The effect of the counterion on water mobility in reverse micelles studied by molecular dynamics simulations

In this study, mobility and structure of water molecules in Aerosol OT (bis(2-ethylhexyl) sulfosuccinate, AOT) reverse micelles with water content w0 = 5 and Na+, K+, Cs+ counterions have been explored with molecular dynamics (MD) simulations. Using the Faeder/Ladanyi model (J. Phys. Chem. B, 2000, 104, 1033) of the reverse micelle interior, MD simulations were performed to calculate the self-intermediate scattering function, FS(Q,t), for water hydrogen atoms that could be measured in a quasielastic neutron scattering experiment. Separate intermediate scattering functions FRS(Q,t) and FCMS(Q,t) were determined for rotational and translational motion. We find that the decay of FCMS(Q,t) is nonexponential and our analysis of the MD data indicates that this behavior arises from decreased water mobility for molecules close to the interface and from confinement-induced restrictions on the range of translational displacements. Rotational relaxation also exhibits nonexponential decay, which is consistent with relatively rapid restricted rotation and slower rotational relaxation over the full angular range. Rotational relaxation is anisotropic, with the O-H bond short-time rotational mobility considerably higher than that of the molecular dipole. This behavior is related to the decreased density of water-water hydrogen bonds in the vicinity of the interface compared to core or bulk water. We find that the interfacial mobility of water molecules is quite different for the three counterion types, but that the core mobility exhibits weak counterion dependence. Differences in interfacial mobility are strongly correlated with structural features, especially ion-water coordination, and the extent of disruption by the counterions of the water hydrogen bond network.     

Overtone spectroscopy of H2O clusters in the V(OH) = 2 manifold: infrared-ultraviolet vibrationally mediated dissociation studies

Spectroscopy and predissociation dynamics of (H2O)2 and Ar-H2O are investigated with vibrationally mediated dissociation (VMD) techniques, wherein upsilon(OH) = 2 overtones of the complexes are selectively prepared with direct infrared pumping, followed by 193 nm photolysis of the excited H2O molecules. As a function of relative laser timing, the photolysis breaks H2O into OH and H fragments either (i) directly inside the complex or (ii) after the complex undergoes vibrational predissociation, with the nascent quantum state distribution of the OH photofragment probed via laser-induced fluorescence. This capability provides the first rotationally resolved spectroscopic analysis of (H2O)2 in the first overtone region and vibrational predissociation dynamics of water dimer and Ar-water clusters. The sensitivity of the VMD approach permits several upsilon(OH) = 2 overtone bands to be observed, the spectroscopic assignment of which is discussed in the context of recent anharmonic theoretical calculations.     

EFFECT OF METAL IONS ON THE LUMINESCENCE OF ACRIDINE DYES BOUND TO DNA

Abstract— The luminescence of acridine dyes intercalated in DNA was studied as a function of the concurrent binding of metal ions to DNA, in an effort to deduce specific site interactions of the dyes. Two dyes, proflavine (PF) and acridine orange (AO), and two metal ions, silver and mercuric, were used. Both ions quench the fluorescence of the dyes in aqueous solution at room temperature. The metal ions have a different effect on the fluorescence of these dyes when they are intercalated between the base pairs of DNA. The fluorescence of AO is decreased when silver is bound, while the fluorescence of PF is enhanced. Since Ag⁺ initially binds to GC sites in DNA, which quench the PF fluorescence, it ostensibly 'turns off' the quenching by DNA at these sites, and this effect is greater than the quenching effect of the silver ion itself. Hg²⁺ ion initially binds to AT sites in DNA. Since both dyes fluoresce from AT sites, Hg²⁺ is expected to quench their fluorescence. This behavior is observed at low r (metal ion/base). At higher r values, however, where Hg²⁺ is expected to begin binding to GC sites, the fluorescence of PF is enhanced. These quenching turn-off effects are tentatively interpreted in terms of a change in the structure of the dye/DNA complex which occurs when a metal ion binds at the intercalation site. At 77 K. no fluorescence enhancement is observed when metal ions bind; Ag⁺ quenches the fluorescence and enhances the phosphorescence of both dyes. Qualitatively similar results are obtained with Hg²⁺.     

Nucleoside und Nucleotide. Teil 16. Verhalten von 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyrimidinon-5′-triphosphat, 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)pyridinon-5′-triphosphat und 4-Amino-1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyridinon-5′-triphosphat gegenüber DNA-Polymerase

Nucleosides and Nucleotides. Part 16. The Behaviour of 1-(2′-Deoxy-β-D -ribofuranosyl)-2(1H)-pyrimidinone-5′-triphosphate, 1-(2′-Deoxy-β-D -ribofuranosyl-2(1H))-pyridinone-5′-triphosphate and 4-Amino-1-(2′-desoxy-β-D -ribofuranosyl)-2(1H)-pyridinone-5′-triphosphate towards DNA Polymerase The behaviour of nucleotide base analogs in the DNA synthesis in vitro was studied. The investigated nucleoside-5′-triphosphates 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyrimidinone-5′-triphosphate (pppM_d), 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppII_d) and 4-amino-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppZ_d) can be considered to be analogs of 2′-deoxy-cytidine-5′-triphosphate. However, their ability to undergo base pairing to the complementary guanine is decreased. When pppM_d, pppII_d or pppZ_d are substituted for pppC_d in the enzymatic synthesis of DNA by DNA polymerase no incorporation of these analogs is observed. They exhibit only a weak inhibition of the DNA synthesis. The mode of the inhibition is uncompetitive which shows that these nucleotide analogs cannot serve as substrates for the DNA polymerase.     

Lower bounds on the cluster size distribution

We rigorously prove that the probabilityP _n that the origin of ad-dimensional lattice belongs to a cluster of exactlyn sites satisfiesP _n > exp(–n ^(d–1)/d ) whenever percolation occurs. This holds for the usual (noninteracting) percolation models for any concentrationp > p _c , as well as for the equilibrium states of lattice spin systems with quite general interactions. Such a lower bound applies also if no percolation occurs, but if it appears in some other phase of the system.     

Translation invariance and instability of phase coexistence in the two dimensional Ising system

It is shown that any Gibbs state of the two dimensional ferromagnetic Ising system is of the form ₊+(1–)_–, with some [0, 1]. This excludes the possibility of a locally stable phase coexistence and of translation symmetry breaking, which are known to occur in higher dimensions. Use is made in the proof of the stochastic aspects of the geometry of the interface lines.Supported in part by the U.S. National Science Foundation under the grant PHY — 7825390     

On bounded solutions of a classical yang-mills equation

We discuss bounded solutions of the equation $$r^2 \left( {\frac{{\partial ^2 u}}{{\partial r^2 }} + \frac{{\partial ^2 u}}{{\partial t^2 }}} \right) = u^3 - u$$ in the halfspacer>0. All solutions depending only ont/r are characterized topologically. Then we prove the existence of infinite dimensional manifolds oft-periodic as well as nonperiodic solutions which are small in a suitable norm.     

Identification of marker proteins for Bacillus anthracis using MALDI-TOF MS and ion trap MS/MS after direct extraction or electrophoretic separation

Direct extraction of bacterial vegetative cells or spores followed by matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI TOF MS) has become popular for bacterial identification, since it is simple to perform and mass spectra are readily interpreted. However, only high-abundance proteins that are of low mass and ionize readily are observed. In the case of B. anthracis spores, small acid-soluble spore proteins (SASPs) have been the most widely studied. Additional information can be obtained using tandem mass spectrometry (MS-MS) to confirm the identity of proteins by sequencing. This is most readily accomplished using ion trap (IT) MS-MS. However, enzymatic digestion of these proteins is needed to generate peptides that are within the mass range of the ion trap. The use of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), or other forms of electrophoresis, allows one to focus on specific proteins of interest (e.g. the high mass exosporium glycoproteins BcIA and BcIB) that provide additional species- and strain-specific discrimination.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Diphosphine-phosphenium coordination complexes representing monocations with pendant donors and ligand tethered dications

Homoatomic P-P coordinate bonding is exploited to prepare the first examples of triphosphorus monocations and tetraphosphorus dications using dimethylphosphenium or diphenylphosphenium Lewis acceptors with diphosphinomethane, diphosphinoethane, diphosphinohexane, or diphosphinobenzene ligands. Solid-state structures and spectroscopic characterization data for complexes involving bis(diphenylphosphino)methane ligands show coordination of only one donor site of the diphosphine ligand in the monocations, and chelate complexation is not observed. Tetraphosphorus dications are observed with longer diphosphines, in which the ligand tethers two phosphenium acceptors. The structural preferences between monocations with pendant phosphines and tethered dications are dependent on intramolecular steric interactions and the flexibility of the tether.