Conformational refinement, diffraction analysis

The success of the gas phase electron diffraction analysis of cis-and /ra 5-decalin (123) is another example of the use of MM calculations as an auxiliary technique. Minimum energy conformations and vibrational ampUtudes were calculated by both the Lifson and Boyd force fields (30,31) and were used as the starting values for refinement of the geometrical and vibrational parameters for the least-squares analysis. The results revealed no appreciable strain in cj5-decalin (123) other than that expected from gauche interactions. 

A combination of stereochemical structural refinement and. T-ray diffraction analysis has been used to determine the crystal stracture of potassium hydroxide-complexed amylose, obtained by heterogeneous deacetylation of amylose acetate. The complex crystallizes as an orthorhombic unit cell with p2,2,2 symmetry and dimensions a = 8.84,6 = 12.31, and c = 22.41 A. The conformation of the amylose chain is a distorted left-hand helix with six o-glucose residues per turn. Each three-residue asymmetric unit is complexed with one molecule of potassium hydroxide and three molecules of water. Extension of the amylose chain probably arises because of the co-ordination of the K ion. 

The geometrical parameters as determined in the electron diffraction analysis are shown in Table 7 The results appeared to be little sensitive to the changing conformational properties of the models. It was of great advantage that the 0...0 distance with great accuracy was available from the microwave spectra. Besides, in addition to the requirement of convergency in the least-squares refinement, an important criterion for any acceptable structure was the consistency with the rotational constants derived from the microwave spectra. It is stressed, however, that such a criterion was considered to a certain limit only. Discrepancies up to 2% were acceptable since the parameters were not corrected for the effects of the intramolecular motion, and, what may be even more important, the standard deviations were relatively large. 

Of great interest to the molecular biologist is the relationship of protein form to function. Recent years have shown that although structural information is necessary, some appreciation of the molecular flexibility and dynamics is essential. Classically this information has been derived from the crystallographic atomic thermal parameters and more recently from molecular dynamics simulations (see for example McCammon 1984) which yield independent atomic trajectories. A diaracteristic feature of protein crystals, however, is that their diffraction patterns extend to quite limited resolution even employing SR. This lack of resolution is especially apparent in medium to large proteins where diffraction data may extend to only 2 A or worse, thus limiting any analysis of the protein conformational flexibility from refined atomic thermal parameters. It is precisely these crystals where flexibility is likely to be important in the protein function. 

A single conformer of trifluoroacetic anhydride, CF3C(0)0C(0)CF3, is indicated by the analysis of gas electron diffraction data, but there is some doubt about the precise structure of this conformer.29 The two C=0 bonds have the synperiplanar orientation, but it is not possible to say whether the equilibrium structure is planar, with C2V symmetry, or distorted to C2 symmetry. The refined effective dihedral angle C-0-C=0 is 18(4)°, reasonably consistent with values of 16.5 and 13.9° given by MP2 and B3LYP calculations with the 6-31G basis set. 

X-ray diffraction techniques are the only way of determining the crystal structure of natural and synthetic polymers, although the x-ray data itself obtained from a crystalline polymeric fiber or film is not sufficient to allow complete refinement of the structure. Conformational analysis and electron diffraction represent complementary methods which will facilitate the determination of the structure. The necessary requirements for the x-ray approach are crystallinity and orientation. X-ray data cannot be Obtained from an amorphous sample which means that a noncrystalline polymeric material must be treated in order to induce or improve crystallinity. Some polymers, such as cellulose andchitin, are crystalline and oriented in the native state.(1 )... 

Since the structure of PAIB has not been determined in detail by diffraction methods, the normal-mode studies [110] were based on a 3io structure obtained from conformational analysis [111] (Figure 5-7). The vibrational studies compared experimental data with predictions for two helices, and the results clearly favored the 3io- over the a-helix. The threefold screw symmetry of this structure results in El and Ez species modes reducing to doubly degenerate E species modes. The main chain force field was the same as that for aj-PLA, with additional force constants refined for the (CH3)2 group. Some modes from the full analysis [110] are compared with those of ai-PLA in Table 5-11. 

A tilt of the molecular core with respect to the column axis is a common feature in these structures. In the very first report on the hexa-alkanoyloxy benzenes [1] it was noted that the X-ray photographs contained a few weak diffraction spots not quite conforming to true hexagonal symmetry, but the quality of the X-ray patterns in these early studies did not warrant a more refined analysis. Subsequently, Frank and Chandrasekhar [11] noted that, when seen under the polarizing microscope, the extinction brushes (or crosses) in the optical textures of the me-sophases do not coincide with the polarizer... 

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