Simulation catalytic effects

The previous chapters taught us how to ask questions about specific enzymatic reactions. In this chapter we will attempt to look for general trends in enzyme catalysis. In doing so we will examine various working hypotheses that attribute the catalytic power of enzymes to different factors. We will try to demonstrate that computer simulation approaches are extremely useful in such examinations, as they offer a way to dissect the total catalytic effect into its individual contributions. 

The overwhelming majority of biomimetics operate in liquid. Their activity depends on the origin of solvents, reaction mixture and cell effects. Gas-phase oxidation processes are less dependent on these effects and in the first approximation can be considered as oxidation under quasi-ideal conditions. It goes without saying that enzymatic reactions do not proceed in gases. However, it is possible to simulate catalytic functions in the gas phase. This simplifies the decoding of the reaction mechanism, not complicated by factors accompanying the liquid-phase oxidation [1],... 

The efficiency of a Vanadium trap additive is illustrated in Figure 5.8 (Si reflects the presence of the zeolite based catalyst while La and V are present on the same additive particle, the V-trap) and the catalytic effect demonstrated in Figure 5.9. The effectiveness of V-traps is particularly difficult to test in the laboratory, because the level of vanadium mobility in commercial units is difficult to simulate, and the competitive reaction to form sulfate is not taken into account by most laboratory testing. 

Test Methods. Since its inception, the Mitchell Method (MM) or slight variations (often referred to as the Modified Mitchell Method) have been en )loyed by researchers evaluating FCC catalyst as a sin )le, inexpensive, and fast procedure by which to simulate the effect of contaminant metals on catalyst performance. As a fallout of more sophisticated catalytic testing in fixed fluid bed reactors, the method of cycUc metals deposition (CMD) has also emerged as a useful method for introducing metal contaminants. 

The computer simulations reported in this chapter are based on the empirical valence bond (EVB) model that will be only briefly described here as it has been extensively discussed elsewhere [1,2], The enzymic reaction of TIM is used as our main example to illustrate both the origin of catalytic effects on PT and methodological aspects of the computational strategy. A more detailed account of the TIM calculations discussed in the next section has recently been reported by Aqvist Fothergill [3]. 

The results from the EVB/FEP/MD simulations of the TIM reaction are summarized in the diagram of Fig. 4 (lower curve). The large catalytic effect... 

Takeuchi et al. 7 reported a membrane reactor as a reaction system that provides higher productivity and lower separation cost in chemical reaction processes. In this paper, packed bed catalytic membrane reactor with palladium membrane for SMR reaction has been discussed. The numerical model consists of a full set of partial differential equations derived from conservation of mass, momentum, heat, and chemical species, respectively, with chemical kinetics and appropriate boundary conditions for the problem. The solution of this system was obtained by computational fluid dynamics (CFD). To perform CFD calculations, a commercial solver FLUENT has been used, and the selective permeation through the membrane has been modeled by user-defined functions. The CFD simulation results exhibited the flow distribution in the reactor by inserting a membrane protection tube, in addition to the temperature and concentration distribution in the axial and radial directions in the reactor, as reported in the membrane reactor numerical simulation. On the basis of the simulation results, effects of the flow distribution, concentration polarization, and mass transfer in the packed bed have been evaluated to design a membrane reactor system. 

In a recent contribution [87] we studied the catalytic effect in polyelectrolyte-electrolyte mixtures by various theoretical techniques. For an isotropic model where the macroions, co-ions and counterions are pictured as charged hard spheres, we employed the HNC approximation, the modified PB and symmetric PB theories. The results for k/k° were compared with the computer simulations for the same quantity. Note that this quantity is much more sensitive to the details of the model and theory than thermodynamic properties like osmotic pressure studied before. The conclusion was that these theories are not well-suited to treat the problem they were capable of reproducing MC values only qualitatively and even this merely for low-charged macroions. 

It is generally accepted (e.g., Ref. 1) that many enzymes have evolved by optimizing kCat/-KM, where Km — ( -i + kcaX)/k and can be approximated as Km % k- /k — K l. However, this observation, and related findings, has not identified the factors responsible for the actual catalytic effect. As will be shown below, the key question is to determine how the activation barrier in the chemical step is reduced. In order to proceed further in a meaningful way, we need a reliable tool to quantify the activation barrier and to relate that with the structure and function of the enzyme. We also need to determine the individual contributions to the overall catalytic effect. Gradually it is becoming clear that this is best accomplished by computer simulation approaches. 

Hwang et al.131 were the first to calculate the contribution of tunneling and other nuclear quantum effects to enzyme catalysis. Since then, and in particular in the past few years, there has been a significant increase in simulations of QM-nuclear effects in enzyme reactions. The approaches used range from the quantized classical path (QCP) (e.g., Refs. 4,57,136), the centroid path integral approach,137,138 and vibrational TS theory,139 to the molecular dynamics with quantum transition (MDQT) surface hopping method.140 Most studies did not yet examine the reference water reaction, and thus could only evaluate the QM contribution to the enzyme rate constant, rather than the corresponding catalytic effect. However, studies that explored the actual catalytic contributions (e.g., Refs. 4,57,136) concluded that the QM contributions are similar for the reaction in the enzyme and in solution, and thus, do not contribute to catalysis. 

Ref. [4], the corresponding rate constants do not show significant dynamical effects. Furthermore, attempts to define dynamical catalytic effect in a different way and to include in such factor nonequilibrium solvation effects [100] have been shown to be very problematic (e.g. Ref. [4]). Similarly, we have shown that the reasonable definition of dynamical effects by the existence of special vibrations that lead coherently to the TS does correspond to the actual simulation in enzyme and solution. 

The critical role played by the Ti catalyst in helping hydrogen cycling in alanates has been an on-going research subject for theoreticians. Ti-doped NaAlH4 system has been most studied as a prototypical system for materials of similar structures. The exact nature of the titanium catalyst action and the location of the Ti atoms still remain unclear however, several different theories have been elucidated to explain the observed reaction dynamics. Three doping hypotheses have been applied to study the catalytic effects with DFT simulations. One is to search for evidence of whether Ti exists as a bulk dopant on the sodium alanate and if... 

---