Nanosilver resonance scattering spectral method for determination of hydroxyl radical and its application

Silver nanoparticles were prepared under a microwave high-pressure condition using citric acid sodium as a reducer while the excess citrate was removed under high speed centrifugation. There is a resonance scattering (RS) peak at 470 nm for silver nanoparticles. In a pH 4.0 HAc-NaAc buffer solution, hydroxyl radicals from the Fenton reaction can oxidize silver nanoparticles to Ag , resulting in the RS intensity decreasing. The decreased RS intensity at 470 nm (△I 470 nm) is linear with respect to the concentration of H2O2 (C) in the range of 0.27-7.56 μmol/L with a detection limit of 0.23 μmol/L. Its regression equation is △I 470 nm = 24.3 C 13.8 with a correlation coefficient of 0.9959. This method was applied to screening the antioxidants with satisfactory results.     

Many-body calculations of low-energy eigenstates in magnetic and periodic systems with self-healing diffusion Monte Carlo: steps beyond the fixed phase

The self-healing diffusion Monte Carlo algorithm (SHDMC) [F. A. Reboredo, R. Q. Hood, and P. R. C. Kent, Phys. Rev. B 79, 195117 (2009); F. A. Reboredo, ibid. 80, 125110 (2009)] is extended to study the ground and excited states of magnetic and periodic systems. The method converges to exact eigenstates as the statistical data collected increase if the wave function is sufficiently flexible. It is shown that the dimensionality of the nodal surface is dependent on whether phase is a scalar function or not. A recursive optimization algorithm is derived from the time evolution of the mixed probability density, which is given by an ensemble of electronic configurations (walkers) with complex weight. This complex weight allows the phase of the fixed-node wave function to move away from the trial wave function phase. This novel approach is both a generalization of SHDMC and the fixed-phase approximation [G. Ortiz, D. M. Ceperley, and R. M. Martin, Phys Rev. Lett. 71, 2777 (1993)]. When used recursively it simultaneously improves the node and the phase. The algorithm is demonstrated to converge to nearly exact solutions of model systems with periodic boundary conditions or applied magnetic fields. The computational cost is proportional to the number of independent degrees of freedom of the phase. The method is applied to obtain low-energy excitations of Hamiltonians with magnetic field. Periodic boundary conditions are also considered optimizing wave functions with twisted boundary conditions which are included in a many-body Bloch phase. The potential applications of this new method to study periodic, magnetic, and complex Hamiltonians are discussed.     

A simple and sensitive resonance scattering spectral method for determination of hydroxyl radical in Fenton system using rhodamine S and its application to screening the antioxidant

Based on resonance scattering (RS) effect of rhodamine dye association particles, a new resonance scattering method for the determination of hydroxyl free radical from Fenton reaction was developed. In HCl-NaAc buffer solution, the OH of Fenton reaction oxidized the excess I⁻ to I₃⁻. The I₃⁻ combined, respectively, with rhodamine B (RhB), butyl rhodamine B (b-RhB), rhodamine 6G (RhG) and rhodamine S (RhS) to form association particles that exhibit stronger resonance scattering effect at 420 nm and 610 nm. However, the RS peak at about 610 nm was interfered with its synchronous fluorescence peak at 580 nm for RhB, 580 nm for b-RhB, 560 nm for RhG and 560 nm for RhS, respectively. The concentration of H₂O₂ in the range of 0.648-21.6 μmol/L, 0.423-13.0 μmol/L, 0.216-13.0 μmol/L and 0.092-13.0 μmol/L was linear to its resonance scattering intensity at 420 nm. Its detection limit was 0.15 μmol/L, 0.10 μmol/L, 0.092 μmol/L and 0.044 μmol/L, H₂O₂, respectively. This RhS RS method was applied to selection of the antioxidant, with satisfactory results.     

Two approaches to the calculation of molecular resonance states: Solution of scattering equations and matrix diagonalization

We have analyzed two approaches to reproduce the resonance expansion of the scattering matrix appropriate for the calculation of molecular resonance states. The first is based on the resonance theory of Siegert-Humblet-Rosenfeld (SHR) and the second on the Fano-Feshbach formalism. The direct method of calculating the resonance expansion characteristics, devised on the basis of the SHR theory, makes it possible to obtain the energies and partial widths (detailed decay rate constants) of resonances. The Fano-Feshbach formalism, on the other hand, elucidates the resonance state as a concept and facilitates the interpretation of calculation results. The use of computational methods is illustrated by the study of the decay of a model triatomic system and of gas-phase nucleophilic substitution reactions. Used in the latter case is the division of all degrees of freedom of the reacting system into the adiabatic and dynamic ones along with an algorithm of inclusion of the restricted dynamical treatment in the calculation of reaction rate constants.     

Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides

A new approach, the hypothetical scanning Monte Carlo (HSMC), for calculating the absolute entropy, S, and free energy, F, has been introduced recently and applied first to fluids (argon and water) and later to peptides. In this paper the method is further developed for peptide chains in vacuum. S is calculated from a given MC sample by reconstructing each sample conformation i step-by-step, i.e., calculating transition probabilities (TPs) for the dihedral and bond angles and fixing the related atoms at their positions. At step k of the process the chain's coordinates that have already been determined are kept fixed (the "frozen past") and TP(k) is obtained from a MC simulation of the "future" part of the chain whose TPs as yet have not been determined; when the process is completed the contribution of conformation i to the entropy is, S(i) approximately -ln Pi(k) TP(k). In a recent paper we studied polyglycine chains, modeled by the AMBER force field with constant bond lengths and bond angles (the rigid model). Decaglycine [(Gly)(10)] was studied in the helical, extended, and hairpin microstates, while (Gly)(16) was treated only in the first two microstates. In this paper the samples are increased and restudied, (Gly)(16) is also investigated in the hairpin microstate, and for (Gly)(10) approximations are tested where only part of the future is considered for calculating the TPs. We calculate upper and lower bounds for F and demonstrate that like for fluids, F can be obtained from multiple reconstructions of a single conformation. We also test a more realistic model of (Gly)(10) where the bond angles are allowed to move (the flexible model). Very accurate results for S and F are obtained which are compared to results obtained by the quasiharmonic approximation and the local states method. Thus, differences in entropy and free energy between the three microstates are obtained within errors of 0.1-0.3 kcal/mol. The HSMC method can be applied to a macromolecule with any degree of flexibility, ranging from local fluctuations to a random coil. The present results demonstrate that the difference in stability, DeltaF(mn)=F(m)-F(n) between significantly different microstates m and n, can be obtained from two simulations only without the need to resort to thermodynamic integration. Our long-term goal is to extend this method to any peptide and apply it to a peptide immersed in a box with explicit water.     

Determination of carbofuran by the quenching effect on resonance light scattering and its application to water and vegetable samples

A new method for the determination of carbofuran (CF) with DNA by a resonance light scattering (RLS) technique was developed. The intensity of RLS (I _RLS) of DNA–HCl system was significantly quenched in presence of CF. A RLS peak at 315.6 nm was found, and the quenched intensity of RLS was proportional to the concentration of CF. The linear range of the calibration curve was ≈0.02–2.0 µg mL^?1 and the detection limit (S/N = 3) 7 ng mL^?1. The CF in river water, cucumbers and rice samples was determined. The recovery rates were in the range of 90.0–111.1, 95.0–106, 93.0–111.0%, respectively. The mechanism of the reaction between CF and DNA is also discussed.     

3D Monte Carlo Simulations of Diffusion Limited Cluster Aggregation up to the Sol-Gel Transition: Structure and Kinetics

Three-dimensional (3D) Monte Carlo simulations of diffusion limited cluster aggregation at different concentrations () show a crossover from a flocculation regime at short times to a percolation regime close to the gel time (t_g). Contrary to suggestions in the literature t_g is independent of the system size (L) for large L. The structural and temporal crossovers between flocculation and percolation take place at characteristic values of the cluster mass (m_c) and the time (t_c) which depend on . After normalisation by these characteristic values the crossovers are independent of except for very small clusters and at short times. The concentration dependence of m_c and t_c indicates that the crossover takes place at a given cumulated volume fraction of the clusters independent of . At low concentrations the -dependence of t_g is determined by the cluster growth in the flocculation regime.     

Comparison of ISO-GUM and Monte Carlo methods for the evaluation of measurement uncertainty: application to direct cadmium measurement in water by GFAAS

The propagation stage of uncertainty evaluation, known as the propagation of distributions, is in most cases approached by the GUM (Guide to the Expression of Uncertainty in Measurement) uncertainty framework which is based on the law of propagation of uncertainty assigned to various input quantities and the characterization of the measurand (output quantity) by a Gaussian or a t-distribution. Recently, a Supplement to the ISO-GUM was prepared by the JCGM (Joint Committee for Guides in Metrology). This Guide gives guidance on propagating probability distributions assigned to various input quantities through a numerical simulation (Monte Carlo Method) and determining a probability distribution for the measurand.In the present work the two approaches were used to estimate the uncertainty of the direct determination of cadmium in water by graphite furnace atomic absorption spectrometry (GFAAS). The expanded uncertainty results (at 95% confidence levels) obtained with the GUM Uncertainty Framework and the Monte Carlo Method at the concentration level of 3.01 μg/L were ±0.20 μg/L and ±0.18 μg/L, respectively. Thus, the GUM Uncertainty Framework slightly overestimates the overall uncertainty by 10%. Even after taking into account additional sources of uncertainty that the GUM Uncertainty Framework considers as negligible, the Monte Carlo gives again the same uncertainty result (±0.18 μg/L). The main source of this difference is the approximation used by the GUM Uncertainty Framework in estimating the standard uncertainty of the calibration curve produced by least squares regression. Although the GUM Uncertainty Framework proves to be adequate in this particular case, generally the Monte Carlo Method has features that avoid the assumptions and the limitations of the GUM Uncertainty Framework.     

A new way to detect the interaction of DNA and anticancer drugs based on the decreased resonance light scattering signal and its potential application

A novel assay has been developed to detect the interaction of DNA and anticancer drugs based on the decreased resonance light scattering (RLS) technique. The proposed method can be used to study those drugs which do not produce a RLS-signal after binding to DNA. RLS was used to monitor the interaction of five anticancer drugs with DNA. The reaction between anticancer drugs and DNA took place in BR buffer solution. From the RLS assay, the sequence of five anticancer drugs activities was as follows: CTX < MTX < Pt < MMC < 5-Fu. Mammary cancer cell DNA (mcDNA) was involved to validate the RLS assay. The results showed that the sensitivities of the five anticancer drugs targeting both mcDNA and ctDNA increased in the same order. However the sensitivity of each drug to mcDNA was higher than that to ctDNA It is a significant innovation of the RLS method to detect the interaction of DNA and anticancer drugs and to obtain drug sensitivity, which provides new strategies to screen DNA targeted anticancer drugs.     

Imidazo[1,2-a]pyrazine inhibitors of phosphoinositide 3-kinase alpha (PI3Kα): 3D-QSAR analysis utilizing the Hybrid Monte Carlo algorithm to refine receptor-ligand complexes for molecular alignment

Phosphoinositide 3-kinase alpha (PI3Kα) is a lipid kinase involved in several cellular functions such as cell growth, proliferation, differentiation and survival, and its anomalous regulation leads to cancerous conditions. PI3Kα inhibition completely blocks the cancer signalling pathway, hence it can be explored as an important therapeutic target for cancer treatment. In the present study, docking analysis of 49 selective imidazo[1,2-a]pyrazine inhibitors of PI3Kα was carried out using the QM-Polarized ligand docking (QPLD) program of the Schrödinger software, followed by the refinement of receptor–ligand conformations using the Hybrid Monte Carlo algorithm in the Liaison program, and alignment of refined conformations of inhibitors was utilized for the development of an atom-based 3D-QSAR model in the PHASE program. Among the five generated models, the best model was selected corresponding to PLS factor 2, displaying the highest value of Q²_test (0.650). The selected model also displayed high values of r²_train (0.917), F-value (166.5) and Pearson-r (0.877) and a low value of SD (0.265). The contour plots generated for the selected 3D-QSAR model were correlated with the results of docking simulations. Finally, this combined information generated from 3D-QSAR and docking analysis was used to design new congeners.     

The stochastic resonance algorithm with the direct current signal as external force and its application to the detection of weak chromatographic peaks

As a potential tool for amplifying weak chromatographic peaks, the stochastic resonance algorithm was developed based upon a counterintuitive physical phenomenon. Therefore, the essential step, parameter optimization, was perplexing and difficult for analysts. In order to avoid optimizing the system parameters on a case‐by‐case basis, an improved algorithm was proposed by introducing a constant or direct current signal into the signal to be measured as the external force. The weak chromatographic peak can be amplified and detected by the new algorithm using the same set of parameters. Two sets of our previous experimental data were reanalyzed by using the developed algorithm and the results were satisfactory. A generalized solution was expected to come into being on account of the new algorithm.     

Nonperturbative quantum simulation of time-resolved nonlinear spectra: Methodology and application to electron transfer reactions in the condensed phase

A quantum dynamical method is presented to accurately simulate time-resolved nonlinear spectra for complex molecular systems. The method combines the nonpertubative approach to describe nonlinear optical signals with the multilayer multiconfiguration time-dependent Hartree theory to calculate the laser-induced polarization for the overall field–matter system. A specific nonlinear optical signal is obtained by Fourier decomposition of the overall polarization. The performance of the method is demonstrated by applications to photoinduced ultrafast electron transfer reactions in mixed-valence compounds and at dye–semiconductor interfaces.     

p-Nitro-N-propylaniline/silica: synthesis, characterization, and its application in matrix solid phase dispersion for multiresidue analysis of pesticides in carrots

A new material for matrix solid phase dispersion (MSPD) was synthesized -- p-nitro-N-propylaniline/silica (pNNPASi) by grafting reactions, characterized by elemental analysis and N(2)-adsorption-desorption isotherms, and tested for multiclass multiresidue analysis of pesticides in wet and freeze-dried carrots. Results obtained applying this new solid phase sorbent to MSPD extraction of ten pesticides (trichlorphon, trifluralin, dicloran, chlorothalonil, prometryn, linuron, captan, procymidone, prochloraz, and deltametrin) in wet carrots showed better results than the ones obtained for freeze-dried samples. Recoveries were in the range of 48-106% and precisions varied from 6 to 20% when wet samples were employed. Comparison between pNNPASi sorbent and C(18) showed better performance of pNNPASi for eight out of ten pesticides tested. The LOQs show that the developed method can be used to detect the pesticides investigated in carrots at concentrations below the maximum residue levels (MRL) established by EU, USEPA, and National Sanitary Surveillance Agency (ANVISA). Linuron, captan, prochloraz, and deltamethrin were found in at least one of the two commercial samples studied in concentrations above the LOQ of this method. Concentrations of the last three pesticides were above the European MRL in one of the commercial samples.     

ChemInform Abstract: Solvent Effect on Relative Gibbs Free Energy and Structural Property of Eu3* to Yb3+ Ion Mutation: A Monte Carlo Simulation Study.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors

Three approximate free energy calculation methods are examined and applied to an example ligand design problem. The first of the methods uses a single simulation to estimate the relative binding free energies for related ligands that are not simulated. The second method is similar, except that it uses only first derivatives of free energy with respect to atomic parameters (most often charge, van der Waals equilibrium distance, and van der Waals well depth) to calculate free energy differences. The last method PROFEC (Pictorial Representation of Free Energy Components), generates contour maps that show how binding free energy changes when additional particles are added near the ligand. These three methods are applied to a benzamidine/trypsin complex. They each reproduce the general trends in the binding free energies, indicating that they might be useful for suggesting how ligands could be modified to improve binding and, consequently, useful in structure-based drug design.     

Time-resolved simultaneous polarized and depolarized light scattering system with high sensitivity to optical anisotropy: application to phase separation of an optically isotropic liquid mixture

Depolarized light scattering is widely used to probe the spatial correlation of optical anisotropy in crystals, liquid crystals, and viscoelastic materials under stress, and a powerful means to study a non-equilibrium pattern evolution process of such a system. To follow the temporal change in the diagonal and off-diagonal contributions of the dielectric tensor, it is highly desirable to measure two-dimensional (2D) polarized (HH: horizontally transmitted, horizontally received) and depolarized (VH: vertically transmitted, horizontally received) scattering patterns simultaneously in a time-resolved manner. We develop a light scattering system with a video-rate time resolution as well as very high sensitivity to optical anisotropy. To detect extremely weak VH scattering from a sample without suffering from residual birefringence of the optical system itself and leakage of strong HH scattering signals, we use an objective lens specially designed for polarizing microscopy and Glan-laser prisms, respectively. This system enables us to experimentally elucidate the origin of VH scattering: we use the ratio of the VH and HH scattering intensity as a fingerprint for whether a 2D VH scattering pattern is caused by (i) optical anisotropy (intrinsic birefringence) or merely by (ii) spatial inhomogeneity of optically isotropic materials. We verify the validity of this method for a process of phase separation in a binary mixture of isotropic liquids. The simultaneous HH and VH measurement allows us to directly estimate the ratio of VH and HH scattering intensity accurately. The careful comparison of this ratio with a simple theory unambiguously demonstrates that the 2D VH scattering pattern is caused by the scattering angle dependence of the diffraction efficiency of light with the two polarization directions. That is, the origin of VH scattering is due to geometrical effects of the inhomogeneous distribution of the refractive index and not due to optical birefringence, as it should be for the optically isotropic sample. This method using the ratio of VH and HH scattering intensity may be widely used for distinguishing the two types of origins for a VH scattering pattern in an unambiguous manner.     

Application of the Monte Carlo method to modeling of kinetic processes with the participation of polyatomic molecules and clusters: 1. Kinetics of energy transfer during collisions of polyatomic molecules

The Monte Carlo method was used to model the collisional energy transfer for polyatomic molecules within the framework of the statistical theory of reactions. A model describing energy transfer through the formation of a statistical collisional complex was suggested. It was assumed that the total energy of the complex was randomized in the course of collisions and statistically distributed among the internal and translational degrees of freedom. The method was verified by comparing the equilibrium distribution functions for the vibrational, rotational, and total energies of the molecule. The mean energy portion and the root-mean-square energy portion transferred per collision, as functions of the total molecular energy, were determined. The relaxation parameters of the population distribution over energy after a sharp increase in the bath-gas temperature were calculated.     

Surface-enhanced Raman scattering and surface-enhanced resonance Raman scattering excitation profiles of Ag-2,2'-bipyridine surface complexes and of [Ru(bpy)3]2+ on Ag colloidal surfaces: manifestations of the charge-transfer resonance contributions to the overall surface enhancement of Raman scattering

Excitation profiles of SERS (surface-enhanced Raman scattering) and/or SERRS (surface-enhanced resonance Raman scattering) spectral bands of two forms of a Ag-bpy (bpy = 2,2'-bipyridine) surface complex and of [Ru(bpy)3]2+ on Ag nanoparticle (hydrosol) surfaces were determined from the spectra excited in the 458-600 nm region and are reported together with the FT-SERS spectra of the Ag-bpy surface complex and FT Raman spectra of [Ru(bpy)3] Cl2. Seven of the observed 11 fundamentals as well as their first overtones and combination bands are selectively enhanced in SERS of the Ag-bpy surface complex formed in the Ag colloid/HCl/bpy system. The profiles of these bands show a common maximum at approximately 540 nm. The selectively enhanced bands of the Ag-bpy surface complex have nearly the same wavenumbers as those enhanced in the SERRS and resonance Raman spectra of [Ru(bpy)3]2+ upon excitation close to the 453 nm maximum of its MLCT absorption band. Moreover, the intensity patterns of the bpy vibrations of the two species match both in resonance (541 nm excitation for Ag-bpy, 458 nm for [Ru(bpy)3]2+) and in off-resonance (458 and 1064 nm for Ag-bpy, 1064 nm for [Ru(bpy)3]2+). The distinct band shapes of the excitation profiles of the selectively enhanced vibrational modes of the Ag-bpy surface complex, as well as the observation of overtones and combination bands in the SERS spectra upon excitation into this "band", are interpreted in terms of a charge-transfer resonance contribution to the overall SERS enhancement. In view of the near-coincidence of the vibrational modes coupled to the resonant electronic transition of Ag-bpy with those coupled to the MLCT transition of [Ru(bpy)3]2+, the resonant electronic transition is tentatively assigned to a Ag metal to bpy (pi*) CT transition.     

Electron transport membrane: Preparation of polypeptide membrane with spacers between the polymer matrix and viologen moiety and their application to an electron transfer reaction

Polypeptide membranes with several lengths of spacers [? (CH₂)_n? ; n = 3, 6, 12] between the polymer matrix and viologen moiety as a functional group were prepared. Reduction of K₃Fe(CN)₆ with Na₂S₂O₄ across the obtained membrane in aqueous media were carried out and reduction rate of K₃Fe(CN)₆ across the membrane of n = 6 was faster than that of n = 3. However, the reduction of the membrane (n = 12) did not proceed chemically and electrochemically at all.