Density-dependent analysis of nonequilibrium paths improves free energy estimates II. A Feynman-Kac formalism

The nonequilibrium fluctuation theorems have paved the way for estimating equilibrium thermodynamic properties, such as free energy differences, using trajectories from driven nonequilibrium processes. While many statistical estimators may be derived from these identities, some are more efficient than others. It has recently been suggested that trajectories sampled using a particular time-dependent protocol for perturbing the Hamiltonian may be analyzed with another one. Choosing an analysis protocol based on the nonequilibrium density was empirically demonstrated to reduce the variance and bias of free energy estimates. Here, we present an alternate mathematical formalism for protocol postprocessing based on the Feynmac-Kac theorem. The estimator that results from this formalism is demonstrated on a few low-dimensional model systems. It is found to have reduced bias compared to both the standard form of Jarzynski's equality and the previous protocol postprocessing formalism.     

SERS spectroscopy and SERS imaging of Shewanella oneidensis using silver nanoparticles and nanowires

Facile and reproducible SERS signals from Shewanella oneidensis were obtained utilizing silver nanoparticles (AgNPs) and silver nanowires (AgNWs). Additionally, SERS images identify the distribution of SERS hot-spots. One important observation is the synergistically enhanced SERS signal when AgNPs and AgNWs are used in conjunction, due to constructively enhanced electromagnetic field.     

Chemistry of condensed thiophenes. IV. Acetylation of phenanthro[4,5-bcd]thiophene

Treatment of phenanthro[4,5-bcd]thiophene ( 2 ) with acetyl chloride and aluminum chloride in nitrobenzene gives acetylation of positions ortho and para to the heteroatomic sulfur atom. In separate experiments, mixtures of 1- and 3-acetyl (50% yield, ratio 1.9:1) or of 1,5-, 1,7-, and 3,5-diacetyl (79% yield, ratio 3:1:1) derivatives were obtained. Isolated as isomerically pure products were the 1-acetyl and the 1,5-diacetyl compounds, as well as the oximes of the 1- and 3-acetyl derivatives. Comparison of these results is made with those reported for nitration of 2 , which also occurs ortho and para to the sulfur atom, and with nitration and acetylation of pyrene (the benzolog of 2 ) which substitutes in the corresponding positions.     

High-performance liquid affinity chromatography for the purification of immunoglobulin A from human serum using jacalin

A high-performance liquid affinity chromatographic method for the purification of serum immunoglobulin A (IgA) using a jacalin column is described. The automated procedure takes about 2 with minimal manipulation. The yields of the isolated IgA and of its IgG and IgM contamination were studied by enzyme-linked immunosorbent assay (ELISA) of 30 sera. Purity was assured by immunoelectrophoresis. The ratio of IgA1 to total IgA was unchanged after purification, as verified by ELISA. The results showed that greater than 90% IgA could be recovered with less than 0.5% total IgG and greater than 2.0% total IgM remaining in the fractions containing purified IgA.     

Chemistry of the phenoxathiins and isosterically related heterocycles. XXXII . The synthesis of 2-azathianthrene and selected analogs

The synthesis of 2-azathianthrene ([1,4]benzodithiino[2,3-c]pyridine), the only remaining monoazathianthrene yet to be reported, is described. Attempts at the direct condensation of disubstituted pyridines with the dianion of 1,2-dimercaptobenzene were generally unsuccessful requiring that the alternative condensation of the dianion with disubstituted pyridine 1-oxides be employed. The title compound was characterized by physical means including ¹³C-nmr spectroscopy. One analog, 4-nitro-2-azathianthrene was also studied by X-ray crystallographic means; the molecule crystallized with two molecules in the asymmetric unit P2₁/n, a = 20.712(3), b = 7.8109(13), c = 13.720(2)Å, β = 107.880(11)°, Z = 8, the data refined to a final R = 0.051 for 3061 reflections. Dihedral angles between the planes of the phenyl rings were 135.00(13) and 132.52(13)° for the two independent molecules contained in the crystal. Close non? bonded S ?O intramolecular contacts were observed in both molecules between the sulfur and nitro-group oxygens. Both nitro groups are twisted out of the plane of the pyridine ring and are oriented at angles of 28.75 and 38.82° respectively.     

Fast determination of the tin content in cassiterite ores by photon activation method

Photon activation analysis has been success-fully applied to the fast and non-destructive analysis of tin in cassiterite ores based on the 159.7 keV gamma line of^123mSn produced in the¹²⁴Sn/γ, n/^123mSn reaction. In order to improve the accuracy of analytical results, corrections for self-absorption and pile-up effects were performed. Under typical conditions /15 μA electron beam current, 15 MeV bremsstrahlung energy, 5 min irradiation time and 10 min measurement/ the sensitivity of the analysis is 10 ppm. The proposed method can be used for routine analysis of tin in geological samples.     

Theoretical studies on the metathesis processes, (Tp(PH3)MR(eta 2-H[bond]CH3)]-->[Tp(PH3)M(CH3)(eta 2-H[bond]R)] (M=Fe,Ru, and Os; R=H and CH3)

Theoretical calculations on the metathesis process, [Tp(PH3)MR(eta 2-H[bond]CH3)] --> [Tp(PH3)M(CH3)(eta 2-H[bond]R)] (M=Fe, Ru, and Os; R=H and CH3), have been systematically carried out to study their detailed reaction mechanisms. Other than the one-step mechanism via a four-center transition state and the two-step mechanism through an oxidative addition/reductive elimination pathway, a new one-step mechanism, with a transition state formed under oxidative addition, has been found. Based on the intrinsic reaction coordinate calculations, we found that the trajectories of the transferring hydrogen atom in the metathesis processes studied are similar to each other regardless of the nature of reaction mechanisms.     

Conformational dependence of the intrinsic acidity of the aspartic acid residue sidechain in N-acetyl- -aspartic acid-N′-methylamide

The sidechain conformational potential energy hypersurfaces (PEHS) for the γ_L, β_L, α_L, and α_D backbone conformations of N-acetyl- -aspartate-N′-methylamide were generated. Of the 81 possible conformers initially expected for the aspartate residue, only seven were found after geometric optimizations at the B3LYP/6-31G(d) level of theory. No stable conformers could be located in the δ_L, _L, γ_D, δ_D, and _D backbone conformations. The ‘adiabatic’ deprotonation energies for the endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide were calculated by comparing their optimized relative energies against those found for the seven stable conformers of N-acetyl- -aspartate-N′-methylamide. Sidechain conformational PEHSs were also generated for the estimation of ‘vertical’ deprotonation energies for both endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide. All backbone–sidechain (N–H⁻O–C) and backbone–backbone (N–HO=C) hydrogen bond interactions were analyzed. A total of two backbone–backbone and four backbone–sidechain interactions were found for N-acetyl- -aspartate-N′-methylamide. The deprotonated sidechain of N-acetyl- -aspartate-N′-methylamide may allow the aspartyl residue to form strong hydrogen bond interactions (since it is negatively charged) which may be significant in such processes as protein–ligand recognition and ligand binding. As a primary example, the molecular geometry of the aspartyl residue may be important in peptide folding, such as that in the RGD tripeptide.     

Solid-phase synthesis of pyrazolines and isoxazolines with sodium benzenesulfinate as a traceless linker

[reaction: see text] The preparation of pyrazoline and isoxazoline derivatives with traceless solid-phase sulfone linker strategy is described. Key steps involved in the solid-phase synthetic procedure include (i) sulfinate S-alkylation, (ii) sulfone anion alkylation, (iii) gamma-hydroxy sulfone --> gamma-ketosulfone oxidation, and (iv) traceless product release via elimination-cyclization. A library of 12 pyrazolines and isoxazolines was synthesized.     

Development and validation of a method for determination of residues of 15 pyrethroids and two metabolites of dithiocarbamates in foods by ultra-performance liquid chromatography-tandem mass spectrometry

This paper reports a novel approach for the detection, confirmation, and quantification of 15 selected pyrethroid pesticides, including pyrethins, and two metabolites of dithiocarbamates in foods by ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS–MS). The proposed method makes use of a modified QuEChERS (quick, easy, cheap, effective, rugged, and safe) procedure that combines isolation of the pesticides and sample cleanup in a single step. Analysis of pyrethroids and dithiocarbamate metabolites was performed by UPLC–MS–MS operated with electrospray and atmospheric pressure chemical ionization, respectively. Two specific precursor–product ion transitions were acquired per target compound in multiple reaction monitoring (MRM) mode. Such acquisition achieved the minimum number of identification points according to European Commission (EC) document no. SANCO/10684/2009, thus fulfilling the EC point system requirement for identification of contaminants in samples. The method was validated with a variety of food samples. Calibration curves were linear and covered from 1 to 800 μg kg⁻¹ in the sample for all target compounds. Average recoveries, measured at mass fractions of 10 and 100 μg kg⁻¹ for pyrethroids and 5 and 50 μg kg⁻¹ for dithiocarbamate metabolites, were in the range of 70–120% for all target compounds with relative standard deviations below 20%. Method limits of quantification (MLOQ) were 10 μg kg⁻¹ and 5 μg kg⁻¹ for pyrethroids and dithiocarbamate metabolites, respectively. The method has been successfully applied to the analysis of 600 food samples in the course of the first Hong Kong total diet study with pyrethroids and metabolites of dithiocarbamates being the pesticides determined.