Catalysis of tRNA Aminoacylation: Single Turnover to Steady-State Kinetics of tRNA Synthetases

Aminoacyl-tRNA synthetases (aaRS) catalyze the bimolecular association reaction between amino acid and tRNA by specifically and unerringly choosing the cognate amino acid and tRNA. There are two classes of such synthetases that perform tRNA-aminoacylation reaction. Interestingly, these two classes of aminoacyl-tRNA synthetases differ not only in their structures but they also exhibit remarkably distinct kinetics under pre-steady-state condition. The class I synthetases show initial burst of product formation followed by a slower steady-state rate. This has been argued to represent the influence of slow product release. In contrast, there is no burst in the case of class H enzymes. The tight binding of product with enzyme for class I enzymes is correlated with the enhancement of rate in presence of elongation factor. EF-TU. In spite of extensive experimental studies, there is no detailed theoretical analysis that can provide a quantitative understanding of this important problem. In this article, we present a theoretical investigation of enzyme kinetics for both classes of aminoacyl-tRNA synthetases. We present an augmented kinetic scheme and then employ the methods of time-dependent probability statistics to obtain expressions for the first passage time distribution that gives both the time-dependent and the steady-state rates. The present study quantitatively explains all the above experimental observations. We propose an alternative path way in the case of class II enzymes showing the tRNA-dependent amino acid activation and the discrepancy between the single-turnover and steady-state rate.

Unraveling siRNA unzipping kinetics with graphene

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (tau) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4742189]

High-temperature kinetics of the reaction between CN and hydrocarbons using a novel high-enthalpy flow tube

More than 70 molecules of varied nature have been identified in the envelopes of carbon-rich stars through their spectral fingerprints in the microwave or far infrared regions. Many of them are carbon chain molecules and radicals, and a significant number are unique to the circumstellar medium. The determination of relevant laboratory kinetics data is critical to keep up with the development of the high spectral and spatial resolution observations and of the refinement of chemical models. Neutralneutral reactions of the CN radical with unsaturated hydrocarbons could be a dominant route in the formation of cyanopolyynes, even at low temperatures and deserve a detailed laboratory investigation. The approach we have developed aims to bridge the temperature gap between resistively heated flow tubes and shock tubes. The present kinetic measurements are obtained using a new reactor combining a high-enthalpy source with a flow tube and a pulsed laser photolysislaser-induced fluorescence system to probe the undergoing chemical reactions. The high-enthalpy flow tube has been used to measure the rate constant of the reaction of the CN radical with propane (C3H8), propene (C3H6), allene (C3H4), 1,3-butadiene (1,3-C4H6), and 1-butyne (C4H6) over a temperature range extending from 300 to 1200 K. All studied reactions of CN with unsaturated hydrocarbons are rapid, with rate coefficients greater than 10-10 cm3 center dot molecule-1 center dot s-1 and exhibit slight negative temperature dependence above room temperature. (c) 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 753766, 2012

Thermal degradation kinetics of thermoresponsive poly(N-isopropylacrylamide-co-N,N-dimethylacrylamide) copolymers prepared via RAFT polymerization

Reversible addition-fragmentation chain transfer polymerization at 70 A degrees C in N,N-dimethylformamide was used to prepare poly(N-isopropylacrylamide-co-N,N-dimethylacrylamide) copolymers in various compositions to afford well-defined polymers with pre-determined molecular weight, narrow molecular weight distribution, and precise chain end structure. The copolymer compositions were determined by H-1 NMR spectroscopy. The reactivity ratios of N-isopropylacrylamide (NIPAM) and N,N-dimethylacrylamide (DMA) were calculated as r (NIPAM) = 0.838 and r (DMA) = 1.105, respectively, by the extended Kelen-Tudos method at high conversions. The lower critical solution temperature of PNIPAM can be altered by changing the DMA content in the copolymer chain. Differential scanning calorimetry and thermogravimetric analysis at different heating rates were carried out on these copolymers to understand the nature of thermal degradation and to determine its kinetics. Different kinetic models were applied to estimate various parameters like the activation energy, the order, and the frequency factor. These studies are important to understand the solid state polymer degradation of N-alkyl substituted polymers, which show great potential in the preparation of miscible polymer blends due to their ability to interact through hydrogen bonding.

``On-the-fly'' kinetics of enzymatic racemization using deuterium NMR in DNA-based chiral oriented media

We report the in situ and real-time monitoring of the interconversion of L- and D-alanine-d(3) by alanine racemase from Bacillus stearothermophilus directly observed by H-2 NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their H-2 quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis Menten model.

Growth kinetics and immune response of chimeric foot-and-mouth disease virus serotype `O' produced through replication competent mini genome of serotype Asia 1, 63/72, in BHK cell lines

Regular vaccinations with potent vaccine, in endemic countries and vaccination to live in non-endemic countries are the methods available to control foot-and-mouth disease. Selection of candidate vaccine strain is not only cumbersome but the candidate should grow well for high potency vaccine preparation. Alternative strategy is to generate an infectious cDNA of a cell culture-adapted virus and use the replicon for development of tailor-made vaccines. We produced a chimeric `O' virus in the backbone of Asia 1 and studied its characteristics. The chimeric virus showed high infectivity titre (>10(10)) in BHK 21 cell lines, revealed small plague morphology and there was no cross reactivity with antiserum against Asia I. The virus multiplies rapidly and reaches peak at 12 h post infection. The vaccine prepared with this virus elicited high antibody titres.

Densification kinetics, phase assemblage and hardness of spark plasma sintered Cu-10 wt% TiB2 and Cu-10 wt% TiB2-10 wt% Pb composites

The present work demonstrates the synthesis of Cu-10 wt% TiB2 composites with a theoretical density of more than 90% by tailoring the spark plasma sintering (SPS) conditions in the temperature range of 400-700 degrees C. Interestingly, 10 wt% Pb addition to Cu-10 wt% TiB2 lowers the sinter density and the difference in the densification behavior of the investigated compositions was discussed in reference to the current profile recorded during a SPS cycle. The sintering kinetics and phase assemblage were also discussed in reference to surface melting of the constituents prior to bulk melting temperature, temperature dependent wettability of Pb on Cu, diffusion kinetics of Cu as well as the formation of various oxides. An important result is that a high hardness of around 2 GPa and relative density close to 92% qtheoretical was achieved for the Cu-10 wt% TiB2-10 wt% Pb composite, and such a combination has never been achieved before using any conventional processing route.

Thermal and Sonochemical Degradation Kinetics of Poly(n-butyl methacrylate-co-alkyl acrylates): Variation of Chain Strength and Stability with Copolymer Composition

The thermal degradation of poly(n-butyl methacrylate-co-alkyl acrylate) was compared with ultrasonic degradation. For this purpose, different compositions of poly (n-butyl methacrylate-co-methyl acrylate) (PBMAMA) and a particular composition of poly(n-butyl methacrylate-co-ethyl acrylate) (PBMAEA) and poly(n-butyl methacrylate-co-butyl acrylate) (PBMABA) were synthesized and characterized. The thermal degradation of polymers shows that the poly(alkyl acrylates) degrade in a single stage by random chain scission and poly(n-butyl methacrylate) degrades in two stages. The number of stages of thermal degradation of copolymers was same as the majority component of the copolymer. The activation energy corresponding to random chain scission increased and then decreased with an increase of n-butyl methacrylate fraction in copolymer. The effect of methyl acrylate content, alkyl acrylate substituent, and solvents on the ultrasonic degradation of these copolymers was investigated. A continuous distribution kinetics model was used to determine the degradation rate coefficients. The degradation rate coefficient of PBMAMA varied nonlinearly with n-butyl methacrylate content. The degradation of poly (n-butyl methacrylate-co-alkyl acrylate) followed the order: PBMAMA < PBMAEA < PBMABA. The variation in the degradation rate constant with composition of the copolymer was discussed in relation to the competing effects of the stretching of the polymer in solution and the electron displacement in the main chain. (C) 2012 Society of Plastics Engineers

Film thickness mediated transition in the kinetics of electric current induced flow of thin liquid metal films

Application of high electric-field between two points in a thin metallic film results in liquefaction and subsequent flow of the liquid-film from one electrode to another in a radially symmetric fashion. Here, we report the transition of the flow kinetics driven by the liquid film thickness varying from 3 to 100 nm. The mechanism of the flow behavior is observed to be independent of the film thickness; however, the kinetics of the flow depends on the film thickness and the applied voltage. An analytical model, incorporating viscosity and varying electrical resistivity with film thickness, is developed to explain the experimental observations. (C) 2014 AIP Publishing LLC.

Specroelectrochemical, Switching Kinetics, and Chronoamperometric Studies of Dibenzyl Derivative of Poly(3,4-propylenedioxythiophene) Thin-Film-Based Electrochromic Device

The dibenzyl derivative of poly(3,4-propylenedioxythiophene) (PProDOT-Bz(2)) thin film is deposited onto ITO-coated glass substrate by electropolymerization technique. The electropolymerization of ProDOT-Bz(2) is carried out by a three-electrode electrochemical cell. The cyclic voltammogram shows the redox properties of electrochemically prepared films deposited at different scan rates. The thin films prepared were characterized for its morphological properties to study the homogeniety. Classic six-layer structure of PProDOT-Bz(2) electrochromic device using this material was fabricated and reported for the first and its characterizations such as spectroelectrochemical, switching kinetics, and chronoamperometric studies are performed. The color contrast of the thin film and the device achieved are 64 and 40%, respectively, at lambda(max) (628 nm). The switching time is recorded and the observed values are 5 s from the coloring state to the bleaching state and vice versa. The chronoamperometry shows that the device performed up to 400 cycles, and it is capable of working up to 35 cycles without any degradation. (C) 2014 Wiley Periodicals, Inc.

Role of surface chemistry in modulating drug release kinetics in titania nanotubes

Surface chemistry and the intrinsic porous architectures of porous substrates play a major role in the design of drug delivery systems. An interesting example is the drug elution characteristic from hydrothermally synthesised titania nanotubes with tunable surface chemistry. The variation in release rates of Ibuprofen (IBU) is largely influenced by the nature of the functional groups on titania nanotubes and pH of suspending medium. To elucidate the extent of interaction between the encapsulated IBU and the functional groups on titania nanotubes, the release profiles have been modelled with an empirical Hill equation. The analysis aided in establishing a probable mechanism for the release of IBU from the titania nanotubes. The study of controlled drug release from TiO2 has wider implication in the context of biomedical engineering. (C) 2014 Elsevier B.V. All rights reserved.

Kinetics of phase separation in polymer mixtures: A molecular dynamics study

We present detailed results from a molecular dynamics (MD) simulation of phase-separation kinetics in polymer mixtures. Our MD simulations naturally incorporate hydrodynamic effects. We find that polymeric phase separation (with dynamically symmetric components) is in the same universality class as segregation of simple fluids: the degree of polymerization only slows down the segregation kinetics. For d = 2 polymeric fluids, the domain growth law is L(t) similar to t(phi) with phi showing a crossover from 1/3 -> 1/2 -> 2/3. For d = 3 polymeric fluids, we see the crossover phi = 1/3 -> 1. Our MD simulations do not yet access the inertial hydrodynamic regime (with L similar to t(2/3)) of phase separation in 3-d fluids. (C) 2014 AIP Publishing LLC.

Pressure induced manifold enhancement of Li-kinetics in FCC fullerene

The reduction of the diffusion energy barrier for Li in electrodes is one of the required criteria to achieve better performances in Li ion batteries. Using density functional theory based calculations, we report a pressure induced manifold enhancement of Li-kinetics in bulk FCC fullerene. Scanning of the potential energy surface reveals a diffusion path with a low energy barrier of 0.62 eV, which reduces further under the application of hydrostatic pressure. The pressure induced reduction in the diffusion barrier continues till a uniform volume strain of 17.7% is reached. Further enhancement of strain increases the barrier due to the repulsion caused by C-C bond formation between two neighbouring fullerenes. The decrease in the barrier is attributed to the combined effect of charge transfer triggered by the enhanced interaction of Li with the fullerene as well as the change in profile of the local potential, which becomes more attractive for Li. The lowering of the barrier leads to an enhancement of two orders of magnitude in Li diffusivity at room temperature making pressurized bulk fullerene a promising artificial solid electrolyte interface (SEI) for a faster rechargeable battery.

A detailed numerical study of NOx kinetics in low calorific value H-2/CO syngas flames

The present study provides an extensive and detailed numerical analysis of NO chemical kinetics in low calorific value H-2/CO syngas flames utilizing predictions by five chemical kinetic mechanisms available out of which four deal with H-2/CO while the fifth mechanism (GRI 3.0) additionally accounts for hydrocarbon chemistry. Comparison of predicted axial NO profiles in premixed flat flames with measurements at 1 bar, 3.05 bar and 9.15 bar shows considerably large quantitative differences among the various mechanisms. However, at each pressure, the quantitative reaction path diagrams show similar NO formation pathways for most of the mechanisms. Interestingly, in counterflow diffusion flames, the quantitative reaction path diagrams and sensitivity analyses using the various mechanisms reveal major differences in the NO formation pathways and reaction rates of important reactions. The NNH and N2O intermediate pathways are found to be the major contributors for NO formation in all the reaction mechanisms except GRI 3.0 in syngas diffusion flames. The GRI 3.0 mechanism is observed to predict prompt NO pathway as the major contributing pathway to NO formation. This is attributed to prediction of a large concentration of CH radical by the GRI 3.0 as opposed to a relatively negligible value predicted by all other mechanisms. Also, the back-conversion of NNH into N2O at lower pressures (2-4 bar) was uniquely observed for one of the five mechanisms. The net reaction rates and peak flame temperatures are used to correlate and explain the differences observed in the peak NO] at different pressures. This study identifies key reactions needing assessment and also highlights the need for experimental data in syngas diffusion flames in order to assess and optimize H-2/CO and nitrogen chemistry. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Phase evolutions, growth kinetics and diffusion parameters in the Co-Ni-Ta system

Diffusion couple experiments are conducted to study phase evolutions in the Co-rich part of the Co-Ni-Ta phase diagram. This helps to examine the available phase diagram and propose a correction on the stability of the Co2Ta phase based on the compositional measurements and X-ray analysis. The growth rate of this phase decreases with an increase in Ni content. The same is reflected on the estimated integrated interdiffusion coefficients of the components in this phase. The possible reasons for this change are discussed based on the discussions of defects, crystal structure and the driving forces for diffusion. Diffusion rate of Co in the Co2Ta phase at the Co-rich composition is higher because of more number of Co-Co bonds present compared to that of Ta-Ta bonds and the presence of Co antisites for the deviation from the stoichiometry. The decrease in the diffusion coefficients because of Ni addition indicates that Ni preferably replaces Co antisites to decrease the diffusion rate. (C) 2014 Elsevier B.V. All rights reserved.