Potential energy switching

These functions allow- the nonbonded potential energy Lo turn off smoothly and systematically, removing artifacts caused by a truncated potential. With an appropriate switching function, the potential function is unaffected except m the region of the switch. 

An alternative way to eliminate discontinuities in the energy and force equations is to use a switching function. A switching function is a polynomial ftmction of the distance by which the potential energy function is multiplied. Thus the switched potential o (r) is related to the true potential t> r) by v r) = v(r)S(r). Some switching functions are applied to the entire range of the potential up to the cutoff point. One such function is ... 

If a molecule is strained, atoms may not be ver y close to the minimum of their individual potential energy wells when the best compromise geometry is reached. In such a case, the geometric criterion does not provide an exit from the loop. Programs are usually written so that they can automatically switch from a geometric minimization criterion to an energy minimization procedure. 

Figure 4. Potential energy of the 7.5 A cutoff potentials (truncate, shift, switch) and the no cutoff potential on the heating portion of the trajectories of (a) the no cutoff simulation and (b) the 7.5 A shift simulation. Continued on next page.

The problem of influence of the electric field intensity on the permittivity of solvents has been discussed in many papers. The high permittivity of water results from the intermolecular forces and is a cumulative property. The electric field intensity is the lowest at the potential of zero charge (pzc), thus allowing water molecules to adsorb in clusters. When the electrode is polarized, the associated molecules, linked with hydrogen bonds, can dissociate due to a change in the energy of their interaction with the electrode. Moreover, the orientation of water molecules may also change when the potential is switched from one side of the pzc to the otha. 

In real systems, for regauging we have to pay for a little switching costs, for example, but this may be minimal compared to the potential energy actually directed or gated upon the system to potentialize it. 

Figure 13.8 Schematic operation of a two-station rotaxane as a controllable molecular shuttle, and idealized representation of the potential energy of the system as a function of the position of the ring relative to the axle upon switching off and on station A. The number of dots in each position reflects the relative population of the corresponding coconformation in a statistically significant ensemble. Structures (a) and (c) correspond to equilibrium states, whereas (b) and (d) are metastable states. An alternative approach would be to modify station through an external stimulus in order to make it a stronger recognition site compared to station A.

Free cw-azobenzene, excited at 480 nm displays a biexponential decay of the excited state Si with time constants of 0.1 ps and 0.9 ps. Here the ultrafast kinetic component dominates the absorption change (it contains 90 % of the whole amplitude). A direct interpretation would relate the fast component to a free isomerizational motion, where the most direct reaction path on the Si and So potential energy surface is used without disturbance. The slower process may be assigned to a less direct motion due to hindrance by the surrounding solvent molecules. This interpretation is supported by the observation of the absorption changes in the APB and AMPB peptides. Here both reaction parts are slowed down by a factor of 2 - 3 and both show similar amplitudes The peptide molecules hinder the motion of the azobenzene switch and slow down considerably the initial kinetics. However, in all samples the transition to the ground state is finished within a few picoseconds. 

---