Theoretical simulation

A catalyst may play an active role in a different sense. There are interesting temporal oscillations in the rate of the Pt-catalyzed oxidation of CO. Ertl and coworkers have related the effect to back-and-forth transitions between Pt surface structures [220] (note Fig. XVI-8). See also Ref. 221 and citations therein. More recently Ertl and co-workers have produced spiral as well as plane waves of surface reconstruction in this system [222] as well as reconstruction waves on the Pt tip of a field emission microscope as the reaction of H2 with O2 to form water occurred [223]. Theoretical simulations of these types of effects have been reviewed [224]. 

A determination of the structural ( , m) parameters of the samples investigated is still needed in order to establish a direct link to theoretical simulations. 

Figure 62. Theoretical simulation of a series of Voltammograms initiated from different cathodic potentials (ranging between -1000 and -3000 mV vs. SCE). (Reprinted from T. F. Otero, H.-J. Grande, and J. Rodriguez, J. Phys. Chem. 101, 8525, 1997, Figs. 3-11, 13. Copyright 1997. Reproduced with permission from the American Chemical Society.)...

The work described in this paper is an illustration of the potential to be derived from the availability of supercomputers for research in chemistry. The domain of application is the area of new materials which are expected to play a critical role in the future development of molecular electronic and optical devices for information storage and communication. Theoretical simulations of the type presented here lead to detailed understanding of the electronic structure and properties of these systems, information which at times is hard to extract from experimental data or from more approximate theoretical methods. It is clear that the methods of quantum chemistry have reached a point where they constitute tools of semi-quantitative accuracy and have predictive value. Further developments for quantitative accuracy are needed. They involve the application of methods describing electron correlation effects to large molecular systems. The need for supercomputer power to achieve this goal is even more acute. 

Indeed, several identifiable resonance fingerprints in experimental observables were found.26-31 Concurrent theoretical simulations and analyses not only confirmed the experimental conjectures, but also provided deeper insights into the nature of this resonance state. For the integral cross-sections, a distinct step for Ec < 1 kcal/mol was observed in the reactive excitation function (i.e. the translation energy dependence of the reactive cross-section) for the HF+D product channel, whereas it is totally absent for the other DF+H product channel.26 Anomalous collision energy dependence of the HF vibration branching was also observed.28 For Ec < 1 kcal/mol more than 90% of the HF products are populated in the v = 2 state. However, as the energetic threshold for the formation of HF( / = 3) from... 

Fig. 8. Theoretical simulation of VCD (top) and IR absorption (bottom) spectra of alanine dodecapeptides for the amide V bands for a fully a-helical conformation (left) and a fully left-handed 3i-helical conformation (right). The simulations are for the same three isotopically labeled (13C on the amide C=0 for four Ala residues selected in sequence) peptides as in Figure 7 N-terminal tetrad (4AL1), middle (4AL2), and C-terminal (4AL4). The 13C feature is the same for all sequences, confirming the experimentally found unfolding of the C-terminus. The agreement with the shapes in Figure 7 is near quantitative. Reprinted from Silva, R. A. G. D., Kubelka, J., Decatur, S. M., Bour, R, and Keiderling, T. A. (2000a). Proc. Natl. Acad. Sci. USA 97, 8318-8323. 2000 National Academy of Science, U.S.A.

Martini S, Bonechi C, Corbini G, Donati A, Rossi C Solution structure of rifaximin and its synthetic derivative rifaximin OR determined by experimental NMR and theoretical simulation methods. Bioorg Med Chem 2004 12 2163-2172. 

FIGURE 14. Theoretically simulated and experimental vibrational circular dichroism (VCD) and infrared (IR) spectra of (2S,3S)-2,3-dimethylaziridine [(2S,3S)-159] carbon tetrachloride in the region 700-1600 cm-1. Reproduced from Reference 149 by permission of the National Research Council of Canada... 

Table 1. Comparison of theoretical, simulation and experimental values of factor q ...

The following articles in the Current Separations Series are an excellent introduction to the topic of simulation Bott, A. W., Fitting experimental cyclic voltammetry data with theoretical simulations using DigiSim 2.1 , Current Separations, 15, 67-71 (1996) Bott, A. W. and Jackson, B. P., Study of ferri-cyanide by cyclic voltammetry using the CV-50w, Current Separations, 15, 25-30(1996). 

Janini, G. M., Metral, C. J., Issaq, H. J., and Muschik, G. M. (1999). Peptide mobility and peptide mapping in capillary zone electrophoresis — experimental determination and theoretical simulation. J. Chromatogr. A 848, 417-433. 

Figure 4.4. Mossbauer spectra of Hox-2.10 hatched marks) prepared from the spectra of D. vulgaris hydrogenase poised at -310 mV. The data were recorded at 4.2 K in a magnetic field of 0.05 T A, or 8 T B applied parallel to the y-rays. Theoretical simulations for the individual iron sites of the [2Fe]H cluster dotted-and-dashed lines, component A dashed lines, component B) and of the [4Fe-4S]e cluster (dotted-and-dashed lines, component C dashed lines, component D) are shown above the experimental data. Solid lines, superpositions of these four simulated spectral components.

Delineation of the operational parameters was achieved using computer simulations as described in Section 4.1.3.1. The values of K j (determined experimentally), the initial reactor volume, and the initial concentration of NADP were fed into the program. Employing the conclusions obtained from the theoretical simulations, the other parameters (i.e., flow rates, concentration range of the substrates, and Vmj values) were calculated according to the output signal desired. 

It is possible to compensate for curvature in theoretical simulation of the rocking curve. If the beam profile is square, then the rocking curve is simply correlated with... 

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