Rate constants fluctuations

We attributed the rate constant fluctuation to conformational interconversion, which had been inferred by Frauenfelder and co-workers in their earlier work on photolysis of heme proteins [18]. We developed a method that made... 

Lu D-H and Hase W L 1989 Monoenergetic unimolecular rate constants and their dependence on pressure and fluctuations in state-specific unimolecular rate constants J. Phys. Chem. 93 1681-3... 

An intrinsic surface is built up between both phases in coexistence at a first-order phase transition. For the hard sphere crystal-melt interface [51] density, pressure and stress profiles were calculated, showing that the transition from crystal to fluid occurs over a narrow range of only two to three crystal layers. Crystal growth rate constants of a Lennard-Jones (100) surface [52] were calculated from the fluctuations of interfaces. There is evidence for bcc ordering at the surface of a critical fee nucleus [53]. 

It has been frequently suggested that dynamical factors are important in enzyme catalysis (Ref. 9), implying that enzymes might accelerate reactions by utilizing special fluctuations which are not available for the corresponding reaction in solutions. This hypothesis, however, looks less appealing when one examines its feasibility by molecular simulations. That is, as demonstrated in Chapter 2, it is possible to express the rate constant as... 

The total Hamiltonian is the sum of the two terms H = H + //osc- The way in which the rate constant is obtained from this Hamiltonian depends on whether the reaction is adiabatic or nonadiabatic, concepts that are explained in Fig. 2.2, which shows a simplified, one-dimensional potential energy surface for the reaction. In the absence of an electronic interaction between the reactant and the metal (i.e., all Vk = 0), there are two parabolic surfaces one for the initial state labeled A, and one for the final state B. In the presence of an electronic interaction, the two surfaces split at their intersection point. When a thermal fluctuation takes the system to the intersection, electron transfer can occur in this case, the system follows the path... 

In a conventional relaxation kinetics experiment in a closed reaction system, because of mass conservation, the system can be described in a single equation, e.g., SCc(t) = SCc(0)e Rt where R = ((Ca) + ( C b)) + kh- The forward and reverse rate constants are k and k t, respectively. In an open system A, B, and C, can change independently and so three equations, one each for A, B, and C, are required, each equation having contributions from both diffusion and reaction. Consequently, three normal modes rather than one will be required to describe the fluctuation dynamics. Despite this complexity, some general comments about FCS measurements of reaction kinetics are useful. 

If Ea is small, then the rate constant of reaction is relatively insensitive to temperature if Ea is large, then k is more sensitive to temperature fluctuations. 

In fluorescence correlation spectroscopy (FCS), the temporal fluctuations of the fluorescence intensity are recorded and analyzed in order to determine physical or chemical parameters such as translational diffusion coefficients, flow rates, chemical kinetic rate constants, rotational diffusion coefficients, molecular weights and aggregation. The principles of FCS for the determination of translational and rotational diffusion and chemical reactions were first described in the early 1970s. But it is only in the early 1990s that progress in instrumentation (confocal excitation, photon detection and correlation) generated renewed interest in FCS. 

Nonequilibrium effects. In applying the various formalisms, a Boltzmann distribution over the vibrational energy levels of the initial state is assumed. The rate constant calculated on the basis of the equilibrium distribution, keq, is the maximum possible value of k. If the electron transfer is very rapid then the assumption of an equilibrium distribution over the energy levels is not valid, and it is more appropriate to treat the nuclear fluctuations in terms of a steady-state rather than an equilibrium formalism. Although a rigorous treatment of this problem has not yet appeared, intuitively it seems that since the slowest nuclear fluctuation will generally be a solvent orientational motion, ke will equal keq when vout keq and k will tend to vout when vout keq (a simple treatment gives l/kg - 1/ vout + 1/keq). These considerations are... 

Other groups may cause shortening of the lifetime. The phosphorescence of parvalbumin is quenched by free tryptophan with a quenching rate constant of about 10s M i s l (D. Calhoun, unpublished results). A more extensive survey of proteins or model compounds with known distances between tryptophans is needed to study how adjacent tryptophans affect the lifetime. It should be noted that at low temperature the phosphorescence lifetime of poly-L-tryptophan is about the same as that of die monomer.(12) This does not necessarily mean that in a fluid solution tryptophan-tryptophan interaction could not take place. Thermal fluctuations in the polypeptide chain may transiently produce overlap in the n orbitals between neighboring tryptophans, thus resulting in quenching. 

Seymour and Klinman (entry 6 in Table 2 see Fig. 5 for a schematic mechanism) measured relative rate constants for the hydride-transfer reaction (H, D, T) from Cl of 2-deoxyglucose to the cofactor FAD. To explore the model for enzymically enhanced mnneling, according to which the enzyme conducts a fluctuational search for an efficient mnneling sub-state, five variants of glucose oxidase, anticipated to have differing capacities for the fluctuational search, were generated. 

If the paramagnetic center is part of a solid matrix, the nature of the fluctuations in the electron nuclear dipolar coupling change, and the relaxation dispersion profile depends on the nature of the paramagnetic center and the trajectory of the nuclear spin in the vicinity of the paramagnetic center that is permitted by the spatial constraints of the matrix. The paramagnetic contribution to the relaxation equation rate constant may be generally written as... 

A chemical relaxation technique that measures the magnitude and time dependence of fluctuations in the concentrations of reactants. If a system is at thermodynamic equilibrium, individual reactant and product molecules within a volume element will undergo excursions from the homogeneous concentration behavior expected on the basis of exactly matching forward and reverse reaction rates. The magnitudes of such excursions, their frequency of occurrence, and the rates of their dissipation are rich sources of dynamic information on the underlying chemical and physical processes. The experimental techniques and theory used in concentration correlation analysis provide rate constants, molecular transport coefficients, and equilibrium constants. Magde" has provided a particularly lucid description of concentration correlation analysis. See Correlation Function... 

Correlation functions are powerful tools in statistical physics, and in the above example they permit one to examine the behavior of a fluctuating system from a reference time back to previous times. Such fluctuations can occur in the concentration of two (or more) interconverting chemical species in dynamic equilibrium, and the technique of concentration correlation analysis permits one to determine the forward and reverse rate constants for their interconversion. See Concentration Correlation Analysis... 

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