Single molecule dynamics and statistical fluctuations of gene regulatory networks: A repressilator

The authors developed a time dependent method to study the single molecule dynamics of a simple gene regulatory network: a repressilator with three genes mutually repressing each other. They quantitatively characterize the time evolution dynamics of the repressilator. Furthermore, they study purely dynamical issues such as statistical fluctuations and noise evolution. They illustrated some important features of the biological network such as monostability, spirals, and limit cycle oscillation. Explicit time dependent Fano factors which describe noise evolution and show statistical fluctuations out of equilibrium can be significant and far from the Poisson distribution. They explore the phase space and the interrelationships among fluctuations, order, amplitude, and period of oscillations of the repressilators. The authors found that repressilators follow ordered limit cycle orbits and are more likely to appear in the lower fluctuating regions. The amplitude of the repressilators increases as the suppressing of the genes decreases and production of proteins increases. The oscillation period of the repressilators decreases as the suppressing of the genes decreases and production of proteins increases.

Efficient synthesis of highly substituted pyrrolin-4-ones via PIFA-mediated cyclization reactions of enaminones

A convenient and efficient synthesis of highly substituted pyrrolin-4-ones is developed via the PIFA-mediated cyclization reactions of readily available enaminones, and a mechanism involving sequential cleavage of N-C bond, formation of new N-C bond, intramolecular addition reaction, and benzilic acid type rearrangement is proposed.

Vilsmeier-Haack reactions of 2-arylamino-3-acetyl-5,6-dihydro-4H-pyrans toward the synthesis of highly substituted pyridin-2(1H)-ones

A facile and efficient one-pot synthesis of highly substituted pyridin-2(IH)-ones was developed via Vilsmeier-Haack reactions of readily available enaminones, 2-arylamino-3-acetyl-5,6-dihydro-4H-pyrans, and a mechanism involving sequential ring-opening, haloformylation, and intramolecular nucleophilic cyclization reactions is proposed.

Thia-michael addition reactions in water using 3-[Bis(alkylthio) methylene]pentane-2,4-diones as odorless and efficient thiol equivalents

3-[Bis(ethylthio)methylene]pentane-2,4-dione (1a) and 3-[bis(benzylthio)methylene]pentane-2,4-dione (1b) have been investigated as non-thiolic and odorless thiol equivalents in thia-Michael addition reactions. In the presence of aqueous p-dodecyl benzenesulfonic acid (DBSA), compound (1) was cleaved and the generated thiols underwent facile conjugate addition to alpha,beta-unsaturated ketones 2 in-situ, affording the corresponding beta-keto sulfides (3) in good yields.

Design of silicone rubber according to requirements based on the multi-objective optimization of chemical reactions

The explicit expression between composition and mechanical properties of silicone rubber was derived from the physics of polymer elasticity, the implicit expression among material composition, reaction conditions and reaction efficiency was obtained from chemical thermodynamics and kinetics, and then an implicit multi-objective optimization model was constructed. Genetic algorithm was applied to optimize material composition and reaction conditions, and the finite element method of cross-linking reaction processes was used to solve multi-objective functions, on the basis of which a new optimization methodology of crosslinking reaction processes was established. Using this methodology, rubber materials can be designed according to pre-specified requirements.

The synthesis and catalytic activity of poly(bis(imino)pyridyl) iron(II) metallodendrimer

The first and second generation carbosilane dendrimers with silicon hydride terminated were synthesized, and then reacted with bis(imino)pyridyl containing allyl [4-CH2==CHCH2-2,6-(Pr2C6H3N)-Pr-i==CMe(C5H3N)MeC==N(2,6-'Pr2C6H3)], in the presence of H2PtCl6 as a hydrosilylation catalyst, to afford the first and second generation carbosilane supported ligands. Complexation reactions with FeCl(2)(.)4H(2)O give rise to iron-containing carbosilane dendrimers with FeCl2 moieties bound on the periphery. The metallodendrimers were used as catalyst precursors, activated with modified methylaluminoxane, for the polymerization of ethylene. In the case of low Al/Fe molar ratio, the metallodendrimers display much higher catalytic activity towards ethylene polymerization and produce much higher molecule weight polyethylenes than the corresponding single-nuclear complex under the same conditions.

Ionic liquid solvent based on cyclic guanidinium cation for nucleophilic displacement reactions

The nucleophilic displacement reaction of n-bromooctane and potassium iodide in ionic liquid based on cyclic guanidinium cation(2) was investigated. The kinetic reasult shows that the rate of the reaction is enhanced in ionic liquid (2). The same reaction in [bmim][PF6](1)(where bmim = 1-butyl-3-methylimidazolium) was also studied. It was found that as a reaction medium ionic liquid (2) is better than (1) for nucelophilic displacement reactions.

Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier.

Coordination reactions in the extraction of cerium(IV) and fluorine(I) by DEHEHP from mixed nitric acid and hydrofluoric acid solutions

The coordination reactions during the solvent extraction of cerium(IV) and fluorine(l) from mixed nitric acid and hydrofluoric acid solutions by di-(2-ethylhexyl)-2-ethylhexylphosphonate, L (DEHEHP) in heptane have been investigated. The extraction data have been analyzed by graphical methods taking into account all plausible species extracted into the organic phase. Different variables influencing the extraction of Ce(IV), such as the concentrations of nitrate ions, hydrofluroric acid, nitric acid, and extractant have been studied. The results demonstrate that DEHEHP can extract not only Ce(NO3)(4) as Ce(NO3)4.2L and HF as HF (.) H2O (.) L, but both together as Ce(HF)(NO3)(4) (.) L. The extraction equilibrium equations are determined according to slope analysis and IR spectra. The equilibrium constants of the extracted complexes have been calculated, taking into account complexation between the metal ion and inorganic ligands in the aqueous phase and all plausible complexes extracted into the organic phase. It is also shown that boric acid, which was added into the mixed solutions to complex with F(I) is not extracted by DEHEHP, and neither does it affect the extraction of cerium(IV) and HF, nor change the extraction mechanism.

Application of impedance spectroscopy for monitoring colloid Au-enhanced antibody immobilization and antibody-antigen reactions

We used colloidal An to enhance the amount of antibody immobilized on a gold electrode and ultimately monitored the interaction of antigen-antibody by impedance measurement. Self-assembly of 6 nm (diameter) colloidal An onto the self-assembled monolayers (SAMs) of 4-aminothiophenol modified gold electrode resulted in an easier attachment of antibody. The redox reactions of [Fe(CN)(6)](4-)/[Fe(CN)(6)](3-) on the gold surface were blocked due to the procedures of self-assembly of 4-aminothiophenol and antibody immobilization, which were investigated by cyclic voltammetry and impedance spectroscopy. The interaction of antigen with grafted antibody recognition layers was carried out by soaking the modified electrode into a phosphate buffer at pH 7.4 with various concentrations of antigen at 37 degreesC for 30 min. The antibody recognition layers and their interactions with various concentrations of antigen could be detected by measurements of the impedance change. The results show that this method has good correlation for detection of Hepatitis B virus surface antigen in the range of 0.5-200 mug/l and a detection limit of about 50 ng/l.

Investigation of facilitated ion-transfer reactions at high driving force by scanning electrochemical Microscopy

The kinetics of facilitated ion-transfer (FIT) reactions at high driving force across the water/1,2-dichloroethane (W/DCE) interface is investigated by scanning electrochemical microscopy (SECM). The transfers of lithium and sodium ions facilitated by dibenzo-18-crown-6 (DB18C6) across the polarized W/DCE interface are chosen as model systems because they have the largest potential range that can be controlled externally. By selecting the appropriate ratios of the reactant concentrations (Kr c(M)+/c(DB18C6)) and using nanopipets as the SECM tips, we obtained a series of rate constants (k(f)) at various driving forces (Delta(O)(W) phi(ML+)(0') - Es, Delta(O)(W) phi(ML+)(0') is the formal potential of facilitated ion transfer and Es is the potential applied externally at the substrate interface) based on a three-electrode system. The FIT rate constants k(f) are found to be dependent upon the driving force. When the driving force is low, the dependence of 1n k(f) on the driving force is linear with a transfer coefficient of about 0.3. It follows the classical Butler-Volmer theory and then reaches a maximum before it decreases again when we further increase the driving forces. This indicates that there exists an inverted region, and these behaviors have been explained by Marcus theory.

Synthesis of fluorene-based oligomeric organoboron reagents via Kumada, Heck, and stille cross-coupling reactions

Boronic pinacol ester group is not reactive in Kumada, Heck and Stille coupling reaction conditions. Fluorene-based sophisticated organoboron compounds were synthesized by means of Palladium catalyzed Kumada, Heck and Stille cross-coupling reactions from halofluorenyl boronic esters.