Introduction

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. Gaussion can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.

Traditionally, proteins and other large biological molecules have been out of the reach of electronic structure methods. However, Gaussian 03’s ONIOM method overcomes these limitations. ONIOM first appeared in Gaussian 98, and several significant innovations in Gaussian 03 make it applicable to much larger molecules.

This computational technique models large molecules by defining two or three layers within the structure that are treated at different levels of accuracy. Calibration studies have demonstrated that the resulting predictions are essentially equivalent to those that would be produced by the high accuracy method.

The ONIOM facility in Gaussian 03 provides substantial performance gains for geometry optimizations via a quadratic coupled algorithm and the use of micro-iterations. In addition, the program’s option to include electronic embedding within ONIOM calculations enables both the steric and electrostatic properties of the entire molecule to be taken into account when modeling processes in the high accuracy layer (e.g., an enzyme’s active site). These techniques yield molecular structures and properties results that are in very good agreement with experiment.

Spin-Spin Coupling
Determining Conformations via Spin-Spin Coupling Constants

Conformational analysis is a difficult problem when studying new compounds for which X-ray structures are not available. Magnetic shielding data in NMR spectra provides information about the connectivity between the various atoms within a molecule. Spin-spin coupling constants can aid in identifying specific conformations of molecules because they depend on the torsion angles with the molecular structure.

Gaussian 03 can predict spin-spin coupling constants in addition to the NMR shielding and chemical shifts available previously. Computing these constants for different conformations and then comparing predicted and observed spectra makes it possible to identify the specific conformations that were observed. In addition, the assignment of observed peaks to specific atoms is greatly facilitated.

Studying Periodic Systems

Gaussian 03 expands the range of chemical systems that it can model to periodic systems such as polymers and crystals via its periodic boundary conditions (PBC) methods. The PBC technique models these systems as repeating unit cells in order to determine the structure and bulk properties of the compound.

For example, Gaussian 03 can predict the equilibrium geometries and transition structures of polymers. It can also study polymer reactivity by predicting isomerization energies, reaction energetics, and so on, allowing the decomposition, degradation, and combustion of materials to be studied. Gaussian 03 can also model compounds’ band gaps.

Predicting Spectra

Gaussian 03 can compute a very wide range of spectra and spectroscopic properties.

These include:

For example, Gaussian 03 computes many of the tensors which contribute to hyperfine spectra. These results are useful for making spectral assignments for observed peaks, something which is usually difficult to determine solely from the experimental data (see the example below). Using theoretical predictions to aid in interpreting and fitting observed results should make non-linear molecules as amenable to study as linear ones.

Modeling Solvent Effects

Modeling Solvent Effects on Reactions and Molecular Properties.

Molecular properties and chemical reactions often vary considerably between the gas phase and in solution. For example, low lying conformations can have quite different energies in the gas phase and in solution (and in different solvents), conformation equilibria can differ, and reactions can take significantly different paths.

Gaussian 03 offers the Polarizable Continuum Model (PCM) for modeling system in solution. This approach represents the solvent as a polarizable continuum and places the solute in a cavity within the solvent.

System Requirements