Rumer's transformation,in biology,as the negation,in classical logic

In this article, we make a connection between the Rumer transformation, used in the study of the genetic code‐doublets, and the negation of classic logic. A unified classification is given, relying on two Klein's 4‐groups describing the symmetries of the 16 doublets of nitrogenous bases and those of the 16 binary connectives of classic logic, both groups being subgroups of a larger noncommutative group with eight elements we identify as the dihedral group D₄. Also, some connections with other works are briefly considered. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Ab initio and DFT modeling of stereoselective deamination of aziridines by nitrosyl chloride

The stereochemical course of the deamination of cis‐2,3‐dimethylaziridine by nitrosyl chloride was investigated at the QCISD/6‐31G(d) level. Calculations reveal that the reaction takes place in two steps. In the first step, the reactants form a pre‐reactive complex, followed by a spiro‐type bicyclic transition state, which on dissociative cycloelimination gives the N‐nitrosoaziridine intermediate. In the second step, this intermediate undergoes cycloreversion through a slightly asynchronous concerted transition state to form an alkene with the same stereochemistry, which is in total agreement with experiment. In the whole reaction, the denitrosation step is found to be rate‐determining. For comparison, geometry optimizations and energies were also obtained at the B3LYP/6‐31G(d) level. It was found that the B3LYP energy results differed significantly from the QCISD ones. To analyze the reason for this difference, B3LYP calculations were repeated by varying the contribution of exact exchange in the Becke functional. With respect to the QCISD results, it has been shown that the functional with 0% exact exchange yields the best activation barriers, whereas the functional with 30% exact exchange is the most suitable one to carry out the complexation and reaction energy calculations. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Interplay of Electronic Structure and Bulk Properties in 2D and 3D Ternary Carbonitrides from First Principles

The changes in electronic structure and hardness as inferred from the bulk modulus are investigated for model structures of ternary compounds XC₃N₃ (X = B, Al, P, As, Ga) within the framework of density functional theory (DFT). The optimisations of the proposed two‐ (2D) and three‐dimensional (3D) structures and the calculations of the bulk moduli are performed by a pseudo potential method. The electronic structures are calculated with the augmented sphere wave method (ASW). The obtained hardness for 2D BC₃N₃ system (B₀ ～ 220 GPa) points to a magnitude close to that of graphitic C₃N₄. For heavier X atoms it decreases rapidly. This is equally observed for the 3D systems examined in the β‐C₃N₄ structure for which B₀(β‐BC₃N₃) amounts to ～330 GPa. Within the magnitude of the well known hard material cubic BN, the BC₃N₃ phases can be predicted as candidates for ultra hard materials. The electronic effect induced by the chemical nature of the X substitutional was examined according to its position in the periodic table i.e. X_III or X_V. Both, band structures and the electron localisation function (ELF) were used for this analysis. The ELF plots show a decreasing covalency with heavier X‐atoms. Potential applications of the devised systems are proposed such as dopings with atoms (Li, rare gas) and molecules (N₂).     

Elucidation of the structures of 3-alkylthio-, 3-benzylthio-, 2-arylthio- and 2-heteroarylthio-N1-(1,3-dimethylbutyl)-N4-phenyl-1,4-phenylenediamines by one- and two-dimensional NMR spectroscopy

Nucleophilic addition of alkyl- and benzylthiols to benzoquinone diimine (1) gave the corresponding 3-alkylthio- or 3-benzylthio-1,4-phenylenediamines (2-5). However, addition of aryl- or heteroarylthiols to 1 formed 2-arylthio- or 2-heteroarylthio-1,4-phenylenediamines (6-14). The structures of 2-14, obtained in 55-91% yields, were confirmed in CDCl3 or DMSO-d6 solution using 1D (NOE difference, coupled 13C NMR spectra, APT and DEPT) and 2D NMR techniques [DQCOSY, NOESY, HETCOR and heteronuclear multiple bond coherence (HMBC)] that resulted in unambiguous proton and carbon NMR resonance assignments. The substituent-induced 13C NMR chemical shift differences were calculated in 2-14 relative to carbon atoms in the model compound N1-(1,3-dimethylbutyl)-N4-phenyl-1,4-phenylenediamine (DMBPPD) (15) (a reduced form of benzoquinone diimine).     

Different catalysis role of in‐loop and out‐of‐loop waters in assisting HNS/HSN proton transfer isomerizations: Bridging vs. surrounding effect

In this work, a density function theory (DFT) study is presented for the HNS/HSN isomerization assisted by 1–4 water molecules on the singlet state potential energy surface (PES). Two modes are considered to model the catalytic effect of these water molecules: (i) water molecule(s) participate directly in forming a proton transfer loop with HNS/HSN species, and (ii) water molecules are out of loop (referred to as out‐of‐loop waters) to assist the proton transfer. In the first mode, for the monohydration mechanism, the heat of reaction is 21.55 kcal · mol^?1 at the B3LYP/6‐311++G** level. The corresponding forward/backward barrier lowerings are obtained as 24.41/24.32 kcal · mol^?1 compared with the no‐water‐assisting isomerization barrier T (65.52/43.87 kcal · mol^?1). But when adding one water molecule on the HNS, there is another special proton‐transfer isomerization pathway with a transition state 10T′ in which the water is out of the proton transfer loop. The corresponding forward/backward barriers are 65.89/65.89 kcal · mol^?1. Clearly, this process is more difficult to follow than the R–T–P process. For the two‐water‐assisting mechanism, the heat of reaction is 19.61 kcal · mol^?1, and the forward/backward barriers are 32.27/12.66 kcal · mol^?1, decreased by 33.25/31.21 kcal · mol^?1 compared with T. For trihydration and tetrahydration, the forward/backward barriers decrease as 32.00/12.60 (30T) and 37.38/17.26 (40T) kcal · mol^?1, and the heat of reaction decreases by 19.39 and 19.23 kcal · mol^?1, compared with T, respectively. But, when four water molecules are involved in the reactant loop, the corresponding energy aspects increase compared with those of the trihydration. The forward/backward barriers are increased by 5.38 and 4.66 kcal · mol^?1 than the trihydration situation. In the second mode, the outer‐sphere water effect from the other water molecules directly H‐bonded to the loop is considered. When one to three water molecules attach to the looped water in one‐water in‐loop‐assisting proton transfer isomerization, their effects on the three energies are small, and the deviations are not more than 3 kcal · mol^?1 compared with the original monohydration‐assisting case. When adding one or two water molecules on the dihydration‐assisting mechanism, and increasing one water molecule on the trihydration, the corresponding energies also are not obviously changed. The results indicate that the forward/backward barriers for the three in‐loop water‐assisting case are the lowest, and the surrounding water molecules (out‐of‐loop) yield only a small effect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Cytotoxic Components from the Leaves of Schefflera Taiwaniana

The isolation and identification of eighteen components from the leaves of Schefflera taiwaniana are presented. Their structures were determined on the basis of spectral data as well as direct comparison with authentic samples. These compounds include two polyacetylenes, one carotenoid‐like, three sesquiterpenes, one diterpene, four triterpenes, two tocopherols, and five alkyl 4‐hydroxycinnamate mixtures. Among these, 4‐hydroxy‐trans‐cinnamic acid docosyl ester and 4‐hydroxy‐cis‐cinnamic acid tetracosyl ester are new compounds. Some of these components exhibit cytotoxic activity.     

Role of resonances in building cross sections: Comparison between the Mittag–Leffler and the T‐matrix Green function expansion approaches

Peaks in collision cross sections are often interpreted as resonances. The complex dilation method, as well as other methods relying on analytic continuation of the scattering formalism, can be used to clarify whether these structures are true resonances in the sense that they are poles of the S‐matrix and the associated Green function. The performance of the Mittag–Leffler expansion and T‐matrix Green function expansion methods are formally and computationally compared. The two methods are applied to two model potentials. Eigenenergies, s‐wave residues, and cross sections are computed with both methods. The resonance contributions to the cross sections are further analyzed by removing the residue contributions from the Mittag–Leffler and Green function expansion sums, respectively. It is suggested that the contribution of a resonance to a cross section should be defined through its S‐matrix residue. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

The Electrochemically Initiated Reaction of Sulfide with N,N‐Diethyl‐p‐phenylenediamine in Dimethylformamide. Part II: Implications for Sensing Strategies

The electrochemically initiated reaction of p‐phenylenediamines with sulfide in aqueous media is well documented. We now report the adaptation of this chemistry into nonaqueous media. This is critically appraised as a means of detecting sulfide. The electrochemically initiated reaction of N,N‐diethyl‐p‐phenylenediamine with sulfide is shown at both macro‐ and platinum microdisk electrodes with quantitative detection of sulfide produced by means of the enhanced currents observed upon its addition. The linear detection range for sulfide is dependent on the concentration of N,N‐diethyl‐p‐phenylenediamine present with a linear range from 28–3290 μM and a limit of detection of 22 μM achievable. This represents a large increase compared to that found previously in aqueous media and offers the prospect of more ready applications in high temperature systems.