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.     

Bifurcations and transition states

Bifurcations of reaction channels are related to valley-ridge inflection points and it is examined what happens when these do not coincide with transition states. Under such conditions there result bifurcating regions. There exist a number of different prototypes for such regions which are discussed explicitly on the basis of the pertinent Taylor expansions. When bifurcations occur close enough to transition states then there result bifurcating transition regions. An example for a bifurcating transition region is exhibited which is obtained from a quantum mechanical ab initio calculation for the ring opening of cyclopropylidene to aliene. In general there exist no orthogonal trajectory patterns which could serve as simplified models for channel bifurcations.Operated for the U.S. Department of Energy by Iowa State University under Contract No. W-7405-ENG-82. This work was supported by the Office of Basic Energy Sciences     

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.     

动力学体系二维数据的秩分析及其应用

详细论证了动力学体系中存在的多种共线性情况,以及在此情况下二维数据阵的秩与独立反应数及组分数的关系.分析了通过增秩这一方式来判断体系组分数的条件.讨论了反应间存在物质交换对数据阵秩的影响.建立起一套通过秩分析判断未知动力学体系中存在的反应组分数、独立反应数以及可能反应机理的方法.将秩分析技术应用到聚苯胺与质子酸反应,初步分析了该体系存在的多种吸光性结构及结构变化.确定了[H＋]=0.01～0.1 mol•L－1范围内,聚苯胺与质子酸反应存在一个三结构两步互变过程.     

除草剂2-甲基-4-氯苯氧乙酸(MCPA)与OH自由基的气相化学反应

采用长光程气体池结合傅里叶变换红外光谱仪测得了除草剂2-甲基|4|氯苯氧乙酸(MCPA)与·OH自由基在23 ℃时的反应速率常数为2.67×10-11  cm3/(s*mol), 以此估算了在大气中·OH自由基浓度为 7×105  mol/cm3时, MCPA与·OH自由基反应导致的大气寿命为14.9 h. 结果表明, 在大气环境中MCPA较容易降解, 不会通过大气输送对环境造成广泛和持久性污染.      

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).     

Qualitative properties of pulsating fronts for reaction–advection–diffusion equations in periodic excitable media

In this paper, we study the pulsating fronts of reaction–advection-diffusion equations with two types of nonlinear term in periodic excitable media. Firstly, for the case with combustion nonlinearity, the unique front is proved to decay exponentially when it approaches the unstable limiting state. Secondly, for the degenerate monostable type nonlinearity, it is shown that the front with critical speed is unique, monotone and decays exponentially at negative end, while the fronts of noncritical speeds decay to zero non-exponentially.     

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.