Computational Chemistry

Brian T. Luke, Ph.D.


Computational Chemistry, and to some extent Molecular Modeling, actually comprises four sub-fields: Quantum Chemistry; Semi-Empirical Quantum Chemistry; Empirical Energy Modeling; and Molecular Graphics. There is definitely some overlap between these categories since many molecular graphics programs act as front-ends to programs in some or all of the other three categories. Similarly, many ab initio quantum chemistry programs allow you to solve for the structure and/or properties of a molecule using a semi-empirical Hamiltonian, and some semi-empirical programs include electron correlation.

Molecular Graphics is obviously the visualization of a molecule, and may also include a graphical representation of some of the molecule's properties. The other three methods represent procedures that try to solve for the structure and properties of a molecule on a computer.

At the highest level, quantum chemical methods attempt to solve the Schrodinger equation as accurately as possible. Unfortunately, this equation can only be explicitly solved for the simplest atom, hydrogen. More precisely, it can only be solved for atoms/ions that contain only a single electron; H, He+, Li2+, and so on. For these systems, this lone electron can occupy one of a number of atomic orbitals. These atomic orbitals are simply probability distributions that determine the likelihood of the electron being in a given positon.

As soon as a second electron is added, a problem arises. Both negatively charged electrons want to get as close to the postive atomic nucleus as possible, but they repel each other. Therefore, if one of the electrons moves close to the nucleus the other is more likely to move further away. This interplay in their motions is known as electron correlation. Unfortunately, the Heisenberg Uncertanty Principle states that there is a minimum uncertanty in the product of a particle's position and its momentum (i.e. velocity), and this uncertanty is large for the electron. Therefore if you know where the electrons are at a given time, the uncertanty in their velocities is large and you do not know where they are an instant later. That is why the electron correlation problem can never be explicitly solved.

At two atoms approach each other, the motions of the electrons in each atom change. Some of the outer electrons, known as the valence electrons, will change their probability distributions so that they can travel between both atoms. Their probability distributions are now known as molecular orbitals. In contrast, the inner electrons in each atom, knwon as the core electrons, will basically stay within their respective atoms.

With this brief background, the differences betweenthe four sub-fields can now be described.

Quantum Chemistry: This level of theory attempts to determine the average distribution of all electrons within a molecule.

Semi-Empirical Quantum Chemistry: This level of theory ignors the core electrons in each atom of the molecule, creating an effective core potential, and only tries to determine the probability distribution of the valence electrons.

Empirical Energy Modeling: This level of theory ignors any explicit treatment of the electrons and uses simplified functions to represent the interactions of atoms within molecules.

Molecular Graphics: This sub-field represent programs which graphically displays the structure and properties of molecules.

Computational Chemistry Links

Computational Chemistry List - Software Related Sites

Molecular Modeling at UCSB

Computational Chemistry Links

U of Minnesota Computational Chemistry

CCL -- Computational Chemistry List, Ltd.

Description of SMILES Notation

Linux4Chemistry - Linux software for chemistry: molecular modeling, visualization, graphic, quantum mechanic, dynamic, kinetic, simulation

Molecular Monte Carlo

Global Instructional Chemistry