Behavior of density functionals with respect to basis set. 3. Basis set superposition error

The impact of basis set superposition error (BSSE) upon molecular properties determined using the density functionals B3LYP, B3PW91, B3P86, BLYP, BPW91, and BP86 in combination with the correlation consistent basis sets [cc-pVnZ, where n = D(2), T(3), Q(4), and 5] for a set of first-row closed-shell molecules has been examined. Correcting for BSSE enables the irregular convergence behavior in molecular properties such as dissociation energies with respect to increasing basis set size, noted in earlier studies, to be improved. However, for some molecules and functional combinations, BSSE correction alone does not improve the irregular convergence behavior.     

Gold nanoparticle based FRET assay for the detection of DNA cleavage

We report gold nanoparticle based FRET assay to monitor the cleavage of DNA by nucleases. Fluorescence signal enhancement is observed by a factor of 120 after the cleavage reaction in the presence of S1 nuclease. The mechanism of distant dependent fluorescence quenching has been discussed. Our experimental results on distance dependent fluorescence quenching match quite well with theoretical findings obtained from the fluorescence quenching model by Gersten and Nitzan (Surf. Sci. 1985, 158, 165). Our experimental observation paradigm for the design of optical based molecular ruler strategies at distances more than double the distances achievable using traditional dipole-dipole Columbic energy transfer based methods.     

Characterization by 27Al NMR, X-ray absorption spectroscopy, and density functional theory techniques of the species responsible for benzene hydrogenation in Y zeolite-supported carburized molybdenum catalysts

Carburized molybdenum catalysts supported on a dealuminated NaH-Y zeolite were prepared by carburization under a 20% methane in hydrogen flow of two precursors obtained by adsorption of molybdenum hexacarbonyl, one containing 5 wt % and the other 10 wt % Mo, and a third one was prepared by impregnation with aqueous ammonium heptamolybdate, containing 5 wt % Mo. The three catalysts displayed very distinct behaviors in the benzene hydrogenation reaction at atmospheric pressure and 363 K. By using XANES spectroscopy at the molybdenum L edge, EXAFS and XANES spectroscopy at the molybdenum K edge, and 27Al solid-state NMR spectroscopy, it was shown that different carburized molybdenum species exist in each sample. In the catalyst containing 10 wt % Mo, formation of molybdenum carbide nanoparticles was observed, with an estimated diameter of 1.8 nm. In the catalyst containing 5 wt % Mo and prepared by carburization of adsorbed molybdenum hexacarbonyl, formation of molybdenum oxycarbide dimers is proposed. In the latter case, density functional theory calculations have led to a dimer structure which is compatible with EXAFS results. In the catalyst prepared by impregnation with ammonium heptamolybdate solution followed by carburization, the molybdenum seems to interact with extraframework alumina to produce highly disordered mixed molybdenum-aluminum oxycarbides.     

Synthesis of an immobilized Bombyx mori pheromone-binding protein liquid chromatography stationary phase

The pheromone-binding protein from the silkworm moth, Bombyx mori (BmorPBP) has been covalently bonded to a liquid chromatographic stationary phase. The resulting column was evaluated using radiolabeled bombykol and the immobilized protein retained its ability to bind this ligand. The data also demonstrate that the BmorPBP column was able to distinguish between four compounds, and rank them in their relative order of affinity for the protein from highest to lowest: bombykol > bombykal > 1-hexadecanol > (Z,E)-5,7-dodecadien-1-ol, and that the immobilized BmorPBP retained its pH-dependent conformational mobility.The results of this study demonstrate that pheromone-binding protein from the silkworm moth, Bombyx mori and an odorant binding protein (OBP) obtained from the female mosquito Culex quinquefasciatoes have been immobilized on a silica support with retention of ligand-binding activity. The data indicate that proteins from non-mammalian organisms can be used to create liquid chromatography affinity columns.     

Ionic dispersion in nanofluidics

An analytical solution for dispersion of ionic and neutral solutes in nanoscale channels is presented. Results suggest that in the presence of relatively thick electrical double layers (EDLs) characteristic of nanofluidics, the dispersion of ionic solutes differs from that of neutral solutes on which previous theory is based. Ionic dispersion for circular cross-section channels is quantified as a function of a valance parameter, the relative EDL thickness, and the form of the velocity profile. Two unique mechanisms governing ionic dispersion in both pressure- and electrokinetically driven flows are identified. The results of the analytical solution, employing the linearized form of the Poisson-Boltzmann equation, are supported and extended by the results of an independent computational model employing the nonlinear Poisson-Boltzmann equation. Applicability of the computational results is not limited by the Debye-Hückel approximation. Collectively, these results indicate that dispersion of ionic species in nanoscale channels is markedly charge dependent, and substantially deviates from that of neutral solutes in the same flow.     

Asymptotics of the dispersion interaction: analytic benchmarks for van der Waals energy functionals

We show that the usual sum of R-6 contributions from elements separated by distance R can give qualitatively wrong results for the electromagnetically nonretarded van der Waals interaction between nonoverlapping bodies. This occurs for anisotropic nanostructures that have a zero electronic energy gap, such as metallic nanotubes or nanowires, and nanolayered systems including metals and graphene planes. In all these cases our analytic microscopic calculations give an interaction falling off with a power of separation different from the conventional value. We discuss implications for van der Waals energy functionals. The new nanotube interaction might be directly observable at submicron separations.     

Combined hydrogen production and storage with subsequent carbon crystallization

We provide evidence of low-temperature hydrogen evolution and possible hydrogen trapping in an anthracite coal derivative, formed via reactive ball milling with cyclohexene. No molecular hydrogen is added to the process. Raman-active molecular hydrogen vibrations are apparent in samples at atmospheric conditions (300 K, 1 bar) for samples prepared 1 year previously and stored in ambient air. Hydrogen evolves slowly at room temperature and is accelerated upon sample heating, with a first increase in hydrogen evolution occurring at approximately 60 degrees C. Subsequent chemical modification leads to the observation of crystalline carbons, including nanocrystalline diamond surrounded by graphene ribbons, other sp2-sp3 transition regions, purely graphitic regions, and a previously unidentified crystalline carbon form surrounded by amorphous carbon. The combined evidence for hydrogen trapping and carbon crystallization suggests hydrogen-induced crystallization of the amorphous carbon materials, as metastable hydrogenated carbons formed via the high-energy milling process rearrange into more thermodynamically stable carbon forms and molecular hydrogen.     

Fluorescent signal amplification of carbocyanine dyes using engineered viral nanoparticles

We report enhancement in the fluorescent signal of the carbocyanine dye Cy5 by using an engineered virus as a scaffold to attach >40 Cy5 reporter molecules at fixed locations on the viral capsid. Although cyanine dye loading is often accompanied by fluorescence quenching, our results demonstrate that organized spatial distribution of Cy5 reporter molecules on the capsid obviates this commonly encountered problem. In addition, we observe energy transfer from the virus to adducted dye molecules, resulting in a highly fluorescent viral nanoparticle. We have used this enhanced fluorescence for the detection of DNA-DNA hybridization. When compared with the most often used detection methods in a microarray-based genotyping assay for Vibrio cholerae O139, these viral nanoparticles markedly increased assay sensitivity, thus demonstrating their applicability for existing DNA microarray protocols.     

Olefin epoxidation with tert-butyl hydroperoxide catalyzed by MoO2X2L complexes: a DFT mechanistic study

DFT calculations suggest that the catalytic epoxidation of olefins by Mo(vi) complexes, modeled by MoO2Br2(MeN=C(H)-C(H)=NMe), in the presence of MeOOH, the model for tert-butyl hydroperoxide, starts with a hydrogen transfer from the peroxide to one of the terminal Mo=O oxygen atoms and the remaining MeOO anion binds as a seventh ligand, forming a five-membered Mo-O(alpha)-O(beta)(Me)...H-O-Mo ring held together by a hydrogen bond. In the second step, a concerted approach of ethylene to the Mo-O(alpha) bond gives rise to an intermediate containing a seven-membered Mo-C-C-O(alpha)-O(beta)(Me)...H-O-Mo ring. In the final step, decomposition of the intermediate leads to the starting complex, alcohol and the epoxide. The activation energy for the addition of the olefin (second step) is the highest one, in agreement with available kinetic studies showing that the catalyst formation is not always a rate-limiting step. DFT calculations also show that the alcohol by-product (MeOH) can react with the starting complex, competing with ROOH and hence leading to the progressive catalyst poisoning, which has been observed experimentally.