In this tutorial, we will demonstrate how to build molecules using GaussView 6.
We will introduce several building techniques, including, rapid building with GaussView fragments,
setting an angle between rings, using point group symmetry to simplify building, docking
two structures, and using alternative templates for tricky building tasks.
In our first example, we will build 2,4,6-trinitrotoluene, commonly known as TNT.
We open the ring fragments panel and select benzene.
Clicking in the view window makes a benzene ring appear.
We now select tetrahedral carbon from the Elements Fragment panel and bond it to the
benzene ring by clicking on one of the hydrogen atoms.
This now forms a toluene molecule.
Moving to the R-Groups Fragment palette, we select the nitro fragment and replace the
hydrogen atoms in these three locations to form the structure of TNT.
We use the clean button to regularize the structure.
However, the actual structure of TNT is planer, so we must adjust the Carbon-Carbon-Nitrogen-Oxygen
dihedral angle to be 180 degrees, thereby twisting the nitro group into the plane.
In this second example, we demonstrate setting an angle between two rings by building
2-phenylpyridine.
To begin, we open the Ring Fragments panel, select pyridine and place it in the view window.
Next, we select benzene from the Ring Fragments palette, and replace the hydrogen to the right
of the nitrogen atom.
Clicking the atom replaces hydrogen with a benzene ring.
We will now set the value of the inter-ring angle by specifying the dihedral angle.
We select Modify Dihedral and click on the appropriate Carbon-Carbon-Carbon-Nitrogen
dihedral.
The Semi-Chem Smartslide window opens when the desired atoms are selected.
Set Atom 1's drop down menu to "Fixed" and Atom 4's to “Rotate Groups.”
Doing this causes only one ring to rotate while the other one remains fixed.
We can modify the dihedral either by using the Slider Tool, or by entering a value in
the text box.
Here, we want the rings to be close to their natural value so we enter 30 degrees in the
text box and then click OK.
2-phenylpyridine is complete.
In this segment, we will now demonstrate how to rapidly build structures using the Point
Group Symmetry feature.
We begin with chromium hexacarbonyl.
We open the Element Fragments panel and place an octahedral chromium in the view window.
Next, we select “Point Group” from the Tools menu in order to open the Point Group
Symmetry dialog.
We click here to enable point group symmetry and see that the current point group is Octahedral.
We would like to constrain our molecule to this point group, so we select Octahedral
from the “Constrain to Subgroup” dropdown, applying the constraint to all changes made,
and we make sure to select “Always track point group symmetry.”
When tracking symmetry is enabled, the current symmetry is listed in the bottom right corner
of the view window.
We are now ready to continue building our molecule.
We select the carbonyl group from the R-Group Fragments palette.
We replace one of the hydrogen atoms with the group.
As you can see, with symmetry enabled, all of the hydrogen atoms in the molecule were
replaced with our selected fragment at the same time.
We confirm that our point group has not changed by looking in the bottom right corner of the
view window.
Finally, we clean our molecule and chromium hexacarbonyl is complete.
Now we are going to build a similar molecule, iron pentacarbonyl.
After creating a New Molecule group, open the Elements Fragment palette.
Then choose the trigonal bipyramidal iron fragment.
We will now open the Point Group Symmetry dialog, and enable Point Group Symmetry.
The molecule currently has D3h symmetry, which we constrain it to.
We close the dialog, and open the R-Group Fragment palette and select the carbonyl ligand.
We click on one of the hydrogen atoms.
Notice how only the symmetry-equivalent atoms are replaced.
When we click on one of the equatorial hydrogen atoms, all 3 remaining hydrogen atoms are
replaced with carbonyl ligands, and iron pentacarbonyl is complete.
In the next example, we will build 3,3'-Dichlorobiphenyl to illustrate a method for building a molecular
structure consisting of docked fragments.
We place a benzene ring in the View window using the Ring Fragments palette.
We select chlorine from the Elements Fragment palette and replace a hydrogen atom.
We want another molecule like this one, so we press the “A” key to select all of
the atoms in the view window.
We use the “CONTROL-C” key combination to copy all of the atoms.
Note that the copied molecule appears in the molecule preview window.
Now, we click inside the view window, and a second molecule appears.
The chlorine atoms in the rings need to be opposite one another.
Holding down the “ALT” key allows us to rotate one of the rings into position.
We use the “ALT-SHIFT” key combination to move one of the rings so that the carbon
atoms to be bonded are in the correct positions, and the hydrogen atoms overlap.
We delete the hydrogen atoms in the overlap region.
Then, we use the Modify Bond tool and select the two carbon atoms to be bonded.
Notice that when the SmartSlide dialog opens, we have the choice of setting multiple types
of bonds, as well as choosing the bond length using the slider below.
We choose the single bond option.
We clean the molecule, but we know 3,3’ dichlorobiphenyl is not planer, so we use
the Modify Dihedral tool to move one of the rings to roughly a 45 degree angle.
3,3’ dichlorobiphenyl is now complete.
In our final example, we will bring together all of the concepts introduced so far in this
video, by building the D2h and C2h isomers of Di-μ-oxo-bis(tetraamine manganese).
This is our completed molecule.
Before building, we’ll take a moment to examine the molecule and plan our building
process.
First, selecting the right template will make building easier at several points.
For example, we will start with a manganese atom having 6 bonds.
We will also use the tetrahedral carbon template when building what will ultimately be the
NH3 groups.
Second, since the molecule consists of two identical fragments, we will build it using
the fragment docking technique we demonstrated earlier.
Third, we will build the overall skeleton of the molecule using carbon atoms, specifying
nitrogens later in the process.
Finally, we will make extensive use the Point Group Symmetry feature to aid in creating
the proper symmetry in the molecular structure.
First, we select the Octahedral Manganese fragment from the element fragments dialog.
You can see that the molecule fragment has all the required bonds for our desired structure.
We rotate it to a position where we are looking down the Hydrogen-Manganese-Hydrogen bond,
and the remaining four hydrogen atoms form an “X” shape.
By clicking in the View window, another Octahedral Manganese fragment appears.
By holding down the “ALT” key, we maneuver the newly placed molecule towards our first
one, overlapping the hydrogen atoms.
We chose oxygen atom from the Element Fragments panel and replace the hydrogen atom here with
an oxygen atom.
We take care to now select the hydrogen atom bonded to the other manganese atom, seen here,
so that the two manganese atoms are bridged with the two oxygen atoms.
Next, we delete the extra hydrogen atoms using the “Delete Valances” tool.
Now we make single bonds between the oxygen atoms and the manganese atoms.
We are now ready to complete the skeleton.
We open the Point Group Symmetry dialog, and click the checkbox to enable symmetry features.
We want D2h symmetry for this structure, but when we check the “Constrain to Subgroup”
dropdown, we can see it is not present.
In this case, we must loosen the tolerance to locate a higher-order point group.
We choose “Do you feel lucky?” and notice that D2h has appeared.
We symmetrize the structure, and then constrain the molecule to D2h symmetry.
After enabling “Always track point group symmetry” we close the dialog.
Notice that the symmetry is listed in the bottom right of the View window.
As we rotate the molecule, we can see that it already resembles the final molecular structure
we are looking to achieve.
Returning to the Element Fragment panel, we chose tetrahedral carbon, and click on one
of the valence hydrogens that project off the y-axis of the manganese atom.
We can see that all four hydrogens have been replaced by methyl groups.
We check to ensure that D2h symmetry is still maintained.
We now click on one of the remaining hydrogen atoms bonded to the manganese atom.
Again, all four atoms are replaced by the methyl groups.
After this last operation, symmetry was lowered, the molecule is now C2.
Again, we symmetrize using the higher-order point groups section and then constrain to
D2h.
After repositioning the molecule, we select a nitrogen atom from the Element Fragments
panel, and replace the carbon in one of the CH3 groups.
Notice how all four equivalent atoms change, and we maintain D2h symmetry.
We click on one of the remaining carbon atoms, and again all four change into Nitrogen atoms.
The D2h isomer of this compound is complete.
We will now build the C2h isomer starting from our D2h isomer.
To begin, we open the Point Group Symmetry dialog, and reduce the symmetry down to C2.
We select C2 and not C2h because we need to rotate the hydrogen atoms through the planes
of symmetry that C2h enforces.
We will impose this higher symmetry point group afterwards.
We constrain the subgroup to C2, and close the dialog.
We need to modify the Nitrogen-Hydrogen bond in two of the equatorial NH3 groups into a
“chasing the tail” configuration.
We choose the Modify Dihedral tool and select the Nitrogen-manganese-Nitrogen-Hydrogen dihedral
shown here.
It is currently around negative 150 degrees.
Since we want to rotate the nitrogen-hydrogen bond, we also make sure that Atom 1 remains
fixed, and that the Atom 4 group rotates.
We move the slider up to 30 degrees.
Finally, we return to the Point Group dialog, and symmetrize with C2h symmetry.
In this case, we actually need to tighten the criteria in order for C2h symmetry to
be applicable.
As we rotate the molecule, you can see that each Nitrogen-Hydrogen is pointing towards
the next nitrogen group, completing the C2h isomer of Di-μ-oxo-bis(tetraamine manganese).
In our next video, we will demonstrate using GaussView to set up and run Gaussian jobs
with molecules we’ve built.