Permeation and gating in proteins: kinetic Monte Carlo reaction path following

We present a new Monte Carlo technique, kinetic Monte Carlo reaction path following (kMCRPF), for the computer simulation of permeation and large-scale gating transitions in protein channels. It combines ideas from Metropolis Monte Carlo (MMC) and kinetic Monte Carlo (kMC) algorithms, and is particularly suitable when a reaction coordinate is well defined. Evolution of transition proceeds on the reaction coordinate by small jumps (kMC technique) toward the nearest lowest-energy uphill or downhill states, with the jumps thermally activated (constrained MMC). This approach permits navigation among potential minima on an energy surface, finding the minimum-energy paths and determining their associated free-energy profiles. The methodological and algorithmic strategies underlying the kMCRPF method are described. We have tested it using an analytical model and applied it to study permeation through the curvilinear ClC chloride and aquaporin pores and to gating in the gramicidin A channel. These studies of permeation and gating in real proteins provide extensive procedural tests of the method.     

Dipole-bound anions of highly polar molecules: ethylene carbonate and vinylene carbonate

Results of experimental and theoretical studies of dipole-bound negative ions of the highly polar molecules ethylene carbonate (EC, C3H4O3, mu=5.35 D) and vinylene carbonate (VC, C3H2O3, mu=4.55 D) are presented. These negative ions are prepared in Rydberg electron transfer (RET) reactions in which rubidium (Rb) atoms, excited to ns or nd Rydberg states, collide with EC or VC molecules to produce EC- or VC- ions. In both cases ions are produced only when the Rb atoms are excited to states described by a relatively narrow range of effective principal quantum numbers, n*; the greatest yields of EC- and VC- are obtained for n*(max)=9.0+/-0.5 and 11.6+/-0.5, respectively. Charge transfer from low-lying Rydberg states of Rb is characteristic of a large excess electron binding energy (Eb) of the neutral parent; employing the previously derived empirical relationship Eb=23/n*(max)(2.8) eV, the electron binding energies are estimated to be 49+/-8 meV for EC and 24+/-3 meV for VC. Electron photodetachment studies of EC- show that the excess electron is bound by 49+/-5 meV, in excellent agreement with the RET results, lending credibility to the empirical relationship between Eb and n*(max). Vertical electron affinities for EC and VC are computed employing aug-cc-pVDZ atom-centered basis sets supplemented with a (5s5p) set of diffuse Gaussian primitives to support the dipole-bound electron; at the CCSD(T) level of theory the computed electron affinities are 40.9 and 20.1 meV for EC and VC, respectively.     

Hawaiian plant studies. XIV. Alkaloids of Ochrosia sandwicensis A. Gray

Two quaternary alkaloids were isolated from Ochrosia sandwicensis A. Gray. One was shown to be hunterburnine -methochloride (I), while the other has been named ochrosandwine and its probable structure is 10-hydroxydihydrocorynantheol methochloride (II). The stereochemistry of the related alkaloid huntrabrine methochloride (IV) is elaborated. Two previously isolated yellow Ochrosia bases were shown to be ellipticine hydrochloride and methoxyellipticine for which the structure-8-methoxyellipticine (V) is suggested. A rapid separation of alkaloids from plant material is described, which involves extraction with hot dilute acetic acid, precipitation with Mayer's reagent and conversion of the complex to the chlorides by anion exchange.     

Ditungsten Siloxide Hydrides, [(silox)(2)WH(n)()](2) (n = 1, 2; silox = (t)BuSiO), and Related Complexes

The addition of 4.0 equiv of Na(silox) to Na[W(2)Cl(7)(THF)(5)] afforded (silox)(2)ClW&tbd1;WCl(silox)(2) (1, 65%). Treatment of 1 with 2.0 equiv of MeMgBr in Et(2)O provided (silox)(2)MeW&tbd1;WMe(silox)(2) (2, 81%). In the presence of 1 atm of H(2), reduction of 1 with 2.0 equiv of Na/Hg in DME provided (silox)(2)HW&tbd1;WH(silox)(2) (3, 70%), characterized by a hydride resonance at delta 19.69 (J(WH) = 325 Hz, (1)H NMR). Exposure of 2 to 1 atm of H(2) yielded 3 and CH(4) via (silox)(2)HW&tbd1;WMe(silox)(2) (4); use of D(2) led to [(silox)(2)WD](2) (3-d(2)). Exposure of 3 to ethylene ( approximately 1 atm, 25 degrees C) in hexanes generated (silox)(2)EtW&tbd1;WEt(silox)(2) (5), but solutions of 5 reverted to 3 and free C(2)H(4) upon standing. NMR spectral data are consistent with a sterically locked, gauche, C(2) symmetry for 1-5. Thermolysis of 3 at 100 degrees C (4 h) resulted in partial conversion to (silox)(2)HW&tbd1;W(OSi(t)Bu(2)CMe(2)CH(2))(silox) (6a, approximately 60%) and free H(2), while extended thermolysis with degassing (5 d, 70 degrees C) produced a second cyclometalated rotational isomer, 6b (6a:6b approximately 3:1). When left at 25 degrees C (4 h) in sealed NMR tubes, 6 and free H(2) regenerated 3. Reduction of 1 with 2.0 equiv of Na/Hg in DME also afforded 6a (25%). When 3 was exposed to approximately 3 atm of H(2), equilibrium amounts of [(silox)(2)WH(2)](2) (7) were observed by (1)H NMR spectroscopy (3 + H(2) right harpoon over left harpoon 7; 25.9-88.7 degrees C, DeltaH = -9.6(4) kcal/mol, DeltaS = -21(2) eu). Benzene solutions of 3 and 1-3 atm of D(2) revealed incorporation of deuterium into the silox ligands, presumably via intermediate 6. In sealed tubes containing [(silox)(2)WCl](2) (1) and dihydrogen (1-3 atm), (1)H NMR spectral evidence for [(silox)(2)WCl](2)(&mgr;-H)(2) (8) was obtained, suggesting that formation of 3 from 1 proceeded via reduction of 8. Alternatively, 3 may be formed from direct reduction of 1 to give [(silox)(2)W](2) (9), followed by H(2) addition. Hydride chemical shifts for 7 are temperature dependent, varying from delta 1.39 (-70 degrees C, toluene-d(8)), to delta 3.68 (90 degrees C). (29)Si{(1)H} NMR spectra revealed a similar temperature dependence of the silox (delta 12.43, -60 degrees C, to delta 13.64, 45 degrees C) resonances. These effects may arise from thermal population of a low-lying, deltadelta, paramagnetic excited state of D(2)(d)() [(silox)(2)W](2)(&mgr;-H)(4) (DeltaE approximately 2.1 kcal/mol, chi(7a) approximately 0.03), an explanation favored over thermal equilibration with an energetically similar but structurally distinct isomer (e.g., [(silox)(2)WH(2)](2)(&mgr;-H)(2), DeltaG degrees approximately 0.69 kcal/mol, chi(7b) approximately 0.25) on the basis of spectral arguments. Extended Hückel and ab initio molecular orbital calculations on model complexes [(H(3)SiO)(2)W](2)(&mgr;-H)(4) (staggered bridged 7a', EHMO), [(H(3)SiO)(2)WH(2)](2) (all-terminal 7b', EHMO), [(H(3)SiO)(2)W](2) (9', EHMO), (HO)(4)W(2)(H(4)) (staggered-bridged 7", ab initio), and (HO)(4)W(2)(H(4)) (bent-terminal 7, ab initio) generally support the explanation of a thermally accessible excited state and assign 7 a geometry intermediate between the all-terminal and staggered-bridged forms.     

Evaluation and validation of the ABI 3700, ABI 3100, and the MegaBACE 1000 capillary array electrophoresis instruments for use with short tandem repeat microsatellite typing in a forensic environment

The demand for high-throughput DNA profiling has increased with the introduction of national DNA databases and has led to the development of automated methods of short tandem repeat (STR) profile production; however, a potential bottleneck still exists at the gel electrophoresis stage. Capillary electrophoresis sequencers capable of processing 96 samples with considerably reduced manual intervention are now available. In this paper, we compare the ABI Prism 377 slab-gel sequencer currently used by the Forensic Science Service with three leading capillary array electrophoresis instruments: the ABI Prism 3700, the Amersham MegaBACE 1000 and the 16-capillary ABI Prism 3100. We describe the experiments used to evaluate and validate these platforms for forensic use with the STR multiplex Ampf/STR SGMplus [1, 2], along with comparative data from the ABI Prism 377 sequencer.     

Using molecular dynamics simulations to identify the key factors responsible for chiral recognition by an amino acid-based molecular micelle

Molecular dynamics (MD) simulations were used to investigate the binding of six chiral compounds to the amino acid-based molecular micelle (MM) poly-(sodium undecyl-(L)-leucine-leucine) or poly(SULL). The MM investigated is used as a chiral selector in capillary electrophoresis. The project goal was to characterize the chiral recognition mechanism in these separations and to move toward predictive models to identify the best amino acid-based MM for a given separation. Poly(SULL) was found to contain six binding sites into which chiral compounds could insert. Four sites had similar sizes, shapes, and electrostatic properties. Enantiomers of alprenolol, propranolol, 1,1′-bi-2-naphthyl-2,2′-diyl hydrogen phosphate, 1,1′-bi-2-naphthol, chlorthalidone, or lorazepam were separately docked into each binding pocket and MD simulations with the resulting intermolecular complexes were performed. Solvent-accessible surface area calculations showed the compounds preferentially associated with binding sites where they penetrated into the MM core and shielded their non-polar atoms from solvent. Furthermore, with five of the six compounds the enantiomer with the most favorable free energy of MM association also experienced the most favorable intermolecular hydrogen bonding interactions with the MM. This result suggests that stereoselective intermolecular hydrogen bonds play an important role in chiral discrimination in separations using amino acid-based MMs.GRAPHICAL ABSTRACT     

Determination of54Mn in foods

⁵⁴Mn is analyzed in complex food ash of high cationic environment. The initial step is an extraction atpH 2.7 with hexane containing di(2-ethylhexyl) phosphoric acid (HDEHP) to complex the⁵⁴Mn and other nuclides. The manganese is reextracted into an alkaline EDTA buffer which is washed with 1% 8-hydroxyquinoline in chloroform containing 5% isoamyl alcohol. The⁵⁴Mn is determined by gamma spectrometry with recoveries ranging from 96.6 to 99.4%.     

Effects of Poly(ethylene glycol) Doping on the Behavior of Pyrene, Rhodamine 6G, and Acrylodan-Labeled Bovine Serum Albumin Sequestered within Tetramethylorthosilane-Derived Sol-Gel-Processed Composites

We investigate the effects of controlled poly(ethylene glycol) (PEG) doping on the behavior of pyrene, rhodamine 6G (R6G), and acrylodan-labeled bovine serum albumin (BSA-Ac) sequestered within tetramethylorthosilicate (TMOS)-derived sol-gel-processed materials. To probe the dipolarity of the local environment within the composite we performed static fluorescence measurements on pyrene as the composites aged. We found that small levels of PEG loading effected significant enhancements in the local dipolarity surrounding the average pyrene molecule. Time-resolved fluorescence anisotropy measurements were used to follow the rotational reorientation dynamics of R6G as the composites aged. As the PEG loading increased, the R6G reorientational mobility increased. Nitrogen adsorption techniques were used to quantify the effects of PEG doping level on the surface area and final xerogel pore features. A large reduction in surface area was observed with PEG doping, but no detectable change in pore size was noted. The effects of PEG doping on a biomolecule were probed by following the time-resolved fluorescence anisotropy decay of BSA-Ac. These results showed that PEG doping resulted in increased biomolecule dynamics relative to that found for a neat, undoped TMOS-derived composites. Together these results show that PEG doping can be used to tune the sol-gel-processed composite dipolarity, alter the mobility of dopants sequestered within the composite, control analyte acessibility to the sensing chemistry, and modulate the internal dynamics within a biodopant.