The Molecular Orbital (MO) Editor
The MOs window. It is used to inspect molecular orbitals (MOs) from Gaussian calculations—MO energy and occupancy diagrams, visualized MO isovalue surfaces—as well as to quickly generate new MOs and/or visually select active-space MOs to be used for CASSCF calculations.
menu path and the button both open theThe MO Editor
This window is used for examining molecular
orbitals visually and potentially rearranging
their occupancies and/or ordering for a subsequent Gaussian
calculation. Here we are
viewing MO 20, one of 5 available surfaces (and 2 selected MOs).
The MOs dialog has its own embedded View window for displaying the molecule and surface corresponding to the currently selected MO (if available). This embedded view is read-only and cannot be used to edit the molecule. In viewing functionality, it functions almost identically to a standard View window in terms of including keyboard and mouse controls for translating, rotating, and zooming the molecule, accessing the context menu, and so on. (See the discussion of manipulating views earlier in this chapter and that concerning surfaces in “Viewing Gaussian Results” for details.)
The size of the Current Surface window can be changed by resizing the entire MOs dialog. Its width can also be adjusted by clicking and dragging on the partition between it and the MO diagram. This adjusts the relative widths of the two windows.
MOs can be selected for visualization, inclusion in future calculation, and other operations by left-clicking on them. Selected MOs are highlighted in yellow. If a surface is available for an MO, a small square appears to the right of the MO. The square is red for the MO whose surface is currently being viewed. Clicking on a different MO’s grey square will change the Current Surface area to show that MO’s surface.
The bottom portion of the window contains four panels:
The Visualize panel is visible in the figure above. The various fields in it specify which orbitals should be visualized, along with two surface generation parameters (the isodensity value and the grid density, via the and fields, respectively). The popup contains items which specify which MOs to visualize; its options are generally self-explanatory with the possible exception of (regenerates the orbitals listed in the field) and (specifies the arbitrary list of orbitals present in the editable field). Note that GaussView attempts to keep the and fields synchronized. Clicking the button will generate the requested orbital surfaces.
The figure below displays the other panels present in the MO Editor (stacked on top of one another), each of which will be discussed in the course of the remainder of this section.
The MO Editor’s New, Calculation, and Diagram Panels
Each panel shows a typical use for it (and not necessarily the default settings).
To the right of the Current Surface is the MO energy and occupancy diagram showing the MOs for the current molecule if available, initially arranged in order of increasing energy. Alpha and Beta electrons are represented by red up and down arrows in a blue box, respectively. Electrons can be moved from one MO to another by dragging them between the corresponding boxes. Electrons can also be added or removed from an MO by right-clicking in the MO box. Manipulating the MO occupancies in this way changes the net charge and/or spin multiplicity of the molecule as appropriate, reflected in the and fields. These fields can also be edited directly, and any changes will be reflected in the MO occupancies. Increasing the charge will remove electrons from the MOs, starting with the HOMO. Decreasing the charge will add electrons to the MOs, starting with the LUMO (or the HOMO if it is singly occupied). Similarly, increasing the spin multiplicity will move electrons from the highest doubly occupied MOs to the lowest virtual MOs, and decreasing the spin multiplicity will move electrons from the lowest-energy singly occupied MOs to the highest-energy singly occupied MOs. Finally, modifying the charge will also affect the spin multiplicity if the charge is changed by an odd number.
Controls in the Calculation panel also serve this purpose. The popup contains two choices:
The Diagram panel controls the orbital diagram. The popup allows you to order orbitals , , or ; the latter is appropriate for creating a CAS active space (see below). The sets the value below which to consider orbital energies as equal. This feature is illustrated below.
Degenerate Orbitals in the MO Editor
This MO display for NH3 illustrates
how degenerate orbitals appear in the orbital display area. Note that
we have
modified the from its default value of 0 to allow GaussView to
detect the degenerate MOs.
The New Gaussian MOs panel allows you to read-in or generate MO data, depending on the setting of the popup. When it is set to , you can read in orbital data from a checkpoint file by specifying its location and then clicking .
When Guess keyword in the Gaussian User’s Reference for more information on the various fields and choices. Clicking will launch a Gaussian job to generate the orbital data (calculation type is Guess=Only).
is set to , the and areas specify the calculation model for generating orbitals. The fields labeled specify the initial guess type, localization method, and wavefunction type, while the desired basis set is specified in the fields below these. The fields in the second line of this panel specify the basis set to use for the Gaussian calculation. Consult the discussion of theThe Permutation List control in the Calculation panel displays the current orbital reordering at any given moment; it is initially empty. The popup in this area offers three choices for orbital reordering:
The Diagram panel contains two additional controls: