Conformational reorientation

Other interesting units that have been incorporated in the electron-donor macro-cyclic component of catenanes are porphyrins (Figure 26) [56]. The compounds containing a free-base porphyrins can be protonated in strongly acidic solutions, causing electrostatic repulsions which result in conformational reorientations and changes in rotation rates [57]. 

A putatively opposing requirement is the necessity to establish fast guest exchange in order to obviate rate limitations in prospected catalytic reactions due to slow association — dissociation processes. This can most easily be achieved in very flexible host molecules, but rigid structures which are not subject to major conformational reorientation on complexing the guest species may meet this requirement as well. 

The derived solution conformation of short neurotoxins (Figures 8 and 9) is in general agreement with the X-ray crystal structure of erabutoxins(46,48), although the amino acid composition of these sea snake toxins differs by ca 30% from that of the terrestrial snake neurotoxins mostly studied by NMR. The conformational reorientation of the fragment 30-34 (3 turn in the central loop. Figure 9)... 

The monolayer resulting when amphiphilic molecules are introduced to the water—air interface was traditionally called a two-dimensional gas owing to what were the expected large distances between the molecules. However, it has become quite clear that amphiphiles self-organize at the air—water interface even at relatively low surface pressures (7—10). For example, x-ray diffraction data from a monolayer of heneicosanoic acid spread on a 0.5-mM CaCl2 solution at zero pressure (11) showed that once the barrier starts moving and compresses the molecules, the surface pressure, 7T, increases and the area per molecule, M, decreases. The surface pressure, ie, the force per unit length of the barrier (in N/m) is the difference between CJq, the surface tension of pure water, and O, that of the water covered with a monolayer. Where the total number of molecules and the total area that the monolayer occupies is known, the area per molecules can be calculated and a 7T-M isotherm constmcted. This isotherm (Fig. 2), which describes surface pressure as a function of the area per molecule (3,4), is rich in information on stabiUty of the monolayer at the water—air interface, the reorientation of molecules in the two-dimensional system, phase transitions, and conformational transformations. 

Molecules that are chiral as a result of barriers to conformational interconversion can be racemized if the enantiomeric conformers are interconverted. The rate of racemization will depend upon the conformational barrier. For example, -cyclooctene is chiral. E-Cycloalkenes can be racemized by a conformational process involving reorienting of the... 

Here the vector rj represents the centre of mass position, and D is usually averaged over several time origins to to improve statistics. Values for D can be resolved parallel and perpendicular to the director to give two components (D//, Dj ), and actual values are summarised for a range of studies in Table 3 of [45]. Most studies have found diffusion coefficients in the 10 m s range with the ratio D///Dj between 1.59 and 3.73 for calamitic liquid crystals. Yakovenko and co-workers have carried out a detailed study of the reorientational motion in the molecule PCH5 [101]. Their results show that conformational molecular flexibility plays an important role in the dynamics of the molecule. They also show that cage models can be used to fit the reorientational correlation functions of the molecule. 

Macromolecules differ from small molecules in a number of critical properties. First, the linear chain structure confers elasticity, toughness, and strength on the solid state system. This is a consequence of the reorientational freedom of the skeletal bonds and of their ability to absorb impact or undergo elastic deformation by means of conformational changes rather than bond cleavage. 

LI ligase s large intrinsic flexibility was revealed by the recent crystal structure of the ligation product of a reduced size variant with two vastly different conformers, differing by reorientation of one of the stems by around 80 A, that were resolved in the same asymmetric cell [106], Based on the presence/absence of specific contacts between distant conserved parts including the ligation site and a totally conserved residue, U38, one of the conformers was postulated to represent the catalytically active or on conformation, the other the inactive or off one [106],... 

The stereoselected Cda conformation of the BPDE i(-) and Il(-) adducts to N6(a) were chosen for study in a reoriented complex with an externally bound pyrene moiety. In Figure 13, the adduct is shown in its optimum orientation in B-DNA with adenine after an anti - syn transformation for which the non-bonded contacts are poor, and with the normal anti base orientation with favorable contacts. The fit improves for the anti base as ax 30°. The orientation of the pyrene moiety is a(BPDE) =31° and the local helical axis of the DNA is oriented at y(DNA) = 15° Calculations were not performed with externally bound BPDE-DNA adducts to 06(G) and NU(C). Calculations of externally bound BPDE I(-)-N6(a) adducts with kinked DNA with ax + 30° yields an orientation a(BPDE) = 31° in good agreement with experimental results for the externally bound component (51). 

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