MOLLIQ-05280; No of Pages 6

Journal of Molecular Liquids xxx (2015) xxx–xxx

Contents lists available at ScienceDirect

Journal of Molecular Liquids

journal homepage: www.elsevier.com/locate/molliq

Solvent effects on the stability and the electronic properties of

histidine/Pd-doped single-walled carbon nanotube biosensor
Nazanin Etminan a, Mehdi Yoosefian b,⁎, Heidar Raissi c, Mohammad Hakimi a
a
Chemistry Department, Payame Noor University, 19395-4697 Tehran, Iran
b
Department of Chemistry, Graduate University of Advanced Technology, Kerman, Iran
c
Department of Chemistry, University of Birjand, Birjand, Iran

a r t i c l e i n f o a b s t r a c t

Article history: The nanobiosensors physical and chemical properties are affected by the nature and the interactions with the
Received 17 November 2015 solvent molecules. To develop a new biosensing concept for the detection of biological agents in both in vivo
Received in revised form 30 November 2015 and in vitro, identifying the non-specific influence of the solvent on the chemical reactivity and the stability of
Accepted 2 December 2015
the nanobiosensors is crucial. In this paper, the self-consistent reaction field theory (SCRF) was used to investi-
Available online xxxx
gate the solvent effects on the structure and electronic properties of the hybride of Pd doped single-walled carbon
Keywords:
nanotube (Pd/SWCNT) and histidine amino acid as a new generation of nanobiosensors. These effects will be
Solvent effects investigated in three polar mediums using density functional theory (DFT) calculations in the combination
Biosensor with the polarizable continuum model (PCM). The emphasis will be on the results of the Quantum Theory
Single-walled carbon nanotube Atoms in Molecule (QTAIM), Natural bond orbital (NBO) and the Frontier Molecular Orbital (FMO) analysis.
Histidine The conceptual DFT based reactivity and stability descriptors, chemical potential, hardness and electrophilicity
index were calculated in different solvents in ground state to study how the structure and electronic properties
will be affected by solvents. Molecular electrostatic potential map was performed by DFT method. The value of
the electrostatic potential is largely responsible for the binding of a substrate to active sites of biosensor. The
presence of heterocyclic organic compound and electronegative atoms in the biological receptor of the His/Pd/
SWCNT nanobiosensor will result in strong solvent-solute interactions. With increasing the electric permittivity
of solvents, the stabilization energies of various conformations of nanobiosensor shifts to lower value because of
the additional attractive interactions between the nanobiosensor and the solvent. The His/Pd/SWCNT presents
high stability with considerable values of stabilization energies, charge transfer and sensible energy bond gap
in polar medium which confirm both in vitro and in vivo biosensing application.
© 2015 Published by Elsevier B.V.

1. Introduction industrial processing and monitoring and environmental pollution

Since 2000 with the first use of carbon nanotube (CNT) as sensor by
Kong et al. [1], individual nanotubes have been demonstrated to be
promising molecular platform in sensing application due to their fast
response time and high sensitivity at room temperature. The excellent
structural and electrical properties of CNTs have stimulated great
focus on the application of these nanomaterials as physical transducers
in biosensors [2].
Higher performance in sensitivity and selectivity will be offered by
biosensors rather than other diagnostic devices. L.L. Clark in Cincinnati
USA, developed the biosensors to measure the dissolve oxygen in
blood [3]. Biosensors comprise of a biological entity as sensing element
combined with a physicochemical detector component. Nanobiosen-
sors are widely used due to their promising applications in clinical and
diagnostic analysis, detection and monitoring of biological processes,
⁎ Corresponding author.
E-mail address: m.yoosefian@kgut.ac.ir (M. Yoosefian).
monitoring [3–9]. The outstanding ability to fast electron transfer
kinetics, compatible size with the biological structures and low detec-
tion limits of single walled carbon nanotubes (SWCNTs) are the great
characteristics in the fabrication of SWCNT-based biosensors. SWCNT,
a cylindrical nanostructure with high aspect ratio, and the greater area
of contact, formed by rolling up a single graphite sheet into a tube, can
enhance the chemical reactivity of biomolecules [10–12]. Because of
the week van der Waals interaction of smooth surface of nanotube
nanotube surface with the adsorbents, the sensitivity and the selectivity
of SWCNT towards a specific analyte could be improved by chemical
functionalization. One of the most effective modification of the surface
of SWCNTs and thus introducing additional electronic states in the
Fermi levels and enhancement of their adsorption potential, is the dop-
ing, i.e. heteroatom substitution into the lattice of SWCNTs [13–16]. The
biocompatibility and the stability of the SWCNT-based biosensors can
improve the sensing behavior of these materials. Denis et al. had theo-
retically investigated the stability of SWCNT [17]. The noncovalent
interaction of amino acids with the doped SWCNTs would change the

http://dx.doi.org/10.1016/j.molliq.2015.12.009
0167-7322/© 2015 Published by Elsevier B.V.

Please cite this article as: N. Etminan, et al., Solvent effects on the stability and the electronic properties of histidine/Pd-doped single-walled
carbon nanotube biosensor, J. Mol. Liq. (2015), http://dx.doi.org/10.1016/j.molliq.2015.12.009
2 N. Etminan et al. / Journal of Molecular Liquids xxx (2015) xxx–xxx

Table 1
Adsorption energies (kcal mol−1) and the dipole moment (D) of complexes in three solvent using PCM model.

Water(ε = 78.39) DMSO(ε = 48.90) Ethanol(ε = 24.55)

Complex Eads Dipole moment Eads Dipole moment Eads Dipole moment

Amine Site −15.435 17.8 −15.606 17.7 −15.968 17.4

Carbonyl site −10.320 12.9 −10.551 12.8 −11.025 12.6
Imidazol ring site −2.737 5.8 −2.742 5.7 −2.772 5.3

electrical conductance of SWCNT-based sensors by charge transfer be-
tween Pd/SWCNT and His adsorbed via the local chemical reactivity
[18] and lead to efficient detection of a variety of biomolecules and fur-
ther progress in biomedical applications. In our previous studies [14],
we have designed a new type of modified nanobiosensors through
doping impurity atom into SWCNT, the His/Pd/SWCNT.
The function of biologically active molecules depends on their struc-
ture and on the intermolecular interaction with the solvent which influ-
ence biological processes. In this study, an attempt has been made to
explore the structural stability, adsorption energies, reactivity parame-
ters and molecular orbital properties in three different polar solvent
medium including, water, DMSO and ethanol and DMSO using PCM. In
continuum models the solvent treated as a continuum, with a uniform
dielectric constant surrounding a solute molecule which is placed in a
cavity and immersed in a continuous medium. The polarization of the
media induced by the solute electric field will react with the solute
system.
Results have been compared to estimate the variation of electronic
properties of investigated nanobiosensor. The study of solvent effects
plays an important role in biocompatibility of these sensors, i.e. the abil-
ity of a sensor to perform with an appropriate host response in a specific
application [19].
2. Computational details
at the same level verified the optimized structures correspond to the
energy minima. Three solvent, water (ε = 78.39), DMSO (ε = 48.9)
and ethanol (ε = 24.55) were selected to study the solvent effects on
titled parameters using Tomasi's polarized continuum (PCM) model
[23]. Adsorption energies in solvent were calculated according to Eq. 1.


Eads ¼ EHis=Pd=SWCNT − EPd=SWCNT þ EHis ð1Þ
were EHis/Pd/SWCNT is the total energy of Pd/SWCNT with histidine
molecule and EPd/SWCNT and EHis are the total energy of Pd/SWCNT and
histidine molecule in relax geometry respectively. The noncovalent in-
teraction of histidine (His) molecule with Pd/SWCNT were considered
via different initial configuration complexes i.e. amine, carbonyl and
imidazole ring sites through the perpendicular direction to SWCNT to
reduce the unfavorable interactions.
The natural bond orbital (NBO) [24] was carried out to quantify
the charge transfer between His and Pd/SWCNT at the same level. AIM
2000 package was employed to deep understanding of the nature of
interactions in different solvent medium via the Bader's quantum theory
of atom in molecules (QTAIM) [25].
Chemical reactivity and stability indexes were calculated as defined
in Eqs. 2–5 according to Koopmans theorem [26]:
 
∂E
μ¼ ð2Þ
∂N VðrÞ;T

Gaussian 03 program package [20] has been used to calculate geom- 2

!
etry optimization and solvent effects. Density functional calculations ∂ E
η¼ ð3Þ
with Beck's three parameter hybrid method (B3) [21] using correlation ∂N2 VðrÞ;T
functional of Lee, Yang, Parr [22] (B3LYP) level have been performed.
Different basis sets were tested and all geometry full optimization S ¼ 1=2η ð4Þ
have been performed with hybrid density functional B3LYP/6-31G(d)
and DGDZVP extra basis set for Pd atom as showed good ability in
study of long range interactions. The absence of imaginary frequency ω ¼ μ 2 =2η ð5Þ

Fig. 1. Optimized geometries of His/Pd/SWCNT a. amine site b. carbonyl site and c. imidazol ring site adsorption with the interatomic distances in angstrom.

Please cite this article as: N. Etminan, et al., Solvent effects on the stability and the electronic properties of histidine/Pd-doped single-walled
carbon nanotube biosensor, J. Mol. Liq. (2015), http://dx.doi.org/10.1016/j.molliq.2015.12.009
 N. Etminan et al. / Journal of Molecular Liquids xxx (2015) xxx–xxx 3

Table 2 3. Result and discussion

Topological parameters for studied His/Pd/SWCNT bionanosensor.

Water DMSO Ethanol 3.1. Optimized configurations

Complex ρ ∇2ρ ρ ∇2ρ ρ ∇2ρ
Adsorption energy is one of the most important parameters in bio-
Amine site 0.0570 0.2229 0.0570 0.2230 0.0571 0.2238
sensing strength investigation. To relate the nanobiosensor applications
Carbonyl site 0.0442 0.2196 0.0443 0.2204 0.0446 0.2220
Imidazol ring site 0.0034 0.0137 0.0035 0.0140 0.0038 0.0150 to the real case, ethanol with moderate polarity and high polar solvent
DMSO and water were selected. The calculated values of the adsorption
energies (Eads) and dipole moments of His/Pd/SWCNT in three environ-
ments for all complexes with DFT/6-31G (d) calculations are given in
Where μ is chemical potential, η is chemical hardness, S is global Table 1. The calculated results showed that the amine site adsorbed
softness and ω is electrophilicity index. configuration which is partially favorable with the largest adsorption
In order to investigate the non-specific interactions of SWCNT based energy propose to be the most stable form in all solvents. It can be
biosensor with the surrounding medium, the solvation energy of all ge- seen that by increasing the electric permittivity of solvent, the adsorp-
ometries calculated from the total energies at the same level of theory tion energy (Eads) and dipole moment values decrease and increase
according to the Eq. 6. respectively. In general, the order of magnitude of physisorption energy
is defined lower than 5 kcal mol−1. Our calculation show that amine site
adsorbed His biosensor possess binding energy within the range of
15.4–15.7 kcal mol−1 and thus they are within the range of chemisorp-
Estab ¼ Ein solvent − Ein gas ð6Þ tion. The more appropriate amine site His/Pd/SWCNT has the largest

Fig. 2. The contour map of His/Pd/SWCNT (a. amine site b. carbonyl site and c. imidazol ring site) biosensor in the three environments.

Please cite this article as: N. Etminan, et al., Solvent effects on the stability and the electronic properties of histidine/Pd-doped single-walled
carbon nanotube biosensor, J. Mol. Liq. (2015), http://dx.doi.org/10.1016/j.molliq.2015.12.009
4 N. Etminan et al. / Journal of Molecular Liquids xxx (2015) xxx–xxx

Table 3 biosensor with high precision. The most important donor-acceptor in-
NBO analysis of some important orbitals and second-order perturbation energy of some teraction and their second-order perturbation energies are listed in
important orbital interactions (intermolecular threshold energy for printing: 4 kcal/mol).
Table 3. The NBO analysis results illustrate that in the amine site
E2 kcal/mol adsorbed His/Pd/SWCNT system, lone pair of N participates as a donor
Donor NBO Acceptor NBO Ethanol DMSO Water and LP* (Pd) atom and σ*(C45-Pd70) interaction as an acceptor is the
strongest intermolecular charge transfer interactions with the energy
Amine site
σ H–N LP*(4) Pd 5.97 5.95 4.4 values that presented in Table 3 in all solvents and in the carbonyl site
σ H–N LP*(4) Pd 4.26 4.33 4.4 adsorbed one, lone pair of O participates as a donor and LP* (Pd) atom
LP(1) N LP*(4) Pd 29.21 29 29.2 as an acceptor are the strongest. It should be mentioned that none
LP(1) N LP*(5) Pd 5.92 6 5.68 investigated threshold found for imidazol ring interaction.
LP(1) N σ* C–Pd 13.97 13.92 13.95

Carbonyl site
LP(1) O LP*(4) Pd 23.56 23.63
LP(2) O LP*(4) Pd 20.79 20.82
LP(2) O σ* C–Pd 9.21 9.17
dipole moment value in water. Optimized geometries of different repre-
sentative His adsorbed site fragments and the interatomic distance
between Pd atom and N, O and imidazole ring are shown in Fig. 1
which are slightly different from those in gas phase.
3.2. QTAIM analysis
The quantum theory of atom in molecules (QTAIM) analysis of the
electronic charge density (ρ) and its Laplacian (∇2ρ) at critical points
which are obtained by integrating the charge density over the atom or-
bitals is used to characterize the nature of bonding interaction [27–31].
Intermolecular interaction of His and Pd/SWCNT is associated with
the appearance of a bond critical point between the Pd atom and His
molecule which studied with AIM analysis. As the solvent-solute inter-
actions are more prominent around the heteroatom especially in polar
solvent, the topological analysis of the electronic charge density of
bond critical points (ρ) and its Laplacian (∇2ρ) were performed of all
complexes (see, Table 2). The positive values of Laplacian of electron
density with the potential energy domination confirmed the closed
shell (non-covalent) interactions in the nanobiosensor structure. The
Laplacian of electron densities (∇2ρ) in the title mediums for the most
active configuration is are 0.22288, 0.22301 and 0.22382 respectively.
Comparison between different complexes showed that the highest
electron density (ρ) and Laplacian of electron density (∇2ρ) observed
in ethanol solvent values which could be attributed to a stronger inter-
action in this solvent. Fig. 2 presents the contour map of the title nano-
biosensor in the three environments.
3.3. NBO analysis
The natural bond orbital (NBO) calculations were used to under-
stand delocalization of electron density from occupied Lewis-type
(donor) NBOs to properly unoccupied non Lewis type (acceptor)
NBOs within the molecule [32–35].
Second-order perturbation stabilization energies, E(2), result from
NBO analysis which calculated at the same level of theory, indicate
the bonding-antibonding interaction between different parts of the
3.4. Frontier molecular orbital analysis and global reactivity descriptors
23.65
20.82
9.16
It is generally known that the properties of bionanosensors may dif-
fer considerably between the gas phase and solution. Continuum model
techniques were used to include solvent effects.
The HOMO–LUMO energy gap, the basic electronic parameter relat-
ed to the FMO, refers to the potential energy difference between the
highest occupied molecular orbital (HOMO) and the lowest unoccupied
molecular orbital (LUMO).
To evaluate solvent effects on the reactivity indices, chemical poten-
tial, chemical hardness and electrophilicity have been calculated in the
homogeneous polar medium using the same level for all complexes
(Table 4). The frontier orbital are shown in Fig. 3.
It can be observed that the order of HOMO–LUMO bond gap for dif-
ferent configurations are car N ring N amine site adsorbed in all three
solvents.
The order of Eg as an important scale of stability in different solvents
are in the order; Water b DMSO b Ethanol which shows that the
bionanosensor tends to have higher stability and lower reactivity
in lower polarized medium. The lower Eg results softer molecules, so
biosensor has been found to be softest in water which indicates the
most biocompatibility.
The electrophilicity index increases with increasing solvent polariz-
ability so if it is desired to increase electrophilicity of bionanosensor to
larger extent, then among the selected solvents, water is the best.
The chemical potential of investigated bionanosensor in title
solvents increases in the order of Water N DMSO N Ethanol which
shows that ethanol increases the electronegativity of active sites.
3.5. Molecular electrostatic potential (MEP) surface
Visualization of variable charge distributions provide deep insight
into intermolecular interactions, molecular properties and prediction
of electrophilic and nucleophilic reactions at the particular site of titled
biosensor. The molecular electrostatic potential graphic representations
for all complexes are depicted in Fig. 4. Electronegativity difference is a
key to determine the nature of a chemical bond.
To interpret the electrostatic potential energy data, a colored spec-
trum, with red as lowest and blue as the highest electrostatic potential
energy values, is employed to convey the varying intensities. The Pd
atom has negative electrostatic potentials susceptible to electrophilic
attack. The yellow-green region of O atom of carbonyl and N atom of

Table 4
Molecular orbital analyses, chemical potential, chemical hardness, softness and electrophilicity calculated in the homogeneous polar medium.

Solvent Complex EHOMO(eV) ELUMO(eV) Eg(eV) μ η S ω

Amine site −4.026 −2.415 1.610 −3.220 0.805 0.621 6.441

Carbonyl site −4.183 −2.486 1.697 −3.335 0.849 0.589 6.552
Water Imidazol ring site −4.146 −2.507 1.639 −3.326 0.820 0.610 6.750
Amine site −4.001 −2.385 1.616 −3.193 0.808 0.619 6.311
Carbonyl site −4.162 −2.464 1.697 −3.313 0.849 0.589 6.467
Ethanol Imidazol ring site −4.145 −2.500 1.646 −3.322 0.823 0.608 6.708
Amine site −4.017 −2.404 1.613 −3.211 0.806 0.620 6.392
Carbonyl site −4.178 −2.478 1.700 −3.328 0.850 0.588 6.515
DMSO Imidazol ring site −4.145 −2.505 1.640 −3.325 0.820 0.610 6.741

Please cite this article as: N. Etminan, et al., Solvent effects on the stability and the electronic properties of histidine/Pd-doped single-walled
carbon nanotube biosensor, J. Mol. Liq. (2015), http://dx.doi.org/10.1016/j.molliq.2015.12.009
 N. Etminan et al. / Journal of Molecular Liquids xxx (2015) xxx–xxx 5

Fig. 4. The molecular electrostatic potential graphic for all complexes, a colored spectrum,
with red as lowest and blue as the highest electrostatic potential energy values (a. amine
site b. carbonyl site and c. imidazol ring site). (For interpretation of the references to color
Fig. 3. HOMO and LUMO compositions of the frontier molecular orbital for His/Pd/SWCNT
in this figure legend, the reader is referred to the web version of this article.)
a. amine site b. carbonyl site and c. imidazol ring site biosensor in the three environments.

Please cite this article as: N. Etminan, et al., Solvent effects on the stability and the electronic properties of histidine/Pd-doped single-walled
carbon nanotube biosensor, J. Mol. Liq. (2015), http://dx.doi.org/10.1016/j.molliq.2015.12.009
6 N. Etminan et al. / Journal of Molecular Liquids xxx (2015) xxx–xxx

Table 5 change of His/Pd/SWCNT induced by charge transfer and solvent effect

The calculated values of total energy, dipole moment, stabilization energy and reorganiza- were investigated for this novel biosensor through DFT, QTAIM, NBO,
tion energy of title biosensor in the gas and three environments.
HOMO-LUMO energies and MPE analysis. The adsorption energies
Amine site Carbonyl site Imidazol ring site decrease by increasing the electric permittivity of the polar solvents
Gas phase(ε = 1) and indicate chemisorption of the His/Pd/SWCNT biosensor in different
Total energy(Etot, Hartree) −8129.791292 −8129.785723 −8129.767809 solvents. In addition the lower HOMO-LUMO energy gap, Eg, indicated
Dipol moment (Debye) 11.97 9.14 3.02 the more reactive and less chemical stable configuration of biosensor
Ethanole(ε = 24.55) in water. The solvent contribution to reorganization energy which con-
Total energy(Etot, Hartree) −8129.827952 −8129.820072 −8129.806917 trol electron-transfer process has an excellent correlation with the ad-
Dipol moment(Debye) 17.36 12.58 5.29 sorption energy. These changes might be useful to design new
Estab(kJ/mol) −96.251 −90.183 −102.678
generation of biosensors based on transition metal doped SWCNTs.
EReorganization 4.695 4.898 0.111
The chemical reactivity of investigated bionanosensor in water me-
DMSO(ε = 48.9) dium can be rationalized from HOMO-LUMO gap and associated index-
Total energy(Etot, Hartree) −8129.82977 −8129.821713 −8129.809266
es of FMO results whereas the values of adsorption energy point out the
Dipol moment(Debye) 17.67 12.81 5.69
Estab(kJ/mol) −101.025 −94.492 −108.844 more stable systems in ethanol medium.
EReorganization 4.374 4.745 0.108

Water(ε = 78.39)
Total energy(Etot, Hartree) −8129.830667 −8129.822513 −8129.810426
Dipol moment(Debye) 17.82 12.92 5.85
Estab(kJ/mol) −103.379 −96.592 −111.891
EReorganization 4.316 4.673 0.108
imidazol ring sites of amine adsorbed complex reflect lowest electro-
static potential which correspond to the area of large depletion of elec-
tron may be a site for electrophilic interactions and the two blue region
of proton may be a site for nucleophillic attack whereas other region
have intermediary electrostatic potentials.
3.6. Solvation and reorganization energies
Nevertheless, carbon nanotubes are generally found to be insoluble
in most solvents including water; however they can be made soluble
by adding hydrophilic groups as a surfactant. The calculated values of
total energy and stabilization energy (Estab) of title biosensor in the
gas and three environments with DFT/B3LYP/6-31G (d) are given in
Table 5. Water plays a critical role in the stabilization of biomolecular
systems [36] and the origin of this stability arises from unique hydrogen
bond capacity of water. In Table 5, the stabilization energy increases
with the increasing electric permittivity of solvents. The calculated
data indicates that the total energy of title biosensor in solvent is
lower than that in the gas phase. In PCM model, while the value of
ε for solvents increases, the total energy value of molecule shifts
to lower value. The biosensor stabilizes due to additional attractive in-
teractions between the solvent and biosensor. The dipole moment
values of biosensor have the largest values in water.
With the framework of DFT, the reorganization energy of investigat-
ed complexes in different solvent medium was calculated and our result
show that maximum deformation will occur in ethanol medium. The
results show an excellent correlation between the reorganization
(X) and the adsorption energy (Y) by
Y ¼ 45:91X2 −60:003X−1:2768Þ and R ¼ 0:96:
4. Conclusion
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Biosensors have incredible potential for the monitoring of biological

agents. In this work the sensing mechanism which is the conductance

Please cite this article as: N. Etminan, et al., Solvent effects on the stability and the electronic properties of histidine/Pd-doped single-walled
carbon nanotube biosensor, J. Mol. Liq. (2015), http://dx.doi.org/10.1016/j.molliq.2015.12.009