GMU Introduction to ArgusLab Questions

Here is a Youtube video that will help in general when answering the questions for Argus lab  

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Introduction to ArgusLab
Part I- Properties of Ethane
To introduce you to the ArgusLab molecular modeling program, you will first build
an ethane molecule, optimize its geometry to determine the low energy
conformation, and then obtain some bond distance and bond angle data for it.
Steps for Using ArgusLab
1. Start ArgusLab.
The screen should be gray with the Building menus in a box at the left hand side of
the ArgusLab window at the top.
Build Menu
If you don’t see the Build Menu, click on the Builder Tool Kit.
2. Open a new molecule window Selecting File→New. The screen should turn
black.
3. Select Atom “C” and Geometry “tetrahedral” from the Building Menu. Make sure
Auto Bonds is set to “On” This is controlled by the
toolbar
button. When it is toggled on, bonds will automatically be drawn between atoms
as you add them to the scene. Right-click the mouse button in the graphics part
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of the molecule window and lay down two Carbon sp3 atoms. A bond will
automatically be made as you add the atoms.
4. Add hydrogens by clicking the
button on the toolbar.
5. Save the molecule. When the File Save dialog comes up, make a new folder and name
it ethane. Double-click the new folder while still in the File Save dialog to open it up
and save the molecule, naming it ethane as well. Accept the default ArgusLab agl file
type.
6. Clean the geometry by clicking the clean
button on the toolbar. You should see
the structure of the molecule changing as its geometry is cleaned.
7. Clean the hybridization by using “Ctrl+B” or selecting “Clean Hybridization” from
the Edit menu. This will check all bond and atom types and set the proper ones; it will
be more critical for aromatic or unsaturated compounds.
8. Click on the
button on the toolbar to put the right mouse button into Select Mode.
Right clicking on the atoms and bonds make sure that the information is correct. (Click
on atom information.) You can also change the atom and bond type at this point.
9. Practice translating, rotating, zooming the molecule using the left mouse button and
the
,
,
,
buttons or the corresponding keyboard shortcuts using the
Shift, Alt and Ctrl keys. More information is provided in the Help Menu and
Tutorials Option.
10. You can modify the length and the torsion angle of a bond by selecting it (yellow
surrounded by a magenta ribbon), using the combination of Ctrl-Alt or Shift-Alt and
the left mouse button.
Optimize the Geometry and/or Minimize the Energy
Important: Before any optimization and calculation make sure that the structure is
correct, the atom and bond types are correct.
11. Optimize the geometry with the PM3 semi-empirical QM method. Click the
optimize geometry button
Geometry dialog box.
on the toolbar. This will bring up the Optimize
12. Click the PM3 radio button in the Hamiltonian group box in the upper left of the
dialog.
13. Click OK. Then click the calculation button
on the toolbar. A PM3 calculation
will run and you should see the geometry of the molecule change as the progress of
the calculation is displayed in the lower-half of the molecule window.
14. Click the save file button
on the toolbar to save this final structure.
15. For basic energy calculations for simple molecules click on the
icon (Single Point
Energy Calculation) and Select UFF (Unified Force Field). This is a Molecular
Mechanics (non-Quantum Mechanical) calculation. Click OK. Then click the
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calculation button
on the toolbar. To see the results click on the
icon,
opening a text file. The energy of the corresponding conformation of the molecule is
usually at the end of the report. The absolute value of the energy is not important.
More important is the energy change corresponding to different conformations and
the change should correlate with the published values. Do not forget to close the results
window after inspecting it.
16. Measuring distances and angles. Select two, three or four atoms using the
left mouse button and the Ctrl Key and from the Monitor menu, select
Distance, Angle, Torsion or click on the corresponding icons
icons. If you make a mistake or want to change something use Edit, Undo.
The sequence of selection of the three atoms defining the correct angle is critical.
To measure a dihedral angle (the angle formed by two intersecting planes, one
containing the first three atoms of the four which are selected, and the second
containing the last three atoms), click sequentially on four atoms in a row on
your structure. For example, click on a H atom, the C atom to which it is bonded,
the second C atom in ethane and a H atom bonded to it. The H-C-C- H dihedral
angle will be displayed on the structure.
Part I Results (10)
Properties of ethane
Optimized Geometry (PM3), Energy (UFF) (kJ/mol)
Distances (Å)
C–C bond distance
C–H bond distance
ANY H–H non-bonded distance
Angles (°)
C–C–H
H–C–H
Three dihedral angles (°)
H–C–C–H
H–C–C–H
H–C–C–H
Omit #17
17. Export, Copy/Paste. To transfer an image on the screen to a Word document
Select File, Export and save the image as a .btm file. Open it in Paint and Select
it at your convenience. If you want to change the color of the background
Select, Settings, Color, Pick Color.
18. Close the file. Select File→Close.
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Part II- Conformational Analysis
Complete the following exercises. Record the results of your analyses in Tables 1–
3 and answer the questions that follow.
Conformations of ethane and 1,2-dichloroethane
1. Build ethane, clean the geometry and verify the H-C-C-H dihedral angle. Since
there are 3 H atoms on each C, there can be 9 dihedral angles. Starting from the
same H atom on one C, you should see dihedral angles of 60°, 120° or -60°, and
180° for the staggered conformation.
2. Calculate and record the energy using UFF.
3. Change and set the dihedral angle to zero for the eclipsed conformation. Rightclick in the Selection mode on the displayed angle and in the Specify Torsion
Angle window enter 0, click Apply and OK. Do not Optimize the Geometry
anymore, but Calculate and record the energy again using UFF.
Note: We are not concerned with the actual value of the energy. Rather, we
will be comparing the energy difference between the staggered and eclipsed
conformations of ethane. The difference between energies is what should be
compared to textbook value. Record the energy of the staggered and eclipsed
conformation in Table I. Convert kilocalories to kilojoules when necessary (1
kcal = 4.184kJ)(Multiply the value in Kcal that the Argus program reports by
4.184 kJ/kcal.)
Table 1 (10)
Ethane
Staggered
Eclipsed
Dihedral
angle (°)
Newman
projection
Energy
(kJ/mol)
Energy
difference
4. Build 1,2 dichloroethane. You can begin this by building ethane, cleaning the
geometry, and cleaning the hybridization of ethane as in steps 2-7 of part I.
5. Click on the
button on the toolbar to put the right mouse button into Select
Mode. Right clicking on the atoms and bonds make sure that the information is
correct. Change a H atom on each C to Cl.
6. You will build, calculate the energy, and constrain the dihedral angle, then
analyze the four conformations of 1,2-dichloroethane obtained by rotation about
the C-C bond (180o, 120o, 60o, 0o). Use this information to complete Table 2. .
7. To constrain the dihedral angle: Select four contiguous atoms in order using the
left mouse button and the Ctrl Key. From the Monitor menu, select Torsion or
click on the corresponding icon
. In the select mode
, click on the
dihedral angle displayed with the right mouse button. Choose “set value” then
type 180 for the staggered conformation. Save it as 1,2 dichloroethanestaggered. Clean the geometry and hybridization and Optimize the geometry
with PM3. Determine the energy of the molecule
with UFF. Do this for each
subsequent conformation: Constrain the dihedral angle, save the conformation
and determine the energy for each of the three conformations with dihedral
angles of 120° for the Cl eclipsing H conformation, 60° for the gauche
conformation, and 0° for the Cl eclipsing Cl conformation
Table 2 (8)
Dichloroethane Dihedral Newman
angle (°) Projection
Staggered-anti
180
Eclipsed
Conformation I
Cl – H eclipsing
120
Staggeredgauche
60
Eclipsed
0
Conformation II
Cl – Cl eclipsing
Energy
(kJ/mol)
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Conformations of 1,2-dichlorocyclohexanes
8. To build the following dichlorocyclohexane molecules, start by using the Rings option
in the Build menu, then add chloro groups in the appropriate locations. Use the
“change atom” function.
trans-1,2-diaxial-dichlorocyclohexane
trans-1,2-diequatorial-dichlorocyclohexane
cis-1,2-dichlorocyclohexane (1 methyl is axial and 1 is equatorial)
a. For each molecule, first build and clean the geometry
record the energy. UFF gives good results in this case.
. Then calculate and
b. Record the energies in Table 3.
Table 3 (15)
Molecule
trans-1,2-diaxialdichlorocyclohexane
trans-1,2-diequatorialdichlorocyclohexane
cis-1,2dichlorocyclohexane
Drawing
(chair forms)
Energy
(kJ/mol)
Energy difference
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Part III Questions – Answer the following questions and turn this in with your lab when you
come to lab next week.
1) a. From your ArgusLab data, considering the difference in energies between the
staggered and eclipsed conformations of ethane, which conformation, staggered
or eclipsed, is more stable? (3)
b. In a Newman projection of the less stable conformation of ethane show the
source of strain. (6)
c. Is the strain due to torsional interactions? Is it due to steric interactions? (2)
2) How do you account for the difference in energies between the two staggered
conformations of 1,2-dichloroethane? How do you account for the difference in
energies for the two eclipsed conformations? Answer these questions by drawing
all four conformations as Newman projections and, on your drawings, indicate
the sources of strain – torsional, steric-gauche, steric-eclipsed.(12)
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3) a. Rank the conformations of 1,2-dichloroethane in terms of stability. Draw a plot
of potential energy versus rotation for the C-C bond in 1,2-dichloroethane. (Like
figure 3-9 in your text.)(10)
b. Do your calculations from ArgusLab agree with your predictions? (2)
4) a. According to ArgusLab, for the trans – 1,2-dichlorocyclohexane stereoisomer,
which conformation of the trans stereoisomer has the lower energy, the diaxial or
the diequatorial conformer? (2)
b. Show the sources of strain in a drawing. Draw both ring-flipped versions of the
trans isomer. (Draw the cyclohexane ring in the chair form.) (10)
c. Draw the cis and trans isomers of 1,2-dichlorocyclohexane in their most stable
conformations. Indicate which isomer has the lower energy. Identify the sources of
strain in the conformations you built. (Draw the ring of cyclohexane in its chair
form.) (10)