Document Type : Original Article
Author
 Nabieh Farhami ^{}
Department of Chemistry, Mahshahr Branch, Islamic Azad University, Mahshahr, Iran
Abstract
The effect of the adsorbed thiophene (T) on the surface of (8,0) zigzag single walled boron nitride nanotubes (BNNTs) was studied using density functional theory calculations in the gas phase. Geometry optimizations were also carried out at the B3LYP/631G (d) level of theory. The Gaussian 09 suites of programs were used. The geometric optimization of (8, 0) BNNTT was performed using the minimum energy criterion in six different configurations of the adsorbed thiophene on the nanotube. Our computer simulations have found that the preferred adsorption site of the molecule is at the end of the nanotube for the T component and all cases have physical interactions. The results showed an increase in polarity due to the proper distribution of electrons. It was also found that the reduction in global hardness, energy gap and electronic chemical potential due to thiophene adsorption leads to an increase in the stability of the (8,0) zigzag BNNTT complex. In this study, natural bond analysis, global softness, ionization potential and electrophilicity index for nanotubes were calculated.
Graphical Abstract
Keywords
Introduction
Boron nitride nanotubes (BNNT) were experimentally synthesized in 1995 [12]. Boron is the only known element to form cage molecule clusters and tetragonal structure. Due to the polar nature of BN bonds, BNNTs nanostructures are expected to have a higher reactivity than their carbon structure [3,4] The BNNTs have special features such as short and open length that make these types of systems suitable for biological applications [3,4]. The BNNTs are semiconductors with wide band gaps and independent of tube diameter and helicity [5,6] that have higher chemical and thermal stability than carbon nanotubes (CNT) [7]. These nanostructures have been used for storage as well as detection of hydrogen molecules [8,9]. Theoretical studies [1015] have shown variation in the magnetic and electronic properties of both nano tubes and nano sheets made up of BN when these structures interact with organic molecules or functional groups. Thiophene is a conjugated heterocyclic compound with the molecular formula C_{4}H_{4}S consisting of a planar fivemembered ring [3,4]. On the other hand, thiophene molecule (T; C4H4S), which belongs to heterocyclic molecules, is present in petroleum products [16,17]. Based on the presenceof delocalized electrons in sulfur and adjacent carbons 1 and 2, we can point to the high reactivity of this molecule (Figure 1). It is possible to change the electronic properties of nanotubes for technological applications. Mills et al. studied the adsorption reactions of thiophene upon Mo_{2}N/ Al_{2}O_{3 }catalysts using FTIR spectroscopy. The experimental studies also showed the reactive adsorption of thiophene on Ni/ZnO structure. Denis and Iribarne studied thiophene adsorption on single wall carbon nanotubes and graphene using the VDWDF and LDA functionals [21]. Peyghan et al. studied adsorption of thiophene on the pristine(6,0) AlN nanotubes in the gas phase using DFT calculations [21] and also Peyghane et al. studied electronic structure and adsorption process of imidazole on (6,0) zigzag boron nitride nanotube [22]. Baei et al. investigated the adsorption of thiophene over Zn_{12}O_{12} nanocage structure [21]. Chigo Anota et al. studied heterocyclic molecules interactions [23].
Figure 1. Exhibition delocalized electrons on sulfur atom and adjacent carbons 1 and 2
We studied thiophene adsorption on the SWBNNT surface with 6 different configurations. Moreover, we researched the quantum molecular descriptors [18,19], energy gap, global softness (s), electronic chemical potential ( ), global hardness ( ), electrophilicity index ( ), [20]^{ }and electronegativity ( ) of the nanotubes.
Simulation models and computational details
The DFT method is the standard model in many Gamess and Gaussian computational chemistry software systems. For modeling, this research used an 8core computer system with 500GB of memory and a 2.3 GHz processor running Windows 7. Calculations were performed by Gaussian09. Calculations were based on the density functional theory (DFT) because this method has a higher calculation speed compared to other methods with the same accuracy. The B3LYP method and the basic set of 631G (# B3LYP/631G) were used for optimization of structures and calculation of interaction energy. The Gaussian software was used to prepare input data and perform calculations. Using a series of graphic softwares such as Nanotube Modeler, HyperChem and GaussView, the desired molecular geometry structure was first drawn. Then, necessary commands were applied to determine the required calculations. Finally, Gaussian09 was introduced as the input file, and in the next Gaussian step, calculations were presented as numbers by solving the Schrödinger electron eqaution. BELYP is a hybrid method in which the electron correlation energy is calculated from Equation (1)
In this work, the main calculations of total energy are first performed to investigate the interactions of (8, 0) BNNT with thiophene. To determine the interaction distance between thiophene and nanotubes (Figure 2), we examined six different geometric configurations.
In the first configuration, the thiophene fragment is directed to the boron atom. In the second configuration, the thiophene is placed parallel to the boron atom. In the third, the thiophene is perpendicular to the central hexagon of the nanotube surface; in the fourth, the thiophene is placed parallel to the central hexagon of the nanotube surface; in the fifth, the fragment is perpendicularly oriented to N of the nanotube end; and in the sixth configuration, the thiophene is perpendicularly oriented to B of the nanotubes end.
Neutrality and multiplicity 1, were considered for the aromatic molecule, BNNT and BNNTthiophene systems. The properties of (8, 0) chiral nanotubes with specifications of length 25nm and diameter 1 A was also studied. The BNNT contains a total of 80 atoms (40N, 40B). The interacting molecule is thiophene. The energy gap is determined as the difference between the HOMO (Highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) orbital energies. The molecular energy adsorbed on the BN nanotubes is defined as follows:
The use of the localized basis sets reliably reduces the amount of required computational work when using them with large vacuum regions in the unit cell. However the finiteness of the localized basis sets leads to a basis set superposition error (BSSE) as described by Tournus and Charlier in a study of benzene on CNT [18]. E (BSSE) is defined as the basis set superposition errors. For measuring the chemical reactivity, we determine the chemical potential as the arithmetic average which shows that the chemical potential of free electron gas is equal to the fermi level and it is considered as the center of the energy gap [14].
The work function is defined as the minimum required energy for removal of an electron from a solid to a point immediately outside the solid surface or the energy required for transfer of an electron from the fermi energy level into the vacuum. This work function is determined as the energy difference between the vacuum level (LUMO orbital) and the fermi level (chemical potential). Work function was calculated and it is equal to 0.393eV.
Figure 2. Six different geometrical configuration BNNTT complexes
Results and Discussion
The geometric optimization (Table 1a,b,c) was performed using previously defined criteria (Figure 3). The results indicated that the atomic structure of the interaction between the BNNT and fragment is in the most stable state in configuration 6, as shown in Table 2. The aim of the present paper is to gain the quantum molecular descriptors and adsorption properties of the nanotube system. The systems studied are BNNTthiophene, BNNT, thiophene, ) Figure 3( that exhibit a semiconductor behavior with energy gap values (HOMOLUMO energy difference) ( eV), ( eV), eV). The system with BNNTT exhibited a gap reduction. The polarity increased from for BNNT to for BNNTT. The electrical conductivity changes are calculated with formula (3), where is the energy gap of the HOMOLUMO difference, is the Boltzmann's constant, is the given temperature [14] and is the electrical conductivity of the complex.
According to the above equation, a larger energy gap at a certain temperature leads to a smaller electrical conductivity.
Figure 3. The geometric optimization of thiophene molecule and BNNT
Table 1a. The optimal energy of thiophene molecule and BNNT
Fragment 


Thiophene 


BNNT (8,0) 
3190.848 

Table 1b. The optimum geometrical parameters for the thiophene
Bond lenght (^{0}A) 
Thiophene 
CH 
1/087 
CC 
1/42 
CC 
1/37 
CS 
1/71 
Table 1c. The optimum geometrical parameters for the BNNT
Bond lenght (^{0}A) 
BNNT 
NB(16) 
1/45 
NB(25) 
1/45 
Table 2. Energy of six configuration for BNNTT complexes
Configuration BNTT 

1 
3739.0224 
2 
3739.0245 
3 
3738.9984 
4 
3739.0273 
5 
3739.0228 
6 
3739.0281 
We studied adsorption behavior of thiophene on the SWBNNT with the (8, 0) zigzag SWBNNT model consisting of (B_{40}N_{40}) atoms. In the first step, the structures were allowed to relax using all atomic geometrical parameters in the optimization at the DFT level of B3LYP exchange functional and 631G (d) standard basis set. We calculated the adsorption energy ( as follows
For the nanotubes, quantum molecular descriptors [1617], electronic chemical potential , global hardness , electrophilicity index [18], energy gap and global softness (s) were calculated as follows:
_{ }
where ) is the ionization potential and ) is the electron affinity of the molecule. The electrophilicity index is a measure of the electrophilic power of a molecule. The quantum molecular descriptors were compared for the BNT and thiophene adsorbed on the (8,0) zigzag BNNT (Table 3). All calculations were carried out using the Gaussian 09 suites of programs.
Table 3. The calculated properties for BNNT and BNNT T complex
Property 
BNNTT^{a} 
BNNT^{b} 
Energy gap 
0.00979 
0.01034 
I 
0.20395 
0.18305 
A 
0.194 
0.1727 
Η 
0.00489 
0.00517 
𝞵 
0.199 
0.1778 
S 
102.145 
96.711 

4.045 
3.0599 
^{a,b} Units are eV
Natural bond orbital analysis
Based on the NBO analysis (Tables 47), NHO direction and bending of the bond (deviation from line of nuclear centers) can be estimated to understand the position of and orbitals. These data are often useful for predicting the direction of geometry changing results from geometric optimization. The direction of a hybrid is specified in terms of the polar and azimuthal angles of the vector describing its pcomponent. The hybrids directions are then compared with the direction of the center lines between two nuclei to determine the bending of those bonds, which are expressed as the deviation angles between these two directions. For adsorbed thiophene (T) on (8, 0) BNNTT, NBO calculations showed that these structures are the dominant Lewis structure. However, based on the advanced valance bond theory, covalentionic resonances are not necessary due to the inclusion of bondpolarity effects in a resonance structure. By this work, for each NAO functions, the core, valence or Rydberg, the orbital occupancy and the orbital energy were shown. It was notable that the occupancies of the Rydberg (Ryd) NAOs are typically much lower than those of the core and valence (Val) NAOs of the natural minimum basis (NMB) set.
Electron delocalization can be defined based on Lewis amount. It can be considered that the maximum value of electric charges in the Lewis orbitals represents a low amount of electric charge which corresponds to the strong effects of electron delocalization. In resonance phenomenon, major and minor percentages combinations may appear in several calculations. Based on perturbation theories of Fock Matrix, it is possible to estimate the donoracceptor (bonding and antibonding) interactions in the NBO foundation: These analyses are carried out through examining all possible interactions among types of lewis donors (Field) with (empty) nonLewis acceptors of NBOs. Their energy is calculated based on secondorder perturbation theories. Since these kind interactions are related to donation of occupancies from the localized Lewis structure to the idealized into the empty nonLewis orbitals, they are introduced as "delocalization" corrections to the zeroorder natural Lewis structures. For any donor (i) and acceptor (j), the stabilization energies E(2) are associated to delocalization. The following equation exhibits the relationship of F Matrix to energy: = where is the donor occupancies and is diagonal orbital energies. In addition, is the Fockmatrix function.
In quantum chemistry, a natural bond orbital or NBO is a calculated bonding orbital with maximum electron density. The NBOs are one of the sequence of natural localized orbital sets that include "natural atomic orbital" (NAO), "natural hybrid orbital" (NHO), "natural bonding orbital" (NBO) and "natural (semi)localized molecular orbital" (NLMO). These natural localized sets are intermediate between basis atomic orbital (AO) and molecular orbital (MO):
Atomic orbital → NAO → NHO → NBO → NLMO → Molecular orbital
Natural (localized) orbitals are used in computational chemistry to calculate the electron density distribution in atoms and the bonds between atoms. They have the "maximumoccupancy character" in localized 1center and 2center regions of the molecule. Natural bond orbitals (NBOs) include the highest possible percentage of the electron density, ideally providing occupancy close to 2.000, the most accurate possible “natural Lewis structure” of . A high percentage of electron density (shown as %ρ_{L}), which is usually for typical organic molecules, corresponds to an precise natural Lewis structure.
The concept of natural orbitals was first proposed by Per Olov Lowdin in 1955, to describe the unique set of orthonormal1electron functions that are inherently the function of Nelectron wave. The bonding NBOs are of the "Lewis orbital"type (occupation numbers near 2); anti bonding NBOs are of the "nonLewis orbital"type (occupation numbers near 0). In an ideal Lewis structure, full Lewis orbitals (two electrons) are complemented by formally empty nonLewis orbitals. Weak occupancies of the valence anti bonds play the primary role in departures from an ideally localized Lewis structure, which means true "delocalization effects. Lewis optimal structures can be found with a computer program that can calculate NBO. A Lewis optimal structure can be defined as a structure with the maximum amount of electric charge in Lewis orbitals (Lewis load).
A low amount of electric charge in Lewis orbitals indicates strong effects of electron delocalization [19]. Table 4 summarizes a variety of information for each cycle: the occupancy threshold for a "good" pair in the NBO search, the total populations of Lewis and non Lewis NBOs, the number of core (CR), 2center bond (BD), 3center bond (3C), and lone pair (LP) NBOs in the natural Lewis structure, the number of lowoccupancy Lewis (L) and highoccupancy (> 0.1e) nonLewis (NL) orbitals, and the maximum deviation (Dev) of any formal bond order for the structure from a nominal estimate (NAO Wiberg bond index). If all orbitals of the formal Lewis structure cross the occupation threshold, the Lewis structure is accepted ((default = 1.90 electrons).
Table 5 allows one to quickly identify the principal delocalizing acceptor orbitals associated to each donor NBO, and their topological relationship to this NBO, i.e., whether attached to the same atom (geminal, " g"), to an adjacent bonded atom (vicinal, "v"), or to a more remote ("r") site. These acceptor NBOs will generally correspond to the principal "delocalization tails" of the NLMO associated to the parent donor NBO.
NBO calculations using occupation numbers of bonding and nonbonding orbitals, occupation number of Energy, Lewis and nonLewis, atomic partial charge are given in Tables 4, 5 and 6.
Table 4. Natural bond orbital analysis

OCCU^{a} 

LE^{b} 

STRUC^{c} 

LOW OCC 
HIGH OCC 

Cycle 
Lewis 
Nonlewis 
CR 
BD 
3C 
LP 
L 
NL 
Dev 
1(1) 
494.91 
29.088 
89 
121 
0 
52 
51 
58 
0.64 
2(2) 
494.91 
29.088 
89 
121 
0 
52 
51 
58 
0.64 
3(1) 
495.22 
28.77 
89 
122 
0 
51 
50 
58 
0.64 
4(2) 
495.22 
28.77 
89 
122 
0 
51 
50 
58 
0.64 
5(1) 
503.109 
20.89 
89 
154 
0 
19 
13 
60 
0.84 
6(2) 
503.148 
20.85 
89 
154 
0 
19 
13 
59 
0.84 
7(3) 
503.187 
20.81 
89 
154 
0 
19 
13 
58 
0.35 
8(4) 
503.187 
20.81 
89 
154 
0 
19 
13 
58 
0.35 
^{a}occupancies; ^{b}Lewis; ^{c}structure
Table 5. Occupied number and energy by using NBO calculations for number nitrogen atoms in adsorbed thiophene molecule
NBO 
Atom 
Occupancy 
E/Kcalmol^{1} 
BD(1) 
(10)NN(20) 
1.74 
0.24327 
(10)NN(80) 
1.73 
0.24341 

(20)NN(30) 
1.73 
0.24365 

(30)NN(40) 
1.73 
0.24366 

(40)NN(50) 
1.74 
0.24353 

(50)NN(60) 
1.74 
0.24328 

(60)NN(70) 
1.74 
0.24331 

CR(1) 
N(10) 
1.99 
14.174 
N(20) 
1.99 
14.175 

N(30) 
1.99 
14.173 

N(40) 
1.99 
14.175 

N(50) 
1.99 
14.176 

LP(1) 
N(10) 
1.95 
0.50647 
N(20) 
1.95 
0.50600 
Table 6. Calculated partial charges by NBO calculation for effective sites of BN nanotube in adsorbed thiophene molecule
Atom 
No 
Charge 
N 
10 
0.32961 
N 
20 
0.32471 
N 
30 
0.35089 
N 
40 
0.33064 
N 
50 
0.31294 
N 
60 
0.31229 
N 
70 
0.32190 
N 
80 
0.34185 
C 
81 
0.41810 
C 
84 
0.42625 
S 
85 
0.61838 
The second order prturbation energy
This analysis is carried out by examining all possible interactions between "filled" (donor) Lewistype NBOs and "empty" (acceptor) nonLewis NBOs, and estimating their energy importance from second order perturbation theory. Since these interactions lead to the donation of occupancy from the localized NBOs of the idealized Lewis structure into the empty nonLewis orbitals (and thus, to departures from the idealized Lewis structure description), they are referred to as "delocalization" corrections to the zerothorder natural Lewis structure. For each donor NBO (i) and acceptor NBO (j), the stabilization energy of associated with delocalization ("2estabilization") i, j is estimated as equation 10:
Where is the energy of the nonLewis NBO (i.e. ), is the energy of the orbital occupied by , and is the occupancy of the orbital . The 'stabilization energy' determined by secondorder perturbation treatments is usually abbreviated as .
Table 7. The second order perturbation energy ( ) for a number of delocalized electrons of bonding, nonbonding and antibonding pairs
NBO 
Donor(i) 
Acceptor(j) 
E_{2}/ Kcal mol^{1} 
CR(2) 
S(85) 
C(81) 
1.59 
S(85) 
C(84 
1.60 

S(85) 
C(84)H(89) 
0.94 

S(85) 
C(81)H(81) 
0.94 

BD(1) 
N(10)N(20) 
C(81)S(85) 
0.08 
N(10)N(80) 
C(81)S(85) 
0.16 

N(20)N(30) 
C(84)S(85) 
0.31 

N(30)N(40) 
C(84)S(85) 
0.23 

N(70)N(80) 
C(81)S(85) 
0.05 

LP 
N(10) 
C(81)S(85) 
0.06 
N(30) 
C(81)H(86) 
0.1 

N(30) 
C(84)S(85) 
0.16 

N(80) 
C(84)H(89) 
0.09 
Conclusion
In this work, the adsorptions of thiophene on zigzag (8,0) BNNT is investigated through density functional theory (DFT) calculations. These calculations indicate that the thiophene cannot be significantly adsorbed on the pristine models of boron nitride and has a poor physical adsorption on the BNNTs. The obtained results showed that the BNNTs can't detect thiophene molecules and the adsorption energy has positive value. This finding suggests that the use of structures doped with some metal atoms such as Gadoped BNNT, Aldoped BNNT and doped nanotubes with other suitabale metals can improve adsorption. The results showed that the preferred site of molecule adsorption is at the end of the nanotube for the T fragment and the increase in polarization is due to the proper dispesion of electrons. The decrease in global hardness, energy gap, electronic and chemical potential due to thiophene adsorption leads to an increment in the stability of the (8,0) zigzag BNNTT complex. Reduction of global hardness, energy gap, electronic and chemical potential resulting from thiophene adsorption leads to increased stability of BNNTT zigzag complex (8,0).
Acknowledgments
Hereby, the author acknowledges Islamic Azad University, Mahshahr Branch, for supporting her to prorate software and computational instrument in informatics lab.
Conflict of interest
The author declares no conflict of interest.
Symbols
energy gap eV
A electron affinity eV
I Ionization Potential eV
Adsorption Energy a.u or j/mol
Greek Letters
Electric conductivity of the complex
Electronic chemical potential
Global hardness
Electrophilicity index
(s) Global softness
Citation N. Farhami. A Computational Study of Thiophene Adsorption on Boron Nitride Nanotube. J. Appl. Organomet. Chem., 2022, 2(3), 163172
https://doi.org/10.22034/jaoc.2022.154821
Copyright © 2022 by SPC (Sami Publishing Company) + is an open access article distributed under the Creative Commons Attribution License(CC BY) license (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.