Torsional angles improper

Another way is to define an improper torsion angle e- (for atoms 1-2-3-4 in Figure 7-11 in combination with a potential lihe V((r- = fc l-cos2fi.-), which has its minima at <> = 0 and 7t. This of course implies the risk that, if the starting geometry is far from reality, the optimi2 ation will perhaps lead to the wrong local minimum. 

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... 

As mentioned in Section 2.2.3, the out-of-plane energy may also be described by an improper torsional angle. For the example shown in Figure 2.6, a torsional angle ABCD may be defined, even though there is no bond between C and D. The out-of-plane oop may then be described by an angle for example as a harmonic function... 

Scheme 2 Newman projections for PTX conformations in terms of the improper torsion angles 0-C2-C3 -N(Bz) and 0-C2-C3 -C(Ph) (< )1, < )2). The front atom is C-2, the unseen back atom, C-3. a The nonpolar conformation as derived by NMR in CDC13. b The polar conformation as observed in the solid state, c T-Taxol conformation bound to 3 tubulin from EC...

Identity reaction, 367 Improper torsional angle, 16 Inactive molecular orbitals, in MCSCF methods, 119... 

Improper torsion angles arise in considering angles about planar centers, for example, sjP carbon atoms. 

There are several ways in which out-of-plane bending terms can be incorporated into a force field. One approach is to treat the four atoms as an improper torsion angle (i.e. a torsion angle in which the four atoms are not bonded in the sequence 1-2-3-4). One way to define an improper torsion for cyclobutane would involve the atoms 1-5-3-2 in Figure 4.9. 

A torsional potential of the following form is then used to maintain the improper torsion angle at 0° or 180° ... 

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