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.     

Singlet exciplexes between a thioxanthone derivative and substituted aromatic quenchers: role of the resonance integral

Fluorescence quenching of a thioxanthone derivative by methyl- and methoxy-substituted benzenes (MeB and MeOB, respectively) is performed in solvents of different polarity. Emissive exciplexes are observed even in polar solvents and provide kinetic and spectroscopic data over a large scale of solvent polarity. These data were subsequently analyzed by use of a new theoretical model that leads to a thermodynamic relationship between exciplex and electron-transfer driving forces Delta G(exc) and Delta G(et), respectively. The remarkable agreement found between this model and both kinetic and spectroscopic data supports its validity. Moreover, the difference observed between MeB and MeOB compounds in quenching efficiency is analyzed by this model and provides the main parameters governing exciplex features, especially the resonance integral between locally excited and charge-transfer states.     

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).     

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.     

Kinetic-catalytic determination of osmium by fluorescence quenching with salicylfluorone and hydrogen peroxide

A highly sensitive and selective fluorescence-quenching kinetic method is proposed for the determination of trace osmium(IV), based on the catalytic effect of osmium(IV) on the salicylfluorone (_ex = 510 nm, _em = 535 nm)-H₂O₂ system at pH 9.3–9.6. Using the fixed time method, osmium(IV) in the range 0.008–0.6 ng/ml can be determined. The detection limit is 0.006 ng/ml. Over thirty anions and cations, including other platinum metal ions, do not interfere, even when present in large excess. The method has been applied successfully for the determination of osmium in a series of synthetic mixtures and refined ore with relative standard deviations of 2–6%.     

Distance-dependent fluorescence quenching ofN-acetyl-l-tryptophanamide by acrylamide

We examined the time-dependent intensity decays ofN-acetyl-l-tryptophanamide (NATA) when collisionally quenched by acrylamide in propylene glycol over a range of temperatures. The intensity decays of NATA became increasingly heterogeneous in the presence of acrylamide. The NATA intensity decays were not consistent with the Collins-Kimball radiation boundary condition (RBC) model for quenching. The steady-state Stern-Volmer plots show significant upward curvature, and quenching of NATA by acrylamide was observed even in vitrified propylene glycol, where translational diffusion cannot occur during the lifetime of the excited state. These frequencydomain and steady-state data indicate a through-space quenching interaction between NATA and acrylamide, and the results are consistent with a rate constant for quenching that depends exponentially on the fluorophore-quencher separation distance. The exponential distance-dependent rate of quenching also explains the upward curvature of the Stern-Volmer plot, and the steady-state data aid in determining the interaction distance between NATA and acrylamide. These results suggest that the distance-dependent quenching rates need to be considered in the interpretation of acrylamide quenching of proteins.     

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.