Potential energy functions bond stretching

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)). 

Most of the molecules we shall be interested in are polyatomic. In polyatomic molecules, each atom is held in place by one or more chemical bonds. Each chemical bond may be modeled as a harmonic oscillator in a space defined by its potential energy as a function of the degree of stretching or compression of the bond along its axis (Fig. 4-3). The potential energy function V = kx j2 from Eq. (4-8), or W = ki/2) ri — riof in temis of internal coordinates, is a parabola open upward in the V vs. r plane, where r replaces x as the extension of the rth chemical bond. The force constant ki and the equilibrium bond distance riQ, unique to each chemical bond, are typical force field parameters. Because there are many bonds, the potential energy-bond axis space is a many-dimensional space. 

According to the namre of the empirical potential energy function, described in Chapter 2, different motions can take place on different time scales, e.g., bond stretching and bond angle bending vs. dihedral angle librations and non-bond interactions. Multiple time step (MTS) methods [38-40,42] allow one to use different integration time steps in the same simulation so as to treat the time development of the slow and fast movements most effectively. 

The force constant that is associated with the stretching vibration of a bond is often taken as a measure of the strength of the bond, although it is more correctly a measure of the curvature of the potential energy function around the minimum (Figure 2.1) that is, the rigidity of the bond. For a diatomic molecule, the frequency of vibration v is determined by the force constant k and the reduced mass /x = + m2), where m and m2 are the masses of... 

The spacings between the various vibrational energy levels depend on the potential energy associated with bond stretching (see Section 9.3.2). The data from the spectroscopic experiments thus permit the derivation of that potential energy function in a straightforward way. 

Before we go on to consider functional forms for all of the components of a molecule s total steric energy, let us consider the limitations of Eq. (2.2) for bond stretching. Like any truncated Taylor expansion, it works best in regions near its reference point, in this case req. Thus, if we are interested primarily in molecular structures where no bond is terribly distorted from its optimal value, we may expect Eq. (2.2) to have reasonable utility. However, as the bond is stretched to longer and longer r, Eq. (2.2) predicts the energy to become infinitely positive, which is certainly not chemically realistic. The practical solution to such inaccuracy is to include additional terms in the Taylor expansion. Inclusion of the cubic term provides a potential energy function of the form... 

A harmonic potential is a good approximation of the bond stretching function near the energy minimum (Fig. 2.7). Therefore, most programs use this approximation (see Eq. 2.6) however the limits of the simplification have to be kept in mind, in those cases where the anharmonicity becomes important. Apart from the possibility of including cubic terms to model anharmonicity fsee the second term in Eq. 2.14), which is done in the programs MM2 and MM3[1,2,2 241, the selective inclusion of 1,3-nonbonded interactions can also be used to add anharmonicity to the total potential energy function. 

Figure 12.10. Potential-energy functions of the S0 state, the locally excited 1 hit states of guanine and cytosine, the lowest1 rnr state, and the tt-jt charge-transfer state of the WC conformer (a), the conformer B (b), and the conformer C (c) of the CG dimer. The PE functions have been calculated along the linear-synchronous-transit proton-transfer reaction path from the S0 minimum to the biradical minimum. Insets show the potential-energy function of the locally excited 1mr state of guanine calculated along the minimum-energy path for stretching of the NH bond...

Some formulations of the potential energy function (e.g., References 27 and 79, and AMBER, CHARMM, and DISCOVER, as well as most force fields used in small-molecule studies) include terms that allow for bond stretching and bond angle bending, that is, for flexible geometry. Hence, the terms in Eq. [1] are augmented by the expression27... 

Figure 28-7 In force field calculations, different levels of approximations are used to reproduce the stretching and compression of chemical bonds The plot shows a Morse potential energy function siipenmposed with various power series approximations (quadratic, cubic, and quartic functions) Note that the bottoms of the curves, representing the bond length for most chemical bonds of interest to medicinal chemists, almost overlap exactly. This nearly perfect fit in the bonding region is the reason simple harmonic functions can be used to calculate tx>nd lengths for unstrained molecular structures in the force lield method.

Molecular mechanics calculations involve summation of the force fields for each type of strain. The original mathematical expressions for the force fields were derived from classical mechanical potential energy functions. The energy required to stretch a bond or to bend a bond angle increases as the square of the distortion ... 

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