Size-expanded yDNA bases: an ab initio study

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.     

A mechanistic rationalization of unusual kinetic behavior in proline-mediated C-O and C-N bond-forming reactions

Kinetic evidence supports the role of the reaction product in the catalytic cycle of proline-mediated alpha-aminoxylation and alpha-amination reactions, providing both design principles as well as a model for the evolution of efficiency in catalysis.     

A comparative first-principles study of the adsorption of a carbon atom on copper and nickel surfaces

The adsorption energies of a carbon atom at the most stable adsorption sites on the Cu and Ni(100), (110) and (111) surfaces have been studied by first-principles calculations. The preference order of the adsorption sites for both Cu and Ni surfaces is the same. The (100) hollow site is the most stable one. The diffusion barriers for a C atom on the three surfaces have also been obtained, with the highest mobility on the (111) surface of both metals. Our investigation shows that the adsorption energies of the C atom on Ni are significantly higher in magnitude than those on Cu for all the three surfaces. This phenomenon is mainly due to the interaction and hybridization between C p-orbits and partially filed d-shell of Ni, which forms a stronger binding.     

Correlated exciton relaxation in Poly(3-hexylthiophene)

Two-color 3 pulse photon echo peak shift (2C-3PEPS) measurements on poly(3-hexylthiophene) (3PHT) demonstrate that spectral regions in the photoluminescence remain correlated with the excitation, despite large differences in energy (>0.5 eV). The observations are explained in terms of exciton-phonon coupling that is dominated by only two motions: one high frequency bond stretch and a low frequency torsional motion. Numerical simulations of the 2C-3PEPS are shown to be consistent with the experimental observations. The results demonstrate that initial intramolecular exciton relaxation in P3HT is not primarily a stochastic process, but is driven by strong, selective exciton-phonon coupling to torsional motions.     

Interplay of Hole Transfer and Host–Guest Interaction in a Molecular Dyad and Triad: Ensemble and Single‐Molecule Spectroscopy and Sensing Applications

A new molecular dyad consisting of a Cy5 chromophore and ferrocene (Fc) and a triad consisting of Cy5, Fc, and β‐cyclodextrin (CD) are synthesized and their photophysical properties investigated at both the ensemble and single‐molecule levels. Hole transfer efficiency from Cy5 to Fc in the dyad is reduced upon addition of CD. This is due to an increase in the Cy5‐Fc separation (r) when the Fc is encapsulated in the macrocyclic host. On the other hand, the triad adopts either a Fc‐CD inclusion complex conformation in which hole transfer quenching of the Cy5 by Fc is minimal or a quasi‐static conformation with short r and rapid charge transfer. Single‐molecule fluorescence measurements reveal that r is lengthened when the triad molecules are deposited on a glass substrate. By combining intramolecular charge transfer and competitive supramolecular interaction, the triad acts as an efficient chemical sensor to detect different bioactive analytes such as amantadine hydrochloride and sodium lithocholate in aqueous solution and synthetic urine.     

Reliability analysis of a single warm-standby system subject to repairable and nonrepairable failures

An n-unit system provisioned with a single warm standby is investigated. The individual units are subject to repairable failures, while the entire system is subject to a nonrepairable failure at some finite but random time in the future. System performance measures for systems observed over a time interval of random duration are introduced. Two models to compute these system performance measures, one employing a policy of block replacement, and the other without a block replacement policy, are developed. Distributional assumptions involving distributions of phase type introduce matrix Laplace transformations into the calculations of the performance measures. It is shown that these measures are easily carried out on a laptop computer using Microsoft Excel. A simple economic model is used to illustrate how the performance measures may be used to determine optimal economic design specifications for the warm standby.     

Structure and function of a lignostilbene-α,β-dioxygenase orthologue from <Emphasis Type="Italic">Pseudomonas brassicacearum</Emphasis>

Background

Stilbene cleaving oxygenases (SCOs), also known as lignostilbene-α,β-dioxygenases (LSDs) mediate the oxidative cleavage of the olefinic double bonds of lignin-derived intermediate phenolic stilbenes, yielding small modified benzaldehyde compounds. SCOs represent one branch of the larger carotenoid cleavage oxygenases family. Here, we describe the structural and functional characterization of an SCO-like enzyme from the soil-born, bio-control agent Pseudomonas brassicacearum.

Methods

In vitro and in vivo assays relying on visual inspection, spectrophotometric quantification, as well as liquid-chormatographic and mass spectrometric characterization were applied for functional evaluation of the enzyme. X-ray crystallographic analyses and in silico modeling were applied for structural investigations.

Results

In vitro assays demonstrated preferential cleavage of resveratrol, while in vivo analyses detected putative cleavage of the straight chain carotenoid, lycopene. A high-resolution structure containing the seven-bladed β-propeller fold and conserved 4-His-Fe unit at the catalytic site, was obtained. Comparative structural alignments, as well as in silico modelling and docking, highlight potential molecular factors contributing to both the primary in vitro activity against resveratrol, as well as the putative subsidiary activities against carotenoids in vivo, for future validation.

Conclusions

The findings reported here provide validation of the SCO structure, and highlight enigmatic points with respect to the potential effect of the enzyme’s molecular environment on substrate specificities for future investigation.

     

Molecular structure of an extremely crowded iron(II) dihydride complex: FeH2(PMePh2)4

The crystal structure of FeH₂(PMePh₂)₄ shows this to exist as thecis isomer in the solid state with major distortions of the FeP₄ skeleton:cis P-Fe-P angles 98.1(1)–107.2(1)° andtrans P-Fe-P angle 143.3(1)°. All hydrogen atoms were refined, and the mean Fe-H separation is 1.59 Å. Long Fe-P distances, 2.187(3)–2.251(3) Å, emphasize the crowding in this molecule. Crystallographic data:a=11.684(4) Å,b=37.793(17),c=9.765(3),=90.81(1)°, andZ=4 in space groupP2₁/n (No. 14).R(F)=6.3% andR _w (F)=6.0% for 2585 observed reflections collected at —162°C.