, (electro)conductive, and other functional crystalline materials, and for the prediction of novel solid forms (polymorphs, co-crystals, solvates) are discussed. Besides, some unusual applications, the potential for further development and limitations of the CCDC software are reported.

Synthesis, Spectroscopic Studies and X-Ray Diffraction of Heptacoordinated Mn(II) and Co(II) Complexes with Ligands Derived from Carbonohydrazide

The ligand 1-(1-(pyridin-2-yl)ethylidene)carbonohydrazide (H4L1) and 1-(pyridin-2-ylmethylene)carbonohydrazide (H4L2) were prepared by reaction of carbonohydrazide with 2-acetylpyridine or pyridine carbaldehyde respectively in a reflux methanol solution. The complexes are prepared by reaction of the ligand with the appropriate metal salt. These complexes are well characterized by elemental analysis, IR and UV spectroscopies and their structure were determined by single X-ray diffraction technic. In the crystal of the dinuclear complex [Mn2(H4L1)2(H2O)4]·Cl4, 1) each Mn(II) center is seven coordinated by two nitrogen atom and one carbonyl atom of the one ligand and one nitrogen atom and one carbonyl oxygen atom of another ligand molecule. The coordination sphere is completed by two water molecules. Each of the carbonyl oxygen atom acts as bridge between the two Mn(II) centers. In the mononuclear complex [Co(H4L2)(NO3)(H2O)2]·(NO3); 2) the Co(II) center is heptacoordinated. The ligand acts in tridentate fashion through two nitrogen atoms and one carbonyl oxygen atom. Two water molecules lie in the apical positions. One nitrate group acts in bidentate manner while the other nitrate group remains uncoordinated. In both complexes the coordination polyhedral are best described as a pentagonal bipyramid. The molecules are linked together in each case by multiple hydrogen bond interaction resulting in a three-dimensional network. The crystallographic data has been deposited in Cambridge Crystallographic Data Centre [CCDC No. 1944387 (complex 1) and 1944386 (complex 2)].

Growth and Characterization of 8-Hydroxy Quinoline Nitrobenzoate

In this work we report the newly formed crystal structure of 8-Hydroxy quinoline nitro benzoate. The systematic investigation has been carried out on the growth and characterizations with a view of using this organic material in semiconductor devices apart from its various biological applications. Single crystals of 8-Hydroxy Quinoline Nitro Benzoate (8-HQNB) were grown successfully by slow evaporation solution growth technique. The new formation of the crystal with molecular formula C16H14N2O6 is confirmed by single crystal X-ray diffraction analysis. The crystallographic data has been deposited in Cambridge Crystallographic Data Centre [CCDC NO. 1005192]. Fourier Transform Infra Red (FTIR) spectroscopic analysis confirms the functional groups of the newly confirmed crystal. The UV-Vis-NIR studies reveal that there is no remarkable absorption in the visible region which proves its suitability for optical applications.