Ab initio stochastic optimization of conformational and many-body degrees of freedom

Moderate to large size molecules in solution have complex energy surfaces due to intramolecular (conformational) and intermolecular (many-body) interactions. The first principles Monte Carlo (FPMC) method, previously shown to effectively locate minimum-energy structures for systems with only many-body complexity, has been extended to address conformational flexibility by adding three new Monte Carlo move types. The primary advantage of the FPMC method is the ability to efficiently locate minimum energy structures of molecules with conformational flexibility in the presence of explicit solvent molecules using highly accurate quantum chemical calculations. The additions to FPMC were validated by studying conformers of glycerol, glyceraldehyde, and a large humic acid monomer unit. The structure of glyceraldehyde in the presence of one and two water molecules was also explored to demonstrate the power of FPMC to study systems with both conformational and many-body degrees of freedom.     

DNA-templated three-branched nanostructures for nanoelectronic devices

Three-branched DNA molecules have been designed and assembled from oligonucleotide components. These nucleic acid constructs contain double- and single-stranded regions that control the hybridization behavior of the assembly. Specific localization of a single streptavidin molecule at the center of the DNA complex has been investigated as a model system for the directed placement of nanostructures. Highly selective silver and copper metallization of the DNA template has also been characterized. Specific hybridization of these DNA complexes to oligonucleotide-coupled nanostructures followed by metallization should provide a bottom-up self-assembly route for the fabrication and characterization of discrete three-terminal nanodevices.     

Synthesis of polystyrene/poly[2-(dimethylamino)ethyl methacrylate-stat-ethylene glycol dimethacrylate] core-shell latex particles by seeded emulsion polymerization and their application as stimulus-responsive particulate emulsifiers for oil-in-water emulsions

Surfactant-stabilized polystyrene (PS) latex particles with a mean hydrodynamic diameter of 155 nm were prepared by aqueous emulsion polymerization using 2,2'-azobis(2-amidinopropane) hydrochloride as a cationic radical initiator. Seeded aqueous emulsion copolymerizations of 2-(dimethylamino)ethyl methacrylate (DMA) and ethylene glycol dimethacrylate (EGDMA) were conducted in the presence of these PS particles to produce two batches of colloidally stable core-shell latex particles, in which the shell comprised a cross-linked P(DMA-stat-EGDMA) overlayer. Both the PS and PS/P(DMA-stat-EGDMA) latexes were characterized in terms of their particle size, morphology, and composition using dynamic light scattering, electron microscopy, and FT-IR spectroscopy, respectively. Using the PS/P(DMA-stat-EGDMA) latex particles as a pH-responsive particulate ('Pickering'-type) emulsifier, polydisperse n-dodecane-in-water emulsions were prepared at pH 8 that could be partially broken (demulsified) on lowering the solution pH to 3. These emulsions were characterized in terms of their emulsion type, mean droplet diameter, and morphology using electrical conductivity and Mastersizer measurements, optical microscopy, and scanning electron microscopy (using critical point drying for sample preparation).     

Enzymes in Organic Synthesis: Application to the Problems of Carbohydrate Recognition (Part 1)

Carbohydrates on cell surfaces are information molecules. Although only seven or eight monosaccharides are commonly used as building blocks in mammalian systems, the multifunctionality of these monomers can lead to the assembly of an immense variety of complex structures. Millions of different tetrasaccharide structures, for example, can be constructed from this small number of building blocks, if branching, the stereochemistry of glycosidic linkages, and the modification of hydroxyl and amino groups are taken into consideration. Oligosaccharides therefore represent an effective class of biomolecules that code for a vast amount of information required in various biological recognition processes, such as intercellular communication, signal transduction, cell adhesion, infection, cell differentiation, development and metastasis. The pace of development of pharmaceuticals based on carbohydrates has, however, been slower than that based on other classes of biomolecules. Part of the reason is the lack of technologies for the study of complex carbohydrates. There is no method to amplify oligosaccharides for sequence analysis. There is no machine available for automated synthesis of oligosaccharides. In addition, the possibly poor bioavailability and difficulties in the large-scale synthesis of carbohydrates have undoubtedly contributed to this slow pace. The enzymatic and chemoenzymatic methods, especially those based on aldolases and glycosyltransferases, described here appear to be useful for the synthesis of mono- and oligosaccaharides and related molecules. Further advances in glycobiology will probably lead to the development of new technologies for the study of carbohydrate recognition and for the synthesis of bioactive carbohydrates and mimetics to control the recognition processes.     

THE EFFECT OF RED AND FAR RED LIGHT ON CAROTENOID AND CHLOROPHYLL FORMATION IN PEA SEEDLINGS

Abstract— Treatment of etiolated pea seedlings with a short exposure to red light caused a stimulation of growth (size and dry wt production) and carotenoid synthesis during the following 48 hr compared with seedlings kept entirely in darkness.The effect is nullified by a following dose of far red light and thus the phenomenon is probably phytochrome-controlled.
Similar treatment with red light one hour before continuous illumination with white light tended to reduce the lag period for chlorophyll synthesis.Again a following dose of far red light reversed this response.     

Ab initio characterization of several states of nitroxylium (NO). Comparison of fragmentation energies of nitroxylium,nitroxyl (NO3), and nitrate

Ab initio calculations have been performed at the self-consistent field (HF) level, and its perturbative extensions up to fourth-order (MPn), for several electronic states of nitroxylium (NO) as well as for a large number of reference species. Geometries are optimized at the HF/DZ and HF/DZP levels (double zeta and double zeta plus polarization bases). The ground state is found to be the D_3h ¹A₁′ state, with the C_2v ¹A₁ (closed Y) state higher by 0.94 eV. The relationship between adding electrons or oxygen atoms to NO⁺ and NO is explored, especially in relation to fragmentation energies of NO (q = 0 or 1). A comparison is drawn between NO and two isoelectronic species, CO₃ and C(CH₂)₃, where no surprises are found.     

Fast directed motion of "fakir" droplets

In this Letter, we report on the motion of water droplets on surfaces decorated with molecular gradients comprising semifluorinated (SF) organosilanes. SF molecular gradients deposited on flat silica substrates facilitate faster motion of water droplets relative to the specimens covered with an analogous hydrocarbon gradient. Further increase in the drop speed is achieved by advancing it along porous substrates coated with the SF wettability gradients. The results of our experiments are in quantitative agreement with a simple scaling theory that describes the faster liquid motion in terms of reduced friction at the liquid/substrate interface.     

A maximum likelihood estimator to distinguish single molecules by their fluorescence decays

We have developed a maximum likelihood estimator to distinguish between similar molecules at the single molecule level based upon fluorescence decay measurements. Time resolved fluorescence measurements for single Rhodamine 6G and tetramethylrhodamine isothiocyanate molecules in fluid flow are derived from time-correlated single photon counting. A maximum likelihood estimator is developed and applied to data from a mixture of molecules. Single molecules are identified and distinguished by their fluorescence time decays. Comparison is made between identification error rates and theoretical predictions. To our knowledge, this is the first reported example of single molecule identification by fluorescence decay in a mixture.     

Structural Study of an Unusual Cubic Pyrochlore Bi1.5Zn0.92Nb1.5O6.92

Single-phase pyrochlore-type specimens of Bi_1.5Zn_0.92Nb_1.5O_6.92 were studied using combined electron, X-ray and neutron powder diffraction techniques. Rietveld refinements using neutron powder diffraction data confirmed an average pyrochlore structure A₂B₂O₆O′ (Fd&3macr;m, a=10.5616(1) Å) with both Bi and Zn mixed on the A-sites. However, refinements revealed significant local deviations from the ideal pyrochlore arrangement which were caused by apparent displacive disorder on both the A and O′ sites. The best fit was obtained with a disordered model in which the A-cations were randomly displaced by ∼0.39 Å from the ideal eight-fold coordinated positions. The displacements occur along the six 〈112〉 directions perpendicular to the O′-A-O′ links. In addition, the O′ ions were randomly displaced by ∼0.46 Å along all 12 〈110〉 directions. Crystal-chemical considerations suggest the existence of short-range correlations between the O′ displacements and both the occupancy of the A-sites (i.e., Bi or Zn) and the directions of the A-cation displacements. The combined A-cation and O′ displacements change the coordination sphere of the A-cations from 8 to (5+3); the resulting coordination environment of the A-cations bears similarities to that of the (5+1)coordinated Zn in zirconolite-like Bi₂Zn_2/3Nb_4/3O₇. The observed displacive disorder in the A₂O′ network of the Bi_1.5Zn_0.92Nb_1.5O_6.92 structure involves atoms associated with the lowest-frequency vibrational bending mode, and is likely responsible for both the high dielectric constant and the dielectric relaxation reported for this compound.