Comparison of the binding stoichiometries of positively charged DNA-binding drugs using positive and negative ion electrospray ionization mass spectrometry

Positive and negative ion electrospray ionization (ESI) mass spectra of complexes of positively charged small molecules (distamycin, Hoechst 33258, [Ru(phen)2dpq]Cl2 and [Ru(phen)2dpqC]Cl2) have been compared. [Ru(phen)2dpq]Cl2 and [Ru(phen)2dpqC]Cl2 bind to DNA by intercalation. Negative ion ESI mass spectra of mixtures of [Ru(phen)2dpq]Cl2 or [Ru(phen)2dpqC]Cl2 with DNA showed ions from DNA-ligand complexes consistent with solution studies. In contrast, only ions from freeDNAwere present in positive ion ESI mass spectra of mixtures of [Ru(phen)2dpq]Cl2 or [Ru(phen)2dpqC]Cl2 with DNA, highlighting the need for obtaining ESI mass spectra of non-covalent complexes under a range of experimental conditions. Negative ion spectra of mixtures of the minor groove binder Hoechst 33258 with DNA containing a known minor groove binding sequence were dominated by ions from a 1:1 complex. In contrast, in positive ion spectra there were also ions present from a 2:1 (Hoechst 33258: DNA) complex, suggesting an alternative binding mode was possible either in solution or in the gas phase. When Hoechst 33258 was mixed with a DNA sequence lacking a high affinity minor groove binding site, the negative ion ESI mass spectra showed that 1:1 and 2:1 complexes were formed, consistent with existence of binding modes other than minor groove binding. The data presented suggest that comparison of positive and negative ion ESI-MS spectra might provide an insight into various binding modes in both solution and the gas phase.

Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism

Significant cleavage by hammerhead ribozymes requires activation by divalent metal ions. Several models have been proposed to account for the influence of metal ions on hammerhead activity. A number of recent papers have presented data that have been interpreted as supporting a one-metal-hydroxide-ion mechanism. In addition, a solvent deuterium isotope effect has been taken as evidence against a proton transfer in the rate-limiting step of the cleavage reaction. We propose that these data are more easily explained by a two-metal-ion mechanism that does not involve a metal hydroxide, but does involve a proton transfer in the rate-limiting step.

Mixed convection over a horizontal plate with streamwise non-uniform surface temperature distribution

Numerical investigation on mixed convection of a two-dimensional incompressible laminar flow over a horizontal flat plate with streamwise sinusoidal distribution of surface temperature has been performed for different values of Rayleigh number, Reynolds number and frequency of periodic temperature for constant Prandtl number and amplitude of periodic temperature. Finite element method adapted to rectangular non-uniform mesh elements by a non-linear parametric solution algorithm basis numerical scheme has been employed. The investigating parameters are the Rayleigh number, the Reynolds number and frequency of periodic temperature. The effect of variation of individual investigating parameters on mixed convection flow characteristics has been studied to observe the hydrodynamic and thermal behavior for while keeping the other parameters constant. The fluid considered in this study is air with Prandtl number 0.72. The results are obtained for the Rayleigh number range of 102 to 104, Reynolds number ranging from 1 to 100 and the frequency of periodic temperature from 1 to 5. Isotherms, streamlines, average and local Nusselt numbers are presented to show the effect of the different values of aforementioned investigating parameters on fluid flow and heat transfer.

High-resolution imaging of ordered mixed-layer clays

HRTEM has been used to examine illite/smectite from the Mancos shale, rectorite from Garland County, Arkansas; illite from Silver Hill, Montana; Na-smectite from Crook County, Wyoming; corrensite from Packwood, Washington; and diagenetic chlorite from the Tuscaloosa formation. Thin specimens were prepared by ion milling, ultra-microtome sectioning and/or grain dispersal on a porous carbon substrate. Some smectite-bearing clays were also examined after intercalation with dodecylamine hydrochloride (DH). Intercalation of smectite with DH proved to be a reliable method of HRTEM imaging of expanded smectite, d(001) 16 A which could then be distinguished from unexpanded illite, d(001) 10 A. Lattice fringes of basal spacings of DH-intercalated rectorite and illite/smectite showed 26 A periodicity. These data support XRD studies which suggest that these samples are ordered, interstratified varieties of illite and smectite. The ion-thinned, unexpanded corrensite sample showed discrete crystallites containing 10 A and 14 A basal spacings corresponding with collapsed smectite and chlorite, respectively. Regions containing disordered layers of chlorite and smectite were also noted. Crystallites containing regular alternations of smectite and chlorite were not common. These HRTEM observations of corrensite did not corroborate XRD data. Particle sizes parallel to the c axis ranged widely for each sample studied, and many particles showed basal dimensions equivalent to > five layers. -J.M.H.

Gas-Phase Transformation of Phosphatidylcholine Cations to Structurally Informative Anions via Ion/Ion Chemistry

Gas-phase transformation of synthetic phosphatidylcholine (PC) monocations to structurally informative anions is demonstrated via ion/ion reactions with doubly deprotonated 1,4-phenylenedipropionic acid (PDPA). Two synthetic PC isomers, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC16:0/18:1) and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (PC18:1/16:0), were subjected to this ion/ion chemistry. The product of the ion/ion reaction is a negatively charged complex, \[PC + PDPA - H](-). Collisional activation of the long-lived complex causes transfer of a proton and methyl cation to PDPA, generating \[PC - CH3](-). Subsequent collisional activation of the demethylated PC anions produces abundant fatty acid carboxylate anions and low-abundance acyl neutral losses as free acids and ketenes. Product ion spectra of \[PC - CH3](-) suggest favorable cleavage at the sn-2 position over the sn-1 due to distinct differences in the relative abundances. In contrast, collisional activation of PC cations is absent of abundant fatty acid chain-related product ions and typically indicates only the lipid class via formation of the phosphocholine cation. A solution phase method to produce the gas-phase adducted PC anion is also demonstrated. Product ion spectra derived from the solution phase method are similar to the results generated via ion/ion chemistry. This work demonstrates a gas-phase means to increase structural characterization of phosphatidylcholines via ion/ion chemistry. Grant Number ARC/CE0561607, ARC/DP120102922

Negative-ion photoelectron spectroscopy, gas-phase acidity, and thermochemistry of the peroxyl radicals CH3OO and CH3CH2OO

Methyl, methyl-d(3), and ethyl hydroperoxide anions (CH3OO-, CD3OO-, and CH3CH2OO-) have been prepared by deprotonation of their respective hydroperoxides in a stream of helium buffer, gas. Photodetachment with 364 nm (3.408 eV) radiation was used to measure the adiabatic electron affinities: EA[CH3OO, (X) over tilde (2)A"] = 1.161 +/- 0.005 eV, EA[CD3OO, (X) over tilde (2)A"] = 1.154 +/- 0.004 eV, and EA[CH3CH2OO, (X) over tilde (2)A"] = 1.186 +/- 0.004 eV. The photoelectron spectra yield values for the term energies: DeltaE((X) over tilde 2A"-(A) over tilde 2A')[CH3OO] = 0.914 +/- 0.005 eV, DeltaE((X) over tilde (2)A"-(A) over tilde 2A') [CD3OO] = 0.913 +/- 0.004 eV, and DeltaE((X) over tilde (2)A"-(A) over tilde (2)A')[CH3CH2OO] = 0.938 +/- 0.004 eV. A localized RO-O stretching mode was observed near 1100 cm(-1) for the ground state of all three radicals, and low-frequency R-O-O bending modes are also reported. Proton-transfer kinetics of the hydroperoxides have been measured in a tandem flowing afterglow-selected ion flow tube k(FA-SIFT) to determine the gas-phase acidity of the parent hydroperoxides: Delta (acid)G(298)(CH3OOH) = 367.6 +/- 0.7 kcal mol(-1), Delta (acid)G(298)(CD3OOH) = 367.9 +/- 0.9 kcal mol(-1), and Delta (acid)G(298)(CH3CH2OOH) = 363.9 +/- 2.0 kcal mol(-1). From these acidities we have derived the enthalpies of deprotonation: Delta H-acid(298)(CH3OOH) = 374.6 +/- 1.0 kcal mol(-1), Delta H-acid(298)(CD3OOH) = 374.9 +/- 1.1 kcal mol(-1), and Delta H-acid(298)(CH2CH3OOH) = 371.0 +/- 2.2 kcal mol(-1). Use of the negative-ion acidity/EA cycle provides the ROO-H bond enthalpies: DH298(CH3OO-H) 87.8 +/- 1.0 kcal mol(-1), DH298(CD3OO-H) = 87.9 +/- 1.1 kcal mol(-1), and DH298(CH3CH2OO-H) = 84.8 +/- 2.2 kcal mol(-1). We review the thermochemistry of the peroxyl radicals, CH3OO and CH3CH2OO. Using experimental bond enthalpies, DH298(ROO-H), and CBS/APNO ab initio electronic structure calculations for the energies of the corresponding hydroperoxides, we derive the heats of formation of the peroxyl radicals. The "electron affinity/acidity/CBS" cycle yields Delta H-f(298)[CH3OO] = 4.8 +/- 1.2 kcal mol(-1) and Delta H-f(298)[CH3CH2OO] = -6.8 +/- 2.3 kcal mol(-1).

Reactions of the hydroperoxide anion with dimethyl methylphosphonate in an ion trap mass spectrometer : evidence for a gas phase alpha-effect

The gas phase degradation reactions of the chemical warfare agent (CWA) simulant, dimethyl methylphosphonate (DMMP), with the hydroperoxide anion (HOO(-)) were investigated using a modified quadrupole ion trap mass spectrometer. The HOO(-) anion reacts readily with neutral DMMP forming two significant product ions at m/z 109 and m/z 123. The major reaction pathways correspond to (i) the nucleophilic substitution at carbon to form \[CH(3)P(O)(OCH(3))O](-) (m/z 109) in a highly exothermic process and (ii) exothermic proton transfer. The branching ratios of the two reaction pathways, 89% and 11% respectively, indicate that the former reaction is significantly faster than the latter. This is in contrast to the trend for the methoxide anion with DMMP, where proton transfer dominates. The difference in the observed reactivities of the HOO(-) and CH(3)O(-) anions can be considered as evidence for an a-effect in the gas phase and is supported by electronic structure calculations at the B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d) level of theory that indicate the S(N)2(carbon) process has an activation energy 7.8 kJ mol(-1) lower for HOO(-) as compared to CH(3)O(-). A similar alpha-effect was calculated for nucleophilic addition-elimination at phosphorus, but this process an important step in the perhydrolysis degradation of CWAs in solution - was not observed to occur with DMMP in the gas phase. A theoretical investigation revealed that all processes are energetically accessible with negative activation energies. However, comparison of the relative Arrhenius pre-exponential factors indicate that substitution at phosphorus is not kinetically competitive with respect to the S(N)2(carbon) and deprotonation processes.

Ion-molecule reactions of O,S-Dimethyl methylphosphonothioate : Evidence for intramolecular sulfur oxidation during VX perhydrolysis

The alkaline perhydrolysis of the nerve agent O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate (VX) was investigated by studying the ion-molecule reactions of HOO(-) with O,S-dimethyl methylphosphonothioate in a modified linear ion-trap mass spectrometer. In addition to simple proton transfer, two other abundant product ions are observed at m/z 125 and 109 corresponding to the S-methyl methylphosphonothioate and methyl methylphosphonate anions, respectively. The structure of these product ions is demonstrated by a combination of collision-induced dissociation and isotope-labeling experiments that also provide evidence for their formation by nucleophilic reaction pathways, namely, (i) S(N)2 at carbon to yield the S-methyl methylphosphonothioate anion and (ii) nucleophilic addition at phosphorus affording a reactive pentavalent intermediate that readily undergoes internal sulfur oxidation and concomitant elimination of CH(3)SOH to yield the methyl methylphosphonate anion. Consistent with previous Solution phase observations of VX perhydrolysis, the toxic P-O cleavage product is not observed in this VX model system and theoretical calculations identify P-O cleavage to be energetically uncompetitive. Conversely, intramolecular sulfur oxidation is calculated to be extremely exothermic and kinetically accessible explaining its competitiveness with the facile gas phase proton transfer process. Elimination of a sulfur moiety deactivates the nerve agent VX and thus the intramolecular sulfur oxidation process reported here is also able to explain the selective perhydrolysis of the nerve agent to relatively nontoxic products.

Turning points, power transfer, and frequency response of mode transitions in RF plasmas

Turning points for transitions between the electrostatic and electromagnetic discharge modes in low-frequency (∼ 500 kHz) inductively coupled plasmas have been identified and cross-referenced using time-resolved measurements of the plasma optical emission intensities, RF coil current, and ion saturation current collected by a single RF-compensated Langmuir probe. This enables one to monitor the variation of the plasma parameters, power transfer efficiency, which accompany the discharge hysteresis. The excitation conditions for the pure and hybrid modes in the plasma are considered, and the possibility of the TMmnl → TEm'n'l' transitions at higher frequencies are discussed.

Onset of transition in mixed convection of a lid-driven trapezoidal enclosure filled with water-Al2O3 nanofluid

A numerical study is carried out to investigate the transition from laminar to chaos in mixed convection heat transfer inside a lid-driven trapezoidal enclosure. In this study, the top wall is considered as isothermal cold surface, which is moving in its own plane at a constant speed, and a constant high temperature is provided at the bottom surface. The enclosure is assumed to be filled with water-Al2O3 nanofluid. The governing Navier–Stokes and thermal energy equations are expressed in non-dimensional forms and are solved using Galerkin finite element method. Attention is paid in the present study on the pure mixed convection regime at Richandson number, Ri = 1. The numerical simulations are carried out over a wide range of Reynolds (0.1 ≤ Re ≤ 103) and Grashof (0.01 ≤ Gr ≤ 106) numbers. Effects of the presence of nanofluid on the characteristics of mixed convection heat transfer are also explored. The average Nusselt numbers of the heated wall are computed to demonstrate the influence of flow parameter variations on heat transfer. The corresponding change of flow and thermal fields is visualized from the streamline and the isotherm contour plots.

Non-Newtonian mixed convection flow from a horizontal circular cylinder with uniform surface heat flux

Mixed convection laminar two-dimensional boundary-layer flow of non-Newtonian pseudo-plastic fluids is investigated from a horizontal circular cylinder with uniform surface heat flux using a modified power-law viscosity model, that contains no unrealistic limits of zero or infinite viscosity; consequently, no irremovable singularities are introduced into boundary-layer formulations for such fluids. The governing boundary layer equations are transformed into a non-dimensional form and the resulting nonlinear systems of partial differential equations are solved numerically applying marching order implicit finite difference method with double sweep technique. Numerical results are presented for the case of shear-thinning fluids in terms of the fluid temperature distributions, rate of heat transfer in terms of the local Nusselt number.

Helix-sheet interconversion in a synthetic pore lining peptide derived from a designed ion channel

We have designed a four-helix protein that is expected to tetramerize in the membrane to form an ion channel with a structurally well defined pore. A synthetic peptide corresponding to the channel lining helix facilitates ion transport across liposomal membranes and largely helical in membranes. Detailed circular dichroism studies of the peptide in methanol, water and methanal-water mixtures reveal that it is helical in methanol, beta-structured in 97.5% water and a combination of these two structures at intermediate compositions of methanol and water. A fluorescence resonance energy transfer study of the peptide shows that the peptide is monomeric in methanol but undergoes extensive anti-parallel aggregation in aqueous solution.

Mixed Convection Boundary Layer Flow Past a Horizontal Circular Cylinder Embedded in a Bidisperse Porous Medium

Adopting a two-temperature and two-velocity model, appropriate to a bidisperse porous medium (BDPM) proposed by Nield and Kuznetsov (2008), the classical steady, mixed convection boundary layer flow about a horizontal, isothermal circular cylinder embedded in a porous medium has been theoretically studied in this article. It is shown that the boundary layer analysis leads to expressions for the flow and heat transfer characteristics in terms of an inter-phase momentum parameter, a thermal diffusivity ratio, a thermal conductivity ratio, a permeability ratio, a modified thermal capacity ratio, and a buoyancy or mixed convection parameter. The transformed partial differential equations governing the flow and heat transfer in the f-phase (the macro-pores) and the p-phase (the remainder of the structure) are solved numerically using a very efficient implicit finite-difference technique known as Keller-box method. A good agreement is observed between the present results and those known from the open literature in the special case of a traditional Darcy formulation (monodisperse system).

Turbulent mixed convection in a shallow enclosure with a series of heat generating components

Turbulent mixed convection flow and heat transfer in a shallow enclosure with and without partitions and with a series of block-like heat generating components is studied numerically for a range of Reynolds and Grashof numbers with a time-dependent formulation. The flow and temperature distributions are taken to be two-dimensional. Regions with the same velocity and temperature distributions can be identified assuming repeated placement of the blocks and fluid entry and exit openings at regular distances, neglecting the end wall effects. One half of such module is chosen as the computational domain taking into account the symmetry about the vertical centreline. The mixed convection inlet velocity is treated as the sum of forced and natural convection components, with the individual components delineated based on pressure drop across the enclosure. The Reynolds number is based on forced convection velocity. Turbulence computations are performed using the standard k– model and the Launder–Sharma low-Reynolds number k– model. The results show that higher Reynolds numbers tend to create a recirculation region of increasing strength in the core region and that the effect of buoyancy becomes insignificant beyond a Reynolds number of typically 5×105. The Euler number in turbulent flows is higher by about 30 per cent than that in the laminar regime. The dimensionless inlet velocity in pure natural convection varies as Gr1/3. Results are also presented for a number of quantities of interest such as the flow and temperature distributions, Nusselt number, pressure drop and the maximum dimensionless temperature in the block, along with correlations.

Efficient Hg and Ag ion detection with luminescent PbS quantum dots grown in poly vinyl alcohol and capped with mercaptoethanol

PbS quantum dots capped with mercaptoethanol (C2H5OSH) have been synthesized in poly vinyl alcohol and used to investigate their photoluminescence (PL) response to various ions such as zinc (Zn), cadmium (Cd), mercury (Hg), silver (Ag), copper (Cu), iron (Fe), manganese (Mn), cobalt (Co), chromium (Cr) and nickel (Ni). The enhancement in the PL intensity was observed with specific ions namely Zn, Cd, Hg and Ag. Among these four ions, the PL response to Hg and Ag even at sub-micro-molar concentrations was quite high, compared to that of Zn and Cd. It was observed that the change in Pb and S molar ratio has profound effect on the sensitivity of these ions. These results indicate that the sensitivity of these QDs could be fine-tuned by controlling the S concentration at the surface. Contrary to the above, Cu quenched the photoluminescence. In Cd based QDs related ion probing, Hg and Cu was found to have quenching properties, however, our PbS QDs have quenching property only for Cu ions. This was attributed to the formation HgS at the surface that has bandgap higher than PbS. Another interesting property of PbS in PVA observed is photo-brightening mechanism due to the curing of the polymer with laser. However, the presence of excess ions at the surface changes its property to photo-darkening/brightening that depends on the direction of carrier transfer mechanism (from QDs to the surface adsorbed metal ions or vice-versa). which is an interesting feature for metal ion detectivity.