Influence of π-stacking on the N7 and O6 proton affinity of guanine

The influence of π-stacking interactions between guanine (G) and the side chain of tyrosine (Tyr) on the N7 and O6 proton affinities of guanine and on the capability of these sites to act as hydrogen bond acceptors is analyzed at the B3LYP-D, M05-2X and MP2 levels of theory. With all methods, results from full geometry optimizations indicate that stacking interactions increase the N7 and O6 proton affinities by about 5–6 kcal mol^?1, the increase being slightly larger for N7. Consistently with these results, hydrogen bond distances between guanine and one water molecule decrease in the stacked system. Moreover, interaction energy between H₂O and (G-Tyr) is found to be 2–3 kcal mol^?1 larger than in G···H₂O. This strengthening arises from the additional Tyr–H₂O stabilizing interactions and from a cooperative interplay between stacking and hydrogen bond forces.     

Connected generalised Sierpiński carpets

Generalised Sierpiński carpets are planar sets that generalise the well-known Sierpiński carpet and are defined by means of sequences of patterns. We present necessary and sufficient conditions, under which generalised Sierpiński carpets are connected, with respect to Euclidean topology.     

Water-catalyzed isomerization of the glycine radical cation. From hydrogen-atom transfer to proton-transport catalysis

The isomerization reactions of the glycine radical cation, from [NH₂CH₂COOH]⁺, I, to [NH₃CHCOOH]⁺, II, or [NH₂CHC(OH)₂]⁺, III, in the presence of a water molecule have been studied theoretically. The water molecule reduces dramatically the energy barriers of the III and IIII tautomerizations owing to a change in the nature of the process. However, the role of the water molecule depends on the kind of isomerization, the catalytic effect being more important for the IIII reaction. As a consequence, the preferred mechanism for the interconversion of glycine radical cation I to the stablest isomer, III, is the direct one-step mechanism instead of the two step (III and IIIII) process found for isolated [NH₂CH₂COOH]⁺. When using ammonia as a solvent molecule, a spontaneous proton-transfer process from [NH₂CH₂COOH]⁺ to NH₃ is observed and so no tautomerization reactions take place. This behavior is the same as that observed in aqueous solution, as has been confirmed by continuum model calculations.Contribution to the Jacopo Tomasi Honorary Issue     

Interpolation of relative retentions as a tool for identification of perhalogenated compounds

Summary Separation of perhalogenated compounds resulting from thermolysis, photolysis or radiolysis of mixtures of halogens in carbon tetrachloride was carried out by programmed temperature gas chromatography. Plots of relative retentions (to CBr₄) vs the number of bromine atoms present for known compounds of the general formula C_xBr_yCl_z (x=1 and 2; y+z=4 or 6) gave three linear correlations (all with r>0.99). These correlations permitted projections of the identities of reaction products for which no standards were available. These projections were later confirmed by CG-MS. *** DIRECT SUPPORT *** A0732166 00010     

Triplet (pi,pi) reactivity of the guanine-cytosine DNA base pair: benign deactivation versus double tautomerization via intermolecular hydrogen transfer

Ab initio computations (CASSCF/6-31G* supported by CAS-PT2 single-point calculations) are used to study the reactivity of the triplet excited state of the guanine-cytosine DNA base pair. When the triplet excitation is centered on cytosine there is a competition between benign deactivation to the ground state and a hydrogen transfer route that can trigger double tautomerization. The calculated barriers favor the benign deactivation, but this route goes through a singlet/triplet intersystem crossing with small spin-orbit coupling. Therefore, the potentially mutagenic, double tautomerization route cannot be ruled out completely, and the two paths are probably an alternative to the well-known cytidine photodimerization reaction.     

Effective way of modeling chemical catalysis: Empirical valence bond picture of role of solvent and catalyst in alkylation reactions

A general methodology for the study of chemical catalysis is presented and demonstrated in a study of Friedel–Crafts‐type alkylation reactions that are constrained to collinear configurations. Ab initio potential energy surfaces in solution and relevant experimental results are used to calibrate general empirical valence bond (EVB) potential surfaces for studies of such reactions. The EVB surfaces allow one to interpolate the ab initio results to studies of the effect of different solvents, substituents, and catalysts on the alkylation reactions. This implicit approach introduces such effects by shifting the diagonal energies of the corresponding resonance structures. Such an EVB/shift approach appears valuable for assessing the effects of different catalysts and solvents on complex chemical reactions. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 607–625, 2000     

Monitoring powder blending in pharmaceutical processes by use of near infrared spectroscopy

One of the goals of the new automated immunoassay analysers is to perform direct analysis in complex matrices thus overcoming traditional limits of homogeneous immunoassays: reduced sensitivity and ability to determine above all proteins and antibodies. The aim of this work was to demonstrate the feasibility of quantitative homogeneous immunoassay for small analytes in a complex matrix with a rapid and easy assay by exploiting an agglutination reaction. We studied the steroid hormone progesterone, and used new technology, the Copalistrade mark, which uses a special optical-sizing flow particle analysis and a semiconductor laser as a light source. We used polystyrene microbeads coated with the antigen as markers and put them in competition with the analyte in solution for the analytical antiserum. We synthesised and tested different conjugates of progesterone-bovine serum albumin, optimising all the experimental parameters. We performed a short pre-treatment of the serum and we obtained a detection limit of 0.011 ngcm(-3) and a working range between 0.026 and 43 ngcm(-3). We estimated human serum specimens and, with minor experimental revisions, the amounts of progesterone found agreed accurately with AutoDELFIAtrade mark analysis. The recoveries are good. All the experimental steps are easy, rapid and enable us to process many samples contemporarily.     

Thermodynamic and stereochemical aspects of the polymerizability of glycolide and lactide

The ring-opening polymerizations of the dilactones glycolide and the S,S- and S,R-stereoisomers of lactide were studied using quantum mechanical methods. The ring strain and the conformational distribution of these cyclic monomers and of the polymers were calculated, and the effect of the medium on the polymerization was predicted, for both bulk and solution. The polymerizability of the three monomers in the gas phase, that is, nonpolar medium, is much greater than that of δ-valerolactone or 1,4-dioxan-2-one. This difference vanishes in the polar medium chloroform, which is attributed to the fact that, while all of these monomers possess polar cis-lactone bonds, the three dilactones possess small dipole moments. The data are combined to give polymerization enthalpy and free energy values. The four stereoregular lactide polymers did not differ significantly in energy. Accordingly, the ability to synthesize any one of these rests on catalyst specificity (“polymer chain-end control”). Although introduction of sterically demanding methyl groups into glycolide is expected to favor coiled conformations and decrease polymerizability, this was not found to be the case. Good agreement of calculated values with experimental data from the literature was achieved.