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Letter

End-Group Induced Charge Transfer in MolecularJunctions: Effect on Electronic-Structure and ThermopowerJanakiraman Balachandran, Pramod Reddy, Barry Dov Dunietz, and Vikram Gavini

J. Phys. Chem. Lett., Just Accepted Manuscript • DOI: 10.1021/jz300668c • Publication Date (Web): 05 Jul 2012

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End-Group Induced Charge Transfer in Molecular

Junctions: Effect on Electronic-Structure and

Thermopower

Janakiraman Balachandran,† Pramod Reddy,∗,‡ Barry D. Dunietz,∗,¶ and Vikram

Gavini∗,†

Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI-48109,

Department of Mechanical Engineering, Department of Materials Science and Engineering,

University of Michigan, Ann Arbor, MI-48109, and Department of Chemistry & Biochemistry,

Kent State University, Kent, OH-44242

E-mail: pramodr@umich.edu; bdunietz@kent.edu; vikramg@umich.edu

∗To whom correspondence should be addressed†Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI-48109‡Department of Mechanical Engineering, Department of Materials Science and Engineering, University of Michi-

gan, Ann Arbor, MI-48109¶Department of Chemistry & Biochemistry, Kent State University, Kent, OH-44242

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Abstract

We analyze triphenyl molecules coupled to gold electrodes through five different end-

groups to understand the effect of end-groups on the thermoelectric properties of molecular

junctions. Our investigation suggests that end-group mediated charge transfer between the

molecule and electrodes plays an important role in the resulting thermoelectric properties. We

find that the direction of charge transfer, which is governedby the electronegativity of the

end-group functionalized molecule, is strongly correlated to the degree of reorganization of

frontier molecular orbitals (HOMO-LUMO). In particular, isocyanide, nitrile and amine end-

group molecular junctions, with charge (electron) transfer out of the molecule, exhibit a strong

overall downward shift in the energies of frontier molecular orbitals. Whereas, thiol and hy-

droxyl end-group molecular junctions, with charge transfer into the molecule, exhibit a smaller

overall downward shift. Finally, our study shows that the sign of the thermopower of molecu-

lar junctions is closely related to the HOMO-LUMO energies and electronegativity of isolated

molecules.

En

erg

y

EEM

EIM

Stabilization

Increased

e-e Repulsion

Stabilization

Decreased

e-e Replusion

EIM

EEM

X X

X

SH

OH

X

NC

CN

NH 2

Charge Gain Charge Loss

Vhot

Vcold

TOC Graphic

Keywords: orbital alignment, electronegativity, molecular thermoelectrics, energy conversion,

molecular electronics

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Nanometer sized molecular junctions (MJs), where a single molecule bridges two metal elec-

trodes, have great potential for advancing future electronic1–3 and energy conversion4–7 technolo-

gies. The end-groups of the MJs play an important role in determining their transport properties

such as electrical conductance and thermopower8–13(also called the Seebeck coefficient). Reliable

experimental measurements of electrical conductance of MJs with different end-groups10,11,14,15

have provided important insights into the effect of end-groups on their conductance. However,

conductance measurements alone cannot delineate the nature of charge transport in the MJs.16

Thermoelectric measurements can provide this additional insight.9,16,17 In particular, a positive

thermopower indicates a scenario where transport is dominated by states immediately below the

Fermi energy (EF ) (HOMO dominated or p-type transport), while a negative thermopower indi-

cates a scenario where transport is dominated by states immediately above theEF (LUMO or

n-type transport).

Recent thermopower measurements12,13,18,19demonstrate the ability to tune the nature of trans-

port in aromatic MJs by changing the end-group. Further, thermoelectric properties have also been

studied using the Green’s function approach in the Landauerformalism of transport.20–22 Such

computational studies12,23–25have provided important insights on the length and end-group depen-

dence of the thermoelectric properties of MJs. However, theunderlying mechanism that relates the

effect of end-groups on the electronic-structure and the resulting thermoelectric properties needs

further elucidation. The present work bridges this gap by illustrating the role of end-groups on the

resultant electronic-structure. Further, this work also provides a qualitative understanding of the

relationship between the pertinent characteristics of isolated molecules (HOMO, LUMO energies,

electronegativity) and the thermopower of MJs created fromthem.

In this work, we begin by analyzing the electronic-structure of triphenyl di-thiol (SS3) and

triphenyl di-isocyanide ((NC)23) molecules (Figure 1(a)) using density functional theory(DFT)

calculations performed with Q-CHEM software26 by employing B3LYP functional27,28and LANL2DZ

basis sets.29–31The computed HOMO and LUMO energy levels of these molecules are presented

in Table 1. These results indicate that the Fermi energy (EF ) of Au, which is∼ -5.2 eV,32 lies in

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the HOMO-LUMO gap of these molecules and is closer to the HOMOenergy level. Interestingly,

recent experimental and computational studies12 suggest that Au-(NC)23-Au junctions exhibit a

LUMO dominated transport, whereas Au-SS3-Au junctions exhibit HOMO dominated transport.

This observation raises an important question:How do end-groups influence the reorganization of

molecular orbital upon contact with electrodes?

Table 1: Computed values of HOMO and LUMO energy levels, charge transfer (∆N) (seeEq. 3), electronegativity (χ), shift of HOMO ( ∆εH) and LUMO ( ∆εL) energy levels of all themolecular systems considered in this work.

System HOMO (eV) LUMO (eV) ∆N χ(eV) ∆εH(eV) ∆εL(eV)SS3 -5.65 -1.14 -0.66 5.13 0.35 0.25

(NC)23 -6.28 -1.93 0.16 4.15 0.9 1.05OO3 -5.47 -0.82 -0.25 5.12 0.24 0.23

(CN)23 -6.53 -2.20 0.12 4.40 0.8 0.86(NH2)23 -4.68 -0.41 0.27 2.57 0.96 0.92

In order to obtain insights into the end-group mediated reorganization of energy levels, we com-

pared the molecular density of states (M-DOS) ofSS3 and(NC)23 before and after making contact

with Au electrodes. Specifically, the M-DOS is calculated for three different scenarios: (a) isolated

molecule (IM); (b) extended molecule (EM), where the molecule is coupled to Au clusters through

the most stable adsorption site (system geometries discussed subsequently); (c) open quantum sys-

tem, where the extended molecule is connected to semi-infinite electrodes. Past work indicates

that the hollow site (Figure S1 in Supporting Information (SI)) and the top site (Figure S2, SI) are

the most stable adsorption sites for theSS323,33 and(NC)2334 molecules respectively . Further,

in the case ofSS3, the hydrogen in the thiol group is assumed to have deprotonated upon contact

with Au. A schematic of the extended molecule system geometry is shown in Figure S4 of the SI,

where the Au clusters include four{111} planes of six Au atoms each, in addition to the contact-

ing Au atoms. For the open quantum system, the effect of semi-infinite electrodes is modeled by

projecting the Green’s functions of electrodes through theself-energy operators onto the extended

molecule. These Green’s functions are calculated using an efficient recursive algorithm.35 In our

calculations, the self-energy operators of the electrodesare computed only atEF , which is com-

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monly referred to as the wide band scheme and has been shown tobe a good approximation for

MJs created from Au electrodes with density of states dominated by thes band.36

We now describe the procedure to compute the M-DOS for the three aforementioned scenarios.

The retarded Green’s function,Gri j (z), that is subsequently used to compute M-DOS, is given by

Gri j (z) = (zSi j −Hi j −ΣLi j −ΣRi j )

−1 z= E+ iη , (1)

whereE is the energy andη is a small imaginary parameter to regularize the Green’s function. In

the above expression,Hi j andSi j denote the Hamiltonian and overlap matrix of the system under

consideration.ΣL/R denote the self-energy operators corresponding to the leftand right leads. In

the case of IM and EM systems theΣL/R are set to zero.

The density of states,D(E), is then obtained fromGr(z) by

D(E) =−1π

Tr (Im[Gr(z)S]) . (2)

To compute M-DOS, the trace in Eq.2 is performed only over theorbitals that are centered on

the molecule. Natural atomic orbital (NAO)37 basis, which is an orthonormal basis with localized

functions, is used for computing the M-DOS.

We begin with our electronic-structure analysis of the SS3 and (NC)23 molecular systems.

The computed M-DOS for the IM, EM and open quantum systems forSS3 and(NC)23 are shown

in Figure 1(b) and 1(c) respectively. A comparison between the M-DOS of IM and EM for both

systems shows that the HOMO and LUMO states of EM shift to lower energies in comparison to

IM. However, it is interesting to note that this downward shift in energies (Table 1) is significantly

larger in the case of(NC)23. In particular, the shift of HOMO and LUMO states in the caseof SS3

is 0.35 eV and 0.25 eV respectively, whereas in the case of(NC)23 these shifts are significantly

larger—0.9 eV for HOMO and 1.05 eV for LUMO. In order to validate the independence of the

obtained results on the choice of basis functions, we repeated our calculations using a second basis

set comprising of the primitive atomic orbitals (Figure S5,SI), whose results are in good agreement

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0

200

400

600

800

0 1 2 3 4

EF

M-

DO

S

−2 −1 0 1 2 30

200

400

600

800

EF

(c)

(b)

M-

DO

S

E − EF (eV)

E − EF (eV)

SS3

(NC)23

HS SH C CNNSS3 (NC)23(a)

Figure 1: (a) Isolated triphenyl di-thiol (SS3) and triphenyl di-isocyanide ((NC)23) molecules. (b)M-DOS ofSS3 molecule in different scenarios (IM, EM and open quantum system). (c) M-DOS of(NC)23 molecule in different scenarios. The M-DOS of the IM, EM andopen quantum system aredenoted by blue-dotted line, red-dashed line and green-continuous line respectively. The purplearrows indicate the magnitude of the M-DOS shift.

with the results obtained using NAO basis. A comparison of the M-DOS of EM and open quantum

systems in Figure 1(b) and 1(c) shows that the energies corresponding to the dominant peaks are

almost identical. In order to verify that this observation is not an artifact of the wide band scheme

adopted in our calculations, a full tight binding computation was also performed (Figure S6, SI)

which did not affect the results. This suggests that for the purpose of understanding the reorgani-

zation of the molecular states, the shifts in the dominant peaks of the EM are representative of the

respective shifts in the open quantum systems.

Although these results demonstrate that end-groups play animportant role in realigning the

molecular orbitals, the dominant mechanism that leads to the differences in the magnitude of these

shifts is yet to be identified. As a first step towards answering this question, we compare the

number of electrons present in the isolated and extended molecular systems. The insights obtained

from such an analysis are also expected to be valid for the open quantum system, since the shift

of the M-DOS is completely captured by the extended molecule. To quantify the change in the

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number of electrons in the IM and EM systems, we define the electrode-coupling inducedcharge

transfer(∆N) as

∆N = NIM −NEM , (3)

whereNIM denotes the number of electrons in the IM, andNEM denotes the number of electrons in

the spatial location of the molecule in the EM system.NEM is computed by expressing the single

particle density matrix̂ρ in the NAO basis and performing the trace only over the orbitals which

are centered on the molecule:

NEM = ∑i∈Mol

ρ̂ii . (4)

This approach is commonly referred to as natural populationanalysis.38 In the case of(NC)23,

NIM is simply obtained from the total number of electrons in the IM. However, in the case ofSS3,

as the hydrogen atoms are assumed to have deprotonated, the electrons contributed by them are

excluded fromNIM .

The ∆N values forSS3 and(NC)23 (see Table 1) indicate that,SS3 molecule gains a 0.66

electron partial charge upon contact with Au atoms. Such a gain in electronic charge is in agree-

ment with recent studies.32,39,40On the other hand,(NC)23 molecule loses 0.16 electron partial

charge to Au atoms. It is interesting to note that the magnitude in the shift of M-DOS between

IM and EM systems is greater for(NC)23 which looses electrons, while the shift is smaller for

SS3 which gains electrons. Based on this observation, we hypothesize that the magnitude of the

shift in M-DOS is correlated to the end-group mediated charge transfer between Au atoms and the

molecule. In particular, the shift in M-DOS is governed by two important factors: (i) the stabi-

lization of energy levels induced by contact to the Au cluster; (ii) the change in electron-electron

interactions (Coulomb repulsion and exchange-correlation effects) arising from the charge trans-

fer. The effect of stabilization is to shift the energy levels to lower energies, whereas the effect of

electron-electron interactions is to increase their energies. In the case ofSS3, the partial electron

gain enhances the electron-electron repulsion, in turn reducing the overall downward shift of the

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energy levels. In the case of(NC)23, the charge transfer is out of the molecule which reduces

the electron-electron repulsion, resulting in a large overall downward shift of the energy levels. A

schematic presentation of the proposed mechanism is shown in Figure 2.

We note that the effect of charge transfer between a moleculeand electrodes, upon contact,

can also be described in terms of interface dipoles.41–44 In fact, past work has invoked this pic-

ture to quantitatively understand the barriers to electron/hole injection at the interface of organic

molecular layers and metal electrodes, in the context of organic light emitting diodes and pho-

tovoltaic devices.45,46 In the present work, the computed M-DOS accounts for both theeffect of

charge transfer and the stabilization of energy levels resulting from the bond formation at the elec-

trodes. Further, we subsequently also relate the resultingelectronic-structure to the thermoelectric

properties of single molecule junctions.

En

erg

y

EEM

EIM

(a) (b)

Stabilization

Increased

e-e Repulsion

Stabilization

Decreased

e-e Replusion

EIM

EEM

Figure 2: (a-b) The molecular orbital of an isolated molecule is initially at EIM indicated byblue dotted ellipse. The stabilization (brown dashed arrow) resulting from contact with Au clusterlowers the energy of the molecular orbital. (a) The partial charge gain (SS3), increases the electron-electron repulsion (orange dotted arrow) resulting in a small overall downward shift (purple doubleheaded arrow) toEEM (red ellipse). (b) The charge loss ((NC)23) decreases the electron-electronrepulsion, in turn resulting in a larger overall downward shift to EEM (red ellipse).

In order to further test the above hypothesis, we extend our study to triphenyl molecules ter-

minated with other end-groups: di-hydroxyl (OO3) and di-nitrile ((CN)23) (Figure 3(a)). Similar

to the thiol end-group, the hydroxyl end-group is assumed tohave deprotonated upon contact with

Au.8 The stable adsorption site forOO3 and(CN)23 are respectively the hollow and top47 sites.

The HOMO-LUMO energy values for the corresponding isolatedmolecules are presented in Ta-

ble 1. Similar to the previous systems, theEF lies in the HOMO-LUMO gap with the HOMO level

being closer to theEF . The∆N values calculated for these systems are shown in Table 1. These

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values suggest that theOO3 molecule gains partial electron from the Au atoms, while the (CN)23

loses partial electron to Au atoms. Following our hypothesis, we expect a smaller overall down-

ward shift in the M-DOS ofOO3, resulting in the HOMO level remaining closer toEF . On the

other hand, for(CN)23, a larger overall downward shift in the M-DOS is predicted resulting in the

LUMO level being closer toEF . The computed M-DOS forOO3 and(CN)23 molecular systems

are shown in Figure 3(b)-3(c), and are in good agreement withthese qualitative predictions.

0 1 2 3 4

EF

(b)

0

200

400

600

800

M-

DO

S

EF

E − EF (eV)

(c)

0

200

400

600

800

M-

DO

S

E − EF (eV)

HO OH N NCCOO3 (CN)23(a)

0 1 2 3-1-2

OO3

(CN)23

Figure 3: (a) Isolated triphenyl di-hydroxyl (OO3) and triphenyl di-nitrile ((CN)23) molecules. (b)The M-DOS ofOO3 molecule in different scenarios (IM, EM and open quantum system). (c) TheM-DOS of(CN)23 molecule in different scenarios. The M-DOS of the IM, EM andopen quantumsystem are denoted by blue-dotted line, red-dashed line andgreen-continuous line respectively.The purple arrows indicate the magnitude of the M-DOS shift.

We next consider the amine end-group that has garnered significant experimental and compu-

tational interest for their ability to form reproducible contacts.10,18,48–50In this study, we choose

triphenyl di-amine molecule ((NH2)23) (Figure 4(a)), whose stable adsorption site correspondsto

the atop site of Au trimer25 (Figure S3, SI). The computed HOMO-LUMO energies of the isolated

molecule are provided in Table 1. Interestingly, unlike theother end-groups, the HOMO level of

the isolated molecule is above theEF of Au electrode. The computed∆N for this molecular system

(see Table 1) indicates that the(NH2)23 molecule loses partial charge to Au atoms. Based on our

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hypothesis, we expect a significant overall downward shift of the M-DOS to lower energies. This

relaxation would move the HOMO level below theEF resulting in HOMO dominated transport.

The computed M-DOS of the(NH2)23 molecular systems (see Figure 4(b)) is indeed consistent

with the proposed hypothesis. We note that our results are inagreement with recent experimental

and computational studies,18,19,25which have indicated that triphenyl and other aromatic molecules

with amine end-groups exhibit HOMO dominated transport.

0 1 2 3 40

200

400

600

800

EF

E − EF (eV)

M-

DO

S

(b)

(a) (NH )2

(NH )2 (NH )

2 23

(NH )2 2

3

Figure 4: (a) Isolated triphenyl di-amine ((NH2)23) molecule. (b) The M-DOS of(NH2)23molecule in different scenarios (IM, EM, open quantum system). The M-DOS of the IM, EMand open quantum system are denoted by blue-dotted line, red-dashed line and green-continuousline respectively. The purple arrows indicate the magnitude of the M-DOS shift.

In all the molecular systems studied in the present work, thepredictions obtained from the pro-

posed hypothesis are in good agreement with detailed electronic-structure calculations. We next

extend our analysis to the relationship between end-group chemistry and charge transfer. The direc-

tion of charge transfer between the molecule and the Au atomsis governed by the electronegativity

(χ) of molecule and that of the Au cluster. We use the Mulliken definition of electronegativity

in the present work, defined as the average of ionization energy (I.E) and electron affinity (E.A),

χ = I .E+E.A2 .51 The χ values for the molecules considered in the present study areprovided in

Table 1. Theχ of Au cluster with{111} layers representing the hollow site configuration (Figure

S1 and S4, SI) is computed to be 4.9 eV, while that of top site configuration (Figure S2 and S4,

SI) is 4.81 eV. Our data indicates thatSS3 andOO3 are more electronegative than the Au clusters.

Hence, there is a tendency for these molecules to gain partial charge from the Au cluster. However,

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theχ of (NC)23, (CN)23 and(NH2)23 is below that of the Au cluster, which implies that there is

a tendency for these molecules to lose electrons to the Au cluster.

Finally, we investigate the effect of end-group mediated electron transfer on the transport prop-

erties of the molecular junctions. We begin with the transmission function,τ(E), which is com-

puted in the Landauer formalism by employing the Green’s function approach:

τ(E) = Tr [ΓRGr(z)ΓLGa(z)] , (5)

whereGa(z) is the advanced Green’s function and is the complex conjugate ofGr(z). The broaden-

ing functionsΓL/R are related toΣL/R throughΓL/R= i[

ΣL/R−Σ†L/R

]

. Our approach to computing

the transmission function is described in the following references.12,20–22,52The computed trans-

mission functions for all the MJs considered in the present study are shown in Figure 5(a)-5(b),

and are in agreement with previous studies.8,23,47,49,53The transmission curves show that inSS3,

OO3 and(NH2)23 molecules, the HOMO peak is closer to theEF resulting in a HOMO domi-

nated transport. While in(NC)23 and(CN)23, the LUMO peak is closer to theEF resulting in

a LUMO dominated transport. These results are consistent with the computed M-DOS for all the

molecular junctions, suggesting a strong correlation betweenτ(E) and M-DOS. The HOMO or

LUMO character of the transport is also validated by performing the transmission eigenchannel

analysis,54 which is presented in the SI (Figure S7-S9).

OO3

SS3

N H( )2 23

0 1 2 3 4-1 E − E

F (eV)

EF

10-1

100

10-2

10-3

10-4

10-5

−3 −2 −1 0 1 2 E − E

F (eV)

EF

100

10-2

10-4

10-6

10-8

(CN)23

(NC)23

τ(E)

Figure 5: (a) The transmission functionτ(E) of SS3,OO3 and(NH2)23 molecular junctions (openquantum systems) plotted as a function of energy. (b)τ(E) of (NC)23 and(NC)23 molecularjunctions plotted as a function of energy.

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The thermopower,S, of a molecular junction at low temperature differentials is related to the

slope of the transmission function (τ(E))16 as:

S=−∆V∆T

= −π2k2

BT3|e|

(

1τ(E)

∂τ(E)∂E

)∣

∣

∣

∣

E=EF

, (6)

wheree is the charge of an electron andT is the average absolute temperature of the junction (cho-

sen to be 300K). The thermopower of the molecular junctions obtained using Eq. 6 is presented in

Table 2. The predicted thermopower is in good agreement withprevious experimental and compu-

tational values.9,12,13,17,19,23,25,53,55The deviations of the computational results from experiments

may arise due to the microscopic variations in the contact details, molecular vibrations,56 and in-

teractions beyond the mean field approximation (especiallyfor amines25) that are not accounted

for in our current models.

Table 2: Thermopower of molecular junctions obtained from Eq. 6, experiments and othercomputations. aThe experimental value corresponds to triphenyl mono-isocyanide. b Thecomputed value neglects the interactions beyond the mean field.

SystemThermopower(S) (µV /K)

This work Experiments Past ComputationsSS3 21.9 15.4±1.012 14.06,23 ∼ 21.153

OO3 26.5 - -(NC)23 -1.6 −1.0±0.4a12 -(CN)23 -6.8 - -(NH2)23 22.5 6.4±0.419 24.3b25

To summarize, our calculations demonstrate a relationshipbetween the chemistry of the end-

groups, the resultant electronic-structure, and the nature of electronic transport. In particular, the

electronegativity of the molecule relative to that of the electrode can be used to determine the

direction of charge transfer between the molecule and the electrode. Further, our studies have

demonstrated a simple qualitative relationship between the direction of charge transfer and the

degree of reorganization of the molecular electronic states, which in turn determines the thermo-

electric properties of molecular junctions. We expect thatthe proposed approach has the potential

to guide the design of molecular junctions with desirable thermoelectric properties.

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ACKNOWLEDGEMENT

V. G. and J. B. gratefully acknowledge the support from College of Engineering at University of

Michigan. B. D. D. gratefully acknowledges support by a DOE-BES award through the Chemical

Sciences Geosciences and Biosciences Division (DE-SC0004924), DE-FG02-10ER16174). P. R.

acknowledges the support by DOE-BES as part of an EFRC at the University of Michigan (DE-

SC0000957).

Supporting Information

Contact models, M-DOS and Eigenchannel analysis. This material is available free of charge via

the Internet at http://pubs.acs.org.

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