Torsion angles determination

Figure 8. Methyl-orientation results for the three methyl groups in N-acetyl-L-leucine. A, x-ray determined p(r) charge density map. B, graph showing relation between the H-C-C-H methyl torsion angles determined from the x-ray results and those determined by using a quantum chemical geometry optimization. The rms error is 8°.

To assess the precision of the distances, angles, and torsion angles determined by an X-ray structure analysis, and to explain why some are more precise than others even if they both are derived from structures with the same / -value (see Chapters 10 and 11). 

Mimicking a p-tum consists in constraining correctly four torsional angles (4>,4>2, P, P2) and four bonds (bonds a-d, cf. Fig. 2.3.3). Bonds a and d direct the entry and the exit of the peptide chain through the turn, respectively, whereas bonds b and c are responsible for the spatial dispositon of the amino acid side chains at position i+1 and i+2 of a turn. The torsional angles determine the backbone geometry of the turn and consequently the shape of the turn hydrogen... 

M. Hong, Torsion Angle Determination by Solid-State NMR , in Modern Magnetic Resonance Part 1, ed. G. A. Webb, Springer, Dordrecht, Netherlands, 2006, p. 723. 

A set of rules determines how to set up a Z-matrix properly, Each line in the Z-matiix represents one atom of the molecule. In the first line, atom 1 is defined as Cl, which is a carbon atom and lies at the origin of the coordinate system. The second atom, C2, is at a distance of 1.5 A (second column) from atom 1 (third column) and should always be placed on one of the main axes (the x-axis in Figure 2-92). The third atom, the chlorine atom C13, has to lie in the xy-planc it is at a distanc e of 1.7 A from atom 1, and the angle a between the atoms 3-1-2 is 109 (fourth and fifth columns). The third type of internal coordinate, the torsion angle or dihedral r, is introduced in the fourth line of the Z-matiix in the sixth and seventh column. It is the angle between the planes which arc... 

Example Yon can monitor improper torsion angles to determine wh ich side of a substrate m olecn le faces the active site of a protein. Select three atoms on the substrate molecule and a fourth in the active site. These atom s define an improper torsion angle. Save th is selection as a named selection. Then observe a plot of this improper torsion angle (in the Molecular Dynam ics Results dialog... 

In the course of the investigations directed at the structural characterization of another type of aza analog of sesquifulvalene, the X-ray structure of the triaza derivative 72a was determined (89CC1086). Tire molecule is effectively planar, the torsion angle between the pyridine and benzimidazole... 

FIGURE 2. The molecular model of dimethyl sulfoxide. The following C—H lengths (A), S—C—H bond angles (deg) and x(C—S—C—H) torsional angles (deg) were determined from microwave spectra by Typke17 ... 

The density of 87O has been determined as 2.15 g cm at 25 °C and calculated from the lattice constants as 2.179 g cm at —110 °C, measured by a single-crystal X-ray diffraction analysis [1, 64, 65]. The 87O molecules are of Cl symmetry and consist of chair-hke seven-membered homocycles with the exocyclic oxygen atom in an axial position see Fig. 2. Most remarkably are the two almost planar groups 0-8-8-8 (torsion angle r=2.9°) and 8-S-8-8 (r=6.3- ). 

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