Effect of morphology of thin DNA films on the electron stimulated desorption of anions

We present a comparison between the electron stimulated desorption (ESD) of anions from DNA samples prepared by lyophilization (an example of poorly organized or nonuniform films) and molecular self-assembly (well-ordered films). The lyophilization (or freeze- drying) method is perhaps the most frequently employed technique for forming DNA films for studies of low-energy electron (LEE) interactions leading to DNA damage; however, this technique usually produces nonuniform films with considerable clustering which may affect DNA configuration and enhance sample charging when the film is irradiated. Our results confirm the general validity of ESD measurements obtained with lyophilized samples, but also reveal limitations of lyophilization for LEE studies on DNA films. Specifically we observe some modulation of structures, associated with dissociative electron attachment, in the anion yield functions from different types of DNA film, confirming that conformational factors play a role in the LEE induced damage to DNA.     

Two-grid finite element method for the dual-permeability-Stokes fluid flow model

In this paper, two-grid finite element method for the steady dual-permeability-Stokes fluid flow model is proposed and analyzed. Dual-permeability-Stokes interface system has vast applications in many areas such as hydrocarbon recovery process, especially in hydraulically fractured tight/shale oil/gas reservoirs. Two-grid method is popular and convenient to solve a large multiphysics interface system by decoupling the coupled problem into several subproblems. Herein, the two-grid approach is used to reduce the coding task substantially, which provides computational flexibility without losing the approximate accuracy. Firstly, we solve a global problem through standard P_k ? P_k??1 ? P_k ? P_k finite elements on the coarse grid. After that, a coarse grid solution is applied for the decoupling between the interface terms and the mass exchange terms to solve three independent subproblems on the fine grid. The three independent parallel subproblems are the Stokes equations, the microfracture equations, and the matrix equations, respectively. Four numerical tests are presented to validate the numerical methods and illustrate the features of the dual-permeability-Stokes model.

     

Modeling and optimization of simultaneous degradation of rhodamine B and acid red 14 binary solution by homogeneous Fenton reaction: a chemometrics approach

This study aimed to propose a mathematical method to investigate and optimize the simultaneous elimination process of multiple organic pollutants using the Fenton process. Hence, the treatment of rhodamine B (RB) and acid red 14 (AR14) dyes in their binary solution was studied. Multivariate curve resolution alternating least square (MCR-ALS), a novel chemometric method, was applied along with correlation constraints to resolute the UV-Vis spectrophotometric data, enabling quantification of investigated dyes despite a high spectral overlapping. Response surface methodology was adopted to assess the model and optimize individual and interactive effects of three independent factors (Fe²⁺, H₂O₂ and initial pH) on the simultaneous elimination of RB and AR14. The values of the regression coefficient for RB and AR14 were determined as 98.48 and 98.67 percent, respectively, revealing the reliability of the obtained polynomial models to predict decolorization efficiencies. Desirability function was employed to optimize the independent variables to attain the highest possible degradation performance for both dyes in their binary solution. At the optimum point of operation ([Fe²⁺] = 143.88 mg/L, [H₂O₂] = 126.89 mg/L and pH = 3.71), degradation efficiencies of RB and AR14 were found as 81.58% and 80.22%, respectively, which were nearly identical to the experimental results.     

Conformational and structural study of N-nicotinyl N′, N″-bis(diisobutyl amine)phosphoric triamide

Single crystals of C5H4NC(O)NHP(O)[N(i-C4H9)2]2 were prepared and investigated by X-ray crystallography. Interestingly, four symmetrically independent conformers were detected in the structure of this compound by X-ray crystallography. The greatest difference in these conformers was different torsion angles. In all conformers, the phosphoryl and carbonyl groups showed anti-configurations, and the two terminal CH3 groups of each alkyl chain in amine parts have different spatial orientations due to their connection to a prochiral carbon atom. The diastereotopic protons of every CH2 moiety in amine groups also have different spatial orientations. Every conformer forms a centrosymmetric dimer with its own symmetrically generated analog via a hydrogen bond. The first conformer connects to others (A, B, and C) via electrostatic interactions and forms a tetramer. All hydrogen bonds and electrostatic interactions result in the formation of a three-dimensional polymeric network in the crystalline lattice of compound. To find the most stable conformer, density functional theory (DFT) calculations were performed. The computationally optimized geometric parameters are in good agreement with the experimental results. According to DFT calculations, B is the most stable conformer with energy of ?987714.07 kcal/mol. In all conformers the electron density of HOMO is localized on P=O and C=O oxygen atoms and some parts of amine groups, while LUMO is localized on the nicotinamide part of the molecule.     

Efficient one-pot synthesis of novel 6′,9′-dihydro-2H,7′H-spiro[pyrimidine-5,8′-[1,3]dioxolo[4,5-f]quinoline]-2,4,6(1H,3H)-trione derivatives under mild and “green” reaction conditions

In this paper, an efficient method is introduced for the synthesis of 7′,9′-disubstituted 6′,9′-dihydro-2H,7′H-spiro[pyrimidine-5,8′-[1,3]dioxolo[4,5-f]quinoline]-2,4,6(1H,3H)-trione derivatives under mild and “green” reaction conditions. The method is based on one-pot multicomponent reaction of an aldehyde, barbituric acid, and benzo[d][1,3]dioxol-5-amine in ethanol as a green and environmentally friendly solvent. The reaction has given the products in the highest isolated yield in the presence of acetic acid as catalyst under reflux conditions. Various aldehydes, bearing electron-donating or -withdrawing functionalities have been used under the optimized conditions and successfully gave the desired products (13 examples) in high isolated yields.     

Spectroscopic studies of dactinomycin and vinorelbine binding to deoxyribonucleic acid and chromatin

Dactinomycin and vinorelbine are anticancer drugs, widely used as chemotherapeutic agents for the treatment of various cancers. This study represents an attempt to compare the effect of these drugs on DNA and soluble chromatin employing UV/vis, fluorescence and circular dichroism spectroscopy techniques. The results demonstrated that the absorbance at 260 and 210 nm was decreased and quenching of drugs with DNA and chromatin chromospheres induced reduction of fluorescence emission intensity. Circular dichroism profiles showed that the binding of drugs induced structural changes in both positive and negative extremes of DNA and chromatin revealing release or displacement of histone proteins from chromatin upon dactinomycin binding whereas vinorelbine preceded the chromatin into compaction. The results suggest that dactinomycin shows higher affinity to DNA compared to chromatin, whereas, vinorelbine recognizes the chromatin structure with higher affinity than free DNA. Also chromatin proteins play a fundamental role in drug-chromatin complex process.     

A Simple,Mild and Efficient One‐Pot Synthesis of 2‐Substituted Benzimidazoles in the Presence of H2O2/HCl under Microwave Irradiation

A simple, fast and efficient method for the preparation of several 2‐substituted benzimidazole derivatives is reported. Compounds were synthesized through a rapid one‐pot synthesis via microwave irradiation, starting from aldehydes and o‐phenylenediamine, in the presence of H₂O₂/HCl system in acetonitrile. The significant features of this method are short reaction times, high yields, easy and quick isolation of the products.     

Synthesis of 1,5‐Disubstituted 1H‐Tetrazole Derivatives via a Three‐Component Reaction of Carbodiimides,Isocyanides, and Trimethylsilyl Azide

The three‐component reaction of isocyanides 1 , carbodiimides 2 , and trimethylsilyl azide ( 3 ) occurs at room temperature, and the produced 1,5‐disubstituted 1H‐tetrazole derivatives 4 are formed in 81–98% yields (Scheme 1, Table). The reaction proceeds smoothly and cleanly under mild conditions, and no side reactions are observed.     

Landscape analysis and efficient metaheuristics for solving the n-queens problem

The n-queens problem is a classical combinatorial optimization problem which has been proved to be NP-hard. The goal is to place n non-attacking queens on an n×n chessboard. In this paper, two single-solution-based (Local Search (LS) and Tuned Simulated Annealing (SA)) and two population-based metaheuristics (two versions of Scatter Search (SS)) are presented for solving the problem. Since parameters of heuristic and metaheuristic algorithms have great influence on their performance, a TOPSIS-Taguchi based parameter tuning method is proposed, which not only considers the number of fitness function evaluations, but also aims to minimize the runtime of the presented metaheuristics. The performance of the suggested approaches was investigated through computational analyses, which showed that the Local Search method outperformed the other two algorithms in terms of average runtimes and average number of fitness function evaluations. The LS was also compared to the Cooperative PSO (CPSO) and SA algorithms, which are currently the best algorithms in the literature for finding the first solution to the n-queens problem, and the results showed that the average fitness function evaluation of the LS is approximately 21 and 8 times less than that of SA and CPSO, respectively. Also, a fitness analysis of landscape for the n-queens problem was conducted which indicated that the distribution of local optima is uniformly random and scattered over the search space. The landscape is rugged and there is no significant correlation between fitness and distance of solutions, and so a local search heuristic can search a rugged plain landscape effectively and find a solution quickly. As a result, it was statistically and analytically proved that single-solution-based metaheuristics outperform population-based metaheuristics in finding the first solution of the n-queens problem.     

The intersection problem for 2-(v,5,1) directed block designs

The intersection problem for a pair of 2-$(v,3,1)$ directed designs and 2-$(v,4,1)$ directed designs is solved by Fu in 1983 and by Mahmoodian and Soltankhah in 1996, respectively. In this paper we determine the intersection problem for 2-$(v,5,1)$ directed designs.