Torsion/torsional improper

A very promising recent approach to modeling angular geometries, the VAL-BOND model[30], is based on Pauling s 1931 paper1311 that established the fundamental principles of directed covalent bonds formed by hybridization. The VALBOND force field, which uses conventional terms for bond stretching, torsions, improper tor-... 

The potential energy surfaces of biological, polymer, and other systems of interest to nanotechnology applications are usually written as sums of interactions between chemically bonded atoms (stretch, bend, torsion, improper torsion, and so on) and non-bonded interactions. MD and other molecular simulation methods require first and sometimes second derivatives of potential energy terms. A potential energy term where is an internal coordinate, has the following first and second derivatives ... 

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... 

An atom lhai hassp h yhridi/alion lends lo be coplanar wilh its attached aloms. This effect isaccoiinled for by improper torsions in Olher force fields and by oiil-of-plane-bending inlcraclions in... 

V these three functional forms, the improper torsion definition is most widely used as it can then be easily included with the proper torsional terms in the force field. However, the... 

An atom that has sp hybridization tends to be coplanar with its attached atoms. This effect is accounted for by improper torsions in other force fields and by out-of-plane-bending interactions in... 

HyperChem uses the improper dihedral angle formed by central atom - neighbor 1 - neighbor 2 - neighbor 3, where the order of neighbors is how they appear in a HIN file. Not all planar atoms customarily have associated improper torsions. The order of atoms is arbitrary but has been consistently chosen by the original authors of the CHARMM force field. The templates contain equivalent CHARMM definitions of improper torsions for amino acids. Improper dihedral angles cannot be defined that do not have a central atom, as is sometimes done in CHARMM calculations. 

Some authors refer to improper dihedrals when discussing dihedral torsion where we would not normally expect full rotation, for example, any of the C-C-C-C linkages in the benzene ring of aspirin. Many MM force fields treat... 

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... 

More complicated cross-terms between the different intramolecular degrees of freedom are also employed in some force fields, but we will not consider them in the following. The dihedral term may also include four-center improper torsion or out-of-plane bending interactions that occur at sp2 hybridized centers.29... 

Energy terms bonds, angles, improper torsions Number of calculated structures 40... 

---