Design of photoactivated DNA oxidizing agents: synthesis and study of photophysical properties and DNA interactions of novel viologen-linked acridines

A new series of photoactivated DNA oxidizing agents in which an acridine moiety is covalently linked to viologen by an alkylidene spacer was synthesized, and their photophysical properties and interactions with DNA, including DNA cleaving properties, were investigated. The fluorescence quantum yields of the viologen-linked acridines were found to be lower than that of the model compound 9-methylacridine (MA). The changes in free energy for the electron transfer reactions were found to be favorable, and the fluorescence quenching observed in these systems is explained by an electron transfer mechanism. Intramolecular electron transfer rate constants were calculated from the observed fluorescence quantum yields and singlet lifetime of MA and are in the range from 1.06x10(10) s(-1) for 1 a (n=1) to 6x10(8) s(-1) for 1 c (n=11), that is, the rate decreases with increasing spacer length. Nanosecond laser flash photolysis of these systems in aqueous solutions showed no transient absorption, but in the presence of guanosine or calf thymus DNA, transient absorption due to the reduced viologen radical cation was observed. Studies on DNA binding demonstrated that the viologen-linked acridines bind effectively to DNA in both intercalative and electrostatic modes. Results of PM2 DNA cleavage studies indicate that, on photoexcitation, these molecules induce DNA damage that is sensitive to formamidopyrimidine DNA glycosylase. These viologen-linked acridines are quite stable in aqueous solutions and oxidize DNA efficiently and hence can be useful as photoactivated DNA-cleaving agents which function purely by the co-sensitization mechanism.     

The Catalytic Oxidative Coupling of Methane

One of the great challenges in the field of heterogeneous catalysis is the conversion of methane to more useful chemicals and fuels. A chemical of particular importance is ethene, which can be obtained by the oxidative coupling of methane. In this reaction CH₄ is first oxidatively converted into C₂H₆, and then into C₂H₄. The fundamental aspects of the problem involve both a heterogeneous component, which includes the activation of CH₄ on a metal oxide surface, and a homogeneous gas-phase component, which includes free-radical chemistry. Ethane is produced mainly by the coupling of the surface-generated CH radicals in the gas phase. The yield of C₂H₄ and C₂H₆ is limited by secondary reactions of CH radicals with the surface and by the further oxidation of C₂H₄, both on the catalyst surface and in the gas phase. Currently, the best catalysts provide 20% CH₄ conversion with 80% combined C₂H₄ and C₂H₆ selectivity in a single pass through the reactor. Less is known about the nature of the active centers than about the reaction mechanism; however, reactive oxygen ions are apparently required for the activation of CH₄ on certain catalysts. There is spectroscopic evidence for surface O^? or O ions. In addition to the oxidative coupling of CH₄, cross-coupling reactions, such as between methane and toluene to produce styrene, have been investigated. Many of the same catalysts are effective, and the cross-coupling reaction also appears to involve surface-generated radicals. Although a technological process has not been developed, extensive research has resulted in a reasonable understanding of the elementary reactions that occur during the oxidative coupling of methane.     

Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

Electroreduction of some pyridine carboxamides on carbon electrodes in aqueous solutions

The electroreductions of the NAD⁺ model compounds nicotinamide (I), N₁-methyl nicotinamide (II), N′-methyl nicotinamide (III) and isonicotinamide (IV) on carbon electrodes have been studied in aqueous media in the pH range 0–12 by linear-sweep cyclic voltammetry (Scheme 1, I-IV). Logarithmic analyses of the reduction peaks were performed by computing the convolution of the current with time as a function of the potential. On the basis of the experimental results it was concluded that the irreversibility of the electron transfers increased when a glassy carbon electrode was used, and this irreversibility being more marked when a plastic formed carbon electrode was employed. The reduction processes occurred with more difficulty on carbon electrodes than on mercury electrodes. Both the reduction and the reoxidation (when occurred) processes changed with respect to those observed on mercury electrodes, being irreversible electron transfers the rate-determining steps in most cases. Thus, for compounds I, II and III at pH < 2 the reductions occurred by the uptake of two electrons and two H⁺ ions, and the rate determining step was found to be the first one-electron transfer, for I and III, and the irreversible second electron transfer, preceded by the uptake of an H+ ion, for II. At pH>3 the processes consisted of electrodimerization reactions, preceded by the protonation of the heterocyclic nitrogen in cases I and III. The second electron transfer of the electroreduction of IV always appeared irreversible, in contrast with that found for mercury electrodes.     

Thermal behaviour of the homopolynuclear glyoxylate complex combinations with Cu(II) and Cr(III)

Homopolynuclear complexes of Cu(II) respectively Cr(III) with the glyoxylate dianion, C₂H₂O₄ ^2-, have been studied in non-isothermal regime in air and nitrogen. The results of the non-isothermal analysis performed for the synthesised complexes, Cu(C₂H₂O₄)·0.5H₂O, respectively [Cr₂(OH)₂(C₂H₂O₄)₂(OH₂)₄]·2H₂O, correlated with the results of the IR and TG analysis of the compounds obtained by thermal treatment from the initial complexes and the results of the GLC and XR analysis have led to the establishment of the thermal decomposition mechanisms for the two studied complexes. The decomposition mechanisms confirm the stoichiometric and structural formulae proposed for the two synthesised homopolynuclear complexes. This revised version was published online in July 2006 with corrections to the Cover Date.     

Zirconium bis(indenyl) sandwich complexes with an unprecedented indenyl coordination mode and their role in the reactivity of the parent bent-metallocenes: a detailed DFT mechanistic study

The mechanisms of three closely related reactions were studied in detail by means of DFT/B3 LYP calculations with a VDZP basis set. Those reactions correspond to 1) the reductive elimination of methane from [Zr(eta5-Ind)2(CH3)(H)] (Ind=C9H7-, indenyl), 2) the formation of the THF adduct, [Zr(eta5-Ind)(eta6-Ind)(thf)] and 3) the interconversion between the two indenyl ligands in the Zr sandwich complex, [Zr(eta5-Ind)(eta9-Ind)], which forms the link between the two former reactions. An analysis of the electronic structure of this species indicates a saturated 18-electron complex. A full understanding of the indenyl interchange process required the characterisation of several isomers of the Zr-bis(indenyl) species, corresponding to different spin states (S=0 and S=1), different coordination modes of the two indenyl ligands (eta5/eta9, eta5/eta5 and eta6/eta9), and three conformations for each isomer (syn, anti, and gauche). The fluxionality observed was found to occur in a mechanism involving bis(eta5-Ind) intermediates, and the calculated activation energy (11-14 kcal mol(-1)) compares very well with the experimental values. Two alternative mechanisms were explored for the reductive elimination of methane from the methyl/hydride complex. In the more favourable one, the initial complex, [Zr(eta5-Ind)2(CH3)(H)], yields [Zr(eta5-Ind)2] and methane in one crucial step, followed by a smooth transition of the Zr intermediate to the more stable eta5/eta9-species. The overall activation energy calculated (Ea=29 kcal mol(-1)) compares well with experimental values for related species. The formation of the THF adduct follows a one step mechanism from the appropriate conformer of the [Zr(eta5-Ind)(eta9-Ind)] complex, producing easily (Ea=6.5 kcal mol(-1)) the known product, [Zr(eta5-Ind)(eta6-Ind)(thf)], a species previously characterised by X-ray crystallography. This complex was found to be trapped in a potential well that prevents it from evolving to the 3.4 kcal mol(-1) more stable isomer, [Zr(eta5-Ind)2(thf)], with both indenyl ligands in a eta5-coordination mode and a spin-triplet state (S=1).     

Damage spreading in a single-component irreversible reaction process: Dependence of the system's immunity on the Euclidean dimension

The spreading of a globally distributed damage, created in the stationary regime, is studied in a single-component irreversible reaction process, i.e., the BK model [Browne and Kleban,Phys. Rev. A 40, 1615 (1989)]. The BK model describes one variant of the A+AA₂ reaction process on a lattice in contact with a reservoir of A species. The BK model has a single parameter, namely the rate of arrival of A species to the lattice (Y). The model, exhibits an irreversible phase transition between a stationary reactive state with production of A₂ species and a poisoned state with the lattice fully covered by A species. The transition takes place at critical points (Y _C ) which solely depend on the Euclidean dimensiond. It is found that the system is immune ford=1 andd=2, in the sense that even 100% of initial damage is healed within a finite healing period (T _H ). Within the reactive regime,T _H diverges when approachingY _C according toT _H (Y _C –Y)^–, with 1.62 and 1.08 ford=1 andd=2, respectively. Ford=3 a frozen-chaotic transition is found close toY _s 0.4125, i.e., well inside the reactive regime 0YY _C 0.4985. Just atY _S the damageD(t) heals according toD(t) t ^–, with 0.71. For the frozen-chaotic transition atd=3 the order parameter critical exponent 0.997 is determined.     

The host-guest chemistry of resorcinarenes

Conformations, acid-base and supramolecular properties of phenolic metacyclophanes obtained from the condensation of resorcinol with aldehydes are discussed, including the mechanisms involved in the formation of these macrocycles. The strong binding of choline-type compounds and the inhibition of acetylcholine hydrolysis with therccc stereoisomers is mechanistically evaluated; arctt isomer shows strong conformational coupling for, e.g., choline binding and simultaneous proton release. The presence of larger alkyl residues at the bottom of therccc macrocycle leads to an additional binding site for small lipophilic substrates, which is independent of the upper complexation center for positively charged substrates. Substitution at the upper rim by carboxylic groups at the 2-position of the phenyl rings yields receptors for, e.g., , -diammonium ions with alternate equatorial and axial arylunits. Positively charged substituents at the upper rim, introduced by aminoalkylation, lead to little change of complexation as a result from their orientation away from the binding center. Aminoacid substituents, for the same reason, do not lead to enantioselective complexation, but allow particularly for strong binding of transition metal ions. Preliminary studies show that resorcinarenes bearing a wide array of positive charges are potent groove binders to ds-DNA without intercalative contributions.This paper is dedicated to the commemorative issue on the 50th anniversary of calixarenes.     

The role of radicals in metal-assisted oxygenation reactions

The oxo-functionalization of organic substrates with the aid of metal oxo moieties is of fundamental importance not only in nature but also in academic and industrial research. Nevertheless the corresponding reaction mechanisms remain among the most enigmatic in chemistry and few of them are understood in detail. Recent research efforts have resulted in significantly improved information: in the cases of many oxygenation reactions evidence has been provided for the occurrence radical intermediates, even though the high selectivity observed suggests to a different mechanism. Examples stem from various areas of chemistry and include processes involving molecular metal oxo complexes, gas-phase and matrix-isolated species, metalloenzymes, and solid-state oxide surfaces. This review treats this seemingly wide variety of systems with the aim of providing an overview of common reactivity patterns and principles, as well as open problems.     

Alternative paths in the ring opening of oxadiaziridine: The diimide N-oxide versus the oxodiimide rearrangement

The ring opening of the oxadiaziridine by cleavage of the N-N bond has been theoretically investigated by SCF calculations improved with limited CI. The possible competition of this reaction with the better known ones (N-O bond cleavage, inversion of the N atom) is discussed. The chemical implications of the formation of a new type of 1,3-dipole are examined.