Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Palladium-catalyzed Heck reactions of styrene derivatives and 2-iodo-p-carborane

p-Carborane has been vinylated on the 2-B-atom in high yields using the Heck reaction. Thus, the reaction between 2-iodo-p-carborane and various styrenes [4-H-, 4-C(6)H(4)-, 4-Cl-, 4-Br-, 4-NO(2)-, 4-CH(3)O-, and 4-CH(3)-] resulted in the production of the corresponding trans-beta-(2-B-p-carboranyl)styrene in DMF solution when reacted in the presence of silver phosphate and the palladacycle Herrmann's catalyst.     

Retention mechanisms and selectivity in internal-surface reversed-phase liquid chromatography. Studies with cyanobacterial peptide toxins

Summary Microcystins-LA,-LR,-RR,-YR and nodularin, cyanobacterial peptide toxins, were separated by internal-surface reversed-phase (ISRP), high-performance liquid chromatography. The capacity factors of the toxins were measured in the range pH 2–8 using acetonitrile, isopropanol or tetrahydrofuran in potassium dihydrogenphosphate mobile phase. The main retention mechanism of the ISRP column was reversed-phase interaction but cation-exchange offered additional selectivity at neutral and slightly acidic pH. At neutral pH (10% modifier, 0.1 M buffer) the elution order was microcystin-LA (two nonpolar residues leucine and alanine as the variable amino acids), nodularin, microcystin-LR,-YR and-RR (two basic arginines as the variable amino acids). The retention times of all toxins except microcystin-RR were substantially longer at acidic pH. At pH 2 (10% modifier, 0.1 M buffer) where the cation-exchange mechanism was inoperative the elution order was changed to microcystin-RR, nodularin, microcystin-LR,-YR and-LA. The best separation was achieved at pH 2 where even two desmethylated microcystin-RR analogs could be separated from microcystin-RR.     

Time-dependent nonlinear optical properties of pyroelectric liquid crystalline polymers

Highly oriented pyroelectric liquid-crystalline polymers were prepared by photopolymerization under the influence of a static electric field from binary mixtures of two acrylate monomers exhibiting chiral smectic C mesomorphism. Both monomers contained nitro groups to yield second order nonlinear optical properties (second harmonic generation) and one of the monomers had two functional groups to yield a crosslinked polymer. The room temperature second order nonlinear susceptibility of the polymers showed during the first two hours a 10 % decrease after which it remained constant during the next 48 days. At elevated temperatures there was a significant difference in the nonlinear optical properties over time between crosslinked and uncrosslinked polymers. The uncrosslinked polymer showed a pronounced loss of second order nonlinear optical activity with time at ≥38°C. The crosslinked polymer showed a much smaller and basically a temperature independent decrease rate in the second order nonlinear optical properties at all the ageing temperatures (23-130°C). Both the loss in mesogen order parameter, very evident for the uncrosslinked polymer, and conformational changes occurring within the mesogens (β mechanism), may account for the observations made.     

Bentley’s conjecture on popularity toplist turnover under random copying

Bentley et al. studied the turnover rate in popularity toplists in a ‘random copying’ model of cultural evolution. Based on simulations of a model with population size N, list length ? and invention rate μ, they conjectured a remarkably simple formula for the turnover rate: $\ell \sqrt{\mu}$ . Here we study an overlapping generations version of the random copying model, which can be interpreted as a random walk on the integer partitions of the population size. In this model we show that the conjectured formula, after a slight correction, holds asymptotically.     

Multicomponent analysis of drinking water by a voltammetric electronic tongue

A voltammetric electronic tongue is described that was used for multicomponent analysis of drinking water. Measurements were performed on drinking water from a tap and injections of the compounds NaCl, NaN₃, NaHSO₃, ascorbic acid, NaOCl and yeast suspensions could be identified by use of principal component analysis (PCA). A model based on partial least square (PLS) was developed for the simultaneously prediction of identification and concentration of the compounds NaCl, NaHSO₃ and NaOCl. By utilizing this type of non-selective sensor technique for water quality surveillance, it will be feasible to detect a plurality of events without the need of a specific sensor for each type of event.     

Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine

DNA-protein cross-linking is one of the many DNA lesions mediated by hydroxyl radicals, the most damaging among the reactive oxygen species in biological systems. Density functional theory methods are employed to investigate the complex reaction mechanisms of the formation of cytosine-tyrosine cross-links as observed in gamma-irradiated aqueous solutions of cytosine and tyrosine, as well as in gamma-irradiated nucleohistone. The majority of the radical addition mechanisms considered are found to have significant barriers and therefore to be thermodynamically unfavorable for the formation of the initial cross-linked product. Our calculated reaction potential energy surfaces suggest that a feasible complete mechanism consists of radical combination forming the initial cross-linked product, a hydrogen shuffle within the initial cross-linked product, and an acid-catalyzed dehydration reaction. Water and hydrogen-bonding interactions are suggested to play a key role in catalyzing the hydrogen-transfer step of the reaction.