Molecular fitting

This chapter will address software systems to interactively fit molecular models to electron density maps and to analyse the resulting models. This chapter is heavily biased toward proteins, but the programs can also build nucleic acid models. First a brief review of molecular modelling and graphics is presented. Next, the best current and freely available programs are discussed with respect to their performance on common tasks. Finally, some views on the future of such software are given. 

O (Kleywegt and Jones, 1997), the successor to FRODO, fits molecular models to maps. It is... 

Fujita, M., Nagao, S., Ogura, K., Guest-induced organization of a 3-dimensional palladium(II) cage-like complex - a prototype for induced-fit molecular recognition. J. Am. Chem. Soc. 1995, 117, 1649-1650. 

Figure 2. Correlation between accessible pore volume and fitted molecular size, estimated based on bimodal gamma function fitting, (a) Filtrsorb-400, (b) Norit ROW 0.8, and (c) Norit ROX 0.8.

The mutual diffusion constant obtained from Stokes-Einstein equation shows a large difference with the values obtained from the measurements of fluorescence quenching reaction and also empirical equations especially in viscous solvents. By using the values of R and D, we estimated the reaction rate constant, kR, and reaction probability in collision complex, rp, when we assumed the yan der W s radii of CNA and CHD estimated from space-fitting molecular model to be 5.0 A and 2.0 A, respectively, that is R=7.0 A in eq.(6).The obtained rp, ko and kR values are listed in Table 2. 

Figure 2.1 The basic steps of macromolecular crystal structure solving are illustrated with respect to the enzyme, PNP MW 30000x3 D. (a) A crystal of human PNP space group R32. (b) Monochromatic oscillation diffraction photograph recorded at the Daresbury SRS resolution limit of outermost diffraction spots =3 A. (c) Electron density map, calculated at 6 A resolution, viewed down the hexagonal c axis. The diameter of the central solvent channel is =130A. Six trimers are visible. (d) A portion of the 3 A electron density map with fitted molecular model. (e) The PNP trimer molecular model, (f) The PNP trimer with bound inhibitor the protein here is represented in ribbon format for a-helix and ft sheet (see chapter 3 for details of macromolecular structure). Based on Ealick et al (1990). These figures kindly supplied by Dr S. Ealick and reproduced with permission.

In Fig. 2a we depict the wideband loss spectrum of water calculated in terms of the hat model for room temperature (27°C). For ice at —7°C a similar calculation (but in a much narrower band) is presented in Fig. 2b. The fitted molecular parameters are presented in Table I (some of these parameters will be determined below). During the lifetime Tor a dipole performs in water and ice about two librations and about six librations in supercooled water (mor = 5.6). 

Murakami, Y. Kikuchi, J. Ohno, T. Hayashida, O. Kojima, M. Syntheses of macrocyclic enzyme models. 7. Octopus cyclophanes having L-aspartate residues as novel water-soluble hosts. Aggregation behavior and induced-fit molecular recognition. J. Am. Chem. Soc. 1990.112 (21). 7672-7681. 

Hu, H., Lu, Z., and Yang, W. (2007]. Fitting molecular electrostatic potentials from quantum mechanical calculations, J. Chem. Theo. Comp. 3, pp. 1004-1013. 

One of the most active areas of research in dehydration reactions is the use of heterogeneous catalysts (such as metal oxides, alumina, and zeolites) to catalyze the elimination of water from alcohols. Not only do the catalysts lower the temperatures required for dehydration, but they can also alter product distributions. For example, dehydration of 2-butanol produced 45% of 1-butene when the dehydration was catalyzed by alumina but 90% of 1-butene when zirconia was the catalyst. A wide variety of mechanisms have been considered for these reactions. The effect of the catalyst is a function of the nature of the acidic and basic sites on the catalyst surface, the size of openings into which organic molecules may fit, molecular shape, and... 

The most convenient way of defining MINDO/3 is in relation to the earlier methods. The basic form of the equations was similar to those in INDO, only in MINDO/3 the origin of the parameters was different. For example, rather than use atomic spearal data to define 17, the one-electron integral was made an adjustable parameter. MINDO/3 had several of these parameters, which were adjusted to give the best fit to experimental data for molecules. Here we see a basic difference between Dewar s methods and those that had gone before. Slater s rules were abandoned instead the orbital exponent was made a parameter, as were the multipliers in the resonance integral, By adjusting the parameters to fit molecular data rather than theory, as with Slater s rules, or spectra, as with the values, a vastly improved result was obtained. 

A different approach towards the incorporation of metal oxide clusters into zeo-litic pores via chemical vapor deposition has been studied extensively by Ozin et al. [236 - 240]. They developed a method denoted as intrazeolite metal carbonyl phototopotaxy . Metal carbonyls are used as precursors to obtain the occluded guest component because of their volatility, fitting molecular dimensions, ease of purification, ready availability, and facile and quantitative conversion to the respective metal oxide materials with minimal contamination by carbon [236, 240]. The metal carbonyl precursors are transformed into the metal oxides by photochemical oxidation. The term phototopotaxy is meant to indicate the similarity of this preparation method to epitactical growth of semiconducting oxide layers on planar surfaces commonly used to form low-dimensional quantum nanostructures for applications in electronic and optical devices [238]. 

---