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Exp3 Quantum Chemical Calculation - Manual

The document discusses using quantum chemical calculations to obtain potential energy curves and orbitals of the H2+ molecule. It provides background on quantum mechanical theories of chemical bonding and introduces the Born-Oppenheimer approximation. The experiment uses the ACE-Molecule solver to calculate the energy and orbitals of H2+ at different atomic distances based on solving the Schrodinger equation numerically.

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56 views8 pages

Exp3 Quantum Chemical Calculation - Manual

The document discusses using quantum chemical calculations to obtain potential energy curves and orbitals of the H2+ molecule. It provides background on quantum mechanical theories of chemical bonding and introduces the Born-Oppenheimer approximation. The experiment uses the ACE-Molecule solver to calculate the energy and orbitals of H2+ at different atomic distances based on solving the Schrodinger equation numerically.

Uploaded by

ritu.kumari141002
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Experiment 3

Quantum Chemical calculation:


The potential energy curves and the orbitals of H2+

1. Objectives
A quantum chemistry solver is used to obtain the energy and orbitals of one
of the simplest molecules, H2+, and the formation of chemical bonding is
analyzed from a quantum-mechanical point of view.

(Refer to Sections 6.1 and 6.2 in Oxtoby 7th ed.)

2. Introduction and Background information

2-1) Quantum picture of the chemical bond


Chemical bond is the attraction to form molecules or solids and it represents
the arrangement of atoms and indicates the geometries of molecules. From a
classical point of view, chemical bonding has been represented by a model
known as the Lewis concept. However, this model cannot explain the electrons
hold the molecule together despite of repulsive force pushing nuclei apart.
Also some molecular properties cannot be described by this classical argument.
Depending on the distance between the atoms, the energy of the molecule
varies, and chemical bonds are formed at distances that maintain the lowest
energy. Let’s consider the progress of forming bond on the simplest system
H2.
Figure 1
In this figure, at distance Re, H2 has minimum energy and it is called bond
length and De is bond dissociation energy. However, according to the
uncertainty principle, the minimum energy that can be experimentally
measured is higher than this level, which has E0. Then measured energy for
bond dissociation is D0. The point at Re is useful for constructing model
potentials and optimizing molecular geometry in calculations.
The effective potential energy can be divided into the following factors in
order to explain how the negative charge existing between nuclei can
overcome the Coulomb repulsion making the nuclei attract toward each other,
which maintains the structure of the molecule; Coulomb repulsion between
two protons, Coulomb repulsion between two electrons, Coulomb attraction
between protons and electrons and kinetic energies of electrons. Then, we can
express effective potential term as sum of average kinetic energy of electrons
and average Coulomb interactions (electron-electron, nuclear-nuclear,
electron-nuclear)
Figure 2
Above figure shows the contribution of average kinetic energy and average
potential energy (Coulomb interactions) to effective potential energy. The
change of the 𝑉𝑉� (eff) will be described in three intervals:

(Interval A)

Figure 4

Figure 5
Black dots: protons, Yellow dots: electrons.
Solid line indicates interaction between the nucleus and the electron which
belongs to same atom, while dashed line indicates interaction between the
nucleus and the electron which was belongs to the other atom.
𝑉𝑉� : As the distance between atoms becomes closer, one electron begins to
interact with a proton at another atom, and the amount of interaction with a
proton at the same atom decreases. The average potential size increases.

Figure 6

Figure 7

: As discussed in Particle-in-a-box model, the electron's kinetic energy


decreases as the size of the box is increased (eq 4.37 in Oxtoby 7th ed).

Since the degree of decrease in kinetic energy is greater than the degree of
increase in potential energy, the effective potential energy decreases and
chemical bonding begins to occur.

(Interval B)
𝑉𝑉� : As the distances between the electron and the nuclei are decrease, average
potential energy decreases.

: The confinement of the electron to the smaller volume yields the increase
of the average kinetic energy.
(Interval C)
𝑉𝑉� : If distance between two nuclei is too small, their high repulsion energy
increase the average potential energy.

: The confinement of the electron to the smaller volume yields the increase
of the average kinetic energy.

One of the purpose of this class is quantitative quantum chemical calculation


of curves at the Figure 1 and Figure2. To do so, we need to solve the well-
known equation, Schrodinger's equation. By solving this equation, we can
obtain the wave functions of the electrons and their corresponding energies
in a given system. In section 2-2) we will look at the basic quantum mechanical
theories for quantitative computation of this curve.

2-2) Quantum chemical calculation


(*This section has brief explanation of a quantum chemistry (or mechanics).
If you want to study more about this subject, refer to chapter 4, 5)

Several experiments have confirmed wave-particle duality, and it has been


found that the motion of the particles is not explained by the classical
mechanics. In classical mechanics, the motion of an object is described
according to Newton's law of motion, while the Schrödinger equation plays a
role in quantum mechanics. You can refer to chapter 4(p168~p169) of Oxtoby
7th ed for the origin of the Schrödinger equation and the validity of it.

� which is
How the physical system is organized determines the form of 𝐻𝐻
called Hamiltonian operator. Then, “solving the Schrödinger equation” means
that finding pair of ψ and corresponding E which satisfies this differential
equation and they are the solutions of it. Generally, it has multiple solutions.
Then we write as

(𝑖𝑖 are integers)

ψ indicates wave function , and it is the amplitude of the wave related to the
motion of a particle. In particular, the wave function in one electron picture is
called orbital. It can have positive, negative or zero values. The points or
region with the zero amplitude of the wave function are called nodes. The
wave function cannot be measured directly. Instead, we use ψ2 as a
probability density of the particle and ψ(x, y, z)2 𝑑𝑑𝑑𝑑 is the probability that the
particle exists in a small volume 𝑉𝑉. This probabilistic interpretation have shown
consistent result of the motion on a microscopic scale.
E is the energy associated with this wave function. Each wave function has
corresponding energy value, which means the system has discrete values. It
shows that the energy quantization is the consequence of Schrödinger
equation. The wave function corresponds to the lowest energy value is called
ground state and others are called excited states.
One of the example system called “Particle-in-a-box” can be described by the
Schrödinger equation and it can be solved exactly (or analytically). You can
practice solving the Schrödinger equation for this model (pp 172–4, Oxtoby
7th ed).

2-3) Using quantum chemical solver


The Schrodinger equation is a kind of differential equation and can be solved
analytically for simple systems, such as the particle-in-a-box model, the
hydrogen atom system or the H2+ molecule system to be covered in the class.
Solving the differential equation analytically means that the exact solution can
be obtained by algebraic operations of the symbols in the equation, calculus,
trigonometry, or other mathematical techniques. However, the Schrödinger
equations of many other systems are complex to solve analytically, and
therefore requires a numerical analysis to obtain approximate solutions instead
of exact solutions. Since, it takes too much time to get the solutions manually
by numerical methods, some research institutes design algorithms of
numerical analysis and obtain the solution with HPC (High performance
computing). Many solvers have been developed which can calculate the
various physical properties of molecules by devising numerical methods and
algorithms. These solvers can expand the quantum mechanical theories and
calculate the physical properties of the material. For example, the three-
dimensional structures and the energies of the molecules which is in ground
and excited state, IR frequencies, and the transition states and so on.
The solver we will use in this class is ACE-Molecule, which is being developed
by the Prof. Woo Youn Kim’s Laboratory in KAIST chemistry department.
To obtain the curves of Figure 1 and Figure 2 using quantum chemical
calculations, we need an important assumption of the Born Oppenheimer
approximation. The curves discussed in the previous section 2-1) also assumed
the Born-Oppenheimer approximation.

Born-Oppenheimer approximation
The mass of the nucleus is much larger than that of the electron. Thus, we can
assume that the motion of electron is much faster than that of the electron,
which means the positions of the nuclei can be fixed. Then, the kinetic energy
of the nucleus is zero and the nucleus-nucleus Coulomb potential energy is
constant. Based on this Born-Oppenheimer approximation, the energy of a
molecule can be calculated as following two steps.

1) Solve the equation for electronic Hamiltonian first. Then we get the
orbitals (single electron’s wave function) and their energies
2) To get the total energy of the molecule, add the nucleus-nucleus
Coulomb potential to the orbital energies.

Following is the schematic diagram to calculate the effective potential energy


curve of diatomic molecules.

3. Requisites
3-1) ACE-Molecule solver, installed in a remote server EDISON.
3-2) An orbital viewer program VESTA.

4. Procedure
(Refer to the PPT file for details)
1) Prepare input files:
One input file and 10 structure files
2) Sign in to EDISON (chem.edison.re.kr).
Account information will be given by the TA.
3) Select the ACE-Molecule (KDFT ver2.0.3) solver
4) Submit your jobs.
One input file and a structure file comprise one simulation job.
5) Download output files and analyze them.

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