Solving stochastic chemical kinetics by Metropolis-Hastings sampling

This study considers using Metropolis-Hastings algorithm for stochastic simulation of chemical reactions. The proposed method uses SSA (Stochastic Simulation Algorithm) distribution which is a standard method for solving well-stirred chemically reacting systems as a desired distribution. A new numerical solvers based on exponential form of exact and approximate solutions of CME (Chemical Master Equation) is employed for obtaining target and proposal distributions in Metropolis-Hastings algorithm to accelerate the accuracy of the tau-leap method. Samples generated by this technique have the same distribution as SSA and the histogram of samples show it''s convergence to SSA     

Influence of copolymer configuration on the phase behavior of ternary blends

The influence of copolymer configuration on the phase behavior of various ternary polymer blends containing a crystallizable polyester, a noncrystallizable polyether, and an acrylic random copolymer of different chain configuration was investigated. In these ternary blends, the acrylic random copolymer is typically added to control rheological properties at elevated temperatures. In fact, the acrylic random copolymers composed of various compositions of MMA and nBMA were found to have different miscibility with polyester as well as polyether, leading to substantially different phase behavior of ternary blends. Remarkable temperature dependence was also found. The mean-field Flory-Huggins theory for the free energy of mixing, extended to ternary polymer blends, was adopted for predicting phase diagrams where the exact spinodal and binodal boundaries could be calculated. Phase diagrams of ternary blends, predicted by the Flory-Huggins formulations and related calculations, were in good agreement with experimental phase diagrams. The differences observed in the rheological processes of various ternary blends with different acrylic copolymers were directly related to changes in miscibility, associated phase behavior, and chain configuration.     

Strong optical nonlinearities of self-assembled polymorphic microstructures of phenylethynyl functionalized fluorenones

The polymorphs of a phenylethynyl functionalized fluorenone derivative, and their controlled self-assembly for microstructures with different morphologies have been studied. These polymorphic microcrystals exhibit very distinctive NLO properties, which are highly correlated to their electronic and supramolecular structures.     

Understanding Chemical Reactivity in Extended Systems:Exploring Models of Chemical Softness in Carbon Nanotubes

Chemical reactivity towards electron transfer is captured by the Fukui function.However,this is not well defined when the system or its ions have degenerate or pseudo-degenerate ground states.In such a case,the first-order chemical response is not independent of the perturbation and the correct response has to be computed using the mathematical formalism of perturbation theory for degenerate states.Spatialpseudo-degeneracy is ubiquitous in nanostructures with high symmetry and totally extended systems.Given the size of these systems,using degenerate-state perturbation theory is impractical because it requires the calculation of many excited states.Here we present an alternative to compute the chemical response of extended systems using models of local softness in terms of the local density of states.The local softness is approximately equal to the density of states at the Fermi level.However,such approximation leaves out the contribution of inner states.In order to include and weight the contribution of the states around the Fermi level,a model inspired by the long-range behavior of the local softness is presented.Single wall capped carbon nanotubes(SWCCNT) illustrate the limitation of the frontier orbital theory in extended systems.Thus,we have used a C360 SWCCNT to test the proposed model and how it compares with available models based on the local density of states.Interestingly,a simple Hü ckel approximation captures the main features of chemical response of these systems.Our results suggest that density-of-states models of the softness along simple tight binding Hamiltonians could be used to explore the chemical reactivity of more complex system,such a surfaces and nanoparticles.     

Total structure determination of grassypeptolide, a new marine cyanobacterial cytotoxin

A collection of the cyanobacterium Lyngbya confervoides off Grassy Key in Florida yielded grassypeptolide (1), a 31-membered macrocyclic depsipeptide with unusually high D-amino acid content, two thiazolines, and one beta-amino acid. We report the rigorous 3D structure determination and conformational analysis in solution and solid state by NMR, MS, X-ray crystallography, chemical degradation, and molecular modeling involving distance geometry and restrained molecular dynamics. Grassypeptolide (1) inhibited cancer cell growth with IC50 values from 1.0 to 4.2 microM.     

Electron paramagnetic resonance (EPR) and stable isotope records of paleoenvironmental conditions during peat formation

EPR spectroscopy was performed on four peat cores (1-2.5 m depth) collected from Yellowstone National Park (USA), Scotland (UK) and Lower Silesia (Poland) to study peat formation process. The stable free radicals identified in all investigated samples are semiquinone type and g-parameters range from 2.0030 to 2.0048. The highest g-values are characteristic of upper well-aerated peat layers and gradually decrease with depth. The lowest g-values are typical of relatively old fens and bogs where anaerobic conditions are expected and carbonization processes are advanced. The decrease in g-parameter value is connected with conjugation of semiquinone units with gradually augmented polyaromatic units in the peat substance. Generally the radical concentration increases with depth (0.05-5x10(17) spins/gram). However the g-values, line width parameters, and spin concentrations exhibit strong variations in some peat layers. Variation of these parameters observed for certain peat horizons correlate with the variation of carbon stable isotopic composition. For the old well-conserved peat deposits (e.g. Scotland/UK, approximately 5600 BP), variation of EPR parameters may be used to study paleo redox conditions.     

Marine chemical ecology

This review covers the recent marine chemical ecology literature for benthic cyanobacteria, macroalgae, sponges, octocorals, molluscs, other benthic invertebrates, fish and seabirds.     

Liquid chromatography-mass spectrometry-based quantification of steroidal glycoalkaloids from Solanum xanthocarpum and effect of different extraction methods on their content

A new liquid chromatography-mass spectrometry (LC-MS)-based method coupled with pressurized liquid extraction (PLE) as an efficient sample preparation technique has been developed for the quantification and fingerprint analysis of Solanum xanthocarpum. Optimum separations of the samples were achieved on a Waters MSC-18 XTerra column, using 0.5% (v/v) formic acid in water (A) and acetonitrile (ACN):2-propanol:formic acid (94.5:5:0.5, v/v/v) (B) as mobile phase. The separation was carried out using linear gradient elution with a flow rate of 1.0mL/min. The gradient was: 0min, 20% B; 14min, 30% B; 20min, 30% B; 27min, 60% B and the column was re-equilibrated to the initial condition (20% B) for 10min prior to next injection. The steroidal glycoalkaloids (SGAs) which are the major active constituents were isolated as pure compounds from the crude methanolic extract of S. xanthocarpum by preparative LC-MS and after characterization were used as external standards for the development and validation of the method. Extracts prepared by conventional Soxhlet extraction, PLE and ultrasonication were used for analysis. The method was validated for repeatability, precision (intra- and inter-day variation), accuracy (recovery) and sensitivity (limit of detection and limit of quantitation). The purpose of the work was to develop a validated method, which can be used for the quantification of SGAs in commercialized S. xanthocarpum products and the fingerprint analysis for their routine quality control.     

Cobalt-catalyzed intermolecular [2 + 2 + 2] cycloaddition for the synthesis of 1,3-cyclohexadienes

A cobalt(I)-catalyzed [2 + 2 + 2] cycloaddition reaction between an internal acceptor-substituted alkyne and a terminal alkene leads to the formation of regiochemically enriched polysubstituted 1,3-cyclohexadiene derivatives in acceptable yields when methyl butynoate is used, whereas regiochemically pure products are formed in good yields form phenyl propyonate. The concurrent cyclotrimerization reaction of the alkyne to the corresponding benzene derivative is dependent on the sterical bulk of the alkyne and is considerably reduced with the sterically more hindered alkyne.     

Concise total synthesis of (+)-crocacin C

The cytotoxic natural product (+)-crocacin C ( 1) has been synthesized in 10 linear steps from commercially available Evans' chiral propionimide in 5% overall yield (8 steps from Evans' chiral dipropionate synthon). No protecting groups were utilized.