The Covalent Bond Revised: 4/22/09

THE COVALENT BOND

INTRODUCTION

This experiment will look at the energies, wave functions, and electron densities of different
forms of dihydrogren: the one electron cation (H2+), the two electron neutral molecule (H2), and
the three electron anion (H2-). The formation of these chemical species is driven by the lowering
of the systems total energy by finding the equilibrium bond length and creating positive
constructive interaction between two atomic wave functions leading to a bonding molecular
wave function. In this experiment, the Spartan computer program will be used to calculate and
map various energy and orbital values. Bond lengths will be constrained (locked at specific
values) to show the relationship between bond length and dihydrogens total energy. The orbital
images for H2+, H2, and H2- will be created and assigned to molecular orbital diagrams.

First, we will discuss the energies involved in bonding. For a covalent bond to form between
two atoms, the energy of the new molecule must be lower than the energy of the separate atoms.
In other words, covalent bond formation occurs when the resulting molecule is more stable than
its components. To completely understand the energies involved in bonding, one must look at
the attractions and repulsions of subatomic particles.

H2+, a 1-electron molecule:

Let us first concentrate on a molecule with only

e
-
one electron, the H2+ molecular ion. It contains
two nuclei H+, that we will label with a and b,
r
H+a H+b and one electron. The distance between the
R
nuclei is labeled R.

The easiest way of dissociating H2+ is to

separate it into 2 fragments, H and H+.
(Separating H2+ into its 3 elementary
constituents H+ + H+ + e- would cost much more
energy.) Hence the dissociation energy (De) of H2+ is the difference between the energy of the
separated fragments H and H+ and that of the molecule at its equilibrium distance (R = Re).

H2, a 2-electron molecule:

- H2 contains two nuclei (labeled a and b) and

e two electrons labeled (1 and 2).
r1 r1 is the coordinate for electron 1 and r2 the
H+a R H+b coordinate for electron 2.
The easiest dissociation is to Ha + Hb
r2

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The Covalent Bond Revised: 4/22/09

A molecule is created when atoms come together to create a more stable, lower energy species.
The two components to the molecular (or atomic) energy are kinetic and potential energy.
Potential energy is energy of position. The position of electrons and nuclei with respect to each
other is a major determinant of molecular stability. Potential energy can be minimized (the
molecule stabilized) by balancing the repulsive and the attractive forces of electrons and nuclei.
See below for a detailed description of those forces.

The potential energy of H2+ consists in 3 terms:

Electron-nuclear attraction (Ha+e-
& Hb+e-) of the negatively charged
-
e electron to each of the positively charged
nuclei gives two negative contributions
H+a H+b (decreasing the potential energy).
Nuclear-nuclear repulsion (Ha+
Hb+) between the two nuclei gives a
positive contribution (increasing the
potential energy).

The potential energy of H2 contains 6 terms:

Electron-nuclear attraction (Ha+e1-,

e1
- Hb+e1-, Ha+e2- &, Hb+e2-) of
the negatively charged electrons to each
H+a H+b
of the positively charged nuclei gives
four negative contributions (decreasing
the potential energy).
Nuclear-nuclear repulsion (Ha+ Hb+)
e2 - between the two nuclei gives a positive
contribution (increasing the potential
energy).
Electron-electron repulsion (e1- e2-)
between the two electrons gives a positive
contribution (increasing the potential
energy).

Kinetic energy is the energy of motion. Within a molecule the movement of electrons and
nuclei are the source of kinetic energy. While the movement of the electron(s) is the major
contributor to the kinetic energy, the movement of nuclei is small in comparison and is usually
ignored. An electrons kinetic energy can be lowered by delocalization. When an electron is
limited to a small volume space near one nuclei it is said to be localized. If the electron can
occupy a volume of space that includes more than one nuclei it is delocalized. In this experiment
the electron is localized around a single hydrogen atom in an atomic orbital. When a covalent
bond is formed the electron is delocalized meaning it can occupy a larger space between the two
nuclei in the molecular orbital. When an electron has a larger volume of space to move in the

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The Covalent Bond Revised: 4/22/09

kinetic energy is lowered. (The velocity of the electron particle drops as does the frequency of
the electron wave.)

Applying these ideas of the potential and kinetic energies, physical intuition how internuclear
separation (bond length) effects molecular energy:
For a large separation the system energy is the sum of the energy of the separated H and
H+ (or H), the molecular energy is zero (i.e. there is no molecule);
For an intermediate separation the molecular energy is lowered (it is more stable) because
the electron(s) can explore the space between the two nuclei: feeling the attraction of both
nuclei instead of only one and in addition its kinetic energy decreases because it is more
delocalized. The molecular energy is negative;
For a small separation the nucleus-nucleus repulsion becomes very important and the
kinetic energy increases again because the space available for the electron(s) is/are much
smaller: the electron-nuclei attraction cannot compensate for these two effects, and the
molecular energy becomes positive.

The resulting energy curve plotted as a function of R, the internuclei distance, has a minimum
(where the H2+ or H2 molecule is most stable). The value of R at this minimum is the equilibrium
bond length, Re, and the value of the energy is De, where De (a positive number) is the bond
dissociation energy.
Energy (kJ/mol)

Internuclear Distance, R ()

Re

-De

Molecular Energy Curve

In this experiment you will use Spartan to constrain (restrict) the bond length of H2 to find the
molecular energy at different points on this curve. The density images will be created to help
visualize the lengthening bond.

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The Covalent Bond Revised: 4/22/09

The energetics of bonding just discussed are directly related to the arrangement and location of
the bonds electron(s). Wave functions (orbitals) mathematically describe an electrons three
dimensional location in space. Wave functions can only be completely solved for a 1 electron
atom or ion. To fully appreciate the complexity of a wave function, take a look at the equation
for a one electron atom (or ion):
nlm(r,,) = Rnl(r) Ylm(,)
radial spherical

Rnl(r) = 4(n l 1)! (2r)l L2l+1 (2r)-r/n

n4[(n+1)!]3 (n) n-l-1 (n)

Ylm(,) = [(2l + 1)(l |ml |)!] P|ml| (cos) + (2)- eiml

[2(l + |ml |)!] l

The above equations use spherical, not Cartesian, coordinates to describe the motion of the
electrons around a center nucleus. Quantum numbers (n, l, and ml) take up different values
depending on the desired orbital of the 1 e- atom. (For example, if n = 1 and l = ml = 0, 1s will
be calculated; if n = 2, l = 1, ml = 0, 2px will be calculated.)

In this experiment we are interested in more than just a one electron atom or ion. These
calculations are increasing more complex and cannot be completely solved. All other wave
functions (or orbitals) must be solved by making approximations. These complex calculations
require the assistance of a computer. Spartan will perform these complex calculations for you by
employing ab initio (from first principles) methods.

One of the approximations that Spartan uses for these calculations is the LCAO-MO (Linear
Combination of Atomic Orbitals Molecular Orbital) method. Molecular orbitals are
approximated as 1-electron molecular wave functions (molecular orbitals) by summing separate
1-electron atomic wave functions (atomic orbitals). In other words, molecular orbitals are
created as a linear combination of atomic orbitals. In this document atomic orbitals are
symbolized by and molecular orbitals as .

Because the H2+ ion has only one electron, the molecular wave functions are relatively simple. If
the H and H+ separation is large, the atoms are still separate and corresponding wave functions
are still atomic wave functions a (if the electron is attached to nucleus a, corresponding to Ha +
H+b) or b (if the electron is attached to nucleus b, corresponding to H+a + Hb). Once the atoms
move closer, approximate molecular wave functions can be constructed by combining the
atomic wave functions a and b as follows:
+ = Ca+ a + Cb+ b = C+ [a + b]
= Ca a Cb b = C [a b]

Ca+, Cb+, and Ca-, Cb are weighting coefficients: indicating the preference of the electron
for a particular nucleus. (The subscripts a & b refer to the nuclei.) For homonuclear
diatomics like H2+, the nuclei are identical so the coefficient is the same for both, allowing
the expression to be simplified.

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The Covalent Bond Revised: 4/22/09

+ is a bonding orbital: The electron is no longer localized around a single nucleus but
delocalized between the two nuclei, which lowers both its potential and its kinetic energy.
The potential energy is lower because of the increased electronic density in the region where
the electron feels the attraction of both nuclei; the kinetic energy is lower because the
electron can explore a larger space between the nuclei. When the sole electron of H2+ is in
this orbital there is covalent bonding.

is an antibonding orbital: A nodal plane (a plane where the probability for finding the
electron is zero) exists in the middle between the nuclei. By creating a region where the
electron is not permitted, the electron is further localized around one or the other nucleus,
increasing its kinetic energy. Furthermore, potential energy is increased when electron
density is decreased between the two atoms. When the sole electron is in this orbital, there is
no bonding.

Because of the addition of a second electron, the calculation for the molecular wave functions of
the H2 molecule is more complex. Each electron will interact interchangeably with each
hydrogen nuclei. To account for this the molecular wave function is as the product of the two 1
electron wave functions (+(r1) for the first electron and +(r2) for the second electron):
I = +(r1) +(r2)

Then, using the LCAO-MO approach, each of these 1 electron wave functions is represented
by a linear combination of atomic orbitals. Because two identical hydrogen atoms are involved
in the bond the weighting coefficients (Ca+ = Cb+ = C1) are the same simplifying the equation:
I = [Ca+a(r1)+Cb+b(r1)][Ca+a(r2)+Cb+b(r2)] = CI[a(r1)+b(r1)][ a(r2)+b(r2)]

The wave function (I) is the lowest energy bonding molecular orbital. This one wave function
is not, however, a complete description of the H2 molecule. The three molecular wave functions
also belong to H2, as well as many others. Note: Expansion of the II, III, and IV using the
LCAO-MO method is beyond the scope of this experiment.

II = +(r1) (r2) + (r1) +(r2)

III = (r1) (r2)
IV = +(r1) (r2) (r1) +(r2)

These wave functions correspond the excited states of the molecule (denoted as H2*). II and
IV have one electron in the bonding MO and one in the antibonding MO, hence they are higher
in energy than I. III places both electrons in the antibonding MO. The electrons in I, II,
and III are in opposite spin states, giving a total magnetic moment (total electronic spin) zero,
called singlet spin state. The two electrons in IV are in the same spin state, called a triplet spin
state. (H2+ is in a doublet spin state because of its one unpaired electron.) Can you create the
molecular orbital diagram for 1, 2, 3, and 4?

Spartan will be used to create pictures and calculate the energies of various molecular orbitals (,
wave functions). Molecular orbitals are listed within Spartan in conjunction with electron filling.

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The Covalent Bond Revised: 4/22/09

The highest energy orbital filled with electrons is called the HOMO (highest occupied molecular
orbital). The lowest energy orbital without electrons is called the LUMO (lowest unoccupied
molecular orbital). Molecular orbitals of lower or higher energy are designated as HOMO(-#) or
LUMO(+#). Spartan demonstrates the phase of orbitals with red and blue coloring. An orbital
has phase because an electron is a wave. When two waves combine in phase their amplitude
increases. Therefore, when two atomic orbitals in the same phase (with the same color) combine
a bonding molecular orbital is created. Conversely, when two atomic orbitals in opposite phases
(two different colors) combine an antibonding molecular orbital is created.

Refer back to the equation for . At the very end of the 3rd line of the equation you will find the
term eiml. The first figure in the exponent is i", a complex number. Complex numbers are
used in wave functions as a way to mathematically describe phase (mentioned above). The
phase of a wave is a given location near the crest of a wave, at the trough of a wave, or
somewhere in between. If two waves meet in phase their amplitudes combine creating a larger
wave. In the same way, when two atomic wave functions (orbitals) meet in phase they create a
larger molecular wave function (orbital). However, a three dimensional volume of space cannot
be described by equations containing complex numbers. To obtain such a description the wave
function () must be squared (removing i) to create the electron density of a molecule (||2).
The result of this mathematical operation on the H2+ ion is shown below.
|+(r) |2 = C+2 |a(r) + b(r) |2 = C+2 [a2(r) + b2(r) + 2 a(r) b(r)]
|(r) |2 = C-2 |a(r) - b(r) |2 = C-2 [a2(r) + b2(r) - 2 a(r) b(r)]

The last terms +2 a b or -2 a b shows constructive (+) or destructive (-) interference

between the two atomic orbitals: in the region between the nuclei, both a and b are important,
so the term +2 a b adds some electron density and the term -2 a b subtracts some electron
density in that region. An electron density plot represents a volume of space where electrons
spend 90% of their time. In Spartan, these plots are gray.

In the experiment you will correlate the following with the Molecular Orbital diagrams for H2+,
H2, and H2*:
Electron Density and HOMO/LUMO Plots for H2. As the bond length (R) is shortened,
the change in electron density of a bonding molecular orbital will be observed and the total
energy will be recorded. Energies of HOMO and LUMO orbitals will be found. The affect
of bond length on these energies will be investigated.
HOMO/LUMO and Electrostatic Potential Plots of H2+, H2, & H2- at Equilibrium Bond
Distances. The relationship of molecular orbital diagrams and bond order to orbitals and
electrostatic potential plots of H2+, H2, & H2- will be found.

This is an at-home experiment. There will be no in-lab time this week. You will need to
purchase and download the Spartan program from Wavefunctions website (follow the link on
the lab manual webpage.) No flow chart or formal write-up of procedures is required for this
experiment. At the next lab meeting, turn in lab notebook (or typed) pages with the
experiment title and your name with the answers to the discussion questions. Tables
containing plots generated from Spartan should also be included.

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The Covalent Bond Revised: 4/22/09

PROCEDURES
Images should be pasted into Word documents posted on the course website.
Note: Holding down the mouse button while over the drawing allows for the rotation and
translation of the molecule.

A. Build Diatomic Hydrogen

1. Double click on the ST icon to launch the program.
2. On the menu bar, click File and then New.
3. In the Model Kit in the left panel, click the Organic tab.
4. In the Model Kit, click H to select hydrogen.
5. In the Workspace area, click anywhere to place hydrogen.
6. Click on the yellow bond to add an additional hydrogen.

B. Setup Equilibrium Geometry Calculations

An Equilibrium Geometry calculation will result in the most stable (lowest energy) form of a
molecule or ion.
1. On the menu bar, click Setup, and then Surfaces.
2. In the Surfaces window, click the Add button.
3. In the Add Surfaces window, the following options should already be selected:
Surface: density
Property: none
Resolution: normal
Click Apply to add the density surface. (This image will show the size of the molecule.
Recall that molecular size is determined by the size of the electron cloud of the molecule.)
4. Change the Surface field to HOMO. (Do not change the Property and Resolution fields.)
Click Apply. (Recall: HOMO stands for highest occupied molecular orbital, the orbital that
contains the outermost, highest energy valence electrons.)
5. Change the Surface field to LUMO. (Do not change the Property and Resolution fields.)
Click Apply. (Recall: LUMO stands for lowest unoccupied molecular orbital, the first
orbital (just above the HOMO in energy) that is not filled with electrons.)
6. Change the Surface field to density. Change the Property field to potential. (Do not change
the Resolution field.) Click Apply. Click OK to close the Add Surfaces window. Leave the
Surfaces window open. (This surface will show where electron density is highest (indicated
by red) where electron density is lowest (indicated by blue) and the values in between
(indicated by a progression of colors from red to blue).)
7. On the menu bar, click Setup, and then Calculations.
8. Select Calculate: Equilibrium Geometry with Hartree-Fock 6-311+G**.
9. Click Submit to exit Calculations window and start the calculation.
10. When the Save As window appears name the file and click on Save. Click OK button to start
the calculations. Almost immediately, a dialog will appear indicating that the calculations
are complete. Click the OK button to clear the dialog.
11. In the Workspace Area, click on the bond between the hydrogen atoms so that it is
highlighted. Note the equilibrium bond length displayed in the lower right hand corner of the
screen.

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The Covalent Bond Revised: 4/22/09

C. Modify and View Surfaces

1. If you have accidentally closed the Surfaces window, go to the Display menu and select
Surfaces.
2. In the Surfaces window, click on the yellow box next to density to display the molecules
surface.
3. Now click on the large gray surface in the Workspace area, from the surface style menu that
appears in the bottom right hand corner of the screen, choose Mesh.
4. Go to the Options menu and choose Colors. Click on the teal background. Drag all 3 color
toggles to the top so that the background is white (this will make for a better printout).
5. Crop the surfaces in MS Word. Paste the gray density surface into the first table provided on
the website. The red and blue HOMO and LUMO plots should be pasted in the second table.
(See directions below.)

Directions for using Crop function in MS Word:

Paste the Spartan surface into MS Word.
Go to the View menu and select Toolbars, then select Picture.
Click on the Spartan plot so the corner handles and frame appear.
Click on the Crop icon . Hold down Ctrl and drag one of the corners inward until
the density plot or MO and only a small amount of the background from the Spartan
program are visible.

D. Variation of Bond Length

1. Close the file created above and repeat the steps in Part A to create another H2 molecule.
2. On the menu bar, click Setup, and then Surfaces.
3. In the Surfaces window, click the Add button.
4. In the Add Surfaces window, the following options should already be selected:
Surface: density
Property: none
Resolution: normal
Click Apply to add the density surface.
5. On the menu bar, click Geometry and then Measure Distance.
6. In the Workspace Area, select the bond by either clicking on the bond between the hydrogen
atoms, or by clicking on one hydrogen atom and then the other.
7. In the lower right corner of the screen, click inside the field indicating the distance. Change
the value displayed to 0.400 and press Enter.
12. On the menu bar, click Setup, and then Calculations. Select Calculate: Energy with
Hartree-Fock 6-311+G**. Click the Submit button.
8. Enter a name for the file in the Save As window. Click OK button to start the calculations.
9. When the dialog appears indicating that the calculations are complete, click OK.
10. Repeat the steps of Part C (cropping and pasting density surface images (the other 3 surfaces
do not need to be generated) into the first table).

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The Covalent Bond Revised: 4/22/09

11. Repeat steps 1 through 10 (closing the preceding file and opening a new file for each bond
length, using bond lengths 0.580, equilibrium bond length (found in Part B), 1.25, 2.10, and
3.20.

E. Potential Energy Well & Effect of Bond Length on E

12. Open the file for the H2 molecule with the smallest bond length (0.400 ). Go to the
Display menu and choose Spreadsheet. A spreadsheet window should open.
13. Go to the Geometry menu and choose Measure Distance. Click on both of the hydrogen
atoms in the H2 molecule. Both atoms should now have a gray coating. Click on the P in
the bottom right hand corner of the screen (next to the distance value). The bond length
value (with more significant figures should show up under the Distance heading.
14. Click Add in the Spreadsheet window. Choose the following: E, E HOMO, and E LUMO.
Your choices will be highlighted if they have been selected. Click Apply then OK. Four
quantities should now be visible on the spreadsheet: Distance, E, E HOMO, and E LUMO.
The spreadsheet window may need to be stretched out to see everything. The definition of
these four quantities is:
Distance: Bond length. This should be basically the same as the values listed in step
7 & 12 of Part D.
E: Molecular Energy. This is the energy required to create the molecule either from
its elements in their standard state (enthalpy of formation, Hf) or from a collection
of separated nuclei and electrons.
E HOMO: Energy of the highest occupied MO. This energy value is implied by the
placement of the MO on a molecular orbital diagram.
E LUMO: Energy of the lowest unoccupied MO. This energy value is implied by the
placement of the MO on a molecular orbital diagram.
15. Right click over the Label column on the left hand side of the Spreadsheet window. Choose
Append Molecule(s) Open the file for the H2 molecule with the next largest bond length
(0.580 ). The Distance, E, E HOMO, and E LUMO values should have appeared in the next
row of the Spreadsheet. Repeat this step until all of the molecules created in Part D have
been appended to the Spreadsheet.
16. Copy the four columns (Distance, E, E HOMO, and E LUMO) by dragging the cursor across
to highlight the cells to be copied. Copy the cells, then open Excel and paste the table into a
worksheet. (Save the changes to the Spartan file you are working on.)
17. Create 2 Excel plots:
Potential Energy Curve (Distance vs. E): This plot will demonstrate how bond length
affects the total energy (E) of a molecule. It is impossible to fit a computer generated
curve to these data points draw a smooth curve by hand on the print out.
Effect of Bond Length on E (Distance vs. E HOMO and E LUMO): This plot will
demonstrate what happens to the HOMO/LUMO energy gap as bond length is increased.
Make sure you fit a two curves on the same plot one to the E HOMO data the other to
the E LUMO data.

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The Covalent Bond Revised: 4/22/09

F. H2+ Calculations
Repeat the steps in Parts A-C. Exceptions to Part B: Set Total Charge to Cation and
Unpaired Electrons to 1. Fill the HOMO, LUMO, and Density Potential surfaces into the
second table (Density surfaces are not needed).

G. H2- Calculations
Repeat the steps in A. through C. Exceptions to Part B: Set Total Charge to Anion and
Unpaired Electrons to 1 and add a HOMO(-) surface. (The HOMO(-) does not need to be
pasted in a table just keep it for reference when completing the postlab.) Fill the HOMO,
LUMO, and Density Potential surfaces into the second table (Density surfaces are not needed).

RESULTS

1. Fill in the first data table in MS Word for H2.

2. Create the two Excel plots for Part E.
3. Fill in the second data table for H2+, H2, and H2- comparing the equilibrium bond lengths,
HOMO, LUMO, and density potential plots. (The 2nd and 3rd columns should have red/blue
plots, the 4th column should have rainbow colored plots.)

DISCUSSION
1. Using only 1s atomic orbitals, create MO diagrams for H2+, H2, and H2-. Sketch the HOMO(-
), HOMO, LUMO, or LUMO(+) surfaces (the red and/or blue surfaces created in Spartan)
next to each molecular orbital energy level. Provide the electron configuration and bond
order for each. Which species is the most stable? Why?

2. What is the calculated equilibrium bond length for H2? How does the data support your
choice? Using the true bond length for H2 (0.7414 ), calculate the percent error for the
value calculated in Spartan.

3. The energy of the HOMOs and LUMOs (E HOMO and E LUMO) are reported relative to the
atomic orbitals used to create the molecule. The energy of the atomic orbitals of each
hydrogen atom is 0 kJ/mol. Use this idea to explain what is seen in the 2nd Excel plot
created in Part E, #17 for the neutral hydrogen molecule (H2).

4. Answer the following questions for H2+, H2, and H2-:

a. What is density, HOMO, & LUMO in terms of the molecular wave function?
b. What is indicated if two colors are present on a HOMO or LUMO plot?
c. Is the electron more delocalized in the HOMO or LUMO plots of H2+ and H2?

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d. What is the relationship between HOMO & LUMO and bonding & antibonding?
(Provide a specific answer for H2+, H2, and H2-.)
e. Which of the three species (H2+, H2, and H2-) has a HOMO with a node?
f. What atomic orbitals create the LUMO for H2-? What orbital for H2+ and/or H2 more
closely resembles the HOMO in H2-?
g. What do the density/potential plots demonstrate about bond order? (Provide a specific
answer for H2+, H2, and H2-.)

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