CHEM461. Lab 01. Computational Chemistry Project.

Access our servers at: http://pchem.c.byui.edu/~halebg/cgi-bin/webmo/login.cgi

Or : http://physicalchemistry.byui.edu/cgi-bin/webmo/login.cgi (Tables 2,4,6)

(Tables 1,3,5)

How do we calculate the most accurate

energies of a boron atom?
Developed by Tricia D. Shepherd1, Ryan C. Fortenberry2, Matthew Kennedy3, and C. David
Sherrill3
Introduction
The eigenfunction solutions to the Schrodinger equation for a multielectron system depend on
the coordinates of all electrons. The orbital approximation says that we can represent a manyelectron eigenfunction in terms of individual electron orbitals, each of which depends only on the
coordinates of a single electron. A basis set in this context, is a set of basis functions used to
approximate these orbitals. There are two general categories of basis sets: Minimal Basis Sets
A basis set that describes only occupied orbitals Extended Basis Sets A basis set that describes
both occupied and unoccupied orbitals
Part A. What is the calculated Hartree Fock energy using a minimal basis set?
1. Go to the New Job menu, and select Create New Job. Click on the small periodic table
icon on the left and select B atom. Place a single B atom by double clicking on the
drawing area. Select the right arrow button at the bottom of the drawing frame to move to
the next step.
2. Select the PSI4 computational engine. Click the right arrow to advance to the next step.
Now we select the options for the computation. For Method, well use the default
Hartree-Fock. For Basis set: STO-3G. For neutral B atom, the atom can only be a
doublet, to which WebMO correctly defaults. We will run our computations with
unrestricted orbitals, so select Unrestricted from the reference dropdown menu. A good
title usually include the atom or molecule studied, the method, and the basis set set. In
Job Title give this job the title: (yourinitials) B HF/STO-3G.
3. Select the right arrow at the bottom of the screen. This should take you to a list of jobs
that the server is running. Your job should be at the top. It may be listed as queued or
running. When the status is listed as Complete, select the View Job icon (magnifying
glass) to the right of the job to display the results of the calculation. Scroll down to the
bottom of the web page (below the drawing area), youll see a summary of Calculated
Quantities. Record the total SCF energy (in Hartrees, Eh, to 6 digits after the decimal).

Department of Chemistry, St. Edwards University, Austin, TX

Department of Chemistry, Georgia Southern University, Statesboro, GA
3
Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry,
and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
2

Page 1

4. For more detailed information, select Raw output from the list of options under Actions
to the left of the molecule viewer. Near the top of the file, record the number of Basis
Functions used for this STO-3G HF energy calculation. Close the output file tab.
Part B. How does the Hartree Fock energy depend on the trial basis set?
The smallest basis-set available is called STO-3G, where STO stands for Slater-type orbital
which is approximated by the sum of 3 Gaussian functions. STO-3G is an example of a
minimal basis set, i.e. it represents the orbitals of each occupied subshell with one basis function.
While basis sets of the form STO-nG were popular in the 1980s, they are not widely used today.
For the same reason that multiple Gaussian functions better approximate a Slater type orbital,
multiple STO-nG functions are found to better approximate atomic orbitals. In practice, inner
shell (core) electrons are still described by a single STO-nG function and only valence electrons
are expressed as the sum of STO-nG type functions.
To understand how to read each basis set, lets consider the next available basis set: 3-21G basis
set. The number before the dash, 3, represents the 3 Gaussian primitives (i.e. a STO-3G)
used to represent the inner shell electrons. The next two numbers represent the valence shell split
into two sets of STO- nG functions one with 2 Gaussian-type orbitals (GTOs) and one with
1 GTO.
1. Under the Molecule Viewer window (between the arrows) select New Job Using This
Geometry. Select the right arrows, until you get to the Job Options tab. For Basis set,
select 3-21G. Submit the energy calculation with the title (yourinitials) B HF/3-21G
and view the output. Record the total SCF energy and the number of basis functions
used.
2. Rationalize the number of basis functions used for the STO-3G and 3-21G calculations.
3. Compare the STO-3G and 3-21G HF energies. Which basis set is more accurate? (Recall
the variational principle states that for a given Hamiltonian operator, any trial
wavefunction will have an average energy that is greater than or equal to the true
corresponding ground state wavefunction. Because of this, the Hartree Fock energy is an
upper bound to the ground state energy of a given molecule.)
Part C. How can we improve the accuracy of the HF energy?
To make an even better approximation of our trial function, we may need to take into account
polarization effects. (This accounts for the unequal distribution of electrons when two atoms
approach each other.) We can include polarization effects by adding STOs of higher orbital
angular momentum, i.e. d type functions are added to describe valence electrons in 2p orbitals.
The presence of polarization functions is denoted by an asterisk. Two asterisks indicate
polarization functions are added to hydrogens. (This would be important if you wanted to

account for hydrogen bonding.) An asterisk in parentheses, (*), symbolizes that polarization
functions are added only to second-row elements.
The presence of diffuse functions is symbolized by the addition of a plus sign, +, to the basis set
designator: 6-31+G. Diffuse functions are also useful for systems in an excited state, for systems
with low ionization potential, and systems with some significant negative charge attached. A
second +, such as 6-31++G, implies diffuse functions added to hydrogens. The use of doublydiffuse basis sets is especially useful if you are working with hydrides (H- ions).
1. Repeat the boron atom energy calculation for each basis set listed in the data table in the
results section. Record the total SCF energy and the number of basis functions used.
2. For each basis set used, identify the type and number of STO-nG functions used for the
core and valence electrons and whether polarized or diffuse functions are included.
Record the total number of orbitals. For the Boron atom, which approximation (choice of
basis set) is the most accurate? How does the accuracy relate to the number of basis
functions used?
Part D. How much correlation energy can we recover?
At the Hartree Fock level of theory, each electron experiences an average potential field of all
the other electrons. In essence, it is a mean field approach that neglects individual electronelectron interactions or electron correlation. Thus, we define the difference between the selfconsistent field energy and the exact energy as the correlation energy. Two fundamentally
different approaches to account for electron correlation effects are available by selecting a
Correlation method: Moller Plesset (MP) Perturbation theory and Coupled Cluster (CC) theory.
1. Based on the calculated SCF energy for the 6-311+G** basis set (see results from Part C)
determine the value of the correlation energy for boron assuming an experimental
energy of -24.608 hartrees4.
2. Select New Job Using This Geometry. Select the right arrows, until you get to the Job
Options tab. For Basis set, select 6-311+G**. Under Method, select MP4. Submit the
energy calculation and view the output. From this single submission, you can record both
the MP2 and MP4 energies.
3. Select New Job Using This Geometry. Select the right arrows, until you get to the Job
Options tab. Under Method, select CCSD(T). Submit the energy calculation and view the
output. From this single submission, you can record both the CCSD and CCSD(T)
energies.
4. For each method, determine the percentage of the correlation energy recovered.

H. S. Schaefer and F. Harris, (1968) Phys Rev. 167, 67

Part E. Can we use DFT (B3LYP) to calculate the electron affinity of boron?
The electron affinity of atom A is the energy released for the process A + e- A- or simply the
energy difference between the anion and the neutral forms of an atom. Note: Electron affinities
are reported as positive values, i.e. EA= -(Eanion-Eneutral).
It was reported5 that the electron affinity of Boron at the B3LYP 6-311+G** level of theory is 0.36 eV. In comparison to the experimental value of 0.28 eV this led to the assumption that
B3LYP does not yield a reasonable electron affinity.
1. Go to the New Job menu, and select Create New Job. Click on the small periodic table
icon on the left and select B atom. Place a single B atom by double clicking on the
drawing area. Select the right arrow button at the bottom of the drawing frame to move to
the next step.
2. Select the PSI4 computational engine. Click the right arrow to advance to the next step.
Now we select the options for the computation. Method: DFT. Functional: B3LYP.
Basis set: 6-311+G**. Submit the calculation and record the energy for neutral boron.
3. Geometry. Select the right arrows, until you get to the Job Options tab. For the anion
calculation you will set the charge to -1. Once we do that, the charge and spin multiplicity
are no longer compatible. For 2 electrons in a set of p orbitals, the multiplicity can only
be 3 (triplet state, unpaired spins) or 1 (singlet state, paired spins). Here, by Hunds rules,
we expect the spins will remain unpaired, leading to a triplet. Submit the energy
calculation and record the energy for boron anion.
4. Calculate the electron affinity. Is this literature result consistent with your calculation? (1
hartree = 27.2116 eV)
5. Repeat the electron affinity calculation of boron, but this time, assume the anion is a
singlet state. What is the reason6 for the reported failure of the B3LYP method?

5
6

B. S. Jursic, (1997) Int. J. Quantum Chem. 61, 93

C. W. Bauschlicher, (1998) Int. J. Quantum Chem. 66, 285

How do we calculate the most accurate energies of atom?

Name __________________________ Date _______________________
Lab Partner __________________________
Lab Partner __________________________

Part A
Boron: STO-3G
Job Number:__________________
SCF Energy:____________________

Number of basis functions:__________________

Part B
Boron: 3-21G
Job Number:__________________
SCF Energy:____________________

Number of basis functions:__________________

Data Analysis
Which basis set is more accurate? Please use complete and correct sentences in your discussion.

Part C
Job Number

Basis Set

SCF Energy

Number of basis functions

6-31G
6-31+G
6-31G*
6-31+G*
6-311G*
6-311+G**
cc-pVDZ
cc-pVTZ

Data Analysis
For the Boron atom, which approximation (choice of basis set) is the most accurate? How does
the accuracy relate to the number of basis functions used?

Part D
Total Correlation Energy:________________
Job Number

Method

Energy

Correlation
Energy

% recovered

MP2
N/A

MP4

N/A

CCSD
CCSD(T)

Part E
Job Number

Boron State

DFT Energy

Neutral
Anion (Triplet)
Anion (Singlet)
Data Analysis
What is the reason for the reported failure of the B3LYP method? Discuss.

Electron Affinity
N/A