Potential energy surface trajectory calculations

Most of these theoretical investigations have been carried out using methyl compounds as the substrate. For example, the Sn2 reaction between OFT and methyl chloride has been investigated for non-linear and linear collisions using ab initio molecular dynamics calculations.105 The potential energy surface was calculated at the MP2/6-311-I— -G(2df,2pd) level of theory and the collision energy was set at 25 kcal mor1. The results for 495 trajectories indicated that the reactants pass from the initial encounter complex to the transition state in 0.02 ps and to the product encounter... 

In the early 1930 s, Eyring and his co-workers made some preliminary studies of the trajectories of systems on potential-energy surfaces, but not much progress could be made until the development of high-speed computers. There has recently been a revival of interest in this field, now known as molecular dynamics. In particular, Karplus, Porter, and Sharma have carried out calculations on the H -b Hg system, using what appears to be a very reliable potential-energy surface. The calculations are quasi-classical in nature the vibrational and rotational states in the Hg molecule are quantized, but the course of the collision is treated classically. 

Classical trajectory calculations for the reaction H2 + I2 HI + HI and its reverse have been carried out for two potential energy surfaces. Such calculations are not easy to perform because of the large number of possible states of reactant species, the mismatch of the masses of H and I atoms, and the low probability of reaction. The light H atoms require small time steps to avoid time-step error and the heavy I atoms require a long time for movement. The probability of reaction of two HI molecules, randomly selected from pairs at 700 K with sufficient total energy to react, is about 1 in 10 [15]. In a thermal system collisions of H2 with I2 (or 21) which result in reaction to form HI + HI are indeed rare events. 

The methods for calculating classical trajectories of molecular collisions are well established, and they are straightforward to apply. Usually, the first step in a simulation is to represent the potential energy surface in an analytical form so that the forces can be rapidly calculated. Given the potential energy surface, the calculation can be viewed as having three parts selection of initial conditions, solution of the equations of motion, and analysis of the trajectories. 

In section III the model H-C-C H + C=G potential energy surfaces and the methodology of the classical trajectory calculations are described. The trajectory unimolecular lifetime distributions and rate constants for the different surfaces are compared in section IV. Also discussed in section IV are the observed quasiperiodic trajectories for some of the potential energy surfaces. The calculated product energy distributions are presented in section V along with a dynamical model which explains the product energy partitioning. 

Figure Al.6.27. Equipotential contour plots of (a) the excited- and (b), (c) ground-state potential energy surfaces. (Here a hamionic excited state is used because that is the way the first calculations were perfomied.) (a) The classical trajectory that originates from rest on the ground-state surface makes a vertical transition to the excited state, and subsequently undergoes Lissajous motion, which is shown superimposed, (b) Assuming a vertical transition down at time (position and momentum conserved) the trajectory continues to evolve on the ground-state surface and exits from chaimel 1. (c) If the transition down is at time 2 the classical trajectory exits from chaimel 2 (reprinted from [52]).

At the time the experiments were perfomied (1984), this discrepancy between theory and experiment was attributed to quantum mechanical resonances drat led to enhanced reaction probability in the FlF(u = 3) chaimel for high impact parameter collisions. Flowever, since 1984, several new potential energy surfaces using a combination of ab initio calculations and empirical corrections were developed in which the bend potential near the barrier was found to be very flat or even non-collinear [49, M], in contrast to the Muckennan V surface. In 1988, Sato [ ] showed that classical trajectory calculations on a surface with a bent transition-state geometry produced angular distributions in which the FIF(u = 3) product was peaked at 0 = 0°, while the FIF(u = 2) product was predominantly scattered into the backward hemisphere (0 > 90°), thereby qualitatively reproducing the most important features in figure A3.7.5. 

Ah initio trajectory calculations have now been performed. However, these calculations require such an enormous amount of computer time that they have only been done on the simplest systems. At the present time, these calculations are too expensive to be used for computing rate constants, which require many trajectories to be computed. Semiempirical methods have been designed specifically for dynamics calculations, which have given insight into vibrational motion, but they have not been the methods of choice for computing rate constants since they are generally inferior to analytic potential energy surfaces fitted from ah initio results. 

Rather than using transition state theory or trajectory calculations, it is possible to use a statistical description of reactions to compute the rate constant. There are a number of techniques that can be considered variants of the statistical adiabatic channel model (SACM). This is, in essence, the examination of many possible reaction paths, none of which would necessarily be seen in a trajectory calculation. By examining paths that are easier to determine than the trajectory path and giving them statistical weights, the whole potential energy surface is accounted for and the rate constant can be computed. 

Most potential energy surfaces are extremely complex. Fiber and Karplus analyzed a 300 psec molecular dynamics trajectory of the protein myoglobin. They estimate that 2000 thermally accessible minima exist near the native protein structure. The total number of conformations is even larger. Dill derived a formula to calculate the upper bound of thermally accessible conformations in a protein. Using this formula, a protein of 150 residues (the approx-... 

The method is composed of the following algorithms (1) transition position is detected along each classical trajectory, (2) direction of transition is determined there and the ID cut of the potential energy surfaces is made along that direction, (3) judgment is made whether the transition is LZ type or nonadiabatic tunneling type, and (4) the transition probability is calculated by the appropriate ZN formula. The transition position can be simply found by... 

Traditionally, trajectory calculations were only performed on previously calculated (or empirically estimated) potential energy surfaces. With the increased computational speed of modern computers, it has also become possible to employ direct dynamics trajectory calculations [34, 35]. In this method, a global potential energy surface is not needed. Instead, from some... 

For both statistical and dynamical pathway branching, trajectory calculations are an indispensable tool, providing qualitative insight into the mechanisms and quantitative predictions of the branching ratios. For systems beyond four or five atoms, direct dynamics calculations will continue to play the leading theoretical role. In any case, predictions of reaction mechanisms based on examinations of the potential energy surface and/or statistical calculations based on stationary point properties should be viewed with caution. 

Fig. 1. Potential energy surface and classical trajectory calculations on the H + H2 hydrogen exchange reaction. Note the orbiting trajectory in the vicinity of Lake Eyring . Despite the unrealistic nature of a well near the transition state of this reaction, many of the modern ideas of chemical reaction theory can be seen in action already in this work. (See Ref. 1.)...

From the point of view of associative desorption, this reaction is an early barrier reaction. That is, the transition state resembles the reactants.46 Early barrier reactions are well known to channel large amounts of the reaction exoergicity into product vibration. For example, the famous chemical-laser reaction, F + H2 — HF(u) + H, is such a reaction producing a highly inverted HF vibrational distribution.47-50 Luntz and co-workers carried out classical trajectory calculation on the Born-Oppenheimer potential energy surface of Fig. 3(c) and found indeed that the properties of this early barrier reaction do include an inverted N2 vibrational distribution that peaks near v = 6 and extends to v = 11 (see Fig. 3(a)). In marked contrast to these theoretical predictions, the experimentally observed N2 vibrational distribution shown in Fig. 3(d) is skewed towards low values of v. The authors of Ref. 44 also employed the electronic friction theory of Tully and Head-Gordon35 in an attempt to model electronically nonadiabatic influences to the reaction. The results of these calculations are shown in... 

Classical trajectory calculations, performed on the PES1 and PESl(Br) potential energy surfaces described above, have provided a detailed picture of the microscopic dynamics of the Cl- + CH3Clb and Cl" + CH3Br SN2 nucleophilic substitution reactions.6,8,35-38 In the sections below, different aspects of these trajectory studies and their relation to experimental results and statistical theories are reviewed. 

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