Search results for: X-ray diffraction crystallography

Authors: Shuang Zhao, Shintaro Ito, Yoshihiro Ohba, Hiroshi Katagiri

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We present the synthesis and single-crystal X-ray crystallography of a Cu(II) complex(bmn-bpy) of a pyridine-naphthoimidazole-based ligand containing two naphthoimidazoles as the chromophores and a vacant coordination site on Cu(II).

Keywords: synthesis, Cu(II) complex, single-crystal X-ray crystallography

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Authors: Noureddine Benharkat, Abdelkader Chouaih, Nourdine Boukabcha

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A thiourea derivative compound was synthesized and subjected to structural analysis using single-crystal X-ray diffraction (XRD). The crystallographic data unveiled its crystallization in the P21/c space group within the monoclinic system. Examination of the dihedral angles indicated a notable non-planar structure. To support and interpret these resulats, density functional theory (DFT) calculations were conducted utilizing the B3LYP functional along with a 6–311 G (d, p) basis set. Additionally, to assess the contribution of intermolecular interactions, Hirshfeld surface analysis and 2D fingerprint plots were employed. Various types of interactions, whether weak intramolecular or intermolecular, within a molecule can significantly impact its stability. The distinctive signature of non-covalent interactions can be detected solely through electron density analysis. The NCI-RDG analysis was employed to investigate both repulsive and attractive van der Waals interactions while also calculating the energies associated with intermolecular interactions and their characteristics. Additionally, a molecular docking study was studied to explain the structure-activity relationship, revealing that the title compound exhibited an affinity energy of -6.8 kcal/mol when docked with B-DNA (1BNA).

Keywords: computational chemistry, density functional theory, crystallography, molecular docking, molecular structure, powder x-ray diffraction, single crystal x-ray diffraction

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Authors: Saleh Gorji, Sahil Gulati, Ana Pakzad

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Continuous electron diffraction tomography, also known as microcrystal electron diffraction (MicroED) or three-dimensional electron diffraction (3DED), is a powerful technique, which in combination with cryo-electron microscopy (cryo-ED), can provide atomic-scale 3D information about the crystal structure and composition of different classes of crystalline materials such as proteins, peptides, and small molecules. Unlike the well-established X-ray crystallography method, 3DED does not require large single crystals and can collect accurate electron diffraction data from crystals as small as 50 – 100 nm. This is a critical advantage as growing larger crystals, as required by X-ray crystallography methods, is often very difficult, time-consuming, and expensive. In most cases, specimens studied via 3DED method are electron beam sensitive, which means there is a limitation on the maximum amount of electron dose one can use to collect the required data for a high-resolution structure determination. Therefore, collecting data using a conventional scintillator-based fiber coupled camera brings additional challenges. This is because of the inherent noise introduced during the electron-to-photon conversion in the scintillator and transfer of light via the fibers to the sensor, which results in a poor signal-to-noise ratio and requires a relatively higher and commonly specimen-damaging electron dose rates, especially for protein crystals. As in other cryo-EM techniques, damage to the specimen can be mitigated if a direct detection camera is used which provides a high signal-to-noise ratio at low electron doses. In this work, we have used two classes of such detectors from Gatan, namely the K3® camera (a monolithic active pixel sensor) and Stela™ (that utilizes DECTRIS hybrid-pixel technology), to address this problem. The K3 is an electron counting detector optimized for low-dose applications (like structural biology cryo-EM), and Stela is also a counting electron detector but optimized for diffraction applications with high speed and high dynamic range. Lastly, data collection workflows, including crystal screening, microscope optics setup (for imaging and diffraction), stage height adjustment at each crystal position, and tomogram acquisition, can be one of the other challenges of the 3DED technique. Traditionally this has been all done manually or in a partly automated fashion using open-source software and scripting, requiring long hours on the microscope (extra cost) and extensive user interaction with the system. We have recently introduced Latitude® D in DigitalMicrograph® software, which is compatible with all pre- and post-energy-filter Gatan cameras and enables 3DED data acquisition in an automated and optimized fashion. Higher quality 3DED data enables structure determination with higher confidence, while automated workflows allow these to be completed considerably faster than before. Using multiple examples, this work will demonstrate how to direct detection electron counting cameras enhance 3DED results (3 to better than 1 Angstrom) for protein and small molecule structure determination. We will also show how Latitude D software facilitates collecting such data in an integrated and fully automated user interface.

Keywords: continuous electron diffraction tomography, direct detection, diffraction, Latitude D, Digitalmicrograph, proteins, small molecules

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Authors: Yalçın Kılıç, İbrahim Kani

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In recent years, interest in the synthesis of coordination compounds has greatly increased due to various application areas (such as catalysis, gas storage, luminescence). Dicarboxylic acids are often used in the synthesis of metal complexes. Bis-thiosalicylate derivative ligands contribute to the synthesis of structures of crystal engineering interest, as they can have both rigid and flexible properties. In addition, these ligands have great potential in terms of catalytic applications with the sulfur and oxygen donor atoms in their structures. In this study, we synthesized a Cu(II) complex [Cu(tsaxyl)(phen)2]•CH3OH (where tsaxyl = 2,2'-(1,2-phylenebis(methylene))bis(sulfanedyl)dibenzoate, phen = 1,10-phenantroline) and characterized through X-ray crystallography. The catalytic activities of Cu(II) complex on oxidation of ethylbenzene, cyclohexane, diphenylmethane, p-xylene were performed in acetonitrile with t-BuOOH as the source of oxygen.

Keywords: complex, crystallography, catalysis, oxidation

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Authors: Minas Balyan

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Nowadays X-ray nonlinear diffraction and nonlinear effects are investigated due to the presence of the third generation synchrotron sources and XFELs. X-ray third order nonlinear dynamical diffraction is considered as well. Using the nonlinear model of the usual visible light optics the third-order nonlinear Takagi’s equations for monochromatic waves and the third-order nonlinear time-dependent dynamical diffraction equations for X-ray pulses are obtained by the author in previous papers. The obtained equations show, that even if the Fourier-coefficients of the linear and the third order nonlinear susceptibilities are zero (forbidden reflection), the dynamical diffraction in the nonlinear case is related to the presence in the nonlinear equations the terms proportional to the zero order and the second order nonzero Fourier coefficients of the third order nonlinear susceptibility. Thus, in the third order nonlinear Bragg diffraction case a nonlinear analogue of the well-known Renninger effect takes place. In this work, the 'third order nonlinear Renninger effect' is considered theoretically.

Keywords: Bragg diffraction, nonlinear Takagi’s equations, nonlinear Renninger effect, third order nonlinearity

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Authors: Christina Roman, Deepak Koirala, Joseph A. Piccirilli

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Phage displaying synthetic Fab libraries have been used to obtain Fabs that bind to specific RNA targets with high affinity and specificity. These Fabs have been demonstrated to facilitate RNA crystallization. However, the antibody framework used in the construction of these phage display libraries contains numerous bulky, flexible, and charged residues, which facilitate solubility and hinder aggregation. These residues can interfere with crystallization due to the entropic cost associated with burying them within crystal contacts. To systematically reduce the surface entropy of the Fabs and improve their crystallization properties, a protein engineering strategy termed surface entropy reduction (SER) is being applied to the Fab framework. In this approach, high entropy residues are mutated to smaller ones such as alanine or serine. Focusing initially on Fab BL3-6, which binds an RNA AAACA pentaloop with 20nM affinity, the SER P server (http://services.mbi.ucla.edu/SER/) was used and analysis was performed on existing RNA-Fab BL3-6 co-crystal structures. From this analysis twelve surface entropy reduced mutants were designed. These SER mutants were expressed and are now being measured for their crystallization and diffraction performance with various RNA targets. So far, one mutant has generated 3.02 angstrom diffraction with the yjdF riboswitch RNA. Ultimately, the most productive mutations will be combined into a new Fab framework to be used in a optimized phage displayed Fab library.

Keywords: antibody fragment, crystallography, RNA, surface entropy reduction

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Authors: Naureen Akhtar

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The stability of the protein in detergent-containing solution is the key for its successful crystallisation. Fluorescence-detection size-exclusion chromatography (FSEC) is a potential approach for screening monodispersity as well as the stability of protein in a detergent-containing-solution. In this present study, covalently linked Green Fluorescent Protein (GFP) to bacterial nitrate transporter, NarU from Escherichia coli was studied for pre-crystallisation trials by FSEC. Immobilised metal ion affinity chromatography (IMAC) and gel filtration were employed for their purification. The main objectives of this study were over-expression, detergent screening and crystallisation of nitrate transporter proteins. This study could not produce enough proteins that could realistically be taken forward to achieve the objectives set for this particular research. In future work, different combinations of variables like vectors, tags, creation of mutant proteins, host cells, position of GFP (N- or C-terminal) and/or membrane proteins would be tried to determine the best combination as the principle of technique is still promising.

Keywords: transporters, detergents, over-expression, crystallography

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Authors: Mona Alharbi

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Melioidosis has emerged as a lethal disease. Unfortunately, the molecular mechanisms of virulence and pathogenicity of Burkholderia pseudomallei remain unknown. However, proteomics research has selected putative targets in B. pseudomallei that might play roles in the B. pseudomallei virulence. BPSL 2418 putative protein has been predicted as a free methionine sulfoxide reductase and interestingly there is a link between the level of the methionine sulfoxide in pathogen tissues and its virulence. Therefore in this work, we describe the cloning expression, purification, and crystallization of BPSL 2418 and the solution of its 3D structure using X-ray crystallography. Also, we aimed to identify the substrate binding and reduced forms of the enzyme to understand the role of BPSL 2418. The gene encoding BPSL2418 from B. pseudomallei was amplified by PCR and reclone in pETBlue-1 vector and transformed into E. coli Tuner DE3 pLacI. BPSL2418 was overexpressed using E. coli Tuner DE3 pLacI and induced by 300μM IPTG for 4h at 37°C. Then BPS2418 purified to better than 95% purity. The pure BPSL2418 was crystallized with PEG 4000 and PEG 6000 as precipitants in several conditions. Diffraction data were collected to 1.2Å resolution. The crystals belonged to space group P2 21 21 with unit-cell parameters a = 42.24Å, b = 53.48Å, c = 60.54Å, α=γ=β= 90Å. The BPSL2418 binding MES was solved by molecular replacement with the known structure 3ksf using PHASER program. The structure is composed of six antiparallel β-strands and four α-helices and two loops. BPSL2418 shows high homology with the GAF domain fRMsrs enzymes which suggest that BPSL2418 might act as methionine sulfoxide reductase. The amino acids alignment between the fRmsrs including BPSL 2418 shows that the three cysteines that thought to catalyze the reduction are fully conserved. BPSL 2418 contains the three conserved cysteines (Cys⁷⁵, Cys⁸⁵ and Cys¹⁰⁹). The active site contains the six antiparallel β-strands and two loops where the disulfide bond formed between Cys⁷⁵ and Cys¹⁰⁹. X-ray structure of free methionine sulfoxide binding and native forms of BPSL2418 were solved to increase the understanding of the BPSL2418 catalytic mechanism.

Keywords: X-Ray Crystallography, BPSL2418, Burkholderia pseudomallei, Melioidosis

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Authors: Takashi Sakai, Yuri Shimomura

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The crystal orientation is a factor that affects the microscopic material properties. Crystal orientation determines the anisotropy of the polycrystalline material. And it is closely related to the mechanical properties of the material. In this paper, for pure copper polycrystalline material, two different methods; X-Ray Diffraction (XRD) and Electron Backscatter Diffraction (EBSD); and the crystal orientation were analyzed. In the latter method, it is possible that the X-ray beam diameter is thicker as compared to the former, to measure the crystal orientation macroscopically relatively. By measurement of the above, we investigated the change in crystal orientation and internal tissues of pure copper.

Keywords: bending, electron backscatter diffraction, X-ray diffraction, microstructure, IPF map, orientation distribution function

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Authors: Héctor González Espinosa, Ricardo Ivan Cordova Chávez, Alejandra Contreras Ramos, Itzia Irene Padilla Martínez, José Guadalupe Trujillo Ferrara, Marvin Antonio Soriano Ursúa

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Boronic acids are able to create diester bonds with carbohydrates because of their hydroxyl groups; in nature, there are some organoborates with these characteristics, such as the calcium fructoborate, formed by the union of two fructose molecules and a boron atom, synthesized by plants. In addition, it has been observed that, in animal cells only the compounds with cis-diol functional groups are capable of linking to boric or boronic acids. The formation of these organoboron compounds could impair the physical and chemical properties of the precursors, even their acute toxicity. In this project, two carbohydrate-derived boron-containing compounds from D-fructose and D-arabinose and phenylboronic acid are analyzed by different spectroscopy techniques such as Raman, Infrared with Fourier Transform Infrared (FT-IR), Nuclear Magnetic Resonance (NMR) and X-ray diffraction crystallography to describe their chemical characteristics. Also, an acute toxicity test was performed to determine their LD50 using the Lorke’s method. It was confirmed by multiple spectra the formation of the adducts by the generation of the diester bonds with a β-D-pyranose of fructose and arabinose. The most prominent findings were the presence of signals corresponding to the formation of new bonds, like the stretching of B-O bonds, or the absence of signals of functional groups like the hydroxyls presented in the reagents used for the synthesis of the adducts. The NMR spectra yielded information about the stereoselectivity in the synthesis reaction, observed by the interaction of the protons and their vicinal atoms in the anomeric and second position carbons; but also, the absence of a racemic mix by the finding of just one signal in the range for the anomeric carbon in the 13C NMR spectra of both adducts. The acute toxicity tests by the Lorke’s method showed that the LD50 value for both compounds is 1265 mg/kg. Those results let us to propose these adducts as highly safe agents for further biological evaluation with medical purposes.

Keywords: acute toxicity, adduct, boron, carbohydrate, diester bond

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Authors: Sergey I. Chizhikov, Vladimir Y. Molchanov, Konstantin B. Yushkov

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We demonstrate a method for adaptive spatial shaping of laser beams by means of acousto-optic Bragg diffraction. Transformation of the angular spectrum during Bragg diffraction is used to convert Gaussian intensity distribution into a flat-top one. Theoretical model is supported by the experiment.

Keywords: acousto-optics, flat top, beam shaping, Bragg diffraction

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Authors: N. Ammouchi

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We have studied the effect of milling time on the structural and hyperfine properties of Ni45Al45Fe10 compound elaborated by mechanical alloying. The elaboration was performed by using the planetary ball mill at different milling times. The as milled powders were characterized by X-ray diffraction (XRD) and Mӧssbauer spectroscopy. From XRD diffraction spectra, we show that the β NiAl(Fe) was completely formed after 24 h of milling time. When the milling time increases, the lattice parameter increases, whereas the grain size decreases to a few nanometres and the mean level of microstrains increases. The analysis of Mӧssbauer spectra indicates that, in addition to a ferromagnetic phase, α-Fe, a paramagnetic disordered phase Ni Al (Fe) solid solution is observed after 2h and only this phase is present after 12h.

Keywords: NiAlFe, nanostructured powders, X-ray diffraction, Mӧssbauer spectroscopy

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Authors: Minas Balyan

Abstract:

In the third-order nonlinear Takagi’s equations for monochromatic waves and in the third-order nonlinear time-dependent dynamical diffraction equations for X-ray pulses for forbidden reflections the Fourier-coefficients of the linear and the third order nonlinear susceptibilities are zero. The dynamical diffraction in the nonlinear case is related to the presence in the nonlinear equations the terms proportional to the zero order and the second order nonzero Fourier coefficients of the third order nonlinear susceptibility. Thus in the third order nonlinear Bragg diffraction case a nonlinear analogue of the well known Renninger effect takes place. In this work, the ‘third order nonlinear Renninger effect’ is considered theoretically and numerically. If the reflection exactly is forbidden the diffracted wave’s amplitude is zero both in Laue and Bragg cases since the boundary conditions and dynamical diffraction equations are compatible with zero solution. But in real crystals due to some percent of dislocations and other localized defects, the atoms are displaced with respect to their equilibrium positions. Thus in real crystals susceptibilities of forbidden reflection are by some order small than for usual not forbidden reflections but are not exactly equal to zero. The numerical calculations for susceptibilities two order less than for not forbidden reflection show that in Bragg geometry case the nonlinear reflection curve’s behavior is the same as for not forbidden reflection, but for forbidden reflection the rocking curves’ width, center and boundaries are two order sensitive on the input intensity value. This gives an opportunity to investigate third order nonlinear X-ray dynamical diffraction for not intense beams – 0.001 in the units of critical intensity.

Keywords: third order nonlinearity, Bragg diffraction, nonlinear Renninger effect, rocking curves

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Authors: Meltem Bolluk, Ismail Duman

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Boron exhibits the properties of high melting temperature (2273K to 2573 K), high hardness (Mohs: 9,5), low density (2,340 g/cm3), high chemical resistance, high strength, and semiconductivity (band gap:1,6-2,1 eV). These superior properties enable to use it in several high-tech areas from electronics to nuclear industry and especially in high temperature metallurgy. Amorphous boron and crystalline boron have different application areas. Amorphous boron powder (directly amorphous and/or α-rhombohedral) is preferred in rocket firing, airbag inflating and in fabrication of superconducting MgB2 wires. The conventional ways to produce elemental boron with a purity of 85 pct to 95 prc are metallothermic reduction, fused salt electrolysis and mechanochemical synthesis; but the only way to produce high-purity boron powders is Chemical Vapour Deposition (Hot Surface CVD). In this study; amorphous boron powders with a minimum purity of 99,9 prc were synthesized in quartz tubes using BCl3-H2 gas mixture by CVD. Process conditions based on temperature and gas flow rate were determined. Thermodynamical interpretation of BCl3-H2 system for different temperatures and molar rates were performed using Fact Sage software. The characterization of powders was examined by using Xray diffraction (XRD), Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM), Stereo Microscope (SM), Helium gas pycnometer analysis. The purities of final products were determined by titration after lime fusion.

Keywords: amorphous boron, CVD, powder production, powder characterization

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Authors: J. O. Bodunrin, S. J. Moloi

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This study reports on the x-ray crystallography (XRD) structure of cadmium-implanted p-type silicon, the current-voltage (I-V) and capacitance-voltage (C-V) characteristics of unimplanted and cadmium-implanted silicon-based diodes. Cadmium was implanted at the energy of 160 KeV to the fluence of 10¹⁵ ion/cm². The results obtained indicate that the diodes were well fabricated, and the introduction of cadmium results in a change in behavior of the diodes from normal exponential to ohmic I-V behavior. The C-V measurements, on the other hand, show that the measured capacitance increased after cadmium doping due to the injected charge carriers. The doping density of the p-Si material and the device's Schottky barrier height was extracted, and the doping density of the undoped p-Si material increased after cadmium doping while the Schottky barrier height reduced. In general, the results obtained here are similar to those obtained on the diodes fabricated on radiation-hard material, indicating that cadmium is a promising metal dopant to improve the radiation hardness of silicon. Thus, this study would assist in adding possible options to improve the radiation hardness of silicon to be used in high energy physics experiments.

Keywords: cadmium, capacitance-voltage, current-voltage, high energy physics experiment, x-ray crystallography, XRD

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Authors: Morteza Mohri Esfahani, Amir S. H. Rozatian, Morteza Mozaffari

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Single phase magnetite nanoparticles and Bi-substituted ones were prepared by mechanochemical processing (MCP). The effects of Bi-substitution on the structural and magnetic properties of the nanoparticles were studied by X-ray Diffraction (XRD) and magnetometry techniques, respectively. The XRD results showed that all samples have spinel phase and by increasing Bi content, the main diffraction peaks were shifted to higher angles, which means the lattice parameter decreases from 0.843 to 0.838 nm and then increases to 0.841 nm. Also, the results revealed that increasing Bi content lead to a decrease in saturation magnetization (Ms) from 74.9 to 48.8 emu/g and an increase in coercivity (Hc) from 96.8 to 137.1 Oe.

Keywords: bi-substituted magnetite nanoparticles, mechanochemical processing, X-ray diffraction, magnetism

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Authors: Mohsen Sanayei, Jerzy Szpunar

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The present study investigates the effects of deformation strain and annealing temperature on the formation of twin boundaries, deformation and recrystallization texture evolution and grain boundary networks and connectivity. The resulting microstructures were characterized using Electron Backscatter Diffraction (EBSD) and X-Ray Diffraction (XRD) both immediately following small amount of deformation and after short time annealing at high temperature to correlate the micro and macro texture evolution of these alloys. Furthermore, this study showed that the process of grain boundary engineering, consisting cycles of deformation and annealing, is found to substantially reduce the mass and size of random boundaries and increase the proportion of low Coincidence Site Lattice (CSL) grain boundaries.

Keywords: coincidence site lattice, grain boundary engineering, electron backscatter diffraction, texture, x-ray diffraction

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Authors: Katharigatta N. Venugopala, Melendhran Pillay, Bander E. Al-Dhubiab

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Tuberculosis (TB) infection is caused mainly by Mycobacterium tuberculosis (MTB) and it is one of the most threatening and wide spread infectious diseases in the world. Benzothiazole derivatives are found to have diverse chemical reactivity and broad spectrum of pharmacological activity. Some of the important pharmacological activities shown by the benzothiazole analogues are antitumor, anti-inflammatory, antimicrobial, anti-tubercular, anti-leishmanial, anticonvulsant and anti-HIV properties. Keeping all these facts in mind in the present investigation it was envisaged to synthesize a series of novel {2-(benzo[d]-thiazol-2-yl-methoxy)-substitutedaryl}-(substitutedaryl)-methanones (4a-f) and characterize by IR, NMR (1H and 13C), HRMS and single crystal x-ray studies. The title compounds are investigated for in vitro anti-tubercular activity against two TB strains such as H37Rv (ATCC 25177) and MDR-MTB (multi drug resistant MTB resistant to Isoniazid, Rifampicin and Ethambutol) by agar diffusion method. Among the synthesized compounds in the series, test compound {2-(benzo[d]thiazol-2-yl-methoxy)-5-fluorophenyl}-(4-chlorophenyl)-methanone (2c) was found to exhibit significant activity with MICs of 1 µg/mL and 2 µg/mL against H37Rv and MDR-MTB, respectively when compared to standard drugs. Single crystal x-ray studies was used to study intra and intermolecular interactions, including polymorphism behavior of the test compounds, but none of the compounds exhibited polymorphism behavior.

Keywords: benzothiazole analogues, characterization, crystallography, anti-TB activity

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Authors: Omoruyi G. Idemudia, Alexander P. Sadimenko

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The need for the development of new sustainable bioactive compounds with unique properties that can become potential replacement for commonly used medicinal drugs has continued to gain tremendous research concerns because of the problems of disease resistant to these medicinal drugs and their toxicity effects. NOS-donor heterocycles are particularly of interest as they have showed good pharmacological activities in the midst of their interesting chelating properties towards metal ions, an important characteristic for transition metal based drugs design. These new compounds have also gained application as dye sensitizers in solar cell panels for the generation of renewable solar energy, as greener water purification polymer for supply and management of clean water and as catalysts which are used to reduce the amount of pollutants from industrial reaction processes amongst others, because of their versatile properties. Di-ketone acylpyrazolones and their azomethine schiff bases have been employed as pharmaceuticals as well as analytical reagents, and their application as transition metal complexes have being well established. In this research work, a new 4-propyl-3-methyl-1-phenyl-2-pyrazolin-5-one-thiosemicarbazone was synthesized from the reaction of 4-propyl-3-methyl-1-phenyl-2-pyrazolin-5-one and thiosemicarbazide in methanol. The pure isolate of the thiosemicarbazone was further reacted with aqueous solutions of palladium and platinum salts to obtain their metal complexes, in an effort towards the discovery of transition metal based synthetic drugs. These compounds were characterized by means of analytical, spectroscopic, thermogravimetric analysis TGA, as well as x-ray crystallography. 4-propyl-3-methyl-1-phenyl-2-pyrazolin-5-one thiosemicarbazone crystallizes in a triclinic crystal system with a P-1 (No. 2) space group according to x-ray crystallography. The tridentate NOS ligand formed a tetrahedral geometry on coordinating with metal ions. Reported compounds showed varying antioxidant free radical scavenging activities against 2, 2-diphenyl-1-picrylhydrazyl DPPH radical at 100, 200, 300, 400 and 500 µg/ml concentrations. The platinum complex have shown a very good antioxidant property against DPPH with an IC50 of 76.03 µg/ml compared with standard ascorbic acid (IC50 of 74.66 µg/ml) and as such have been identified as a potential anticancer candidate.

Keywords: acylpyrazolone, free radical scavenging activities, tridentate ligand, x-ray crystallography

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Authors: S. Nqayi

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Understanding the structural, electronic, and magnetic properties of nanomaterials is essential for developing next-generation electronic and spintronic devices, contributing to the progress of nanoscience and nanotechnology applications. Multiferroic materials, with intimately coupled ferroic-order parameters, are widely considered to breed fascinating physical properties and provide unique opportunities for the development of next-generation devices, like multistate non-volatile memory. In this study, we are set to investigate the structural, electronic, and magnetic properties of the frustrated Feᴵᴵ/Smⱽᴵ sublattice in relation to the widely studied perovskites for spintronics applications. The atomic composition, microstructure, crystallography, magnetization, thermal, and dielectric properties of a pyrochlore Sm₂Fe₂O₇ system synthesized using sol-gel methods are currently being investigated. Precursor powders were dissolved in citric acid monohydrate to obtain a solution. The obtained solution was stirred and heated using a magnetic stirrer to obtain the gel phase. Then, the gel was dried at 200°C to remove water and organic compounds and form an orange powder. The X-ray diffraction analysis confirms that the structure crystallized as a pyrochlore structure with a tetragonal F4mm (107) symmetry. The presence of Fe³⁺/Fe⁴⁺ mixed states is also revealed by XPS analysis.

Keywords: nanostructures, multiferroic materials, pyrochlores, spintronics

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Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from x-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for x-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across x-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: biomacromolecular structure, coenzyme, electron density discrepancy analysis, x-ray crystallography

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Authors: Karthika Chandran, Pulkit Prakash, Amitabh Das, Santhosh P. N.

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Rare earth orthoferrites (RFeO₃) exhibit interesting and useful magnetic properties like multiferroicity, magnetodielectric coupling, spin reorientation (SR) and exchange bias. B site doped RFeO₃ are attracting attention due to the complex and tuneable magnetic transitions. In this work, 45% Mn-doped HoFeO₃ polycrystalline sample (HoFe₀.₅₅Mn₀.₄₅O₃) was synthesized by a solid-state reaction method. The magnetic structure and transitions were studied by magnetization measurements and neutron powder diffraction methods. The neutron diffraction patterns were taken at 13 different temperatures from 7°K to 300°K (7°K and 25°K to 300°K in 25°K intervals). The Rietveld refinement was carried out by using a FULLPROF suite. The magnetic space groups and the irreducible representations were obtained by SARAh module. The room temperature neutron diffraction refinement results indicate that the sample crystallizes in an orthorhombic perovskite structure with Pnma space group with lattice parameters a = 5.6626(3) Ǻ, b = 7.5241(3) Ǻ and c = 5.2704(2) Ǻ. The temperature dependent magnetization (M-T) studies indicate the presence of two magnetic transitions in the system ( TN Fe/Mn~330°K and TSR Fe/Mn ~290°K). The inverse susceptibility vs. temperature curve shows a linear behavior above 330°K. The Curie-Weiss fit in this region gives negative Curie constant (-34.9°K) indicating the antiferromagnetic nature of the transition. The neutron diffraction refinement results indicate the presence of mixed magnetic phases Γ₄(AₓFᵧG

Keywords: neutron powder diffraction, rare earth orthoferrites, Rietveld analysis, spin reorientation

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Authors: Shahriar Ghammamy, Mehrnoosh Saboony

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Purpose: To evaluate the spectral specification (IR-XRD and SEM) of nano-ciprofloxacin that prepared by up-down method (satellite mill). Methods: the ciprofloxacin was minimized to nano-scale with satellite mill and its characterization evaluated by Infrared spectroscopy, XRD diffraction and semi electron microscope (SEM). Expectation enhances the antibacterial property of nano-ciprofloxacin in comparison to ciprofloxacin. IR spectrum of nano-ciprofloxacin compared with spectrum of ciprofloxacin, and both of them were almost agreement with a difference: the peaks in spectrum of nano-ciprofloxacin were sharper than peaks in spectrum of ciprofloxacin. X-Ray powder diffraction analysis of nano-ciprofloxacin shows the diameter of particles equal to 90.9nm. (on the basis of Scherer Equation). SEM image shows the global shape for nano-ciprofloxacin.

Keywords: antibiotic, ciprofloxacin, nano, IR, XRD, SEM

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Authors: Shahriar Ghammamy, Mehrnoosh Saboony

Abstract:

Purpose: to evaluate the spectral specification(IR-XRD and SEM) of nano ciprofloxacin that prepared by up-down method (satellite mill). Methods: the ciprofloxacin was minimized to nano-scale with satellite mill and it,s characterization evaluated by Infrared spectroscopy, XRD diffraction and semi electron microscope (SEM). Expectation: to enhance the antibacterial property of nano ciprofloxacin in comparison to ciprofloxacin.IR spectrum of nano ciprofloxacin compared with spectrum of ciprofloxacin, and both of them were almost agreement with a difference: the peaks in spectrum of nano ciprofloxacin was sharper than peaks in spectrum of ciprofloxacin. X-Ray powder diffraction analysis of nano ciprofloxacin showes the diameter of particles equal to 90.9 nm (on the basis of scherrer equation). SEM image showes the global shape for nano ciprofloxacin.

Keywords: antibiotic, ciprofloxacin, nano, IR, XRD, SEM

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Authors: Jaroslav Fiala, Jaroslav Kaiser, Pavel Zlabek, Vaclav Mentl

Abstract:

The X-ray diffraction technique was recognized as a useful tool for the assessment of material degradation degree after a long-time service. In many industrial applications materials are subjected to degradation of mechanical properties as a result of real service conditions. The assessment of the remnant lifetime of components and structures is commonly based on correlated procedures including numerous destructive, non-destructive and mathematical techniques that should guarantee reasonable precise assessment of the current damage extent of materials in question and the remnant lifetime assessment. This paper summarizes results of an experimental programme concentrated on mechanical properties degradation of welded components. Steel an Al-alloy test specimens of base metal, containing welds and simple weldments were fatigue loaded at room temperature to obtain Woehler S-N curve. X-ray diffraction technique was applied to assess the degradation degree of material as a result of cyclic loading.

Keywords: fatigue loading, material degradation, steels, AL-alloys, X-ray diffraction

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Authors: G. Farkas, K. Mathis, J. Pilch, P. Minarik

Abstract:

Deformation mechanisms in an Mg-Al-Ca alloy reinforced with short alumina fibres were studied by acoustic emission and in-situ neutron diffraction method. The fibres plane orientation with respect to the loading axis was found to be a key parameter, which influences the acting deformation processes, such as twinning or dislocation slip. In-situ neutron diffraction tests were measured at different temperatures from room temperature (RT) to 200°C. The measurement shows the lattice strain changes in the matrix and also in the reinforcement phase depending on macroscopic compressive deformation and stress. In case of parallel fibre plane orientation, the increment of compressive lattice strain is lower in the matrix and higher in the fibres in comparison to perpendicular fibre orientation. Furthermore, acoustic emission results indicate a larger twinning activity and more frequent fibre cracking in sample with perpendicular fibre plane orientation. Both types of mechanisms are more dominant at elevated temperatures.

Keywords: neutron diffraction, acoustic emission, magnesium based composite, deformation mechanisms

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Authors: Nompumelelo P. Mathebula, Roger A. Sheldon, Daniel P. Pienaar, Moira L. Bode

Abstract:

The preparation of enantiopure Morita-Baylis-Hillman (MBH) adducts remains a challenge in organic chemistry. MBH adducts are highly functionalised compounds which act as key intermediates in the preparation of compounds of medicinal importance. MBH adducts are prepared in racemic form by reacting various aldehydes and activated alkenes in the presence of DABCO. Enantiopure MBH adducts can be obtained by employing Enzymatic kinetic resolution (EKR). This technique has been successfully demonstrated in our group, amongst others, using lipases in either hydrolysis or transesterification reactions. As these methods only allow 50% of each enantiomer to be obtained, our interest grew in exploring other enzymatic methods for the synthesis of enantiopure MBH adducts where, theoretically, 100% of the desired enantiomer could be obtained.Dehydrogenase enzymes can be employed on prochiral substrates to obtain optically pure compounds by reducing carbon-carbon double bonds or carbonyl groups of ketones. Ketoreductases have been used historically to obtain enantiopure secondary alcohols on an industrial scale. Ketoreductases are NAD(P)H-dependent enzymes and thus require nicotinamide as a cofactor. This project focuses on employing ketoreductase enzymes to selectively reduce ketones derived from Morita-Baylis-Hillman (MBH) adducts in order to obtain these adducts in enantiopure form.Results obtained from this study will be reported. Good enantioselectivity was observed using a range of different ketoreductases, however, reactions were complicated by the formation of an unexpected by-product, which was characterised employing single crystal x-ray crystallography techniques. Methods to minimise by-product formation are currently being investigated.

Keywords: ketoreductase, morita-baylis-hillman, selective reduction, x-ray crystallography

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Authors: Omoruyi Gold Idemudia, Alexander P. Sadimenko

Abstract:

The synthesis of N-heterocycles with novel properties, having broad spectrum biological activities that may become alternative medicinal drugs, have been attracting a lot of research attention due to the emergence of medicinal drug’s limitations such as disease resistance and their toxicity effects among others. Acylpyrazolones have been employed as pharmaceuticals as well as analytical reagent and their application as coordination complexes with transition metal ions have been well established. By way of a condensation reaction with amines acylpyrazolone ketones form a more chelating and superior group of compounds known as azomethines. 4-propyl-3-methyl-1-phenyl-2-pyrazolin-5-one was reacted with phenylhydrazine to get a new phenylhydrazone which was further reacted with aqueous solutions of palladium and platinum salts, in an effort towards the discovery of transition metal based synthetic drugs. The compounds were characterized by means of analytical, spectroscopic, thermogravimetric analysis TGA, as well as x-ray crystallography. 4-propyl-3-methyl-1-phenyl-2-pyrazolin-5-one phenylhydrazone crystallizes in a triclinic crystal system with a P-1 (No. 2) space group based on x-ray crystallography. The bidentate ON ligand formed a square planar geometry on coordinating with metal ions based on FTIR, electronic and NMR spectra as well as magnetic moments. Reported compounds showed antibacterial activities against the nominated bacterial isolates using the disc diffusion technique at 20 mg/ml in triplicates. The metal complexes exhibited a better antibacterial activity with platinum complex having an MIC value of 0.63 mg/ml. Similarly, ligand and complexes also showed antioxidant scavenging properties against 2, 2-diphenyl-1-picrylhydrazyl DPPH radical at 0.5mg/ml relative to ascorbic acid (standard drug).

Keywords: acylpyrazolone, antibacterial studies, metal complexes, phenylhydrazone, spectroscopy

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Authors: Saja M. Nabat Al-Ajrash, Charles Browning, Rose Eckerle, Li Cao

Abstract:

Three preceramic polymer formulations for potential use in 3D printing technologies were investigated. The polymeric precursors include an allyl hydrido polycarbosilane (SMP-10), SMP-10/1,6-dexanediol diacrylate (HDDA) mixture, and polydimethylsiloxane (PDMS). The rheological property of the polymeric precursors, including the viscosity within a wide shear rate range was compared to determine the applicability in additive manufacturing technology. The structural properties of the polymeric solutions and their photocureability were investigated using Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC). Moreover, thermogravimetric analysis (TGA) and X-ray diffraction (XRD) were utilized to study polymeric to ceramic conversion for versatile precursors. The prepared precursor resin proved to have outstanding photo-curing properties and the ability to transform to the silicon carbide phase at temperatures as low as 850 °C. The obtained ceramic was fully dense with nearly linear shrinkage and a shiny, smooth surface after pyrolysis. Furthermore, after pyrolysis to 1350 °C and TGA analysis, PDMS polymer showed the highest onset decomposition temperature and the lowest retained weight (52 wt%), while SMP.10/HDDA showed the lowest onset temperature and ceramic yield (71.7 wt%). In terms of crystallography, the ceramic matrix composite appeared to have three coexisting phases, including silicon carbide, and silicon oxycarbide. The results are very promising to fabricate ceramic materials working at high temperatures with complex geometries.

Keywords: preceramic polymer, silicon carbide, photocuring, allyl hydrido polycarbosilane, SMP-10

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Authors: Hanan Alenezi

Abstract:

Membrane performance depends on the kind of solvent used in preparation. A membrane made by Polyetherimide (PEI) was evaluated for gas separation using X-Ray Diffraction (XRD), Scanning electron microscope (SEM), and Energy Dispersive X-Ray Spectroscopy (EDS). The purity and the thickness are detected to evaluate the membrane in order to optimize PEI membrane preparation.

Keywords: Energy Dispersive X-Ray Spectroscopy (EDS), Membrane, Polyetherimide PEI, Scanning electron microscope (SEM), Solvent, X-Ray Diffraction (XRD)

Procedia PDF Downloads 145