Isoenergy contour

Fig. 6. Kainate-iGluR2-SlS2 complex, including isoenergy contours according to GRID (16) - methyl probe (beige, -3.0 kcal/mol), water probe (cyan, -10.0 kcal/mol), and anionic oxygen probe (magenta, -11.0 kcal/mol).

As an example of this technique we can compare the computed and the experimental X-ray diffraction intensity for liquid water at T=298°K (see, for example, E, Clementi, Lecture Notes in Chemistry, Vol, 2, Springer Verlag, 1976), In the same way we can consider water around amino acids. For example, in Fig, 1 we present the isoenergy contour... 

Fig. 1. Isoenergy contours of amino acids in water. Contour interval 1 Kcal/mole.

Fig. 2. Left Isoenergy contour diagram (energies in kJ/mol) for the interaction of Na+ with [18] crown-6 and one H20 molecule,5). The conformation of the crown ether and the position of the water molecule were fixed as found experimentally 171). Right same view of the structure of the NaSCN [18] crown-6 H20 complex as determined by X-ray crystallography171 . The distance between the position of the energy minimum (left) and the found position of Na+ (right) amounts to 11 pm...

Grids of target-probe interaction energy values can be read into many molecular graphics programs which can display the MIFs as isoenergy contours or project the energies onto molecular surfaces. 

Data analysis options include the preparation of isoenergy contour maps (CMAPS), linear energy vs. rotation angle plots (LINPLOT) and tables of local energy minima, statistical thermodynamic probabilities, and entropy terms to enable the reporting of "free" energies in addition to "conformational" energies. 

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

Figure 17 Energy grid map of a(l-3) linkage in trisaccharide 2. Isoenergy contours are scaled at 1 kcal/mol intervals up to 6 kcal/mol above the global minimum energy.

Figure9.1 Model 2D PES U s,R) ofthe symmetrical A---H A fragment. Closed loops (1—4) are isoenergy contour lines in arbitrary units.

Fig. 3.3 The isoenergy contours are shown for the double well model dark curves) together with the corresponding curves for the Verlet modified Hamiltonian light curves)...

The early topological analyses of potential energy hypersurfaces have been based on isoenergy contours [8,15] defined indirectly by the energy gradients using an... 

In Figure 1 we depict the PES for rotation of the tp, ip torsion angles of N-acetylalanine N-methylamide. The isoenergy contours shown on a plot of vs. (similar to isobars on a weather map) are depicted in the same color and indicate quite clearly where the minima and saddle points are located. 

Figure 1 Contour plot of 4> vs. i/r torsion angles for Al-acetylalanine yV-methylamide. Isoenergy contours are color coded according to the energy (red = high, purple = low). The global minimum, two local minima and saddle points, and a maximum are labeled. Structures of the global minimum, the local minimum on the top right, and the connecting saddle point are depicted helow the contour plot...

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