How To: Build Molecules

 

Basic Molecule Building Tutorials

Placing Elements and Fragments

The GaussView molecule building tools always operate on the active View window. In general, GaussView begins and remains in its insert/replace mode, unless one of the options described below explicitly calls for it to act in a different manner. Clicking in an open area of the View window adds the current atom or fragment to the window as a distinct fragment. Clicking on an existing atom adds the current item to the existing structure at the indicated point, usually replacing it (other options are discussed later).

The desired atom or fragment is chosen using one of the Element, Functional Groups, Rings and Biological Fragments buttons and then selecting one of the choices from the resulting palette. The current item always appears in the Current Fragment area of the GaussView control window and/or the Active Fragment area of the standalone Builder palette. Clicking on either the Active Fragment area on the standalone Builder palette or on the fragment name above the main window’s Current Fragment area opens the palette corresponding to the selected fragment type.

Note that the standalone Builder palette is opened with the View=>Builder menu item and can be made to always stay on top of all other open windows by checking the Builder Dialog Stays on Top checkbox in the Window Behavior Preferences (accessed with the File=>Preferences menu path).

The Element Fragments Palette

The Element Fragments palette allows you to select an element from the periodic table. The various possible coordination patterns for the selected element are shown at the bottom of the window below. The default element type is tetrahedral carbon.

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The Element Fragments Palette

The available hybridization (connectivity) variations for the selected element appear along the bottom of the palette. In this case, the current atom type is pentavalent sulfur.

The R-Group Fragments Palette

The R-Group Fragments window allows you to select from a series of AM1-optimized functional group fragments. The default group is carbonyl (formaldehyde).

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The R-Group Fragments Palette

Use this palette to select the desired functional group.

Note that several of the fragments use non-traditional bonding. These fragments include a five-member ring with an open bond perpendicular to the plane of the ring: a n5-cyclopentadienyl ligand for use in constructing organometallic systems.

The Rings Palette

The Ring Fragments window allows you to select from a series of AM1-optimized ring structures. The default ring is benzene.

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The Ring Fragments Palette

Use this palette to select the desired ring system.

The Biological Fragments Palette

The Biological Fragments palette presents a set of AM1-preoptimized fragments useful to biological researchers: the amino acids and various DNA bases. The default biological fragment is Alanine Central Residue.

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Selecting Biological Fragments

Use the various fields in this window to select amino acids and DNA bases.

The Type field allows you to select either Amino Acid or Nucleoside. When Amino Acid is selected, the left popup menu below the Type field can be used to select the desired amino acid, and the right popup menu in that line allows you to specify the structural form as Central Fragment, Amino-Terminal Fragment or Carboxyl-Terminal Fragment (the last two are the N-terminated and C-terminated forms, respectively).

When the Type field is set to Nucleoside, the left popup menu below the Type field can be used to select the desired DNA base (nucleic acid fragment), and the right popup menu in that line allows you to specify the structural form as Central Fragment, C3’-Terminal Fragment, C5’-Terminal Fragment or Free Nucleoside.

Making Palettes Sticky

The various palettes in GaussView can be used in a modal (dialog box behavior) or amodal (floating palette behavior) manner. The thumbtack icon in the upper left corner of the window shows whether the palette will close when another one is selected (or a non-building context is entered). The green pushed-in tack indicates that the palette is “tacked” to the desktop (i.e., “sticky”): i_tacked.tif ; the red upward pointing tack similarly indicates modal operation: i_notack.tif .

Modifying Bonds and Angles

Read more about Modifying Bonds and Modifying Angles.

Undo and Redo

The Edit=>Undo and Edit=>Redo menu paths may be used to reverse or reinstate a previous molecule modification or other action. The Undo button and the Redo button may be used for the same purposes.

Viewing and Adjusting Structure Parameters

The Builder toolbar/window includes the following buttons for viewing and modifying the structural parameters of molecules: Bond, Angle, Dihedral, Inquire, Add Valence, Delete Atom, and Invert About Atom. In addition, other buttons and their corresponding menu items also affect molecular structure—including Clean, Rebond, and Symmetrize—and display.

Inquire Mode

The Inquire button allows you to request geometric information directly from the View window when you click on the atoms of interest. Note that the selected atoms do not need to be bonded. The structural information appears in the View window’s status bar, as in Figure 14. The number of atoms that you select affects the resulting display on the View window:

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Inquire Mode Display

This display shows the value of the selected bond angle in the window’s lower left corner.

Adding and Deleting Valences

The Add Valence button attaches additional valences (shown as hydrogen atoms) to the center clicked with the mouse. The new valences will be placed as far as possible from the other atoms attached to the center.

Similarly, the Delete Atom button removes atoms and open valences. When used, the function will eliminate the selected atom and all single valences (hydrogens) attached to it. It may also be used to remove a dangling bond by clicking on the bond stick.

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Deleting a Dangling Bond (Open Valence)

The Delete Atom button may be used to remove atoms and dangling bonds. An example of the latter is shown at the top of the molecule. Clicking on it will remove the open valence.

Invert About Atom (Mirror Invert)

The Invert About Atom button allows you to reverse the symmetry of a molecule with respect to a selected atom.

invert.tif

Inverting a Structure About an Atom

Clicking on the nitrogen atom with the Invert About Atom tool will result in the structure on the right.

Cleaning Structures

The Clean button and Edit=>Clean menu items both adjust the geometry of the molecule, based on a defined set of rules, to more closely match chemical intuition. The results are only approximations and are not intended to be perfect. Geometries may require adjustment for non-classical cases such as transition states.

The GaussView clean function may be customized via the Clean Controls Preferences panel.

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Customizing the Clean Function

You can use this preference panel to modify and customize how the GaussView clean function operates.

The default clean settings attempt to achieve a balance that produces expected “normal” results. Altering the settings in Clean Controls Preferences can cause unexpected and undesirable results, so please read the following sections carefully before making any changes.

The following controls are available in the dialog. The fields in the Rel. Weights column are:

The checkboxes at the bottom of the window have the following effects:

The fields in the Opt. Controls column are:

It is important to remember that the various components of the clean force field are relative. Changing one weight will affect the behavior of the other weights. For example, an excessive non-bond weight will produce longer bonds. Similarly, an excessive hard angle weight could affect the 2-center dihedrals.

You can disable any set of terms by assigning a weight of 0.0. For example, disabling the 1-center dihedral term can result in faster cleaning, but the resulting tertiary structure may not be as nice. Do not disable the bond weight or hard angle terms. The former should be kept high relative to the other terms.

Clean Performance Tips

If the clean function is too slow on your system, try these settings:

Poor performance of the clean function can also be a symptom of a memory shortage on the system.

Rebonding Structures

The Rebond button and Edit=>Rebond menu path both initiate a rebonding process in which GaussView reidentifies bonded atoms, based on a distance algorithm. Note that Gaussian usually does not use the bond information on the screen for calculations. This information is presented primarily to make it convenient for you to visualize the chemistry of the molecule.

Imposing Symmetry

The Point Group Symmetry dialog is used to specify the desired symmetry for a molecular structure. It is reached via the Tools=>Point Group menu path. The controls have the following meanings:

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Imposing Symmetry on a Molecular Structure

In this example, GaussView has identified the current point group of this distorted benzene molecule as C1. It also recognizes that the C2v point group might also be appropriate. Clicking the Symmetrize button will apply the specified point group to the structure. The Tolerance field can be used to tighten or relax the symmetry identification process. In this case, loosening the tolerance allows GaussView to identify the highest applicable point group as D6h.

The Symmetrize button (on the toolbar) and the Edit=>Symmetrize menu item both immediately impose the maximum identifiable point group on the current structure, using the most recent Tolerance setting from the Point Group Symmetry dialog for this molecule (or the default of Normal). They also have the side effect of enabling point group symmetry for the molecule (again, using the previous settings, if any).

The View window status bar will indicate any identified and constrained symmetry for the molecule.

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Symmetry-Related Status Bar Displays

Four views of the symmetry information section of the status bar for the triazine molecule: (a) symmetry has not been turned on; (b) molecule symmetry (D3h) but no symmetry constraint (C1); (c) molecule symmetry (D3h) and structure constrained to D3 symmetry; and (d) molecule symmetry and constraint symmetry are both D3h.

Pasting Molecules into the View Window

The Edit=>Cut and Edit=>Copy menu items and the corresponding Cut and Copy buttons can be used to cut or copy the entire structure in the current model to the system clipboard. Note that any atom selection within the model is ignored.

The Edit=>Delete menu item and the Delete Molecule button can be used to remove the structure in the current model, discarding it without copying it anywhere.

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There are several options for pasting molecules from the clipboard. The Edit=>Paste menu item accesses a slideoff menu containing three items. These items can also be reached via the small downward-pointing triangle on the Paste button. Clicking on the Paste icon itself (avoiding the triangle’s panel) selects the Replace Molecule item.

The items on the Paste submenu are:

Placing a Fragment in a Centroid Position

The Place Fragment at Centroid of Selected Atoms item on the Builder context menu (reached by right clicking in an open area of a View window) will place the current element, R-group, ring, or biological fragment at the centroid position defined by the currently selected atoms. For example, to place an atom inside a C60 cage, select all of the atoms in the molecule, select the desired atom from the Element Fragments palette (specifying the bare atom type), right click in an open area of the view, and select Builder=>Place Fragment at Centroid of Selected Atoms. This process is illustrated below:

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Placing a Centroid Atom in C60

Note that if you simply want to define the centroid location without immediately placing any atoms there, you can use the dummy atom (element type X) to do so.