Determination of some trace metals with a new synthesized polymer resin by FAAS in various tea and herbal plants samples

In this work, a new polymer resin with a functional groups capable of holding trace metals has been synthesized. The structure of polymer resin has been examined by BET-N₂ method analyzer, IR spectrometer, scanning electron microscope (SEM) and elemental microanalyser. The synthesized polymer resin was used for the simultaneous separation and preconcentration of the trace metals from various tea and herbal plants samples. After extraction process, flame atomic absorption spectrometry (FAAS) was used to determine the trace metals. The analytical parameters and solid phase extraction (SPE) performance such as pH, sample volume, flow rates of sample, flow rates of eluent, concentration, volume and type of eluent and effect of interference ions, were investigated. The limits of detection (DL) of the SPE procedure for trace metals, were calculated to be (3s) in the range of 0.9?4.0 μg L^?1 (n = 21) and the factors of preconcentration (PF) were obtained at 200 for Cd, Co, Cu, Fe, Ni and Zn, and at 50 for Cr, Mn and Pb ions and the relative standard deviation (RSD) at ≤ 2% (n = 11).     

Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins

The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants.     

Ru(II) with chelating containing N4-type donor quadridentate Pd-oxime metal complexes: Syntheses, spectral characterization, thermal and catalytic properties

Five new metal complexes [Pd(LH)₂] (1), [Pd(L)₂Ru₂(bpy)₄](ClO₄)₂ (2), [Pd(L)₂Ru₂(phen)₄](ClO₄)₂ (3), [Pd(L)₂Ru₂(dafo)₄](ClO₄)₂ (4) and [Pd(L)₂Ru₂(dcbpy)₄](ClO₄)₂ (5), (where, L = ligand, bpy = 2,2′-bipyridine, phen = 1,10-phenantroline, dafo = 4,5-diazafluoren-9-one and dcbpy = 3,3′-dicarboxy-2,2′-bipyridine) have been isolated and characterized by UV-VIS, FT-IR, ¹H NMR, magnetic susceptibility measurements, elemental analysis, molar conductivity, X-ray powder techniques, thermal analyses and their morphology studied by SEM measurements. IR spectra show that the ligand acts in a tetradentate manner and coordinates N₄ donor groups of LH₂ to Pd^II ion. The disappereance of H-bonding (O−H···O) in the trinuclear Ru^II-Pd^II-Ru^II metal complexes, the Ru^II ion centered into the main oxime core by the coordination of the imino groups while the two Ru^II ions coordinate dianionic oxygen donors of the oxime groups and linked to the ligands of bpy, phen, dafo and dbpy. The X-powder results show that 1 metal complex is indicating crystalline nature, not amorphous nature. Whereas, the X-ray powder pattern of the ligand (LH₂) with 2, 3,4 and 5 exhibited only broad humps, indicating its amorphous nature. The catalytic activity of three different complexes were tested in the Suzuki coupling reaction. The 1, 4 and 5 metal complexes catalyse Suzuki coupling reaction between phenylboronic acid and arylbromides affording biphenyls. Also, the thermal results shown that the most stable complex is 1 compound while the less stable is 4 compound.     

Novel vic-dioxime ligands and their poly-metal complexes bearing 1,8-diamino-3,6-dioxaoctane: synthesis, characterization, spectroscopy and electrochemistry

Three novel vic-dioxime ligands containing the 1,8-diamino-3,6-dioxaoctane group, N,N′-(1,8-diamino-3,6-dioxaoctane)-p-tolylglyoxime (L¹SL¹H₄), N,N′-(1,8-diamino-3,6-dioxaoctane)-phenylglyoxime (L²SL²H₄), and N,N′-(1,8-diamino-3,6-dioxaoctane)-glyoxime (L³SL³H₄) have been prepared from 1,8-diamino-3,6-dioxaoctane with anti-p-tolylchloroglyoxime, anti-phenylchloroglyoxime or anti-monochloroglyoxime. Polynuclear complexes [M(L ^x SL ^x )] _n or [M(L ^x SL ^x )(H₂O)] _n (x = 1, 2 and 3), where M = Cu^II, Co^II, and Ni^II, have been obtained with 1:1 metal/ligand ratio. The Cu^II and Ni^II poly-metal complexes of these ligands are proposed to be square planar, while also the prepared Co^II complexes are proposed to be octahedral with two water molecules as axial ligands. The detection of H-bonding in the [Ni(L¹SL¹)] _n , [Ni(L²SL²)] _n and [M(L³SL³)(H₂O)] _n metal complexes by FT i.r. spectra revealed the square planar or octahedral [MN₄·H₂O)] _n coordination of poly-nuclear metal complexes. [MN₄] _n coordination of the [Ni(L¹SL¹)] _n and [Ni(L²SL²)] _n complexes were also determined by ¹H-n.m.r. spectroscopy. The ligands and poly-metal complexes were characterized by elemental analyses, FT-i.r., u.v.-vis., ¹H and ¹³C-n.m.r. spectra, magnetic susceptibility measurements, molar conductivity, cyclic voltammetry, and differential pulse voltammetric (DPV) techniques.     

Synthesis and EPR studies of porphyrazines with bulky substituents

Magnesium porphyrazinate substituted with eight 4-tert-butylphenylthio-groups on the peripheral positions has been synthesized by cyclotetramerization of 1,2-bis(4-tert-butylphenylthio)maleonitrile in the presence of magnesium butanolate. The metal-free derivative was obtained by its treatment with trifluoroacetic acid and further reaction of this product with copper(II) acetate, zinc(II) acetate and cobalt(II) acetate led to the metal porphyrazinates (M = Cu, Zn, Co). These new compounds have been characterized by elemental analysis, together with FT-IR, ¹H NMR, UV–Vis spectral data. By using EPR technique, room temperature paramagnetic properties of Cu(II) doped porphyrazine sample as powder and solution forms were measured. The first-derivative EPR signals taken from as powder and solution forms shows that the sample is axially symmetric. The trend g_∥ > g_⊥ > 2 indicates that the unpaired electron is located mainly in the _dx2-y2${\mathrm{d}}_{x^2-y^2}$ orbital (²B₁ as ground state).     

Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers

Determination of genetic stability of in vitro-grown plantlets is needed for safe and large-scale production of mature trees. In this study, genetic variation of long-term micropropagated mature pistachio developed through direct shoot bud regeneration using apical buds (protocol A) and in vitro-derived leaves (protocol B) was assessed via DNA-based molecular markers. Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) were employed, and the obtained PIC values from RAPD (0.226), ISSR (0.220), and AFLP (0.241) showed that micropropagation of pistachio for different periods of time resulted in “reasonable polymorphism” among donor plant and its 18 clones. Mantel’s test showed a consistence polymorphism level between marker systems based on similarity matrices. In conclusion, this is the first study on occurrence of genetic variability in long-term micropropagated mature pistachio plantlets. The obtained results clearly indicated that different marker approaches used in this study are reliable for assessing tissue culture-induced variations in long-term cultured pistachio plantlets.     

A multi-objective genetic algorithm for a bi-objective facility location problem with partial coverage

In this study, we present a bi-objective facility location model that considers both partial coverage and service to uncovered demands. Due to limited number of facilities to be opened, some of the demand nodes may not be within full or partial coverage distance of a facility. However, a demand node that is not within the coverage distance of a facility should get service from the nearest facility within the shortest possible time. In this model, it is assumed that demand nodes within the predefined distance of opened facilities are fully covered, and after that distance the coverage level decreases linearly. The objectives are defined as the maximization of full and partial coverage, and the minimization of the maximum distance between uncovered demand nodes and their nearest facilities. We develop a new multi-objective genetic algorithm (MOGA) called modified SPEA-II (mSPEA-II). In this method, the fitness function of SPEA-II is modified and the crowding distance of NSGA-II is used. The performance of mSPEA-II is tested on randomly generated problems of different sizes. The results are compared with the solutions of the most well-known MOGAs, NSGA-II and SPEA-II. Computational experiments show that mSPEA-II outperforms both NSGA-II and SPEA-II.     

Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein–ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate binders from nonbinders in virtual screening and to more accurately predict the ligand binding modes prior to the more computationally expensive FEP calculations of binding affinity.     

Synthesis of 2-(2,3,4-trimethoxyphenyl)-1-(substituted-phenyl)acrylonitriles: in vitro anticancer activity against MCF-7, PC-3 and A2780 cancer cell lines

A series of 2-(2,3,4-trimethoxyphenyl)-1-(substituted-phenyl)acrylonitrile (2–9) were designed and synthesized to develop new cancer drugs. The structures of synthesized compounds 2–9 were described by using melting point, mass (MALDI-TOF-MS), FT-IR, elemental analysis, ¹H, ¹³C, ¹³C-APT and 2D NMR spectroscopy. The in vitro anticancer activities of 2–9 against human breast cancer (MCF-7), human prostate cancer (PC-3) and human ovarian cancer cells (A2780) were investigated by [3-(4,5-dimethylthiazol)-2-yl]-2,5-diphenyl-2H-tetrazolium bromide] (MTT) assay method. Additionally, the LogIC₅₀ values of these compounds on A2780, MCF-7 and PC-3 cell lines were calculated by using inhibition % values by the GraphPad Prism 6 program on a computer. The results indicated that these compounds have high anticancer activity against MCF-7, PC-3 and A2780 cell lines (especially A2780 cell lines, p < 0.05).