Continuing the nearly 40-year tradition of the Gaussian series of electronic structure programs, Gaussian 16 offers new methods and capabilities which allow you to study ever larger molecular systems and additional areas of chemistry. GaussView 6 offers a rich set of building and visualization capabilities. We highlight some of the most important features on this page.

Explore New Substances and Environments: Green Fluorescent Protein

GFP is a protein that fluoresces bright green when exposed to light in the blue-to-ultraviolet range. The chromophore is shown in the inset below. The molecule was first isolated in the jellyfish species Aequorea victoria, which is native to the Pacific northwest coast of North America. Since then, it has been studied extensively, and variants of the molecule with enhanced fluorescence properties have been engineered.

GFP consists of a chromophore within a protein chain composed of 238 amino acids. The isolated chromophore is not fluorescent, so modeling it in its protein environment is essential. GFP’s fluorescence cycle involves an initial excitation to its first excited state, a proton transfer reaction on the S₁ potential energy surface, and finally a relaxation back to the ground state.

The following features of Gaussian 16 and GaussView 6 are useful for modeling fluorescence in this compound:

GaussView can directly open files from the Protein Data Bank (PDB files). It can add hydrogens to the retrieved structure when imported or at a later time. You can also view, manipulate and modify the structure using the PDB chain, residue type and/or number, and other PDB substructure information present in the original file. Residue and other information can be retained throughout molecule editing and job execution. The molecule can be modeled via MO:MM calculations using Gaussian’s ONIOM facility: GaussView makes it easy to define ONIOM layers based on many different criteria. For this molecule, assigning atoms by PDB residue is often the most straightforward. GaussView identifies molecular mechanics atoms types and partial charges automatically in most cases. It is also simple to locate atoms missing types and to specify/modify types and charges as desired. Gaussian incorporates standard MM parameters for Amber and other force fields and also allows you to define MM parameters as needed. Gaussian’s ONIOM electronic embedding feature includes all of the effects of the protein environment without neglecting terms in the MM coupling with the chromophore QM treatment. Explicit solvent molecules can be included in the calculation (e.g., water molecules above). GaussView can directly open files from the Protein Data Bank (PDB files). It can add hydrogens to the retrieved structure when imported or at a later time. You can also view, manipulate and modify the structure using the PDB chain, residue type and/or number, and other PDB substructure information present in the original file. Residue and other information can be retained throughout molecule editing and job execution.

• Gaussian can optimize the geometries of the minima and transition structures on the excited state PES with TD-DFT. GaussView includes features for setting up reliable QST2/QST3 transition structure optimizations with minimum effort.
• An IRC calculation in Gaussian can follow the corresponding S₁ PES reaction path, which can then be animated in GaussView.
• Gaussian can perform vibrational frequency analysis in order to predict the IR/Raman spectra and normal modes. A variety of other spectra are also available, including vibronic spectra. GaussView can display plots of the predicted spectra and animate the associated normal modes (as applicable).
• GaussView makes it easy to examine the results of one calculation and then set up and initiate the next calculation in sequence via an intuitive interface to all major Gaussian 16 features.

[Thompson14] and [Petrone16] are excellent studies of GFP using the previous version of Gaussian. See chapter 9 of [Foresman15] for a detailed tutorial about preparing PDB files for use with the ONIOM facility in Gaussian.