Enzymatic amplification in a bioinspired, autonomous signal cascade

A two-step reaction cascade is applied to the sequence-specific detection of DNA by enzymatic amplification of the molecular into an optical signal.     

Isothermal cycling and cascade signal amplification strategy for ultrasensitive colorimetric detection of nucleic acids

Microchimica Acta - We have designed a novel isothermal cascade signal-amplification strategy for ultrasensitive colorimetric determination of nucleic acids. It is based on double-cycling...     

Additivity of noise propagation in a protein cascade

Stochastic fluctuations in a protein synthetic cascade are investigated using standard Omega-expansion technique. For the steady-state sensitivity, we show the conditions that result in the ultrasensitive "all-or-none" behavior, and for the noise propagation, we show clearly that (i) for any one given protein species in this cascade, the contributions of fluctuations in upstream proteins to its noise should be additive; and (ii) the output noise levels can vary as a function of the input concentrations and cascade length. Our results provide a possible theoretical explanation for the previous experimental studies.     

Analogies between point mechanics and chemical reaction kinetics

A few rather interesting analogies are shown between classical point mechanics and chemical reaction kinetics. The approach used is that of the differential geometry.

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The association reaction between C2H and 1-butyne: a computational chemical kinetics study

The potential energy surfaces (PES) for the reaction of the C(2)H radical with 1-butyne (C(4)H(6)) have been studied using the CBS-QB3 method. Density functional B3LYP/cc-pVTZ and M06-2X/6-311++G(d,p) calculations have also been performed to analyze the reaction energetics. For detailed theoretical calculation on the total reaction mechanism, the initial association reactions on more and less substituted C atoms of 1-butyne are treated separately followed by a variational transition state theory (VTST) calculation to obtain reaction rates. The successive unimolecular reactions from the association reaction complexes are subjected to Rice-Ramsperger-Kassel-Marcus (RRKM) calculations for reaction rate constants and product branching ratios. The calculated rate constants in the temperature range 70-295 K for both the association reactions are found to be highly temperature dependent at low temperatures, which is contrary to the experimental findings of temperature independent association rates. We have explained this observation with the help of variational nature of the transition states, and we found a "loose" transition state at low temperatures. The calculated product branching ratios for the unimolecular reactions generally agree with the available experimental data, although some channels show a significant method dependency and therefore the correlation with experiment is lost to some extent. Our detailed reaction energetics calculations confirm that the C(2)H + C(4)H(6) reaction proceeds without an entrance barrier and leads to the important products ethynylallene + CH(3), 1,3-hexadiyne + H, 3,4-hexadiene-1-yne + H, 2-ethynyl-1,3-butadiene + H, 3,4-dimethylenecyclobut-1-ene + H and fulvene + H exothermic by 25-75 kcal mol(-1), with strong dependence of the product distribution on the association mode of C(2)H with C(4)H(6), making these reactions fast under low temperature conditions of Titan's atmosphere. Therefore this study can provide a detailed picture of the complex hydrocarbon formation mechanism in the upper atmosphere.     

Complex chemical kinetics in single enzyme molecules: Kramers's model with fractional Gaussian noise

A model of barrier crossing dynamics governed by fractional Gaussian noise and the generalized Langevin equation is used to study the reaction kinetics of single enzymes subject to conformational fluctuations. The direct application of Kramers's flux-over-population method to this model yields analytic expressions for the time-dependent transmission coefficient and the distribution of waiting times for barrier crossing. These expressions are found to reproduce the observed trends in recent simulations and experiments.     

The influence of the photoacid-generator structure on chemical amplification in a resist

The effect of structure of a photoacid generator (triarylsulfonium and diaryliodonium salts) on the trends of image formation in a chemically amplified resist based on a methyl methacrylate copolymer with methacrylic acid and ethoxyethyl methacrylate was studied. It was shown that the type and quality of image in the resist depend on the structure of the Brönsted acid produced upon UV irradiation, on postexposure bake temperature, and on exposure radiation energy.     

Combination of precipitation preconcentration and chemical amplification of the signal in flow-injection determination of nanogram amounts of phosphorus

Coprecipitation of ion pairs of quadruply charged molybdovanadophosphoric heteropoly anions and cations of Brilliant Green with the ion pairs of the same dye and paramolybdate ions was used for determining nanogram amounts of phosphorus present as orthophosphates. Filtering of the sol through a column with a filter made of fibrous polypropylene provides on-line preconcentration of phosphorus, eliminates the effect of collector, and makes it possible to elute the concentrate for subsequently measuring the signal in the flow mode. A combination of this technique with chemical amplification of the analytical signal lowers the limit of detection to 0.05 ng of phosphorus in 2 mL.     

On the interplay between chemical reactions and phase transitions for molecules adsorbed on solid surfaces

We use Monte Carlo simulations to examine the manner in which reagent aggregation affects the reaction rate between molecules adsorbed on a solid surface. We discuss the temperature and concentration dependence of the rate of product formation.     

响应性凝胶与非线性化学反应相互作用研究进展

本文综述了响应性凝胶与非线性反应动力学相互作用的研究进展,从实验及理论方面评述了pH振荡器中响应胶的振荡行为、P(NIPAAm-co-Ru(bpy)3)共聚凝胶中Belousov-Zhabotinsky(BZ)化学反应引起的膨胀-收缩振荡、行波和纳米制动器的制备及生理条件下凝胶自振荡行为,成为化学能向机械能转化的智能材料领域中活跃的研究方向; 同时凝胶的响应性作用于非线性化学反应可控制反应动力学的分岔行为.最后对该研究领域的发展方向和应用前景进行了展望.     

Is there any convergence between the differential and integral procedures used in chemical kinetics,particularly in nonisothermal kinetics?

Some contradictions concerning the classification of the methods to evaluate nonisothermal kinetic parameters into differential and integral ones are analyzed. Using the theorem of media for integrals, the equivalence between the methods that use the integration on low ranges of variables and the differential methods is shown. Concerning the magnitude of the range of change of variables on which the integration of the rate equation is performed, the applicability of the isoconversional methods that use approximate expressions of the temperature integral (Simpson's formula, formula based on the theorem of media for integrals) was analyzed. Our results were verified for simulated data (which are not affected by the experimental errors) as well as for the nonisothermal data for the thermal decomposition of ammonium perchlorate. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 339–344, 2006     

Pre-equilibrium approximation in chemical and photophysical kinetics

For most mechanisms of chemical reactions and molecular photophysical processes the time evolution of the concentration of the intervening species cannot be obtained analytically. The pre-equilibrium approximation is one of several useful approximation methods that allow the derivation of explicit solutions and simplify numerical solutions. In this work, a general view of the pre-equilibrium approximation is presented, along with the respective analytical solution. It is also shown that the kinetic behavior of systems subject to pre-equilibration can be obtained by the application of perturbation theory. Several photophysical systems are discussed, including excimer formation, thermally activated delayed fluorescence, and external-heavy atom quenching of luminescence.     

Matrix and convolution methods in chemical kinetics

Two new approaches for writing kinetic equations in the matrix form or directly in the integrated form are presented here. While the first method allows to derive the kinetic rate matrix of kinetic systems of any kind in a direct and straightforward way, the second approach applies to species that are consumed solely through first order steps, regardless of the complexity of their formation pathways.     

The simulation of molecular weight distributions in polyreaction kinetics by discrete Galerkin methods

This article describes the development of a comprehensive solver for the differential equations arising from the modeling of molecular weight distributions in polyreactions. Based on a series of numerical developments, the software package PREDICI combines new directions in mathematics, chemical computing and implementation. The algorithm is based on a so-called discrete Galerkin h-p-method, which allows the efficient treatment of numerous polymerization reaction types. The abilities of the new concept are demonstrated on challenging examples.     

离子对色谱法研究吡咯并喹呤醌与D-丝氨酸反应的化学动力学

D-丝氨酸(DSer)作为一种新的神经递质存在于胶质细胞,在中枢神经系统疾病中发挥重要的作用;吡咯并喹呤醌(PQQ)能够促进神经因子的产生和神经保护作用。采用离子对色谱法测定吡咯并喹呤醌(PQQ)与DSer反应中游离PQQ的浓度,通过化学反应动力学研究PQQ与DSer的作用,为PQQ在神经递质的调节作用机制提供重要的信息。采用四丁基溴化铵为离子对试剂,PQQ与DSer孵育反应后各物质在Amethyst C18-P柱上的分离度较好,平均回收率为94.2%～99.3%,相对标准偏差为1.05%～2.03%。PQQ-DSer反应的平均速率常数分别为0.032 h~1 (25 ℃)、0.07 h~1(37 ℃)、0.17 h~1(50 ℃);平均反应活化能为54.7 kJ/mol;半衰期分别为22.0 h(25 ℃)、9.8 h(37 ℃)和3.99 h(50 ℃)。动力学结果显示PQQ对脑内DSer的平衡具有重要的调节作用。该方法简便、可靠。     

反应NH~4ClO~4+Mg+K~2Cr~2O~7的非线性化学动力学1: 固相振 荡燃烧的实验现 象

在外界环境条件恒定的情况下,反应体系NH~4ClO~4+Mg+K~2Cr~2O~7的燃烧过程是不均匀的,燃烧和光强呈周期性的强弱变化,给出了典型的化学振荡现象。本文介绍了NH~4ClO~4+Mg+K~2Cr~2O~7体系的固相振荡燃烧配方,对新配方进行了实验,研究了这个体系的固相振荡燃烧现象的非线性特性,分析了固相化学振荡的非线性化学反应动力学机理。