Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal–chemical modeling, formation of first cells, and geological clues

Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal–chemical modeling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular sieve silicalite-ZSM-5-(mutinaite). Calculation of binding and activation energies for catalytic assembly into polymers is progressing for a chemical composition with one catalytic Al–OH site per 25 neutral Si tetrahedral sites. Internal channel intersections and external terminations provide special stereochemical features suitable for complex organic species. Polymer migration along nano/micrometer channels of ancient weathered feldspars, plus exploitation of phosphorus and various transition metals in entrapped apatite and other microminerals, might have generated complexes of replicating catalytic biomolecules, leading to primitive cellular organisms. The first cell wall might have been an internal mineral surface, from which the cell developed a protective biological cap emerging into a nutrient-rich “soup.” Ultimately, the biological cap might have expanded into a complete cell wall, allowing mobility and colonization of energy-rich challenging environments. Electron microscopy of honeycomb channels inside weathered feldspars of the Shap granite (northwest England) has revealed modern bacteria, perhaps indicative of Archean ones. All known early rocks were metamorphosed too highly during geologic time to permit simple survival of large-pore zeolites, honeycombed feldspar, and encapsulated species. Possible microscopic clues to the proposed mineral adsorbents/catalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments.

Synaptonemal complex (SC) component Zip1 plays a role in meiotic recombination independent of SC polymerization along the chromosomes.

Zip1 is a yeast synaptonemal complex (SC) central region component and is required for normal meiotic recombination and crossover interference. Physical analysis of meiotic recombination in a zip1 mutant reveals the following: Crossovers appear later than normal and at a reduced level. Noncrossover recombinants, in contrast, seem to appear in two phases: (i) a normal number appear with normal timing and (ii) then additional products appear late, at the same time as crossovers. Also, Holliday junctions are present at unusually late times, presumably as precursors to late-appearing products. Red1 is an axial structure component required for formation of cytologically discernible axial elements and SC and maximal levels of recombination. In a red1 mutant, crossovers and noncrossovers occur at coordinately reduced levels but with normal timing. If Zip1 affected recombination exclusively via SC polymerization, a zip1 mutation should confer no recombination defect in a red1 strain background. But a red1 zip1 double mutant exhibits the sum of the two single mutant phenotypes, including the specific deficit of crossovers seen in a zip1 strain. We infer that Zip1 plays at least one role in recombination that does not involve SC polymerization along the chromosomes. Perhaps some Zip1 molecules act first in or around the sites of recombinational interactions to influence the recombination process and thence nucleate SC formation. We propose that a Zip1-dependent, pre-SC transition early in the recombination reaction is an essential component of meiotic crossover control. A molecular basis for crossover/noncrossover differentiation is also suggested.

Real time measurements of elongation by a reverse transcriptase using surface plasmon resonance.

A rapid direct assay for polymerase-induced elongation along a given template is an obligate requirement for understanding the processivity of polymerization and the mode of action of drugs and inhibitors on this process. Surface plasmon resonance can be used to follow the association and the dissociation rates of a given reverse transcriptase on DNA.RNA and DNA.DNA hybrids immobilized on a biotin-streptavidin surface. The addition of nucleotides complementary to the template strand produces an increase in the local mass, as deduced from an increase in the measured signal, due to elongation of the primer strand that allows an estimation of both the extent and rate of the polymerization process. The terminator drug 3'-deoxy-3'-azidothymidine triphosphate completely abolishes the increase in signal as would be expected from an inhibition of elongation. This technique provides a sensitive assay for the affinities of different polymerases for specific templates and for the effects of terminators of the elongation process.

Living cationic polymerization

The kinetics of the polymerization of styrene iniated by 1-chloro-1-phenyltehane/tin (IV) chloride in the presence of tetrabutylammonium chloride have been studied. Dilatometry studies at 25 °C were conducted and the orders of reaction were established. Molecular weight studies were conducted for these experiments using size exclusion chromatography. These studies indicated that transfer/termination reactions were present. The observed kinetics may be explained by a polymerization mechanism involving a single propagating species which is present in low concentrations. Reactions at 0 °C and -15 °C have shown that a "living" polymerization could be obtained at low temperatures. A method was derived to study the kinetics of a "living" polymerization by following the increase in degree of polymerization with time. Polymerizations of styrene were conducted using 1,4-bis(bromomethyl)benzene as a difunctional co-catalyst. These reactions produced polymers with broad or bimodal molecular weight distributions. These observations may be explained by the rate of initiation being slower than the rate of propagation or the presence of transfer/termination reactions. Reactions were conducted using a co-catalyst using a co-catalyst produced by the addition of 1,1-diphenylethane to 1,4-bis(bromomethyl)benzene. Size exclusion chromatography studies showed that the polymers produced had a narrower molecular weight distribution than those produced by polymerizations initiated by 1,4-bis(bromomethyl)benzene alone. However the polydispersity was still observed to increase with reaction time. This may also be explained by slow initiation compared to the rate of propagation. Polymerizations initiated by both bifunctional initiators were examined using the method of studying reaction kinetics by following the change in number average degree of polymerization. The results indicated that a straight line relationship could also be obtained with a non-living polymerization.

Living cationic polymerization of styrene monomers

This thesis describes an experimental investigation of synthesis of polystyrene under various polymerization conditions such as solvent polarity, temperature, initial concentrations of initiator, catalyst, monomer and added salts or co-catalyst, which was achieved using the living cationic polymerization technology in conjunction with gel permeation chromatography (GPC) and NMR spectroscopy. Polymerizations of styrene were conducted using 1-phenyl ethylchloride (1-PEC) as an initiator and tin tetrachloride (SnCI4) as a catalyst in the presence of tetra-n-Butylammonium chloride (nBu4NCI). Effects of solvent polarity varied by mixing dichloromethane (DCM) and less polar cyclohexane (C.hex), temperature, initial concentrations of SnC14, 1-PEC and nBu4NCI on the polymerizations were examined, and the conditions under which a living polymerization can be obtained were optimised as: [styrene]o ~ 0.75 - 2 M; [1-PEC]o ~ 0.005 - 0.05 M; [SnCI4Jo ~ 0.05 - 0.4 M; [nBu4NCIJo ~ 0.001 - 0.1 M; DCM/C.hex ~ 50/0 - 20/30 v/v; T ~ 0 to -45°C. Kinetic studies of styrene polymerization using the Omnifit sampling method showed that the number average molecular weight (Mn) of the polymers obtained increased in direct proportion to monomer conversion and agreed well with the theoretical Mn expected from the concentration ratios of monomer to initiator. The linearities of both the 1n([MJoI[M]) vs. time plot and the Mn vs. monomer conversion plot, and the narrow molecular weight distribution (MWD) measured using GPC demonstrated the livingness of the polymerizations, indicating the absence of irreversible termination and transfer within the lifetimes of the polymerizations. The proposed 'two species' propagation mechanism was found to apply for the styrene polymerization with 1-PEC/SnCI4 in the presence of nBu4NCl. The further kinetic experiments showed that living styrene polymerizations were achieved using the 1-PEC/SnCI4 initiating system in mixtures of DCM/C.hex 30/20 v/v at -15°C in the presence of various bromide salts, tetra-n-butylammonium bromide, tetra-n-pentylammonium bromide, tetra-n-heptylammonium bromide, and tetra-n-octylammonium bromide, respectively. The types of the bromide salts were found to have no significant effect on monomer conversion, Mn, polydispersity and initiation efficiency. Living polymerizations of styrene were also achieved using titanium tetrachloride (TiCI4) as a catalyst and 1-PEC as an initiator in the presence of a small amount of 2,6-di-tert-butylpyridine or pyridine instead of nBu4NCl. GPC analysis showed that the polymers obtained had narrow polydispersities (P.D. < 1.3), and the linearities of both the In([MJo/[MJ) vs. time plot and the Mn vs. monomer conversion plot demonstrated that the polymerizations are living, when the ratio of DCM and C.hex was less than 40 : 10 and the reaction temperature was not lower than -15°C. The reaction orders relative to TiCl4 and 1-PEC were estimated from the investigations into the rate of polymerization to be 2.56 and 1.0 respectively. lH and 13C NMR analysis of the resultant polystyrene would suggest the end-functionality of the product polymers is chlorine for all living polymerizations.

Reversible addition–fragmentation chain transfer polymerization of 2-chloro-1,3-butadiene

Controlled polymerization of 2-chloro-1,3-butadiene using reversible addition–fragmentation chain transfer (RAFT) polymerization has been demonstrated for the first time. 2-Chloro-1,3-butadiene, more commonly known as chloroprene, has significant industrial relevance as a crosslinked rubber, with uses ranging from adhesives to integral automotive components. However, problems surrounding the inherent toxicity of the lifecycle of the thiourea-vulcanized rubber have led to the need for control over the synthesis of poly(2-chloro-1,3-butadiene). To this end, four chain transfer agents in two different solvents have been trialed and the kinetics are discussed. 2-Cyano-2-propylbenzodithioate (CPD) is shown to polymerize 2-chloro-1,3-butadiene in THF, using AIBN as an initiator, with complete control over the target molecular weight, producing polymers with low polydispersities (Mw/Mn < 1.25 in all cases).

Controlled RAFT polymerization and zinc binding performance of catechol-inspired homopolymers

Incorporation of catechols into polymers has long been of interest due to their ability to chelate heavy metals and their use in the design of adhesives, metal-polymer nanocomposites, antifouling coatings, and so on. This paper reports, for the first time, the reversible addition-fragmentation chain transfer (RAFT) polymerization of a protected catechol-inspired monomer, 3,4-dimethoxystyrene (DMS), using commercially available trithiocarbonate, 2-(dodecylthiocarbonothioylthio)-2-methylpropionic acid (DDMAT), as a chain transfer agent. Our identified RAFT system produces well-defined polymers across a range of molecular weights (5-50 kg/mol) with low molar mass dispersities (Mw/Mn < 1.3). Subsequent facile demethylation of poly(3,4-dimethoxystyrene) (PDMS) yields poly(3,4-dihydroxystyrene) (PDHS), a catechol-bearing polymer, in quantitative yields. Semiquantitative zinc binding capacity analysis of both polymers using SEM/EDXA has demonstrated that both PDMS and PDHS have considerable surface binding (65% and 87%, respectively), although the films deposited from PDMS are of a better quality and processability due to solubility and lower processing temperatures. © 2014 American Chemical Society.

Detailed analysis of a conservative difference approximation for the time fractional diffusion equation

Diffusion equations that use time fractional derivatives are attractive because they describe a wealth of problems involving non-Markovian Random walks. The time fractional diffusion equation (TFDE) is obtained from the standard diffusion equation by replacing the first-order time derivative with a fractional derivative of order α ∈ (0, 1). Developing numerical methods for solving fractional partial differential equations is a new research field and the theoretical analysis of the numerical methods associated with them is not fully developed. In this paper an explicit conservative difference approximation (ECDA) for TFDE is proposed. We give a detailed analysis for this ECDA and generate discrete models of random walk suitable for simulating random variables whose spatial probability density evolves in time according to this fractional diffusion equation. The stability and convergence of the ECDA for TFDE in a bounded domain are discussed. Finally, some numerical examples are presented to show the application of the present technique.

Determination of preventive maintenance lead time using hybrid analysis

The time for conducting Preventive Maintenance (PM) on an asset is often determined using a predefined alarm limit based on trends of a hazard function. In this paper, the authors propose using both hazard and reliability functions to improve the accuracy of the prediction particularly when the failure characteristic of the asset whole life is modelled using different failure distributions for the different stages of the life of the asset. The proposed method is validated using simulations and case studies.

Effective Cell-Centred Time-Domain Maxwell's Equations Numerical Solvers

This research work analyses techniques for implementing a cell-centred finite-volume time-domain (ccFV-TD) computational methodology for the purpose of studying microwave heating. Various state-of-the-art spatial and temporal discretisation methods employed to solve Maxwell's equations on multidimensional structured grid networks are investigated, and the dispersive and dissipative errors inherent in those techniques examined. Both staggered and unstaggered grid approaches are considered. Upwind schemes using a Riemann solver and intensity vector splitting are studied and evaluated. Staggered and unstaggered Leapfrog and Runge-Kutta time integration methods are analysed in terms of phase and amplitude error to identify which method is the most accurate and efficient for simulating microwave heating processes. The implementation and migration of typical electromagnetic boundary conditions. from staggered in space to cell-centred approaches also is deliberated. In particular, an existing perfectly matched layer absorbing boundary methodology is adapted to formulate a new cell-centred boundary implementation for the ccFV-TD solvers. Finally for microwave heating purposes, a comparison of analytical and numerical results for standard case studies in rectangular waveguides allows the accuracy of the developed methods to be assessed.