Simple harmonic potential function

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)). 

The TRIPOS force fields in the SYBYL and Alchemy programs and the Chem-X, CHARMm, and COSMIC force fields all employ a simple harmonic potential (Eq. [1]) for bond stretching/compression. The CVFF, DREIDING, and UFF force fields support a Morse potential as well as a harmonic potential. The harmonic function is the default in DREIDING and UFF. 

The classical harmonic oscillator in one dimension was illustrated in Seetfon 5.2.2 by the simple pendulum. Hooke s law was employed in the fSfin / = —kx where / is the force acting on the mass and k is the force constant The force can also be expressed as the negative gradient of a scalar potential function, V(jc) = for the problem in one dimension [Eq. (4-88)]. Similarly, the three-dimensional harmonic oscillator in Cartesian coordinates can be represented by the potential function... 

These potential energy terms and their attendant empirical parameters define the force field (FF). More complicated FFs which use different and/or more complex functional forms are also possible. For example, the simple harmonic oscillator expression for bond stretching can be replaced by a Morse function, Euorse (3), or additional FF terms may be added such as the stretch-bend cross terms, Estb, (4) used in the Merck molecular force field (MMFF) (7-10) which may be useful for better describing vibrations and conformational energies. 

This can be seen from elementary considerations. The distortion of the surrounding medium that leads to the intermediate state with energy WH can be described by simple harmonic motion, with a parameter x for the displacement, a potential energy px2 and a wave function of the form r=const xexp(—ax2). The probability P 2 of a configuration with potential energy WH is thus... 

M for a simple harmonic oscillator where v, the vibrational quantum i AUmber has values 0, 1.2, 3, etc. The potential function F(r) for simple < harmonic motion as derived from Hooke s law is given by... 

The central potential can be a simple harmonic oscillator potential/(r) kr2 or more complicated such as a Yukawa function f(r) (e a,/r) 1 or the Woods-Saxon function that has a flat bottom and goes smoothly to zero at the nuclear surface. The Woods-Saxon potential has the form... 

The potential energy of such an oscillator can be plotted as a function of the separation r, or, for a normal mode in a polyatomic molecule, as a function of a parameter characterizing the phase of the oscillation. For a simple harmonic oscillator, the potential energy function is parabolic, but for a molecule its shape is that indicated in Figure 2.6. The true curve is close to a parabola at the bottom, and it is for this reason that the assumption of simple harmonic motion is justified for vibrations of low amplitude. 

Fig. 3.4 Simple harmonic motion, (a) Displacement xand velocity vas a function of time t. (b) Variation of potential and kinetic energies during the motion.

The first derivatives of a potential energy function define the gradient of the potential and the second derivatives describe the curvature of the energy surface (Fig. 3.4). In most molecular mechanics programs the potential functions used are relatively simple and the derivatives are usually determined analytically. The second derivatives of harmonic oscillators correspond to the force constants. Thus, methods using the whole set of second derivatives result in some direct information on vibrational frequencies. 

Such a potential energy function gives rise to the famihar parabolic curve (Figure 22) where the curvature of the function is related to the force constant. The success of this simple harmonic model in treating surface atom vibrations lies in the relatively small displacement of surface atoms during a period of vibration. For some crystal properties, such as thermal expansion at elevated temperature, anharmoitic contributions to the potential must be included for an accurate description. 

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.

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