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.

Encapsulation of transition metal species into zeolites and molecular sieves as redox catalysts: Part I-preparation and characterisation of nanosized TiO2, CdO and ZnO semiconductor particles anchored in NaY zeolite

In this paper, we report the preparation and characterisation of nanometer-sized TiO2, CdO, and ZnO semiconductor particles trapped in zeolite NaY. Preparation of these particles was carried out via the traditional ion exchange method and subsequent calcination procedure. It was found that the smaller cations, i.e., Cd2+ and Zn2+ could be readily introduced into the SI′ and SII′ sites located in the sodalite cages, through ion exchange; while this is not the case for the larger Ti species, i.e., Ti monomer [TiO]2+ or dimer [Ti2O3]2+ which were predominantly dispersed on the external surface of zeolite NaY. The subsequent calcination procedure promoted these Ti species to migrate into the internal surface of the supercages. These semiconductor particles confined in NaY zeolite host exhibited a significant blue shift in the UV-VIS absorption spectra, in contrast to the respective bulk semiconductor materials, due to the quantum size effect (QSE). The particle sizes calculated from the UV-VIS optical absorption spectra using the effective mass approximation model are in good agreement with the atomic absorption data.

Diurnal variation of small and large ion concentrations in an urban location

A Neutral cluster and Air Ion Spectrometer (NAIS) was used to monitor the concentration of airborne ions on 258 full days between Nov 2011 and Dec 2012 in Brisbane, Australia. The air was sampled from outside a window on the sixth floor of a building close to the city centre, approximately 100 m away from a busy freeway. The NAIS detects all ions and charged particles smaller than 42 nm. It was operated in a 4 min measurement cycle, with ion data recorded at 10 s intervals over 2 min during each cycle. The data were analysed to derive the diurnal variation of small, large and total ion concentrations in the environment. We adapt the definition of Horrak et al (2000) and classify small ions as molecular clusters smaller than 1.6 nm and large ions as charged particles larger than this size...

Observation of ions and particles near busy roads using a Neutral Cluster and Air Ion Spectrometer (NAIS)

Motor vehicles emit large quantities of ions in the form of both charged particles and molecular cluster ions. While, the health effects of inhalation of charged particles is largely unexplored, the concentrations near busy roads and the distance to which these particles and ions are carried have important implications for the exposure of the large percentage of the population that lives close to such roadways. We measured ion concentrations using a neutral cluster and air ion spectrometer (NAIS) near seven busy roads carrying on the average approximately 7000 vehicles hr-1 including about 15% heavy duty diesel vehicles. In this study, charged particle concentrations were measured as a function of downwind distance from the road for the first time. We show that, at a moderate wind speed of 2.0 m s-1, mean charged particle concentrations at the kerb were of the order of 2x104 cm-3 and, more importantly, decreased as d 0.6 where d is the distance from the road. While cluster ions were rapidly depleted by attachment to particles and were not carried to more than about 20 m from the road, elevated concentrations of charged particle were detected up to at least 400 m from the road. Most of the charge on the downwind side was carried on the larger particles, with no excess charge on particles smaller than about 10 nm. At 30 nm, particles carried more than double the charge they would normally carry in equilibrium. There are very few measurements of ions near road traffic and this is the first study of the spatial dispersion of charged particles from a road.

Reaction of Aromatic Peroxyl Radicals with Alkynes: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach

The reaction of the aromatic distonic peroxyl radical cations N-methyl pyridinium-4-peroxyl (PyrOO center dot+) and 4-(N,N,N-trimethyl ammonium)-phenyl peroxyl (AnOO center dot+), with symmetrical dialkyl alkynes 10?ac was studied in the gas phase by mass spectrometry. PyrOO center dot+ and AnOO center dot+ were produced through reaction of the respective distonic aryl radical cations Pyr center dot+ and An center dot+ with oxygen, O2. For the reaction of Pyr center dot+ with O2 an absolute rate coefficient of k1=7.1X10-12 cm3 molecule-1 s-1 and a collision efficiency of 1.2?% was determined at 298 K. The strongly electrophilic PyrOO center dot+ reacts with 3-hexyne and 4-octyne with absolute rate coefficients of khexyne=1.5X10-10 cm3 molecule-1 s-1 and koctyne=2.8X10-10 cm3 molecule-1 s-1, respectively, at 298 K. The reaction of both PyrOO center dot+ and AnOO center dot+ proceeds by radical addition to the alkyne, whereas propargylic hydrogen abstraction was observed as a very minor pathway only in the reactions involving PyrOO center dot+. A major reaction pathway of the vinyl radicals 11 formed upon PyrOO center dot+ addition to the alkynes involves gamma-fragmentation of the peroxy O?O bond and formation of PyrO center dot+. The PyrO center dot+ is rapidly trapped by intermolecular hydrogen abstraction, presumably from a propargylic methylene group in the alkyne. The reaction of the less electrophilic AnOO center dot+ with alkynes is considerably slower and resulted in formation of AnO center dot+ as the only charged product. These findings suggest that electrophilic aromatic peroxyl radicals act as oxygen atom donors, which can be used to generate alpha-oxo carbenes 13 (or isomeric species) from alkynes in a single step. Besides gamma-fragmentation, a number of competing unimolecular dissociative reactions also occur in vinyl radicals 11. The potential energy diagrams of these reactions were explored with density functional theory and ab initio methods, which enabled identification of the chemical structures of the most important products.

Ion-molecule reactions reveal facile radical migration in peptides

Ion-molecule reactions between molecular oxygen and peptide radicals in the gas phase demonstrate that radical migration occurs easily within large biomolecules without addition of collisional activation energy.

Heat of formation of the hydroperoxyl radical HOO via negative ion studies

We present a determination of Delta(f)H(298)(HOO) based upon a negative. ion thermodynamic cycle. The photoelectron spectra of HOO- and DOO- were used to measure the molecular electron affinities (EAs). In a separate experiment, a tandem flowing afterglow-selected ion flow tube (FA-SIFT) was used to measure the forward and reverse rate constants for HOO- + HCdropCH reversible arrow HOOH + HCdropC(-) at 298 K, which gave a value for Delta(acid)H(298)(HOO-H). The experiments yield the following values: EA(HOO) = 1.078 +/- 0.006 eV; T-0((X) over tilde HOO - (A) over tilde HOO) = 0.872 +/- 0.007 eV; EA(DOO) = 1.077 +/- 0.005 eV; T-0((X) over tilde DOO - (A) over tilde DOO) = 0.874 +/- 0.007 eV; Delta(acid)G(298)(HOO-H) = 369.5 +/- 0.4 kcal mol(-1); and Delta(acid)H(298)(HOO-H) = 376.5 +/- 0.4 kcal mol(-1). The acidity/EA thermochemical cycle yields values for the bond enthalpies of DH298(HOO-H) = 87.8 +/- 0.5 kcal mol(-1) and Do(HOO-H) = 86.6 +/- 0.5 kcal mol(-1). We recommend the following values for the heats of formation of the hydroperoxyl radical: Delta(f)H(298)(HOO) = 3.2 +/- 0.5 kcal mol(-1) and Delta(f)H(0)(HOO) = 3.9 +/- 0.5 kcal mol(-1); we recommend that these values supersede those listed in the current NIST-JANAF thermochemical tables.

Molecular genetic investigation of mitochondrial dysfunction in relation to migraine susceptibility

The aim of this research was to assess the role of genetic variation in mitochondrial function and how this relates to migraine pathophysiology. Using our unique Norfolk Island population, a custom in-house next generation sequencing methodology was developed. This data for the first time showed that there is a molecular genetic link between mitochondrial dysfunction and migraine susceptibility. This work has provided the foundation for further studies aimed at utilising the identified markers in improved migraine diagnostic and therapeutic strategies.

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.

Void Geometry Driven Spin Crossover in Zeolite-Encapsulated Cobalt Tris(bipyridyl) Complex Ion

The cobalt(II) tris(bipyridyl) complex ion encapsulated in zeolite-Y supercages exhibits a thermally driven interconversion between a low-spin and a high-spin state-a phenomenon not observed for this ion either in solid state or in solution. From a comparative study of the magnetism and optical spectroscopy of the encapsulated and unencapsulated complex ion, supported by molecular modeling, such spin behavior is shown to be intramolecular in origin. In the unencapsulated or free state, the [Co(bipy)(3)](2+) ion exhibits a marked trigonal prismatic distortion, but on encapsulation, the topology of the supercage forces it to adopt a near-octahedral geometry. An analysis using the angular overlap ligand field model with spectroscopically derived parameters shows that the geometry does indeed give rise to a low-spin ground state, and suggests a possible scenario for the spin state interconversion.

Gel-coated ion-exchange resin: A new kinetic model

Regenerable 'gel-coated' cationic resins with fast sorption kinetics and high sorption capacity have application potential for removal of trace metal ions even in large-scale operations. Poly(acrylic acid) has been gel-coated on high-surface area silica (pre-coated with ethylene-vinyl acetate copolymer providing a thin barrier layer) and insolubilized by crosslinking with a low-molecular-weight diepoxide (epoxy equivalent 180 g) in the presence of benzyl dimethylamine catalyst at 70 degrees C, In experiments performed for Ca2+ sorption from dilute aqueous solutions of Ca(NO,),, the gel-coated acrylic resin is found to have nearly 40% higher sorption capacity than the bead-form commercial methacrylic resin Amberlite IRC-50 and also several limes higher rate of sorption. The sorption on the gel-coated sorbent under vigorous agitation has the characteristics of particle diffusion control with homogeneous (gel) diffusion in resin phase. A new mathematical model is proposed for such sorption on gel-coated ion-exchange resin in finite bath and solved by applying operator-theoretic methods. The analytical solution so obtained shows goad agreement with experimental sorption kinetics at relatively low levels (< 70%) of resin conversion.

Ultrafast Solvation Dynamics of an Ion in the gamma-Cyclodextrin Cavity: The Role of Restricted Environment

A detailed study of the solvation dynamics of a charged coumarin dye molecule in gamma-cyclodextrin/water has been carried out by using two different theoretical approaches. The first approach is based on a multishell continuum model (MSCM). This model predicts the time scales of the dynamics rather well, provided an accurate description of the frequency-dependent dielectric function is supplied. The reason for this rather surprising agreement is 2-fold. First, there is a cancellation of errors, second, the two-zone model mimics the heterogeneous microenvironment surrounding the ion rather well. The second approach is based on the molecular hydrodynamics theory (MI-IT). In this molecular approach, the solvation dynamics has been studied by restricting the translational motion of the solvent molecules enclosed within the cavity. The results from the molecular theory are also in good agreement with the experimental results. Our study indicates that, in the present case, the restricted environment affects only the long time decay of the solvation time correlation function. The short time dynamics is still governed by the librational (and/or vibrational) modes present in bulk water.

Dynamics of the ammonium ion in the ferroelectric transition in sodium ammonium selenate, NaNH4SeO4·2H2O-an E.S.R. study

E.S.R. investigations of γ-irradiated ferroelectric Sodium ammonium selenate, NaNH4SeO4•2H2O and its deuteriated analogue in powder and single crystal forms have led to a deeper understanding of the nature of the ferroelectric transition of 180 K. A number of paramagnetic species formed due to γ-irradiation have been identified on the basis of their g-factors and hyperfine features from 77Se. The radical SeO4 has been used as a microprobe in studying the phase transition.

Bile Acid Derived PET-Based Cation Sensors: Molecular Structure Dependence of their Sensitivity

A number of bile acid derived photoinduced electron transfer (PET) based sensors for metal ions are prepared. A general strategy for designing the sensor with a modular nature allows for making different molecules capable of sensing different metal ions by a change in the fluorophore and receptor unit. Keeping the basic molecular structure the same, different bile acid base fluoroionophores were prepared inorder to achieve the highest sensitivity toward the metal ions. Thesensors showed similar binding constants for the same metal ion, but the degree Of fluorescence enhancement upon addition of the metal salts were different. The sensitivities of the sensors towards a certain metal were determined from the observed fluorescence enhancement upon addition of the metal salt.