Steric conflict

For small-molecule, metal-carbon monoxide complexes, the carbon monoxide ligand is almost always in a linear conformation and perpendicular to the metal. If one assumed bonding of CO to Hb or Mb in its normal linear, perpendicular mode, steric conflicts as illustrated in Figure 4.20 would occur and thus one might predict... 

Moderate steric conflict of CO)j i with Hj, in conjunction with a maximum in V W>) produces a ridge at = 60° which divides the allowed regions into the subsidiary minima at /, / and III. III. A similar ridge in the L-Ala map is much less pronounced because of the larger bond angle at the nitrogen atom. 

Figure 11-2. Steric interference. (A) To avoid steric violations in placing die centers of mass of two spheres in space, their separation must be greater than one sphere diameter. (B) For nonspherical molecules, steric violations are determined by a complex coupling of center of mass positions and orientations (for rods) or chain conformations (for polymers), (a) and (b) show two identical center of mass positions for two molecules. In (a) the relative orientations lead to no steric conflict, while die configurations in (b) are impossible because of steric violations. The figure is taken from Chan and Dill [18] with permission...

Based on these results, it appears that substitution of F or Cl for H has an appreciable effect on the band structure of the chain. The band gap for (-CH-CF) is somewhat higher than expected in comparison with (-CF-CF) and (-CH-CH-CF-CF). However, such variation is expected given the great sensitivity of the calculated E values to small changes in structural geometry (6). Substitution or Cl for H has a pronounced effect on the value of E. Specifically, the E values for (-CC1-CC1) and (-CH-CC1) are significantly lower than that calculated for (CH-CH). However, due to the large size of the Cl atom relative to H and F, steric conflicts will effectively... 

The value of the rotational angle will have a direct influence on the extent of steric interactions between substituent atoms (Figure 1). Specifically, as increases from 0 (trans) to 180 (cis), the interatomic distances 1...3 and 2...4 will increase while 1...4 and 2...3 will decrease. Of these, the 1...4 interaction in the c conformation is particularly critical since here contacts are encountered with the potential for severe steric conflicts. In fact, for (-CC1-CC1) the c conformation is essentially precluded since the 1...4 interactions are exclusively Cl...Cl. In (-CH-CC1) and (-CH CH-CCl CCl), the Cl...Cl interactions are replaced by... 

H.. .C1 which reduce the steric conflicts encountered in the planar conformations, but only slightly so. 

It should be noted once again that correct geometry is no guarantee of correct structure prediction. In some cases, it may be better to tolerate a few steric conflicts or bad dihedral angles, rather than to minimize the struc-... 

The side-chain of Tyr99 adopts different conformations in the two crystal structures of nXa reported to date [11, 16], In both structures Tyr99 is in steric conflict with canonical substrate binding in the S2-S4 sites. These observations suggest a critical role of Tyr99 and spatially neighboring amino acids in the substrate-dependent activity of nXa. In particular, Lys98 is likely to electrostatically interfere with the basic substrate preference of fiXa. 

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