Potential energy surface atom mechanism

The origin of a torsional barrier can be studied best in simple cases like ethane. Here, rotation about the central carbon-carbon bond results in three staggered and three eclipsed stationary points on the potential energy surface, at least when symmetry considerations are not taken into account. Quantum mechanically, the barrier of rotation is explained by anti-bonding interactions between the hydrogens attached to different carbon atoms. These interactions are small when the conformation of ethane is staggered, and reach a maximum value when the molecule approaches an eclipsed geometry. 

Molecular mechanical force fields use the equations of classical mechanics to describe the potential energy surfaces and physical properties of molecules. A molecule is described as a collection of atoms that interact with each other by simple analytical functions. This description is called a force field. One component of a force field is the energy arising from compression and stretching a bond. 

Reality suggests that a quantum dynamics rather than classical dynamics computation on the surface would be desirable, but much of chemistry is expected to be explainable with classical mechanics only, having derived a potential energy surface with quantum mechanics. This is because we are now only interested in the motion of atoms rather than electrons. Since atoms are much heavier than electrons it is possible to treat their motion classically. Quantum scattering approaches for small systems are available now, but most chemical phenomena is still treated by a classical approach. A chemical reaction or interaction is a classical trajectory on a potential surface. Such treatments leave out phenomena such as tunneling but are still the state of the art in much of computational chemistry. 

Consider a reactant molecule in which one atom is replaced by its isotope, for example, protium (H) by deuterium (D) or tritium (T), C by C, etc. The only change that has been made is in the mass of the nucleus, so that to a very good approximation the electronic structures of the two molecules are the same. This means that reaction will take place on the same potential energy surface for both molecules. Nevertheless, isotopic substitution can result in a rate change as a consequence of quantum effects. A rate change resulting from an isotopic substitution is called a kinetic isotope effect. Such effects can provide valuable insights into reaction mechanism. 

Iti Chapter 1, we dealt at length with molecular mechanics. MM is a classical model where atoms are treated as composite but interacting particles. In the MM model, we assume a simple mutual potential energy for the particles making up a molecular system, and then look for stationary points on the potential energy surface. Minima correspond to equilibrium structures. 

Figure 14. Classical trajectories for the H + H2(v = l,j = 0) reaction representing a 1-TS (a-d) and a 2-TS reaction path (e-h). Both trajectories lead to H2(v = 2,/ = 5,k = 0) products and the same scattering angle, 0 = 50°. (a-c) 1-TS trajectory in Cartesian coordinates. The positions of the atoms (Ha, solid circles Hb, open circles He, dotted circles) are plotted at constant time intervals of 4.1 fs on top of snapshots of the potential energy surface in a space-fixed frame centered at the reactant HbHc molecule. The location of the conical intersection is indicated by crosses (x). (d) 1-TS trajectory in hyperspherical coordinates (cf. Fig. 1) showing the different H - - H2 arrangements (open diamonds) at the same time intervals as panels (a-c) the potential energy contours are for a fixed hyperradius of p = 4.0 a.u. (e-h) As above for the 2-TS trajectory. Note that the 1-TS trajectory is deflected to the nearside (deflection angle 0 = +50°), whereas the 2-TS trajectory proceeds via an insertion mechanism and is deflected to the farside (0 = —50°).

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. 

For a system containing a larger number of atoms, the general picture of the potential energy surface and the transition state also applies. For example, in the second reaction step in the mechanism of ethane pyrolysis in Section 6.1.2,... 

In some situations we have performed finite temperature molecular dynamics simulations [50, 51] using the aforementioned model systems. On a simplistic level, molecular dynamics can be viewed as the simulation of the finite temperature motion of a system at the atomic level. This contrasts with the conventional static quantum mechanical simulations which map out the potential energy surface at the zero temperature limit. Although static calculations are extremely important in quantifying the potential energy surface of a reaction, its application can be tedious. We have used ah initio molecular dynamics simulations at elevated temperatures (between 300 K and 800 K) to more efficiently explore the potential energy surface. 

In principal one can calculate the electronic energy as a function of the Cartesian coordinates of the three atomic nuclei of the ground state of this system using the methods of quantum mechanics (see Chapter 2). (In subsequent discussion, the terms coordinates of nuclei and coordinates of atoms will be used interchangeably.) By analogy with the discussion in Chapter 2, this function, within the Born-Oppenheimer approximation, is not only the potential energy surface on which the reactant and product molecules rotate and vibrate, but is also the potential... 

The isotope independent potential energy surface was evaluated using a mixed quantum mechanics/molecular mechanics (QM/MM) method. The system (N atoms) was partitioned into Nqm quantum mechanical atoms and Nmm classical mechanical atoms. Nqm consisted of the 15 atom substrate (phospho-D-glycerate)... 

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