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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].

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.

1

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)

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

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)

2

1.3.4 SILICON HYDRIDE

Appearance : tetrahedral

3

1.4. PRESENT WORK

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

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].

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.

4

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

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.

5

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

Ab-initio method

Density functional theory (DFT)

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

6

are of moderate size. However, semi empirical methods are also applied to solids and

Nanostructures, but with different parameterization.

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.

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.

7

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:

Unrestricted Hartree Fock (UHF)

8

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.

9

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.

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.

10

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

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

H0 F + 0 ( H F )

0 2.8

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:

11

N N/2

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

k=1 J =1

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.

12

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.

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.

13

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.

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:

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

14

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

[n0] can be written explicitly in

terms of the ground-state density n0,

V[n0] = V(r) n0 (r) d3r 2.19

can be written explicitly in

terms of the density n,

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

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.

15

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,

16

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].

Where,

N = Normalization constant

r =Radius in angstroms

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)

number beyond what is required by the atom in its electronic ground state allow

orbitals to change not size , but also shape)

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

17

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.

STO-3G

STO-4G

STO-6G

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

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

18

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

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.

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

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.

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.

SV(P)

SVP

21

TZVPP - Valence triple-zeta plus polarization

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.

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.

molecular geometry.

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.

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.

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.

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.

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 )

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

(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

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

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

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

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

GRAPH

33

1.5

0.5

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).

36

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