The Fluorescence Properties and Lifetime Study of G-quadruplexes Single- and Double-labeled with Pyrene

We report steady state fluorescence and lifetime emission studies of d(GGTTGGTGTGGTTGG) (TBA) and d(GGGTTAGGGTTAGGGTTAGGG) (Htelom) oligonucleotides labeled with pyrene through a 3-aminopropyl linker. Such G-rich sequences are able to self-assemble into G-quadruplexes, especially in the presence of specific cations like potassium. A comparative studies with single- and double-labeled G-quadruplexes were carried out. For each probe we have measured fluorescence decays for emission wavelength of 390 and 480 nm in the varying concentration of potassium ion. We have calculated average lifetimes <τ> for every system as well as the fractional distribution α_i of emitting species.     

Formation of PAHs and soot platelets: multiconfiguration theoretical study of the key step in the ring closure–radical breeding polyyne‐based mechanism

Polyynes of general formula H? (C?C? )_nH are known to play a significant role in combustion and pyrolysis, possibly being intermediates in the formation of polycyclic aromatic hydrocarbons (PAHs) and soot. They have also been detected in astrophysical investigations. The key step in the polyyne‐based radical breeding mechanism for PAH growth is a cyclization, put forward by Krestinin, which implies disruption of electron couples, plausibly expected to be energy demanding. We explore the electronic features and energy requirements of such a process by quantum mechanical multiconfiguration methods (CASSCF and CASPT2). The features of the wavefunction are analyzed, and the free energy barriers are estimated over a wide range of temperatures, for three molecular models. The initial radical adduct A, generated by H ^. , HC?C ^. (ethynyl), or HC?C? C ^. H₂ ( propargyl ) addition to butadiyne (BD, HC?C? C?CH), undergoes a cyclization with the generation of two new radical centers. However, in most of the cases, one of these new singly occupied sp² orbitals has some overlap with the unpaired electron lobe already existent in A: some sort of bonding builds up and consequently the triradical character cannot be large. Only one model suggests a possible role of the radical breeding mechanism during combustion. Copyright © 2009 John Wiley & Sons, Ltd.     

Same-sign W pair production as a probe of double-parton scattering at the LHC

We study the production of same-sign W boson pairs at the LHC in double parton interactions. Compared with simple factorised double parton distributions (dPDFs), we show that the recently developed dPDFs, GS09, lead to non-trivial kinematic correlations between the W bosons. A numerical study of the prospects for observing this process using same-sign dilepton signatures, including W ^± W ^± jj, diboson and heavy flavour backgrounds, at 14 TeV centre-of-mass energy is then performed. It is shown that a small excess of same-sign dilepton events from double parton scattering over a background dominated by single scattering W ^± Z(γ ^*) production could be observed at the LHC.     

On the Existence and the Profile of Nodal solutions of Elliptic Equations Involving Critical Growth

We study the existence of sign changing solutions to the slightly subcritical problem

Chemistry of palladium phosphinite (PPh(2)(OR)) and phosphonite (P(OPh)(2)(OH)) complexes: catalytic activity in methoxycarbonylation and Heck coupling reactions

The new phosphinite and phosphonite complexes (1-8) are very efficient catalysts for the methoxycarbonylation of iodobenzene and Heck cross-coupling of bromobenzene with butyl acrylate. High catalytic activity of these complexes can be explained by their in situ transformations during the reaction, stimulated by the presence of water, acid (HCl) or base (NEt(3)). Hydrolysis of phosphinite palladium complexes of the form trans-PdCl(2)[PPh(2)(OR)](2) (R = C(6)F(5), 2, (t)Bu 3, or O-menthyl 4) results in the formation of the dimeric complex [mu-ClPd(PPh(2)OH)(PPh(2)O)](2) 5, which is deprotonated by NEt(3), producing a polymeric complex of formula [Pd(P(O)PPh(2))(2)](n) 8. The reverse reaction, protonolysis of 8 with HCl, leads back to 5 and the monomeric complex 5a. The phosphinite complex PdCl(2)[PPh(2)(OBu)](2)1 with a more lipophilic ligand, PPh(2)(OBu), does not undergo hydrolysis under the same conditions. In the reaction of PdCl(2)(cod) with P(OPh)(2)(OH), the new dimer [mu-ClPd(P(OPh)(2)OH)(P(OPh)(2)O)](2) 6 was obtained, whereas reaction of Pd(OAc)(2) with P(OPh)(2)(OH) leads to the polymeric complex [Pd[P(O)(OPh)(2)](2)](n) 7. Protonolysis of 7 with HCl results in the formation of 6.     

Coordination ability of trans-cyclohexane-1,2-diamine-N,N,N',N'-tetrakis(methylenephosphonic acid) towards lanthanide(III) ions

The proton and metal complex equilibria of trans-cyclohexane-1,2-diamine-N,N,N',N'-tetrakis(methylenephosphonic acid) (CDTP) with lanthanide(iii) ions, where Ln(III) = La(III), Nd(III), Sm(III), Eu(III), Gd(III), Tb(III), Ho(III) and Lu(III) were studied. The stoichiometry, protonation and complex formation constants were determined by potentiometric titration at 25.0 degrees C and ionic strength of 0.1 mol dm(-3) (KCl). All metal ions form several species: [LnH4L]-, [LnH3L](2-), [LnH2L](3-), [LnHL](4-), [LnL](5-), [LnH(-1)L](6-) and [LnH(-2)L](7-) in the pH range between 2 and 11. The stability constants log beta(LnL) were found to be between 14.7 and 16.7. The studied complexes were also characterized by spectroscopic methods (31P NMR, UV-Vis absorption and emission spectroscopy). These studies allowed to reveal a distinct structural change of the Ln(III)-CDTP complex which occurs between protonated and hydroxy species in solutions at pH around 7.5. The major change is caused by the involvement of both nitrogen donors in the metal ion coordination occurring in ML species. The data obtained from UV-Vis spectroscopy allowed to draw conclusions about complex symmetry and to estimate a number of coordinated water molecules. The hydration number or more precisely the number of two OH oscillators was found to be approximately one in all species formed over the pH range between 5 and 10. The structure of the major hydroxy complex was supported by X-ray crystallographic data. The crystal structures of the Eu(III) and Tb(III) complexes clearly show that the CDTP ligand is coordinated to the Ln(III) ion by two nitrogen and four oxygen atoms in such a way that only one oxygen atom from each phosphonic group is placed in the lanthanide inner sphere. The monomeric complex anion is connected to a symmetry related ion through short hydrogen bonds formed by two hydroxy ions and one water molecule. In this way the two neighbouring anions form a quasi-dimer in which one of the Ln(III) ion is seven-coordinate (two N atoms, four O atoms and one hydroxy ion) and the other is eight-coordinate (two N atoms, four O atoms, one hydroxy ion and one water molecule).     

Chemically stable films for combinatorial fluorosensor arrays

Sensor arrays are useful for many purposes. Our interests include quasi-distributed intrinsic fiber optic arrays, those distributed along the length of an optical fiber. We have demonstrated an optical time-of-flight approach to distinguishing the fluorescence output of such arrays, as well as a synthesis of combinatorial libraries that takes advantage of a support of linear morphology to make numerous compounds in a simple manner without information loss in the synthesis. To unite these research areas, we needed an optical fiber cladding material that meets demanding synthetic and optical requirements. We have chosen the Meldal SPOCC polymer support as the best candidate for such a material and report here our initial results with this material.     

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

Parametrization and testing of a new all-atom force field for organic molecules and peptides with fixed bond lengths and bond angles are described. The van der Waals parameters for both the organic molecules and the peptides were taken from J. Phys. Chem. B 2003, 107, 7143 and J. Phys. Chem. B 2004, 108, 12181. First, the values of the 1-4 nonbonded and electrostatic scale factors appropriate to the new force field were determined by computing the conformational energies of six model molecules, namely, ethanol, ethylamine, propanol, propylamine, 1,2-ethanediol, and 1,3-propanediol with different values of these factors. The partial atomic charges of these molecules were obtained by fitting to the electrostatic potentials calculated with the HF/6-31G quantum-mechanical method. Two different charge models (single- and multiple-conformation-derived) were also considered. We demonstrated that the charge model has a stronger effect on the conformational energies than the 1-4 scaling. The choice of a charge model affected the conformational energies of even the smallest molecules considered, whereas the effect of the 1-4 electrostatic or nonbonded scaling was apparent only for 1,3-propanediol. The best agreement with high-level ab initio data was obtained with the multiple-conformation-derived charges and with no scaling of the 1-4 nonbonded or electrostatic interactions (scale factors of 1.0). Next, the torsional parameters of a large number of neutral and charged organic molecules, assumed to be models of the side chains of the 20 naturally occurring amino acids, were computed by fitting to rotational energy profiles obtained from ab initio MP2/6-31G calculations. The quality of the fits was high with average errors for torsional profiles of less than 0.2 kcal/mol. To derive the torsional parameters for the peptide backbone, the partial atomic charges of the 20 neutral and charged amino acids were obtained by fitting to the electrostatic potentials of terminally blocked amino acids using the HF/6-31G quantum-mechanical method. Then, the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe were computed using MP2/6-31G//HF/6-31G quantum-mechanical methods. The phi-psi energy map of Ac-Ala-NMe was used for refinement of the nonbonded parameters for the backbone nitrogen and hydrogen bonded to it. Subsequently, the main-chain torsional parameters were obtained by fitting the molecular mechanics energies to the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe. The transferability of the entire force field was demonstrated by reproducing the main energy minima of terminally blocked Ala3 from the literature. The performance of the force field was also evaluated by simulating crystal structures of small peptides. By comparison of simulated and experimental data, examination of the torsional-angle and atom-positional root-mean-square deviations of the energy-minimized crystal structures from the corresponding X-ray model structures demonstrated high accuracy of the force field.     

The effect of photomask resolution on separation efficiency on microfabricated devices

Separation quality on glass microfluidic devices fabricated from photomasks of different optical resolutions was compared by measuring the dispersion (apparent diffusion) coefficients of a set of standard compounds separated on these devices. Currently, the channel manifolds of most microfluidic devices are patterned using chrome photomasks. A much cheaper, more robust alternative to chrome photomasks are laser photoplotted masks. The primary disadvantage to using laser photoplots is that the optical resolution of these masks is not as high as that of chrome masks, and this feature increases the side-wall roughness of etched channel manifolds patterned using such masks. The increased wall roughness may affect the fluid flow within the channels and, therefore, the separation quality. To determine the effect of increased sidewall channel roughness, microchip channel manifolds were patterned in soda lime glass using a chrome photomask and laser photoplots printed at resolutions of 620, 1240, 3100 and 6200 dots per centimetre (dpc). Separations were performed on these devices using dilute solutions of fluorescently labeled amino acids. The peak variances of the amino acids were calculated at increasing distances down the separation channel and plotted as a function of migration time. From this plot, dispersion coefficients of the analytes were measured. This allowed for a reliable, relatively easy, direct separation analysis among microchips fabricated from the various photomasks. After multiple separations using microchips fabricated from each resolution mask, we found that the change in sidewall surface roughness did not significantly affect the dispersion coefficients measured, and thus the separation quality. The lower mask resolution limit, rather, was governed by the fidelity to which the mask could capture the original CAD design.