scholarly journals Synthesis and crystal structure of cytotoxic copper(II) complex with 1,10-phenanthroline-5,6-dione and isothiazole derivative

2022 ◽  
Vol 11 (4) ◽  
pp. 531-539
Author(s):  
Yu. A. Golubeva ◽  
K. S. Smirnova ◽  
L. S. Klyushova ◽  
V. I. Potkin ◽  
E. V. Lider
Keyword(s):  
Ir Spectroscopy ◽  
Cytotoxic Activity ◽  
Cell Lines ◽  
Anticancer Agents ◽  
Diffraction Data ◽  
Density Functional ◽  
Breast Adenocarcinoma ◽  
High Dose ◽  
X Ray Diffraction ◽  
X Ray

Oligopyridine based copper(II) complexes are of interest to scientists as possible anticancer agents due to promising cytotoxic and DNA binding/cleaving properties. In this study, copper(II) complex [Cu(phendione)L2]·C2H5OH with 1,10-phenanthroline-5,6-dione (phendione) and 4,5-dichloro-isothiazole-3-carboxylic acid (HL) was synthesized and characterized by elemental analysis, IR-spectroscopy, X-ray powder diffraction and single-crystal X-ray diffraction. According to X-ray diffraction data, obtained compound is mononuclear complex with square pyramidal coordination environment of the central atom which is surrounded by two isothiazolate molecules and one phendione ligand. The X-ray diffraction data are confirmed by IR-spectroscopy data showing the presence of characteristic stretching vibration bands of the carbonyl and carboxyl groups of oligopyridine ligand and isothiazolate ions, respectively. Density functional theory (DFT) calculations for complex were carried out using the ADF software package to perform geometry optimization and frequency calculations that were in a good agreement with experimental IR spectrum. Cytotoxicity of complex and initial reagents was tested in vitro against HepG2 (human hepatocellular carcinoma) and MCF-7 (human breast adenocarcinoma) cell lines. The complex showed high dose-dependent cytotoxic activity with the IC50 values of 0.60±0.03 µM and 0.96±0.13 µM, respectively, which is higher than the activity of cisplatin against these cell lines. The activity of the complex is due to the presence of phendione ligand, which exhibits a similar cytotoxic activity.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

scholarly journals CRYSTAL STRUCTURE OF BIS[1-(DIAMINOMETHYLENE)-THIOURON-1-IUM] SULFATE

2017 ◽  
Vol 60 (1) ◽  
pp. 45
Author(s):  
Yuliya V. Butina ◽  
Elena A. Danilova ◽  
Maxim V. Dmitriev ◽  
Aleksey V. Solomonov
Keyword(s):  
Crystal Structure ◽  
Ir Spectroscopy ◽  
Diffraction Data ◽  
Crystalline State ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Tautomeric Forms ◽  
Structural Database ◽  
Derivatives Of

For citation:Butina Yu.V., Danilova E.A., Dmitriev M.V., Solomonov А.V. Crystal structure of bis[1-(diaminomethylene)-thiouron-1-ium] sulfate. Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol. 2017. V. 60. N 1. P. 45-49. In this work crystal data of bis[1-(diaminomethylene)-thiouron-1-ium] sulfate is shown. This compound was characterized by IR spectroscopy and elemental analysis. The monocrystal of this compound was obtained and the structure was confirmed by single X-ray analysis. Moreover, the work describes potential application of synthesized compound. Comparative characteristics of thiourea and its known salts are demonstrated. It is known, that derivatives of thiourea have several tautomeric forms, which can be different in crystalline state or in solution. Therefore, changed scheme of the synthesis of 2-imino-4-thiobiuret is proposed. Elemental cell of crystal consists of two 1-(diaminomethylene)thiouron-1-ium cations and one sulfat anion. A full set of X-ray diffraction data was deposited in the Cambridge Structural Database (deposit CCDC 1421710) and it can be gotten from the site www.ccdc.cam.ac.uk/data_request/cif.

Powder X-ray diffraction of bendamustine hydrochloride monohydrate, C16H22Cl2N3O2Cl·H2O

2018 ◽  
Vol 34 (1) ◽  
pp. 74-75
Author(s):  
J. A. Kaduk ◽  
K. Zhong ◽  
T. N. Blanton ◽  
S. Gates-Rector ◽  
T. G. Fawcett
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Argonne National Laboratory ◽  
Lymphocytic Leukemia ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrochloride Monohydrate

Bendamustine hydrochloride monohydrate (marketed as Treanda®) is a nitrogen mustard purine analog alkylator used in the treatment of chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphomas. Commercial bendamustine hydrochloride monohydrate crystallizes in the monoclinic space group P21/c (14), with a = 4.71348(4) Å, b = 47.5325(3) Å, c = 8.97458 (5) Å, β = 96.6515(8)°, V = 1997.161(23) Å3, and Z = 4. A reduced cell search in the Cambridge Structural Database yielded a previously reported crystal structure (Allen, 2002), which did not include hydrogens (Reck, 2006). In this work, the sample was ordered from Santa Cruz Biotechnology, and analyzed as received. The room-temperature crystal structure was refined using synchrotron (λ = 0.413896 Å) powder diffraction data, density functional theory (DFT), and Rietveld refinement techniques. Hydrogen positions were included as part of the structure, and recalculated during the refinement. The diffraction data were collected on beamline BM-11 at the Advanced Photon Source, Argonne National Laboratory. Figure 1 shows the powder X-ray diffraction pattern of the compound. The pattern is included in the Powder Diffraction File as entry 00-064-1508.

Powder X-ray diffraction of Metastudtite, (UO2)O2(H2O)2

2016 ◽  
Vol 31 (1) ◽  
pp. 71-72 ◽  
Author(s):  
Mark A. Rodriguez ◽  
Philippe E. Weck ◽  
Joshua D. Sugar ◽  
Thomas J. Kulp
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
First Principles ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Unit Cells

There has been some confusion in the published literature concerning the structure of Metastudtite (UO2)O2(H2O)2 where differing unit cells and space groups have been cited for this compound. Owing to the absence of a refined structure for Metastudtite, Weck et al. (2012) have documented a first-principles study of Metastudtite using density functional theory (DFT). Their model presents the structure of Metastudtite as an orthorhombic (space group Pnma) structure with lattice parameters of a = 8.45, b = 8.72, and c = 6.75 Å. A Powder Diffraction File (PDF) database entry has been allocated for this hypothetical Metastudtite phase based on the DFT modeling (see 01-081-9033) and aforementioned Dalton Trans. manuscript. We have obtained phase pure powder X-ray diffraction data for Metastudtite and have confirmed the model of Weck et al. via Rietveld refinement (see Figure 1). Structural refinement of this powder diffraction dataset has yielded updated refined parameters. The new cell has been determined as a = 8.411(1), b = 8.744(1), and c = 6.505(1) Å; cell volume = 478.39 Å3. There are only subtle differences between the refined structure and that of the first-principles model derived from DFT. Notably, the b-axis is significantly contracted in the final refinement as compared with DFT. There were also subtle changes to the U1, O1, and O3 atom positions. Tabulated powder diffraction data (d's and I's) for the Metastudtite have been derived from the refined model and these new values can serve to augment the PDF entry 01-081-9033 with a more updated entry based on observed X-ray powder diffraction data.

Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculations

2009 ◽  
Vol 65 (5) ◽  
pp. 639-646 ◽  
Author(s):  
Edward E. Ávila ◽  
Asiloé J. Mora ◽  
Gerzon E. Delgado ◽  
Ricardo R. Contreras ◽  
Luis Rincón ◽  
...  
Keyword(s):  
Solid State ◽  
Diffraction Data ◽  
Density Functional ◽  
Simulated Annealing Algorithm ◽  
Theoretical Calculations ◽  
Tight Binding ◽  
Van Der Waals Interactions ◽  
Am1 Calculations ◽  
X Ray Diffraction ◽  
X Ray

The molecular and crystalline structure of ethyl 1′,2′,3′,4′,4a′,5′,6′,7′-octahydrodispiro[cyclohexane-1,2′-quinazoline-4′,1′′-cyclohexane]-8′-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem. 38, 1223–1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N—H...S and C—H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions.

Powder X-ray diffraction of capecitabine, C15H22FN3O6

2019 ◽  
Vol 34 (3) ◽  
pp. 282-283 ◽  
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Diffraction Data ◽  
Density Functional ◽  
National Laboratory ◽  
Argonne National Laboratory ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Acta Cryst ◽  
X Ray ◽  
Data Density ◽  
Structure Determinations

Capecitabine (Xeloda) is a chemotherapy drug used to treat breast, gastric, and colorectal cancers. Commercial capecitabine crystallizes in the orthorhombic space group P212121 (#19) with a = 5.20587(3), b = 9.52324(4), c = 34.79574(21) Å, V = 1725.062(12) Å3, and Z = 4. A reduced cell search in the Cambridge Structural Database (Groom C. R., Bruno, I. J., Lightfoot, M. P., and Ward, S. C. (2016) Crystallogr. Sect. B: Struct. Sci., Cryst. Eng. Mater.72, 171–179) yielded three previous structure determinations (Rohlicek, J., Husak, M., Gavenda, A., Jegorov, A., Kratochvil, B., and Fitch, A. (2016). Acta Cryst. Sect. E: Crystallgr. Commun.72, 879–880, BOVDUM; Malińska, M., Krzeczyński, P., Czerniec-Michalik, E., Trzcińska, K., Cmoch, P., Kutner, A., and Woźniak, K. (2014). J. Pharm. Sci.103, 587–593, BOVDUM01 and BOVDUM02), using synchrotron powder data and later single crystal data at two temperatures. In this work, the sample was ordered from United States Pharmacopeial Convention (lot # G0J205), and analyzed as-received. The room temperature (295 K) crystal structure was refined using synchrotron (λ = 0.413914 Å) powder diffraction data, density functional theory (DFT), and Rietveld refinement techniques. Hydrogen positions were included as part of the structure, and were re-calculated during the refinement. The diffraction data were collected on a beamline 11-BM at the Advanced Photon Source, Argonne National Laboratory and the powder X-ray diffraction pattern of the compound is provided. The agreement of the Rietveld-refined and DFT-optimized structures is poorest in the pentyl side chain, consistent with the disorder observed previously.

Structural investigation ofN,N′-methylenebisacrylamideviaX-ray diffraction assisted by crystal structure prediction

2015 ◽  
Vol 48 (2) ◽  
pp. 550-557 ◽  
Author(s):  
Claudia Graiff ◽  
Daniele Pontiroli ◽  
Laura Bergamonti ◽  
Chiara Cavallari ◽  
Pier Paolo Lottici ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Structure Prediction ◽  
Density Functional ◽  
Geometry Optimization ◽  
Lattice Energy ◽  
Strong Interactions ◽  
Crystal Structure Prediction ◽  
X Ray Diffraction ◽  
X Ray

The crystal structure ofN,N′-methylenebisacrylamide was determined through the geometry optimization of the molecular unit with density functional theory and conformational analysis, and then through the calculation of the packingviaa crystal structure prediction protocol, based on lattice energy minimization. All the calculated structures were ranked, comparing their powder pattern with the laboratory low-quality X-ray diffraction data. Rietveld refinement of the best three proposed structures allowed the most probable crystal arrangement of the molecules to be obtained. This approach was essential for disentangling the twinning problems affecting the single-crystal X-ray diffraction data, collected on samples obtainedviarecrystallization of powder, which definitely confirmed the predicted model. It was found thatN,N′-methylenebisacrylamide shows a monoclinic structure in the space groupC2/c, with lattice parametersa= 17.822 (12),b= 4.850 (3),c= 19.783 (14) Å, β = 102.370 (9)°,V= 1670 (2) Å3. Two strong interactions between the amide protons and the carbonyl groups of neighbouring molecules were found along thebaxis, determining the crystal growth in the form of wires in this direction. This work provides a further example of how computational methods may help to investigate low-quality molecular crystals with standard diffraction techniques.

scholarly journals Ab initio and DFT study on Cu (II) complex salicylate derivative

2014 ◽  
Vol 70 (a1) ◽  
pp. C1442-C1442
Author(s):  
Karthikeyan Natarajan ◽  
Sathya Duraisamy ◽  
Sivakumar Kandasamy
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray

X -ray diffraction becomes a routine process these decades for determining crystal structure of the materials. Most of the crystal structures solved nowadays is based on single crystal X-ray diffraction because it solves the crystal and molecular structures from small molecules to macro molecules without much human intervention. However it is difficult to grow single crystals of sufficient size and quality for conventional single-crystal X-ray diffraction studies. In such cases it becomes essential that structural information can be determined from powder diffraction data. With the recent developments in the direct-space approaches for structure solution, ab initio crystal structure analysis of molecular solids can be accomplished from X-ray powder diffraction data. It should be recalled that crystal structure determination from laboratory X-ray powder diffraction data is a far more difficult task than that of its single-crystal counterpart, particularly when the molecule possesses considerable flexibility or there are multiple molecules in the asymmetric unit. Salicylic acid and its derivatives used as an anti-inflammatory drug are known for its numerous medicinal applications. In our study, we synthesized mononuclear copper (II) complex of salicylate derivative. The structural characterization of the prepared compound was carried out using powder X-ray diffraction studies. Crystal structure of the compound has been solved by direct-space approach and refined by a combination of Rietveld method using TOPAS Academic V4.1. Density Functional Theory (DFT) calculations have to be carried in the solid state for the compound using GaussianW9.0 in the frame work of a generalized-gradient approximation (GGA). The geometry optimization was to be performed using B3LYP density functional theory. The atomic coordinates were taken from the final X-ray refinement cycle.

The Structure of Amorphous Hydrogenated Silicon:Carbon Alloys Using X-Ray and Neutron Scattering and Computer Simulation - The Effect of Hydrogen Dilution

1992 ◽  
Vol 270 ◽  
Author(s):  
T. M. Burke ◽  
P. J. R. Honeybone ◽  
D. W. Huxley ◽  
R. J. Newport ◽  
Th. Frauenheim ◽  
...  
Keyword(s):  
Computer Simulation ◽  
Diffraction Data ◽  
Density Functional ◽  
Real Space ◽  
X Ray Diffraction ◽  
X Ray ◽  
Space Resolution ◽  
Silicon Carbon ◽  
Two Samples ◽  
Silane Precursor

ABSTRACTNeutron and X-ray diffraction techniques have been applied to the study of two samples of a-Si:C:H. Both samples were prepared using conventional glow discharge methods, but the hydrocarbon/silane precursor gas was diluted with hydrogen in one case. Analysis of the X-ray diffraction data gives a clear picture of the silicon network, since the scattering profile is dominated by the Si-Si correlations. The high real-space resolution neutron diffraction data, however allows one to comment on the effect of this dilution on the silicon-carbon bonding morphology, and in particular on the degree to which the additional hydrogen enhances hetero-coordination. In addition we present the results of a preliminary computer simulation study of the structure of a-C:H and a-Si:H using an approximate molecular dynamic density functional theory, and discuss its viability in the study of the more complex a-Si:C:H ternary alloy.

scholarly journals Structural study of new cytotoxic heteroleptic Copper (II) complexes

2014 ◽  
Vol 70 (a1) ◽  
pp. C1229-C1229
Author(s):  
Natalia Alvarez ◽  
Sebastián Iglesias ◽  
Diana Viñas ◽  
María Torre ◽  
Eduardo Kremer ◽  
...  
Keyword(s):  
Cell Lines ◽  
Copper Complexes ◽  
Biological Activities ◽  
Copper Ion ◽  
Chemical Properties ◽  
Metastatic Breast ◽  
Breast Adenocarcinoma ◽  
Phen Ligand ◽  
X Ray Diffraction ◽  
X Ray

The widespread success of Cisplatin in the treatment of several neoplasias has arisen the interest in coordination compounds as drugs for the treatment of cancer. In the search for new compounds with antitumor activity, copper coordination complexes are being studied by our group. This work presents the synthesis and structural characterization of four new copper complexes with general stoichiometry [Cu(L-dipeptide)(phen)]·nH2O and their cytotoxicity against tumor cell lines. Single crystal X-ray diffraction experiments show that the copper ion is situated in a distorted squared pyramidal environment. The phen ligand is perpendicular to the plane defined by the coordinated dipeptide, therefore exposed and potentially available for interaction with biological molecules, e.g. DNA. The availability of the phen ligand and the physico-chemical properties of the complexes are modulated by the dipeptide. Complementary techniques (elemental analysis, infrared and UV-vis spectroscopies) were used to further characterize the complexes in solid state and aqueous solution, confirming that the coordination is maintained in solution. Lipophilicity and DNA binding constants were also measured, being able to discriminate between the behavior of even the complexes containing the ala-phe and phe-ala dipeptide. All the complexes induce cell death in the cell lines of human cervical adenocarcinoma, human metastatic breast adenocarcinoma and human lung epithelial carcinoma. Among the six complexes studied, [Cu(ala-phe)(phen)] presents the lowest half maximal inhibitory concentration (IC50) values. In an attempt to increase the activity, studies are presently being carried out using 2,9-dimethyl-10-phenanthroline. X-ray diffraction studies on the latter show slight deviations in the coordination geometries and different results are expected in their biological activities. Acknoledgements: CSIC, CAPES-UdelaR, PEDECIBA.

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