Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files.
Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run.
Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths.

GaussView supports all Gaussian 03 features, and it includes graphical facilities for generating keywords and options, molecule specifications and other input sections for even the most advanced calculation types. GaussView makes it simple to set up ONIOM layers, unit cells for Periodic Boundary Conditions jobs, CASSCF active spaces, molecule specifications for transition structure optimizations using the STQN method, and so on. We’ll look at many of them in the following pages.

Here, we are preparing an ONIOM calculation on a HIV protease fragment with an inhibitor. We need to assign atoms to ONIOM layers and then specify Gaussian keywords and options.
Setting up the input file for an ONIOM job is very simple in GaussView. You simply click the ONIOM check box and then specify the method and basis set for each layer using the corresponding tab on the Method panel. The job type and other options are set using the various tabs in this dialog.
Atoms are assigned to layers using the Layer Selection Tool (and layers defined in existing job files are recognized and preserved). We have already placed the inhibitor in the High layer. These atoms are displayed in ball and stick mode, and ones in the Low layer appear as tubes.
Currently, the atoms in residue number 50 in both chains are selected (highlighted). We selected then in a single step using the Select PDB Group dialog (reached by clicking the Layer Selection Tool’s Select PDB Group button). Once selected, atoms can be assigned to the desired layer using the controls in the Layer Selection Tool dialog

Building Molecules

GaussView includes an advanced Molecule Builder. You can use it to rapidly sketch in molecules and examine them in three dimensions. You can build molecules by atom, ring, group, amino acid and nucleoside, and you can also open PDB and other standard molecule files (hydrogen atoms can be added automatically with excellent accuracy and reliability).

Here, we are building spiroselenurane. This window shows the completed molecule.
We have already placed an iso-indene ring into the Builder window and changed the appropriate atoms from carbon to oxygen and selenium. We are about to add a second iso-indene ring to the structure at the selenium atom. When we click on it, the second ring will appear, and the selenium atom will become part of both rings. Afterwards, we will adjust the angle of the two rings and then add the methyl groups.
The current fragment appears in the Builder’s display area. We have selected the connection point as the selenium atom by moving the hot spot in the iso-indene ring.
Although we are adding a ring to our structure, we can also display other Builder palettes as desired.

Setting Up Gaussian 03 Calculations

GaussView’s Gaussian Calculation Setup window allows you to set up Gaussian 03 jobs in a simple and straightforward manner. All of the features of Gaussian 03 are supported by the interface, enabling you to prepare input for any job type.

The Gaussian Calculation Setup window’s Method panel allows you to select the theoretical method, basis set, and charge and spin multiplicity. Other panels allow you to specify the type of calculation (Job Type), Title section (Title), job resource locations and settings (Link 0). Each panel presents context sensitive options appropriate to the selected calculation type.
Specifying input options for PCM calculations is quite simple. In this panel, we specify the desired Self-Consistent Reaction Field method (IEFPCM in this case), and select the solvent from a pop-up menu.
Once all panels are ready, you can use the Submit button to start the job immediately or the Edit button to examine the generated input file in a text editor

Visualizing Gaussian Results

GaussView can graphically display a variety of Gaussian calculation results, including the following:

Molecular orbitals
Atomic charges
Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties. Surfaces may be displayed in solid, translucent and wire mesh modes.
Surfaces can be colored by a separate property.
Animation of the normal modes corresponding to vibrational frequencies.
Animation of the steps in geometry optimizations, potential energy surface scans, intrinsic reaction coordinate (IRC) paths, and molecular dynamics trajectories from BOMD and ADMP calculations.

Displaying Surfaces


The NMR shielding densities for the methine proton (surface 1) and the phenyl proton (surface 2) in in-[3(4,10)][7]metacyclophane, plotted on an isosurface of current density magnitude. Shielding density increases from red (deshielding) to blue (shielding). The molecule itself is displayed to the right. See R. A. Pascal Jr., C. G. Winans and D. Van Engen, J. Am. Chem. Soc., 111, 3007 (1989).
The electrostatic potential painted charge density surface for 21-thiaporphyrin, a potential anti-cancer photochemotherapy agent. See E. P. Zovinka and D. R. Sunseri, J. Chem. Ed., 79, 1331 (2002). Using a translucent surface makes it easier to correlate structure and properties.

Viewing Spectra

GaussView can display a variety of computed spectra, including IR, Raman, NMR and VCD. Here we see the VCD spectra for two conformations of spiropentyl acetate, a chiral derivative of spiropentane. See F. J. Devlin, P. J. Stephens, C. Österle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).

Visualizing and Manipulating Molecular Orbitals

	GaussView 3.0 can display multiple views of the same molecular structure simultaneously. Here we examine 6 molecular orbitals in separate windows (orbitals 65-69, starting at the upper left and moving across and then down).

The MO Editor (right) allows you to reorder orbitals. We are using this dialog to select orbitals for a CASSCF calculation. Clicking on an orbital highlights it and makes it part of the active space. Electrons may also be moved between orbitals by dragging them. For example, we have moved an electron from the HOMO (orbital 66) to the (new) LUMO (orbital 68). GaussView automatically adjusts the spin multiplicity as necessary. The Gaussian Calculation Setup window can receive information from the MO Editor and add the corresponding keywords and input to the Gaussian job file.

Animating Optimizations and Reaction Paths

GaussView 3.0 introduces several new animation capabilities in addition to displaying molecular vibrations corresponding to normal modes present in earlier versions. These new animation sequences can be viewed with GaussView, and the individual frames can be saved for import into animation/movie editing software.

Steps from a geometry optimization of benzene. We began with a distorted, nonplanar, nonsymmetric structure which optimized quickly to the actual geometry. The entire optimization sequence can be animated in GaussView when the calculation is complete.

This sequence displays a series structures from an Intrinsic Reaction Path (IRC) calculation of the 1,2 hydrogen shift reaction in which formaldehyde transforms into trans hydroxycarbene. This job type begins at a transition structure and follows the potential energy surface path down to the reactants and products. In this case, the first (leftmost) frame shows a structure that is close to formaldehyde, structures very similar to the transition structure appear in frames 4 and 5, and a structure tending toward the product appears in the final frame. Animating the reaction path from an IRC calculation makes it easy to identify the specific reactants and products that are connected by a given transition state structure.

Setting Up Jobs for Periodic Systems

Gaussian 03 can perform Periodic Boundary Conditions (PBC) calculations in order to model periodic systems in condensed phases such as polymers, surfaces and crystals. GaussView 3.0 provides a rich PBC facility for creating the molecule specifications for such calculations, and the program takes care of creating the appropriate Gaussian 03 input from your graphically defined unit cell.

Here we are building a face-centered cubic unit cell for diamond crystal. We begin by specifying the current (empty) model as a three-dimensional periodic system in the PBC Editor’s Symmetry panel. We also choose to constrain the structure to the appropriate space group for diamond, selecting the latter from the pop-up menu. The bounding box then appears in the model window (lower left corner of the dialog).

Since diamond crystal is so highly symmetric, building its unit cell is very simple. We simply place a carbon atom at the origin, and the other atoms required by symmetry are added auto-matically (see the window at the far right)

All of the atoms in the unit cell now appear in the table. Our next step is to add bonds between the atoms in the cell and to atoms in adjacent cells (see the window at the left).

Once our unit cell is complete, we can choose to view multiple replicas of it. Here, we display 3 cells in each direction. The reference cell’s boundaries are visible at the lower left.

It is equally easy and convenient to set up unit cells for one and two dimensional periodic systems. The window at the left shows a unit cell for a trans polyacetylene polymer, and the first window on the right displays the simplest one for a graphite surface. The window at the far right illustrates a larger unit cell created by combining nine of the smaller cells (three replicas in each direction).

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