ON THE MOLECULAR COMPLEXITY OF THE HOT CORES IN ORION-A - GRAIN SURFACE-CHEMISTRY AS THE LAST REFUGE OF THE SCOUNDREL

We have modeled the gas phase chemistry of warm molecular material around protostars that is seeded with evaporating grain mantles. We show that the release of simple molecules into the gas drives ion-molecule and neutral chemistries which can account for many of the complex 0-bearing and N-bearing molecules observed in hot cores. Initial grain mantle components and secondary product molecules are identified, and the observational consequences are discussed.

Molecular Logic Gates and Luminescent Sensors Based on Photoinduced Electron Transfer

The competition between Photoinduced electron transfer (PET) and other de-excitation pathways such as fluorescence and phosphorescence can be controlled within designed molecular structures. Depending on the particular design, the resulting optical output is thus a function of various inputs such as ion concentration and excitation light dose. Once digitized into binary code, these input-output patterns can be interpreted according to Boolean logic. The single-input logic types of YES and NOT cover simple sensors and the double- (or higher-) input logic types represent other gates such as AND and OR. The logic-based arithmetic processors such as half-adders and half-subtractors are also featured. Naturally, a principal application of the more complex gates is in multi-sensing contexts.

Low pressure carbon dioxide solubility in pure electrolyte solvents for lithium-ion batteries as a function of temperature. Measurement and prediction

Experimental values for the carbon dioxide solubility in eight pure electrolyte solvents for lithium ion batteries – such as ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonate (DMC), ethyl methyl carbonate (EMC), diethyl carbonate (DEC), ?-butyrolactone (?BL), ethyl acetate (EA) and methyl propionate (MP) – are reported as a function of temperature from (283 to 353) K and atmospheric pressure. Based on experimental solubility data, the Henry’s law constant of the carbon dioxide in these solvents was then deduced and compared with reported values from the literature, as well as with those predicted by using COSMO-RS methodology within COSMOthermX software and those calculated by the Peng–Robinson equation of state implemented into Aspen plus. From this work, it appears that the CO2 solubility is higher in linear carbonates (such as DMC, EMC, DEC) than in cyclic ones (EC, PC, ?BL). Furthermore, the highest CO2 solubility was obtained in MP and EA solvents, which are comparable to the solubility values reported in classical ionicliquids. The precision and accuracy of the experimental values, considered as the per cent of the relative average absolute deviations of the Henry’s law constants from appropriate smoothing equations and from literature values, are close to (1% and 15%), respectively. From the variation of the Henry’s law constants with temperature, the partial molar thermodynamic functions of dissolution such as the standard Gibbs free energy, the enthalpy, and the entropy are calculated, as well as the mixing enthalpy of the solvent with CO2 in its hypothetical liquid state.

Nonadiabatic forces in ion-solid interactions:The initial stages of radiation damage

The Born-Oppenheimer approximation is the keystone for molecular dynamics simulations of radiation damage processes; however, actual materials response involves nonadiabatic energy exchange between nuclei and electrons. In this work, time dependent density functional theory is used to calculate the electronic excitations produced by energetic protons in Al. We study the influence of these electronic excitations on the interatomic forces and find that they differ substantially from the adiabatic case, revealing a nontrivial connection between electronic and nuclear stopping that is absent in the adiabatic case. These results unveil new effects in the early stages of radiation damage cascades.

Investigation into mercury bound to biothiols:structural identification using ESI-ion-trap MS and introduction of a method for their HPLC separation with simultaneous detection by ICP-MS and ESI-MS

Mercury in plants or animal tissue is supposed to occur in the form of complexes formed with biologically relevant thiols (biothiols), rather than as free cation. We describe a technique for the separation and molecular identification of mercury and methylmercury complexes derived from their reactions with cysteine (Cys) and glutathione (GS): Hg(Cys)(2), Hg(GS)(2), MeHgCys, MeHgGS. Complexes were characterised by electrospray mass spectrometry (MS) equipped with an ion trap and the fragmentation pattern of MeHgCys was explained by using MP2 and B3LYP calculations, showing the importance of mercury-amine interactions in the gas phase. Chromatographic baseline separation was performed within 10 min with formic acid as the mobile phase on a reversed-phase column. Detection was done by online simultaneous coupling of ES-MS and inductively coupled plasma MS. When the mercury complexes were spiked in real samples (plant extracts), no perturbation of the separation and detection conditions was observed, suggesting that this method is capable of detecting mercury biothiol complexes in plants.

Low pressure carbon dioxide solubility in lithium-ion batteries based electrolytes as a function of temperature. Measurement and prediction

We present in this study the effect of nature and concentration of lithium salt, such as the lithium hexafluorophosphate, LiPF6; lithium tris(pentafluoroethane)-trifluorurophosphate LiFAP; lithium bis(trifluoromethylsulfonyl)imide, LiTFSI, on the CO2 solubility in four electrolytes for lithium ion batteries based on pure solvent that include ethylene carbonate (EC), dimethyl carbonate (DMC), ethyl methyl carbonate (EMC), diethyl carbonate (DEC), as well as, in the EC:DMC, EC:EMC and EC:DEC (50:50) wt.% binary mixtures as a function of temperature from (283 to 353) K and atmospheric pressure. Based on experimental solubility values, the Henry’s law constant of the carbon dioxide in these solutions with the presence or absence of lithium salt was then deduced and compared with reported values from the literature, as well as with those predicted by using COSMO-RS methodology within COSMOThermX software. From this study, it appears that the addition of 1 mol · dm-3 LiPF6 salt in alkylcarbonate solvents decreases their CO2 capture capacity. By using the same experimental conditions, an opposite CO2 solubility trend was generally observed in the case of the addition of LiFAP or LiTFSI salts in these solutions. Additionally, in all solutions investigated during this work, the CO2 solubility is greater in electrolytes containing the LiFAP salt, followed by those based on the LiTFSI case. The precision and accuracy of the experimental data reported therein, which are close to (1 and 15)%, respectively. From the variation of the Henry’s law constant with temperature, the partial molar thermodynamic functions of dissolution such as the standard Gibbs energy, the enthalpy, and the entropy, as well as the mixing enthalpy of the solvent with CO2 in its hypothetical liquid state were calculated. Finally, a quantitative analysis of the CO2 solubility evolution was carried out in the EC:DMC (50:50) wt.% binary mixture as the function of the LiPF6 or LiTFSI concentration in solution to elucidate how ionic species modify the CO2 solubility in alkylcarbonates-based Li-ion electrolytes by investigating the salting effects at T = 298.15 K and atmospheric pressure.

A Neutron Diffraction and Molecular Dynamics Investigation of Acetate-based Ionic Liquids as Solvents for Glucose

The liquid state structure of the ionic liquid, 1-ethyl-3-methylimidazolium acetate, and the solute/solvent structure of glucose dissolved in the ionic liquid at a 1: 6 molar ratio have been investigated at 323 K by molecular dynamics simulations and neutron diffraction experiments using H/D isotopically substituted materials. Interactions between hydrogen-bond donating cation sites and polar, directional hydrogen-bond accepting acetate anions are examined. Ion-ion radial distribution functions for the neat ionic liquid, calculated from both MD and derived from the empirical potential structure refinement model to the experimental data, show the alternating shell-structure of anions around the cation, as anticipated. Spatial probability distributions reveal the main anion-to-cation features as in-plane interactions of anions with imidazolium ring hydrogens and cation-cation planar stacking. Interestingly, the presence of the polarised hydrogen-bond acceptor anion leads to increased anion-anion tail-tail structuring within each anion shell, indicating the onset of hydrophobic regions within the anion regions of the liquid.

Analog of Rabi oscillations in resonant electron-ion systems

Quantum coherence between electron and ion dynamics, observed in organic semiconductors by means of ultrafast spectroscopy, is the object of recent theoretical and computational studies. To simulate this kind of quantum coherent dynamics, we have introduced in a previous article [L. Stella, M. Meister, A. J. Fisher, and A. P. Horsfield, J. Chem. Phys. 127, 214104 (2007)] an improved computational scheme based on Correlated Electron-Ion Dynamics (CEID). In this article, we provide a generalization of that scheme to model several ionic degrees of freedom and many-body electronic states. To illustrate the capability of this extended CEID, we study a model system which displays the electron-ion analog of the Rabi oscillations. Finally, we discuss convergence and scaling properties of the extended CEID along with its applicability to more realistic problems. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3589165]

Molecular rearrangement reactions in the gas phase triggered by electron attachment

Bond formation and rearrangement reactions in gas phase electron attachment were studied through dissociative electron attachment (DEA) to pentafluorotoluene (PFT), pentafluoroaniline (PFA) and pentafluorophenol (PFP) in the energy range 0-14 eV. In the case of PFA and PFP, the dominant processes involve formation of [M - HF](-) through the loss of neutral HF. This fragmentation channel is most efficient at low incident electron energy and for PFP it is accompanied by a substantial conformational change of the anionic fragment. At higher energy, HF loss is also observed as well as a number of other fragmentation processes. Thermochemical threshold energies have been computed for all the observed fragments and classical trajectories of the electron attachment process were calculated to elucidate the fragmentation mechanisms. For the dominant reaction channel leading to the loss of HF from PFP, the minimum energy path was calculated using the nudged elastic band method.

Robust nonadiabatic molecular dynamics for metals and insulators

We present a new formulation of the correlated electron-ion dynamics (CEID) scheme, which systematically improves Ehrenfest dynamics by including quantum fluctuations around the mean-field atomic trajectories. We show that the method can simulate models of nonadiabatic electronic transitions and test it against exact integration of the time-dependent Schrodinger equation. Unlike previous formulations of CEID, the accuracy of this scheme depends on a single tunable parameter which sets the level of atomic fluctuations included. The convergence to the exact dynamics by increasing the tunable parameter is demonstrated for a model two level system. This algorithm provides a smooth description of the nonadiabatic electronic transitions which satisfies the kinematic constraints (energy and momentum conservation) and preserves quantum coherence. The applicability of this algorithm to more complex atomic systems is discussed.

Irradiation of oxygen and water ices at by 4 keV singly and doubly charged ions; sputtering and molecular synthesis

The icy surfaces of dust grains in the Interstellar Medium and those of comets, satellites and Kuiper Belt Objects are continuously exposed tophoton and charged particle irradiation. These energetic particles maysputter and induce chemical changes in the ices and the underlyingsurfaces.In the present work 258 nm thick O2 and H2O ices were deposited at 10 K with the thickness measured by a laser interferometer method. Asimple model fit to the reflected laser intensity as measured by aphotodiode detector enabled the refractive index of the ices to bedetermined. The ices were then irradiated with various singly and doublycharged ions such as He+, 13C+, N+, O+ , Ar+, 13C2+, N2+ and O2+ at 4keV. The decrease in ice thickness as a function of ion dose wasmonitored by a laser interferometer and the model used to determine thesputtering yield as shown in Figure 1.In the case of O2 ice thesputtering yields increased with increasing ion mass in good agreementwith a model calculation [Fama, J, Shi, R.A Baragiola, Surface Sci.,602, 156 (2007)]. In the case of O2 ice, O2+ has a significant lowersputtering yield when compared to O+. The sputtering yields for O2 icewere found to be at least 9 times larger compared to those for H2O ice.For H2O ice the sputter yields for C, N and O ions were found todecrease with increasing mass. Doubly charged C, N and O ions which werefound to have the same sputtering yield as the singly charged ionswithin the experimental errors. A preliminary TPD study was carried outusing a QMS to detect the desorbed species from water ice afterirradiation by 6 × 10^15 ions of 13C+ and 13C2+. The formation of13CO and 13CO2 was observed with the yield of 13CO almost of a factor of100 larger than of 13CO2. This is in contrast to our earlier work whereonly CO¬2 was observed.

Comparative biochemical analysis of three members of the Schistosoma mansoni TAL family: Differences in ion and drug binding properties

The tegumental allergen-like (TAL) proteins from Schistosoma mansoni are part of a family of calcium binding proteins found only in parasitic flatworms. These proteins have attracted interest as potential drug or vaccine targets, yet comparatively little is known about their biochemistry. Here, we compared the biochemical properties of three members of this family: SmTAL1 (Sm22.6), SmTAL2 (Sm21.7) and SmTAL3 (Sm20.8). Molecular modelling suggested that, despite similarities in domain organisation, there are differences in the three proteins’ structures. SmTAL1 was predicted to have two functional calcium binding sites and SmTAL2 was predicted to have one. Despite the presence of two EF-hand-like structures in SmTAL3, neither was predicted to be functional. These predictions were confirmed by native gel electrophoresis, intrinsic fluorescence and differential scanning fluorimetry: both SmTAL1 and SmTAL2 are able to bind calcium ions reversibly, but SmTAL3 is not. SmTAL1 is also able to interact with manganese, strontium, iron(II) and nickel ions. SmTAL2 has a different ion binding profile interacting with cadmium, manganese, magnesium, strontium and barium ions in addition to calcium. All three proteins form dimers and, in contrast to some Fasciola hepatica proteins from the same family; dimerization is not affected by calcium ions. SmTAL1 interacts with the anti-schistosomal drug praziquantel and the calmodulin antagonists trifluoperazine, chlorpromazine and W7. SmTAL2 interacts only with W7. SmTAL3 interacts with the aforementioned calmodulin antagonists and thiamylal, but not praziquantel. Overall, these data suggest that the proteins have different biochemical properties and thus, most likely, different in vivo functions.

Oscillator strengths and transition probabilities for the W xlv ion

In this paper we present oscillator strengths and transition probabilities for W xlv transitions between levels arising from configurations 3d¹⁰4s²,4p²,4d², 3d¹⁰4k4l (k = s,p,d,f and l = p,d,f), 3d⁹4s²4l (l = p,d,f) and 3d⁹4s4p². The model used to calculate these contained all configurations which can be constructed from the available orbitals (up to n = 4), with either a 3d¹⁰ or 3d⁹ core. The calculations were performed with the configuration interaction CIV3 program with the inclusion of relativistic effects achieved through the use of the Breit-Pauli approximation. We compare our ab initio energy levels, oscillator strengths and transition rates with other experimental and theoretical values available in the literature. There is generally good agreement when only levels with 3d¹⁰ cores are considered. The literature is sparse for levels in which the 3d-subshell is opened: for the majority of the fine-structure lines considered, there is either no comparison data available or substantial differences are found. This paper also investigates how the inclusion of relativistic effects can result in a significant redistribution of the oscillator strength from the LS calculations.

AaeAP1 and AaeAP2: Novel Antimicrobial Peptides from the Venom of the Scorpion, Androctonus aeneas: Structural Characterisation, Molecular Cloning of Biosynthetic Precursor-Encoding cDNAs and Engineering of Analogues with Enhanced Antimicrobial and Anticancer Activities

The main functions of the abundant polypeptide toxins present in scorpion venoms are the debilitation of arthropod prey or defence against predators. These effects are achieved mainly through the blocking of an array of ion channel types within the membranes of excitable cells. However, while these ion channel-blocking toxins are tightly-folded by multiple disulphide bridges between cysteine residues, there are additional groups of peptides in the venoms that are devoid of cysteine residues. These non-disulphide bridged peptides are the subject of much research interest, and among these are peptides that exhibit antimicrobial activity. Here, we describe two novel non-disulphide-bridged antimicrobial peptides that are present in the venom of the North African scorpion, Androctonus aeneas. The cDNAs encoding the biosynthetic precursors of both peptides were cloned from a venom-derived cDNA library using 3'- and 5'-RACE strategies. Both translated precursors contained open-reading frames of 74 amino acid residues, each encoding one copy of a putative novel nonadecapeptide, whose primary structures were FLFSLIPSVIAGLVSAIRN and FLFSLIPSAIAGLVSAIRN, respectively. Both peptides were C-terminally amidated. Synthetic versions of each natural peptide displayed broad-spectrum antimicrobial activities, but were devoid of antiproliferative activity against human cancer cell lines. However, synthetic analogues of each peptide, engineered for enhanced cationicity and amphipathicity, exhibited increases in antimicrobial potency and acquired antiproliferative activity against a range of human cancer cell lines. These data clearly illustrate the potential that natural peptide templates provide towards the design of synthetic analogues for therapeutic exploitation.