Molecular dynamics averaging of Xe chemical shifts in liquids

The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.     

Aerobic alcohol oxidation catalyzed by a new, oxygen-bridged heterometallic compound [PPh4][Ru(N)Me2(μ2-O)2Pd((−)-sparteine)]

The reaction between the new hydroxy compound [PPh₄][Ru(N)(OH)₂Me₂] and Pd(OSiMe₃)₂((−)-sparteine) produces (Me₃Si)₂O, H₂O and a new heterobimetallic compound [PPh₄][Ru(N)Me₂(μ₂-O)₂Pd((−)-sparteine)] in good yield. The Ru/Pd bimetallic compound catalyzes the oxidation of aryl and allyl alcohols to the corresponding carbonyl compound in air and the rearrangement of allylic alcohols unsaturated aldehydes. It also oxidizes PPh₃ to O-PPh₃ under O₂.     

The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage

The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial alpha-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.     

Synthesis of some dibenzodiazepinone derivatives as potent and m2-selective antimuscarinic compounds

Two series of 5-[[4-[4-(dialkylamino)butyl]-l-cyclohexyl]acetyl], and 5-[(dialkylamino)acyl]-10,11-dihydro-5H- dibenzo[b,e][1,4]diazepin-11-ones were synthesized as potential m2-selective ligands 1,2. Their affinity and selectivity for the muscarinic cholinergic receptor m-AChR subtypes were determined. Replacing a nitrogen with CH in the piperidine ring of 5-[[4-[4-(dialkylamino)butyl]-l-piperidinyl]acetyl]-10,11-dihydro-5H-dibenzo-[b,e][1,4]diazepin-11-ones 3 significantly altered the affinity and selectivity to the muscarinic receptor subtypes.     

Propagating transverse electric and transverse magnetic modes in liquid crystal-clad planar waveguides

ABSTRACT

In a planar dielectric waveguide, weak confinement of a propagating mode in a high index core leads to a measurable evanescent interaction with the cladding. In this work, we study the effect of a reorientable anisotropic cladding on the behaviour of Transverse Electric (TE) and Transverse Magnetic (TM) mode polarisations using a liquid crystal (LC)-clad waveguide architecture. The polarised evanescent field of a guided mode interacts with a voltage-tunable birefringent LC cladding to deflect an out-coupled beam. Experimental measurements are coupled with a theoretical framework and show good consistency with simulation results. We isolate the effect of mode confinement by changing the thickness of the high index core. Interactions between the LC index ellipsoid and the mode polarisation are probed by changing the initial alignment of the LC. Finally, we examine the difference in deflection between TE and TM modes, which incorporates both a change in mode confinement and a difference in LC index components.     

Gas-phase reactions of mono- and dichlorophenols

Reactions occurring within the high-pressure mass spectrometer source during argon-enhanced negative-ion mass Spectrometry (NIMS) of mono- and dichlorophenols result in the formation of adduct ions. The reactants for the formation of the adduct ions are derived solely from the chlorophenol. High-resolution accurate mass -measurements of the adducts and comparison of the argon NIMS of the phenols with the argon-enhanced NIMS of authentic chlorinated phenoxyphenol and dichlorodioxin suggest that gas-phase intermolecular and intramolecular nucleophilic substitutions are occurring. The products of the source reactions reflect the stability of the gas-phase species involved and may be compared with the photolysis and pyrolysis reaction products of chlorophenols, chlorinated phenoxyphenols and chlorophenates reported in the literature.     

Cyano-bridged hexanuclear Fe4M2 (M = Ni, Co, Mn) clusters: spin-canted antiferromagnetic ordering of Fe4Ni2 cluster

Heterobimetallic hexanuclear cyano-bridged complexes, [{Fe(Tp)(CN)3}4{M(MeCN)(H2O)2}(2)].10H2O.2MeCN [M = Ni (1), Co (2), Mn (3); Tp = hydrotris(1-pyrazolyl)borate], have been synthesized in H2O-MeCN solution. Complexes 1-3 are isostructural and hexanuclear with [{Fe(Tp)(CN)3}4{M(MeCN)(H2O)2}2] units linked by hydrogen bonds to form a 2D-structure in the solid state. Complex 1 is a canted antiferromagnet that undergoes a field-induced spin-flop-like transition at approximately 1 T and 2 K. At 4.45 K 1 has a transition to paramagnetic state of noninteracting S = 4 magnetic clusters. However, 2 and 3 show antiferromagnetic intracluster coupling. Facile loss of solvent from 2 alters the local symmetry resulting in changing the intracluster interaction from antiferro- to ferromagnetic.     

Performance validation of step-isothermal calorimeters

Isothermal calorimetry is becoming indispensable as a tool for the study of a wide variety of systems. As with all scientific instruments it is essential that robust calibration routines be developed in order to validate the data obtained. Chemical test reactions offer many advantages over (the traditionally used) joule effect heating methods, not least because they have the potential to validate instrument performance (i.e. they can be used to assess all aspects of calorimeter operation). In this work the results of a validation exercise, conducted by Thermal Hazard Technology as part of an installation routine, using the base catalysed hydrolysis of methyl paraben are discussed. In the case described, a systematic misreporting of the reported temperature of a calorimeter was identified, caused by an upgrade to the calorimeter's firmware, a discrepancy which may not have been noted using traditional electrical calibration methods and one which highlights the importance of both manufacturers and end-users adopting chemical test reactions into their test and validation routines.     

Muonium chemistry: kinetics of the gas phase reaction Mu + F2 → MuF + F from 300 to 400 K

The MSR (muonium spin rotation) technique was used to measure the chemical reaction rate for Mu + F₂ → MuF + F in N₂ moderator at ≈ 1 atm from 295 to 383 K giving the Arrhenius expression: log₁₀k (?/mole s) = (10.83 ± 0.20) - (200 ± 50)/T, with k = (1.46 ± 0.11) × 10¹⁰ ?/mole s at 300 K. This is at least 6.8 times the room temperature rate constant for the analogous H atom reaction. The measured activation energy and enhancement over the H reaction rate are indicative of significant tunnelling in the Mu reaction, in agreement with the recent collinear quantum mechanical calculations of Connor et al.