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A Charge Density Analysis on Quarter Thiophene

Molecular Nanowire Under Applied Electric Field: A
Theoretical Study

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DOI: 10.1166/jctn.2013.2705

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 Copyright 2013 American Scientic Publishers Journal of
All rights reserved Computational and Theoretical Nanoscience
Printed in the United States of America Vol. 10, 111, 2013

A Charge Density Analysis on Quarter

Thiophene Molecular Nanowire Under Applied
Electric Field: A Theoretical Study
K. Selvaraju, M. Jothi, and P. Kumaradhas
Department of Physics, Periyar University, Salem 636011, India

A Quantum chemical calculation and charge density analysis on gold and thiol substituted quarter
thiophene molecular nanowire have been carried out using high level Density Functional Theory
(DFT) with the basis set LANL2DZ coupled with the Baders theory of atoms in molecules to under-
stand its charge density and energy density distributions for the zero and various applied electric
elds. The applied electric eld (0.030.13 V 1 ) altered the geometrical conformation, charge
density distribution and the electronic energy levels of molecular wire. The bond topological analysis
performed for zero and various applied electric elds characterizes, the terminal Au S, S C as
well as the central bonds of the quarter thiophene molecule. The eld highly polarizes the molecule
and this effect increases the dipole moment of the molecule from 2.69 to 13 D. For the zero bias,
the HOMOLUMO gap is 1.713 eV, as the eld increases this gap rapidly decreases to 1.172 eV.
The electrostatic potential maps for various applied electric eld shows the charge accumulated
regions of the molecule. The IV characteristics of the molecule have been studied against various
applied elds.
Keywords: Molecular Nanowire, Charge Density, HOMOLUMO Gap, ESP, IV Characteristics.

1. INTRODUCTION
Recent developments in nanoscience and nanotechnology
facilitate the molecular electronics research. Today molecu-
lar electronics is not only fascinating topic of basic research
but it has an enormous potential for future data process-
ing technologies.1
2 Molecular wire is one of the key com-
ponents of molecular electronics and it is being used as
interconnects3 in all nano-electronic devices. Molecular
wire is a highly conducting single molecule or an assembly
of molecules capable to effectively and electronically cou-
ple the terminal sites so as to mediate energy and charge
transport over long distance.4 Hence, the basic goal is to
measure and control the electron transport through a sin-
gle molecule5
6 attached between two electrodes. Gener-
ally, conjugated polymers like oligomers and thiophenes,
exhibit small HOMOLUMO gap,7 which is less than
3 eV. These molecules are having delocalized  elec-
trons and hence higher conductivity.8 In the electrode
moleculeelectrode system, the organic molecules exhibit
discrete electronic energy levels and substitution of iso-
lated heavy metal atoms at either ends, vary the electronic
Author to whom correspondence should be addressed.
RESEARCH ARTICLE
energy levels of the molecule. Thus, the contact between
the electrode and the molecule plays a crucial role in the
electron-transport properties of molecules.9 However, the
experimental determination of conduction and charge trans-
port properties in single molecule level is still a challenging
task, since several kinds of uncontrollable experimental
factors are inuence the resulting values in substantial
way.10
11 To overcome such difculties, the quantum chem-
ical calculations and theoretical charge density analysis
are essential to relate the charge transport properties more
precisely with the electrode-molecule junction.10 So far,
the reported theoretical research papers1215 explain the
effect of external electric eld (EF) on the quarter thio-
phene molecule using thiol atom as terminal atom (elec-
trode) for applying EF. In the present study, we report
the charge density as well as the energy density distribu-
tion and the effect of Au metal atom in thiol linked quar-
ter thiophene molecule for different levels of applied EF
by using quantum chemical calculations and charge den-
sity analysis. In the following sections, we describe the
computational details, charge density and energy density
distribution, electrostatic potential (ESP), density of states
(DOS), molecular dipole moment and IV characteristics
of quarter thiophene molecule.

J. Comput. Theor. Nanosci. 2013, Vol. 10, No. 2 1546-1955/2013/10/001/011 doi:10.1166/jctn.2013.2705 1

 A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field
2. COMPUTATIONAL DETAILS
The Au and thiol substituted quarter thiophene molecule
has been optimized for the zero bias and applied eld
of ve biasing steps 0.03, 0.05, 0.08, 0.10 and 0.13 V
1 with positive pole on the left end and negative
pole on the right end of the molecule by Density Func-
tional Theory (DFT) method1618 using Gaussian03 pro-
gram package.19
20 The same procedure is repeated for
reversing the EF with same biasing steps. A combina-
tion of Beckes three parameters exchange function and
Lee, Yang and Parr gradient-corrected correlation function
(B3LYP hybrid function) is applied for whole DFT calcu-
lation along with LANL2DZ (Los Alamos National Labo-
ratory of Dual Zeta) basis set,1921 which provide effective
core potential and the detailed description of the effect of
heavy metal atoms in the molecule.20
21 All geometry opti-
mizations were performed via Berny algorithm in redun-
dant internal co-ordinates. The threshold convergence for
maximum force, root mean square (RMS) force, maximum
displacement and root mean square (RMS) displacement
are 0.00045, 0.0003, 0.001 and 0.0012 au respectively. The
self consistency of non-interactive wave function was per-
formed with a requested convergence on the density matrix
of 108 and 106 for the RMS and maximum density
matrix error between the iterations.22 As a part of Hamilto-
nian an external dipolar eld is set to compute the effect of
voltage. The electron density bcp r, Laplacian of charge
density  2 bcp r, bond ellipticity  and the eigen val-
RESEARCH ARTICLE
ues i were calculated for various applied eld using
EXT94b routine incorporated to the AIMPAC software.23
DENPROP and wfn2plots program packages have been
used to plot the deformation density and Laplacian of
electron density maps. The HOMOLUMO and Electro-
static potential (ESP) maps were plotted using GVIEW.24
To determine the density of states (DOS) at various applied
EF the GaussSum program25 has been used.
3. RESULTS AND DISCUSSION
3.1. Structural Aspects
The optimized geometry of Au and S substituted quarter
thiophene molecular wire for the zero and the applied EFs
are illustrated in Figure 1. This molecular wire has four
aromatic rings and the Au atoms are attached at the ends
of the molecule through thiol atoms. The thiol atom forms
an excellent link between the conjugated quarter thiophene
molecule and the Au atom.26 Normally, the conducting
molecules are very sensitive to the applied external EF
and the eld also alters the conformation of the molecules,
which leads to considerable change in the transport prop-
erties of the molecules.27 Further, the bond length alter-
nation due to the applied EF plays an important role in
determining the conductance of molecular wires.28 Hence,
it is essential to compare the zero eld geometry of the
2 J. Comput. Theor. Nanosci. 10, 111, 2013
Selvaraju et al.
molecule with the applied elds to understand its structural
stability over the range of applied EF.
For the zero eld, the C C bond distances of four
rings and the C C bonds which links the aromatic rings
in the molecule are 1.39 and 1.43 respectively;
when the eld applied these distances are slightly mod-
ied, the maximum observed variation is 0.007 . The
zero eld distances of S C bonds in the aromatic rings
are 1.82 ; as the eld increases, the maximum varia-
tion observed is 0.005 . Similarly, the applied EF altered
the bond distances of terminal S C bonds, which are
found to be unequal on both ends. In the left-end (L-end),
the distance increases from 1.785 to 1.792 , while in
the right-end (R-end), the distance decreases from 1.785
to 1.772 ; notably the variation in the R-end is slightly
greater than the L-end and the difference is 0.013 .
The zero and the applied eld distances of Au S bonds
are found unequal. As the eld increases, the distance in
the L-end decreases from 2.424 to 2.413 , while in the
R-end, the distance increases from 2.423 to 2.450 ; how-
ever the variations in both ends are also unequal. And,
for the maximum applied eld (0.13 V 1 , the varia-
tions at L- and R-ends are 0.011 and 0.027 respectively.
This large difference attributes, the applied eld length-
ening the Au S bond through by shrinking the S C
bond distance in the wire (Table-I) and the distances of
S C and Au S bonds are very close to the previously
reported values.29
30 Figure 2 shows the variation of bond
lengths for different applied EF with reference to zero
eld, which includes the variation of Au S bond of quar-
ter thiophene molecule. Further, the applied eld not much
altered the bond angles of the molecule and is almost
equal to the predicted angles for the zero eld. However,
the eld made a signicant variation in the bond angles
of the terminal (S C S and Au S C) bonds. At the
L-end, the zero eld bond angle for the S(1) C(1) S(3)
bonds is 121.9 , as the eld increases (0.13 V 1 , this
angle slightly decreases to 121.5 ; while in the R-end,
S(2) C(16) S(6) bond angle gradually increases from
121.9 to 122.2 . The variation around C(1) may be due
to the rotation of S(1) C(1) bond at the L-end. However,
we didnt observe any notable angular variations found in
the terminal S C C bonds. When the eld increases,
the angle of terminal Au S C bonds present in both
ends increases; the maximum variation in the L-end termi-
nal bond is 0.2 , whereas in the R-end this value rapidly
increases to 1.4 .
On compared with the left and right terminal bonds, the
applied eld made little twist in the C C C C bonds
of the rings as well as the backbone bonds of the molecule;
the maximum difference of torsion angle between zero
and the applied eld is 0.3 . For the zero eld, the tor-
sion angles of thiol linked S C C C bonds is 175.9 ;
when the eld increases, in the L-end, this angle decreases
from 175.7 to 173.8 , whereas in the R-end, it increases
from 175.8 to 176.5 . For the zero eld, the torsion angles
Selvaraju et al. A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field

Fig. 1. Optimized geometry, deformation density and Laplacian of electron density maps of Au and S substituted quarter thiophene molecule for
the zero and applied EF (0.13 V 1 ). In deformation density maps, the positive contours (solid lines) and negative contours (dotted lines) and zero
contours (dashed lines) are drawn at 0.05 e3 intervals. Laplacian of electron density maps the contours are drawn in logarithmic scale, 3 0 2N e5 .

of Au S C C bonds in L- and R-ends are 97.7 and
98.9 respectively; as the eld increases, the corresponding
observed variations are 1.6 and 1.7 . On compared with the
L-end, the variation in the terminal group of the R-end has
been signicantly varied, which indicates that this group is
highly sensitive to the positive eld than the negative eld.
Figure 1 shows the exact conformational difference of zero
and the applied eld structures. The structural compari-
almost insensitive to the applied eld. The selected geo-
metrical parameters are presented in Table I.
3.2. Charge Density Distribution
Using Quantum theory of atoms in molecules (QTAIM)
the relation between the topology of electron density and
the chemical concepts of molecules can be accurately

son on various elds reveals that, relatively the terminal
groups are found to be very sensitive to the EF on com-
pared with the central quarter thiophene molecule as it is
Table I. Geometrical parameters (,  ) of the terminal bonds of Au and
S substituted quarter thiophene molecule for the various applied electric
elds (V 1 .
Applied electric eld
RESEARCH ARTICLE
quantied.18 Table II shows the bond topological parame-
ters of quarter thiophene molecule for zero and various lev-
els of applied EF. The critical point search in the molecule,
found a (3
1) type of bond critical point (bcp) for all
bonds, which implies that the presence of covalent type
chemical bonds30 exists in the molecule. Figure 1 displays
the deformation density20 of quarter thiophene molecular

Bonds 0.00 0.03 0.05 0.08 0.10 0.13

Bond lengths
S(1)C(1) 1.785 1.787 1.789 1.790 1.791 1.792
S(2)C(16) 1.785 1.783 1.780 1.778 1.776 1.772
Au(1)S(1) 2.424 2.420 2.417 2.415 2.415 2.413
Au(2)S(2) 2.423 2.428 2.433 2.438 2.443 2.450
Bond angles
S(1)C(1)S(3) 121.9 121.8 121.7 121.7 121.6 121.5
S(2)C(16)S(6) 121.9 122.0 122.0 122.1 122.1 122.2
S(1)C(1)C(4) 127.6 127.6 127.6 127.6 127.6 127.6
S(2)C(16)C(15) 127.5 127.6 127.6 127.6 127.6 127.7
Au(1)S(1)C(1) 104.6 104.6 104.6 104.7 104.8 104.8
Au(2)S(2)C(16) 104.7 104.8 105.0 105.2 105.5 106.1
Torsion angles
S(1)C(1)C(4)C(3) 175.9 175.7 175.1 174.6 174.1 173.8
S(2)C(16)C(15)C(14) 175.8 175.8 176.2 176.5 176.6 176.5
Au(1)S(1)C(1)C(4) 97.7 96.7 97 97.6 96.1 96.2
Au(2)S(2)C(16)C(15) 98.9 99 97.5 97.6 98.3 97.3
Au(1)S(1)C(1)S(3) 86.5 87.7 88.3 88.1 90.5 90.3 Fig. 2. Showing the bond length variation of Au and S substituted quar-
Au(2)S(2)C(16)S(6) 85.4 85.1 86.1 85.7 84.8 85.6 ter thiophene molecule of for zero and various applied EFs.

J. Comput. Theor. Nanosci. 10, 111, 2013 3

 RESEARCH ARTICLE

4
Table II. Bond topological parameters of Au and S substituted quarter thiophene molecule for zero and various applied EFs.

 2
bcp rb

bcp ra Applied electric eldd c

Bonds 0.00 0.03 0.05 0.08 0.10 0.13 0.00 0.03 0.05 0.08 0.10 0.13 0.00 0 03 0 05 0.08 0.10 0 13

Ring 1
C(1)C(4) 1.976 1.977 1.979 1.980 1.978 1.978 18 240 18 257 18 286 18 294 18 269 18 266 0.201 0 202 0 202 0 202 0 201 0 199
C(2)C(3) 1.960 1.961 1.963 1.964 1.962 1.961 18 080 18 099 18 134 18 149 18 128 18 118 0.196 0 197 0 197 0 197 0 196 0 194
S(3)C(1) 1.060 1.061 1.062 1.063 1.064 1.065 4 300 4 337 4 348 4 357 4 362 4 377 0.215 0 215 0 215 0 215 0 215 0 215
Ring 2
C(5)C(6) 1.974 1.974 1.973 1.970 1.966 1.963 18 343 18 33 18 314 18 273 18 203 18 159 0.200 0 200 0 199 0 197 0 195 0 191
C(7)C(8) 1.972 1.972 1.972 1.970 1.967 1.963 18 285 18 285 18 293 18 276 18 224 18 180 0.200 0 200 0 199 0 198 0 195 0 192
S(4)C(8) 1.060 1.061 1.060 1.059 1.058 1.057 4 660 4 649 4 641 4 629 4 615 4 599 0.218 0 218 0 218 0 218 0 217 0 217
Ring 3
C(9)C(12) 1.972 1.970 1.967 1.963 1.957 1.953 18 284 18 251 18 204 18 132 18 036 17 975 0.200 0 199 0 198 0 195 0 192 0 188
C(10)C(11) 1.974 1.973 1.971 1.968 1.964 1.959 18 337 18 327 18 303 18 261 18 197 18 133 0.200 0 199 0 197 0 195 0 192 0 189
S(5)C(9) 1.060 1.062 1.063 1.062 1.062 1.062 4 660 4 659 4 662 4 658 4 647 4 646 0.218 0 217 0 217 0 217 0 216 0 216
Ring 4
C(13)C(14) 1.960 1.957 1.953 1.948 1.943 1.938 18 076 18 04 17 971 17 897 17 814 17 738 0.196 0 194 0 192 0 189 0 187 0 183
C(15)C(16) 1.976 1.973 1.970 1.966 1.962 1.957 18 232 18 199 18 145 18 086 18 013 17 940 0.201 0 199 0 198 0 196 0 193 0 191
S(6)C(16) 1.060 1.058 1.056 1.055 1.053 1.050 4 320 4 302 4 281 4 261 4 242 4 193 0.215 0 215 0 215 0 215 0 215 0 214
Ring connectors
C(8)C(9) 1.809 1.810 1.812 1.815 1.821 1.825 16 048 16 066 16 096 16 155 16 251 16 316 0.118 0 118 0 119 0 12 0 123 0 125
C(10)C(13) 1.809 1.811 1.815 1.821 1.826 1.831 16 055 16 082 16 158 16 246 16 333 16 403 0.112 0 113 0 115 0 118 0 121 0 124
Terminal bonds
S(1)C(1) 1.070 1.072 1.068 1.065 1.063 1.059 6 030 5 948 5 855 5 789 5 825 5 749 0.199 0 199 0 199 0 201 0 21 0 212
S(2)C(16) 1.070 1.079 1.083 1.065 1.063 1.059 6 030 6 189 6 413 5 789 5 825 5 749 0.199 0 205 0 217 0 201 0 21 0 212
A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field

Au(1)S(1) 0.500 0.503 0.506 0.508 0.508 0.510 3 020 3 036 3 054 3 074 3 091 3 115 0.117 0 117 0 116 0 116 0 116 0 115
Au(2)S(2) 0.500 0.496 0.492 0.487 0.483 0.476 3 020 3 007 2 994 2 986 2 987 2 983 0.117 0 117 0 117 0 117 0 117 0 116
Notes: a The electron density bcp (e3 , b Laplacian of electron density  2 bcp (e5 , c Bond ellipticity (, d Applied electric eld (V 1 .

J. Comput. Theor. Nanosci. 10, 111, 2013

Selvaraju et al.
Selvaraju et al. A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field

wire, shows, the charge accumulation for zero and applied
elds, and the differences.
The zero eld electron density [bcp r] at the bcp of all
aromatic C C bonds ranges from 1.96 to 1.976 e3 ;
whereas for the applied eld, these values are slightly
varied, the maximum variation is 0.058 e3 . Similarly,
the zero eld electron density bcp r of the C C bonds
connecting the rings are 1.809 e3 ; for the applied
eld, this bond density increases to 1.831 e3 . The S C
bond density for the zero eld is 1.07 e3 , and for the
applied eld, it slightly decreases to 1.059 e3 . Notably,
the S C bond density is small, indicates that the charges
of these bonds are move away from the inter-nuclear axis,
which conrm its dominant -bond nature.11 This can
be well understood from the Laplacian of electron den-
-type bond character.18 The mean value of
sity and the bond ellipticity.31 The Au S bond density
at zero eld is 0.5 e3 , whereas for the applied eld,
the density increases (0.50.51 e3  in the L-end, but
in R-end it decreases from 0.496 to 0.476 e3 ; however,
the variation is found to be very small. The C H bond
density is 1.78 e3 , which varies slightly as the eld
increases. The effect of electric eld in the quarter thio-
phene molecule not much altered the bond densities of
the molecule. Relatively, the variations are small for the
applied eld and are found to be very prominent and sys-
tematic (Table II). The increase or decrease of bond den-
sities of the molecule not made any signicant change in
the bond charge accumulation of the molecule.
concentrated than the L-end. For the zero eld, the Lapla-
cian of Au S bond is 3.02 e5 , when the eld increases,
at the L-end this value sharply increases to 3.115 e5
but at the R-end it decreases to 2.983 e5 . Over all, the
Laplacian of electron density distribution in the Au substi-
tuted molecular wire (AuS-molecule-SAu), reveals that
the applied eld depletes the charges at the bcps of C C
bonds, whereas this effect is found little more in the ter-
minal bonds, specically it is high at the R-end.
The anisotropy of electron density distribution at the bcp
of molecules can be calculated from the bond ellipticity
 = 1 /2  1, where 1
2 are the negative eigen val-
ues of Hessian matrix.16 The high ellipticity value implies
large anisotropy of bonding density and hence strong devi-
ations from
 for C C bonds is found very small and the values are
around 0.2. As the eld increases, the bond ellipticity of
S C bond at both ends of the wire increases gradually
from 0.199 to 0.212. On comparing with Au S bonds, the
 value of S C bond is found relatively high (Table II)
for the applied eld, this shows, the densities are seems to
be highly anisotropy.
3.3. Energy Density
To derive the necessary and sufcient conditions for
bonding in molecules, we have to consider both ener-
getic as well as electrostatic aspects of chemical bonds.32
Therefore, here we have calculated the energy density dis-

RESEARCH ARTICLE
The Laplacian of electron density [ 2 bcp r] at the bcp
tribution of quarter thiophene molecule, which is directly
are being used to characterize the charge concentration or
related to Laplacian of electron density.11
32 When the
depletion of chemical bonds.20 In the present study, the Laplacian of electron density is positive, the kinetic energy
Laplacian of electron density at the bcp of all bonds in density is dominant, which leads to the depletion of bond
the molecule has been calculated to understand whether charge; if it is negative, the potential energy density dom-
the charges at the bcp of the bonds are concentrated or inates, and the accumulation of negative charge expected
depleted when the molecules exposed to external electric to happen.32
33 The total energy density in the bonding
eld. The calculated Laplacian of electron density for the
applied EF along with the zero elds are presented in
Table II. Figure 1 shows the Laplacian of electron density
for zero and the maximum applied eld (0.13 V 1 ). For
the zero eld, the predicted Laplacian of electron density
for the aromatic C C bonds are 18 e5 ; whereas
for the applied eld, these values are become little less
negative, indicates, the charges of these bonds are slightly
depleted. Similar trend is found in the C C bonds, which
are connecting the rings in the molecule, in which Lapla-
cian for zero eld is 16 e5 ; for the applied eld,
the maximum variation observed is 0.348 e5 . The zero
eld Laplacian of electron density for the C H bonds is
20 5 e5 , the high negative value of Laplacian, indi-
cates the charge concentration, and the applied eld alter
this charge concentration. The S C bond charges are less
concentrated for the zero eld, its corresponding Lapla-
cian is 6 03 e5 ; as the eld increases, this value
decreases to 5 749 e5 ; however, the observed varia- Fig. 3. Showing the energy density variation of Au and S substituted
tion indicates that the charges at the R-end are slightly quarter thiophene molecule for zero and various applied EFs.

J. Comput. Theor. Nanosci. 10, 111, 2013 5

 A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field Selvaraju et al.

Table III. Selected total bond energy density (H 3  for the various slightly decreases to 1 942 H 3 [C(13)C(14)]. The
applied electric elds (V 1 . energy density distribution in the terminal heavy atom
Bonds 0 00 0 03 0 05 0 08 0 10 0 13 bonds, (Au S and S C) are signicantly less on com-
pared with the bonds in the quarter thiophene molecule.
Ring 1
C(1)C(4) 2 015 2 018 2 022 2 023 2 02 2 021
Of course, the small values are attributed to the nature of
C(2)C(3) 1 987 1 989 1 993 1 994 1 99 1 988 bonds, however, for the applied eld, the variation between
S(3)C(1) 0 648 0 652 0 653 0 654 0 655 0 657 both types of bonds is found to be opposite. For the applied
Ring 2 eld the density H r of S C bonds vary from 0.84 to
C(5)C(6) 2 015 2 015 2 014 2 009 2 000 1 994 0.818 H 3 . In the L-end Au S bond density increases
C(7)C(8) 2 012 2 012 2 011 2 007 1 999 1 991
S(4)C(8) 0 662 0 661 0 66 0 659 0 658 0 656
from 0.143 to 0.148 H 3 , whereas the same at the
Ring 3 R-end decreases from 0.143 to 0.13 H 3 . Figure 3
C(9)C(12) 2 012 2 009 2 003 1 995 1 982 1 974 shows the variation of energy density for various applied
C(10)C(11) 2 014 2 012 2 007 2 001 1 991 1 981 and the zero electric elds. The complete values of energy
S(5)C(9) 0 662 0 662 0 663 0 662 0 661 0 661 density distribution of the molecule are given in Table III.
Ring 4
C(13)C(14) 1 987 1 982 1 973 1 964 1 953 1 942
C(15)C(16) 2 014 2 009 2 002 1 993 1 983 1 974 3.4. Atomic Charges
S(6)C(16) 0 65 0 648 0 646 0 644 0 642 0 637
Ring connectors Generally, Mullikan population analysis (MPA) and Nat-
C(8)C(9) 1 665 1 667 1 672 1 678 1 69 1 698 ural population analysis (NPA) methods34
35 are used to
C(10)C(13) 1 666 1 669 1 678 1 688 1 699 1 709 calculate the atomic charges of atoms in molecules. Both
Terminal bonds
methods are basis set dependent, in which a small change
S(1)C(1) 0 84 0 833 0 824 0 818 0 824 0 818
S(2)C(16) 0 84 0 857 0 88 0 818 0 824 0 818 in basis set can cause a large change in the calculated net
Au(1)S(1) 0 143 0 145 0 146 0 147 0 147 0 148 charges. However, in NPA model the charges are estimated
Au(2)S(2) 0 143 0 141 0 139 0 136 0 147 0 13 on the basis of natural orbital population, it provides bet-
ter charge distribution. Further, both models predict almost
negative charge for all C-atoms in the molecule. The MPA
region Hr is expressed as H r = Gr + V r, where charges of all C-atoms vary with the increase of eld,
V r is the potential energy density and Gr is the local which ranges from 0.025 to 0.475e. The linker S(1)-
kinetic energy density.11 In the case of quarter thiophene atom possess very less positive MPA charge, as the eld
RESEARCH ARTICLE

molecule, Gr is positive, V r is negative and the total
energy density H r is negative, implies that V r dom-
inates for all cases. Relatively, the predicted zero eld
energy density H r for the C C bond in the aromatic
ring is high (2 H 3  on compared with the other
bonds in the molecule; as the eld increases this value
increases this value increases from 0.113 to 0.13e; whereas
the charge of S(2) decreases from 0.112 to 0.087e. For the
applied eld, the charge of Au atom at the L-end varies
from 0.057 to 0.027e, this effect is opposite for the
Au present at the R-end where the value increases from
0.056 to 0.164e. For the zero eld, the NPA charge

Table IV. Selected values of atomic charges (e) of Au and S substituted quarter thiophene molecule for the various applied electric elds (V1 .

Applied electric eld

0 0 03 0 05 0 08 0 1 0 13 0 0 03 0 05 0 08 0 1 0 13

Atoms MPA NPA

C(1) 0 474 0 475 0 474 0 472 0 473 0 473 0 366 0 364 0 361 0 358 0 355 0 35
C(2) 0 072 0 073 0 074 0 076 0 077 0 078 0 189 0 193 0 197 0 201 0 205 0 209
C(5) 0 033 0 032 0 03 0 028 0 026 0 025 0 184 0 18 0 175 0 17 0 165 0 16
C(8) 0 049 0 051 0 053 0 055 0 056 0 058 0 183 0 187 0 192 0 196 0 199 0 202
C(9) 0 049 0 048 0 046 0 044 0 043 0 041 0 183 0 178 0 174 0 169 0 165 0 161
C(10) 0 033 0 035 0 036 0 038 0 039 0 04 0 184 0 188 0 192 0 194 0 197 0 199
C(13) 0 072 0 07 0 069 0 069 0 068 0 068 0 188 0 185 0 181 0 177 0 175 0 172
C(16) 0 472 0 472 0 474 0 474 0 473 0 473 0 366 0 368 0 371 0 372 0 374 0 375
S(3) 0 268 0 27 0 272 0 273 0 276 0 278 0 382 0 385 0 387 0 389 0 392 0 394
S(4) 0 217 0 217 0 218 0 219 0 22 0 221 0 35 0 35 0 351 0 351 0 352 0 353
S(5) 0 217 0 216 0 216 0 216 0 216 0 216 0 35 0 349 0 348 0 348 0 347 0 346
S(6) 0 268 0 267 0 265 0 263 0 261 0 259 0 382 0 38 0 378 0 376 0 373 0 37
S(1) 0 113 0 117 0 12 0 123 0 126 0 13 0 067 0 068 0 07 0 071 0 073 0 075
S(2) 0 112 0 108 0 104 0 099 0 093 0 087 0 067 0 066 0 066 0 065 0 066 0 066
Au(1) 0 057 0 04 0 023 0 007 0 009 0 027 0 172 0 191 0 21 0 228 0 247 0 266
Au(2) 0 056 0 074 0 093 0 114 0 137 0 164 0 172 0 151 0 128 0 104 0 078 0 046

6 J. Comput. Theor. Nanosci. 10, 111, 2013

Selvaraju et al. A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field

for all C-atoms are found almost negative; when the eld
increases, the charges are also increases. For the applied
eld, the NPA charge of S(1) atom is found less negative
and increases from 0.067 to 0.075e, but the charge of
S(2) atom is 0.067e, which is almost remains same for
the increase of eld. For the applied eld, the charge of
Au-atom at the L-end increases gradually from 0.172 to
0.266e, while at the R-end this effect is also opposite as
noticed in MPA charges and the charge decreases from
0.172 to 0.046e. On the whole, large variation of charges in
the terminal atoms have been observed for various applied
EFs. The difference of charge distribution for zero and
various applied EF is presented in Table IV.

3.5. Molecular Orbital Analysis
The charge transport properties of the molecule36 are deter-
mined by the difference of charge density between the
highest occupied molecular orbital (HOMO) and lowest
unoccupied molecular orbital (LUMO) which is known as
HOMOLUMO gap (HLG). Hence, it is essential to exam-
ine the variations in HLG and molecular orbital energy
levels36
37 for the applied EF. Figure 4 shows the spatial
Fig. 6. Energy level diagram showing the HLG for zero and various
applied electric elds.
redistribution of quarter thiophene molecular orbital for
the zero and the maximum applied EF (0.13 V 1 ). The
applied EF partially localizes the frontier orbitals (HOMO
and LUMO) of the molecules, which are opposite to each
other and are very symmetric when the direction of the

RESEARCH ARTICLE
Fig. 4. Isosurface representation of molecular orbitals of Au and S substituted quarter thiophene molecule for zero and applied electric eld
(0.13 V 1 .

(a) (b)

Fig. 5. DOS of Au and S substituted quarter thiophene molecule for (a) zero and (b) applied EF (0.13 V 1 .

J. Comput. Theor. Nanosci. 10, 111, 2013 7

 A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field Selvaraju et al.

eld is reversed. For the applied eld (00.13 V 1 ),
the HLG decreases from 1.713 to 1.172 eV. This varia-
tion is also conrmed from the spectrum of density of
states (DOS). Figures 5(a), (b) shows the complete DOS
of Au substituted molecule, in which, the HOMO (green
lines) and the LUMO (blue lines) and the HLG are shown.
Notably, the presence of gold atoms in the molecule broad-
ens the DOS peaks. For the zero eld, the HLG is 1.71 eV,
RESEARCH ARTICLE
when the eld increases from 0.03 to 0.13 V1 , the
HOMO and LUMO levels become closer, the correspond-
ing value of HLG is 1.17 eV. Presumably, the signi-
cant decrease of HLG may facilitate for large electron
conduction38
39 through the molecule, hence, the Au sub-
stituted quarter thiophene molecule may perform as an ef-
cient molecular nanowire. Figure 6 illustrates the energy
levels of the molecule for various applied EFs.

Fig. 7. Molecular electrostatic potential of Au and S substituted quarter thiophene molecule for zero and various applied electric elds (00.13 V 1 .

8 J. Comput. Theor. Nanosci. 10, 111, 2013

Selvaraju et al. A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field

3.6. Electrostatic Potential

Figure 7 shows the isosurface representation of ESP40 of
Au substituted quarter thiophene molecule. The Au S
bond regions exhibit high negative ESP which are the neg-
ative charged regions of the molecule, and it also explicitly
reects the opposing contributions from the nuclei and the
electrons.41
42 For the zero bias, the negative ESP is con-
centrated around the S-atoms, which are present at either
ends of the molecule, and the rest of the molecule car-
ries positive ESP. For the increase of positive eld from
00.10 V 1 , the negative ESP at the L-end decreases
for each biasing step and it disappears, while at the R-end,
the negative ESP increases and spread around the right
edge of the molecule. As the eld increases to 0.13 V 1 ,
the negative ESP spread completely around the R-end of
the molecule; this shows that when the eld increases the Fig. 8. Molecular dipole moment for zero and various applied electric
charges are seems to drift from left to right. Similarly, elds.
the negative ESP regions are moved from R- to L-end of
the molecule when the eld is reversed. The ESP map
clearly shows the effect of substitution and the applied EFs
in quarter thiophene molecule.
3.7. Molecular Dipole Moment
The external EF eld polarizes43 the molecule, which leads
to change the dipole moment of the molecule. Hence,
it is necessary to nd out the dipole moment of the
molecule for various applied EFs. The variations of molec-
L (2)
ular dipole moment for the various applied EF were ana-
lyzed by Kirtman et al.44 and found a linear character.
is the tunneling decay parameter which can be deter-
However, this linearity no longer exists beyond certain
applied eld and it is unimportant since no molecular elec-
tronic device works under such high voltages.45 Here, we
= 1/h2 1/2 2m  1/2 (3)
have calculated the dipole moment of the molecule for
zero as well as various applied EFs. The resultant molec-
ular dipole moment () for zero bias is 2.69 debye, which
increases almost linearly with the increase of eld. The
molecule becomes highly polarized for the higher eld
(0.13 V 1 ). Figure 8 shows the variation of x, y and
z components of dipole moment (x
y , and z ) and the
resultant molecular dipole moment () for various applied
EFs, the large variation of x-component,43 may be due to
the application of eld along x-direction.
3.8. IV Characteristic Curve
The currentvoltage (IV) characteristic curve generally
used to determine the basic parameters of electronic
devices.46 Here, we have evaluated the IV characteris-
tics of the quarter thiophene molecule using the Landaure
formula.47 The tunneling electric current (I) has been cal-
culated for various applied EF. The resistance (R) and
the linear conductance (G) of the electrodemolecule
electrode junctions can be expressed as43
4749
where (h/2e2  = 12 91 K is the quantum of resistance,
Tl and Tr are the charge transport efciency across the
left and right contacts and Tm is the electron transmission
through the molecule itself. Since there is no charge injec-
tion barrier in the molecule, the left and right contacts
electron transmission can be neglected. Tm can be approx-
imated by the expression
Tm = exp
RESEARCH ARTICLE
where L is the potential barrier width (molecular length)
and
mined by
where, m is the effective mass of electron (m = 0 16m0 ,
m0 is the free electron mass,  is the symmetry parame-
ter of potential prole ( = 1 for symmetric molecule)5052
and  is the potential barrier height for tunneling through
the HOMO or the LUMO level. For a particular external
applied EF,  is half of the HLG and L is the distance
between the two terminal Au atoms of the molecular wire.
Here, we have calculated the resistance of the molecular
wire from the above expression (1). For the various applied
electric elds (E), the bias voltage (V ) across the molecule
of length L have been calculated from the expression
V = EL. Further, using Ohms law, (I = V /R) the current
(I) ows through the wire has been calculated for each
applied eld. Using these parameters, the IV character-
istics of the quarter thiophene molecule has been stud-
ied. Figure 9 illustrates the IV characteristics of quarter
thiophene molecule for the various applied EFs. The IV
characteristic of quarter thiophene molecule reveals that,
as the bias voltage increases, the current increases gradu-
ally showing the nonlinear behavior of the molecule. Since
the molecule is symmetric, the characteristic curve is also
R = G1 = h/2e2 1/Tl Tr Tm  = 12 91 K/Tl Tr Tm (1) almost symmetric for both directions of the applied EFs.

J. Comput. Theor. Nanosci. 10, 111, 2013 9

 A Charge Density Analysis on Quarter Thiophene Molecular Nanowire Under Applied Electric Field
Fig. 9. IV Characteristics of Au and S substituted quarter thiophene
molecule for various applied electric elds.
4. CONCLUSION
The present theoretical study on quarter thiophene molec-
ular wire describes the bond topological parameters and
the electrical characteristics for zero and various external
applied elds. For the applied eld, the Au S bond length
at the R-end is found slightly longer than the L-end; this
difference may be due to the gold atom at the L-end expe-
riences stronger electric eld than the same at the R-end.
The bond topological analysis shows the variation of elec-
tron density bcp r and Laplacian  2 bcp r for zero and
RESEARCH ARTICLE
the various applied elds; though the variations are small,
in most cases it is found to be systematic and almost uni-
form variation. When the eld increases, the hybridization
of molecular levels broaden the DOS and decreases the
HLG from 1.713 to 1.17 eV, the large decrease of band gap
at the high eld, facilitates to have high electrical conduc-
tivity. The IV characteristic curve is found very symmetric
for both directions of applied EFs, it explicitly shows the
nonlinear behavior of quarter thiophene molecule. The EF
polarizes the molecule, in consequence of that the dipole
moment of the molecule increases from 2.69 to 13 D. Over
all, the terminal groups of the quarter thiophene molecule
are found to be very sensitive to applied eld on compared
with the molecular region.
Acknowledgments: The author K. Selvaraju thanks
University Grants Commission (UGC), India, for granting
Teacher Fellowship (FDP) to carry out this research.
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Received: 7 December 2011. Accepted: 4 January 2012.
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