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.     

Some Tris[(triorganophosphine)gold(I)]-oxonium and -Organoimonium Tetrafluoroborates with Bulky Substituents

Tris{[tri(2-methylphenyl)phosphine]gold(I)}-, tris{[tri(2,4,6-trimethylphenyl)phosphine]gold(I)}- and tris{[tri(cyclohexyl)phosphine]gold(I)}-oxonium tetra-fluoroborate ( 1?3 ) have been prepared from the corresponding (phosphine)gold(I) chlorides, silver oxide, and sodium tetrafluoroborate in acetone. These oxonium salts are excellent aurating agents for primary amines. Thus in the reaction with 1, t -butylamine ^tBuNH₂ and aniline PhNH₂ are readily converted into the tri nuclear imino complexes {[(2-MeC₆H₄)₃P]Au}₃N^tBu⁺BF₄^? ( 4 ) and {[(2-MeC₆H₄)₃P]Au}₃NPh⁺BF ( 5 ) in high yields. With 3 , both aniline and 8-amino-quinoline also give the tri nuclear complexes, i.e. {[(c-C₆H₁₁)₃P]Au}₃ NPh⁺BF ( 6 ) and {[(c-C₆H₁₁)₃P]Au}₃N(C₉H₆N)⁺BF ( 7 ). Auration of aniline with the most sterically hindered reagent 2 yields only the bi nuclear complex {[2,4,6-Me₃C₆H₂)₃P] · Au}₂N(Ph)H⁺BF ( 8 ). The reagents 1?3 and the Products 4 – 8 have been characterized by analytical and NMR spectroscopic data, and the crystal structures of compounds 4 and 6 have been determined by single crystal x-ray diffraction. In the cations of 4 , a triangle of gold atoms with short Au — Au contacts [3.036(1), 3.107(1), and 3.214(1) Å] forms a steep pyramid with the nitrogen atom, in which the angles Au? N? Au are all much smaller than the tetrahedral standard of 109.7°: 94.8(4), 98.1(4), and 103.0(4)°. This triangular Au₃ unit is staggered relative to the three methyl groups of the ^tBu substituent at nitrogen. The results for 6 are similar [Au — Au: 3.037(1), 3.071(1), and 3.222(1) Å; Au? N? Au: 95.3(3), 96.5(3), and 103.6(3)°]. Variable temperature NMR studies of compounds 3 and 8 show hindered rotation of the mesityl groups about the P? C bonds of the ligands originating from the steric congestion within each tertiary phosphine.     

Antimalarial activity of n(6)-substituted adenosine derivatives (part 2)

We have investigated the in vitro antimalarial activity of a new series of adenosine derivatives. The results show that N(6)-(1-naphthylmethyl)-5'-deoxy-5'-(amido)adenosines as well as N(6)-(4-phenylbenzyl)-5'-deoxy-5'-(amido)adenosines display significant activity against the malaria-causing parasites, with the sterically demanding bisubstituted species reported being active in most cases in the low-micromolar range. The novel compounds with unusual substitution pattern were obtained applying an efficient convergent polymer-assisted solution-phase (cPASP) synthesis protocol. Thus, we were able to prepare a series of substituted derivatives in parallel that would have been difficult to synthesize by standard techniques. The scope and limitations of the synthetic methodology are discussed.     

Parallelization of three-center electron repulsion integrals

The parallelization of the three-center electron repulsion integrals arising from the variational fitting of the Coulomb potential is presented. A scheme for dynamical load balancing of the corresponding loop structure is discussed. The implementation in the density functional theory program deMon using the message passing interface is described. The efficiency of the parallelization is analyzed by selected benchmark calculations     

Evaluation of Hofmeister effects on the kinetic stability of proteins

Dissolved salts are known to affect properties of proteins in solution including solubility and melting temperature, and the effects of dissolved salts can be ranked qualitatively by the Hofmeister series. We seek a quantitative model to predict the effects of salts in the Hofmeister series on the deactivation kinetics of enzymes. Such a model would allow for a better prediction of useful biocatalyst lifetimes or an improved estimation of protein-based pharmaceutical shelf life. Here we consider a number of salt properties that are proposed indicators of Hofmeister effects in the literature as a means for predicting salt effects on the deactivation of horse liver alcohol dehydrogenase (HL-ADH), alpha-chymotrypsin, and monomeric red fluorescent protein (mRFP). We find that surface tension increments are not accurate predictors of salt effects but find a common trend between observed deactivation constants and B-viscosity coefficients of the Jones-Dole equation, which are indicative of ion hydration. This trend suggests that deactivation constants (log k(d,obs)) vary linearly with chaotropic B-viscosity coefficients but are relatively unchanged in kosmotropic solutions. The invariance with kosmotropic B-viscosity coefficients suggests the existence of a minimum deactivation constant for proteins. Differential scanning calorimetry is used to measure protein melting temperatures and thermodynamic parameters, which are used to calculate the intrinsic irreversible deactivation constant. We find that either the protein unfolding rate or the rate of intrinsic irreversible deactivation can control the observed deactivation rates.     

In-depth analysis of glass fibers

Two types of commercial glass fibers were subjected to attack in strongly basic KOH solutions. The resulting leach solutions were analysed for Na, Ca, and Si. This showed that the corrosion process attacks the fibers incongruently. Although there are some distinct differences in the performance of these fibers, to a first approximation both types behave similarly. Further, the fibers were depth profiled using a recently developed SNMS technique for fiber in-depth analysis. This showed that both types of fibers behave in a quite dissimilar manner. The fibers were weathered already without any treatment. Although both fibers show alkali ion exchange and network splitting processes, on one of the fiber layers enriched in SiO₂, Fe₂O₃, and CaO are formed by a redeposition process from the leach solution.Dedicated to Professor Dr. rer. nat. Dr. h.c. Hubertus Nickel on the occasion of his 65th birthday     

Organic functionalization of carbon nanotubes

A very general and versatile method for functionalizing different types of carbon nanotubes is described, using the 1,3-dipolar cycloaddition of azomethine ylides. Approximately one organic group per 100 carbon atoms of the nanotube is introduced, to yield remakably soluble bundles of nanotubes, as seen in transmission electron micrographs. The solubilization of the nanotubes generates a novel, interesting class of materials, which combines the properties of the nanotubes and the organic moiety, thus offering new opportunities for applications in materials science, including the preparation of nanocomposites.     

Fabrication of magnetically separable mesostructured silica with an open pore system

Magnetically separable mesostructured silica with an unobstructed pore system was fabricated through the deposition of cobalt nanoparticles on the outer surface of the submicron-sized silica particles. These cobalt nanoparticles were further protected by a nanometer-thick carbon shell against acid erosion. Due to the fact that the magnetic particles are grafted on the outer surface of the porous silica, the pores are still accessible for further modification, which could widen the application range of porous silica.     

A new approach to the design of surface treatments for reinforcing agents

A new approach for design of improved interfacial bonding between carbon fibers and polymeric matrices is described. In this method the affinity of surface-treated carbon fibers to various polymer matrices is simulated by analyzing the adsorption characteristics of model compounds, typical of the polymer units, onto very high surface area carbon fibers. The affinity can be evaluated by the use of Thermogravimetric Analysis (TGA) to measure adsorption–desorption characteristics. Since high surface area, activated carbon fibers (ACF) can be chemically treated to obtain acidic, basic, nonpolar or highly polar surfaces, it should be possible to assess the interactions of chemically modified surfaces with model compounds such as methanol (MeOH), acetone, dimethylformamide (DMF), dimethylether, tetrahydrofuran (THF) and water. Some preliminary results are presented, indicating that surface treatments for carbon fibers other than oxidation may lead to enhanced bonding with polymeric matrices.