Normal potential energies

The calculation of potential energy curves is of further interest in that one can examine normal potential energy curves that produce a stable molecule (e.g., H2 and HeH+), molecules that produce a transition state during the dissociation process (metastability as in He2 ", Fig. 12), and unstable molecules as in He2. Just as for H2, it is imperative to use the UHF method to obtain correct dissociation of He2 ". This dication has been detected experimentally. ... 

The following derivation is modified from that of Fowler and Guggenheim [10,11]. The adsorbed molecules are considered to differ from gaseous ones in that their potential energy and local partition function (see Section XVI-4A) have been modified and that, instead of possessing normal translational motion, they are confined to localized sites without any interactions between adjacent molecules but with an adsorption energy Q. 

Figure 6. Diabatic and corresponding adiabatic potential energy along a relevant reaction coordinate for normal electron transfer...

The combination is in this case an out-of-phase one (Section I). This biradical was calculated to be at an energy of 39.6 kcal/mol above CHDN (Table ni), and to lie in a real local minimum on the So potential energy surface. A normal mode analysis showed that all frequencies were real. (Compare with the prebenzvalene intermediate, discussed above. The computational finding that these species are bound moieties is difficult to confimi experimentally, as they are highly reactive.)... 

For vei y small vibronic coupling, the quadratic terms in the power series expansion of the electronic Hamiltonian in normal coordinates (see Appendix E) may be considered to be negligible, and hence the potential energy surface has rotational symmetry but shows no separate minima at the bottom of the moat. In this case, the pair of vibronic levels Aj and A2 in < 3 become degenerate by accident, and the D3/, quantum numbers (vi,V2,/2) may be used to label the vibronic levels of the X3 molecule. When the coupling of the... 

For molecules with an even number of electrons, the spin function has only single-valued representations just as the spatial wave function. For these molecules, any degenerate spin-orbit state is unstable in the symmetric conformation since there is always a nontotally symmetric normal coordinate along which the potential energy depends linearly. For example, for an - state of a C3 molecule, the spin function has species da and E that upon... 

The basic idea of NMA is to expand the potential energy function U(x) in a Taylor series expansion around a point Xq where the gradient of the potential vanishes ([Case 1996]). If third and higher-order derivatives are ignored, the dynamics of the system can be described in terms of the normal mode directions and frequencies Qj and Ui which satisfy ... 

Amadei et al. 1993] Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential Dynamics of Proteins. Proteins 17 (1993) 412-425 [Balsera et al. 1997] Balsera, M., Stepaniants, S., Izrailev, S., Oono, Y., Schiilten, K. Reconstructing Potential Energy Functions from Simulated Force-Induced Unbinding Processes. Biophys. J. 73 (1997) 1281-1287 [Case 1996] Case, D.A. Normal mode analysis of protein dynamics. Curr. Op. Struct. Biol. 4 (1994) 285-290... 

Fig. 3. Curves calculated using (8) for a series of increasing a values. The curves were calculated using tr = 0.6 nm and e = 0.4 kj/mol. Note that for a = 0.0 the normal 6-12 Lennard Jones potential energy function is recovered.

Harmonic analysis (normal modes) at given temperature and curvature gives complete time behavior of the system in the harmonic limit [1, 2, 3]. Although the harmonic model may be incomplete because of the contribution of anharmonic terms to the potential energy, it is nevertheless of considerable importance because it serves as a first approximation for which the theory is highly developed. This model is also useful in SISM which uses harmonic analysis. 

For each pair of interacting atoms (/r is their reduced mass), three parameters are needed D, (depth of the potential energy minimum, k (force constant of the par-tictilar bond), and l(, (reference bond length). The Morse ftinction will correctly allow the bond to dissociate, but has the disadvantage that it is computationally very expensive. Moreover, force fields arc normally not parameterized to handle bond dissociation. To circumvent these disadvantages, the Morse function is replaced by a simple harmonic potential, which describes bond stretching by Hooke s law (Eq. (20)). 

At normal bond lengths, the LHK solution usually degenerates to the situation where the two spatial orbitals become identical. The LHK solution for Hp, for example, has a smooth potential energy... 

The following illustration shows the potential energy surface for vibrational motion along one normal mode ... 

As a simple example of a normal mode calculation consider the linear triatomic system ir Figure 5.16. We shall just consider motion along the long axis of the molecule. The displace ments of the atoms from their equilibrium positions along this axis are denoted by It i assumed that the displacements are small compared with the equilibrium values Iq and th( system obeys Hooke s law with bond force constants k. The potential energy is given by ... 

The potential energy curve in Figure 6.4 is a two-dimensional plot, one dimension for the potential energy V and a second for the vibrational coordinate r. For a polyatomic molecule, with 3N — 6 (non-linear) or 3iV — 5 (linear) normal vibrations, it requires a [(3N — 6) - - 1]-or [(3A 5) -F 1]-dimensional surface to illustrate the variation of V with all the normal coordinates. Such a surface is known as a hypersurface and clearly cannot be illustrated in diagrammatic form. What we can do is take a section of the surface in two dimensions, corresponding to V and each of the normal coordinates in turn, thereby producing a potential energy curve for each normal coordinate. 

If we use a contour map to represent a three-dimensional surface, with each contour line representing constant potential energy, two vibrational coordinates can be illustrated. Figure 6.35 shows such a map for the linear molecule CO2. The coordinates used here are not normal coordinates but the two CO bond lengths rj and r2 shown in Figure 6.36(a). It is assumed that the molecule does not bend. 

---