Recent results from PHOBOS on particle production at high p T

A selection of experimental results from the PHOBOS Collaboration relevant for probing high-energy nuclear collisions with high transverse momentum particles is presented. The inclusive yields of charged particles and comparisons between nuclear and elementary collisions already reveal a large amount of parton energy loss in the hot and dense medium created in heavy ion collisions. Remarkable scaling and factorization features are observed, unifying the data taken at various collision energies, centralities and nuclear sizes. To further analyze the nature of the energy loss, a measurement of pseudorapidity (Δη) and azimuthal angle (Δφ) correlations between high transverse momentum charged hadrons (p _T >2.5 GeV/c) and all associated charged particles is presented at both short-range (small Δη) and long-range (large Δη) over a continuous detector acceptance covering −4<Δη<2. Various near- and away-side features of the correlation structure are discussed as a function of centrality in Au + Au collisions at  GeV. The results provide new information about the longitudinal (Δη) extent of the near-side ‘ridge’ structure, first observed by the STAR Collaboration over a narrower η range. In central Au + Au collisions the ridge structure extends to at least Δη=4, and its strength completely diminishes as collisions become more peripheral. Presenter of the paper on the 3rd International Conference on Hard and Electromagnetic Probes of High-Energy Nuclear Collisions, 8–14 June 2008, Illa da Toxa (Galicia-Spain).     

The Mechanism of Nonenzymatic Template Copying with Imidazole‐Activated Nucleotides

The emergence of the replication of RNA oligonucleotides was a critical step in the origin of life. An important model for the study of nonenzymatic template copying, which would be a key part of any such pathway, involves the reaction of ribonucleoside‐5′‐phosphorimidazolides with an RNA primer/template complex. The mechanism by which the primer becomes extended by one nucleotide was assumed to be a classical in‐line nucleophilic‐substitution reaction in which the 3′‐hydroxyl of the primer attacks the phosphate of the incoming activated monomer with displacement of the imidazole leaving group. Surprisingly, this simple model has turned out to be incorrect, and the dominant pathway has now been shown to involve the reaction of two activated nucleotides with each other to form a 5′–5′‐imidazolium bridged dinucleotide intermediate. Here we review the discovery of this unexpected intermediate, and the chemical, kinetic, and structural evidence for its role in template copying chemistry.     

Aptamers selected for higher-affinity binding are not more specific for the target ligand

Previous study of eleven different in vitro-selected RNA aptamers that bind guanosine triphosphate (GTP) with K(d)s ranging from 8 microM to 9 nM showed that more information is required to specify the structures of the higher-affinity aptamers. We are interested in understanding how the more complex aptamers achieve higher affinities for the ligand. In vitro selection produces structural solutions to a functional problem that are are as simple as possible in terms of the information content needed to define them. It has long been assumed that the simplest way to improve the affinity of an aptamer is to increase the shape and functional group complementarity of the RNA binding pocket for the ligand. This argument underlies the hypothesis that selection for higher-affinity aptamers automatically leads to structures that bind more specifically to the target molecule. Here, we examined the binding specificities of the eleven GTP aptamers by carrying out competition binding studies with sixteen different chemical analogues of GTP. The aptamers have distinct patterns of specificity, implying that each RNA is a structurally unique solution to the problem of GTP binding. However, these experiments failed to provide evidence that higher-affinity aptamers bind more specifically to GTP. We suggest that the simplest way to improve aptamer K(d)s may be to increase the stability of the RNA tertiary structure with additional intramolecular RNA-RNA interactions; increasingly specific ligand binding may emerge only in response to direct selection for specificity.     

TNA synthesis by DNA polymerases

Threose nucleic acid (TNA), which has a repeat unit one atom shorter than that of DNA, is capable of Watson-Crick base pairing with DNA, RNA, and TNA. Because of its chemical simplicity, TNA is considered to be a possible progenitor of RNA. As an initial step toward developing the molecular tools necessary to investigate the functional capabilities of TNA by in vitro selection, we have screened a variety of DNA polymerases for TNA synthesis activity on a DNA template. We wish to report that several polymerases show surprisingly good ability to synthesize TNA using alpha-l-threofuranosyl thymidine-3'-triphosphate as a substrate.     

Characterization of clean and oxidized (100)LaB6

We have studied clean and oxidized (100)LaB₆ grown from aluminum melts by making Auger, LEED, evaporation and work function measurements on well-defined surfaces. The clean surface shows no La enrichment when initially heated as high as 1700°C. Its LEED pattern is 1 × 1, indicating no surface reconstruction. Langmuir evaporation studies up to temperatures of 1700°C show only La and B evaporating non-congruently, and LaO. The activation energy for B evaporation from LaB₆ (and from CeB₆ and EuB₆ also) is abot 5.5 eV, very close to that from elemental B. The rare-earth activation energies, however, vary, being highest for the rare-earth whose pure metal vapor pressure is lowest. Oxidation was carried out at room temperature using O₂ pressures up to 10^?7 Torr and at 1000°C using O₂ pressures up to 10^?4 Torr. At room temperature oxygen adsorption proceeeds to a saturated value indicated from LEED behavior to be about one monolayer. It produces a monotonic work function increase, which also saturates (at 1.40 V), varying linearly with the oxygen uptake. Oxidation at 1000°C is much more extensive than at room temperature, involving at least several monolayers, and results in a work function increase of 2.42 V. Results are discussed in terms of a terminal plane composed of La atoms, and adsorbed oxygen which, when given sufficient mobility, prefers bonding to La atoms at sites atop the B octahedra.     

Low-temperature phase transition in [Mn(OS(CH3)2)6](ClO4)2 studied by single crystal X-ray diffraction, infrared absorption and Raman scattering spectroscopies

Single crystal X-ray diffraction studies of [Mn(OS(CH3)2)6](ClO4)2 have shown that the low temperature phase transition, detected by differential scanning calorimetry (DSC) at about 223 K, is associated with the crystal symmetry's reduction from an orthorhombic crystallographic system (Fdd2, No. 43) to a monoclinic one (Cc, No. 9). The analysis of the full width at half maximum of the bands connected with: δd(OClO)F2 and ρ(CH3) vibrational modes in the FT-IR and FT-RS spectra, respectively, registered in the function of temperature, proved that the reorientational motions of ClO4- anions and CH3 groups from (CH3)2SO ligands, began to slow down at temperatures below the phase transition at about 223K. Mean values of activation energy for ClO4- reorientation in the high temperature phase I and low temperature phase II are: Ea(I)≈14 kJ mol(-1) and Ea(II)≈10 kJ mol(-1), respectively. Analogous values for CH3 reorientation are: Ea(I)≈23 kJ mol(-1) and Ea(II)≈1 kJ mol(-1), respectively.     

The revision of intermolecular interactions in 1,3‐dinitrobenzene crystal—the role of nitro groups in optical nonlinearity

Polarized Fourier transform‐infrared (FT‐IR) reflectance spectra and powder Raman spectra have been measured for 1,3‐dinitrobenzene crystal in order to revise the assignments of bands by means of the oriented gas model reinforced with quantum chemical [density functional theory (DFT)] calculations. Longitudinal optical/transverse optical (LO‐TO) splitting of some bands is observed indicating medium strong, long‐range, dipole–dipole interactions. The analysis of overtones in the polarized FT‐NIR spectra has allowed us to estimate the anharmonicity of vibrations in the crystal. The molecular motions of the nitro groups are analyzed on the basis of temperature‐dependent polycrystalline IR spectra. Based on the values of the energy difference (Δν_el) between the forbidden A_1g→B_2u transition in the benzene molecule in the gas phase and the first electronic transition in 1,3‐dinitrobenzene, it has been concluded that the intermolecular interactions are medium strong. The nitro group interactions are proposed to play the main role in the optical nonlinearity. Copyright © 2010 John Wiley & Sons, Ltd.     

Quantification of Salicylates and Flavonoids in Poplar Bark and Leaves Based on IR,NIR, and Raman Spectra

Poplar bark and leaves can be an attractive source of salicylates and other biologically active compounds used in medicine. However, the biochemical variability of poplar material requires a standardization prior to processing. The official analytical protocols used in the pharmaceutical industry rely on the extraction of active compounds, which makes their determination long and costly. An analysis of plant materials in their native state can be performed using vibrational spectroscopy. This paper presents for the first time a comparison of diffuse reflectance in the near- and mid-infrared regions, attenuated total reflection, and Raman spectroscopy used for the simultaneous determination of salicylates and flavonoids in poplar bark and leaves. Based on 185 spectra of various poplar species and hybrid powdered samples, partial least squares regression models, characterized by the relative standard errors of prediction in the 4.5–9.9% range for both calibration and validation sets, were developed. These models allow for fast and precise quantification of the studied active compounds in poplar bark and leaves without any chemical sample treatment.