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INTRODUCTION

1.1. NONCOVALENT INTERACTIONS

Noncovalent interactions are of great importance in chemistry and biochemistry .They are
responsible for the formation, stability and biological activity of many macromolecules in living
systems. The hydrogen bond (HB)[1] probably the most widely studied and analyzed class of
noncovalent interactions. In, recent years, much attention has been paid to a specific
intermolecular interaction involving tetra, pnicogen, chalcogen and halogen atoms. A tetral
bond refers to the noncovalent interaction (NCI) between a group-IV atom (C, Si, Ge or Sn) in a
molecule with a Lewis base centre on other. The formation of tetral bonding can be explained by
a region of positive electrostatic potential which is present on the outermost portion of some
covalently bonded group IV atom surface, opposite to the covalent bond. This electron-deficient
region is referred as a -hole.

The dihydrogen bond is a special kind of HB, arising from the close approach of a
protonic H atom and a hydridic H atom. This interaction is typically characterized by unusually
short H.H internuclear separation that is less than or equal to the sum of the Vander Waals radii
of the two hydrogen atoms, and a normally linear R-H.H bond angle. Dihydrogen bonding has
been identified in a variety of systems and the concept of dihydrogen bonding has become
important in many fields, although the study of it is far smaller than that of conventional HBs.
The Origin of dihydrogen bond has been studied with many methods including natural bond
orbital, quantum theory of atoms in molecules and energy decomposition analysis[2].

1.2 COOPERACTIVE EFFECTS

When two or more noncovalent interactions coexist in a complex, they can mutually
enhance each others strength and, thus, cooperative effects occur. Cooperative effects between
the noncovalent interactions are currently a topic of wide ranging interest due to their extremely
important role in chemical reactions, molecular recognition and regulation of biochemical
processes[3]. Cooperative effects in open-chains of halogen bond, chalcogen bond, pnicogen bond
and tetral bond interactions has been reported. The coopreativity between two different -hole
interactions has been extremely studied.

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1.3 PROPERTIES OF MOLECULES
1.3.1 SODIUM HYDRIDE
Chemical formula : NaH
IUPAC name : sodium hydride
Melting point : 300c(572F;573K) decomposes
Molar mass : 23.99771 g/mol-1
Solubility : insoluble in ammonia, benzene
Appearance : white or grey solid
Crystal structure : FCC (NaCl)

1.3.2 MAGNESIUM HYDRIDE


Chemical formula : HMgH
IUPAC name : magnesium hydride
Melting point : 923 k (650c, 1202F)
Molar mass : 26.3209 g/mol-1
Solubility : insoluble in ether
Appearance : white crystal
Crystal structure : tetragonal

1.3.3 BERYLLIUM HYDRIDE


Chemical formula : HBeH
IUPAC name : beryllium hydride
Melting point : 250C (482F; 523 K) decomposes
Molar mass : 11.03 g/mol-1
Solubility : insoluble in diethyl ether, toluene
Appearance : amorphous white solid
Crystal structure : FCC (NaCl)

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1.3.4 SILICON HYDRIDE

Chemical formula : H4Si

IUPAC name : silicon hydride

Melting point : -185c (-301.0 F ; 88.1 K)

Molar mass : 32.12 g/mol-1

Solubility : soluble in water reacts slowly

Appearance : tetrahedral

Crystal structure : colorless

1.3.5 LITHIUM HYDRIDE

Chemical formula : HLi

IUPAC name : lithium hydride

Melting point : 688.7c (1,271 F; 573 K) decomposes

Molar mass : 7.95 g/mol-1

Solubility : slightly soluble in dimethylformamide react with ammonia

Appearance : colorless to gray solid

Crystal structure : FCC (NaCl-type)

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1.4. PRESENT WORK

1. To analyze the geometry of the binary XH3Si.NCH and NCH.HM


(X=Li,Na,Cl,Br) and (M=Li,Na,BeH,MgH)complexes using quantum chemical methods.

2. To calculate the total and interaction energy of these complexes.

3. To analyze the Mullikan atomic charges of individual atoms

1.5 COMPUTATIONAL DETAILS

The geometries of monomers and complexes are fully optimized at B3LYP/augcc-pVTZ


level of theory. The interaction energy of all optimized complexes are calculated using
B3LYP/augcc-pVTZ method. They have been computed as the difference between the total
energies of the complexes and have been corrected for energy using the counterpoise method.
The interaction energy is calculated using the formula[4].

Eint (corr) = EAB (AB) [EA (AB) + EB (AB) ]

In this equation, the term EB (AB) is the energy of the complexes with the basis set of
monomers A and B, EB (AB) is the energy of monomers A with the full dimer basis set by setting
the appropriate nuclear charges to zero, which is located at the same intermolecular
configurations as in the complex, with similar to other.

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QUANTUM CHEMICAL METHODS

Quantum chemical methods[5] are powerful tools used to study the molecular
structure and reactions of chemical systems with the aid of computers. It allows experimental
determination of molecular properties such as bond length, bond angle, dipole moment, chemical
hardness etc. Experimentally some methods can be used to model not only stable molecules,
but also short lived, unstable intermediates and transition state. Thus, they can provide
information about molecule and reactions, which is impossible to obtain through observation.

Molecular mechanics
Electronic structure theory

2.1 MOLECULAR MECHANICS

Molecular mechanics consider molecules as a collection of atomic masses held


together by sticky forces. These represent the electron holding the atoms to form molecule. In
molecular mechanics each atom stimulated as a single particle. Each particle is assigned a radius,
polarizability and a constant net charge, and potential energy function is used to calculate
binding constant, protein folding kinetics, protonation equilibrium, and active side co-ordination
and to design binding site. The goal of molecular mechanics is to build a computer model of
reality. This is done with potential energy function. Parameters are then selected for that
potential function so that molecules whose structures, energies and properties are, known can be
reproduced with degrees of prison. Once that has been accomplished, the molecular model may
be used to computer structures, energies and properties of unknown molecules. Molecular
mechanics[6] has several limitations. It is necessary to have access to a data set of known, related
molecules to use parameterization. Thus, the discovery of completely new molecular species
with this computational method is not possible. Also molecular mechanics cannot account for
bond making or bond breaking, because of the way it implicitly treat electrons. Finally, the
motion less structure computed is not very realistic, so many scientist implement molecular
dynamics to achieve better model molecules.

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2.1.1 ELECTRONIC STRUCTURE METHOD

The first step in solving the schrodinger equation with the electronic molecular
Hamiltonian, which is called the electronic structure of molecule, implies essentially its chemical
properties. The electronics structure of the molecule is determined by the equation of quantum
mechanics. There are three major classes of electronics structure method used to solve the
Schrodinger equation for many electron systems.

They are

Semi empirical method


Ab-initio method
Density functional theory (DFT)

2.2. SEMI- EMPRICAL METHOD

Semi empirical quantum chemistry methods are based on the Hartree Fock
formalism, but make many approximations and obtain some parameters from empirical data.
They are very important in computational chemistry for treating large molecules where the full
Hartree Fock method without the approximation is too expensive. The use of empirical
parameters appears to allow some inclusion of electron correlation effects into the methods.
Within the framework of Hartree Fock calculation, some pieces of information (such as two
electron integrals) are sometimes approximated or completely omitted. In order to correct for this
loss, semi empirical methods are parameterized, that is their results are fitted by a set of
parameter, normally in such a way as to produce results that best agree with experimental data,
but sometimes to agree with ab initio results . Semi empirical methods follow what are often
called empirical methods where the two electron part of the Hamiltonian is not explicitly
included. For - electron systems, this was the Huckel method proposed by Erich Huckel. For all
valence electron systems, the extended Huckel method was proposed by Roald Hoffmann. Semi
empirical calculations are much faster than their abintio counterparts, mostly due to the use of
the zero differential overlap approximation. Their results, however, can be very wrong if the
molecule being computed is not similar enough to the molecules in the database used to
parameterize the method. Semi empirical type calculations have been most successful in the
description of organicchemistry, where only a few elements are used extensively and molecules

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are of moderate size. However, semi empirical methods are also applied to solids and
Nanostructures, but with different parameterization.

2.3. AB INITIO METHOD

Ab initio quantum chemistry[7] methods are computational chemistry methods


based on quantum chemistry. The term ab initio was first used in quantum chemistry by Robert
parr and coworkers,including David Craig in a semiempirical study on the excited states of
benzene. Ab initio electronic structure methods have the advantage that they can be made to
cover the exact solution, when all approximations are sufficiently small in magnitude and when
the finite set of basic functions tends towards the limit or a complete set. In this case,
configuration interaction where all possible configurations are included tends to the exact non
relativistic solution of electronic Schrodinger equation. The convergence however is usually not
monochromatic and sometimes the smallest calculation gives the result for some properties. The
downside of ab initio methods is their computational cost they often take enormous amount of
computer time, memory, and disk space. The simplest type of ab initio electronic structure
calculations is the Hartree Fock (HF) scheme, in which the instantaneous Columbic electron
electron repulsion is not specifically taken into account. Only its average effect (mean field) is
included in the calculations. This is a variation procedure; therefore, the obtained approximate
energies, expressed in terms of the systems wave functions, are always equal to or greater than
the exact energy, and tend to a limiting value called the Hartree Fock limit as the size of the
basis is increased.

Many types of calculations begin with a Hartree Fock calculations and


subsequently correct for electron electron repulsion, referred to also as an electronic
correlation. Moller plesset perturbation theory (MPn) and coupled cluster theory (CC) are
examples of these post Hartree fock methods. In some cases, particularly for bond breaking
processes, theHartree Fock method is inadequate and this single-determinant reference function
is not a good basis for post HartreeFock methods .It is then necessary to start with a wave
function that includes more than one determinant such as multi configurational self consistent
field (MCSCF) and methods have been developed that use these multi determinant references
for improvements.

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2.3.1. THE FOCK METHODS

In computational physics and chemistry, the Hartree Fock (HF) method [8] is a
method of approximation for the determination of the wave function and the energy of a quantum
many body system in a stationary state. The Hartree Fock method often assumes that the
exact, N body wave functions of the systems can be approximated by a single Slater
determinant (in the case where the particles are fermions) or by a single permanent (in the case
of bosons) of N spin orbitals. By invoking the variation method, one can derive a set of N-
coupled equations for the N spin orbitals. A solution of these equation yields the Hardee Fock
wave function and energy of the system. Especially in the older literature, the Hartree Fock
method is also called the self consistent field method (SCF). In deriving what is now called the
Hartree equation as approximate solutions of the Schrodinger equation. Hartree required the final
field as computed from the charge distribution to be self consistent with the assumed initial
field. Thus, self consistency was a requirement of the solution. The equations are almost
universally solved by means of an iterative method, although the fixed point iteration algorithm
does not always coverage. This solution scheme is not the only one possible and is not an
essential feature of the Hartree Fock method.

The Hartree Fock method finds its typical application in the solution of the
Schrodinger equations for atoms, molecules, nanostructures and solids but it has a found
widespread use in nuclear physics. In atomic structure theory, calculations may be for a spectrum
with many excited energy levels and consequently the Hartree Fock method for atoms assumes
the wavefunction as a single configuration state function with well-defined quantum number and
that the energy level is not necessarily the ground state. For both atoms and molecules, the
Hartree Fock solution is the central starting point for most methods that describe the many
electron system more accurately. Where the atom or molecules is a closed shell system with al
orbitals (atomic or molecular) doubly occupied. Open shell systems, where some of the
electrons are not paired, can be dealt with by one of two Hartree Fock methods:

Restricted open shell Hartree Fock (ROHF)


Unrestricted Hartree Fock (UHF)

2.3.2 HARTREE FOCK SELF CONSISTENT FIELD THEORY


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The Hartree Fock method is typically used to solve the time independent Schrodinger
equation for a multi electron atom or molecule as described in the Born Oppenheimer
approximation[9]. since there are no known solutions for many electron systems (there are
solution for one electron systems such as hydrogenic atoms and the diatomic hydrogen cation),
the problem is solved numerically. Due to which the nonlinearities introduced by the Hartree
Fock approximation, the equations are solved using a nonlinear method such as iteration, which
method such as iteration, which gives rise to the name self consistent field method. The
Hartree fock method makes five major simplifications in order to deal with this task:
The Born Oppenheimer approximation is inherently assumed. The full
molecular wave function is actually a function of the coordinates of each of the
nuclei, in addition to those of the electrons.
Typically, relativistic effects are completely neglected. The momentum operator is
assumed to be completely non relativistic.
The variation solution is assumed to be a liner combination of a finite number of
basis function, which are usually (but not always) chosen to be orthogonal. The
finite basis set is assumed to be approximatelycomplete.
Each energy eigenfunction is assumed to be describable by a since
Slaterdeterminant, an antisymmetrized product of one electron wave functions
(i.e., orbitals)
The mean field approximation is implied. Effects arising from deviations from
this assumption , known as electron correlation , are completely neglected for the
electrons of opposite spin , but are taken into account for electrons of parallel spin
Electron correlation should not be confused with electron exchange , which is
fully accounted for in the Hartree Fock method .
Relaxation of the last two approximation give rise to many so called post Hartree
Fock methods .The electron electron repulsion term of the electronic molecular Hamiltonian
involves the coordinates of two different electrons , it is necessary to reformulate it in an
approximate way . Under this approximation , (outlined under Hartree Fock algorithm ), all of
the terms of the exact Hamiltonian except the Nuclear nuclear repulsion term are re
expressed as the sum of one electron operators outlined below , for closed shell atoms or
molecules (with two electrons in each spatial orbital) . The "(1)" following each operator symbol
simply indicates that the operator is 1-electron in nature.

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2

N/2
F [ {J}] (1) = Hcore (1) + jj(1) kj(1) ] ..2.1

J =1

Where

F [ {J } ] (1)
is the one-electron Fock operator generated by the orbitals J ,and
Hcore (1) = -1/2 2/1-za/rla ..2.2
is the one-electron core Hamiltonian. Also jj (1)is the Coulomb operator, defining the electron-
electron repulsion energy due to each of the two electrons in the jth orbital.kj(1)is the exchange
operator, defining the electron exchange energy due to the antisymmetry of the total n-electron
wave function. This (so called) "exchange energy" operator, K, is simply an artifact of the Slater
determinant. Finding the HartreeFock one-electron wave functions is now equivalent to solving
the eigenfunction equation:
F (1) i(1) = ii(1) ..2.3

Where i(1) U are a set of one-electron wave functions, called the HartreeFock molecular
orbitals.

2.4 MOLLER PLESSET PERTURBATION THEORY

Mller Plesset perturbation theory (MP)[10] is one of several quantum chemistry post-
HartreeFock ab initio methods in the field of computational chemistry. It improves on
the HartreeFock method by adding electron correlation effects by means of Rayleigh
Schrdinger perturbation theory (RS-PT), usually to second (MP2), third (MP3) or fourth (MP4)
order. Its main idea was published as early as 1934 by Christian Mller and Milton S. Plesset.

2.4.1 RAYLEIGHSCHRDINGER PERTURBATION THEORY (RS-PT)

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The MP perturbation theory is a special case of RS perturbation theory. In RS theory one
considers an unperturbed Hamiltonian operator H0, to which a small (often external)
perturbation Vis added

H = H0 + V .2.4

Here, is an arbitrary real parameter that controls the size of the perturbation. In MP theory, the
zeroth-order wave function is an exact eigenfunction of the Fock operator, which thus serves as
the unperturbed operator. The perturbation is the correlation potential. In RS-PT the perturbed
wave function and perturbed energy are expressed as a power series in :

= Lim i( i) .2.5

E = Lim i E ( i) .2.6

Substitution of these series into the time-independent Schrdinger equation gives a new
educationas m

(H0 + V )( i( i ) ) = ( i E ( i) ) ( i( i) ) .2.7

Equating the factors of kin this equation gives a kth-order perturbation equation, where k = 0, 1,

2,... m.

2.4.2.MOLLERPLESSETPERTURBATIONORIGINAL

FORMULATION

The MP-energy corrections are obtained from RayleighSchrdinger (RS) perturbation


theory with the unperturbed Hamiltonian defined as the shifted Fock operator,

H0 F + 0 ( H F )
0 2.8

and the perturbation defined as the correlation potential,

V H - H0 H - ( F + 0 ( H F )
0 ) 2.9

Where the normalized Slater determinant 0 is the lowest Eigenstate of the Fock operator:

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N N/2

F0 = f ( k ) o=2 C i 0 2.10
k=1 J =1

Here N is the number of electrons in the molecule under consideration (a factor of 2 in


the energy arises from the fact that each orbital is occupied by a pair of electrons with opposite
spin), H is the usual electronic Hamiltonian, f(K) is the one-electron Fock operator, and i is the
orbital energy belonging to the doubly occupied spatial orbital i.
Since the Slater determinant 0 is an eigenstate of F, it follows readily that

F0 0 F
00 =0 H00 = H00 H
00 , 2.11

i.e. the zeroth-order energy is the expectation value of H with respect to 0, the Hartree-Fock
energy. Similarly, it can been seen that in this formulation the MP1 energy

EMP1 0 V
0 = 0 2.12

Hence, the first meaningful correction appears at MP2 energy. In order to obtain the MP2
formula for a closed-shell molecule, the second order RS-PT formula is written in a basis of
doubly excited Slater determinants. (Singly excited Slater determinants do not contribute because
of the Brillouin theorem). After application of the SlaterCondon rules for the simplification
of N-electron matrix elements with Slater determinants in bra and ket and integrating out spin, it
becomes
EMP2 i,j,a.bi j v a b a b v i j / Ci+ CjCaCb ..2.13

Where i and j are canonical occupied orbitals and a and b are virtual (or
unoccupied) orbitals. The quantities i, j, a, and b are the corresponding orbital energies.
Clearly, through second-order in the correlation potential, the total electronic energy is given by
the HartreeFock energy plus second-order MP correction: E EHF + EMP2. The solution of the
zeroth-order MP equation (which by definition is the HartreeFock equation) gives the Hartree
Fock energy. The first non-vanishing perturbation correction beyond the HartreeFock treatment
is the second-order energy.

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2.4.3 USE OF MOLLER PLESSET PERTURBATION METHODS

Second (MP2), third (MP3), and fourth (MP4) order MllerPlesset calculations are
standard levels used in calculating small systems and are implemented in many computational
chemistry codes. Higher level MP calculations, generally only MP5, are possible in some codes.
However, they are rarely used because of their cost. Systematic studies of MP perturbation
theory have shown that it is not necessarily a convergent theory at high orders. Convergence can
be slow, rapid, oscillatory, regular, highly erratic or simply non-existent, depending on the
precise chemical system or basis set. The density matrix for the first-order and higher MP2 wave
function is of the type known as response density, which differs from the more usual expectation
value density. The eigenvalues of the response density matrix (which are the occupation numbers
of the MP2 natural orbitals) can therefore be greater than 2 or negative. Unphysical numbers are
a sign of a divergent perturbation expansion. Additionally, various important molecular
properties calculated at MP3 and MP4 level are no better than their MP2 counterparts, even for
small molecules.

2.5. DENSITY FUNCTIONAL THEORY (DFT) METHOD

Density functional theory (DFT)[11] is a computational quantum mechanical modeling


method used in physics, chemistry and materials science to investigate the electronic
structure (principally the ground state) of many-body systems, in particular atoms, molecules,
and the condensed phases. Using this theory, the properties of a many-electron system can be
determined by using functionals, i.e. functions of another function, which in this case is the
spatially dependent electron density. Hence the name density functional theory comes from the
use of functional of the electron density. DFT is among the most popular and versatile methods
available in condensed-matter physics, computational physics, and computational chemistry.

DFT has been very popular for calculations in solid-state physics since the 1970s.
However, DFT was not considered accurate enough for calculations in quantum chemistry until
the 1990s, when the approximations used in the theory were greatly refined to better model
the exchange and correlation interactions. Computational costs are relatively low when compared
to traditional methods, such as exchange only HartreeFock theory and its descendants based on
the complex many electron wave function.

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Despite recent improvements, there are still difficulties in using density functional theory
to properly describe intermolecular interactions (of critical importance to understanding chemical
reactions), especially Vander Waals forces (dispersion); charge transfer excitations; transition
states, global potential energy surfaces, dopant interactions and some other strongly
correlated systems and in calculations of the band gap and ferromagnetism in
semiconductors. Its incomplete treatment of dispersion can adversely affect the accuracy of DFT
(at least when used alone and uncorrected) in the treatment of systems which are dominated by
dispersion (e.g. interacting noble gas atoms) or where dispersion competes significantly with
other effects (e.g. in bimolecular). The development of new DFT methods designed to overcome
this problem, by alterations to the functional or by the inclusion of additive terms to account for
both core and valence electrons or by the inclusion of additive terms, is a current research topic.

2.5.1 DERIVATION AND FORMULATION

As usual in many-body electronic structure calculations, the nuclei of the treated


molecules or clusters are seen as fixed (the BornOppenheimer approximation), generating a
static external potential V in which the electrons are moving. A stationary electronic state is then
described by a wave function (r 1..rN) satisfying the many-electron time-
independent Schrdinger equation:

H [ T + V + U ] (-h2 /2 mii2 ) + JN V(ri ) + I<J U(ri , rj) = ..2.14

where, for the N-electron system, H is the Hamiltonian[12,13], E is the total energy, T is the
kinetic energy, V is the potential energy from the external field due to positively charged nuclei,
and U is the electron-electron interaction energy. The operators T and U are called universal
operators as they are the same for any N-electron system, while V is system dependent. This
complicated many-particle equation is not separable into simpler single-particle equations
because of the interaction term U.

There are many sophisticated methods for solving the many-body Schrdinger equation
based on the expansion of the wave function in Slater determinants. While the simplest one is
the HartreeFock method, more sophisticated approaches are usually categorized as post-
HartreeFock methods. However, the problem with these methods is the huge computational

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effort, which makes it virtually impossible to apply them efficiently to larger, more complex
systems.

Here DFT provides an appealing alternative, being much more versatile as it provides a
way to systematically map the many-body problem, with U, onto a single-body problem
without U. In DFT the key variable is the electron density n(r) which for a normalized is given
by
n(r) N d3 r2. d3 rN* (r1,r2 .rN) (r1,r2.rN ) (r1,r2.rN ) 2.15
This relation can be reversed, i.e., for a given ground-state density n0(r) it is possible, in
principle, to calculate the corresponding ground-state wave function 0 (r1.rN). In other
words, is a unique functional of H0

0 = n0 .2.16
and consequently the ground-state expectation value of an observable O is also a functional of n0
n0n0
n0 .2.17
In particular, the ground-state energy is a functional of n0
E0 = E[n0] = [ n0 ] T+ V + U
[ n0 ] .2.18

Where the contribution of the external potential < [n0] V


[n0] can be written explicitly in
terms of the ground-state density n0,
V[n0] = V(r) n0 (r) d3r 2.19

More generally, the contribution of the external potential < V


can be written explicitly in
terms of the density n,

V [n] = V (r) n (r) d3r. 2.20

The functional T [n] and U[n] are called universal functional, while V[n] is called a non-
universal functional, as it depends on the system under study. Having specified a system, i.e.,
having specified V, one then has to minimize the functional

E[n] = T[n] + U[n] + V(r)n(r)d3r 2.21

With respect to n(r), assuming one has got reliable expressions for T[n] and U[n]. A
successful minimization of the energy functional will yield the ground-state density n0 and thus
all other ground-state observables.

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The variation problems of minimizing the energy functional E n can be solved by
applying the Lagrangian method of undetermined multipliers. [12] First, one considers an energy
functional that doesn't explicitly have an electron-electron interaction energy term,

Where the second term denotes the so-called Hartree term describing the electron-
electron Coulomb repulsion, while the last term VXC is called the exchange-correlation potential.
Here, VXC includes all the many-particle interactions. Since the Hartree term and VXC depend
on n (r) which depends on the i, which in turn depend on VS, the problem of solving the Kohn
Sham equation has to be done in a self-consistent (i.e., iterative) way. Usually one starts with an
initial guess for n(r), then calculates the corresponding V and solves the KohnSham equations
for the i. From these one calculates a new density and starts again. This procedure is then
repeated until convergence is reached. A non-iterative approximate formulation called Harris
functional DFT is an alternative approach to this.
In the present study, B3LYP of density functional theory has been applied to study the
nature of bonding in XH3Si.NCH and NCH.HM complexes.

BASIS SET

A basis set in chemistry is a set of functions (called basis functions) which are combined
in linear combinations (generally as part of a quantum chemical calculation) to create orbitals,

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which are explained as a linear combination of such functions with the weights or coefficient to
be determined. Usually these functions are atomic orbital in that they are centered on atoms.
Otherwise, the functions are centered on bonds or lone pairs. Pairs of functions centered in the
lobes of a p orbital have also been used. Additionally, basis set composed of sets of plane waves
down to a cutoff wavelength are often used, especially in calculations involving systems with
periodic boundary conditions[14].

Basis Function = N * e-alpha*r

This expression given as Slater type orbital (STO)

STO = ( 3/0.5) e (-r)

Where,

N = Normalization constant

alpha = Orbital exponent

r =Radius in angstroms

The different kinds of basis sets are,

The minimal basis set (includes one basis function for each set occupied atomic
orbital with distinct principal and angular momentum quantum number) split
valence basis set (includes two or more sizes of basis function for each valance
orbital )

Double zeta (dz) basis set (a split valance set that includes exactly twice as many
Functions as the minimal basis set)

Extended basis set (the set larger than that double zeta basis set)

Polarized basis set (incorporates basis functions of higher angular quantum


number beyond what is required by the atom in its electronic ground state allow
orbitals to change not size , but also shape)

3.1. MINIMAL BASIS SETS

The most common minimal basis set is STO-nG, where n is an integer. This n value
represents the number of Gaussian primitive functions comprising a single basis function. In

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these basis sets, the same number of Gaussian primitives functions comprises core and valence
orbitals. Minimal basis sets typically give rough results that are insufficient for research-quality
publication, but are much cheaper than their larger counterparts.

Commonly used minimal basis sets[15] of this type are:

STO-3G

STO-4G

STO-6G

STO-3G* - Polarized version of STO-3G

There are several other minimum basis sets that have been used such as the MidiX basis sets

3.2. SPLIT-VALANCE BASIS SETS

During most molecular bonding, it is the valence electrons which principally take part in
the bonding. In recognition of this fact, it is common to represent valence orbitals by more than
one basis function (each of which can in turn be composed of a fixed linear combination of
primitive Gaussian functions). Basis sets in which there are multiple basis functions
corresponding to each valence atomic orbital are called valence double, triple, quadruple-zeta,
and so on, basis sets (zeta, , was commonly used to represent the exponent of an STO basis
function). Since the different orbitals of the split have different spatial extents, the combination
allows the electron density to adjust its spatial extent appropriate to the particular molecular
environment. Minimum basis sets are fixed and are unable to adjust to different molecular
environments.

3.3. POPLE BASIS SETS

The notation for the split-valence basis sets arising from the group of John Pople is
typically X-YZg. In this case, X represents the number of primitive Gaussians comprising each
core atomic orbital basis function. The Y and Z indicate that the valence orbitals are composed of

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two basis functions each, the first one composed of a linear combination of Y primitive Gaussian
functions, the other composed of a linear combination of Z primitive Gaussian functions. In this
case, the presence of two numbers after the hyphens implies that this basis set is a split-valence
double-zeta basis set. Split-valence triple- and quadruple-zeta basis sets are also used, denoted
as X-YZWg, X-YZWVg, etc. Here is a list of commonly used split-valence basis sets [16] of this
type:

3-21G

3-21G* - Polarized

3-21+G - Diffuse functions

3-21+G* - With polarization and diffuse functions

4-21G

4-31G

6-21G

6-31G

6-31G*

6-31+G*

6-31G(3df, 3pd)

6-311G

6-311G*

6-311+G*

19
The 6-31G* basis set (defined for the atoms H through Zn) is a valence double-zeta
polarized basis set that adds to the 6-31G set six d-type Cartesian-Gaussian polarization
functions on each of the atoms Li through Ca and ten F-type Cartesian Gaussian polarization
functions on each of the atoms Sc through Zn.

3.4. CORRELATION CONSISTENT BASIS SETS

Some of the most widely used basis sets are those developed by Dunning and coworkers
since they are designed to converge systematically to the complete-basis-set (CBS) limit using
empirical extrapolation techniques. For first- and second-row atoms, the basis sets are cc-pVNZ
where N=D, T, Q, 5, 6, (D=double, T=triples, etc.). The 'cc-p', stands for correlation-consistent
polarized' and the 'V' indicates they are valence-only basis sets. They include successively larger
shells of polarization (correlating) functions (d, f, g, etc.)[17,18]. More recently these 'correlation-
consistent polarized' basis sets have become widely used and are the current state of the art for
correlated or post-HartreeFock calculations. Examples of these are:

cc-pVDZ - Double-zeta

cc-pVTZ - Triple-zeta

cc-pVQZ - Quadruple-zeta

cc-pV5Z - Quintuple-zeta, etc.

aug-cc-pVDZ, etc. - Augmented versions of the preceding basis


sets with added diffuse functions.

For period-3 atoms (Al-Ar), additional functions are necessary; these are the cc-pV (N+d)
Z basis sets. Even larger atoms may employ pseudopotential basis sets, cc-pVNZ-PP, or
relativistic-contracted Douglas-Kroll basis sets, cc-pVNZ-DK.These basis sets can be augmented
with core functions for geometric and nuclear property calculations, and with diffuse functions
for electronic excited-state calculations, electric field property calculations, and long-range
interactions, such as Vander Waals forces. A recipe for constructing additional augmented

20
functions exists; as many as five augmented functions have been used in second
hyperpolarizability calculations in the literature. Because of the rigorous construction of these
basis sets, extrapolation can be done for almost any energetic property, although care must be
taken when extrapolating energy differences as the individual energy components may converge
at different rates.

H-He Li-Ne Na-Ar

cc-pVDZ [2s1p] 5 func. [3s2p1d] 14 func. [4s3p1d] 18 func.

cc-pVTZ [3s2p1d] 14 func. [4s3p2d1f] 30 func. [5s4p2d1f] 34 func.

cc-pVQZ [4s3p2d1f] 30 func. [5s4p3d2f1g] 55 func. [6s5p3d2f1g] 59 func.

To understand how to get the number of functions take the cc-pVDZ basis set for H:
There are two s (L = 0) orbital and one p (L = 1) orbital that has 3 components along the z-axis
(mL = -1, 0, 1) corresponding to px, py and pz. Thus, five spatial orbitals in total. Note that each
orbital can hold two electrons of opposite spin.

3.5. OTHER SPLIT VALENCE BASIS SET

Some other basis sets are:

SV(P)

SVP

DZV - Valence double-zeta

TZV - Valence triple-zeta

21
TZVPP - Valence triple-zeta plus polarization

QZVPP - Valence quadruple-zeta plus polarization

3.6. PLANE WAVE BASIS SET

In addition to localized basis sets, plane-wave basis sets can also be used in quantum-
chemical simulations. Typically, a finite number of plane-wave functions are used, below a
specific cutoff energy which is chosen for a certain calculation. These basis sets are popular in
calculations involving periodic boundary conditions. Certain integrals and operations are much
easier to code and carry out with plane-wave basis functions than with their localized
counterparts.

In practice, plane-wave basis sets are often used in combination with an 'effective core
potential' or pseudo potential, so that the plane waves are only used to describe the valence
charge density. This is because core electrons tend to be concentrated very close to the atomic
nuclei, resulting in large wave function and density gradients near the nuclei which are not easily
described by a plane-wave basis set unless a very high energy cutoff, and therefore small
wavelength, is used. This combined method of a plane-wave basis set with a core pseudo
potential is often abbreviated as a PSPW calculation[19].

Furthermore, as all functions in the basis are mutually orthogonal and are not associated
with any particular atom, plane-wave basis sets do not exhibit basis-set superposition error.
However, they are less well suited to gas-phase calculations. Using Fast Fourier Transforms, one
can work with plane-wave basis sets in reciprocal space in which not only the aforementioned
integrals, such as the kinetic energy, but also derivatives are computationally less demanding to
be carried out. Another important advantage of a plane-wave basis is that it is guaranteed to
converge in a smooth, monotonic manner to the target wave function, while there is only a
guarantee of monotonic convergence for all Gaussian-type basis sets when used in variation
calculations. (An exception to the latter point is the correlation consistent basis sets.) The
properties of the Fourier Transform allow a vector representing the gradient of the total energy
with respect to the plane-wave coefficients to be calculated with a computational effort that
scales as NPW*in(NPW) where NPW is the number of plane-waves. When this property is

22
combined with separable pseudo potentials of the Kleinman-Bylander type and pre-conditioned
conjugate gradient solution techniques, the dynamic simulation of periodic problems containing
hundreds of atoms becomes possible.

3.7. REAL SPACE BASIS SET

On the same principle as the plane waves but in real space, there are basis sets whose
functions are centered on a uniform mesh in real space. This is the case for the finite difference,
the functions sins or wavelets. In the case of the latter, it is possible to have an adaptive mesh
closer to the nucleus using the scaling properties of wavelets. These methods use functions that
are localized which allow the development of order N methods[20].

The basis set aug-cc-pVTZ has been employed to optimize the complexes in the present
study.

23
RESULTS AND DISCUSSION

4.1 GEOMETRY

The linear NCH molecule is made to interact with the symmetric top molecules such as
SiH4, SiH3F, SiH3Cl and SiH3Br. Further, NCH is interacted with asymmetric top molecules like
LiH, NaH, BeH2 and MgH2 to analyze the nature of bonding that exists during the interaction.
The structures are fully optimized using the B3LYP/aug-cc-pVTZ level of theory and the
optimized structures are shown in Figure 1. The existence of hydrogen bonds is noted in all the
complexes.

4.2 GEOMETRICAL PARAMETERS

The three dimensional arrangement of atoms that constitute a molecule is called as


molecular geometry.

4.2.1. BOND LENGTH

The bond length is defined as the average distance between the centre of two atoms
bonded together in a molecule. The bond lengths are calculated using B3LYP/aug-cc-pVTZ level
of theory. The observed values of bond length for all the chosen molecules are given in the
Table-1. The estimated Si.N binding distances in the XH 3Si.NCH complexes are in the
range of 3.15-3.63, which are much smaller than the sum of the Vander Waals radii of the Si
and N atoms (3.65) along the sequence of X=H>Cl>Br. However, the Si.N binding

24
distances in the FH3Si.NCH complex is much larger than the sum of the Vander Walls radii of
the Si and N atoms.

The optimized H-H binding distances are estimated to be 1.76, 1.94 and 2.07, 1.76 in
the NCH.HLi, NCH.HNa, NCH.HBeH and NCH.HMgH complexes. That is the two
types of interaction have a cooperative effect on each other.

4.2.2. BOND ANGLE

It is defined as the angle formed between three atoms across at least two bonds .The
torsion angle is the angle between two planes four atoms bonded together in a straight chain. The
torsion angle is the angle between two plane formed by the first three atoms and the plane
formed by the last three atoms. The bond angles for the optimized structures of molecules are
given in the Table-2. The X-Si.N and C-H.H angle is close to 180 in all optimized
complexes which confirms that the complex exhibit linear structure.

4.3. ENERGETICAL PARAMETERS

4.3.1. TOTAL ENERGY

The total energy values of the complexes have been calculated at B3LYP/aug-cc-pVTZ
level of theory and are listed in Table-3. They have been computed as the difference between the
total energy of the complexes and the interaction energy of the isolated monomers and have been
corrected for basis set superposition error (BSSE) using the counter poise method. The total
energy of XH3Si.NCH(X=H, F, Cl, Br) complexes lies in the range -385.3820 to -2959.0638
Hartree. The calculated total energy of NCH.HM (M=Li, Na, BeH, MgH) lies in the range
-101.5634 to -294.7383 Hartree. H4Si.NCH, BrH3Si.NCH, NCH.HLi and NCH.HMgH
are found to possess similar energy values. The calculated interaction energy of NCH.HM
complexes ranges from -1.69 to -8.40 Kcal/mol and become more negative in the order of
M=Na>Li>HMgH>HBeH. The shorter the H.H distance, larger the interaction energy. This is
observed in NCHHM (M=Li,Na) with the presence of shorter H.H distance.

Earlier studies of Esrafili[21] shows that the Si.N and H.H distances are shorter than
the present study. Hence, larger interaction energy is noted. The result shows that MP2\aug-cc-

25
pVTZ level of theory gives better result than B3LYP\aug-cc-pVTZ to describe the molecular
structures of XH3Si.NCH.HM(X=H, Fl, Cl, Br; M=Li ,Na, Cl, Br) complexes.

4.3.2. DIPOLE MOMENT

The electric dipole moment () is a measurable physical property of a polar molecule.


The dipole moment of a molecule is the sum of the individual bond on the nature of the atoms
and on their arrangement. The calculated values shown in Table-4, shows that the halogenated
complexes FH3Si.NCH,ClH3Si.NCH and BrH3Si.NCH have dipole moment around 5.3 to
5.6 Debye which are found to be larger than H 4Si.NCH complex. NCH.HM (M=Li,Na)
have on overall larger dipole moment of nearly 10 Debye ,whereas NCH.HM (M=BeH,MgH)
have less dipole moment around 4.

4.3.3. MULLIKEN ATOMIC CHARGE

A widely used method to analyse SCF wave function is population analysis introduced by
Mulliken. He proposed a method that apportions the electrons of an n-electron molecule into net
population nr in the basis function. Mulliken charges arise from the Mulliken population analysis
and provide a means of estimating partial atomic charges from calculations carried out by the
methods of computational chemistry, particularly these based on the linear combination of
atomic orbital and molecular orbital and molecular orbital method, and are routinely used as
variables in regression procedure. The distribution of charges among various atoms in the
complexes are shown in Table- 5.The charge distribution among various atoms are shown in
Graph-1. Mulliken populations[22] can be used to characterise the electronic charge distribution in
a molecule and the bonding, antibonding and nonbonding nature of the molecular orbital for
particular pairs of an atom.

26
TABLES

TABLE 1

Bond length (R in ) for binary XH3Si.NCH and NCH.HM complexes ( X=H,F,Cl,Br ) and
( M=Li,Na,BeH,MgH )

COMPLEX RSiN COMPLEX RH.H


H4Si.NCH 3.6336 NCH.HLi 1.7676
FH3SiNCH 3.7308 NCH.HNa 1.7686
ClH3SiNCH 3.1530 NCH.HBeH 2.0722
BrH3SiNCH 3.1632 NCH.HMgH 1.9470

TABLE 2

Bond angle ( in degree) for binary XH3Si.NCH and NCH.HM complexes ( X=H,F,Cl,Br )
and ( M=Li,Na,BeH,MgH)

COMPLEX
H4Si.NCH 178
FH3SiNCH 179
ClH3SiNCH 179
BrH3SiNCH 179
NCH.HLi 179
NCH.HNa 179
NCH.HBeH 179
NCH.HMgH 179

27
TABLE 3

Total energy (E in Hartree), interaction energy (Eint in kcal/mol ) for binary XH3Si.NCH
and NCH.HM complexes ( X=H,F,Cl,Br ) and ( M=Li,Na,BeH,MgH )

COMPLEX E Eint
H4Si.NCH -385.3820 -0.31
FH3SiNCH -484.7323 -2.08
ClH3SiNCH -845.0724 -3.13
BrH3SiNCH -2959.0638 -3.71
NCH.HLi -101.5634 -8.34
NCH.HNa -256.3475 -8.40
NCH.HBeH -109.3900 -1.69
NCH.HMgH -294.7383 -3.45

TABLE 4

Dipole moment of ( in Debye) XH3Si.NCH and NCH.HM complexes(X=H,F,Cl,Br) and


(M=Li, Na, BeH ,MgH)

COMPLEX
H4Si.NCH 3.4618
FH3SiNCH 5.2733
ClH3SiNCH 5.4994
BrH3SiNCH 5.5798
NCH.HLi 10.0791
NCH.HNa 10.7902
NCH.HBeH 3.5499
NCH.HMgH 3.9655

28
TABLE 5

Mulliken atomic charge distribution of binary XH3Si.NCH and NCH.HM complexes


(X=H,F,Cl,Br ) and (M=Li, Na, BeH ,MgH)

COMPLEX ATOM MULLIKEN ATOM MULLIKEN


CHARGE CHARGE
Si 1.3564 N -0.1741
H -0.2955 C -0.4482
H4Si.NCH H -0.2944 H 0.6350
H -0.2977
H -0.4763
Si 1.1290 N -0.2684
H -0.1357 C -0.4111
FH3SiNCH H -0.1358 H 0.6498
H -0.1332
F -0.6942
Si 1.0894 N -0.1952
H -0.1904 C -0.4164
ClH3Si.NCH H -0.1903 H 0.6343
H -0.1904
Cl -0.5498
Si 1.0820 N -0.1809
H -0.1926 C 0.2148
BrH3Si.NCH H -0.1937 H 0.0000
H -0.1929
Br -0.5366

COMPLEX ATOM MULLIKEN ATOM MULLIKEN

29
CHARGE CHARGE
N -0.5162 H 0.6395
NCH.HLi C -0.3944 Li 0.1464
H 0.1246
N -0.4944 H 0.0463
NCH.HNa C -0.4050 Na 0.4351
H 0.4180
N -0.5145 H 0.2585
NCH.HBeH C -0.2845 Be -0.1404
H 0.7548 H -0.0739
N -0.5451 H -0.2337
NCH.HMgH C -0.2301 Mg 0.2294
H -0.1129 H 0.8924

FIGURES

30
(a) H4Si.NCH

(b) FH3Si.NCH

31
(c) ClH3Si.NCH

(d) BrH3Si.NCH

(e) NCH.HLi

32
(f) NCH.HNa

(g) NCH.HBeH

(h) NCH.HMgH

Figure 1: Optimized structures of X-H3SiNCHHM(X=H,F,Cl and Br) & (M=Li,Na,MgH


and BeH) complexes calculated at B3LYP/augcc-pVTZ level of theory

GRAPH

33
1.5

0.5

Mulliken atomic charge

0
Si H H H H F Cl Br N C H H Li Na Mg Be H

-0.5

-1

Atoms

GRAPH 1: Mulliken atomic charge of binary complexes XH3Si....NCH (X=H, F, Cl and Br) &
(M=Li, Na, MgH and BeH)

CONCLUSION

34
The molecular structure of eight binary molecules such as H 4Si, FH3Si, ClH3Si, BrH3Si,
HLi,HNa, HBeH, HMgH, has been optimized using B3LYP/aug-cc-pVTZ level of theory. The
structure of H4Si, FH3Si, ClH3Si and BrH3Si shows that they are symmetric top molecules while,
HLi, HNa, HBeH, HMgH are asymmetric top molecules. Further, the symmetric and asymmetric
top molecules are made to interact with each other. The interactions show the existence of
dihydrogen bonds in the complexes. The geometrical parameters such as bond angle and bond
length are calculated and analyzed. The calculated Si.N and H..H binding distances in the
XH3Si.NCH.HM complexes are always shorter than those of isolated XH 3Si.NCH and
NCHHM complexes, the two type of interactions have a cooperative effect on each other. The
energetical parameters are also analyzed. The interaction energy has been computed as the
difference between the total energies of the complexes and the energy of the isolated monomers
and have been corrected for basic set super position error (BSSE) using the counter poise
method. The calculated interaction energy of NCH.HM complexes ranges from -1.692 to
-8.40 kcal/mol and become more negative in the order of M =Na>Li>HMgH>HBeH. It can be
concluded that shorter the HH distance, larger the interaction energy. The calculated dipole
moment shows that NCH.HM (M =Li,Na) have an overall dipole moment of nearly 10 Debye,
whereas NCH.HM (M =BeH, MgH) have practically less dipole moment around 4. The
Mulliken atomic charges are also analyzed from the optimized geometry. The study can be
further extended in the future to gain knowledge on molecular properties and nature of the bonds
present in the complexes.

REFERENCES

35
1) S.Scheiner, Hydrogen Bonding. A Theoretical perspective(Oxford University press, New
York, (1997).
2) M.D. Esrafili, H. Behzadi, j. Beheshitan, and N.L. Hadipour, J. Mol. GRAPH. Model.
27,326 (2008).
3) M.D. Esrafili, H. Behzadi, and N.l. Hadipour, Biophys. Chem. 133, 11 (2008).
4) A. Bauza, R. Ramis, and A. Frontera, Comput. Theor. Chem. 1038, 67 (2014).
5) S. Zahn, R. Frank, E. Hey- Hawkins, and B. Kirchner, chem.: Eur.J. 17, 6034 (2001).
6) I. Alkorta, G. Sanchez-sanz, J. Elgureoo, and J.E.DelBene, J. Chem. Theory Comput. 8,
2320 (2012).
7) I. Alkorta. J. Elguero, and J.E. Del Bene, J. Phys. Chem. A 117, 10497 (2013).
8) G.Aruldhas, quantum Chemistry 2nd edition.
9) N.Rosch, 2003. Counterpoise correction Technical University of Munich, Quantum
Chemistry Laboratory. Retived 14 May 2010.
10) W.Wang, BJi, and Y.Zhang, J Phys .Chem. A 113,8132 (2009)
11) M.D Esrafili and F. Mohammadian-Sabet,Chem. Phys.Lett.634,210(2015)
12) T.Clark, M.Hennemann, J.S Murray and P.Politzer, J.Mol. Model. 13,291 (2007)
13) P.Metrangolo, G.Resnat8i, T. Pilatii, and S. Biella, Halogen Bonding in crystal
Engineering (Springer Verlag, Berlin, 2008).
14) P. Metrangolo, J.S. Murray, T. Pilati, P. Politzer, G. Resnati, and G. Terraneo, Cryst. Eng.
Comm. 13, 6593 (2011).
15) P. Pliter and J.s. Murray, Theor. Chem. Acc.108, 134 (2002).
16) J.S. Murray, P. Lane, and O. Politzers, J. Mol. Model. 15,723 (2009).
17) J.S. Murray, P.Lane, T. Clark, K.E. Riley, and P. Politzer, J. Mol. Model. 18, 541 (2012).
18) A. Bundhun, P. Ramasami, J. Murray, and P. Politzer, J. Mol. Model. 19, 2739 (2013).
19) D. Mani and E. Arunan, Phys. Chem. Chem. Phys. 15, 14377 (2013).
20) Q. Li, X. Guo, X. Yang, W. Li, J. cheng, and H. B. Li, Phys. Chem. Chem. Phys. 16,
11617 (2014).
21) M.D. Esrafiliand F. Mohammadian Sabet, J. Mol. Model. 21 (1), 60 (2015).
22) M.D,Edrafili, R. Nurazar, and F. Mohammadiam Sebet, Mol. Phys. 113,3703
(2015).

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