Comparison to experimental

Nonnal mode analysis was first applied to proteins in the early 1980s [1-3]. Much of the literature on normal mode analysis of biological molecules concerns the prediction of functionally relevant motions. In these studies it is always assumed that the soft normal modes, i.e., those with the lowest frequencies and largest fluctuations, are the ones that are functionally relevant. The ultimate justification for this assumption must come from comparisons to experimental data. Several studies have been made in which the predictions of a normal mode analysis have been compared to functional transitions derived from two X-ray conformers [4-7]. These smdies do indeed suggest that the low frequency normal modes are functionally relevant, but in no case has it been found that the lowest frequency normal mode corresponds exactly to a functional mode. Indeed, one would not expect this to be the case. 

Kinetic gelation simulations seek to follow the reaction kinetics of monomers and growing chains in space and time using lattice models [43]. In one example, Bowen and Peppas [155] considered homopolymerization of tetrafunctional monomers, decay of initiator molecules, and motion of monomers in the lattice network. Extensive kinetic simulations such as this can provide information on how the structure of the gel and the conversion of monomer change during the course of gelation. Application of this type of model to polyacrylamide gels and comparison to experimental data has not been reported. 

Gougousi et al. showed that it is possible to find a set of plausible rate coefficients so that Eq. 28 gives a reasonable fit to their data for different H2 concentrations. Figure 10 shows a comparison to experimental values of p (ne) for the following set of rate coefficients ... 

In the past decade, vibronic coupling models have been used extensively and successfully to explain the short-time excited-state dynamics of small to medium-sized molecules [200-202]. In many cases, these models were used in conjunction with the MCTDH method [203-207] and the comparison to experimental data (typically electronic absorption spectra) validated both the MCTDH method and the model potentials, which were obtained by fitting high-level quantum chemistry calculations. In certain cases the ab initio-determined parameters were modified to agree with experimental results (e.g., excitation energies). The MCTDH method assumes the existence of factorizable parameterized PESs and is thus very different from AIMS. However, it does scale more favorably with system size than other numerically exact quantum... 

There are few reported comparisons to experimental pressure drop data taken by the same workers. An exception is Calis et al. (2001) who compared CFD, the Ergun correlation and experimental data for N — 1-2. They found 10% error between CFD and experimental friction factors, but the Ergun equation... 

A number of approaches are available to extrapolate low-temperature equilibrium constants. Various aspects of this problem have been discussed and some comparisons to experimental data have been made. See, for example, Criss and Cobble (12), Iielgeson (13), MacDonald (1), and Manning and Melling (3). We are not, however, aware of any recent comprehensive evaluation, error analysis or overall assessment. We summarize below what we believe to be the present situation. 

Recently, other CFD models have been published. The model of Siegel et al. ° used an agglomerate approach instead of the porous-electrode approach of the other CFD models. They showed that the agglomerate approach enables good comparisons to experimental data and showed the effects of agglomerate radius and membrane loading on perfor-... 

However, one should keep in mind that simplified models of the actual physical systems are routinely used and that molecular-level modeling techniques involve various levels of approximations. In principle, computational chemistry can only disprove, and never prove, a particular reaction mechanism. In practice, however, a computational investigation may still, in many cases, be a useful guide as to the likeliness of a given reaction pathway. Comparison to experimental information and to computational studies of alternative reaction mechanisms will help establish the kind of trust (or lack thereof) that should be put into a particular reaction mechanism obtained by computational chemistry. 

A residual interaction that is also quite simple has been developed and applied with good results. Recall that the nucleon-nucleon force is attractive and very short ranged, so one might image that the nucleons must be in contact to interact. Thus, the simplest residual interaction is an attractive force that only acts when the nucleons touch or a 8 interaction (in the sense of a Kronecker 8 from quantum mechanics). This can be written as V(r, r%) = a where a is the strength of the interaction, and the 8 function only allows the force to be positive when the nucleons are at exactly the same point in space. In practice, the strength of the potential must be determined by comparison to experimental data. Notice,... 

This chapter is divided into three main sections, focusing respectively on the simulation of the single cell (Section 6.2), of the tube (Section 6.3) and of the bundle (Section 6.4). In each section, the results obtained from the simulation model are reported, and Sections 6.2 and 6.3 also discuss a comparison to experimental data provided by RRFCS. 

The root mean square deviation for measured versus estimated pKa values for 214 azo dyes and related aromatic amines was 0.62 pKa units. In comparison to experimental errors... 

Transition-state theory has been applied to numerous reactions. In order to evaluate the accuracy of the theory in direct comparison to experimental results, highly accurate data for the activated complex is required as basic input to the theory. To that end, we can, e.g., consider the simple reaction D + H2 —> HD + H the rate constant at 1000 K (a temperature where tunneling plays a minor role) is 1.78 x 10-12 cm3/(molecule s) (see Problem 6.8) which is in excellent agreement with the experimental value 2.13 x 10-12 cm3/(molecule s) (with an experimental uncertainty of about 25%). 

Fig. 1.10. Band alignment between II-VI compounds according to density functional theory calculations by Wei and Zunger [95]. The energy of the valence band maximum of ZnS is arbitrarily set to 0 eV. A comparison to experimental results is presented in Fig. 4.18 in Sect. 4.3.1 (page 150)...

Erhart and Albe also calculated zinc diffusion in ZnO [130]. The results are displayed in Fig. 1.18 together with a comparison to experimental data. Depending on chemical potential and Fermi level position either zinc vacancy or zinc interstitial diffusion can dominate. In the case of n-type material, where the Fermi level is close to the conduction band, zinc diffusion is mostly accomplished via the vacancy mechanism. 

The four PBPK models that are highlighted in this section of the profile have each contributed to the overall understanding of the pharmacokinetics of benzene. For instance, the Medinsky model addresses species differences in benzene kinetics using mice and rats. The Travis model specifically addresses human pharmacokinetics of benzene in comparison to experimental animal data, whereas the Bois and Paxman model addresses the effect of exposure rate on benzene metabolism. Finally, the Sun model addresses the formation of hemoglobin-benzene derived adducts in the blood, as a tool in monitoring benzene exposure. Each of these models in discussed in detail below. 

A theoretical determination of vibrational absorption and Raman spectra of 3-methylindole radicals has been carried out in comparison to experimentally measured spectra for 3-methylindole (Table 28) to provide specific spectroscopic markers for the detection of neutral or cationic tryptophan radicals in biological systems <2001CPH(265)13>. Among isatin derivatives, substitution at C-5 has relatively greater influence on the electron density and the force constant of the amide than of the ketone carbonyl group (Table 29) <2001SAA469>. 

For comparison to experimental data, the susceptibility of the Heisenberg S = 1/2 ferromagnetic chain in zero field can be expressed as a power series expansion in powers of J/ 2T) with the coefficients fi known for the first one hundred terms. ... 

Nielsen E, Ekeroth E, Eriksen TE, Jonsson M. (2008) Simulation of radiation induced dissolution of spent nuclear fuel using the steady-state approach. A comparison to experimental data. J Nucl Mater 374 286-289. 

Nonhomogeneous behavior was also predicted by Levine and Zou (343), who began with the oxidation/reduction model of Sales et al. (272) for CO/O2 on polycrystalline Pt and introduced CO surface diffusion. This model predicted one-dimensional, stable traveling waves on the Pt surface. Because no experimental measurements have been performed for traveling waves on polycrystalline catalysts at atmospheric pressures, no comparison to experimental data was possible. 

---