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Band structure engineering of a molecular wire system composed of dimercaptoacetoamidobenzene, its derivatives, and gold clusters
Computational Materials Science 27 (2003) 166–174 www.elsevier.com/locate/commatsci
Band structure engineering of a molecular wire system composed of dimercaptoacetoamidobenzene, its derivatives, and gold clusters M. Nolan, J.A. Larsson, J.C. Greer
*
NMRC, University College, Lee Maltings, Prospect Row, Cork, Ireland
Abstract The properties of molecular devices can be engineered through modification of the conformation of the molecule and through chemical substitution. The following study presents the results of density functional theory studies of the properties of a metal–molecule assembly resulting from the interaction between an organic molecular linker, dimercaptoacetoamidobenzene and thirteen atom ‘‘magic number’’ gold nanoclusters. Bonding between two gold nanoclusters, changing the conformation of the linker molecule and the effect of chemical substitution in the linker are assessed through considering the geometry and electronic structure of the resulting assemblies. Changing the conformation in the molecule leads to significant changes in the electronic structure of the metal–linker–metal complex. Chemical substitution in the molecular wire also has an effect on the electronic structure; however, energy level shifts are larger for conformational changes than for chemical substitution. Ó 2002 Elsevier Science B.V. All rights reserved. Keywords: Molecular wire; Energy levels; Gold clusters
1. Introduction The interactions between organic molecules and metal surfaces and nanoparticles via thiol linkers are of fundamental importance in nanotechnology and molecular electronics [1–4]. These interactions have received much attention experimentally and quantum chemically [1–11]. Quantum chemical calculations have addressed the issues of the bonding configuration of the thiol molecule on the
*
Corresponding author. Tel.: +353-21-904305; fax: +353-214270271/270271. E-mail address: [email protected] (J.C. Greer).
gold surfaces [5–7,11] and the resulting electronic structure and its impact on electronic transport properties [8–11]. A density functional theory (DFT) study of the interaction between the thiol molecule dimercaptoacetoamidobenzene (DMAAB), which is a potential nanoparticle linker, and thirteen atom gold nanoclusters is presented in this paper. We also study conformational effects introduced by rotation about a carbon–carbon bond in the linker molecule. The derivatives formed by substitution with chlorine and methyl on the 2 and 5 positions of the phenyl ring in DMAAB, denoted DMAAB(Cl) and DMAAB(CH3 ), are studied in order to examine the effect of chemical substitution.
0927-0256/03/$ - see front matter Ó 2002 Elsevier Science B.V. All rights reserved. doi:10.1016/S0927-0256(02)00441-X
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174 H
R
O H H A B
SH
H N
N
H
H
S Au
167
H
Au
O
R
H
Au Au
Au
Au
Au
Au
Au
Au
Au
Au Au
(a) Au Au
Au Au Au Au Au
Au
O H
H
H N
N H
S Au Au
Au
Au Au
H
H
H
Au
S H
H
Au Au
H
O
Au Au Au Au Au Au Au Au
Au
Au
(b)
Au AuAu
Au Au
AuAuAu AuAu
AuAu Au
H
O
S HH
H H N HH
N H H
H
O
Au
S
Au Au Au Au Au Au Au Au Au Au
Au
(c)
Au
Fig. 1. (a) Molecular structure of the hollow-site bonding configuration of Au13 –DMAAB in C1 symmetry. The R groups signify possible substituents, in this case H, CH3 and Cl. Structure of the hollow-site bonding configuration, in C2 symmetry, of (b) cis Au13 – DMAAB–Au13 , and (c) trans Au13 –DMAAB–Au13 . Cis and trans labels the configuration of the CA –CB bonds, as marked in Fig. 1(a).
Fig. 1(a) shows the Au13 –DMAAB complex, whereby the R groups signify the positions on the phenyl ring where chemical substitution takes
place: CA and CB label the carbon–carbon bond about which rotation occurs when examining conformational effects. Fig. 1(b) shows the cis
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Au13 –DMAAB–Au13 complex where both CA –CB bonds are in the cis (sulfur relative to the nitrogen atom) conformation. Fig. 1(c) shows the trans Au13 –DMAAB–Au13 complex, where the CA –CB bonds are in the trans conformation. In the following, we discuss the effect that bonding of the thiol molecule to two gold clusters has on the geometry, electronic structure and charge distributions of the metal–molecule complex, when compared to bonding to a single gold cluster. Conformational effects, described above, modify the geometry in the gold cluster–linker molecule interfacial region and have a notable effect on the electronic structure and interfacial charge distributions. Thus, conformational effects are expected to modify transport properties and the utilisation of this effect may be useful for tuning of device properties. Finally, chemical substitution on the aromatic ring of the linker molecule induces a strong modification to the electronic structure and charge distributions, and can also influence transport properties.
2. Methods For the metal cluster, a thirteen atom gold cluster with octahedral symmetry has been used throughout this study. All DFT calculations were performed with the Becke 3 parameter–Lee Yang Parr (B3–LYP) [12,13] exchange-correlation functional. We have used a valence double-zeta polarised basis set as catalogued in the TURBO-
MOLE library [14]. A relativistic effective core potential [15] with sixty core electrons has been used for all gold atoms allowing full treatment of the gold 5s, 5p, 5d and 6s electrons [5]. For all the metal–molecule complexes studied, the sulfur atom is bonded to a hollow-site on a (1 1 1) face of the Au13 nanocluster, which has been determined to be the most favourable bonding site for thiols on Au13 [11]. The complexes with a single metal cluster have C1 symmetry, while those including two clusters have C2 symmetry.
3. Results and discussion 3.1. Bonding configurations of the metal–molecule complexes Relevant geometrical parameters for all the metal–molecule complexes studied in this work are listed in Table 1. Fig. 2 displays bond distances in the interfacial region of the gold cluster–molecular linker complex. In the complexes with one gold cluster the thiolate sulfur bonds to the gold cluster, while the thiol sulfur is terminated by a hydrogen atom. With the exception of the trans Au13 – DMAAB–Au13 complex, the thiolate sulfur to carbon bond distances are all very similar. The most notable effect of bonding DMAAB to the gold cluster can be seen in the changes in the bond distances between the gold atoms bonded to the thiolate sulfur (in Fig. 2 and Table 1). These gold–gold bond distances elongate by 24–25%
Table 1 Bond lengths for the gold–linker complexes studied Au13 –DMAAB
Au13 –DMAAB– Au13 cis
Au13 –DMAAB– Au13 trans
Au13 –DMAAB(CH3 )
Au13 – DMAAB(Cl)
(Au–Au) r/A
3.623 3.641 3.672
3.630 3.640 3.668
3.523 3.727 3.772
3.609 3.616 3.696
3.626 3.654 3.681
(S–Au) r/A
2.550 2.556 2.559
2.552 2.552 2.607
2.534 2.558 2.599
2.552 2.570 2.579
2.555 2.574 2.592
(S–C) r/A
1.849 1.836a
1.849
1.833
1.850 1.840a
1.848 1.833a
a
Where two S–C bond distances are given, the longer one is for the thiolate sulfur.
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174
Fig. 2. Bonding in the interfacial region of the gold cluster– molecular linker complexes.
upon interaction with the molecule. In all cases, but for the trans conformation the interfacial geometry is slightly different. The distance between these gold atoms in trans Au13 –DMAAB–Au13 correspond to a wider range of bond elongations of 20–27%. The cis conformation of Au13 –DMAAB–Au13 (1(b)) is energetically more favourable, with the trans conformation (1(c)) lying 90 meV higher in energy. The trans conformation could be a more representative bonding geometry for many experimental arrangements of single molecular wires, such as break junctions and electromigration generated gaps. We conclude that, within the same conformation, the addition of a second cluster and chemical substitution on the molecule have little effect on the interfacial geometry, whereas conformational effects strongly modify the bond lengths at the interfacial region. 3.2. Electronic structure of metal–molecule complexes The orbital energy levels of Au13 –DMAAB are shown in Fig. 3, and compared to the energy levels of a single gold atom, the Au13 cluster, and the DMAAB molecule. Fig. 4 indicates the evolution of the energy levels as the molecule bonds to one cluster, and to two clusters in cis and trans conformation. Fig. 5 displays the orbital energy levels of the Au13 –DMAAB, the Au13 –DMAAB(CH3 ) and the Au13 –DMAAB(Cl) complexes. Table 2 shows the energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the complexes and the
169
energies of the first orbitals of the complexes derived from the HOMO and LUMO of DMAAB (see the sketch accompanying Table 2). When the gold cluster and the molecule bond, in all cases the resulting complex has a wider HOMO–LUMO gap than the bare cluster indicating that the gold cluster has lost some of its metallic properties, and the metal–molecule complex has a substantial molecular character. It can be deduced from Fig. 3 that HOMO, HOMO 1 and the unoccupied levels up to LUMO þ 9 of Au13 –DMAAB are of metallic origin. HOMO 2 of Au13 –DMAAB is derived from the HOMO of DMAAB. The energy of this orbital increases by 80 meV upon interaction with the metal cluster. HOMO 4 is the first orbital with a contribution from orbitals on both the gold cluster and DMAAB. HOMO 1 of the free molecule contributes to this orbital, undergoing an increase in energy of 130 meV upon bonding to the gold cluster. LUMO þ 10 of the complex is derived from the LUMO of DMAAB. Other unoccupied orbitals of the metal–molecule complex with a contribution from molecular levels are LUMO þ 12 and LUMO þ 13. These levels have contributions from the molecular LUMO þ 1 and gold cluster based gold 6s orbitals. When DMAAB is bonded to two gold clusters, some of the energy levels such as HOMO/ HOMO 1 (the analogue of which is HOMO of Au13 –DMAAB) and HOMO 2=HOMO 3 (HOMO 1 of Au13 –DMAAB) align, while others, such as HOMO 4 (HOMO 2 of Au13 – DMAAB), remain non-degenerate. This is indicated in Fig. 4, where the orbital levels joined by a full line are doubly degenerate (for the complexes with two clusters), while those joined by a dashed line are non-degenerate. This degeneracy of the levels reveals that there are little or no interactions between the two Au13 clusters through the linker molecule. The non-degenerate orbitals show strong contributions from the linker molecule, while the degenerate levels arise from equivalent orbitals localized on the gold clusters. In the cis conformation, all the energy levels of the complex are lowered upon bonding to the second cluster; the energy lowering for the doubly degenerate orbitals is on the order of 20 meV, while for the
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Fig. 3. Orbital energy levels of (from left to right) the Au atom, the Au13 nanocluster, Au13 –DMAAB complex and DMAAB showing the composition of the MOs of the metal–molecule complex. The dashed line across the figure shows the position of the HOMO of the Au13 cluster.
non-degenerate orbitals it is approximately 0.14 eV. This shows that the energy levels with molecular contributions are shifted more strongly in energy in the cis Au13 –DMAAB–Au13 complex (1b) than in the one cluster complex (1a). For trans Au13 –DMAAB–Au13 all the orbital energies, with the exception of HOMO 4, increase in energy by approximately 0.2 eV, compared to the cis configuration. HOMO 4, which is derived from the HOMO of DMAAB, is lowered in energy by 0.3 eV, as can be seen in Fig. 4. A similar change is found for the HOMO orbitals of free cis and trans DMAAB. For the unoccupied orbitals, all those
up to and including LUMO þ 16 for the complexes with two clusters show only gold character and are doubly degenerate. Similar to LUMO þ 10 of Au13 –DMAAB, LUMO þ 17 for the cis and the trans Au13 –DMAAB–Au13 complex has primarily a contribution from the LUMO of DMAAB. The energies of the orbitals joined by full lines within Fig. 5, e.g. the HOMO and HOMO 1 levels, are localised on the gold clusters and are little affected by chemical substitution. These orbitals undergo an increase in energy of 20 meV for Au13 –DMAAB(CH3 ) and less then 50 meV for Au13 –DMAAB(Cl), compared to Au13 –DMAAB.
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174
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Fig. 4. Orbital energy levels for (left to right) Au13 –DMAAB, cis Au13 –DMAAB–Au13 and trans Au13 –DMAAB–Au13 . The dashed lines indicate those orbitals with a molecular contribution.
However, those orbitals joined with a dashed line in Fig. 5, e.g. HOMO 2 and HOMO 4, have strong contributions from the molecular linker. The energy shifts for these orbitals are significantly larger than for the MOs with no molecular contribution and would be expected, since substitution on the phenyl ring will only significantly perturb the orbitals of the complex with a contribution from the linker molecule. The energy shifts demonstrate how chemical substitution in the molecular linker affects the electronic structure. Lowlying unoccupied orbitals joined by the solid line within Fig. 5, which are made up of purely gold 6s and sulfur contributions, show little energy change
upon chemical substitution. The first DMAAB LUMO derived orbitals of the Au13 –DMAAB, Au13 –DMAAB(CH3 ) and Au13 –DMAAB(Cl) complexes are LUMO þ 10, LUMO þ 9 and LUMO þ 8, respectively. The energy gap between the first orbitals derived from the HOMO and LUMO of the linker molecule is given in Table 2 for all the complexes studied and is indicated in the accompanying schematic (Fig. 6). In Au13 –DMAAB this energy gap is 0.18 eV smaller than the gap between the HOMO and LUMO of free DMAAB. The energy gap increases by 30 meV for cis Au13 –DMAAB–Au13 and by 0.51 eV for the trans conformation, both compared to
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Fig. 5. Orbital energy levels for (left to right) Au13 –DMAAB, Au13 –DMAAB(CH3 ) and Au13 –DMAAB(Cl). The dashed lines indicate those orbitals with a molecular contribution.
Au13 –DMAAB. This small change in cis Au13 – DMAAB–Au13 is due to a uniform down shift in HOMO 4 (the linker derived HOMO) and LUMO þ 17 (the linker derived LUMO) of approximately 0.13 eV. The larger shift in trans Au13 – DMAAB–Au13 is caused by a significant down shift of 0.44 eV of HOMO 4 and an opposite up shift of 0.07 eV of LUMO þ 17. The energy gap derived from the linker molecule in Au13 –DMAAB(CH3 ) and Au13 – DMAAB(Cl) decreases by 0.20 eV and increases by 0.15 eV compared to Au13 –DMAAB, respectively. The increase in the energy gap for Au13 – DMAAB(Cl) is caused by a bigger down shift in
HOMO 2 (0.36 eV) than in LUMO þ 8 (0.22 eV) with regard to Au13 –DMAAB; these are the orbitals derived from the HOMO and LUMO of the linker molecule, respectively. The decrease in the linker molecule derived energy gap in Au13 – DMAAB(CH3 ) is due to an up shift in the occupied level ðHOMO 2Þ of 0.14 eV and a down shift in the unoccupied level ðLUMO þ 9Þ of 0.06 eV, again with respect to Au13 –DMAAB. The changes in the orbital levels of the chemically substituted derivatives of Au13 –DMAAB can be seen in Table 2 to be analogous with the differences between DMAAB(Cl) and DMAAB(CH3 ) compared to DMAAB. From our calculations, we see
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174
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Table 2 Energies of HOMO, LUMO and the HOMO–LUMO gap for the molecules and the energy gap between the first HOMO and LUMO derived levels Au13 HOMOAu LUMOAu HLGAu HOMOM LUMOM HLGM
DMAAB
DMAAB(CH3 )
DMAAB(Cl)
)4.85 )4.60 0.15 )5.92 )0.96 4.96
)5.78 )1.04 4.74
)6.32 )1.48 4.84
1(a) R ¼ H
1(b)
1(c)
1(a) R ¼ CH3
1(a) R ¼ Cl
)5.63 )3.63 2.00 )5.84 )1.06 4.78
)5.65 )3.65 2.00 )5.98 )1.17 4.81
)5.45 )3.43 2.02 )6.28 )0.99 5.29
)5.61 )3.61 2.00 )5.70 )1.12 4.58
)5.58 )3.58 2.00 )6.20 )1.28 4.92
All energies are in electron volt. The accompanying schematic (Fig. 6) shows the relationship between the energy quantities given in the table (the energies are not to scale). The energies of the HOMO, LUMO and the HOMO–LUMO gap for the Au13 cluster and the metal–molecule complexes studied. The energies of the HOMO, LUMO and HLG for the isolated DMAAB molecule and its derivatives (rows 2–4). For the complexes 1(a–c), the energies of the first orbitals derived from the HOMO and LUMO of the free molecule and the resulting energy gap between these orbitals are given.
LUMO M
HLG M
LUMO Au HLG Au HOMO Au
HOMO M Au13
Metal-Molecule Complex
Free Molecule
(not to scale) Fig. 6. Schematic to accompany Table 2.
that the change in the molecular linker derived energy gap compared to Au13 –DMAAB is small for cis Au13 –DMAAB–Au13 , moderate for Au13 – DMAAB(Cl) and Au13 –DMAAB(CH3 ) and largest for trans Au13 –DMAAB–Au13 . 3.3. Charge distributions Mulliken partial atomic charges for the complexes studied are given in Table 3. The two sulfur atoms in the free DMAAB derivatives have a net negative charge of 0.10. With the exception of the
trans Au13 –DMAAB–Au13 complex, there is a negative charge of 0.31 on the thiolate sulfur and a negative charge of 0.17 on the carbon atom bonded to the thiolate sulfur in the metal–molecule complexes. In the trans conformation, the sulfur is less negatively charged, while the carbon increases its negative charge. The overall S–C charge remains approximately constant, but the charge becomes more evenly distributed over the S–C bond. Similarly, for the three gold atoms directly bonding to sulfur, the total charge in the trans Au13 –DMAAB–Au13 complex is more uniformly distributed. For both the cis and trans Au13 – DMAAB–Au13 a charge of 0.11 electron is transferred from each gold cluster to the linker. This is twice that for Au13 –DMAAB and reveals that charge transfer from the gold clusters is additive. For the substituted DMAAB derivatives, the interfacial charges are little changed compared to Au13 –DMAAB, and this is due to the charge redistributions on the phenyl ring being too far away from the interfacial region to cause any significant change. The partial atomic charges on the substituted phenyl rings in Au13 –DMAAB(Cl) and Au13 –DMAAB(CH3 ) are insignificantly changed with regard to DMAAB(Cl) and DMAAB(CH3 ), respectively. The charge transfer from the gold cluster is 0.09 and only affects the thiolate group and its nearest neighbours. Note also that the charges on the chlorine atoms and the methyl groups are negative and positive, respectively, as one would expect given their chemical nature.
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Table 3 Mulliken charges for the metal–molecule complexes studied in the present work
a
S Cb Rc
DMAAB
DMAAB(CH3 )
DMAAB(Cl)
1(a) R ¼ H
1(b)
1(c)
1(a) R ¼ CH3
1(a) R ¼ Cl
)0.10 )0.35 0.12
)0.10 )0.36 0.13
)0.09 )0.36 )0.08
)0.31 )0.17 0.08 0.09 0.31 0.26 0.24 0.20 )0.70
)0.31 )0.17 0.09
)0.25 )0.22 0.09
0.31 0.26 0.24 0.55 0.70
0.29
)0.32 )0.17 0.09 0.10 0.32 0.25 0.22 0.21 )0.71
)0.31 )0.17 )0.05 )0.08 0.31 0.25 0.25 0.52 )0.73
Bonding Aud
Moleculee Au10 e
0.33
0.33
0.63
0.56 )0.76
a
S stands for the thiolate sulfur. C for the carbon bonded to the thiolate sulfur. c R stands for the substituent on the ring and can be H, CH3 or Cl. d Bonding Au denotes the three gold atoms bonded directly to the sulfur atom. e Molecule and Au10 denote the sum of the charges on the remaining atoms of the molecular and the cluster moieties. b
4. Conclusions Electronic structure engineering of molecular devices can be accomplished through conformational changes and chemical substitution and this work considers the role of these effects in the modification of the properties of a linker molecule. We have shown that conformational changes in the molecule and chemical substitution lead to a shift in the orbital energy levels of the metal–molecule–metal complex studied, and consequently result in a change in the charge distributions. The shift in orbital energies induced through conformational changes is larger than that induced through chemical substitution. Our study serves to gauge the relative importance of the effect of conformational changes and chemical substitution on the properties of metal–organic molecule–metal complexes assembled by thiolate bonding. Acknowledgements We thank Dr. Jurina Wessels of SONY for encouragement and support. This work has been funded by the European Union through the Information SocietyÕs Technology (IST) Program, within the Future and Emerging Technologies Advanced Research InitiativeÕs NANOTCAD project (IST–1999–10828), and the Improving Human Potential (IHP) Research Training Net-
work (RTN) ATOMCAD (HPRN–CT–2000– 00028).
References [1] A.S. Martin, J.R. Sambles, G.J. Ashwell, Phys. Rev. Lett. 70 (1992) 218. [2] A. Dhirani, P.-H. Lin, P. Guyot-Sionnest, R.W. Zehner, L.R. Sita, J. Chem. Phys. 106 (1997) 5249. [3] M.A. Reed, C. Zhou, C.J. Muller, T.P. Burgin, J.M. Tour, Science 278 (1997) 252. [4] J. Chen, M.A. Reed, A.M. Rawlett, J.M. Tour, Science 286 (1999) 1550. [5] H. Sellers, A. Ulman, Y. Shindman, J.E. Eilers, J. Am. Chem. Soc. 115 (1993) 9389. [6] K.M. Beardmore, J.D. Kress, N. Gronbech-Jensen, A.R. Bishop, Chem. Phys. Lett. 286 (1998) 40. [7] H. Gr€ onbeck, A. Curioni, W. Andreoni, J. Am. Chem. Soc. 122 (2000) 3839. [8] E. Emberley, G. Kirczenow, Phys. Rev. B 58 (1998) 10911. [9] S.N. Yaliraki, A.E. Roitberg, C. Gonzalez, V. Mujica, M.A. Ratner, J. Chem. Phys. 112 (1999) 6997. [10] A. Johansson, S. Stafstr€ om, Chem. Phys. Lett. 322 (2000) 301. [11] J.A. Larsson, M. Nolan, J.C. Greer, J. Phys. Chem. 107B (2002) 7311. [12] A.D. Becke, J. Chem. Phys. 98 (1993) 5486. [13] C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1988) 785. [14] A. Schafer, H. Horn, R. Ahlrichs, J. Chem. Phys. 97 (1992) 2571; A. Schafer, C. Huber, R. Ahlrichs, J. Chem. Phys. 100 (1994) 5829. [15] D. Andre, H. H€ausermann, M. Dolg, H. Stoll, H. Preuss, Theor. Chim. Acta 77 (1990) 123.
Band structure engineering of a molecular wire system composed of dimercaptoacetoamidobenzene, its derivatives, and gold clusters M. Nolan, J.A. Larsson, J.C. Greer
*
NMRC, University College, Lee Maltings, Prospect Row, Cork, Ireland
Abstract The properties of molecular devices can be engineered through modification of the conformation of the molecule and through chemical substitution. The following study presents the results of density functional theory studies of the properties of a metal–molecule assembly resulting from the interaction between an organic molecular linker, dimercaptoacetoamidobenzene and thirteen atom ‘‘magic number’’ gold nanoclusters. Bonding between two gold nanoclusters, changing the conformation of the linker molecule and the effect of chemical substitution in the linker are assessed through considering the geometry and electronic structure of the resulting assemblies. Changing the conformation in the molecule leads to significant changes in the electronic structure of the metal–linker–metal complex. Chemical substitution in the molecular wire also has an effect on the electronic structure; however, energy level shifts are larger for conformational changes than for chemical substitution. Ó 2002 Elsevier Science B.V. All rights reserved. Keywords: Molecular wire; Energy levels; Gold clusters
1. Introduction The interactions between organic molecules and metal surfaces and nanoparticles via thiol linkers are of fundamental importance in nanotechnology and molecular electronics [1–4]. These interactions have received much attention experimentally and quantum chemically [1–11]. Quantum chemical calculations have addressed the issues of the bonding configuration of the thiol molecule on the
*
Corresponding author. Tel.: +353-21-904305; fax: +353-214270271/270271. E-mail address: [email protected] (J.C. Greer).
gold surfaces [5–7,11] and the resulting electronic structure and its impact on electronic transport properties [8–11]. A density functional theory (DFT) study of the interaction between the thiol molecule dimercaptoacetoamidobenzene (DMAAB), which is a potential nanoparticle linker, and thirteen atom gold nanoclusters is presented in this paper. We also study conformational effects introduced by rotation about a carbon–carbon bond in the linker molecule. The derivatives formed by substitution with chlorine and methyl on the 2 and 5 positions of the phenyl ring in DMAAB, denoted DMAAB(Cl) and DMAAB(CH3 ), are studied in order to examine the effect of chemical substitution.
0927-0256/03/$ - see front matter Ó 2002 Elsevier Science B.V. All rights reserved. doi:10.1016/S0927-0256(02)00441-X
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174 H
R
O H H A B
SH
H N
N
H
H
S Au
167
H
Au
O
R
H
Au Au
Au
Au
Au
Au
Au
Au
Au
Au Au
(a) Au Au
Au Au Au Au Au
Au
O H
H
H N
N H
S Au Au
Au
Au Au
H
H
H
Au
S H
H
Au Au
H
O
Au Au Au Au Au Au Au Au
Au
Au
(b)
Au AuAu
Au Au
AuAuAu AuAu
AuAu Au
H
O
S HH
H H N HH
N H H
H
O
Au
S
Au Au Au Au Au Au Au Au Au Au
Au
(c)
Au
Fig. 1. (a) Molecular structure of the hollow-site bonding configuration of Au13 –DMAAB in C1 symmetry. The R groups signify possible substituents, in this case H, CH3 and Cl. Structure of the hollow-site bonding configuration, in C2 symmetry, of (b) cis Au13 – DMAAB–Au13 , and (c) trans Au13 –DMAAB–Au13 . Cis and trans labels the configuration of the CA –CB bonds, as marked in Fig. 1(a).
Fig. 1(a) shows the Au13 –DMAAB complex, whereby the R groups signify the positions on the phenyl ring where chemical substitution takes
place: CA and CB label the carbon–carbon bond about which rotation occurs when examining conformational effects. Fig. 1(b) shows the cis
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Au13 –DMAAB–Au13 complex where both CA –CB bonds are in the cis (sulfur relative to the nitrogen atom) conformation. Fig. 1(c) shows the trans Au13 –DMAAB–Au13 complex, where the CA –CB bonds are in the trans conformation. In the following, we discuss the effect that bonding of the thiol molecule to two gold clusters has on the geometry, electronic structure and charge distributions of the metal–molecule complex, when compared to bonding to a single gold cluster. Conformational effects, described above, modify the geometry in the gold cluster–linker molecule interfacial region and have a notable effect on the electronic structure and interfacial charge distributions. Thus, conformational effects are expected to modify transport properties and the utilisation of this effect may be useful for tuning of device properties. Finally, chemical substitution on the aromatic ring of the linker molecule induces a strong modification to the electronic structure and charge distributions, and can also influence transport properties.
2. Methods For the metal cluster, a thirteen atom gold cluster with octahedral symmetry has been used throughout this study. All DFT calculations were performed with the Becke 3 parameter–Lee Yang Parr (B3–LYP) [12,13] exchange-correlation functional. We have used a valence double-zeta polarised basis set as catalogued in the TURBO-
MOLE library [14]. A relativistic effective core potential [15] with sixty core electrons has been used for all gold atoms allowing full treatment of the gold 5s, 5p, 5d and 6s electrons [5]. For all the metal–molecule complexes studied, the sulfur atom is bonded to a hollow-site on a (1 1 1) face of the Au13 nanocluster, which has been determined to be the most favourable bonding site for thiols on Au13 [11]. The complexes with a single metal cluster have C1 symmetry, while those including two clusters have C2 symmetry.
3. Results and discussion 3.1. Bonding configurations of the metal–molecule complexes Relevant geometrical parameters for all the metal–molecule complexes studied in this work are listed in Table 1. Fig. 2 displays bond distances in the interfacial region of the gold cluster–molecular linker complex. In the complexes with one gold cluster the thiolate sulfur bonds to the gold cluster, while the thiol sulfur is terminated by a hydrogen atom. With the exception of the trans Au13 – DMAAB–Au13 complex, the thiolate sulfur to carbon bond distances are all very similar. The most notable effect of bonding DMAAB to the gold cluster can be seen in the changes in the bond distances between the gold atoms bonded to the thiolate sulfur (in Fig. 2 and Table 1). These gold–gold bond distances elongate by 24–25%
Table 1 Bond lengths for the gold–linker complexes studied Au13 –DMAAB
Au13 –DMAAB– Au13 cis
Au13 –DMAAB– Au13 trans
Au13 –DMAAB(CH3 )
Au13 – DMAAB(Cl)
(Au–Au) r/A
3.623 3.641 3.672
3.630 3.640 3.668
3.523 3.727 3.772
3.609 3.616 3.696
3.626 3.654 3.681
(S–Au) r/A
2.550 2.556 2.559
2.552 2.552 2.607
2.534 2.558 2.599
2.552 2.570 2.579
2.555 2.574 2.592
(S–C) r/A
1.849 1.836a
1.849
1.833
1.850 1.840a
1.848 1.833a
a
Where two S–C bond distances are given, the longer one is for the thiolate sulfur.
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174
Fig. 2. Bonding in the interfacial region of the gold cluster– molecular linker complexes.
upon interaction with the molecule. In all cases, but for the trans conformation the interfacial geometry is slightly different. The distance between these gold atoms in trans Au13 –DMAAB–Au13 correspond to a wider range of bond elongations of 20–27%. The cis conformation of Au13 –DMAAB–Au13 (1(b)) is energetically more favourable, with the trans conformation (1(c)) lying 90 meV higher in energy. The trans conformation could be a more representative bonding geometry for many experimental arrangements of single molecular wires, such as break junctions and electromigration generated gaps. We conclude that, within the same conformation, the addition of a second cluster and chemical substitution on the molecule have little effect on the interfacial geometry, whereas conformational effects strongly modify the bond lengths at the interfacial region. 3.2. Electronic structure of metal–molecule complexes The orbital energy levels of Au13 –DMAAB are shown in Fig. 3, and compared to the energy levels of a single gold atom, the Au13 cluster, and the DMAAB molecule. Fig. 4 indicates the evolution of the energy levels as the molecule bonds to one cluster, and to two clusters in cis and trans conformation. Fig. 5 displays the orbital energy levels of the Au13 –DMAAB, the Au13 –DMAAB(CH3 ) and the Au13 –DMAAB(Cl) complexes. Table 2 shows the energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the complexes and the
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energies of the first orbitals of the complexes derived from the HOMO and LUMO of DMAAB (see the sketch accompanying Table 2). When the gold cluster and the molecule bond, in all cases the resulting complex has a wider HOMO–LUMO gap than the bare cluster indicating that the gold cluster has lost some of its metallic properties, and the metal–molecule complex has a substantial molecular character. It can be deduced from Fig. 3 that HOMO, HOMO 1 and the unoccupied levels up to LUMO þ 9 of Au13 –DMAAB are of metallic origin. HOMO 2 of Au13 –DMAAB is derived from the HOMO of DMAAB. The energy of this orbital increases by 80 meV upon interaction with the metal cluster. HOMO 4 is the first orbital with a contribution from orbitals on both the gold cluster and DMAAB. HOMO 1 of the free molecule contributes to this orbital, undergoing an increase in energy of 130 meV upon bonding to the gold cluster. LUMO þ 10 of the complex is derived from the LUMO of DMAAB. Other unoccupied orbitals of the metal–molecule complex with a contribution from molecular levels are LUMO þ 12 and LUMO þ 13. These levels have contributions from the molecular LUMO þ 1 and gold cluster based gold 6s orbitals. When DMAAB is bonded to two gold clusters, some of the energy levels such as HOMO/ HOMO 1 (the analogue of which is HOMO of Au13 –DMAAB) and HOMO 2=HOMO 3 (HOMO 1 of Au13 –DMAAB) align, while others, such as HOMO 4 (HOMO 2 of Au13 – DMAAB), remain non-degenerate. This is indicated in Fig. 4, where the orbital levels joined by a full line are doubly degenerate (for the complexes with two clusters), while those joined by a dashed line are non-degenerate. This degeneracy of the levels reveals that there are little or no interactions between the two Au13 clusters through the linker molecule. The non-degenerate orbitals show strong contributions from the linker molecule, while the degenerate levels arise from equivalent orbitals localized on the gold clusters. In the cis conformation, all the energy levels of the complex are lowered upon bonding to the second cluster; the energy lowering for the doubly degenerate orbitals is on the order of 20 meV, while for the
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M. Nolan et al. / Computational Materials Science 27 (2003) 166–174
Fig. 3. Orbital energy levels of (from left to right) the Au atom, the Au13 nanocluster, Au13 –DMAAB complex and DMAAB showing the composition of the MOs of the metal–molecule complex. The dashed line across the figure shows the position of the HOMO of the Au13 cluster.
non-degenerate orbitals it is approximately 0.14 eV. This shows that the energy levels with molecular contributions are shifted more strongly in energy in the cis Au13 –DMAAB–Au13 complex (1b) than in the one cluster complex (1a). For trans Au13 –DMAAB–Au13 all the orbital energies, with the exception of HOMO 4, increase in energy by approximately 0.2 eV, compared to the cis configuration. HOMO 4, which is derived from the HOMO of DMAAB, is lowered in energy by 0.3 eV, as can be seen in Fig. 4. A similar change is found for the HOMO orbitals of free cis and trans DMAAB. For the unoccupied orbitals, all those
up to and including LUMO þ 16 for the complexes with two clusters show only gold character and are doubly degenerate. Similar to LUMO þ 10 of Au13 –DMAAB, LUMO þ 17 for the cis and the trans Au13 –DMAAB–Au13 complex has primarily a contribution from the LUMO of DMAAB. The energies of the orbitals joined by full lines within Fig. 5, e.g. the HOMO and HOMO 1 levels, are localised on the gold clusters and are little affected by chemical substitution. These orbitals undergo an increase in energy of 20 meV for Au13 –DMAAB(CH3 ) and less then 50 meV for Au13 –DMAAB(Cl), compared to Au13 –DMAAB.
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174
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Fig. 4. Orbital energy levels for (left to right) Au13 –DMAAB, cis Au13 –DMAAB–Au13 and trans Au13 –DMAAB–Au13 . The dashed lines indicate those orbitals with a molecular contribution.
However, those orbitals joined with a dashed line in Fig. 5, e.g. HOMO 2 and HOMO 4, have strong contributions from the molecular linker. The energy shifts for these orbitals are significantly larger than for the MOs with no molecular contribution and would be expected, since substitution on the phenyl ring will only significantly perturb the orbitals of the complex with a contribution from the linker molecule. The energy shifts demonstrate how chemical substitution in the molecular linker affects the electronic structure. Lowlying unoccupied orbitals joined by the solid line within Fig. 5, which are made up of purely gold 6s and sulfur contributions, show little energy change
upon chemical substitution. The first DMAAB LUMO derived orbitals of the Au13 –DMAAB, Au13 –DMAAB(CH3 ) and Au13 –DMAAB(Cl) complexes are LUMO þ 10, LUMO þ 9 and LUMO þ 8, respectively. The energy gap between the first orbitals derived from the HOMO and LUMO of the linker molecule is given in Table 2 for all the complexes studied and is indicated in the accompanying schematic (Fig. 6). In Au13 –DMAAB this energy gap is 0.18 eV smaller than the gap between the HOMO and LUMO of free DMAAB. The energy gap increases by 30 meV for cis Au13 –DMAAB–Au13 and by 0.51 eV for the trans conformation, both compared to
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Fig. 5. Orbital energy levels for (left to right) Au13 –DMAAB, Au13 –DMAAB(CH3 ) and Au13 –DMAAB(Cl). The dashed lines indicate those orbitals with a molecular contribution.
Au13 –DMAAB. This small change in cis Au13 – DMAAB–Au13 is due to a uniform down shift in HOMO 4 (the linker derived HOMO) and LUMO þ 17 (the linker derived LUMO) of approximately 0.13 eV. The larger shift in trans Au13 – DMAAB–Au13 is caused by a significant down shift of 0.44 eV of HOMO 4 and an opposite up shift of 0.07 eV of LUMO þ 17. The energy gap derived from the linker molecule in Au13 –DMAAB(CH3 ) and Au13 – DMAAB(Cl) decreases by 0.20 eV and increases by 0.15 eV compared to Au13 –DMAAB, respectively. The increase in the energy gap for Au13 – DMAAB(Cl) is caused by a bigger down shift in
HOMO 2 (0.36 eV) than in LUMO þ 8 (0.22 eV) with regard to Au13 –DMAAB; these are the orbitals derived from the HOMO and LUMO of the linker molecule, respectively. The decrease in the linker molecule derived energy gap in Au13 – DMAAB(CH3 ) is due to an up shift in the occupied level ðHOMO 2Þ of 0.14 eV and a down shift in the unoccupied level ðLUMO þ 9Þ of 0.06 eV, again with respect to Au13 –DMAAB. The changes in the orbital levels of the chemically substituted derivatives of Au13 –DMAAB can be seen in Table 2 to be analogous with the differences between DMAAB(Cl) and DMAAB(CH3 ) compared to DMAAB. From our calculations, we see
M. Nolan et al. / Computational Materials Science 27 (2003) 166–174
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Table 2 Energies of HOMO, LUMO and the HOMO–LUMO gap for the molecules and the energy gap between the first HOMO and LUMO derived levels Au13 HOMOAu LUMOAu HLGAu HOMOM LUMOM HLGM
DMAAB
DMAAB(CH3 )
DMAAB(Cl)
)4.85 )4.60 0.15 )5.92 )0.96 4.96
)5.78 )1.04 4.74
)6.32 )1.48 4.84
1(a) R ¼ H
1(b)
1(c)
1(a) R ¼ CH3
1(a) R ¼ Cl
)5.63 )3.63 2.00 )5.84 )1.06 4.78
)5.65 )3.65 2.00 )5.98 )1.17 4.81
)5.45 )3.43 2.02 )6.28 )0.99 5.29
)5.61 )3.61 2.00 )5.70 )1.12 4.58
)5.58 )3.58 2.00 )6.20 )1.28 4.92
All energies are in electron volt. The accompanying schematic (Fig. 6) shows the relationship between the energy quantities given in the table (the energies are not to scale). The energies of the HOMO, LUMO and the HOMO–LUMO gap for the Au13 cluster and the metal–molecule complexes studied. The energies of the HOMO, LUMO and HLG for the isolated DMAAB molecule and its derivatives (rows 2–4). For the complexes 1(a–c), the energies of the first orbitals derived from the HOMO and LUMO of the free molecule and the resulting energy gap between these orbitals are given.
LUMO M
HLG M
LUMO Au HLG Au HOMO Au
HOMO M Au13
Metal-Molecule Complex
Free Molecule
(not to scale) Fig. 6. Schematic to accompany Table 2.
that the change in the molecular linker derived energy gap compared to Au13 –DMAAB is small for cis Au13 –DMAAB–Au13 , moderate for Au13 – DMAAB(Cl) and Au13 –DMAAB(CH3 ) and largest for trans Au13 –DMAAB–Au13 . 3.3. Charge distributions Mulliken partial atomic charges for the complexes studied are given in Table 3. The two sulfur atoms in the free DMAAB derivatives have a net negative charge of 0.10. With the exception of the
trans Au13 –DMAAB–Au13 complex, there is a negative charge of 0.31 on the thiolate sulfur and a negative charge of 0.17 on the carbon atom bonded to the thiolate sulfur in the metal–molecule complexes. In the trans conformation, the sulfur is less negatively charged, while the carbon increases its negative charge. The overall S–C charge remains approximately constant, but the charge becomes more evenly distributed over the S–C bond. Similarly, for the three gold atoms directly bonding to sulfur, the total charge in the trans Au13 –DMAAB–Au13 complex is more uniformly distributed. For both the cis and trans Au13 – DMAAB–Au13 a charge of 0.11 electron is transferred from each gold cluster to the linker. This is twice that for Au13 –DMAAB and reveals that charge transfer from the gold clusters is additive. For the substituted DMAAB derivatives, the interfacial charges are little changed compared to Au13 –DMAAB, and this is due to the charge redistributions on the phenyl ring being too far away from the interfacial region to cause any significant change. The partial atomic charges on the substituted phenyl rings in Au13 –DMAAB(Cl) and Au13 –DMAAB(CH3 ) are insignificantly changed with regard to DMAAB(Cl) and DMAAB(CH3 ), respectively. The charge transfer from the gold cluster is 0.09 and only affects the thiolate group and its nearest neighbours. Note also that the charges on the chlorine atoms and the methyl groups are negative and positive, respectively, as one would expect given their chemical nature.
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Table 3 Mulliken charges for the metal–molecule complexes studied in the present work
a
S Cb Rc
DMAAB
DMAAB(CH3 )
DMAAB(Cl)
1(a) R ¼ H
1(b)
1(c)
1(a) R ¼ CH3
1(a) R ¼ Cl
)0.10 )0.35 0.12
)0.10 )0.36 0.13
)0.09 )0.36 )0.08
)0.31 )0.17 0.08 0.09 0.31 0.26 0.24 0.20 )0.70
)0.31 )0.17 0.09
)0.25 )0.22 0.09
0.31 0.26 0.24 0.55 0.70
0.29
)0.32 )0.17 0.09 0.10 0.32 0.25 0.22 0.21 )0.71
)0.31 )0.17 )0.05 )0.08 0.31 0.25 0.25 0.52 )0.73
Bonding Aud
Moleculee Au10 e
0.33
0.33
0.63
0.56 )0.76
a
S stands for the thiolate sulfur. C for the carbon bonded to the thiolate sulfur. c R stands for the substituent on the ring and can be H, CH3 or Cl. d Bonding Au denotes the three gold atoms bonded directly to the sulfur atom. e Molecule and Au10 denote the sum of the charges on the remaining atoms of the molecular and the cluster moieties. b
4. Conclusions Electronic structure engineering of molecular devices can be accomplished through conformational changes and chemical substitution and this work considers the role of these effects in the modification of the properties of a linker molecule. We have shown that conformational changes in the molecule and chemical substitution lead to a shift in the orbital energy levels of the metal–molecule–metal complex studied, and consequently result in a change in the charge distributions. The shift in orbital energies induced through conformational changes is larger than that induced through chemical substitution. Our study serves to gauge the relative importance of the effect of conformational changes and chemical substitution on the properties of metal–organic molecule–metal complexes assembled by thiolate bonding. Acknowledgements We thank Dr. Jurina Wessels of SONY for encouragement and support. This work has been funded by the European Union through the Information SocietyÕs Technology (IST) Program, within the Future and Emerging Technologies Advanced Research InitiativeÕs NANOTCAD project (IST–1999–10828), and the Improving Human Potential (IHP) Research Training Net-
work (RTN) ATOMCAD (HPRN–CT–2000– 00028).
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