THE JOURNAL OF CHEMICAL PHYSICS 125, 214709 2006

Propensity rules for inelastic electron tunneling spectroscopy of single-molecule transport junctions
Alessandro Troisia
Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom and Centre of Scientic Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom

Mark A. Ratnerb
Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113 and Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113

Received 27 April 2006; accepted 16 October 2006; published online 7 December 2006 Using a perturbative approach to simple model systems, we derive useful propensity rules for inelastic electron tunneling spectroscopy IETS of molecular wire junctions. We examine the circumstances under which this spectroscopy that has no rigorous selection rules obeys well dened propensity rules based on the molecular symmetry and on the topology of the molecule in the junction. Focusing on conjugated molecules of C2h symmetry, semiquantitative arguments suggest that the IETS is dominated by ag vibrations in the high energy region and by out of plane modes au and bg in the low energy region. Realistic computations verify that the proposed propensity rules are strictly obeyed by medium to large-sized conjugated molecules but are subject to some exceptions when small molecules are considered. The propensity rules facilitate the use of IETS to help characterize the molecular geometry within the junction. 2006 American Institute of Physics. DOI: 10.1063/1.2390698

I. INTRODUCTION

The interaction of the nuclear motions with electron transport across a molecular junction gives rise to a variety of phenomena whose understanding is crucial for the correct interpretation of the conductance properties.1 In a recent overview an attempt was made to classify the different manifestations of the nuclear degrees of freedom in transport measurements at the single-molecule level.2 The most complex cases occur when the energy of the electron injected from the electrodes is close to an electronic resonance with one molecular level. In these cases such phenomena as double-barrier tunneling into vibronic states3,4 or polaronic transport5,6 can be observed, depending on the strength of the interaction spectral density between the molecule and the electrodes. In the low voltage regime, inelastic electron tunneling spectroscopy IETS spectra can be recorded at low temperature.716 Here, molecular vibrations modulate the tunneling matrix element between states localized on the left and right electrodes, and this modulation is related to the small probability that the electron tunnels inelastically though the molecule, losing or gaining a quantum of vibrational energy. IETS are displayed as plots of d2I / dV2 versus V, and inelastic peaks appear in such plots, reecting which molecular vibrations are most effective in modulating the tunneling probability. The simpler interpretation14 is that
a b

Electronic mail: a.troisi@warwick.ac.uk Electronic mail: ratner@chem.northwestern.edu

IETS corresponds to the opening of a new, inelastic channel, so that there is an increase in the current as voltage is increased and a peak in d2I / dV2. IETS is an extremely promising technique because it allows an unmistakable proof of the presence of the molecule inside the junction and can provide information about the structure of the junctions. Such measurements at the single-molecule level are relatively recent, and the richness of information they provide structure/bonding requires an appropriate theoretical approach. Interpretation of IETS is not trivial, since there are no strict selection rules derived by the theory and propensity rules have not been clearly identied. Numerical approaches for the interpretation of the IETS spectra have been proposed by several groups.1726 In one recent paper27 we showed that a numerical approach based on a perturbative treatment of the tunneling is able to reproduce correctly the spectra of three molecules measured by Kushmerick et al.15 Numerical treatments are valuable for understanding transport experiments in molecular electronics, but it is also very useful to derive simple principles more closely related to intuition, which can guide interpretation of the results. For example, in infrared IR spectroscopy, the most intense modes modulate most strongly the molecular electric dipole and, without much calculation, it is relatively easy to predict which vibrations are more likely to give strong infrared absorption. Selection rules are strictly obeyed in both Raman and IR spectroscopies and greatly simplify the assignment of the vibrational modes of symmetric molecules. Lorente et al.18
2006 American Institute of Physics

0021-9606/2006/125 21 /214709/11/$23.00

125, 214709-1

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214709-2

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reported elegant work on IETS of deuterated acetylenes absorbed on Cu 111 . The experiments were based on scanning tunneling microscopy STM measurements, for which the molecular energies are pinned to the metal, the transport involves tunneling through vacuum to the STM tip, and the resulting currents are in the nanoampere range. Then the analysis can be based on the Tersoff-Hamann limit, depending only on state densities. We are concerned here with the molecular junction case, where the molecule bridges the interelectrode space, the spectral density is comparable at both molecular termini, currents are in the microampere range, and the Tersoff-Hamann approach28 is not appropriate. Herein we use the Landauer-Imry approach29,30 to tunneling transport to derive a series of propensity rules for IETS that can be used to predict the activity of a given vibrational mode. The derivation is perturbative, assuming that the conductance is much smaller than the quantum conductance and the electrodes are at equilibrium during the measurement. The set of propensity rules will be deduced applying the general formalism outlined in Sec. II to model systems Sec. III and applying standard point group theory. Some calculations on realistic systems will be used in Sec. IV to verify the validity of the propensity rules.
II. BACKGROUND A. Elastic conductance

dependence can be expressed in a Taylor series expansion around the equilibrium position Q = 0 we use dimensionless coordinates , Gij E, Q Gij E,0 + Gij E, Q Q Q . 3

The matrix G , with Gij = 2 / 2 Gij E , Q / Q Q =0, quanties the importance of the inelastic channel involving the vibrational mode . The inelastic contribution to the conductance due to mode , separated in left to right L R and in right to left R L tunneling, is ginel LR E = gc Tr
L

EG E

G E

, 4a

ginel RL E = gc Tr

G E

EG E

, 4b

and the inelastic current from mode I

inel

is 5a dE, 5b

=I

inel LR

inel RL

Iinel LR =

ginel LR E fL E 1 fR E e

We will recall here the general formalism for the perturbative simulation of IETS for a wider discussion see Refs. 19 and 23 . The elastic component of the conductance can be written as31,32 gel E = gc Tr
L

Iinel RL =

ginel RL E fR E 1 fL E e

dE. 5c

EGE

EGE

The elastic and inelastic components are additive in this limited model; therefore, I = Iel + Iinel . 6

where gc is the quantum conductance and L and R are twice the imaginary part of the self-energy matrices associated with the interaction of the molecular subsystem with the left and right electrodes. G is the matrix representation of the retarded Green function operator, related to the molecular Hamiltonian H as G E = EHi
+ 1 0 .

The elastic contribution to the current is Iel =

gel E f L E f R E dE, e

Equations 5 imply that the inelastic channel opens when and it stays open for larger the applied bias is equal to bias. A plot of d2I / dV2 versus V therefore shows a peak for / e or / e and the integral below the peak is V= ginel LR or ginel RL the proof is given in Appendix B . At low bias, the energy dependence in Eqs. 1 and 4 can be neglected and E set to EF. The integrated intensity W of the peak due to mode in an IETS spectrum d2I / dV2 versus V is W = gc Tr
L

where f L = f E + e L and f R = f E + e R are the Fermi functions of the left and right electrodes, modied by the external potential L or R applied to the respective electrode.
B. Inelastic channel

EF G EF

EF G EF

C. Localized representation

The interaction of the tunneling electron with the vibrational levels can be treated perturbatively, allowing exchange of a single vibrational quantum per tunneling electron and assuming that the molecule is in its ground vibrational state low temperature limit . These assumptions are discussed in Ref. 19 where a detailed derivation of the following equations is given. Greens function matrix elements are parametrically dependent on the set of normal modes Q ; this

Any basis set appropriate for the one-electron wave function can be used to build the matrices in Eqs. 1 and 7 . It is convenient to consider localized atomic orbitals. Since we use a linear combination of atomic orbitals/molecular orbital descriptor overall, this choice of basis can still describe delocalization within the molecule. We assume geometry for the junction as illustrated in Figs. 1 and 2. The coupling matrix element between an atomic orbital far from the electrode and the electrode states

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214709-3

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R LL R CL R RL R LC R CC R RC R LR R CR R RR

J. Chem. Phys. 125, 214709 2006

0 0 = 0 0 0 0

0 0
R RR

9b

This form of the two matrices permits a basis set transformaR tion that makes both L and RR diagonal. Then the trace LL in the expression of the elastic conductance Eq. 1 can be written as a summation over two indices g E = gc
FIG. 1. Schematic of a molecular junction and of the three portions that are treated with different computational approaches: i accurate density functional theory DFT calculations of the isolated molecule M are used to evaluate the molecular vibrations and the intramolecular Hamiltonian matrix elements, ii a tight binding Hamiltonian is used to evaluate the LDOS on the surface of the bare electrodes E , and iii a cluster calculation including few gold atoms is used to compute the metal-molecule Hamiltonian matrix element at the interface I .
L mm

m L n R

R nn

E Gmn E

10

Equation 10 is essentially a sum over the tunneling channels m-n: the electron is coupled to the left electrode through orbital m and to the right electrode through orbital n. Note that all the elements of the summation are positive there is no interference between tunneling channels, all the interference is incorporated into the term Gmn E . In this representation, the intensity W of the peak due to mode is W = gc
L mm

is negligible coupling falls exponentially with interatomic distance . Mathematically, recalling the denition of L for R is similar :
L ij

m L n R

R nn

1 2

Gmn E Q

11

E =2

V iV * j E E

is an index running over the left electrode states and the V j are the molecular or atom/electrode couplings , it is clear that L is nonzero only for i and j close to the electrode. We ij can partition the space of the atomic orbitals in three subspaces L, C, and R where L and R contain the orbitals interacting only with the left and right electrodes, respectively, and C is the space of the central atomic orbitals not interacting with either electrode. Of the nine blocks that form the matrices L and R only one is non-null:
L LL L CL L RL L LC L CC L RC L LR L CR L RR L LL

As we will see at the end of the next section and in Appendix A the localized representation allows simple inclusion of symmetry considerations in the evaluation of W .

III. MODEL SYSTEMS A. Point groups in molecular junctions

0 0 0 0 , 0 0 9a

0 0

FIG. 2. Model system used to compute the coupling matrix element between the molecule and the electrode. The benzenethiolate molecule is on the fcc adsorption site of the Au9 cluster and the CS bond is perpendicular to the surface. The geometry of the adsorbed molecule was optimized at the B3LYP/ 6-31G* level, keeping frozen the coordinates of the gold atoms.

It is probably very common that a realistic molecular junction has no rigorous symmetry element, because of the poorly dened structure of the electrodes in many experiments break junctions, cross-bar junction , the interaction with other molecules e.g., in self-assembled monolayers , and the coordinative molecule-electrode interaction that causes frequent uctuation of the interfacial geometry.33 Nevertheless, it is convenient to describe the symmetry propensity rules in the idealized case where both electrodes preserve the maximum allowed degree of symmetry of the molecule in the junction. Two types of molecular symmetry element can be found in a molecular junction: i symmetry elements that interchange the left and right electrode interfaces like the inversion center, a symmetry plane, or C2 rotation axis parallel to the electrodes and ii symmetry elements that transform the left and right electrode interfaces into themselves e.g., symmetry planes or rotational axis perpendicular to the electrodes . When one of the elements of the rst group is present the junction is electrically symmetric since the left and right electrodes are equivalent. We will rst discuss the system where there is one symmetry element of the rst type, but the conjugated planar molecule may possess the second set of symmetry elements, and, at the end of Sec. IV, we will provide some guidelines for the general case. These symmetry elements are illustrated in Fig. 3.

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J. Chem. Phys. 125, 214709 2006

FIG. 3. Using the HS CH v CH2 CH2 v CH SH molecule as an example, the symmetry operations that help dene the propensity rules are illustrated.

B. Linear symmetric tight binding chain

We consider a linear chain of atoms with one orbital j per site j, each interacting with its neighbor. Vij = i H j is the coupling matrix element between adjacent sites i and j. We assume that there is one molecular symmetry element for example a C2 rotation axis parallel to the electrodes that exchanges left and right electrode-molecule interfaces. Only the rst 1 and last N atoms of the chain interact, respectively, with the left and right electrodes, so that the elastic conductance for this system is gel E = gc
L 11

G1N E V j,j+1 Q G1N E . = V j,j+1 Q Q Q j=1,N1

16

R NN

E G1N E

, is

12

and the intensity of the inelastic peak due to mode W = gc

L 11

The elements of the summation in Eq. 16 corresponding to symmetry related j , j + 1 couples are identical if the mode Q transforms as the totally symmetric representation while they are opposite in sign and cancel each other if the mode is not totally symmetric. For example, the following chart considers an idealized symmetric molecule described by four atomic orbitals. The arrows exemplify a symmetric Qs, a and antisymmetric Qa, b mode obtained by combining the motion of atoms 2 and 3 along their bond.

R NN

1 2

G1N E Q

13

If the system has a symmetry element S that interchanges 1 and N , i.e., S 1 = N , it is easy to verify that only totally symmetric vibrational modes lead to non-null G1N E / Q matrix elements. In fact, building the symmetrized combinations + = 1 + N and = 1 N the matrix element of interest can be written as34 1 GE/ Q N =
1 4

GE/ Q GE/ Q

14

that is non-null only if Q transforms as the totally symmetric representation, because G transforms as the totally symmetric representation the general case with more than one symmetry element relating 1 and N is discussed below . It is convenient to conrm this nding in a more intuitive manner. Using the Dyson equation35 we express the matrix element G1N E and G1N E / Q as G1N E = E E1 E E1
L 11

In the evaluation of Eq. 14 for the symmetric mode Qs, the symmetry related terms containing V12 / Qs and V34 / Qs are identical and add up. The evaluation of Eq. 14 for the antisymmetric mode gives zero because the symmetry related terms containing V12 / Qa and V34 / Qa are opposite in sign and cancel the term containing V23 / Qa is zero in the antisymmetric case .

C. Branched symmetric tight binding chain with one site in contact with the electrodes

E EN

R NN j=1,N1

V j,j+1 Q , E Ej 15

The previous observation holds also if the chain of atoms contains branches or loops, as long as there is a single atomic orbital interacting with each electrode as in the four

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J. Chem. Phys. 125, 214709 2006

examples below the electrode in contact with atoms 1 and 6 is omitted :

tional modes sketched in d and e are not likely to give strong signals in the IETS measurements because they do not inuence the main tunneling path. Experimental evidence in support of this conclusion comes from the comparison of the IETS measurement of dithiolates,14 where the CH groups behave as side group and give a negligible CH stretching signal at 3000 cm1, with the IETS measurement of monothiolates,15 where the CH3 terminal group is along the most favorable transmission path and the CH stretching signal is very intense. Further experiments are certainly necessary for a more quantitative assessment of the role of side groups in IETS measurements.
D. Symmetric tight binding chain with more than one site in contact with the electrodes

Each node of the graphs above represents an atomic orbital and connected nodes correspond to interacting orbitals. If there is more than one path connecting sites 1 and N conventionally in contact with the electrode the matrix element G1N E , evaluated via the Dyson equation, is similar to that of Eq. 15 except that a summation over all the possible paths from 1 to N needs to be included: G1N E =
paths P

In this case more than one Greens function matrix element should be computed following Eq. 10 : g E = gc
m L n R L mm

R nn

E
paths P

P Gmn E

19

E E1 E E1 VP
j=1,M j ,P j+1 j L 11

E EN =
paths P

R NN P G1N E . 17

E EP

The conductance is the sum of the always positive contributions of each tunneling channel m-n, each resulting from P the interference of the terms Gmn E connecting the electronic states m and n, on the left and right electrodes through the coupling path P. The inelastic tunneling peak has intensity W = gc
L mm

P j is the jth element of a vector containing the ordered list of neighboring atoms from 1 to N, i.e., it describes a step along a specic tunneling path. We have indicated with P G1N E the contribution to Greens function matrix element given by the path P. Considering for example graph e above, the most important paths are 1-2-5-6 and 1-2-3-4-5-6. Assuming a similar coupling between neighbors, the former p has a much larger G1N E and dominates the transport. The derivative with respect to the nuclear coordinates is G1N E Q =
paths P j=1,M

m L n R

R nn

1 2

paths P

P Gmn E Q

20 It is easy to verify that the existence of more than one tunneling channel also makes the contribution of antisymmetric modes non-null. In chart 3, symmetric and antisymmetric combinations are shown for a system with two sites in contact with each electrode. While the coupling through the symmetric path 1-2-3-4 is modulated only by the symmetric modes for the same reason valid for the a and b examples , the coupling through the asymmetric path 1-2-3-5 is modulated by both symmetric and antisymmetric modes.

VP

j ,P j+1

Q VP

P G1N E j ,P j+1

Q VP

18a

=
paths P j=1,M

P G1P

j ,P j+1

P GP

j+1 N

. 18b

This example demonstrates the expected result that if an electron path for the tunneling is more favorable, the vibrations that modulate it are also more effective in mediating the inelastic tunneling. In fact, a vibration Q that mostly modulates a given coupling Vkl, i.e., with a large Vkl Q / Q , will affect the matrix element G1N E / Q only if there is a path P P with large G1N E that contains the coupling Vkl. For the practical point of view, side groups attached to a molecular wire give weaker signals in IETS while the most important signals derive from the vibrations that inuence the most favorable transmission path. Considering chart 2, the vibra-

More formally, in a system with only one molecular symmetry element that interchanges the orbitals interacting with the right and left electrodes, if the orbitals m and n in contact with the electrodes are not related by a symmetry operation, the matrix element Gmn E / Q is in general non-null regardless of the symmetry property of Q . Although this lack of selection rules in the general case might seem distressing, it is very often the case that one tunneling channel dominates the transport because one m-n orbital couple is related to a much larger matrix element Gmn E . As

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214709-6

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J. Chem. Phys. 125, 214709 2006

seen in Eq. 18 the larger inelastic tunneling matrix elements Gmn E / Q are associated with larger Gmn E so that the inelastic intensity Wa can be considered as originating from a single tunneling channel. When this happens and if the orbitals m and n are related by a symmetry element the totally symmetric modes will dominate strongly the IETS signal. Next, we will see why this situation is relatively common for molecular wires.
E. Planar conjugated molecules

modes that transform as the au or bg representation. To estimate the intensity of these modes we can consider again the case of a linear chain of atoms, but this time we assume that each site has one orbital and several other orbitals, as for a generic conjugated molecule. The IETS matrix element and a orbital on the between a orbital on one end 1 of the molecule is composed of contribuother end N tions of the form
P G1 ,P j

VP

j ,P

j+1

P GP

j+1 ,N

E ,

21

An important subset of molecules studied in molecular electronics3638 consists of planar conjugated systems in contact with the electrodes through a SAu link. We assume that, together with the symmetry plane that contains the molecule, there is a symmetry element that interchanges the two electrode-molecule interfaces, so that the point group of the overall molecular system is C2h or C2v see Fig. 3 . We will discuss only the C2h point group in the following because it is more common but the results can be easily transferred to the isomorphic C2v group. To an excellent degree of approximation the only important matrix elements for the elastic and inelastic channels, Gmn E and Gmn E / Q , are the ones where m and n are orbitals localized on the sulfur atom in contact, respectively, with the left and right electrodes. The m and n orbitals may be either symmetric -type or antisymmetric -type with respect to the molecular symmetry plane.39 Group theory can be used to determine the symmetry of the vibrational modes that give non-null Gmn E / Q matrix elements details are given in Appendix A . It is convenient to distinguish three cases: i When both m and n are -type orbitals, the vibrations that transform as the ag or bu representation give non-null matrix elements. However, if m and n are symmetry related orbitals interchanged by a C2 axis only the totally symmetric modes give a non-null Green function derivative. If a molecule interacts with the electrodes by a SAu contact, only two symmetry related orbitals interact with the electrode, corresponding to the pz valence orbital of the sulfur atom.40 Consequently only ag modes modulate the Gmn E / Q matrix elements between equivalent orbitals. Since the channel through the system is the dominating channel, the ag vibrations that more effectively modulate the tunneling matrix elements are expected to be the most intense in an IETS measurement ag vibrations in planar conjugated molecules are in plane motions involving CC and CH stretchings and CCC and CCH bendings. It is expected that CC stretching and CCC bending combinations would give the strongest contribution to the IETS spectra. ii When m and n are both -type orbitals, the modes transforming as the ag or bu representations lead to non-null Gmn E / Q matrix elements. However, the contribution of the channel to the total current is small and decreases as the size of the conjugated molecule increases so that the tunneling channel are exinelastic peaks related to the pected to be very weak. iii When m is of type and n of type or vice versa the vibrational modes that modulate the matrix elements are those responsible for the - mixing, i.e., out of plane

where P j is a orbital and P j + 1 a orbital along one particular coupling path see Eq. 18b . Each term like the one in Eq. 21 corresponds to a path of the tunneling electron divided in two portions, one through the orbitals from 1 to P j and another through the orbitals from P j to N while the term V P j ,P j+1 Q / Q is responsible for the - mixing . It can be argued that these contributions are larger for conjugated systems when the longest part of the path is through the system, i.e., when the P j orbital is very close to the electrode. This argument suggests that, among the out of plane vibrations, the most active in IETS are the ones with the largest component on atoms close to the electrode.
F. Summary

The considerations of this section can be summarized as giving the following propensity rules for IETS: i If there is a single tunneling channel, only the totally symmetric modes are active in the IET spectroscopy, or equivalently, the greater is the dominance of a single tunneling channel the stricter is the propensity rule that favors totally symmetric modes. Vibrations that do not modify the interelectrode coupling along the main tunneling paths are less active in IETS. For example, the modes that involve mostly side-group motions of a molecular wire are less active in IETS. Vibrations localized on atoms that do not contribute to the important tunneling paths are also less active in IETS. If a system is present, the largest contribution to the IETS is given by the totally symmetric vibrations that orbitals ag modulate the interaction between modes in C2h systems . The contribution of the out of plane modes au or bg in C2h can be important when the tunneling path involves orbitals of type at one end and at the other. Then it is largest for modes with a stronger component close to the electrodes. The bu modes are the least intense, visible only if the conjugation is not too extended. Table I presents a summary view of the propensity rules.

ii

iii

IV. REALISTIC EXAMPLES

We present a small set of accurate calculations of the IETS spectra to verify the validity of the propensity rules suggested in the previous section. We will consider two

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J. Chem. Phys. 125, 214709 2006

TABLE I. Summary of the principal propensity rules for IETS in a metal/molecule/metal junction. Symmetry of the m-n couple with respect to the molecular plane Are the m and n orbitals related by the C2 axis? Yes No Yes No No cannot be Active modes according to group theory Ag A g, B u Ag A g, B u A u, B g

Other considerations Very weak because of energy denominator There is only one orbital per sulfur pz , so m and n must be symmetry related

Modes seen experimentally None Ag

A u, B g

groups of molecules belonging to the C2h group and depicted in Figs. 4 and 5. A series of conjugated polyenes, terminated with thiol groups, is studied to investigate systematically the effect of conjugation length on the IET spectra. We com-

puted also the IET spectra of benzene dithiolate and two molecular wires of the type prepared by Tours group, containing the phenyl ring parasubstituted with ethynyl groups. The second set of molecules is more similar to that investi-

FIG. 4. Simulated spectra of three all-trans polyene dithiolates showed at the left of each spectrum in the 60 1900 cm1 range. Peaks in red, blue, and cyan correspond to vibrational modes of symmetry ag, au, and bg, respectively. The peaks deriving from the bu vibrations are not observed for any of these molecules. The line length is proportional to the calculated intensity.

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214709-8

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J. Chem. Phys. 125, 214709 2006

FIG. 5. Simulated IET spectra of three conjugated compounds shown on the left in the 60 2500 cm1 range. The same color code as in Fig. 4 is used here to label the symmetry of the vibrational modes associated with each peak. bu vibrations in green are observed only for the shortest molecule of the series see text .

gated experimentally in Ref. 41. Detailed and satisfactory comparisons between some experimental measurement and calculations performed with the method described above have been presented elsewhere.27 Here we will use this set of molecules to discuss the general patterns arising from the computed IET spectra and to validate through accurate numerical calculations the propensity rules derived from the qualitative arguments of the previous section.
A. Computational details

ii

Most of the computational details are similar to those presented in Ref. 27. We improved the computation of the self-energy and the metal-molecule interaction using an approach close to that presented in Ref. 42 or 43 Three different kinds of calculation have been performed to compute separately i the isolated molecule properties, ii the molecule-electrode interaction, and iii the electrode local density of states see also Fig. 1 : i Isolated molecule computations are employed to compute the vibrational frequencies of the molecule and the matrix elements Gnm E and Gnm E / Q from rst principles at the 6-31G* / B3LYP level. We have therefore not included the effect of the gold substrate on the molecular vibrations. Calculations have been performed on the indicated compounds withSH terminations instead of theSAu electrode .44

iii

To compute the electrode-molecule interaction, we performed a cluster calculation again at the B3LYP level on a model system made by nine gold atoms and a benzene thiolate. We assumed that the S atoms are in a fcc-like adsorption site, and that the SC bond is perpendicular to the surface see Fig. 2 . We used a SAu distance of 2.85 . We used the 6-31G* basis set for the organic part of the cluster and the Lanl2mb basis set45,46 and pseudopotential for the gold atoms. This cluster was used to compute the Hamiltonian matrix elements between the S and the Au atomic orbitals. These SAu matrix elements are assumed to be similar for all investigated systems. This approximation is plausible since we consider only molecules where the sulfur is connected to an sp2 or sp carbon of a conjugated system. The local density of states LDOS at the Fermi energy on the gold surface is needed, together with the matrix element computed in ii to obtain the matrices of Eqs. 1 and 7 according to

L ij

=2
k

VkiV* LDOS EF k . kj

22

Here k is an index running on the molecular orbitals on the left electode, i and j correspond to orbitals on

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214709-9

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FIG. 6. Comparison of the calculated and observed Ref. 15 IETSs for the phenylene-ethynylene trimer dithiol. The calculation included Gaussian broadening of 100 cm1, but the intensities and frequencies are directly calculated in the isolated molecule using DFT the frequencies here have been scaled by the recommended factor of 0.961 for B3LYP calculations . The bar lines show the unbroadened calculation results: the peak heights are proportional to the calculated intensities, and their color indicates the symmetry with the same code as in Fig. 4 and 5.

the molecule, and the Vik are the couplings between these two groups of orbitals computed in step ii . The LDOS was computed using a tight binding TB model for metallic gold and a very large cluster of atoms to simulate the LDOS on the Au 111 gold surface. The TB parameters were obtained from rst principles B3LYP using small cluster calculations with the same pseudopotential and basis set used for gold in the calculation of the molecule-metal interaction.42 The approach outlined above is quite general, and its accuracy can be systematically improved by increasing the portion of the system considered in i as the molecule to include a few atoms from the electrode. It is, however, very difcult to perform a frequency analysis on a cluster containing a molecule and few metal atoms because the optimized structures are very far from the actual structure at the interface. Here we took the simplest route, neglecting the effect of the electrode on the molecular vibrations and excluding from the calculation the vibrations of the AuS interface. The symmetry considerations we are focusing on are not affected by this approximation. We report here the computed spectra, with each mode represented as a vertical bar on the energy axis with height proportional to its intensity. The effect of broadening5,16,2427,41 will not be considered. All modes related to the CH stretching are not very active in agreement with propensity rule ii , and the spectra are only displayed in the low frequency 2500 cm1 range. The position of the electrode Fermi level with respect to the molecular levels was set to 3.8 eV, a value intermediate between the highest occupied molecular orbital HOMO and lowest unoccupied molecular orbital of all considered systems. We observed previously23 that the exact value of EF does not alter the structure of the computed spectra if changed within a reasonable range the IETSs are essentially independent of the choice of EF when its distance from the HOMO and LUMO is larger than 0.4 eV .

B. Results

The simulated spectra of the all-trans polyene dithiolate series are collected Fig. 4. We used different colors to indicate signals arising from vibrations belonging to different irreducible representations, as described in the gure caption. In Sec. II, qualitative arguments led to the propensity rule that the totally symmetric ag vibrations would be the most important in the IETS spectra, followed by the vibrations belonging to the au or bg representation. We predicted that the weakest contribution would be given by the bu vibrations, noting that the validity of these propensity rules increases with the length of the conjugated portion of the molecule increased dominance of the channel . The simulated spectra of octatetraene and hexatriene dithiolates reported in Figs. 4 a and 4 b conrm the validity of the predictions. The bu transitions are effectively forbidden for all the polyenes considered here more than 30% of all modes are of bu type . This trend conrms the reasoning in the previous section: there are no strict selection rules, but some denite propensity rules appear when one channel dominates the transport. Since the au or bg vibrations correspond to out of plane modes that are usually at a lower frequency than the ag in plane combination of stretching and bending, the spectra appear separable into two regions: the low frequency region 0 800 cm1 where the au and bg transitions are seen and the high frequency region 800 2000 cm1 dominated by the ag modes. Figure 5 collects the simulated spectra of the aromatic molecules studied in the C2h group.47 The spectra of these molecules obey the same trend seen for the polyenes, with a high frequency region of ag transitions and a low frequency region where the au and bg are seen. Transitions of bu symmetry appear in the simulated spectra of the benzene dithiolate, the shortest molecule considered here, evidently because the transport and the inelastic channel through the orbitals of the systems is not completely negligible for very short molecules. Several complications make the low frequency region of the spectra more difcult to assign: the region has a higher density of modes and their energy can be seriously affected by the approximation that the electrodes

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214709-10

A. Troisi and M. A. Ratner

J. Chem. Phys. 125, 214709 2006

do not affect the molecular vibrations. Moreover at low bias the recorded spectra suffer from a still unexplained feature the so-called zero-bias feature48 ZBF that covers the inelastic tunneling signal at the lowest frequencies. On the other hand the high frequency region seems to be dominated by very few modes so that many features of the spectra can be assigned very condently and rationalized well by the propensity rules. Extensive comparisons with experimental IETS will be given elsewhere. Figure 6 demonstrates, by direct comparison, that the current perturbative formalism indeed accurately calculates IETS for single-molecule junctions and that the propensity rules developed here work. In this case the frequencies have been scaled by the recommended factor 0.961 for this level of computational theory49 and an empirical Gaussian broadening of 100 cm1 was applied to each peak. The possibility of predicting from rst principles the broadening of IETS signals is discussed in Ref. 50.
C. Generalization and conclusion

broader experimental use. Further joint experimental and theoretical work may be necessary for the clarication of several aspects of IETS.
ACKNOWLEDGMENTS

We are grateful to the Research Council UK, to the MOLEAPPS program of DARPA, to the NASA URETI program, to the Northwestern MRSEC, to the NSF International Division, and to the DoD MURI/DURINT program for support of this research.
APPENDIX A: NON-NULL MATRIX ELEMENTS FOR JUNCTIONS BELONGING TO THE C2h POINT GROUP

We consider the generic atomic orbitals sL and sR of i i type closer, respectively, to the left and right electrodes and the atomic orbitals pL and pR of type also closer to the i i left and right electrodes, respectively. We assume that the L-R pairs are related by the C2 symmetry element, i.e., C2 sL = sR and C2 pL = pR , and we dene the symmetrized i i i i combination: s+ = sL + sR i i i s = sL sR i i i p+ = pL + pR i i i p = pL pR i i i Ag , Bu , Au , Bg A1a A1b A1c A1d

The discussion above covers most situations that can be found in practical metal/molecule/metal junctions. The generalization to different symmetry groups is straightforward. One has to consider the orbitals localized close to both electrodes and use group theory to evaluate which pairs of orbitals on the left and right electrodes are coupled by which normal modes, using reasoning similar to that in Appendix A. Computation or intuition can suggest which orbital pairs might give larger contributions to the conductance and to the inelastic channel. In fact, the most intense modes in IETS are associated with the vibrations that most effectively modulate the overall coupling among orbitals in contact with the electrodes and are connected by an efcient tunneling path at the Fermi energy. The IETS spectrum can yield structural information about the molecule in the junction. The propensity rules describe modications that may be observed if the molecule were to isomerize, as well as differences that will occur for or , single or differing interfacial geometry or binding multiple site . We have shown that is possible to dene propensity rules for IET spectroscopy that could guide the assignment of experimental spectra. Such rules are more strictly obeyed for larger conjugated molecules while it is more probable that the interpretation of the results for very small junctions will require accurate computational modeling. These simple rules could contribute to an intuitive understanding of the experimental IETS measurements, one of the prerequisites for its

in parentheses we have indicated the irreducible representation of the symmetrized combination . The matrix elements of the operator O between two orbitals localized on opposite ends of the molecule are sL O sR = i j
1 4

s+ O s+ s+ O s + s O s+ i j i j i j A2a

s O s , i j pL O pR = j i
1 4

p+ O p+ p+ O p + p O p+ i j i j i j A2b

p O p , i j sL O pR = i j
1 4

s+ O p+ s+ O p + s O p+ i j i j i j A2c

s O p . i j The symmetry properties of Eqs. A1 imply that

sL O sR i j pL O pR i j sL O pR i j

0 0 0

if O transforms as the Ag or Bu representation, if O transforms as the Ag or Bu representation, if O transforms as the Au or Bg representation.

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214709-11

Inelastic electron tunneling spectroscopy

17 18

J. Chem. Phys. 125, 214709 2006 N. Mingo and K. Makoshi, Phys. Rev. Lett. 84, 3694 2000 . N. Lorente, M. Persson, L. J. Lauhon, and W. Ho, Phys. Rev. Lett. 86, 2593 2001 . 19 A. Troisi, M. A. Ratner, and A. Nitzan, J. Chem. Phys. 118, 6072 2003 . 20 A. Pecchia and A. Di Carlo, Nano Lett. 4, 2109 2004 . 21 Y. C. Chen, M. Zwolak, and M. Di Ventra, Nano Lett. 4, 1709 2004 . 22 Y. C. Chen, M. Zwolak, and M. Di Ventra, Nano Lett. 5, 621 2005 . 23 J. Jiang, M. Kula, W. Lu, and Y. Luo, Nano Lett. 5, 1551 2005 . 24 T. Yamamoto, K. Watanabe, and S. Watanabe, Phys. Rev. Lett. 95, 065501 2005 . 25 N. Sergueev, D. Roubtsov, and H. Guo, Phys. Rev. Lett. 95, 146803 2005 . 26 G. C. Solomon, A. Gagliardi, A. Pecchia, T. Frauenheim, A. Di Carlo, J. R. Reimers, and N. S. Hush, J. Chem. Phys. 124, 094704 2006 . 27 A. Troisi and M. A. Ratner, Phys. Rev. B 72, 0333408 2005 . 28 J. Tersoff and D. R. Hamann, Phys. Rev. B 31, 805 1985 . 29 R. Landauer, IBM J. Res. Dev. 1, 223 1957 . 30 M. Buttiker, Y. Imry, R. Landauer, and S. Pinhas, Phys. Rev. B 31, 6207 1985 . 31 A. Nitzan and M. A. Ratner, Science 300, 1384 2003 . 32 S. Datta, Quantum Transport Cambridge University Press, Cambridge, 2005 . 33 G. K. Ramachandran, T. J. Hopson, A. M. Rawlett, L. A. Nagahara, A. Primak, and S. M. Lindsay, Science 300, 1413 2003 . 34 1 and N are assumed to be real. 35 A. Nitzan, Annu. Rev. Phys. Chem. 52, 681 2001 . 36 Z. J. Donhauser, B. A. Mantooth, K. F. Kelly et al., Science 292, 2303 2001 . 37 M. A. Reed, C. Zhou, C. J. Muller, T. P. Burgin, and J. M. Tour, Science 278, 252 1997 . 38 D. K. James and J. M. Tour, Chem. Mater. 16, 4423 2004 . 39 This is true also if we consider the representation in which L and R are diagonal, and the symmetry of the metal surface does not destroy the symmetry of the molecule. In general m and n are linear combination of atomic orbitals not necessarily localized only on the S atoms but localized on the left and right ends of the molecule not overlapping . If the metal surface does not lower the symmetry of the molecule m and n can be classied as or . 40 Our reasoning in Sec. III assumes that we are dealing with a minimum basis set. We note however, that the realistic calculations in Sec. IV employ an extended basis set 6-31G* , with more than the minimum number of atomic orbitals to describe the electronic structure of the molecule. 41 J. G. Kushmerick, D. B. Holt, J. C. Yang, J. Naciri, M. H. Moore, and R. Shashidhar, Phys. Rev. Lett. 89, 086802 2002 . 42 P. S. Damle, A. W. Ghosh, and S. Datta, Phys. Rev. B 64, 201403 2001 . 43 Y. Xue, S. Datta, and M. A. Ratner, J. Chem. Phys. 115, 4292 2001 . 44 To exclude without ambiguity from the normal modes the ones involving the H atoms of theSH group their mass was set to innity in the frequency calculation. 45 P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 1985 . 46 P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 1985 . 47 Although this series of dithiolates in gas phase belong to the D2h point group, we study them within the highest point group compatible with the Au 111 gold surface they are contacted with in the fcc adsoption site. 48 D. T. Zimmerman, M. B. Weimer, and G. Agnolet, Appl. Phys. Lett. 75, 2500 1999 . 49 G. Rauhut and J. Pulay, J. Phys. Chem. 99, 3093 1995 . 50 A. Nitzan, Nano Lett. 4, 1605 2004 .

However, in the case of SAu termination there is not more than one contributing -type orbital on the left and right sulfur atoms, and the only relevant matrix elements are of type pL O pR , that are non-null only if O transforms as the i i totally symmetric representation. For the applications in this paper it is sufcient to recall that Greens function operator transforms as the totally symmetric mode, and the operator G E / Q transforms as the mode does.
APPENDIX B: THE INTENSITIES OF IETS PEAKS

The integral below one peak of an IET spectrum occurring at V = / e is simply the difference between the conductance measured for frequencies above and below the peak V is an arbitrary small voltage interval . In fact,
/e+ V

W =
/e V

d 2I dV dV2 dI dV

dI dV dI dV

V=

/e+ V

V= inel

/e V

inel V= /e+ V

dI dV

.
V= /e V

B1

The last equality derives from the observation that only the changes around V inelastic conductance due to mode / e if no other vibrational modes are active in the in= terval /e V /e+ V .
G. Cuniberti, G. Fagas, and K. E. Richter, Introducing Molecular Electronics: A brief overview Springer, Berlin, 2005 . 2 A. Troisi and M. A. Ratner, Small 2, 172 2006 . 3 X. H. Qiu, G. V. Nazin, and W. Ho, Phys. Rev. Lett. 92, 206102 2004 . 4 H. Sumi, J. Phys. Chem. B 102, 1833 1998 . 5 A. S. Blum, J. G. Kushmerick, D. P. Long et al., Nat. Mater. 4, 167 2005 . 6 M. Galperin, M. A. Ratner, and A. Nitzan, Nano Lett. 5, 125 2005 . 7 R. C. Jaklevic and J. Lambe, Phys. Rev. Lett. 17, 1139 1966 . 8 C. J. Adkins and W. A. Phillips, J. Phys. C 18, 1313 1985 . 9 E. L. Wolf, Principles of Electron Tunneling Spectroscopy Oxford University Press, New York, 1985 . 10 K. W. Hipps and U. Mazur, J. Phys. Chem. 97, 7803 1993 . 11 B. C. Stipe, M. A. Rezaei, and W. Ho, Science 280, 1732 1998 . 12 H. J. Lee and W. Ho, Science 286, 1719 1999 . 13 J. Gaudioso, L. J. Lauhon, and W. Ho, Phys. Rev. Lett. 85, 1918 2000 . 14 W. Y. Wang, T. Lee, I. Kretzschmar, and M. A. Reed, Nano Lett. 4, 643 2004 . 15 J. G. Kushmerick, J. Lazorcik, C. H. Patterson, R. Shashidhar, D. S. Seferos, and G. C. Bazan, Nano Lett. 4, 639 2004 . 16 J. G. Kushmerick, D. L. Allara, T. E. Mallouk, and T. S. Mayer, MRS Bull. 29, 396 2004 .
1

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