Scanning Tunneling Microscopic Characterization of an 

Engineered Organic Molecule

by Govind Mallick, Pamela Kaste, and Shashi P. Karna

ARL-TR-5639 August 2011

Approved for public release, distribution unlimited.
NOTICES

Disclaimers

The findings in this report are not to be construed as an official Department of the Army position 

unless so designated by other authorized documents.

Citation of manufacturer’s or trade names does not constitute an official endorsement or 

approval of the use thereof.

Destroy this report when it is no longer needed. Do not return it to the originator.
Army Research Laboratory

Aberdeen Proving Ground MD 21005-5069

ARL-TR-5639 August 2011

Scanning Tunneling Microscopic Characterization of an 

Engineered Organic Molecule

Govind Mallick

Vehicle Technology Directorate, ARL

Pamela Kaste and Shashi P. Karna

Weapons and Materials Research Directorate, ARL

Approved for public release; distribution unlimited. 
ii

REPORT DOCUMENTATION PAGE Form Approved

OMB No. 0704-0188

Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the 

data needed, and completing and reviewing the collection information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing the 

burden, to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. 

Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid 

OMB control number.

PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS.

1. REPORT DATE (DD-MM-YYYY)

August 2011

2. REPORT TYPE 3. DATES COVERED (From - To)

01 January to 30April 2011

4. TITLE AND SUBTITLE

Scanning Tunneling Microscopic Characterization of an Engineered Organic 

Molecule

5a. CONTRACT NUMBER

5b. GRANT NUMBER

5c. PROGRAM ELEMENT NUMBER

6. AUTHOR(S)

Govind Mallick, Pamela Kaste, and Shashi P. Karna

5d. PROJECT NUMBER

5e. TASK NUMBER

5f. WORK UNIT NUMBER

7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)

U.S. Army Research Laboratory

ATTN: RDRL-VT

Aberdeen Proving Ground MD 21005-5069

8. PERFORMING ORGANIZATION

 REPORT NUMBER

ARL-TR-5639

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S)

11. SPONSOR/MONITOR'S REPORT

 NUMBER(S)

12. DISTRIBUTION/AVAILABILITY STATEMENT

Approved for public release; distribution unlimited.

13. SUPPLEMENTARY NOTES

14. ABSTRACT

Surface topology and electron transport properties of self-assembled monolayer (SAM) of an engineered molecule 4,4'-[1,4-

phenylenebis(methylidynenitrilo)]bisbenzenethiol (PMNBT) and 1-dodecanethiol (dDT) adsorbed on Au substrates have been 

investigated by scanning tunneling microscopy (STM) at ambient conditions. The electrical measurements of hexadecanethiol 

(hDT), which is similar in length to PMNBT, have also been compared. The -bond dominated PMNBT molecule was 

engineered using first-principle ab initio molecular orbital theory. The estimated conductance, (dI/dV)v=0.75 = 123.91nS for 

PMNBT, is over an order of magnitude larger than the corresponding value (7.15nS) for dDT and two orders of magnitude 

larger (0.078nS) than hDT. The tunneling current (I) as a function of the applied bias (V) between STM tip and SAM of 

PMNBT exhibits asymmetric behavior. A combination of electronic and geometrical effects in the molecule and at the 

molecule-metal interface is proposed to be responsible for the observed asymmetric I-V characteristics. The increased 

conductance in PMNBT is also explained in terms of its nearest available electronic states.

15. SUBJECT TERMS

PMNBT, AFM, STM, hDT, dDT, SAM

16. SECURITY CLASSIFICATION OF: 

17. LIMITATION

OF ABSTRACT

UU

18. NUMBER

OF PAGES

22

19a. NAME OF RESPONSIBLE PERSON

Govind Mallick

a. REPORT

Unclassified

b. ABSTRACT

Unclassified

c. THIS PAGE

Unclassified

19b. TELEPHONE NUMBER (Include area code)

(410) 306-4735

Standard Form 298 (Rev. 8/98)

Prescribed by ANSI Std. Z39.18
iii

Contents

List of Figures iv

List of Tables iv

Acknowledgment v

1. Introduction and Background 1

2. Materials and Methods 2

3. Results and Discussions 5

4. Conclusions 9

5. References 10

List of Symbols, Abbreviations, and Acronyms 12

Distribution List 13
iv

List of Figures

Figure 1. Stick model of the PMNBT molecule (a), and its highly occupied molecular 

orbitals (HOMO) (b), and lowest unoccupied molecular orbitals (LUMO) (c); 

(HOMO-LUMO) = 7.0343 eV. The N-C-C6H4-C-N moiety of the optimized molecule 

is out of plane by 32.88oindicating the asymmetric nature of the molecule (1c)......................2

Figure 2. Schematic diagram of proposed STM characterization (a). STM topographical 

image of 50 x 50 nm2scan area showing SAM of dDT (b) and PMNBT (c) molecules on 

Au surface. The height profiles shown in (d) and (e) indicate average lengths of 1.2 and 

2.1 nm of dDT and PMNBT, respectively.................................................................................3

Figure 3. The grazing angle FTIR spectra of a reference sample of PMNBT crystals 

(bottom), and a SAM film of PMNBT (top) molecules on the Au surface. .............................4

Figure 4. The current (I) as a function of bias voltage (V) at set point tunneling current and 

sample bias of 2 nA and 0.13 V, respectively of (a) PMNBT, (b) hDT, and (c) dDT on Au 

substrate; arrows in the upper left insets indicate spots where the currents were measured. 

Lower right insets show the histograms for the most frequently occurring current 

magnitude at 0.75 V. Average STM I-V curves (2nd order) for PMNBT (green), hDT 

(maroon), and dDT (blue) molecules along with bare gold are shown in (d)............................4

List of Tables

Table 1. Estimated g0=(dI/dV)V=0.75 and corresponding resistance, R0 of the molecules. ..............7

Table 2. Average asymmetry in the current distribution observed in the three samples. ...............7
v

Acknowledgment

This research was supported by the U.S. Army Research Laboratory (ARL) Director’s Research 

Initiative (DRI), the Defense Advanced Research Projects Agency (DARPA)-MoleApps 

program, and the Air Force Office of Scientific Research-Defense University Research Initiative 

in Nanotechnology. Shashi P. Karna thanks Professor Paras Prasad and Dr. Qingdong Zheng for

valuable discussions, and suggestions and their contributions of 

phenylenebis(methylidynenitrilo)]bisbenzenethiol (PMNBT) molecules. Shashi P. Karna and 

Govind Mallick thank Raymond Woo and Ravi Pandey for valuable discussions and suggestions,

and Sarah Lastella and Anubhav Srivastava for their valuable contributions.
vi

INTENTIONALLY LEFT BLANK.
1

1. Introduction and Background

Rectification of electrical current between two metal electrodes by suitably engineered organic 

molecules was first proposed by Aviram and Ratner (1), who showed from semi-classical 

theoretical calculations that an organic molecule with (donor)-(spacer)-(accepter) 

architecture, sandwiched between two metal electrodes, would allow electrons to tunnel only 

from the donor to the acceptor side of the molecule. The Aviram-Ratner model has since been 

verified in several experimental (2–7) and theoretical investigations (7, 8) involving suitably 

engineered donor (D)acceptor (A) substituted organic molecules. Recently, there have also 

been reports of rectification behavior by molecules that do not contain DA architectures, but are 

assembled between dissimilar metal contacts. When probed by scanning tunneling microscopy 

(STM), copper-4,4’,4”,4’”-tetraaza-29H,31H-phthalocyanine molecules adsorbed on graphite

(9), 3,10-didocecylperylene also adsorbed on graphite (10), and oligo(phenylene ethynylene) 

molecules adsorbed on gold (Au)(111) and silver (Ag)(111) substrates (11) have been shown to 

exhibit rectification of tunnel current. Rectification by oligo(phenylene ethynylene) molecules 

adsorbed between Au cross-wire junctions (12) and chemical vapor-deposited (CVD) single wall 

carbon nanotubes (SWCNTs), previously thought to be symmetric structures, have also been 

recently reported (13, 14).

We report the STM observation of rectification by a newly designed and synthesized 4,4'-[1,4-

phenylenebis(methylidynenitrilo)]bisbenzenethiol (PMNBT) molecule adsorbed on thin film Au 

substrate. Alkanethiol molecules [CH3(CH2)n–1SH] form a robust self-assembled monolayer 

(SAM) on Au surfaces and are studied explicitly. STM (15) and conducting atomic force 

microscopy (cAFM) (16) have been used to study the electron transport (ET) through 

alkanethiols at room temperature. In this study, we have designed and modeled the PMNBT 

molecule using first principle ab initio methods. The ET properties of the SAM of the 

synthesized PMNBT molecule, along with the SAMs of hexadecanethiol (hDT) and 

dodecanethiol (dDT) on a thin film Au substrate, were measured using STM at ambient 

conditions. Although similar in size, because PMNBT is a -bonded molecule and hDT is not, 

the current (I)–voltage (V) characteristics are different, as would be expected. Tunnel current 

through PMNBT molecules exhibits almost twice as much asymmetric IV characteristic as the 

hDT and dDT molecules. We attribute the observed rectification by the PMNBT molecule to its 

highly delocalized -electron in the highest occupied molecular orbital (HOMO) and electronrich (Donor) characteristics of the S atom chemisorbed on Au surface.
2

2. Materials and Methods

Theoretical calculations were performed using an ab initio Hartree-Fock (HF)-based effective 

core potential (ECP), with a CEP-121G minimal basis set to obtain the equilibrium structure of 

the Au-PMNBT-Au (Au-S-C6H4-N=CH-C6H4-CH=N-C6H4-S-Au) molecule. The optimized 

structure, along with its corresponding HOMO and lowest unoccupied molecular orbital 

(LUMO), are shown in figure 1. The overall length (RAu-Au) of the molecule was computed to be 

2.16 nm.

Figure 1. Stick model of the PMNBT molecule (a), and its highly occupied molecular orbitals (HOMO) (b), and 

lowest unoccupied molecular orbitals (LUMO) (c); (HOMO-LUMO) = 7.0343 eV. The N-C-C6H4-CN moiety of the optimized molecule is out of plane by 32.88o

indicating the asymmetric nature of the 

molecule (1c).

The PMNBT molecule was synthesized (17) by condensation between two equivalents of 4-

aminothiophenol and one equivalent of 1,4-benzenedicarboxaldehyde, with a yield of 85%. The 

molecular structure of the compound, shown in figure 1a, was confirmed by 1H NMR, 13C NMR,

and elemental analyses. The absorption maximum (λmax) and the extinction coefficient of 

PMNBT in THF are 315 nm and 1.2 × 104 M

–1

cm–1, respectively. The commercially available 

Au substrate (Molecular Imaging, Tempe, AZ) with an average roughness of ~0.3 nm was used 

as the surface upon which the SAMs of PMNBT, hDT, and dDT were deposited. The Au 

substrate as obtained was first treated with UV/Ozone to remove any assortment of organic 

contaminants from the surface. For the preparation of the hDT and dDT SAMs, the Au substrate 

was separately incubated in a 1 mM ethanol solution of 1-hexadecanethiol (Acros Organics, 

92%) and 1-dodecanethiol (Aldrich, 98%) for an overnight period of more than 12 h. 

Subsequently, the film was rinsed with ethanol and dried in air. A 1.13 × 10–3 M solution of 

PMNBT (molecular weight = 348 g/mol) was prepared in tetrahydrofuran (THF). The SAMs of 

PMNBT were prepared by incubating a clean Au (mentioned previously) substrate in the THF
3

solution. The substrate was rinsed with THF and air-dried. The surface topologies of the bare and 

molecule adsorbed substrates were characterized by STM conductance spectroscopy (CP-II, 

Veeco Inc.), as shown in the schematic diagram in figure 2a. The STM topologies (figures 2b 

(dDT) and 2c (PMNBT)) and respective height profiles (figures 2d and 2e) allowed the

identification of the regions on the substrate surface with bundles of adsorbed molecules (hDT–

not shown).

Figure 2. Schematic diagram of proposed STM characterization (a). STM topographical image of 50 x 50 nm2

scan area showing SAM of dDT (b) and PMNBT (c) molecules on Au surface. The height profiles

shown in (d) and (e) indicate average lengths of 1.2 and 2.1 nm of dDT and PMNBT, respectively.

For further verification of molecules on the Au substrates, Fourier Transform Infrared (FTIR) 

spectroscopy was performed. A Thermo Nicolet Nexus 870 FTIR, with a grazing angle 

attachment and wide-band MCT detector, was used. Figure 3 shows the spectra obtained for 

SAM of PMNBT (top), which was compared to raw crystal PMNBT molecules (bottom). 

The STM IV measurements were then performed at clearly marked areas of SAMs of PMNBT 

(figure 4a), hDT (figure 4b), and dDT (figure 4c), respectively. In the STM measurements, 

freshly cut platinum/iridium (Pt/Ir) tips were used for each sample. The tip was lowered to the 

sample for a set tunnel current of 2 nA at a tip-to-sample bias of 0.13 V. In the IV trace, data 

taken at the same points for over 100 traces were averaged in order to reduce random noise, 

especially in the high bias region. Figure 4d shows the average second-order STM I-V curves of 

each molecule. 0.6 nm/Div 1.0 nm/Div

10 nm

10 nm

2.50

2.00

1.00

1.50

0 1 0 20 nm

n m

1.20

1.00

0.80

n m

0 1 0 2 0 3 0 n m

(a)

(c)

(b)

(d)

STM Probe

Au

Au

S

S Au

Au

S

S

Au

Au

S

S

Au

Au

S

S

A

Vdc

(e)
4

Figure 3. The grazing angle FTIR spectra of a reference sample of PMNBT crystals (bottom), 

and a SAM film of PMNBT (top) molecules on the Au surface.

Figure 4. The current (I) as a function of bias voltage (V) at set point tunneling current and sample bias of 2 nA 

and 0.13 V, respectively of (a) PMNBT, (b) hDT, and (c) dDT on Au substrate; arrows in the upper 

left insets indicate spots where the currents were measured. Lower right insets show the histograms

for the most frequently occurring current magnitude at 0.75 V. Average STM I-V curves (2

nd order) 

for PMNBT (green), hDT (maroon), and dDT (blue) molecules along with bare gold are shown in (d).
5

3. Results and Discussions

The line spectra and the height measurements in the STM images were used to identify the 

bundle of the hDT, dDT, and PMNBT molecules (figure 2). The average heights of the 

individual peaks were ~2.0 nm and ~1.2 nm for hDT and dDT, respectively, representing the 

approximate size of the two molecules. The respective reported chain lengths with Au-thiol 

bonding are 1.8 nm and 1.4 nm (18). In case of the PMNBT SAM (figure 2c), the height of the 

individual spike was about 2.1 nm, representing the approximate length (2.16 nm) of the 

optimized PMNBT molecule (figure 1). The measured root mean square (rms) roughness for the 

50 × 50 nm2scan area of the bare Au surface was 0.060±0.0041 nm, and that with adsorbed 

hDT and dDT were 0.048±0.02 nm and 0.058±0.014 nm, respectively. The almost identical 

roughness of the aforementioned three surfaces reflects the close-packed self-assembly of hDT 

and dDT with the formation of SAM. The PMNBT molecules, on the other hand, were less 

uniformly adsorbed on the surface and, thus, add to the measured surface roughness (rms = 

0.17±0.011 nm). The difference in the density and uniformity of the SAM of the two molecules 

could be related to the difference in their chemical bonding and molecular structure. In the case 

of hDT and dDT, the molecular charge density has a small spatial extension due to -type 

bonding in the backbone, resulting in a rather short-range Coulomb field, thus allowing a denser 

packing of molecules. In contrast, the charge density in the -conjugated backbone of PMNBT 

has large overall spatial extension below and above the molecular plane, creating greater 

intermolecular repulsion and steric hindrance, which leads to a less densely packed monolayer 

formation. It is worth noting that a greater intermolecular repulsion between -electron 

conjugated systems may also induce conformational changes in adsorbed molecules, adding to 

the non-uniformity, and also to the electrical properties of the SAM. 

The FTIR spectra of PMNBT, showing relative absorbance values, are provided in figure 3. In 

case of PMNBT, a reference spectrum of the PMNBT crystals is compared to spectrum of the 

SAM film. The amount of material probed in the case of the SAM film is significantly less, and 

the quality of the spectrum is not as good as for the crystals; nonetheless, the spectral features are 

comparable, indicating that the SAM deposition was successful. The bands between 2000–

1600 cm–1are indicative of the –C=N stretch and phenyl ring substitution overtones. The peaks 

above 3000 cm–1are indicative of the C-H stretch of the aromatic ring of PMNBT. The FTIR 

spectra of many thiols have a unique band between 2550 cm–1and 2600 cm–1, which, although 

weak, is distinctly indicative of the S-H stretch. It is not always present, however, and 

unfortunately none of the compounds in this study exhibited it. Had it been present, it could 

potentially have been used to track the extent to which the SAMs are bonded to the Au, since the 

S-H bond break prior to Au-S bond formation. In the case of the hDT and dDT, the molecules 

consist primarily of C-C and C-H bonds, their FTIR spectra are dominated by these absorbances, 

and the S-H bands are not evident. For the case of aromatic thiols, we observed that nearly all of 
6

the halogen-substituted aromatic thiols exhibited the S-H stretching mode, but that it was often 

not found in the amino-substituted compounds. Nonetheless, the FTIR did serve to confirm the 

presence of the SAM molecules on the Au substrate.

The tunnel current (I), as a function of applied tip bias (V), was measured at more than 10 spots 

(some of the spots are indicated by arrows in the upper left insets in figure 4) on each SAM 

sample. Each I-V trace was an average of 100 scans at any spot. The I-V curves for the PMNBT, 

hDT, and dDT SAMs are shown in figures 4a, 4b, and 4c, respectively. The measured tunnel 

current through the SAMs of -bonded molecules (hDT and dDT), as well as PMNBT 

molecules, exhibit a noticeable distribution in magnitude. However, the hDT and dDT SAMs 

show a much narrower spread in current magnitude than the PMNBT. The lower right insets in 

figures 4a, 4b, and 4c show the statistical distribution of the measured current values at +0.75 V, 

from which it is clear that the most frequently occurring current value for PMNBT is around 

24 nA. The hDT and dDT SAMs exhibit a rather uniform distribution of measured tunnel 

current, with the most frequent tunnel current having a magnitude of ~0.005 nA for hDT and 

~1.5 nA for dDT. The most frequently occurring current value in the hDT molecules is smaller 

by a factor of about two than that in the dDT molecules. Both hDT and dDT molecules are 

-bonded molecules and, hence, are expected to be virtually insulating molecules. However, the 

dDT molecules are smaller in length (~1.2 nm) compared to the hDT (~2.0 nm) molecules; the 

tunnel current is much smaller in hDT. On the other hand, the most frequently occurring tunnel 

current values for -bonded PMNBT molecules are about three orders of magnitude higher than 

hDT molecules and one order of magnitude higher than dDT. The observation of large tunneling 

current via PMNBT compared to hDT and dDT is a consequence of the highly delocalized -

electron charge distribution in PMNBT molecules. 

The values of transconductance, go = (dI/dV), and corresponding quantum resistance, Ro, 

estimated from the measured I-V traces at an applied bias of 0.75 V are listed in table 1. Though 

go and Ro are generally measured at zero applied bias, we measured at the applied bias of 

+0.75 V. This was done to avoid the low signal-to-noise ratio regime of the STM (18). Our 

estimated value of go for dDT is about two orders of magnitude smaller than that reported earlier 

by Labonté et al (18) from a similar experiment but using an applied bias of –1.5 V. The 

difference in the value of go (and Ro) in the two measurements could be due to differences in 

experimental conditions, including different bias voltages, SAM preparation, and quality of the 

film, as well as the sensitivity of the STM. However, our measured go and Ro for dDT, which has 

been extensively studied, is within an order of magnitude of the literature values (18). It is noted 

that the value of go for the -bonded molecule PMNBT is almost four orders of magnitude larger 

than -bonded hDT and almost two orders of magnitude larger than dDT molecules. A large 

magnitude of go for PMNBT makes it an attractive candidate for molecular-scale electronics 

applications. 
7

Table 1. Estimated g0=(dI/dV)V=0.75 and corresponding resistance, R0 of the molecules.

Substrate (dI/dV)V=0.75 (S) R0 ()

hDT 7.79x10–11 1.66x1014

dDT 7.15x10–91.81x1012

PMNBT 1.24x10–71.04x1011

An interesting part of the measured tunnel currents in the molecular SAMs is the asymmetry 

with respect to the polarity of the bias voltage. The estimated distribution of the tunnel current 

with respect to the positive and negative bias voltages for the molecular SAMs, as well as the 

bare Au substrate, is listed in table 2. Asymmetric behavior in the I–V curves is observed for bare 

Au (11.0%), and the SAMs of hDT (24.9%) and dDT molecules (19.0%). In comparison, the 

PMNBT SAM molecule exhibits a significantly more pronounced asymmetry (40.6%) of the 

tunnel current. We also note that the I-V curves for the PMNBT molecules show three distinct 

behaviors (marked in figure 4a). Although, no specific reason is apparent, there could be several 

significant contributing factors. As indicated by the marked arrows in the upper-left inset of 

figure 4a, there are three different regimes where the I-V curves were measured which are 

differentiated by the brightness. The brightest spots, indicated by 1, represent the maximum 

current, whereas the arrows marked 3 represent the lowest current. Moreover, the -bonded 

PMNBT molecules have the tendency to change their geometrical conformation in response to 

external perturbation, leading to varying current magnitudes (19). Nonetheless, it is worth noting 

the prominent rectification in each region of current. This observed rectifying behavior in the 

case of PMNBT SAM can be seen more clearly in figure 4d, where the best second-order fit to 

the measured I-V curves for the SAMs of hDT (maroon), dDT (blue), and PMNBT (green) on the 

Au(111) substrate are plotted together. For reference, the corresponding I-V curve (yellow) for 

bare Au is also plotted. The magnitude of the current in the case of bare Au is much larger than 

those for the molecular SAMs.

Table 2. Average asymmetry in the current distribution observed in the three samples. 

Gold 11.0%

hDT 24.9%

dDT 19.0%

PMNBT 40.6%

The observation of a large current rectification by PMNBT molecules, and not by hDT or dDT 

under similar experimental conditions, can be understood from the consideration of the physical 

and electronic structures of the STM probe-SAM-substrate system. Three possible factors can 

potentially contribute to the observed asymmetry in the measured tunnel current through 

PMNBT: (i) asymmetry due to a difference in the chemical nature (and chemical potential) of the 

substrate (Au) and the STM tip (Pt/Ir), (ii) difference in the electronic structure of the molecule-
8

substrate (Au) and molecule-STM tip interfaces, and (iii) electric-field induced change in 

conformation of the molecule. While the difference in the chemical nature of the substrate and 

STM tip will certainly have an effect due to different work functions of the metals, it alone 

cannot account for the observed asymmetry in the case of PMNBT. If this alone were the case, 

one would also observe similar behavior in hDT or dDT, especially since this molecule has a 

single –SH group and, hence, becomes somewhat asymmetric. The difference in the electronic 

structure and the charge distribution at the molecule-Au interface and at the molecule-Pt/Ir 

junction due to difference in chemical bonding at the two interfaces may induce D-A

characteristics in the otherwise symmetric molecule, thus creating a medium for rectifying tunnel 

current. Indeed, the ab initio calculation (figure 1), which yielded an optimized Au-PMNBT-Au,

suggests substantial charge (0.22e-) transfer from Au to sulfur (S) atoms. The charge at the S 

atom is mainly localized in the HOMO-1 level, which is a low-conjugated sp-type orbital with 

slight contributions from Au 4s shell. Thus, one would expect transfer of charge from Au to the 

S-end of the chemisorbed molecule, thus making the molecule electron rich (donor) at the Aumolecule interface. Since no bonds are formed at the STM side of the molecule, no effective 

charge transfer takes place, thus the molecule acquires an effective electron deficient (acceptor) 

characteristic at the molecule-air-Pt/Ir end. Due to this “induced” D-A characteristic of the 

molecule, the electrons will easily tunnel from the molecule to STM tip under positive tip-bias, 

but not vice versa, resulting in the observed rectification behavior. The ability of this charge to 

easily tunnel through the molecule, and to the Pt/Ir tip at positive bias, is facilitated by the highly 

delocalized nature of the HOMO (figure 1b), which is only 0.6 eV higher than the S atom 

containing the extra charge. A similar mechanism has also been proposed as a possible reason 

for the observed rectification in a previous experiment (11) on oligo (phenylethynyl) benzothiol 

and appears to be consistent with the present observation. 

A conformational change of the conjugated- electron system is known to affect its electrical 

transport properties. It has been shown on the basis of quantum mechanical calculations that a 

planar geometry, in which the -orbitals in the molecule are parallel, gives a larger tunnel current

(19) and electron transfer probability (20) through the molecule than a non-planar geometry. In 

order for the conformational change to cause rectification of tunnel current, one would expect 

that under a positive tip bias, the molecules (at least a great fraction of them) under the STM tip 

acquire an electrically favorable (planar) geometry, while the same is not true under reversed 

bias. The ab initio molecular orbital calculations do suggest that under equilibrium conditions, 

the molecule has a non-planar ground state geometry (figure 1c), with the middle diimino 

(-N=CH-C6H4-CH=N-) moiety rotated by ~33o with respect to the molecular plane containing 

the two terminal phenyl rings. The difference in the total energy between the planar and the 

stable non-planar ground state geometry is calculated to be ~0.25 eV with HF and ~0.18 eV with 

density functional theory. Thus, it is possible that under applied bias, a number of molecules 

change their state from a non-planar to a planar geometry, therefore facilitating enhanced 

electron transport. More detailed experimental and theoretical investigations and analyses are 

required to exactly establish the underlying physical mechanism of the observed rectification. 
9

However, the asymmetry due to charge transfer to the molecule at the Au-molecule interface 

appears to be the dominant mechanism, as also suggested by Dhirani et al. (11) in the case of 

oligo(phenylenacytelene)benzothiol.

4. Conclusions

In summary, we have performed STM measurements on electron tunneling characteristics of 

SAMs of a newly engineered -conjugated molecule, PMNBT, together with the much studied 

-bonded, hDT, and dDT molecules. Both hDT and dDT molecules form close packed SAMs,

as expected. PMNBT molecules also form somewhat patterned SAM. The PMNBT molecule 

exhibits a large tunneling current due to its highly conjugated -electron structure. The PMNBT 

molecule also exhibits prominent rectification of the tunnel current, which appears to result from 

a combination of electronic and geometrical effects in the molecule and at the molecule-metal 

interface. In contrast, the tunneling current through the -bonded hDT and dDT SAMs has much 

smaller magnitude and exhibits very little asymmetry in the I–V curves. The PMNBT molecules, 

due to a large magnitude of tunnel current and rectifying property, may be useful for molecularscale electronics applications.
10

5. References

1. Aviram, A.; Ratner, M. A Molecular Rectifiers. Chem. Phys. Lett. 1974, 29, 277–283.

2. Geddes, N. J.; Sambles, J. R.; Jarvis, D. J.; Parker, W. G.; Sandman, D. J. Fabrication and 

Investigation of Asymmetric Current-voltage Characteristics of Metal/Langmuir-Blodgett 

Monolayer/Metal Structure. Appl. Phys. Lett. 1990, 56, 1916–1918.

3. Martin, A. S.; Sambles, J. R.; Ashwell, G. J. Molecular Rectifier. Phys. Rev. Lett. 1993, 70, 

218–221.

4. Fisher, C. M.; Burland, M.; Roth, S.; Klitzing, K. V. Organic Quantum Wells: Molecular 

Rectification and Single-electron Tunneling. Europhys. Lett. 1994, 28, 129–134.

5. Metzger, R. M.; Chen, B.; Hopfner, U.; Lakshmikantham, M. V.; Vuillame, D.; Kawai, T.; 

Wu, X.; Tachibana, H.; Hughes, T. V.; Sakurai, H.; Baldwin, J. W.; Hosch, C.; Cava, M. P.; 

Brehmer, L.; Ashwell, G. J. Unimolecular Electrical Rectification in Hexadecylquinolinium 

Tricyanoquinodimethanide. J. Am. Chem. Soc. 1997, 119, 10455–10466.

6. Metzger, R. M.; Chen, B.; Vuillame, D.; Laxmikantam, M. V.; Hopfner, U.; Kawai, T.; 

Baldwin, J. W.; Wu, X.; Tachibana, H.; Sakurai, H.; Cava, M. P. Observation of 

Unimolecular Electrical Rectification in Hexadecylquinolinium Tricyanoquinodimethanide.

Thin Solid Films 1998, 326, 326–330.

7. Elbing, M.; Ochs, R.; Koentopp, M.; Fischer, M.; Hänisch, C. von.; Weigend, F.; Evers, F.; 

Weber, H. B.; Mayor, M. A Single-molecule Diode. Proc. Natl. Acad. Sci., 2005, 102, 

8815–8820.

8. He, H.; Pandey, R.; Mallick, G.; Karna, S. P. Asymmetric Currents in a Donor-BridgeAcceptor Single Molecule: Revisit of the Aviram-ratner Diode. J. Phys. Chem. C, 2009, 

113, 1575–1579. 

9. Pomerantz, M.; Aviram, A.; McCorkle, R. A.; Li, L.; Schrott, A. G. Rectification of STM 

Current to Graphite Covered with Phthalocyanine Molecules. Science, 1992, 255, 1115–

1118.

10. Stabel, A.; Herwig, P.; Mullen, K.; Rabe, J. P. Diode Like Current-voltage Curves for a 

Single Molecule-tunneling Spectroscopy with Submolecular Resolution of Alkylated Pericondensed Hexabenzo Coronene. Angew. Chem. Int. Ed. Engl., 1995, 34, 1609–1611.

11. Dhirani, A.; Lin, P.-H.; Guyot-Sinnoset, P.; Zehner, R. W.; Sita, L. R. Self-assembled 

Molecular Rectifiers. J. Chem. Phys., 1997, 106, 5249–5253.
11

12. Kusmerick, J. G.; Holt, D. B.; Yang, J. C.; Naciri, J.; Moore, M. H.; Shashidhar, R. Metalmolecule Contacts and Charge Transport Across Monomolecular Layers: Measurement and 

Theory. Phys. Rev. Lett. 2002, 89, 086802 (1–4).

13. Mallick, G.; Griep, M, Lastella, S.; Sahoo, S.; Hirsch, S.; Ajayan P. M.; Karna, S. P. Diodelike Properties of As-grown Chemical Vapor Deposited Single-walled Carbon Nanotubes. J 

of Nanosc. and Nanotech. 2010, 10, 6062–6066.

14. Mallick, G.; Griep, M. H.; Ajayan P. M.; Karna, S. P. Alternating Current-to-Direct Current 

Power Conversion by Single-wall Carbon Nanotube Diodes. Appl. Phys. Letts. 2010, 96, 

233109 (1–4).

15. Bumm, L. A.; Arnold, J. J.; Dunbar, T. D.; Allara, D. L.; Weiss, P. S. Electron Transfer 

through Organic Molecules. J. Phys. Chem. B 1999, 103, 8122–8127.

16. Wold, D. J.; Haag, R.; Rampi, M. A.; Frisbie, C. D. Distance Dependence of Electron 

Tunneling through Self-assembled Monoloayers Measured by Conducting Probe Atomic 

Force Microscopy: Unsaturated versus Saturated Molecular Junctions. J. Phys. Chem. B

2002, 106, 2813–2816.

17. Moutloali, R. M.; Nevondo, F. A.; Darkwa, J.; Iwuoha , E. I.; Henderson, W. Bimetallic 

Nickel Complexes with Bridging Dithiolated Schiff Base ligands: Synthesis Mass Spectral 

Characterization and Electrochemistry. J. Organomet. Chem. 2002, 656, 262–269.

18. Labonte, A. P.; Tripp, S. L.; Reifenberger, R.; Wei, A. Scanning Tunneling Spectroscopy of 

Insulating Self-assembled Monolayers on Au(111). J. Phys. Chem. B 2002, 106, 8721–8725.

19. Pati, R.; Karna, S. P. Current Switching by Conformational Change in a  Molecular 

Wire. Phys. Rev. B 2004, 69, 155419 (1–5).

20. Pati, R.; Karna, S. P. Ab Initio Hartree-Fock Study of Electron Transfer in Organic 

Molecules. J. Chem. Phys. 2001, 115, 1703–1715.
12

List of Symbols, Abbreviations, and Acronyms

Ag silver

ARL U.S. Army Research Laboratory

Au gold

cAFM conducting atomic force microscopy

CVD chemical vapor deposited

DARPA Defense Advanced Research Projects Agency

dDT dodecanethiol

DRI Directors’s Research Initiative

ECP effective core potential

ET electron transport

FTIR Fourier Transform Infrared

hDT hexadecanethiol

HF Hartree-Fock

HOMO highest occupied molecular orbital

Ir iridium

LUMO lowest unoccupied molebular orbital

PMNBT ,4'-[1,4-phenylenebis(methylidynenitrilo)]bisbenzenethiol

Pt platinum

S sulfur

SAM self-assembled monolayer

STM scanning tunneling microscopy

SWCNTs single wall carbon nanotubes

THF tetrahydrofuran
13

NO. OF

COPIES ORGANIZATION

1 ADMNSTR

ELEC DEFNS TECHL INFO CTR

ATTN DTIC OCP

8725 JOHN J KINGMAN RD STE 0944

FT BELVOIR VA 22060-6218

1 CD OFC OF THE SECY OF DEFNS

ATTN ODDRE (R&AT) 

THE PENTAGON

WASHINGTON DC 20301-3080

1 US ARMY RSRCH DEV AND ENGRG 

CMND

ARMAMENT RSRCH DEV & ENGRG 

CTR 

ARMAMENT ENGRG & TECHNLGY 

CTR

ATTN AMSRD AAR AEF T J MATTS

BLDG 305

ABERDEEN PROVING GROUND MD 

21005-5001

1 US ARMY INFO SYS ENGRG CMND

ATTN AMSEL IE TD A RIVERA

FT HUACHUCA AZ 85613-5300

1 COMMANDER

US ARMY RDECOM

ATTN AMSRD AMR 

W C MCCORKLE

5400 FOWLER RD

REDSTONE ARSENAL AL 35898-5000

1 NASA GLENN

ATTN RDRL VT M VALCO

21000 BROOKPARK ROAD

MAIL STOP 21-2

CLEVELAND, OH 44139-3191

1 US GOVERNMENT PRINT OFF

DEPOSITORY RECEIVING SECTION

ATTN MAIL STOP IDAD J TATE

732 NORTH CAPITOL ST NW

WASHINGTON DC 20402

NO. OF

COPIES ORGANIZATION

1 US ARMY RSRCH LAB

VTD-ODIR

ATTN RDRL VT

BLDG 4603

ABERDEEN PROVING GROUND, MD 

21005-5069

31 US ARMY RSRCH LAB

ATTN RDRL VT G MALLICK

(10 HCS)

ATTN RDRL WM (A)

ATTN RDRL WM S KARNA

(10 HCS)

ATTN RDRL WML B P KASTE

(10 HCS)

BLDG 4600

ABERDEEN PROVING GROUND MD 

21005

3 US ARMY RSRCH LAB

ATTN IMNE ALC HRR 

MAIL & RECORDS MGMT

ATTN RDRL CIO LL TECHL LIB

ATTN RDRL CIO MT TECHL PUB

ADELPHI MD 20783-1197

TOTAL: 42 (1 ELEC, 1 CD, 40 HCS)
14

INTENTIONALLY LEFT BLANK.