Solvent channel units

Figure 2.18 Identified inhibitors of TGFpRl identified through inhibitor hybridisation. The red region shows the selectivity pocket fragment, the hinge region binding element is black and the solvent channel unit is coloured blue.

MIR), requires the introduction of new x-ray scatterers into the unit cell of the crystal. These additions should be heavy atoms (so that they make a significant contribution to the diffraction pattern) there should not be too many of them (so that their positions can be located) and they should not change the structure of the molecule or of the crystal cell—in other words, the crystals should be isomorphous. In practice, isomorphous replacement is usually done by diffusing different heavy-metal complexes into the channels of preformed protein crystals. With luck the protein molecules expose side chains in these solvent channels, such as SH groups, that are able to bind heavy metals. It is also possible to replace endogenous light metals in metal-loproteins with heavier ones, e.g., zinc by mercury or calcium by samarium. 

Fig. 5. The arrangement of the electron density in a tetragonal crystal of human serum albumin. Prominent features of the molecular packing arrangement are large (90 x 90 A) solvent channels (shown in white) that pass through the crystal parallel to the crystallographic c axis. The unit cell and symmetry operations parallel to the c axis are illustrated. Reproduced with permission from Carter et al. (1989) American Association for the Advancement of Science (AAAS).

The first step is to introduce heavy atoms into the protein crystal. This is usually done by soaking the crystals in a solution containing 0.1—10 mmol 1 1 of the heavy atom compound (Hg, Pt, Au, U compounds are often used) but sometimes the macromolecule is also co-crystallized with the heavy atom compound. As discussed in Section 9.03.4, protein crystals contain large solvent channels, which allow the diffusion of small molecules within the crystal. An important caveat is that the binding of the heavy atom compound must not distort the crystal appreciably neither the overall unit cell dimensions nor the conformation of the macromolecule. If it does, the underlying assumption that we can subtract away the protein component is false. In other words, the native (no heavy atom) and derivative (with heavy atom) must be isomorphous, and the techniques are called in general isomorphous replacement. 

The resolution limit of the sample is not necessarily correlated with the mosaic spread. As is evident from figure 2.1 (c) with the PNP crystal relatively few intermolecular contacts make up the crystal periodicity. The unit cells could be perfectly aligned one with another but the protein surface projecting into solvent is able to flop around in the solvent channels. Hence, the angular rocking width of the crystal can be small indicating perfection, but the resolution limit could be relatively poor. In the case of PNP the crystal diffracts only to a resolution limit of 2.8A. 

The crystal structures of the 2 1 solvates formed by phenylbutazone with benzene, cyclohexane, 1,4-dioxane, tetrahydrofuran, and tetrachloromethane were found to be isostructural, while the structure of the chloroform solvate differed [57]. In all of the solvatomorphs, the solvent molecules were found to be located in channels along the (0 1 0) direction, and their inclusion served to increase the length of the unit cell along the n-axis. The solvent inclusion was also found to alter the //-angle. 

Figs. 12 and 13 show the crystal structure of 6-Gd. Four of the linear POM-catalyst dicarboxylic acid units, 5, are linked by di-lanthanide paddle wheel junctions (Fig. 12) into the open-framework material 96). Fig. 13 shows the large channels in 6-Gd. These are filled with dimethylformamide (DMF) molecules that are hard to remove (the boiling point of DMF at 1.0 atmosphere — 151 °C). Thus while the solvent-accessible internal volume of 6-Gd is 50.5% of the crystal... 

Figure 4 Distribution of channels containing one, two, three, four, five, or six dye molecules in equilibrium as a function of the dye concentration in the solvent, calculated by means of Eq. (12) for = 7.75 X 10, [M/] = 1.9 X lO m, = 100, and Aq = 4.4 X 10 M. The free dye concentration is expressed in units of the total number...

The Soxhlet extraction procedure is a semicontinuous process, which allows the buildup of the solvent in the extraction chamber for 5 to 20 min. The solvent surrounds the sample and is then siphoned back into the boiling flask (Fig. D 1.1.1). Multiextractor units are available for extraction of lipids from several different samples or replicate runs of the same material. The procedure provides a soaking effect and does not permit channeling. The fact that polar and bound lipids are not removed is a drawback to the procedure (see Background Information). 

Crystals, however, are not always so perfectly ordered. Atomic mobility exists within the crystal lattice however, it is greatly reduced relative to the amorphous state. Partial loss of solvent from the lattice can result in static disorder within the lattice where the atomic positions of a given atom can deviate slightly within one asymmetric unit of the unit cell relative to another. Lattice strain and defects occur for many reasons. Solvents can be present within channels of the lattice in sites not described by the symmetry of the crystal structure itself, resulting in disordered solvent molecules or incommensurate structures and potentially nonstoichiometric solvates or hydrates. 

But in the real world, one doesn t ordinarily perform the extraction immediately. By going to a 6-channel pump (Figure 2), one can expand the usefulness of the cleanup system by adding more unit operations. One can now start with a diluent (to get the sample into the correct concentration range), add the sample to this air-segmented stream and mix it in coil "M", then add the organic solvent and perform the extraction in coil "E". 

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