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.     

On the Thermodynamic Thermal Properties of Quercetin and Similar Pharmaceuticals

The thermodynamic properties of pharmaceuticals are of major importance since they are involved in drug design, processing, optimization and modelling. In this study, a long-standing confusion regarding the thermodynamic properties of flavonoids and similar pharmaceuticals is recognized and clarified. As a case study, the thermal behavior of quercetin is examined with various techniques. It is shown that quercetin does not exhibit glass transition nor a melting point, but on the contrary, it does exhibit various thermochemical transitions (structural relaxation occurring simultaneously with decomposition). Inevitably, the physical meaning of the reported experimental values of the thermodynamic properties, such as the heat of fusion and heat capacity, are questioned. The discussion for this behavior is focused on the weakening of the chemical bonds. The interpretations along with the literature data suggest that the thermochemical transition might be exhibited by various flavonoids and other similar pharmaceuticals, and is related to the difficulty in the prediction/modelling of their melting point.     

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.     

DFT-calculated structures based on 1H NMR chemical shifts in solution vs. structures solved by single-crystal X-ray and crystalline-sponge methods: Assessing specific sources of discrepancies

DFT calculations of ¹H NMR chemical shifts, using various functionals and basis sets, the conductor-like polarizable continuum model and discrete solute-solvent hydrogen bond interactions have been used to derive the solution structures of methyl salicylate and methyl 2,5-dihydroxybenzoate. We demonstrate that very good agreement between experimental and computed ¹H NMR chemical shifts can be obtained for various basis sets. The DFT structures in solution were compared with the recently reported X-ray structure, solved by the crystalline-sponge method, of the methyl salicylate and the single-crystal X-ray structure of methyl 2,5-dihydroxybenzoate. It is demonstrated that the information provided by ¹H NMR chemical shifts about the solution structure is significantly more precise than that obtained by the single-crystal X-ray and the crystalline-sponge methods.     

Monitoring fuel quality: a case study for quinizarin marker content of unleaded petrol marketed in Greece

Fuel adulteration and cross-contamination lead to low-quality fuel products, which may cause increased environmental pollution, loss of taxes and engine problems. An establishment of a quality monitoring mechanism based on laboratory measurements may reveal problematic areas of the fuel supply chain. For the purposes of this work, 97 unleaded petrol samples were measured in order to quantify mass concentration of quinizarin, a substance used in Greece to easily mark the presence of 95 Research Octane Number unleaded petrol in other types of automotive fuels. The samples were obtained from petroleum retail stations selling different brands of fuels and located in different geographic regions of Greece. Statistical analysis of the results revealed quinizarin mass concentrations below the 3 mg L^?1 legislation specification limit and significant differences between brands and geographic regions, which may attributed to the structure of the fuel supply chain in Greece in combination with quinizarin properties and way of handling. Moreover, certain approaches were used for the calculation of decision limits for assessing compliance or non-compliance. These approaches take measurement reproducibility or estimated in-house uncertainty into account, in order to minimize the probability of false rejection.     

Theoretical study of gallium nitride molecules, GaN2 and GaN4

The electronic and geometric structures of gallium dinitride GaN 2, and gallium tetranitride molecules, GaN 4, were systematically studied by employing density functional theory and perturbation theory (MP2, MP4) in conjunction with the aug-cc-pVTZ basis set. In addition, for the ground-state of GaN 4( (2)B 1) a density functional theory study was carried out combining different functionals with different basis sets. A total of 7 minima have been identified for GaN 2, while 37 structures were identified for GaN 4 corresponding to minima, transition states, and saddle points. We report geometries and dissociation energies for all the above structures as well as potential energy profiles, potential energy surfaces and bonding mechanisms for some low-lying electronic states of GaN 4. The dissociation energy of the ground-state GaN 2 ( X (2)Pi) is 1.1 kcal/mol with respect to Ga( (2)P) + N 2( X (1)Sigma g (+)). The ground-state and the first two excited minima of GaN 4 are of (2)B 1( C 2 v ), (2)A 1( C 2 v , five member ring), and (4)Sigma g (-)( D infinityh ) symmetry, respectively. The dissociation energy ( D e) of the ground-state of GaN 4, X (2)B 1, with respect to Ga( (2)P) + 2 N 2( X (1)Sigma g (+)), is 2.4 kcal/mol, whereas the D e of (4)Sigma g (-) with respect to Ga( (4)P) + 2 N 2( X (1)Sigma g (+)) is 17.6 kcal/mol.     

Theoretical study on the electronic states of NaLi

Configuration interaction calculations have been carried out on electronic states of the NaLi molecule and the cation NaLi(+). Potential energy curves are presented for the lowest nine (1)Sigma(+), seven (1)Pi, four (1)Delta, eight (3)Sigma(+), seven (3)Pi, and four (3)Delta states of NaLi as well as for the lowest ten (2)Sigma(+), six (2)Pi, and two (2)Delta states of NaLi(+). The results of the present many-electron configuration interaction calculations on the cation are in support of previous core-polarization effective potential calculations. The present calculations on the NaLi molecule are complementary to previous theoretical work on this system, including recently observed electronic states that had not been calculated previously as well as an investigation of nonadiabatic effects leading to spectral perturbations. Furthermore, ab initio potential energy curves of the neutral and the ground state of the cation are employed to determine quantum defect that may be employed to generate potential energy curves for nd and (n+1)p (for n>3) Rydberg states of NaLi. The present results on the 3 (1)Pi and 4 (1)Pi states are in good agreement with recent experimental work, whereas on the basis of theoretical data, the recently observed state 5 (1)Pi is better described as 6 (1)Pi.