The experimental and theoretical QM/MM study of interaction of chloridazon herbicide with ds-DNA

We report a multispectroscopic, voltammetric and theoretical hybrid of QM/MM study of the interaction between double-stranded DNA containing both adenine-thymine and guanine-cytosine alternating sequences and chloridazon (CHL) herbicide. The electrochemical behavior of CHL was studied by cyclic voltammetry on HMDE, and the interaction of ds-DNA with CHL was investigated by both cathodic differential pulse voltammetry (CDPV) at a hanging mercury drop electrode (HMDE) and anodic differential pulse voltammetry (ADPV) at a glassy carbon electrode (GCE). The constant bonding of CHL-DNA complex that was obtained by UV/vis, CDPV and ADPV was 2.1×10(4), 5.1×10(4) and 2.6×10(4), respectively. The competition fluorescence studies revealed that the CHL quenches the fluorescence of DNA-ethidium bromide complex significantly and the apparent Stern-Volmer quenching constant has been estimated to be 1.71×10(4). Thermal denaturation study of DNA with CHL revealed the ΔTm of 8.0±0.2°C. Thermodynamic parameters, i.e., enthalpy (ΔH), entropy (ΔS°), and Gibbs free energy (ΔG) were 98.45 kJ mol(-1), 406.3 J mol(-1) and -22.627 kJ mol(-1), respectively. The ONIOM, based on the hybridization of QM/MM (DFT, 6.31++G(d,p)/UFF) methodology, was also performed using Gaussian 2003 package. The results revealed that the interaction is base sequence dependent, and the CHL has more interaction with ds-DNA via the GC base sequence. The results revealed that CHL may have an interaction with ds-DNA via the intercalation mode.     

Green synthesis and biological activity investigation of new derivatives of spiroisatins

In this research, the synthesis of novel derivatives of spiroisatins in high yields was investigated. These new compounds were synthesized using a multicomponent reaction (MCR) of isatin, malononitrile, acetophenone derivatives, diethyl oxalate, primary amines, and Et₃N in aqueous media. Under similar conditions, spiropyrroloisatins were prepared using MCRs of synthesized spiroistins. The antioxidant activity of newly synthesized spiroisatins is due to having an NH group which was evaluated by two procedures. Also, the antimicrobial activity of newly generated spiroisatins was evaluated by a disk distribution process utilizing two kinds of Gram-negative bacteria and Gram-positive bacteria and bacterial growth was stopped using these compounds. The advantages of this method are short reaction times, high yields of products, and the easy separation of catalyst and product using simple procedures.     

DFT, NBO, and NRT analysis of alkyl and benzyl β-silyl substituted cations: carbenium ion vs. silylium ion

The effect of β-trimethylsilyl (TMS) substituent on the structure, stability, natural charges, electrostatic potential map, natural bond orders, rotational energy barrier, and hyperconjugative interactions of five acyclic β-silyl carbocation derivatives of RR′C⁺–CH₂Si(Me)₃ including α-dimethyl 1 (R,R′ = Me), α-methyl phenyl 2 (R = Me, R′ = Ph), α-methyl para-aminophenyl 3 (R = Me, R′ = p-NH₂Ph), α-methyl para-nitrophenyl 4 (R = Me, R′ = p-NO₂Ph) and diphenyl 5 (R,R′ = Ph) was investigated in the gas phase and in solution using polarized continuum model (PCM) at B3LYP/6-311 ++G** level of theory. The resonance structures weighting of cations 1–5 were determined using natural resonance theory (NRT). The contribution of carbenium ion (RR′C⁺–CH₂Si(Me)₃) and silylium ion (RR′C=CH₂ Si(Me) ₃ ⁺ ) to the stability depend upon substituents. The former form dominants when R,R′ = Ph, but the latter is major the contributor when R,R′ = Me. The weighting of carbocation forms of β-silyl benzyl cation overwhelms silylium cation due to the delocalization of positive charge on the phenyl ring. The calculated molecular orbital (MO) diagrams, energy decomposition analysis (EDA) and ²⁹Si and ¹³C nuclear magnetic resonance (NMR) chemical shifts complement these predictions.     

Adsorption and diffusion of Xenon in a granulated nano-NaY zeolite

Henry??s law constant and crystal diffusivity of xenon in the granulated nano-NaY zeolite were measured by the pulse gas chromatography method. For this purpose the moments of response peaks of xenon were analyzed. The effect of extra column parts of the utilized chromatographic system was also considered by analyzing the moments of the response peak which was obtained by pulse injection of inert gas of helium into the carrier gas of nitrogen. In addition, the measurement of average velocity of the carrier gas regarding the pressure drop in the extra column parts of the system attributed to precise results. By carrying out the experiments at various temperatures in the range of 30?C110?°C the heat of adsorption and activation energy of crystal diffusivity were estimated. In order to find the binder effect on the adsorption of and diffusion into granules, the aforementioned parameters were also measured for the binderless granules of macron sized NaY zeolite. Results revealed that although the adsorption of xenon on the binder of bentonite was negligible, the diffusion resistance created by this binder was significant such that the effective crystal diffusivity in the granules with 25?% binder was determined to be 96 percent lower than the granules with no binder.     

Co-adsorption of CO molecules at the open ends of MgO nanotubes

Equilibrium geometries, stabilities, and electronic properties of the adsorption of a CO molecule along with two or three CO co-adsorptions at the open ends of MgO nanotubes have been investigated through density functional calculations. It was found that the interaction of CO molecule with ends of the tube is much stronger than that of with its exterior surface. It was also found that adsorption of the second CO molecule at the end of the tube is independent of the first adsorbed CO molecule, while the prior adsorption process impacts the third adsorption. This phenomenon was described based on the frontier molecular orbital analysis, showing that the third CO molecule has to interact with high energetic unoccupied orbitals instead of the LUMO. Furthermore, it was revealed that similar to CO adsorption on the exterior surface of the tube, the adsorption at its open ends is electronically harmless.     

Synthesis and application of glutaric dihydrazide modified multiwalled carbon nanotubes for selective solid-phase extraction and preconcentration of Cu(II), Zn(II), Ni(II), and Fe(III)

An SPE method for selective separation-preconcentration of Cu(ll), Zn(II), Ni(II), and Fe(III) on multiwalled carbon nanotubes (MWCNTs) modified by glutaric dihydrazide prior to flame atomic absorption spectrometric determination was investigated. The adsorption was achieved quantitatively on MWCNTs at pH 5.0, and then the retained metal ions on the adsorbent were eluted with 1 M HNO3. The effects of analytical parameters including pH of the solution, eluent type, sample volume, and matrix ions were investigated for optimization of the presented procedure. The adsorption capacity of the adsorbent at optimum conditions was found to be 33.6, 29.2, 22.1, and 36.0 mg/g for Cu(ll), Zn(ll), Ni(ll), and Fe(lll), respectively. The LOD values of the method were 0.21, 0.11, 0.24, and 0.27 microg/L for Cu(ll), Zn(ll), Ni(ll), and Fe(lll), respectively. The RSDs were lower than 3.01%. The method was applied for the determination of analytes in soil, river water, and wastewater samples with satisfactory results.     

Parameterization of 241Am and 230Th alpha particle energy in dependence on distance traveled in air

A new method is introduced in this paper for calculating alpha particle energy versus traveled distance (APETD) in air as emitted from ²⁴¹Am and ²³⁰Th sources as well as the alpha range versus its energy and its energy versus distance. This method is to derive the stated relevant equations and in particular to speed up the calculation of E(x) by a Monte-Carlo simulation. By a fitting procedure, an analytical formula E(x) was determined in terms of a series of powers of distance x. Then a randomly sampled x can be quickly transformed into a corresponding energy E. The APETD calculations were run on a Microsoft Windows 7 32?bit operating system with a maximum usable memory of 3?GB. The results of calculations for alphas of the above two radionuclides in air compared to those of others using a different method are in good agreement. The above stated equations as derived in this paper are presented and the process time for applying the new method has been greatly improved.     

Theoretical study of the effects of substitution,solvation, and structure on the interaction between nitriles and methanol

We report an investigation on intermolecular interactions in R? CN ··· H? OCH₃ (R = H, CH₃, F, Cl, NO₂, OH, SH, SCH₃, CHO, COCH₃, CH₂Cl, CH₂F, CH₂OH, CH₂COOH, CF₃, SCOCH₃, SCF₃, OCHF₂, CH₂CF₃, CH₂OCH₃, and CH₂CH₂OH) complexes using density functional theory. The calculations were conducted on B3LYP/6‐311++G** level of theory for optimization of geometries of complexes and monomers. An improper hydrogen bonding (HB) in the H₃CO? H ··· NC? R complexes was observed in that N atom of the nitriles functions acts as a proton acceptor. Furthermore, quantum theory of “Atoms in Molecules” (AIM) and natural bond orbital (NBO) method were applied to analyze H‐bond interactions in respective complexes. The electron density (ρ) and Laplacian (?²ρ) properties, estimated by atoms in molecules calculations, indicate that H ··· N bond possesses low ρ and positive ?²ρ values, which are in agreement with partially covalent character of the HBs, whereas O? H bonds have negative ?²ρ values. In addition, the weak intermolecular force due to dipole–dipole interaction (U) is also considered for analysis. The examination of HB in these complexes by quantum theory of NBO method fairly supports the ab initio results. Natural population analysis data, the electron density, and Laplacian properties, as well as, the ν(O? H) and γ(O? H) frequencies of complexes, calculated at the B3LYP/6‐311++G** level of theory, are used to evaluate the HB interactions. The calculated geometrical parameters and conformational analysis in water phase solution show that the H₃CO? H ··· NC? R complexes in water are more stable than that in gas phase. The obtained results demonstrated a strong influence of the R substituent on the properties of complexes. Numerous correlations between topological, geometrical, thermodynamic properties, and energetic parameters were also found. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Solvent‐free synthesis of 2H‐pyrans: One‐pot reactions of dithiocarbamates,alkyl propiolates,and isocyanides

A novel, convenient, and an efficient approach to the synthesis of 2H‐pyrans has been reported based on the multicomponent reaction. Solvent‐free condition for the reaction of dithiocarbamates, alkyl propiolates and isocyanides lead to the formation of 2H‐pyrans in good yields. In these reactions, synthesis of 2H‐pyrans is possible based on the one‐pot reaction and without using any catalyst. The mild reaction conditions and high yields of the products exhibit the good synthetic advantage of these methods. J. Heterocyclic Chem., lpar;2011).