Generalised expressions for the association and dissociation rate constants of molecules with multiple binding sites

ABSTRACT

Many proteins exhibit multiple binding patches. A patch may harbour a key chemical modification site, but may also simply act as a trap for the binding to another site. Here we consider the scenario in which one molecule (enzyme) binds another molecule (substrate) which contains two sites. We present microscopic expressions for the rate at which the enzyme binds to a particular site on the substrate, both for the scenario in which the enzyme directly binds the site without first visiting the other site, and for the case in which it may visit the other site an arbitrary number of times before binding to the site of interest. We also present the expressions for the corresponding dissociation reactions. These expressions can be used to compute in a single rare-event simulation of the dissociation pathway not only both the intrinsic and effective dissociation rate constants but also both association rate constants.     

Field electron emission images of multi-walled carbon nanotubes

Field electron emission microscope images from multi-walled carbon nanotubes can typically be characterized by the presence of five pentagons surrounding a sixth central pentagon. The observations of bright line centered interference patterns between adjacent pentagons in the field electron emission microscope images of multi-walled carbon nanotubes have been reported in the literature. We have observed a shift from bright to dark line centered interference patterns and associated this with the presence of surface adsorption. In order to identify the origin of the contaminant, multi-walled carbon nanotubes were dosed with H₂, H₂O, CO and O₂ and then imaged in the field electron emission microscope. Only the samples exposed to O₂ showed a shift from a bright line centered pattern between adjacent pentagons of a clean surface to a dark line centered pattern when one pentagon was contaminated or a bright line centered pattern when both adjacent pentagons become contaminated. The results of the experimental studies and the modeling of the changes in the field emission pattern as phase shifts in the wave function of the tunneling electrons due to modifications in the surface work function are presented.     

First nucleation steps during deposition of SiO2 thin films by plasma enhanced chemical vapour deposition

The initial nucleation stages during deposition of SiO₂ by remote plasma enhanced chemical vapour deposition (PECVD) have been monitored by XPS inelastic peak shape analysis. Experiments have been carried out on two substrates, a flat ZrO₂ thin film and a silicon wafer with a native silicon oxide layer on its surface. For the two substrates it is found that PECVD SiO₂ grows in the form of islands. When the SiO₂ particles reach heights close to 10 nm they coalesce and cover completely the substrate surface. The particle formation mechanism has been confirmed by TEM observation of the particles grown on silicon substrates. The kinetic Monte Carlo simulation of the nucleation and growth of the SiO₂ particles has shown that formation of islands is favoured under PECVD conditions because the plasma species may reach the substrate surface according to off-perpendicular directions. The average energy of these species is the main parameter used to describe their angular distribution function, while the reactivity of the surface is another key parameter used in the simulations.     

High-temperature measurements of the rates of the reactions CH2O + Ar → Products and CH2O + O2 → Products

The two-channel thermal decomposition of formaldehyde [CH₂O], (1a) CH₂O + Ar → HCO + H + Ar, and (1b) CH₂O + Ar → H₂ + CO + Ar, was studied in shock tube experiments in the 2258-2687 K temperature range, at an average total pressure of 1.6 atm. OH radicals, generated on shock heating trioxane-O₂-Ar mixtures, were monitored behind the reflected shock front using narrow-linewidth laser absorption. 1,3,5 trioxane [C₃H₆O₃] was used as the CH₂O precursor in the current experiments. H-atoms formed upon CH₂O and HCO decomposition rapidly react with O₂ to produce OH via H + O₂ → O + OH. The recorded OH time-histories show dominant sensitivity to the formaldehyde decomposition pathways. The second-order reaction rate coefficients were inferred by matching measured and modeled OH profiles behind the reflected shock. Two-parameter fits for k_1a and k_1b, applicable in this temperature range, are:

     

纳米氧化锌的过饱和控制生长与大小分布控制.

"在非水介质中合成了纳米氧化锌,测定了纳米氧化锌的紫外吸收光谱,并用有效质量模型计算了粒子大小,开发并命名了一种称之为纳米粒子过饱和控制生长的技术,该技术涉及将小的纳米粒子悬浊液加入到大的粒子悬浊液中,结果因为不同大小粒子间的溶解度差异小的粒子将全部溶解,大的粒子将整体长大,大粒子悬浊液的粒子数将保持不变,大粒子的生长速度显著比Ostwald老化的高．该技术最显著的特征是只要最初两悬浊液粒子大小的差异足够大,分布不是太宽,则粒子大小的分布将会因为粒子如此长大而变窄．"     

Some insights in the sonochemical preparation of cobalt nano-particles

The preparation of cobalt nano-particles from a solution of Co(CO)₃(NO) in n-decane under ultrasonication with a frequency of 20 kHz yielded cobalt particles of a size of ca. 5 nm. The presence of either silica or oleic acid in the solution reduced the particle size to ca. 3 and 2 nm, respectively. The resulting particle size is independent of the ultrasonication time, initial Co(CO)₃(NO) concentration, ultrasound intensity and solution temperature. It is postulated that bubble collapse generates multiple nucleation sites resulting in the formation of cobalt particles with a rather uniform particle size distribution.     

Role of cationic gemini surfactants toward enhanced ninhydrin–tryptophan reaction

In this paper we report the effect of dicationic ‘gemini’ surfactants (CH₃)₂C₁₆H₃₃N⁺? (CH₂)_m? N⁺C₁₆H₃₃(CH₃)₂, 2Br^? (where m = 4, 5, 6) on the reaction of ninhydrin with DL ‐tryptophan. The gemini surfactant micellar media are comparatively more effective than their conventional monomeric counterpart cetyltrimethylammonium bromide (CTAB) micelles. Also, whereas typical rate constant (k_ψ) increase and leveling‐off regions, just like CTAB, are observed with geminis, the latter produce a third region of increasing k_ψ at higher concentrations. These subsequent increases are ascribed to changes in micellar morphologies, consistent with changes in ¹H NMR line widths. Quantitative kinetic analysis of the rate constant–[surfactant] data has been performed on the basis of modified pseudophase model. Copyright © 2007 John Wiley & Sons, Ltd.     

Non-linear scission/recombination kinetics of living polymerization

Living polymers are formed by reversible association of primary units (unimers). Generally the chain statistical weight involves a factor σ < 1 suppressing short chains in comparison with free unimers. Living polymerization is a sharp thermodynamic transition for σ ≪ 1 which is typically the case. We show that this sharpness has an important effect on the kinetics of living polymerization (one-dimensional association). The kinetic model involves i) the unimer activation step (a transition to an assembly-competent state); ii) the scission/recombination processes providing growth of polymer chains and relaxation of their length distribution. Analyzing the polymerization with no chains but unimers at t = 0 , with initial concentration of unimers M ≳ M ^* (M^* is the critical polymerization concentration), we determine the time evolution of the chain length distribution and find that: 1) for M ^* ≪ M ≪ M ^*/σ the kinetics is characterized by 5 distinct time stages demarcated by 4 characteristic times t₁, t₂, t₃ and t^*; 2) there are transient regimes (t ₁ ≲ t ≲ t ₃) when the molecular-weight distribution is strongly non-exponential; 3) the chain scissions are negligible at times shorter than t₂. The chain growth is auto-accelerated for t ₁ ≲ t ≲ t ₂ : the cut-off chain length (= polymerization degree 〈n〉_w N ₁ ∝ t ² in this regime. 4) For t ₂ < t < t ₃ the length distribution is characterized by essentially 2 non-linear modes; the shorter cut-off length N₁ is decreasing with time in this regime, while the length scale N₂ of the second mode is increasing. (5) The terminal relaxation time of the polymer length distribution, t^*, shows a sharp maximum in the vicinity of M^*; the effective exponent is as high as ∼ σ^-1/3 just above M^*.     

A detonation stability formulation for arbitrary equations of state and multi-step reaction mechanisms

A general normal-mode linear stability formulation of steady planar detonation waves is presented that is valid both for an arbitrary equation of state and for multi-step, multi-species chemical kinetics. The general formulation can be used for many purposes, including an examination of gaseous detonation stability with complex reaction kinetics in which the individual reacting species have variable thermochemical properties. In the present paper, we consider two cases that could not be obtained by previous one-step chemistry, polytropic gas formulations: the first concerns the effect of a difference in heat capacities between product and fuel species, as well as a possible mole change, in a single-step irreversible reaction. The second examines the effects of exothermic or endothermic heat release/absorption in the chain-initiation stage of a model three-step reaction.