Molecular modelling potential energy

In this section, we introduce the model Hamiltonian pertaining to the molecular systems under consideration. As is well known, a curve-crossing problem can be formulated in the adiabatic as well as in a diabatic electronic representation. Depending on the system under consideration and on the specific method used, both representations have been employed in mixed quantum-classical approaches. While the diabatic representation is advantageous to model potential-energy surfaces in the vicinity of an intersection and has been used in mean-field type approaches, other mixed quantum-classical approaches such as the surfacehopping method usually employ the adiabatic representation. 

Applications of atomic charges in computational chemistry are far-ranging, and include most calculations that employ molecular mechanical potential energy functions. Here, we limit our attention to a few selected applications which illustrate the advantages of different charge models. 

Comparison of stretching frequencies (cm ) from a molecular orbital calculation and from two model potential energy surfaces. 

The SPC/E model approximates many-body effects m liquid water and corresponds to a molecular dipole moment of 2.35 Debye (D) compared to the actual dipole moment of 1.85 D for an isolated water molecule. The model reproduces the diflfiision coefficient and themiodynamics properties at ambient temperatures to within a few per cent, and the critical parameters (see below) are predicted to within 15%. The same model potential has been extended to include the interactions between ions and water by fitting the parameters to the hydration energies of small ion-water clusters. The parameters for the ion-water and water-water interactions in the SPC/E model are given in table A2.3.2. 

Molecular dynamics consists of the brute-force solution of Newton s equations of motion. It is necessary to encode in the program the potential energy and force law of interaction between molecules the equations of motion are solved numerically, by finite difference techniques. The system evolution corresponds closely to what happens in real life and allows us to calculate dynamical properties, as well as thennodynamic and structural fiinctions. For a range of molecular models, packaged routines are available, either connnercially or tlirough the academic conmuinity. 

How can we apply molecular dynamics simulations practically. This section gives a brief outline of a typical MD scenario. Imagine that you are interested in the response of a protein to changes in the amino add sequence, i.e., to point mutations. In this case, it is appropriate to divide the analysis into a static and a dynamic part. What we need first is a reference system, because it is advisable to base the interpretation of the calculated data on changes compared with other simulations. By taking this relative point of view, one hopes that possible errors introduced due to the assumptions and simplifications within the potential energy function may cancel out. All kinds of simulations, analyses, etc., should always be carried out for the reference and the model systems, applying the same simulation protocols. 

If the system can only be modeled feasibly by molecular mechanics, use the potential energy curve-crossing technique or a force held with transition-structure atom types. 

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