Modeling an SN2 Reactions with Quantum Chemistry.docx -...

Lucas Paquin
CHEM 166A
April 30
th
, 2018
Modeling an S
N
2 Reaction with Quantum Chemistry
Introduction
For this experiment, the software program Jaguar from Schrödinger, Inc. was used on a
computer. Quantum calculations were run to optimize the molecular models, and calculate the
energies as well as the vibrational frequencies for the following reaction:
Figure 1: S
N
2 reaction of CH
3
F + F -
For this reaction, it can be assumed that in the reactant/product state, the two molecules
CH
3
F and F - do not have any interaction. Therefore, the total energy of the reactant/product state
is the sum of individual molecules’ energies. There could be two intermediate states, which are
complexes of the reactants and products respectively. In addition, a transition state (TS) should
bridge the two intermediate states.
Given the difficulty of solving the exact solution of the Schrödinger equation, theories for
quantum calculations introduce approximations as a matter of practice. The Hartree-Fock Self
Consistent Field (HF) method often assumes that the exact N-body wave function of the system
can be approximated by a single Slater determinant of N spin-orbitals. Using the variational
method, one can derive a set of N-coupled equations for the N spin orbitals. A solution of these
equations yields the Hartree–Fock wave function and energy of the system. The solution is
expected to be improved in multiple HF calculations. Based on the perturbation theory, the
Møller–Plesset perturbation theory (LMP2) is one of the post-Hartree–Fock methods for
quantum chemistry. The LMP2 method improves on the Hartree–Fock method by adding second
order correction. Finally, most quantum chemistry calculations require a basis set, which
contains a set of functions to approximate the “real” wave function. In short, before a quantum