Coarse master equation from Bayesian analysis of replica molecular dynamics simulations

We use Bayesian inference to derive the rate coefficients of a coarse master equation from molecular dynamics simulations. Results from multiple short simulation trajectories are used to estimate propagators. A likelihood function constructed as a product of the propagators provides a posterior distribution of the free coefficients in the rate matrix determining the Markovian master equation. Extensions to non-Markovian dynamics are discussed, using the trajectory "paths" as observations. The Markovian approach is illustrated for the filling and emptying transitions of short carbon nanotubes dissolved in water. We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference.     

A multireference coupled-cluster potential energy surface of diazomethane, CH(2)N(2)

The intrinsically multireference dissociation of the C-N bond in ground-state diazomethane (CH(2)N(2)) at different angles has been studied with the multireference Brillouin-Wigner coupled-cluster singles and doubles (MRBWCCSD) method. The morphology of the calculated potential energy surface (PES) in C(s)() symmetry is similar to a multireference perturbational (CASPT3) PES. The MRBWCCSD/cc-pVTZ H(2)C-N(2) dissociation energy with respect to the asymptotic CH(2)(?(1)A(1)) + N(2)(X(1)Sigma(g)(+)) products is D(e) = 35.9 kcal/mol, or a zero-point corrected D(0) = 21.4 kcal/mol with respect to the ground-state CH(2)(X(3)B(1)) + N(2)(X(1)Sigma(g)(+)) fragments.     

The preparation of 1-benzoyl-6,7-dimethoxy-5-keto-1,2,2a,3,4,5-hexahydrobenz[cd]indole

The synthesis of 1 - benzoyl - 6,7 - dimethoxy - 5 - keto - 1,2,2a,3,4,5 - hexahydrobenz[cd]indole (10) is described. Reduction of the pyrrole ring of 3 - (5',6' - dimethoxy - 3' - indolyl)propanoic acid (6) with borane pyridine complex and a proton source, followed by N-benzoylation furnished the corresponding indoline derivative 3 - (1' -benzoyl - 5', 6' - dimethoxy - 3' - indolinyl)propanoic acid (7). This acid was cyclized with PPA to the target tricyclic ketone (10).     

Impact of biological factors on binding media identification in art objects: identification of animal glue in the presence of Aspergillus niger

The materials and especially organic materials used for creation of art objects can be utilized by various microorganisms for their growth and facilitate the microbial colonization of the object. An understanding of the chemical alterations in artefacts caused by the presence of microorganisms can be crucial for correct identification of the materials initially used for the artefact creation--nowadays an important step in restoration and/or art-historical investigation of the art object. The present article describes a model experiment in which we investigated the possible chemical alterations in animal glue films used as substrate for growth of the fungus Aspergillus niger. The sterilized animal glue solution was poured into Petri dishes, inoculated with Aspergillus niger, and subsequently incubated at 15 degrees C for 0, 7, 9, 14, and 28 days. After interruption of incubation, the content of the Petri dish was analyzed for amino acid composition by the GC-MS based method. It was found that the growth of Aspergillus niger on animal glue films did not cause significant changes in the amino acid composition of the film and had no impact on animal glue identification.     

Review of Fluorescence Spectroscopy in Environmental Quality Applications

Fluorescence spectroscopy is an optical spectroscopic method that has been applied for the assessment of environmental quality extensively during the last 20 years. Most of the earlier works have used conventional light sources in spectrofluorometers to assess quality. Many recent works have used laser sources of light for the same purpose. The improvement of the energy sources and of the higher resolution spectrometers has led to a tremendous increase in applications. The motivation for the present review study is the increasing use of laser sources in environmental applications. The review is divided in two parts. The fundamental principles of fluorescence spectroscopy are described in the first part. The environmental applications are described in the second part.     

Polybrominated diphenyl ethers (PBDEs) in marine sediment of Thermaikos Gulf,Greece

Polybrominated diphenyl ether (PBDE) concentrations were determined in marine sediment samples collected from 7 different locations around Thermaikos Gulf in north Greece. PBDEs were detected in all sampling sites and their average total concentration (ΣPBDEs) ranged from 0.26 to 4.92?ng?g^?1?d.w. Concentrations were an order of magnitude higher in locations outlining the inner part of the Gulf, which were also closer to industrial areas, sewage treatment plant discharges, the city's harbour and landfill area. These findings suggest pollution in the aquatic ecosystem from industrial and urban activities in the area. Congener profiles exhibit predominance of BDE-209, while concentrations of other PBDE congeners were usually lower, when compared to similar studies from other countries globally, indicating that Thermaikos Gulf is among the low-polluted areas. Statistical analysis showed significant differences among the higher polluted sampling stations. Statistically significant differences also existed between sampling stations with high and low PBDE concentrations. Correlations between congeners suggested local contamination sources; however, specific point sources of pollution were not established.     

Hypercoordination in Organotin Chemistry – A Novel O,C,O-Coordinating Ligand

Recent results are reported on the application of the novel O,C,O-coordinating pincer ligand {2,6-[P(O)(OEt)₂]₂-4-tert-Bu-C₆H₂} (A) for the synthesis of hypercoordinate organotin(IV) compounds ASnR₃ (R = Ph, Cl), heteroleptic stannylenes ASnR (R = Cl, CH₂SiMe3) and intramolecularly coordinated 1,2,5-oxaphosphastannolanes.     

The effect of aging and natural organic matter on the Th(OH)4 solubility

The solution chemistry of actinides, particularly hydrolysis, is of major importance in the design of nuclear waste repositories and in relation to nuclear fuel reprocessing cycles. In this study the formation and solubility of the Th(OH)₄ solid phase has been investigated as a function of the aging time and the presence of natural organic matter (e.g. humic acid) in 0.1 M NaClO₄, at weak acid pH and under normal atmospheric conditions. Th(OH)₄ has been prepared by alkaline precipitation and characterized by TGA, ATR–FTIR, XRD, and solubility measurements. According to the experimental data Th(OH)₄ is stable and remains the solubility limiting solid phase even in the presence of increased humic acid concentration in solution. Increasing humic acid concentration doesn’t affect the crystallite size and the solubility product of Th(OH)₄. Th(OH)₄ solubility is basically pH depended and governed by the presence of colloidal species. However, solid phase aging, which in absence of humic acid favors crystallinity, affects significantly the Th(OH)₄ solubility.