Potential energy function transferability

A number of more general force fields for the study of small molecules are available that can be extended to biological molecules. These force fields have been designed with the goal of being able to treat a wide variety of molecules, based on the ability to transfer parameters between chemical systems and the use of additional terms (e.g., cross terms) in their potential energy functions. Typically, these force fields have been optimized to... 

Of the biomolecular force fields, AMBER [21] is considered to be transferable, whereas academic CHARMM [20] is not transferable. Considering the simplistic form of the potential energy functions used in these force fields, the extent of transferability should be considered to be minimal, as has been shown recently [52]. As stated above, the user should perform suitable tests on any novel compounds to ensure that the force field is treating the systems of interest with sufficient accuracy. 

Therefore, two parts of any molecular mechanics package that have a direct influence on a particular optimized structure, i. e., on the nuclear coordinates of a specific energy minimum on the calculated potential energy surface, are the mathematical functions and the corresponding parameters. The potential energy functions and the force field parameters are interrelated and, therefore, the parameters may not, in general, be transferred from one force field into another. 

Most force fields used in coordination chemistry, in respect of the organic part of the molecules, are based on or are at least similar to the MM2 11 or AMBER 11 parameterization schemes, or mixtures thereof. However, it is of importance to stress again that transferring parameters from one force field to another without appropriate checks is not valid. This is not only a question of the different potential energy functions that may be used, but it is also a consequence of the interrelatedness of the entire set of parameters. Force field parameters imported from any source, whether a well-established force field or experimental data, should only be used as a starting point for further parameter refinement. 

Fig. 1 Energy levels for CO/Cu 001) showing the energy bands of the substrate and potential energy functions of the adsorbate CO with its axis perpendicular to the surface. The variable x refers to the frustrated-translation vibration of the center of mass of CO parallel to the surface, and q here is the distance from the center of mass of CO to the surface. Following an initial substrate photoexcitation, its de-excitation transfers energy into the adsorbate, which relaxes to the ground vibronic states.

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...

Figure 13 Potential energy surfaces for electron transfer reactions. Hamionic oscillator potential energy functions for reactants and product are shown, including the nuclear wave functions, which are shaded. The dark shaded region indicates the magnitude of overlap of the nuclear wave functions, which is the Franck-Condon factor, (a) is the normal region, (b) is the activationless region and (c) is the inverted region as defined in the text. (Ref. 72. Reproduced by permission of Namre Publishing Group, www.nature.com)...

The techniques collectively termed molecular mechanics (MM) employ an empirically derived set of equations to describe the energy of a molecule as a function of atomic position (the Born—Oppenheimer surface). The mathematical form is based on classical mechanics. This set of potential energy functions (usually termed the force field) contains adjustable parameters that are optimized to fit calculated values of experimental properties for a known set of molecules. The major assumption is, of course, that these parameters are transferable from one molecule to another. Computational efficiency and facile inclusion of solvent molecules are two of the advantages of the MM methods. 

Starting point is QM calculation within the framework of density-functional theory (DFT) (Hohenberg and Kohn, 1964 Kohn and Sham, 1965 Payne et al., 1992). DFT-based energy calculations can be used to evaluate the parameters of classical interatomic interaction potentials, which can be used to perform MS, MC, and MD simulations such ab initio potential parametrization is a key to improving the transferability of the classical force field. In Fig. 1, an interatomic potential energy function for Si-H interactions is given as an example of such a parametrization (Ohira et al., 1995). 

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