In this video, we will demonstrate the basic building and molecule manipulation tools in
GaussView. Our topics include: Building with Fragments
Modifying bond lengths, bond angles, and dihedrals angles
Understanding Bonds and Inverting Molecules
GaussView includes 4 palettes containing a variety of pre-built fragments for building
molecules. We will demonstrate some of them by building
acetylsalicylic acid, the active ingredient in aspirin.
The Ring Fragments palette contains a group of commonly-used rings. Here we add benzene
to the view window. Similar to the Ring fragments, the R-Group
Fragments palette provides a group of common fragments for building. First, we will pin
the palette open. In this mode, the palette stays open after you select an item, rather
than automatically closing. When the pin icon is engaged, it turns from red to green and
its orientation changes. We select the carboxyl fragment and then click
on the hydrogen atom at the top of the ring. We then clean the structure, causing the new
group to rotate into the plane of the ring.
We continue with the carboxyl fragment. Before we add it to the molecule, we change the hot
atom, which is indicated by the blue highlighting in the current fragment area. The indicated
atom will be incorporated at the location where you click within the molecule.
By default, the hot atom for this group is the carbon atom. We change it to the singly-bonded
oxygen atom, and then click on the hydrogen atom adjacent to the carbon bonded to the
carboxyl group. The Element Fragment panel provides access
to individual elements from the periodic table. We select carbon, and then choose its tetrahedral
hybridization from the list at the bottom of the palette. When we click the hydrogen
atom in the group we just added, it is replaced by a methyl group.
Our molecule is now complete.
In our next example, we will be modifying a glycine molecule to conform to an optimized
structure from the literature.
This is our starting structure. We begin by selecting the Modify Angle button and modifying
the C-C-H angle to 124 degrees.
We next select the C-C-N angle. When the SmartSlide dialog appears, we change the Atom 1 dropdown
to Fixed. As we drag the slider, notice how the Nitro group moves. When we change Atom
3 to Rotate atom, only the Nitrogen will move. However, we want to rotate the group, so we
revert the Atom 3 dropdown to Rotate Group. We set the value to 119 degrees.
The Modify Dihedral tool is used in a similar way to modify dihedral angles. We will modify
the Hydrogen atom bonded to the Oxygen to change its orientation. We select the Modify
Dihedral tool, change the Atom 1 dropdown to Fixed, and set the value to 180 degrees.
We use the Modify Dihedral tool again in order to convert this dioxygen difluoride
trans conformer into a cis form. We click on the F-O-O-F dihedral angle. When the Smartslide
appears, we drag the slider to approximately 0 degrees.
In our next example, we illustrate the available bond types as we build a starting structure
for a transition state optimization for an SN2 reaction.
The Modify Bond Tool facilitates the shifting of bond lengths and other properties. When
the tool is active, selecting two atoms opens the bond SmartSlide dialog.
There are several different bond types to choose from:
not bonded, single, double and triple bonds,
resonance bonds, and half bonds.
Half bonds are used to indicate weak interactions such as hydrogen bonding.
In order to build the transition structure, we first lengthen this C-O bond, and then
change its type to weak bond. We create another weak bond between the Chlorine
atom and the ethyl group. We then close the dialog, and clean the structure.
We’ll now take a moment to discuss several bonding concepts and how they relate to Gaussian
calculations and GaussView operations. Bonds are a useful, intuitive chemical concept,
but they are ultimately subjective. They are not physically observable.
Bonds are defined from a molecule’s structural data, most commonly using the distances between
atomic nuclei. GaussView and similar programs provide bond
representations as a visualization aid. GaussView determines bonding from connectivity information
in the input file, if it is present. For Gaussian input files, connectivity information is present
when the Geom=Connectivity keyword is included. Note that Gaussian .Log files do not include
any connectivity data. When no connectivity information is present
in the file, GaussView will infer bonding from atomic distance data. It uses a table
of atomic pair distances to identify bonded atoms and bond types. This data is also used
by the Clean function. It can be customized in the GaussView Preferences, but this feature
is appropriate only for expert users. In some unusual structures, expected bonds
will not be present. In these cases, you must use atomic distances and your chemical intuition
to determine if the expected bond interactions exist.
GaussView uses provided bond type data in three main areas:
First, the Clean function uses the specified bond types to set bond lengths.
Second, the Bond SmartSlide lets you specify bond types and bond lengths. However, changing
the bond type does not change the bond length unless you use the Clean function. Likewise,
changing the bond length will not change the bond type unless you use the Rebond function.
Third, the default in the Gaussian Calculation Setup is to include connectivity information
in all Gaussian 16 input files. Finally, we consider how Gaussian uses connectivity
information provided in the input file. It is important to note that ab initio methods
do not consider bond types at all.
However, connectivity information is used in building internal coordinates, which can
be helpful for geometry optimizations. For this reason, the best practice is to include
the connectivity information in .GJF files.
Finally, be aware that geometry optimizations do not update input connectivity as the nuclei
move, so changes in bonding may not be displayed.
The Invert About Atom tool allows us to invert the molecular structure about a selected atom.
This is the molecule we will use: aeroplysinin-1. Using the View->Stereochemistry menu path,
we see that stereochemistry is displayed over the 2 chiral center atoms, indicating that
this is the (R,R) diastereomer.
Using the Invert about Atom tool, we click on a chiral center, changing its character
from R to S, and then back again. The Edit=>Mirror Invert menu item will invert
the entire molecule, in this case changing it into the (S,S) form.