Conformational energy contour maps

Fig. 2. Conformational energy contour map of JV-acetyl-Giy-W -methylamide (A), N-acetyl-Ala-AT-methylamide (B) (taken from Zimmerman et al., 1977), and N-acetyl-a-Aib-...

Figure 9 Conformational energy contour map of N-acetyl-N -methylalanine amide, for x1 = 60°. Locations of minima are indicated by the filled circles. The contour lines are labeled with energy in kcal/mol above the minimum-energy point at (4>,

The quantity U , i , x is computed by summing over the ECEPP energies of all pairs of nonbonded atoms of the whole molecule. Equations [11] and [12] are used to compute conditional free energy (4>,i]i) contour maps, similar to standard conformational energy (< >, ) contour maps, for each residue of the polypeptide. The probable conformation of the /th residue is taken as the one of lowest conditional free energy, and the probable conformation of the whole polypeptide chain is assumed to be the combination of the probable conformations of the individual residues. 

Amylose. A conformational energy contour map for a dimeric segnent of an amylosic chain is shown in Figure 2. The Hybl... 

MAECIS also contains a molecular conformation analysis system (4). This system allows the user to generate all possible conformations of the current molecule over a series of single bond rotations. Energy contour maps can be obtained for the various conformations and this allows for the selection of low energy conformations for further manipulation or calculations. 

Figure 7. (A) CAMSEQ/M produced conformational isoenergy contour map (B) procedure for calculating probabilities and entropies (C) plot of energy vs.

In either event once an analysis is complete the scientist can ask for the low energy conformations, look at energy contour maps, place the molecule in various conformations for visual inspection, etc. 

Table 3 Conformational Characteristics of DME as Estimated from the Potential Energy Contour Map (Figure 2) for a Temperature of 25 °C ...

Figure 4. Conformational map for dihydropyran. Because of the double bond, 4 atoms are always almost coplanar and a limited number of conformations is probable. The energy contours are at 2 kcal/mol intervals, starting 1 kcal/mol above the minima. The favored conformations are half-chairs, and the easiest paths of transition between the two are through the boat forms. The symmetry of this energy map applies only to dihydropyran, and not to derivatives which cause increases and decreases in the sizes of the allowed (low-energy) areas. This map was calculated with MMP2(85) at increments of 0.1 A shift of the two non-planar atoms. Three of the carbon atoms were held in a plane while C6 and 01 were held at specific distances above and below the plane. Otherwise, the structure was fully relaxed at each increment. The reader may enjoy plotting the indicated path of conformational interchange (pseudorotation) on a copy of Figure 3.

Figure 10. Relaxed (adiabatic) conformational energy map for p-maltose as computed by Brady and coworkers.i3 Contours are drawn at 2,4,6, 8, and 10 kcal/mol above the minimum near < ), y = -60°, -40°. The p-maltose structure may be derived from that of p-cellobiose in Fig. 1 by inversion of the stereochemical configuration at Cl.

The bold contours indicate nonbonded conformational energy in kcal/mol, the thin lines indicate the number of residues per turn (n), and the dashed lines indicate the axial rise per residue (h), in Angstroms. The position of the conformation of the KOH-amylose is shown in the map by a filled circle (l l). 

Figure 13. Map of conformational energy for rotations about the Si-Si skeletal bonds in polysilane, [SiHz-Jn- The energies (in kilocalories per mole) relative to the minima (designated by the plus signs) are shown as contour lines. (Reproduced from reference 60. Copyright 1986 American Chemical Society.)...

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