Computational Chemistry Tutorial: G09 Job Execution and Visualization with GaussView 6.0

Running G09 Job

• To run a G09 job, click the RUN button in the Job Entry window, and the output file will have a .out extension.
• The output file must be saved before closing the G09 program.

Visualization of G09 Output

• GaussView 6.0 is used to visualize the G09 output.
• The .out file can be opened in GaussView 6.0, displaying the input molecule on the view screen.

Computational Methods in Chemistry

• Computational chemistry employs mathematical models like Finite Element Method (FEM) and Simplex method.
• These methods use matrices to divide N-dimensional space into smaller sub-systems, each describable by N linear equations.
• Solutions are obtained iteratively, starting with an initial guess and recursively solving equations until convergence.
• Convergence is reached when subsequent iterations yield the same result as the previous one.

Basis Set and Theoretical Model

• The basis set selection affects the quality of initial guesses.
• The theoretical model influences matrix calculations.
• Approximation methods are developed for multiple-electron systems, requiring researchers to understand their validity and accuracy.

Schrödinger Equation

• The Schrödinger equation is an eigen equation involving the Hamiltonian operator (Ĥ), wave function (Ψ), and energy (E).
• The equation forms the basis for computational methods in chemistry.

Quantum Mechanics

• The wave function (Ψ) describes electron behavior as a wave, offering a probabilistic description of electron positions.
• Physically relevant solutions of the Schrödinger equation require the wave function to be continuous, single-valued, normalizable, and antisymmetric with respect to electron interchange.

Input for G09

• The input for G09 can have extensions: .gjf, .bcf, .com, or .txt.
• The input can be done manually or come from another software, such as ChemDraw (3D), Avogadro, or GaussView.
• G09's input consists of several parts, shown in Figure 1.

Computational Chemistry and Quantum Mechanics

• Computational chemistry relies on approximations due to the complexity of solving quantum mechanical equations.
• Accurate results demand powerful computers, and analytical solutions could streamline computations.
• While some aspects, like the hydrogen atom's behavior, are known precisely, approximations are often necessary.

Uses of Computational Chemistry

• Computational chemistry models molecular systems before laboratory synthesis.
• These models can eliminate unsuitable compounds, saving time, labor, and reducing waste.
• Computational methods provide insights into molecular properties and bonding that may be challenging to obtain experimentally.
• Experimental chemists increasingly utilize computational modeling to deepen understanding of compounds.