Torsional potentials

Via) hindering potential (torsional potential) as a function of the torsional angle a [59Lin, 68Dre] Via) = Na) N 2... 

Hindering potential (torsional potential) for two equivalent methyl groups showing mutual perturbations [91Mey]... 

To calculate N (E-Eq), the non-torsional transitional modes have been treated as vibrations as well as rotations [26]. The fomier approach is invalid when the transitional mode s barrier for rotation is low, while the latter is inappropriate when the transitional mode is a vibration. Hamionic frequencies for the transitional modes may be obtained from a semi-empirical model [23] or by perfomiing an appropriate nomial mode analysis as a fiinction of the reaction path for the reaction s potential energy surface [26]. Semiclassical quantization may be used to detemiine anliamionic energy levels for die transitional modes [27]. 

By combining the Lagrange multiplier method with the highly efficient delocalized internal coordinates, a very powerfiil algoritlun for constrained optimization has been developed [ ]. Given that delocalized internal coordinates are potentially linear combinations of all possible primitive stretches, bends and torsions in the system, cf Z-matrix coordinates which are individual primitives, it would seem very difficult to impose any constraints at all however, as... 

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

Figure 2-102. Dependence of the potential energy ctirve of n-butane on the torsion angle r between carbon atoins C2 and C3.

Figure 2-108. Derivation of a syrMbolic potential energy function from the torsion angle distribution of a torsion fragment.

The origin of a torsional barrier can be studied best in simple cases like ethane. Here, rotation about the central carbon-carbon bond results in three staggered and three eclipsed stationary points on the potential energy surface, at least when symmetry considerations are not taken into account. Quantum mechanically, the barrier of rotation is explained by anti-bonding interactions between the hydrogens attached to different carbon atoms. These interactions are small when the conformation of ethane is staggered, and reach a maximum value when the molecule approaches an eclipsed geometry. 

It is noteworthy that it is not obligatory to use a torsional potential within a PEF. Depending on the parameterization, it is also possible to represent the torsional barrier by non-bonding interactions between the atoms separated by three bonds. In fact, torsional potentials and non-bonding 1,4-interactions are in a close relationship. This is one reason why force fields like AMBER downscale the 1,4-non-bonded Coulomb and van der Waals interactions. 

Figure 7-10. Two examples of torsional potentials plotted using Eq, (24) with the parameters rt = 2, V = 5.0, y = Fi (solid line), and n = 3. = 3.0, y = 0 (broken line). All other V, ...

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. 

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

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