Size-expanded DNA bases: an ab initio study of their structural and electronic properties

The size-expanded DNA bases, xA, xC, xG, and xT, are benzo-homologue forms of the natural DNA bases; i.e., their structure can be seen as the fusion of a natural base and a benzene ring. Recently, a variety of DNAs, known as xDNAs, have been synthesized in which size-expanded and natural bases are paired. In this paper we use second-order M?ller-Plesset perturbation theory and density functional theory to investigate the structural and electronic properties of xA, xC, xG, and xT and their natural counterparts. We find that whereas natural and size-expanded bases have both nonplanar amino groups the latter have also nonplanar aromatic rings. When density functional theory is used to investigate the electronic properties of size-expanded and natural bases, it is found that the HOMO-LUMO gap of the size-expanded bases is smaller than that of the natural bases. Also, xG should be easier to oxidize than G.     

The hydroxyl radical reaction rate constants and atmospheric reaction products of three siloxanes

The relative rate technique has been used to measure the hydroxyl radical (OH) reaction rate constant of hexamethyldisiloxane (MM, (CH₃)₃Si-O-Si(CH₃)₃), octamethyltrisiloxane (MDM, (CH₃)₃Si-O-Si(CH₃)₂-O-Si(CH₃)₃), and decamethyltetrasiloxane (MD₂M, (CH₃)₃Si-O-Si(CH₃)₂-O-Si(CH₃)₂-O-Si(Ch₃)₃). Hexamethyldisiloxane, octamethyltrisiloxane, and decamethyltetrasiloxane react with OH with bimolecular rate constants of 1.32 ± 0.05 × 10⁻¹² cm³molecule⁻¹s⁻¹, 1.83 ± 0.09 × 10⁻¹² cm³ molecule⁻¹s⁻¹, and 2.66 ± 0.13 × 10⁻¹² cm³molecule⁻¹s⁻¹, respectively. Investigation of the OH + siloxane reaction products yielded trimethylsilanol, pentamethyldisiloxanol, heptamethyltetrasiloxanol, hexamethylcyclotrisiloxane, octamethylcyclotetrasiloxane, and other compounds. Several of these products have not been reported before because these siloxanes and the proposed reaction mechanisms yielding these products are complicated. Some unusual cyclic siloxane products were observed and their formation pathways are discussed in light of current understanding of siloxane atmospheric chemistry. © 1997 John Wiley & Sons, Inc. Int J Chem Kinet 29: 445–451, 1997.     

The Characterization of Organic Modified Montmorillonite and Its Filled PMMA Nanocomposite

Thermogravimetric analysis (TG) and Fourier transform infrared (FTIR)results of commercial montmorillonite were compared to that exchanged with trimethyloctadecyl quaternary ammonium chloride (SCPX2048), both were treated up to500°C. The time-of-flight mass spectrometer (TOF/MS) results of SCPX2048 trapped under300 and 500°C were compared with that of N,N,Ntrimethyl-1-dodecanammonium chloride(A 18-50) trapped under 200 and 300°C. The degradation mechanism of organic modified montmorillonite was proposed. PMMA-clay nanocomposite was synthesized through intercalation method and its properties were examined by both TG and DSC techniques. The thermal stability and glass transition temperature of montmorillonite filled PMMA increase comparing with that of the pure PMMA. This revised version was published online in July 2006 with corrections to the Cover Date.     

Chemical biology: the promise, and confusion, of adolescence.

It takes time for any new scientific discipline to gain momentum, and chemical biology is no exception. But with the formation of new training programs and interdisciplinary departments, the changes are coming.     

The hydroxyl radical reaction rate constant and products of cyclohexanol

The gas phase reaction of the hydroxyl radical (OH) with cyclohexanol (COL) has been studied. The rate coefficient was determined to be (19.0 ± 4.8) × 10⁻¹² cm³ molecule⁻¹ s⁻¹ (at 297 ± 3 K and 1 atmosphere total pressure) using the relative rate technique with pentanal, decane, and tridecane as the reference compounds. Assuming an average OH concentration of 1 × 10⁶ molecules cm⁻³, an atmospheric lifetime of 15 h is calculated for cyclohexanol. Products of the OH + COL reaction were determined to more clearly define COL's atmospheric degradation mechanism. The observed products and their formation yields were: cyclohexanone (0.55 ± 0.06), hexanedial (0.32 ± 0.15), 3‐hydroxycyclohexanone (0.31 ± 0.14), and 4‐hydroxycyclohexanone (0.08 ± 0.04). Consideration of the potential reaction pathways suggests that each of these products is formed via hydrogen abstraction at a different site on the COL ring. The products and their relative amounts are discussed in light of the predicted yields for each reaction channel. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 108–117, 2001     

Chromatographic investigation of the effect of dissolved carbon dioxide on the glass transition temperature of a polymer and the solubility of a third component (additive)

The effect of dissolved carbon dioxide on the glass transition temperature of a polymer, PMMA, has been investigated using molecular probe chromatography. The probe solute was iso-octane, and the specific retention volumes of this solute in pure PMMA and mixtures of PMMA with CO₂ were measured over a temperature range of 0 to 180°C and CO₂ pressures from 1 to 75 atm. The amount of CO₂ dissolved in the polymer was calculated from a model fit to previously published solubility data determined chromatographically. Classical van't Hoff-type plots were used to determine the glass transition temperature of CO₂-impregnated PMMA from low pressure up to 46 atm of CO₂. Solvent-induced plasticization was observed with the glass transition temperature decreasing by about 40°C. At some pressures, glass transitions at low temperatures could not be determined from the van't Hoff plots because of the proximity of the polymer glass transition temperature to the gas–liquid transition temperature for CO₂. For these pressures, a new method was developed to determine the glass transition composition. The glass transition pressure was then calculated from the measured composition and temperature using an isotherm model. In every case, the glass transition temperature decreased linearly with increasing concentration of CO₂ in the polymer. However, at higher compositions, the glass transition pressure decreased with increasing composition and decreasing temperature. The observed retention volume of iso-octane with PMMA in a glassy state was correlated with an adsorption model developed from a theory for liquid–solid chromatography derived by Martire. This model accurately described the observed decrease in retention of iso-octane by adsorption on the surface of glassy PMMA with increasing concentration of CO₂ dissolved in the polymer. © 1998 John Wiley & Sons, Inc. J. Polym. Sci. B Polym. Phys. 36: 2537–2549, 1998