Simulation techniques potential energy surfaces

Computer simulation techniques offer the ability to study the potential energy surfaces of chemical reactions to a high degree of quantitative accuracy [4]. Theoretical studies of chemical reactions in the gas phase are a major field and can provide detailed insights into a variety of processes of fundamental interest in atmospheric and combustion chemistry. In the past decade theoretical methods were extended to the study of reaction processes in mesoscopic systems such as enzymatic reactions in solution, albeit to a more approximate level than the most accurate gas-phase studies. 

Nonpolar and dipolar altitudinal rotors (compounds 2 and 3 in Fig. 17.3) have been synthesized. 19F NMR spectroscopy showed that the barrier to rotation in 3 was extremely low in solution. Both systems have then been immobilized on Au(l 11) surfaces and studied with a variety of techniques.57 The results obtained indicated that for a fraction of molecules the static electric field from the scanning tunneling microscopy (STM) tip could induce an orientation change in the dipolar rotor but not in the nonpolar analog (for a recent example of an azimuthal molecular rotor controlled by the STM tip, see Reference 58). Compound 3 can exist as three pairs of helical enantiomers because of the propeller-like conformation of the tetra-arylcyclobutadienes. For at least one out of the three diastereomers, an asymmetric potential energy surface can be predicted by molecular dynamics simulations on application of an alternating electric field.55... 

In order to test the (in)correctness of the Marcus solvent model, we have carried out extensive MD simulations of a bond-breaking electron-transfer reaction in water at a platinum electrode. Figure 10a shows the computer simulated potential energy surface obtained by a two dimensional umbrella sampling technique. Analysis of the results in Figure 10a brings to light two important effects of the solvent the Marcus model does not account for. 

For simple fluids composed of small molecules, the current equilibrium simulation techniques are highly accurate and the computational tools exist for carrying out long enough simulations of a sufficiently large system to obtain experimental accuracy. Thus, for these systems the accuracy of the potential energy surface is normally the factor that will restrict the accuracy that can be achieved for the determination of their properties. 

First-principles simulations are techniques that generally employ electronic structure calculations on the fly . Since this is a very expensive task in terms of computer time, the electronic structure method is mostly chosen to be density functional theory. Apart from the possibility of propagating classical atomic nuclei on the Born-Oppenheimer potential energy surface represented by the electronic energy V (R ) = ji(R ), another technique, the Car-Parrinello method, emerged that uses a special trick, namely the extended Lagrangian technique. The basic idea... 

In the classical trajectory approach, if a potential energy surface is available, one prescribes initial conditions for a particular trajectory. The initial variables are selected at random from distributions that are representative of the collisions process. The initial conditions and the potential energy function define a classical trajectory which can be obtained by numerical integration of the classical equations of motion. Then another set of initial variables is chosen and the procedure is repeated until a large number of trajectories simulating real collision events have been obtained. The reaction parameters can be obtained from the final conditions of the trajectories. Details of this technique are given by Bunker.29... 

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