Zero-finder methods derived using Runge-Kutta techniques

In this paper some families of zero-finding iterative methods for nonlinear equations are presented. The key idea to derive them is to solve an initial value problem applying Runge-Kutta techniques. More explicitly, these methods are used to solve the problem that consists in a differential equation in what appears the inverse function of the one which zero will be computed and the condition given by the value attained by it at the initial approximation. Carrying out this procedure several families of different orders of local convergence are obtained. Furthermore, the efficiency of these families are computed and two new families using like-Newton’s methods that improve the most efficient one are also given.     

Aryl-O reductive elimination from reaction of well-defined aryl-Cu(III) species with phenolates: the importance of ligand reactivity

Well-defined aryl-Cu(III) species undergo rapid reductive elimination upon reaction with phenolates (PhO(-)), to form aryl-OPh cross-coupling products. Kinetic studies show that the reaction follows a different mechanistic pathway compared to the reaction with phenols. The pH active cyclized pincer-like ligand undergoes an initial amine deprotonation that triggers a faster reactivity at room temperature. A mechanistic proposal for the enhanced reactivity and the role of EPR-detected Cu(II) species will be discussed in detail.     

Carbon nanoparticles in lateral flow methods to detect genes encoding virulence factors of Shiga toxin-producing <Emphasis Type="Italic">Escherichia coli</Emphasis>

The use of carbon nanoparticles is shown for the detection and identification of different Shiga toxin-producing Escherichia coli virulence factors (vt1, vt2, eae and ehxA) and a 16S control (specific for E. coli) based on the use of lateral flow strips (nucleic acid lateral flow immunoassay, NALFIA). Prior to the detection with NALFIA, a rapid amplification method with tagged primers was applied. In the evaluation of the optimised NALFIA strips, no cross-reactivity was found for any of the antibodies used. The limit of detection was higher than for quantitative PCR (q-PCR), in most cases between 10⁴ and 10⁵ colony forming units/mL or 0.1–0.9 ng/μL DNA. NALFIA strips were applied to 48 isolates from cattle faeces, and results were compared to those achieved by q-PCR. E. coli virulence factors identified by NALFIA were in very good agreement with those observed in q-PCR, showing in most cases sensitivity and specificity values of 1.0 and an almost perfect agreement between both methods (kappa coefficient larger than 0.9). The results demonstrate that the screening method developed is reliable, cost-effective and user-friendly, and that the procedure is fast as the total time required is <1 h, which includes amplification.     

Nuclear shieldings with the SSB-D functional

The recently reported SSB-D functional [J. Chem. Phys. 2009, 131, 094103] is used to check the performance for obtaining nuclear magnetic resonance (NMR) shielding constants. Four different databases were studied, which contain a diversity of molecules and nuclear shielding constants. The SSB-D functional is compared with its "parent" functionals (PBE, OPBE), the KT2 functional that was designed specially for NMR applications and the coupled cluster CCSD(T) method. The best performance for the experimentally most-used elements ((1)H, (13)C) is obtained for the SSB-D and KT2 functionals.     

Experimental and theoretical study of N-hexylcytosine and N-hexylcytosinium nitrate: the crucial role of hydrophobic and anion–π interactions

We report the synthesis and X-ray characterization of N¹-hexylcytosine (1) and N¹-hexylcytosinium nitrate (2). N¹-hexylcytosine (1) does not follow the same behaviour previously described for N¹-hexylthymine and N¹-hexyluracil in the solid state. This different behavior has been analyzed by means of density functional theory (DFT) calculations including the latest available correction for dispersion (D3). In addition hydrophobic and anion–π noncovalent interactions play a key role in stabilizing the 3D architectures of the compounds, which have been energetically studied using theoretical calculations and compared with similar structures retrieved from the Cambridge Structural Database (CSD). The anion–π–anion binding mode observed for nitrate in compound 2 is also observed in several crystal structures involving cytosine ring coordinated to transition metals.     

The Mechanism of Stereospecific C?H Oxidation by Fe(Pytacn) Complexes: Bioinspired Non‐Heme Iron Catalysts Containing cis‐Labile Exchangeable Sites

A detailed mechanistic study of the hydroxylation of alkane C? H bonds using H₂O₂ by a family of mononuclear non heme iron catalysts with the formula [Fe^II(CF₃SO₃)₂(L)] is described, in which L is a tetradentate ligand containing a triazacyclononane tripod and a pyridine ring bearing different substituents at the α and γ positions, which tune the electronic or steric properties of the corresponding iron complexes. Two inequivalent cis‐labile exchangeable sites, occupied by triflate ions, complete the octahedral iron coordination sphere. The C? H hydroxylation mediated by this family of complexes takes place with retention of configuration. Oxygen atoms from water are incorporated into hydroxylated products and the extent of this incorporation depends in a systematic manner on the nature of the catalyst, and the substrate. Mechanistic probes and isotopic analyses, in combination with detailed density functional theory (DFT) calculations, provide strong evidence that C? H hydroxylation is performed by highly electrophilic [Fe^V(O)(OH)L] species through a concerted asynchronous mechanism, involving homolytic breakage of the C? H bond, followed by rebound of the hydroxyl ligand. The [Fe^V(O)(OH)L] species can exist in two tautomeric forms, differing in the position of oxo and hydroxide ligands. Isotopic‐labeling analysis shows that the relative reactivities of the two tautomeric forms are sensitively affected by the α substituent of the pyridine, and this reactivity behavior is rationalized by computational methods.     

Analysis of Chemical and Biological Features Yields Mechanistic Insights into Drug Side Effects

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Highlights? Biological and chemical traits are flagged in >1,000 drug side effects ? Mechanistic insights are gained for most of the phenotypes ? Chemical features can account for unspecific or intricate biological phenomena ? Blending chemistry and biology helps in anticipating adverse events     

Performance of 3D‐space‐based atoms‐in‐molecules methods for electronic delocalization aromaticity indices

Several definitions of an atom in a molecule (AIM) in three‐dimensional (3D) space, including both fuzzy and disjoint domains, are used to calculate electron sharing indices (ESI) and related electronic aromaticity measures, namely, I_ring and multicenter indices (MCI), for a wide set of cyclic planar aromatic and nonaromatic molecules of different ring size. The results obtained using the recent iterative Hirshfeld scheme are compared with those derived from the classical Hirshfeld method and from Bader's quantum theory of atoms in molecules. For bonded atoms, all methods yield ESI values in very good agreement, especially for C–C interactions. In the case of nonbonded interactions, there are relevant deviations, particularly between fuzzy and QTAIM schemes. These discrepancies directly translate into significant differences in the values and the trends of the aromaticity indices. In particular, the chemically expected trends are more consistently found when using disjoint domains. Careful examination of the underlying effects reveals the different reasons why the aromaticity indices investigated give the expected results for binary divisions of 3D space. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Routes of π-electron delocalization in 4-substituted-1,2-benzoquinones

The substituent effect in 4-substituted-1,2-benzoquinone is investigated by means of modeling using B3LYP hybrid functional in conjunction with the 6-311+G(d,p) basis set. The interrelation between different types of substituents, X = NO, NO(2), CN, CHO, H, Me, OMe, OH, NH(2), NHMe and N(Me)(2), and both CO groups has been characterized both qualitatively and then quantitatively by means of several measures of π-electron delocalization (HOMA, MCI, DI, FLU) based on structural and electronic properties of 4-substituted-1,2-benzoquinones chosen for analysis. Results of this analysis clearly show that only the meta-placed CO group is affected by substituents, whereas the para-placed CO group is rather insensitive to substitution. These observations may help to explain diversified chemical properties (including reactivity) of CO centers in o-benzoquinone derivatives. Among others, they may explain differences in proton-accepting properties of carbonyl O atoms, as it is shown for simple models in which carbonyl groups in o-benzoquinone act as proton acceptors in H-bonds of O···H-F type.