Chapter Two
Chapter Two
Theoretical study
2.1 Introduction
Molecular modeling methods in physics and theoretical chemistry are widespread
for examining many computational properties such as energies of molecules, molecular
geometry, electronic structure, electron and charge distribution, infrared (IR), ultraviolet
(UV), and nuclear magnetic resonance (NMR) spectra, physical properties, catalytic drugs,
and other molecular systems. Perhaps the best of these methods is the density functional
theory test (DFT) [31].
Because of the success of the DFT test in atomic and molecular physics issues and
solid state calculations, this method has proven successful even in nuclear calculations, so it is
a method approved by many physicists [33].
Theoretical physicists and chemists use four main methods in their calculations: they include
molecular mechanics methods, semi-empirical (SE) methods, ab-initio methods and density
functional theory methods. The key to theoretical physics is molecular quantum mechanics
[34].
2.2 Quantum mechanics theory
It is part of modern physics and is concerned with studying the behavior of matter,
including light at the atomic and subatomic levels. This theory tries to explain the behavior of
the atom and its basic components, while classical physics is concerned with studying the
phenomenal things and their mechanics, such as determining location, velocity, momentum,
and momentum. A property confined to objects, as waves do not have momentum, and this is
possible in classical physics, while this thing is not possible in quantum mechanics, because it
is not possible to determine the location of subatomic objects with high accuracy along with
their momentum at the same time, and this is confirmed by the principle of inaccuracy of
Heisenberg [35].
2.3 Heisenberg Uncertainty Principle
One of the most important principles of quantum theory was formulated by the
German theoretical physicist Heisenberg in 1927, which states that it is not possible to
calculate two measured characteristics of a quantum system with the same accuracy at the
same time [36].
{
−
ℏ 2 2 Ze 2
2m
∇ −
r }
ψ (r )=Eψ (r )
...........................(5)
Where:
: Plank constant (h) divided by 2 . and : The wave function of an electron.
^
H Ψ (r)= E Ψ (r) ...............................(6)
The Hamiltonian operator with a large number of electron can be expressed in a similar
way. It is the sum of the kinetic energy operators of the nucleus and electrons, as well as the
potential energy operator denoted by the many Coulomb interactions by the following
equation [42]
N 2n 2n N 2n N
1 1 2 1
H =− ∑
T
∇ A − ∑ ∇ 2p + ∑ r −1
pd −∑ ∑ Z A r Ap + ∑ Z A Z B R AB
−1 −1
2 A MA 2 p p<d A p A <B ......
..(7)
Where MA is the mass of nucleus A , m electronic mass, ZA, ZB are the charges
on nuclei A and B, respectively, rpd is the distance between p and d electrons,
and RAB is the distance between nuclei A and B. The general form of
Schrödinger equation will be[43]
HT(1,2,…,N,1,2,..,n) Ψ(1,2,…,N,1,2,..,n)=EΨ(1,2,…,N,1,2,..,n) ...............(8)
WhereΨ(1,2,…,N,1,2,..,n) is the entire wave function for all particles in the
molecule and is the overall energy of the system.
2. Normalize.
3. Form a complete set.
Completeness refers to the ability to create the "delta function," which is the
sharpest possible function of the unit area, from the whole set of eigen functions.
The energy of a wave function can be calculated using the Hamiltonian
operator's predicted value [44,45].
E=¿ ^
H>¿
∫ ¿
Ψ H^ Ψ dv
...................................(10)
∫ Ψ ¿ Ψ dv
The wave function Ψ describes the many-particle systems.
When applying the Pauli exclusion principle in solving the Schrödinger equation for
many-electron atoms, molecules, or solids. The wave function becomes asymmetric. The
physicist Hartree was the first to derive the many-electron Schrödinger equations, and the
entire wave function, according to Hartree, can be approximated as a series of one-electron
wave functions [46] .
n
Ψ tot =∏ Ψ i (x ) ........................( 11)
i=1
When Hartree solved the non-time dependent Schrödinger equation, he did not take into
account the Pauli exclusion principle so Fock and Slater updated this method to include the
effect of electron exchange and the exclusion principle; So he used Slater's determinant, and
the wave function resulted, including systems consisting of n electrons, as shown below [47]
| |
Ψ 1 (x 1) Ψ 2 ( x 1) … Ψ n ( x 1)
1 Ψ 1 (x 2) Ψ 2 ( x 2) ⋯ Ψ n ( x 2)
Ψ ( 1,2 ,… , n )= ...................(12)
√n ! ⋮ ⋮ ⋱ ⋮
Ψ 1 (x n) Ψ 2 ( x n) ⋯ Ψ n ( x n)
Hartree-Fock equations, are a type of self-consistent field equation. These equations are
formatted as follows:
[ H core + ∑ ( 2 J j −K j ) ]Ψ i=∑ ε ij Ψ j i=1,…,n
j j ............................(13)
FΨ =∑ ε ij Ψ j i=1 , … , n ..............................(14)
j
Empirical wave functions are used to interchange potential integrals and differential equations
and to solve the N Hartree-Focke equations. Solving the n equations results in a new set of
wave functions. Then, the new wave functions are used to calculate a new set of possible
integrals. The cyclic approach is repeated for the estimated wave functions or potential
integrals to remain unchanged, because the final wave functions produce potential integrals,
which in turn produce identical wave functions within a given admission, at the equations.
( 16 ), this approach is known as the self-consistent field method [48,49].
2.7 Density functional theory ( DFT)
The quantum mechanical method of density functional theory (DFT) is frequently
used to study the electronic structure of many-electron systems in physics and chemistry. It is
presently one of the most important techniques for determining the ground state properties of
metals, semiconductors, and insulators [50].
Thomas Fermi's model provided the basis for density theory. In 1927, Thomas and Fermi
described the energy of an atom as a function of electron density, integrating that with
standard equations, nuclear, electron, and electron–electron interactions can be expressed in
terms of electron density [51]. The system is only affected by three coordinates, regardless of
the number of electrons in it [50]
N=∫ ρ ( r⃗ ) d ⃗r ...........................(15)
The ground state energy can be calculated by DFT, the ground state properties depend on the
electron density. The electronic density corresponds to the fine ground conditions of the
system when the total energy is low [52, 53].
Runge and Gross discussed how excited states are obtained using TD-
DFT. The starting point of studying time-dependent systems is the time-
dependent Schrodinger equation. The TD- DFT is straight related to the
∂
Schrodinger equation [iℏ ∂t Ψ ( r⃗ , t ) = ^
H Ψ ( r⃗ , t )] where the Hamiltonian is known to
be[58,59,60]:
^
H=Τ^ + V
^ elec . elec. + V
^ ext . ( r⃗ , t ) … … … … … … … … … … … .(16)
Here, ^
H consists of the kinetic energy operator Τ^ , electron-electron repulsion
^ ^ ^ (⃗r ) is
V elec . elec. (Coulomb operator) and the external potential V ext . ( r
⃗ ) .Where V ext .
The densities of the system rise from a fixed first stateΨ ( t 0 )=Ψ ( 0). The
first state, Ψ ( 0) , is arbitrary, it must not be the ground-state or some other eigen
state of the first potential V^ ext . (⃗r ,t 0 ) = V^ 0 (⃗r ).The R-G theorem indicates that there
exists an one-to-one correspondence between the time-dependent external
potentialV^ ext . (⃗r ,t ), and the time-dependent electron density ρ( r⃗ , t), for systems
developing from a fixed first many-body state. Translation to it, the density
determines the external potential, and next helps in obtaining the time-dependent
many-body wave functions[57,58].
As this wave-function controls all observables of the systemas
animportant, the saying point is that all observables are functionals of ρ( r⃗ , t).
The statement of the theorem is the “densities ρ( r⃗ , t) and ρ' ( ⃗r ,t )evolving from the
same initial state Ψ ( 0) under the effect of two potentials V^ ext . (⃗r ,t ) and V^ 'ext . ( r⃗ , t )are
always different provided that the potentials differ by additional than a chastely
time-dependent function[58,59,61]:
^ (⃗r ,t )= V
V ^ 'ext . ( r⃗ , t )+ C ( t ) … … … … … … … … … … … .(18)
ext .
Where the C ( t ) allows increase to wave functions that are different only by
a phase factor exp (−iC ( t ) ), therefore, the same electronic density is stable. R-G
theorem states that the density is a functional of the external potential and of the
first wave function on the space of potentials differing by more than the addition
of C ( t ).
… … … … … . … .(19)
B 3 LYP LSDA HF B 88 LYP LSDA
E XC =( 1−a ) E X +a E XC +b E X +c E C + ( 1−c ) EC
Where the three parameters (a=0.20, b=0.72 and c=0.81), these values were
found by fitting the experimental data. The first parameter (a) specified the
amount of exact exchange, while (b) and (c) control the contribution of
exchange and correlation.
Basis Sets 2.10
The STO’s are exponential that mimic the exact eigen functions of the
hydrogen atom where in 1930 the physicist John C. Slater, who introduced
them. The STO’s can be defined in spherical polar coordinates as[70,71,72]:
STO n−1 −ξ r⃗
χ =N ⃗r e Y lm (θ , φ ) … … … … … ….. … .(20)
classified as below:
HOMO and LUMO and their resultant energy gap did not only determine
the path the molecules interacts with other species, but their energy gap helps
label the chemical reactivity and kinetic constancy of the molecule. A molecule
with a small frontier orbital gap is more polarizable and is generally related with
a high chemical reactivity, low kinetic stability and it is also termed as a soft
molecule[72,84].
The total energy ET signifies the sum of total kinetic and potential
energy of the system, at the relax structure where the total energy of the
molecule must be at the lowest value because the molecule is at the equilibrium
position, which means the resulting of the real forces is zero[83,85].
The ionization potential (Ionization Energy I E ) for a molecule is the quantity of
energy needed to remove an electron from an atom or molecule and expressed as
the energy difference between the positive charged energy E+¿ ¿ and the neutral En
( I E =E+¿−E ¿). The HOMO and LUMO energy were also used to compute I E in the
n
Within the plan of the DFT, one of the global amounts is chemical
potential ( x ), it measures the escapeetendency of an electronic cloud. It is a
constant, through all space, for the ground state of an atom, molecule or solid,
and equals the slope of the energy versus N curve at constant potential v (⃗r ):
x=
[ ]
∂E
v … … … … … … … … .(26)
∂ N (r⃗ )
1 ∂X
H= ( ) … … … … ….. … .(28)
2 ∂ N V (⃗r )
In terms of I E and E A , the hardness is half of the energy gap between two frontier
orbitals[87,89]:
I E −E A
H= … … … … … … … … .(29)
2
The hard molecule has a large energy gap. The theoretical meaning of
chemical hardness has been providing by the DFT as the second derivative of
electronic energy with respect to the number of electrons N , for a constant
potential V ( r⃗ )[88,89]:
H=
[ ] [ ]
1 ∂2 E
2 ∂ N2
=
V (⃗r )
1 ∂x
2 ∂N V (⃗r )
… … … … … … … .(30)
The soft molecules have a small energy gap and this means small
excitation energies to the various of excited states, their electron density changes
more simply than hard molecules, and due to that, soft molecules will be more
reactive than hard molecules. The electronic softness S is a property of
molecules that measures the degree of chemical reactivity. It is the inverse of H
[88,91]:
( ) ( )
2
1 ∂ N ∂N
S= = = … … … … … ..(31)
2H ∂E
2
V ( ⃗r)
∂K V ( ⃗r)
( )
2
∂ E
∝a ,b = ( a , b=x , y , z ) … … … … … … ...(35)
∂ Fa∂ Fb
The polarizability⟨ ∝ ⟩is calculated as the mean value and given as in the
following equation[95]:
1
⟨ ∝ ⟩= ( ∝ XX +∝ yy +∝ zz ) … … … … … … ….. … .(36)
3
Here ∝ XX , ∝ yy∧∝ZZ denoted the eigen values of the polarizability tensor.
The dipole moment ( P) signifies the first derivative of the energy with respect to
an applied electric field. It is a measure of the asymmetry in molecular charge
distribution. The unit Measurement of dipole moment is Debye (1 Debye =
Coulomb .meter ). In quantum mechanical account of dipole moment,
−30
3.336 ×10
∂E
EF = [ ∂ N ] 𝑣 (r) .......................................( 37).
1
EF ≈ 2 (E HOMO + E LUMO ) .....................................(38)
The valence band is an energy band that lies below the conduction band. When the
valence band is filled to the brim with electrons and the conduction band is devoid of any
electron, the material loses its electrical conductivity. Therefore, there must be some voids
within the valence band to conduct electricity, or the presence of some electrons in the
conduction band. One of these spaces is called an electron hole.
In order for an electron to move from the valence band to the conduction band it needs energy
at least equal to the band gap. In order to fall from the conduction band to the valence band, it
must lose energy at least equal to the bandgap in the form of light (photon) or heat (phonon).
This process is called (electron injection). If the bandgap is direct, the electron releases its
energy in the form of a photon. If the bandgap is indirect, release its energy in the form of a
phonon. The transfer of electrons between the conduction and valence bands is used in several
applications, the most important of which are the solar cell, lasers, masers, and the luminous
diode [102].
and this process can be calculated through the following equation:
All calculations in this study have been performed by using the Gaussian
09package of Programs, GaussView 5.0.8, Gauss Sum 3.0 and other assistant
programs.These programs are described as below:
Gaussian 09 (G09) Program 2.15.1
The Gaussian program is acomputational software package initially
published by John Pople in 1970. Gaussian program is a very high-end quantum
mechanical software package. The “09” mentions to the year 2009 in which the
software was published[107].
Gaussian is capable of running all of the major methods in molecular
modeling, including molecularmechanics,ab-initio, semi-empirical, HF and
DFT. Moreover, excited state computes can be done by different methods in this
program[108].
The name originatesGaussian comes from the use of the Gaussian Type
Orbitals that Gaussian's originator, John Pople, used to try to overcome the
computational difficulties that get up from the use of Slater Type Orbitals. A
number of researchers, such as S.F. Boys and Isaiah Shavitt, Pople, quite
brilliantly, recognized that the (relatively) simple, substitution of a series of
Gaussian functions for the Slater function, would greatly simplify the rest of the
calculation of the Schrödingerequation. Pople (1998) was awarded the Nobel
Prize in chemistry (along with Walter Kohn) for this work[107,108].
Gauss View Program 2.15.2
Gauss View was designed to import the input files for the Gaussian
program and also used to prove the output files for Gaussian program in the
dimensional photo, Gaussian view which not used as calculation program, but it
is simplicity the work on Gaussian program and supply the users three major
advantages.First: enable the user to draw the molecules including the big one,
also enable the rotation, transferring and changing it size easily and the mouse.
Second:Gaussian view permits to achieve many of the Gaussian calculation,
making the complex input preparation for the routine work and the advanced
method.Third: Gaussian view permits the inspection of Gaussian calculations
results using variety of geometrical techniques and this involved the balanced
molecular patterns electronic density surfaces[107,108].