Physical Chemistry II Introduction to Spartan quantum-chemistry software

The instructions in this tutorial were tested on Spartan06, which is installed in room 318 of the
UMD Chemistry building. Although the instructions are expected to work on the Student Edition,
there may be some discrepancies regarding the graphical user interface. For more information at any
point, please consult the Spartan Student Edition Spartan Student Overview,
http://downloads.wavefun.com/SpartanStudentOverview.pdf .

Viewing and manipulating molecules

Start Spartan.
Download the Spartan ethane file, ethane.spartan.
Use the File/Open menu in Spartan to open the ethane molecule.
Mouse control of a selected molecule:
select molecule click on the molecule (left mouse button)
rotate molecule press the left button and move the mouse
translate molecule press the right button and move the mouse
scale molecule press both the Shift key (mac: apple and option keys) and the right button
and move the mouse vertically
Try translating, rotating and scaling the ethane molecule.
Spartan offers several models with which to view molecules.
Click on Model on the menu bar. Try a few of the renderings offered.

Distances, angles and dihedral angles can be measured.

To measure distance, either choose measure distance from the Geometry menu, or click on
the
icon. Then select two atoms. The distance between the two atoms selected will
appear in the lower right-hand corner of the Spartan window. The C-C distance is 1.53
Angstroms.
To measure an angle, either choose measure angle from the Geometry men, or click on the
angle button. Then select three atoms. The angle (first atom to second atom to third atom)
will appear. Note that the order in which the atoms are selected matters.
The H-C-H angle is 107.5.
The dihedral angle formed by four atoms can be measured using either
the Geometry menu or the dihedral-angle button, then selecting four
atoms. The H-C-C-H dihedral angle shown at right is 60.

SpartanIntroTutorial.odt

Energy, symmetry, dipole moment, and atomic charge are available in the Properties window found
on the Display menu. Click on Display/Properties.
The energy of this
molecule (within the
method used to calculate
it) is -79.8387304
Hartree. (The au,
atomic unit, of energy is
Hartree. 1 Hartree =
2625.5 kJ/mol.) Spartan
recognizes the molecule
as belong to the D3d point
group. Note that Spartan, as other quantum-chemical codes, is not always able to recognize a
molecule's full symmetry. The dipole moment is stated to be 0.0 Debye, which is correct for
nonpolar ethane.
To see an atomic charge (or other atomic property) click on one of the atoms. Then
Display/Properties will display properties of the atom rather than of the entire molecule. A carbon
atom in ethane, for example,
has electrostatic charge
-0.274 (in units of e, the
electron charge).

Assignment 1: Download and open the file HOOH.spartan, which contains hydrogen peroxide.
Measure the O-O bond length and the H-O-O-H dihedral angle.Copy an image of the molecule to
the windows clipboard simply by choosing Copy from Spartan's Edit menu, and then pasting
the image into other software (e.g., Word, Excel, or Paint). Use Display/Properties to find the dipole
moment of HOOH. Turn in an image of the molecule along with the O-O bond length, the H-O-O-H
dihedral angle, and the dipole moment. (These are calculated values, not necessarily the same as
experimental values.)

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Building an organic molecule, acetonitrile (CH3CN).

Click on the new file button, or choose New on the File menu. A blank drawing area will
appear, with molecule-building tools at the right. By default, the organic
template opens. The inorganic tab will be described below.
Click on tetrahedral sp3 hybridized carbon from the library
of atomic fragments. The fragment icon is highlighted, and a model
of the fragment appears at the top of the model kit. Bring the cursor
anywhere on Spartan's drawing window and click. An sp3 carbon with four free
valences, which are represented by yellow lines attached to the atom, will
appear.
Return to the build tools. Click on sp carbon. Then move the mouse to the
drawing area and click on any one of the sp3 carbon's free valences. The sp
carbon will bond to that free valence.
Finally, select a triple-bonding nitrogen atom from the build menu and add it to
the triple-bonding free valence on the recently-added carbon atom.

All atoms except hydrogens have been added to the molecule.

Now click the minimize button,
. That will add hydrogen atoms to satisfy
free valences. It also adjusts bond angles and distances based on approximate
molecular mechanics. The result is a good representation of acetonitrile. It can be
refined with quantum-chemical calculations.

Close the drawing window by clicking on the V (view) button. (One can return to the build
window by clicking on the + button.)

SpartanIntroTutorial.odt

Set up a quantum-chemical
calculation for acetonitrile, as
follows. Click on Calculations on
the Setup menu. A dialog box
similar to that shown at right,
which is from Spartan06, should
appear.
Equilibrium geometry is used to
optimize bond angles, bond
lengths, and dihedral angles so as
to achieve the lowest energy
possible with the selected method.
The Hartree-Fock method is a
basic ab initio quantummechanical method. It is often used as a first approach to refining molecular properties. The basis
set 6-31G* is a medium-size basis set suitable for initial work. If we want to calculate vibration
frequencies, IR must be checked. To calculate thermodynamic functions (enthalpy, entropy, etc.)
both IR and Thermodynamics must be checked. For this calculation, select the Hartree-Fock method
with the 6-31G* basis set and IR frequencies.
When the calculations dialog box is ready, click on Submit (not OK). Unless you have already
saved the molecule, Spartan will prompt for a file name. A name such as acetonitrile will work.
Spartan will state that calculations have started. When calculations are done, Spartan will say so.
Display/properties will show Energy = -131.9275 Hartree.
Choosing Spectra from the Display menu
will display a list of vibration frequencies,
their symmetries ("Type") and calculated
infrared intensities. Frequencies are given in
wavenumbers, cm-1. The lowest-frequency
vibration of acetonitrile is 425 cm-1 and is
doubly degenerate. By clicking on the yellow
box next to that frequency, you will see that it
is a C-C-N bending mode. (To stop the
animation, uncheck the yellow box.)
Assignment 2: Create acetonitrile. Optimize the geometry (equilibrium geometry calculation)
using density functional theory (DFT) with the B3LYP functional and the 6-31G* basis set. Turn in
two results: the charge on the nitrogen atom, and the highest vibration frequency (in cm-1).

SpartanIntroTutorial.odt

Building an Inorganic Molecule, OCS

Use File/New or the new-page icon to open a new drawing area.
Choose the inorganic tab on the molecule-building toolbox.
When using the inorganic tools, first choose an atom (e.g., C) and
then choose bonding valence and geometry. For example, to enter
a carbon that will be bonded linearly to two substituents, choose
C and the linear divalent pattern.
Click in the drawing area. A
divalent carbon atom will appear.
Choose singly-bonded oxygen.
Bond it to one of the free valences
on the carbon atom.
Lastly, choose singly-bonded sulfur and attach it to the remaining
free valence on carbon.
Clicking on the Minimize button will cause Spartan to attempt to
improve the bond lengths and angle.
Should a molecule need alteration, there are three handy buttons.
erase, make bond, break bond
The left button is to erase a free valence or an atom. To erase the oxygen, for example, first click on
the erase button, then on the oxygen atom. That leaves a -C-S fragment.

Now add a sulfur atom anywhere in the free drawing area. To do this, first select a sulfur atom and a
bonding type. For practice, choose divalent sulfur, an intentional mistake. Then click on the Insert
button. Then move the mouse to an open area and click to insert a sulfur atom. The result is shown
at right, below.
We can form a C-S sulfur bond. First click on the make bond icon, which is
shown above. Then click on one of the free valences on the lone sulfur atom, and
then click on the free valence on carbon. A bond will be drawn.
Click on the erase button, and then on the extra free valence on
the sulfur atom. That will remove the dangling free valence.
It remains to change one of the sulfur atoms to oxygen. One way
to do this is to choose an O atom from the inorganic build toolbox. Then doubleclick on one of the two sulfur atoms. That atom will be changed to an oxygen
atom.

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Finally, improve the geometry by using the minimize button.

Energy-minimizing the

structure above improved bond lengths but the molecule remained bent.

Use the V (view) button to return to the general viewing screen. Open the Setup/Calculation
dialog box. Set up a calculation: Equilibrium geometry using Hartree-Fock theory and the 6-31G*
basis set.. Choose IR as well, so that vibration frequencies will be calculated. Submit the
calculation.
At the end of the calculation, SCO will be linear, which is its equilibrium geometry.

View the vibration frequencies by using Display/Spectra. Note that all four
frequencies are real numbers. If the linear geometry were unstable (i.e., if
bending lowered the energy) at least one of the frequencies would be
imaginary. In the list of frequencies, an imaginary frequency would be
labeled with a lower-case i.
Assignment 3: Build MgOH+. This
cation is linear. To build a cation,
proceed as for a neutral species. In
the Setup/Calculations dialog box,
specify the total charge on the
species, cation in this case.
Use the Hartree-Fock theory with
the 6-31G* basis set to calculate the
equilibrium geometry and the
vibration frequencies.
Turn in the following: An image of your MgOH+, the Mg-O bond length, and the lowest vibration
frequency (in cm-1).

SpartanIntroTutorial.odt

Reaction thermodynamics, partial hydrogenation of acetylene.

HCCH(g) + H2(g) H2CCH2(g)
To calculate E for a reaction, calculate the energy of each species individually.Each molecule's
geometry must be optimized (i.e., equilibrium geometry calculated). The zero-point vibrational
energy should be added to each molecule's electronic energy. It is essential that calculations for all
molecules use the same theory and the same basis set. Then take the energy difference, products
minus reactants. The resulting E is the energy change at absolute zero temperature, E(0). Let
Ei(0) = Ei + (ZPE)i, the sum of the total electronic energy, Ei, and the vibrational zero-point energy
of species i. The electronic energy Ei is the energy that is shown in the Display/Properties box. The
zero-Kelvin reaction energy, E(0) = ( i Ei(0)), where i is the stoichiometric coefficient of
species i.
The reaction enthalpy can be calculated at 298K. One first calculates the enthalpy correction Hi
=Hi -Ei , for each species. The correction Hi includes zero-point vibrational energy. Then H
equals the sum, products minus reactants, of Ei + Hi. H298 = [i (Ei + Hi)].
Use this tutorial as an opportunity to calculate E(0) and H298.
Begin by constructing acetylene, hydrogen and ethene. Having all three molecules on the Spartan
screen at once works. Each is saved in its own file. Spartan will not confuse them. For each
molecule, do an equilibrium geometry calculation using density functional theory with the B3LYP
functional and the 6-31G* basis set. Check the IR and Thermodynamics boxes on the Calculations
dialog box.

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After a calculation finishes, choose Output on the Display menu. A text file that summarizes
the calculation will be displayed. The output file for the hydrogen calculation is below.
SPARTAN '06 MECHANICS PROGRAM: PC/x86
129
Frequency Calculation
Reason for exit: Successful completion
------ lines deleted -------------------Job type: Geometry optimization.
Method: RB3LYP
confirming that the DFT B3LYP method was used
Basis set: 6-31G(D)
which is the same as 6-31G*
---- lines deleted -----Optimization:
Step
Energy
Max Grad.
Max Dist.
1
-1.1754839
0.000557
0.001080
2
-1.1754842
0.000148
0.000389
The last energy in the Optimization list is the final total electronic energy of the molecule, in au.
------ more lines deleted -----------Standard Thermodynamic quantities at 298.15 K and 1.00 atm
Term
ZPE
Enthalpy
Entropy
Cv
kJ/mol
kJ/mol
J/mol.K
J/mol.K
-------------------------------Total Vibrations
26.6576
0.0000
0.0000
0.0000
Ideal Gas
2.4789
Translation
3.7184 117.4876
12.4716
Rotation
2.4789
12.7643
8.3144
---------------------------Totals
35.3339 130.2519
20.7860
Zero-point vibration energy (ZPE)
Enthalpy correction, including ZPE
------more lines were deleted ------Below are data copied from the output files for hydrogen, acetylene, and ethene.
Note that the atomic unit of Hartree, multiplied by 2625.50, equals kJ/mol.
energy (au) E (kJ/mol) ZPE (kJ/mol) E+ZPE (kJ/mol) Hi= Hcorr
(kJ/mol)
-3086.24

26.66

-3059.58

35.33

-3050.91

acetylene

-77.325652 -203018.50

69.97

-202948.53

80.13

-202938.37

ethene

-78.587448 -206331.34

134.46

-206196.88

144.93

-206186.41

-226.60

37.83

E(0)=-188.77

29.47

H=-197.13

hydrogen

-1.175484

H=E+Hcorr
(kJ/mol)

productsreactants

The E(0) value calculated above is for zero temperature for all molecules and their vibrations in
their ground states. The H value calculated above is for 298K. It includes (through statistical
thermodynamics) vibrational, rotational and translational energy.

SpartanIntroTutorial.odt

For comparison, H298 from tabulated enthalpies of formation at 298K is

H298 = 52.5 -228.2 0.0 = -175.7 kJ/mol (CRC Handbook, 71st ed., page 5-10.)
Some molecules have unpaired electron spins. A famous case is molecular oxygen, O2, which has
two unpaired electron spins in its ground state. That is, the ground state of O2 is a triplet state. Spin
multiplicity (singlet, doublet,
triplet, and so on) is specified in
Spartan in the Setup/Calculations
dialog box.
In most molecules having an even
number of electrons, the electron
spins are paired and the spin
multiplicity is singlet. Singlet
multiplicity is Spartan's default.
Any molecule that has an odd
number of electrons (e.g., ClO2)
cannot have singlet multiplicity.
For a single unpaired electron, set the multiplicity to doublet.
Calculating reaction energy requires a method that includes electron correlation. The two commonly
available methods are Moller-Plesset Perturbation theory (MP2) and density functional theory
(DFT). MP2 theory is a post-Hartree-Fock theory comparable to DFT/B3LYP theory. MP2 may be
slightly more robust. It is often less accurate.
Assignment 4: Calculate E(0) for dichlorine monoxide reacting with molecular oxygen to form
chlorine dioxide in the gase phase: 2 Cl2O + 3 O2 4 ClO2 . The spin multiplicity of dichlorine
monoxide is singlet. Use second-order Moller-Plesset perturbation theory (MP2) with the 6-31G*
basis set for all three molecules. Turn in images of the geometry-optimized molecules, their energies
and zero-point energies, and the overall E(0) for the reaction. Give all energies in kJ/mol.

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