Kinetic transition

State is that assembly of atoms or moieties that closely resembles the reactant(s), such that only a relatively small reorganization will generate the reactant(s). Analogously, a late transition state more closely resembles the structure of the reaction product(s). See Chemical Kinetics Transition State Theory Potential Energy Surface Hammond Principle Transition Structure... 

TRANSIENT-STATE KINETIC METHODS CHEMICAL KINETICS TRANSITION COORDINATE REACTION COORDINATE PHYSICAL ORGANIC CHEMISTRY NOMENCLATURE... 

TRANSITION STATE THEORY POTENTIAL ENERGY SUREACE HAMMOND PRINCIPLE TRANSITION STRUCTURE CHEMICAL KINETICS TRANSITION-STATE ANALOGUES MOLECULAR SIMILARITY... 

Semiempirical calculations have been used to calculate kinetic, transition-state, thermodynamic, and physicochemical parameters for acridin-9-amine (18a) and its tautomer, acridin-9( 10//)-iminc (18b).27... 

The second relaxation process has a specific saddle-like shape and manifests itself in the temperature range of —50°C to +150°C. This relaxation process is thought to be a kinetic transition due to water molecule reorientation in the vicinity of a defect [155]. 

Often the key entity one is interested in obtaining in modeling enzyme kinetics is the analytical expression for the turnover flux in quasi-steady state. Equations (4.12) and (4.38) are examples. These expressions are sometimes called Michaelis-Menten rate laws. Such expressions can be used in simulation of cellular biochemical systems, as is the subject of Chapters 5, 6, and 7 of this book. However, one must keep in mind that, as we have seen, these rates represent approximations that result from simplifications of the kinetic mechanisms. We typically use the approximate Michaelis-Menten-type flux expressions rather than the full system of equations in simulations for several reasons. First, often the quasi-steady rate constants (such as Ks and K in Equation (4.38)) are available from experimental data while the mass-action rate constants (k+i, k-i, etc.) are not. In fact, it is possible for different enzymes with different detailed mechanisms to yield the same Michaelis-Menten rate expression, as we shall see below. Second, in metabolic reaction networks (for example), reactions operate near steady state in vivo. Kinetic transitions from one in vivo steady state to another may not involve the sort of extreme shifts in enzyme binding that have been illustrated in Figure 4.7. Therefore the quasi-steady approximation (or equivalently the approximation of rapid enzyme turnover) tends to be reasonable for the simulation of in vivo systems. 

We have carried out MD simulations for the 3-d binary soft-sphere model with N=500 atoms in a cubic cell. First, we have simulated a liquid equilibrium at Feff = 0.8 then with using the configuration at the final step of this run, the system was quenched down to Teff = 1.50 (quenching process) followed by annealing MD simulation at this Fefr over ten million time steps. This Feg- is still lower than Fj (=1.58, the glass transition), but slightly higher than F (=1.45, kinetic transition) in the supercooled fluid phase. 

Kinetic transitions between well-defined micromorphologies are usually dominated not by second order but by first order thermodynamics. Recent ideas have shown how propagating fronts of the new nucleating phase may be responsible for the limiting rate. ... 

Fig. 13.7. Fluctuations in the dwell time before the 10-bp bursts, (a) Probability distributions for the dweii times before the 10-bp bursts in Fig. 13.4b as a function of [ATP]. Peaked distributions are indicative of multiple rate-limiting kinetic transitions. [ATP] decreases from 250 to 5 xM left to right, (b) The effective number of rate-limiting transitions, Umin, as a function of [ATP]. The values at low and high [ATP] indicate the minimum number of ATP binding events and of nonbinding events that must occur during each dwell, 2 and 4 respectively. Modified from [74]...

First-order solid-state amorphization occurs due to an entropy catastrophe [39] causing melting of superheated graphite and decompressed diamond below Pg when the entropy of the ordered crystal would exceed the entropy of the disordered liquid. This condition is resolved with the occurrence of a kinetic transition to a (supercooled) glass whereby the exact kinetic conditions during carbon transformation will be critically Pg-depen-dent [39]. It is important to consider the crystal to liquid transition and the effect of a superheated crystal whereof the ultimate stability is determined by the equality of crystal and liquid entropies [40]. When this condition is met, a solid below its Pg will melt to an amorphous solid, particularly... 

FIGURE 12.19 Reduced electrophoretic mobility (Pg/p max) of cationic poly(NIPAM) and anionic poly(NIP-MAM) microgel latexes as a function of temperature (10" A/ NaCl). p axis measured far from the electro-kinetic transition temperature (Te x). 

The diffusive kinetics of geminate pairs have been predicted to show a time-dependent decaying behavior [117-122]. Early experiments showed, in contrast, a decay, with a being dependent on the proton concentration [123]. Experiments on longer time ranges with improved sensitivity are prerequisites for an accurate determination of the asymptotic behavior [124]. In fact, recent measurements on HPTS have demonstrated the validity of the theoretically predicted decay law (see Fig. 14.4) [125]. For 5-(methanesulfonyl)-l-naphthol a kinetic transition from power law to exponential has been reported due to a short photobase lifetime [126]. 

In a like fashion, the activities and final concentrations at which sorption kinetics change from anomalous to Case II (uptake linear with time) were estimated for several penetrants in PVC (4). Figure 8, for example, shows that this kinetic transition occurs at a penetrant activity of about 0.9 in the TCE/PVC system. It appears that Case II kinetics are observed only when the final uptake is at least equal to Cg i.e., when the polymer/penetrant system undergoes the glass-rubber transition during the sorption process. 

More realistic kinetic behavior in implicit solvent simulations can be obtained with the Langevin thermostat [18] where stochastic collisions and friction forces provide kinetic energy transfer to and from the solute in an analogous fashion to explicit solute-solvent interactions. As a result, kinetic transition rates similar to rates from explicit solvent simulations can be recovered with an appropriate choice of the friction constant [2]. 

A versatile and classical method for studying kinetic reactions and other kinetic phenomena on short time scales is the use of a stopped-flow apparatus (SFA) for fast reproducible mixing and then to apply, e.g., spectroscopic methods for detection. In this technique, the reactants are rapidly mixed in a mixing chamber, usually under full turbulent flow that ensures fast homogenization on length scales down to nanometers [99]. Provided that short, synchronized acquisitions can be made. X-ray or neutron scattering can be used to probe kinetic transitions and other processes directly by measuring the temporal evolution of the intensity of the (mixed) sample. 

Time resolved X-ray and neutron scattering have also been used to elucidate the kinetic behavior in many surfactant systems 14, 15), For the case of dissolution kinetics transitions between micelle and vesicle structures have been studied during homogeneous dilution of the solvent 16), Transient structures such as disks have been observed during such a transition. 

This model for the thermal rearrangement of l-phenylbicyclo[2.2.1]hex-ene provides an explanation for the stereochemistry observed in the [1,3] methyl shift. More important, it also brings into question some of the common assumptions of reaction kinetics. Transition state theory is based on the premise that the redistribution of internal kinetic energy is faster than is the progress of a collisionally activated reactant over a potential energy surface to a transition state and then to a product. If this assumption is not valid, then the... 

Simulating the kinetic transition of a polymeric system from the melt to the glass has been a modeling target for many years (69,131,176,248,370-379). Any of the techniques that have been discussed for performing either dynamic MC or MD is capable of 5uelding densities that exhibit the characteristic knee at Tg. Simulations, just as in the real world, give Tg s that depend on the rate of... 

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